Amazonia Seasons Have an Influence in the Composition of Bacterial Gut Microbiota of Mangrove Oysters (Crassostrea gasar).

The mangrove oysters (Crassostrea gasar) are molluscs native to the Amazonia region and their exploration and farming has increased considerably in recent years. These animals are farmed on beds built in the rivers of the Amazonia estuaries and, therefore, the composition of their microbiome should be directly influenced by environmental conditions. Our work aimed to evaluate the changes in bacterial composition of oyster's microbiota at two different seasons (rainy and dry). For this purpose, we amplified and sequenced the V3-V4 regions of the 16S rRNA gene. Sequencing was performed on the Illumina MiSeq platform. According to the rarefaction curve, the sampling effort was sufficient to describe the bacterial diversity in the samples. Alpha-diversity indexes showed that the bacterial microbiota of oysters is richer during the rainy season. This richness is possibly associated with the diversity at lower taxonomic levels, since the relative abundance of bacterial phyla in the two seasons remained relatively constant. The main phyla found include Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Similar results were found for the species Crassostrea gigas, Crassostrea sikamea, and Crassostrea corteziensis. Beta-diversity analysis showed that the bacterial composition of oyster's gut microbiota was quite different in the two seasons. Our data demonstrate the close relationship between the environment and the microbiome of these molluscs, reinforcing the need for conservation and sustainable management of estuaries in the Amazonia.

Epigenetic Field Cancerization in Gastric Cancer: microRNAs as Promising Biomarkers.

Background: The biological role of microRNAs (miRNAs) in field cancerization is unknown. To investigate the involvement of miRNAs in gastric field cancerization, we evaluated the expression profile of ten miRNAs and their diagnostic value. Methods: We used three groups of FFPE gastric samples: non-cancer (NC), cancer adjacent (ADJ) and gastric cancer (GC). The expression profiles of hsa-miR-10a, -miR-21, -miR-29c, -miR-135b, -miR-148a, -miR-150, -miR-204, -miR-215, -miR-483 and -miR-664a were investigated using qRT-PCR. The results obtained by qRT-PCR were validated in Small RNA-Seq data from the TCGA database. The search for target genes of the studied miRNAs was performed in the miRTarBase public database and miRTargetLink tool, using experimentally validated interactions. In addition, we also performed the functional analysis of these genes using enrichment in KEGG pathways. The potential as biomarker was evaluated using a receiver operating characteristic (ROC) curve and the derived area under the curve (AUC>0.85) analysis. Results: The miRNAs hsa-miR-10a, -miR-21, -miR-135b, hsa-miR-148a, -miR-150, -miR-215, -miR-204, -miR-483 and -miR-664a were up-regulated in ADJ and GC compared to NC (P<0.03); and hsa-miR-21 and -miR-135b were up-regulated in GC compared to ADJ (P<0.01). Hsa-miR-148a, -miR-150, -miR-215, -miR-483 and -miR-664a were not differentially expressed between GC and ADJ, suggesting that both share similar changes (P>0.1). The TS-miR hsa-miR-29c was up-regulated in ADJ compared to NC and GC (P<0.01); we did not observe a significant difference in the expression of this miRNA between NC and GC. This feature may be an antitumor mechanism used by cancer-adjacent tissue because this miRNA regulates the BCL-2, CDC42 and DMNT3A oncogenes. The expression level of hsa-miR-204 was associated with Helicobacter pylori infection status (P<0.05). Functional analysis using the genes regulated by the studied miRNAs showed that they are involved in biological pathways and cellular processes that are critical for the establishment of H. pylori infection and for the onset, development and progression of GC. hsa-miR-10a, -miR-21, -miR-135b, -miR-148a, -miR-150, -miR-215, -miR-483 and -miR-664a were able to discriminate NC from other tissues with great accuracy (AUC>0.85). Conclusion: The studied miRNAs are closely related to field cancerization, regulate genes important for gastric carcinogenesis and can be potentially useful as biomarkers in GC.

Effect of ancestry on interleukin-10 haplotypes in chronic periodontitis.

Chronic periodontitis is caused by an inflammatory reaction of the periodontal tissues and alveolar bone. This inflammation is caused by periodontopathic bacteria located in the subgingival biofilm, resulting in inflammatory reactions that may lead to loss of attachment. This tissue destruction is a consequence of host immune and inflammatory responses to specific periodontal pathogens and their metabolic products. Cytokines modulate the immune response, altering its efficiency in the competition against pathogens and increasing periodontal susceptibility. This study investigated genetic polymorphisms in Interleukin 10 (A-1082G, C-819T and C-592A) in 205 individuals from an admixed Brazilian population. A significantly increased risk of developing chronic periodontitis was observed in individuals with low IL-10 production and Amerindian ancestry. These results suggest that the polymorphisms A-1082G, C-819T, and C-592A, which are associated with ancestry, are involved in the susceptibility to the development of chronic periodontitis in an admixed northern Brazilian population.

A multicentric association study between 39 genes and nonsyndromic cleft lip and palate in a Brazilian population.

PURPOSE: The aim of this study was to use the TaqMan OpenArray system to evaluate associations between 39 genes and the etiology of nonsyndromic cleft lip and palate (NSCLP) in a Brazilian population. MATERIAL AND METHODS: This case-control association study was designed with 80.11% statistical power according to logistic regression (GPOWER software). The case group had 182 patients with NSCLP enrolled in the Brazilian Database on Orofacial Clefts. The controls included 355 healthy individuals with no history of oral clefting in the past three generations. All samples were genotyped for 253 tag single nucleotide polymorphisms (tagSNPs) in 39 genes, including two that had recently been associated with this process. The association analysis was performed using logistic regression and stepwise regression. The results were corrected for multiple testing [Bonferroni correction and False Discovery Rate (FDR)]. RESULTS: Twenty-four SNPs in 16 genes were significantly associated with the etiology of NSCLP, including MSX1, SPRY1, MSX2, PRSS35, TFAP2A, SHH, VAX1, TBX10, WNT11, PAX9, BMP4, JAG2, AXIN2, DVL2, KIF7, and TCBE3. Stepwise regression analysis revealed that 11 genes contributed to 15.5% of the etiology of NSCLP in the sample. CONCLUSION: This is the first study to associate KIF7 and TCEB3 with the etiology of NSCLP. New technological approaches using the same design should help to identify further etiological susceptibility variants.

Present Insights on Cardiomyopathy in Diabetic Patients.

The pathogenesis of diabetic cardiomyopathy (DCM) is partially understood and is likely to be multifactorial, involving metabolic disturbances, hypertension and cardiovascular autonomic neuropathy (CAN). Therefore, an important need remains to further delineate the basic mechanisms of diabetic cardiomyopathy and to apply them to daily clinical practice. We attempt to detail some of these underlying mechanisms, focusing in the clinical features and management. The novelty of this review is the role of CAN and reduction of blood pressure descent during sleep in the development of DCM. Evidence has suggested that CAN might precede left ventricular hypertrophy and diastolic dysfunction in normotensive patients with type 2 diabetes, serving as an early marker for the evaluation of preclinical cardiac abnormalities. Additionally, a prospective study demonstrated that an elevation of nocturnal systolic blood pressure and a loss of nocturnal blood pressure fall might precede the onset of abnormal albuminuria and cardiovascular events in hypertensive normoalbuminuric patients with type 2 diabetes. Therefore, existing microalbuminuria could imply the presence of myocardium abnormalities. Considering that DCM could be asymptomatic for a long period and progress to irreversible cardiac damage, early recognition and treatment of the preclinical cardiac abnormalities are essential to avoid severe cardiovascular outcomes. In this sense, we recommend that all type 2 diabetic patients, especially those with microalbuminuria, should be regularly submitted to CAN tests, Ambulatory Blood Pressure Monitoring and echocardiography, and treated for any abnormalities in these tests in the attempt of reducing cardiovascular morbidity and mortality.

Population stratification effect on cancer susceptibility in an admixed population from Brazilian Amazon.

BACKGROUND/AIM: Many efforts have been made to identify candidate genes involved in cancer susceptibility. The present study aimed to investigate the association between Arg194Trp (XRCC1), Ala222Val (MTHFR) and Arg521Lys (EGFR) polymorphisms (SNPs) and their susceptibility to gastric and breast carcinoma cancer in patients from Brazilian Amazon, controlling population structure interference. MATERIALS AND METHODS: The SNPs were genotyped by TaqMan® SNP Genotyping Assays. Ancestry was estimated by analysis of a panel with 48 ancestry informative markers. RESULTS: Logistic regression analysis showed an inverse association with a 10% increase in African and European ancestry and cancer risk (odds ratio (OR)=1.919 and 0.676, respectively). In a preliminary Chi-square analysis a positive association between Arg521Lys (EGFR) polymorphism and carcinoma susceptibility was found (p=0.037); however, when two different methodologies to control population structure bias were utilized, this association was lost (p=0.064 and p=0.256). CONCLUSION: Genetic ancestry influence gastric and breast cancer risk and highlight the importance of population structure inference in association studies in highly admixed populations, such as those from Brazilian Amazon.

The genomic ancestry of individuals from different geographical regions of Brazil is more uniform than expected.

Based on pre-DNA racial/color methodology, clinical and pharmacological trials have traditionally considered the different geographical regions of Brazil as being very heterogeneous. We wished to ascertain how such diversity of regional color categories correlated with ancestry. Using a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms we estimated individually the European, African and Amerindian ancestry components of 934 self-categorized White, Brown or Black Brazilians from the four most populous regions of the Country. We unraveled great ancestral diversity between and within the different regions. Especially, color categories in the northern part of Brazil diverged significantly in their ancestry proportions from their counterparts in the southern part of the Country, indicating that diverse regional semantics were being used in the self-classification as White, Brown or Black. To circumvent these regional subjective differences in color perception, we estimated the general ancestry proportions of each of the four regions in a form independent of color considerations. For that, we multiplied the proportions of a given ancestry in a given color category by the official census information about the proportion of that color category in the specific region, to arrive at a "total ancestry" estimate. Once such a calculation was performed, there emerged a much higher level of uniformity than previously expected. In all regions studied, the European ancestry was predominant, with proportions ranging from 60.6% in the Northeast to 77.7% in the South. We propose that the immigration of six million Europeans to Brazil in the 19th and 20th centuries--a phenomenon described and intended as the "whitening of Brazil"--is in large part responsible for dissipating previous ancestry dissimilarities that reflected region-specific population histories. These findings, of both clinical and sociological importance for Brazil, should also be relevant to other countries with ancestrally admixed populations.

A multiplex PCR for 11 X chromosome STR markers and population data from a Brazilian Amazon Region.

The analysis of X-STR polymorphisms has received the attention of several researchers, mainly due to its applicability to the investigation of complex kinship cases. Although many X-STRs have been validated for forensic use, little is known about the variations of these polymorphisms in different populations of the world. The present work describes a new multiplex system that allows the simultaneous analysis of 11 X-STR markers, for use both in paternity determination and more complex forensic cases. The loci investigated include DXS9895, DXS7132, DXS6800, DXS9898, DXS6789, DXS7133, DXS7130, HPRTB, GATA31E08, DXS7423, and DXS10011, which together afford a power of discrimination in the order of 0.999999. In addition, this work presents the genotyping results obtained for a sample of 324 individuals (182 males and 142 females) from the admixed population of Belém, Pará, located in the Brazilian Amazon Region.

Mitochondrial DNA mapping of social-biological interactions in Brazilian Amazonian African-descendant populations

The formation of the Brazilian Amazonian population has historically involved three main ethnic groups, Amerindian, African and European. This has resulted in genetic investigations having been carried out using classical polymorphisms and molecular markers. To better understand the genetic variability and the micro-evolutionary processes acting in human groups in the Brazilian Amazon region we used mitochondrial DNA to investigate 159 maternally unrelated individuals from five Amazonian African-descendant communities. The mitochondrial lineage distribution indicated a contribution of 50.2 percent from Africans (L0, L1, L2, and L3), 46.6 percent from Amerindians (haplogroups A, B, C and D) and a small European contribution of 1.3 percent. These results indicated high genetic diversity in the Amerindian and African lineage groups, suggesting that the Brazilian Amazonian African-descendant populations reflect a possible population amalgamation of Amerindian women from different Amazonian indigenous tribes and African women from different geographic regions of Africa who had been brought to Brazil as slaves. The present study partially mapped the historical biological and social interactions that had occurred during the formation and expansion of Amazonian African-descendant communities.

Nucleotide variability of HV-I in Afro-descendents populations of the Brazilian Amazon Region.

The analysis of genetic variation in the nucleotide sequences of mitochondrial DNA, provides unique information about the population diversity and human identification. In this study, the mitochondrial DNA sequences of the first hypervariable region (HV-I) were analyzed in 243 unrelated individuals of seven Afro-descendents populations of the Amazon Region. Sequence polymorphisms were detected using PCR and direct sequencing analysis. A total of 133 different haplotypes were found determined by 97 variable nucleotides. Each one of the three more frequent haplotypes was shared by 9 samples and 91 sequences were unique. The genetic diversity was estimated to 0.9898+/-0.0016 and the probability of two random individuals showed identical mitochondrial DNA (mtDNA) haplotypes were 1.2%.

Study of AZFc partial deletion gr/gr in fertile and infertile Japanese males.

A recurrent partial azoospermia factor C (AZFc) deletion, called gr/gr, has been reported to be a male infertility risk factor. A specific type of Y chromosome observed in approximately 30% of Japanese males (haplogroup D derived at YAP+) is believed to have a fixed gr/gr deletion. A recent study claimed that spermatogenic failure is more likely in males with D Y chromosomes, because of the gr/gr deletion, the presence of which is not well characterized among D haplogroup chromosomes. We therefore decided to perform a systematic study of the frequency of the gr/gr deletion in the Japanese. We studied fertile and infertile males to investigate the possibility of different gr/gr frequencies. The deletions were detected by use of single tagged-sequences (STSs) and the D haplogroup sub-lineages typing were done by use of the biallelic markers M174, M64, M116.1, 12f2.2, M15, M151, and M125. Analysis of gr/gr deleted Y chromosomes showed that all are classified as haplogroup D2, suggesting a lineage association. The subtype D2b1 was most frequent among the Japanese, in control and infertile samples. The haplogroups D2b2, D*, and D1 were not found in any population group. Remarkably, we observed no statistical difference between haplogroup D sub-lineages of the infertile and control groups, although the statistical power of this study is low. This study suggests lack of significant evidence of increased infertility risk in haplogroup D Japanese males. We were also able to establish the ancestral chromosome that suffered a gr/gr deletion, and propose a new Y chromosome phylogeny for haplogroup D and its derivatives. In summary, we were able to define the frequency of gr/gr deletion in Japanese males and show that the gr/gr deletion was probably present in the ancestral Y chromosome that entered Japan at least 12,000 years ago.

Nucleotide variability of HV-I in admixed population of the Brazilian Amazon Region.

The analysis of genetic variation in the nucleotide sequences of mitochondrial DNA has been used as a tool in the study of history of different human populations, as Amerindians, Afro-descendents populations and furthermore admixed populations. In this study, the mitochondrial DNA was analyzed in 158 unrelated individuals in an admixed population of the Amazonian Region: Santarém-PA-Brazil. The polymorphisms were detected using both levels, analysis of restriction enzyme and direct sequencing. We observed a total of 49 different haplotypes were found determined by 46 variable nucleotides. The more frequent haplotypes (Hap03) was shared by five samples and 43 sequences were unique. The genetic diversity was estimated to 0.989+/-0.0067 and the probability of two random individuals showed identical mitochondrial DNA (mtDNA) haplotypes were 2.8%.

Genetic characterization of the population of São Luís, MA, Brazil

Five loci (vWA1, F13A1, D12S67, Apo-B and D1S80) were investigated by polyacrylamide gel electrophoresis followed by silver staining in a sample of 177 individuals from the population of São Luís, State of Maranhão, Brazil. A total of 70 different alleles were identified. A statistically significant deviation from the Hardy-Weinberg equilibrium was observed in a single locus (F13A1, p = 0.0075). The average heterozygosity (H) was estimated at 77.7 percent, the mean number of alleles per locus as 14. The PD (capacity of genotype differentiation at each locus) ranged from 88.9 percent (vWA1) to 96.7 percent (F13A1). The combined PE (power of exclusion) of these five loci was 99.8 percent. In terms of racial admixture (42 percent European, 39 percent Indian, and 19 percent African Black ancestry), São Luís presented an estimate similar to Belém, another trihybrid Amazonian population.

Dissimilarities in the process of formation of Curiaú, a semi-isolated Afro-Brazilian population of the Amazon region.

The genetic consequences of the social policy of the past in relation to the formation of Afro-Brazilian societies are interesting and have been studied at various biological levels (classical polymorphisms and the mitochondrial and nuclear levels. These allow the estimation of the contribution of African genes and the participation of other ethnic groups in the formation of these communities. With this objective, uniparental systems of exclusively maternal (mtDNA) or paternal (Y-DNA) inheritance in the Curiaú community were analyzed. The results demonstrate a differential contribution of the maternal and paternal genetic systems. Thirty-three sequences were identified by mtDNA analysis; 53% showing an African and 47% an Amerindian origin. For the paternal system, 57% were of African, 37% of European, and 6% of Amerindian origin.

Genetical-demographic data from two amazonian populations composed of descendants of african slaves: Pacoval and Curiau

The Amazon region of Brazil includes communities founded by escaped slaves, some of which still remain relatively isolated. We studied two such Afro-Brazilian communities (Pacoval and Curiau), in the rural area of Alenquer, Pará, and in the metropolitan region of Macapá, Amapá, respectively. Among 12 blood loci, alleles considered as markers of African ancestry, such as HBB*S, HBB*C, TF*D1, HP*2M, ABO*B, RH*D-, and CA2*2 were found at frequencies that are expected for populations with a predominantly African origin. Estimates of interethnic admixture indicated that the degree of the African component in Curiau (74 per cent) is higher than that of Pacoval (44 per cent); an Amerindian contribution was not detected in Curiau. Estimated values of African ancestry fit well with the degree of isolation and mobility of the communities. Pacoval exhibited a high proportion of immigrants among the parents and grandparents of the individuals studied, whereas persons living in Curiau exhibited a low level of mobility, despite its location in the metropolitan area of Macapá city, suggesting a relatively strong barrier against the interethnic admixture in this population. In addition, analysis of genetic data in a sub-sample consisting of individuals whose parents and grandparents were born in the study site, and that probably represents the populations two generations ago, indicated that gene flow from non-black people is not a recent event in both populations.