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Technological advances in recent decades, especially in molecular genetics, have enabled the detection of genetic DNA markers associated with productive characteristics in animals. However, the prospection of polymorphisms based on DNA sequencing is still expensive for the reality of many food-producing regions around the world, such as Brazil, demanding more accessible prospecting methods. In the present study, the Fourier transform infrared spectroscopy (FTIR) and machine learning algorithms were used to identify single nucleotide polymorphism (SNP) in animal DNA. The fragments of bovine DNA with well-known polymorphisms were used as a model. The DNA fragments were produced and genotyped by PCR-RFLP and classified according to the genotype (homozygous or heterozygous). FTIR spectra of DNA fragments were analyzed by principal component analysis (PCA) and machine learning algorithms. The best results exhibited 75-95% accuracy in the classification of bovine genotypes. Therefore, FTIR spectroscopy and multivariate analysis can be used as an alternative tool for prospecting polymorphisms in animal DNA. The method can contribute with studies to identify genetic markers associated with animal production and indirectly with food production itself, and reduce pressure on available natural resources., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The tribe Gochnatieae is restricted to America. A recent molecular study including over 60% of the species of the tribe was carried out to untangle evolutionary relationships among the taxa. Eight supported clades were recovered as monophyletic genera, while Gochnatia s.l. was revealed as paraphyletic and currently restricted to the Central Andes. Gochnatia rotundifolia was not included in this phylogeny since extracted DNA from few and old collections from Brazil was unusuable. Since Cabrera's treatment of Gochnatia s.l., this species has received special attention due to its distinct morphological characters when compared with the other monophyletic genera of Gochnatieae. Therefore, this paper aims to provide new evidence that supports Gochnatia rotundifolia to be described as a separate monospecific genus based on a morphological study and a maximum parsimony (MP) analysis. A total of 21 species were studied. The leaf venation was analysed using digital X‐ray capture (VIVA–Varian Image viewing & Aquisition). Seventeen morphological characters obtained from vegetative and floral parts of the plants were included in the data matrix. Our results reinforce the placement of Gochnatia rotundifolia within the tribe Gochnatieae. Gochnatia rotundifolia is consistently recovered in a clade as sister to the Cnicothamnus‐Richterago group. The species differs from the other genera of the tribe by an actinodromous basal leaf venation with three primary veins, and pappus elements composed by (50–)60–75 bristles, sometimes almost flat setae, arranged in 2 or 3 series, unequal in length. Our results support Gochnatia rotundifolia as the sole species Vickia rotundifolia comb. nov. in a new genus of Gochnatieae, Vickia gen. nov. The new genus is described, illustrated, and a generic identification key for the tribe Gochnatieae is provided. [ABSTRACT FROM AUTHOR]

The drug-resistant temporal lobe epilepsy (TLE) has recently been associated with single nucleotide variants (SNVs) in microRNA(miR)-146a (MIR-146A) (rs2910164) and Sodium Voltage-Gated Channel Alpha Subunit 1 (SCN1A) (rs2298771 and rs3812718) genes. Moreover, no studies have shown an association between these SNVs and susceptibility to drug-resistant and drug-responsive TLE in Brazil. Thus, deoxyribonucleic acid (DNA) samples from 120 patients with TLE (55 drug-responsive and 65 drug-resistant) were evaluated by real-time polymerase chain reaction (RT-PCR). A total of 1171 healthy blood donor individuals from the Online Archive of Brazilian Mutations (ABraOM, from Portuguese Arquivo Brasileiro On-line de Mutações), a repository containing genomic variants of the Brazilian population, were added as a control population for the studied SNVs. MIR-146A and SCN1A relative expression was performed by quantitative RT-PCR (qRT-PCR). The statistical analysis protocol was performed using an alpha error of 0.05. TLE patient samples and ABraOM control samples were in Hardy–Weinberg equilibrium for all studied SNVs. For rs2910164, the frequencies of the homozygous genotype (CC) (15.00% vs. 9.65%) and C allele (37.80% vs. 29.97%) were superior in patients with TLE compared to controls with a higher risk for TLE disease [odds ratio (OR) = 1.89 (95% confidence interval (95%CI) = 1.06–3.37); OR = 1.38 (95%CI = 1.04–1.82), respectively]. Drug-responsive patients also presented higher frequencies of the CC genotype [21.81% vs. 9.65%; OR = 2.58 (95%CI = 1.25–5.30)] and C allele [39.09% vs. 29.97%; OR = 1.50 (95%CI = 1.01–2.22)] compared to controls. For rs2298771, the frequency of the heterozygous genotype (AG) (51.67% vs. 40.40%) was superior in patients with TLE compared to controls with a higher risk for TLE disease [OR = 2.42 (95%CI = 1.08–5.41)]. Drug-resistant patients presented a higher AG frequency [56.92% vs. 40.40%; OR = 3.36 (95%CI = 1.04–17.30)] compared to the control group. For rs3812718, the prevalence of genotypes and alleles were similar in both studied groups. The MIR-146A relative expression level was lower in drug-resistant compared to drug-responsive patients for GC (1.6 vs. 0.1, p-value = 0.049) and CC (1.8 vs. 0.6, p-value = 0.039). Also, the SCN1A relative expression levels in samples from TLE patients were significantly higher in AG [2.09 vs. 1.10, p-value = 0.038] and GG (3.19 vs. 1.10, p-value < 0.001) compared to the AA genotype. In conclusion, the rs2910164-CC and rs2298771-AG genotypes are exerting significant risk influence, respectively, on responsive disease and resistant disease, probably due to an upregulated nuclear factor kappa B (NF-kB) and SCN1A loss of function. [ABSTRACT FROM AUTHOR]

Background: Plasmodium vivax is the main species responsible for human malaria in Brazil, and one of its manifestations is splenic malaria, though there are still challenges in its diagnosis. The present study aimed to standardize Plasmodium sp. DNA extraction from histological slices of spleen and diagnosis using real-time qPCR. Methods: This study performed a microtomy of a paraffin-embedded spleen as a positive control for P. vivax from a patient who had been previously diagnosed with the parasite. The sample was deparaffinized with xylol and ethanol, then DNA extraction was performed with two commercial kits. qPCR was carried out with the Taqman system for detection of Plasmodium sp. and was made species-specific using PvmtCOX1 gene. From 2015 to 2019, 200 spleen samples were obtained from trauma patients subjected to splenectomy in Manaus, Amazonas. All the samples were tested for cell-free human DNA (cfDNA). Results: The deparaffinization and the Plasmodium vivax DNA extraction method was successfully standardized, and the control sample was positive for P. vivax. Of the 200 samples, all qPCRs were negative, but they were positive for human PCR. Conclusion: Paraffinization is practical and efficient for the preservation of samples, but the formation of bonds between proteins and DNA makes extraction difficult. Despite this, in this study, it was possible to standardize a method of DNA extraction for detecting P. vivax. [ABSTRACT FROM AUTHOR]

Tapaculos of the genus Scytalopus are secretive birds which tunnel like mice through dense understory of humid forest in the Andes, Central America, and south-eastern Brazil. Their agoraphobic habits make Scytalopus species highly sensitive to habitat discontinuities, so they are well suited for analyzing diversification patterns in montane forest biota. This study uses DNA sequence data to test hypotheses about past speciation events. The DNA data support that allopatric and parapatric populations with different songs represent different species. The high degree of phylogenetic resolution obtained by DNA-data permits a better description of geographical patterns of endemism. The data suggests that the commonly observed biogeographic pattern, where related species have long linear distributions along the Andes in different altitudinal zones, arose by divergence in disjunct isolates rather than by parapatric divergence. The approach seems well suited for identifying areas that have a special role for the diversification process. The paper finally discusses how detailed phylogenetic studies can be used to test interpretations of biogeographic patterns of high relevance for pinpointing top priority areas for conservation.

Simple Summary: The flat mite family Tenuipalpidae includes 41 genera and more than 1100 species worldwide, and is considered one of the most important families of phytophagous mites. The Ultratenuipalpus is a small genus with 25 known species present in almost all zoogeographic regions. Here, a new species Ultratenuipalpus parameekeri Castro, Ochoa & Feres sp. nov. is described from specimens collected on ferns from Brazil. It represents the first species of the genus described from the country. The type species of the genus Ultratenuipalpus meekeri (De Leon) is redescribed based on types and newly collected material from Mexico. Highly detailed low-temperature scanning electron image (LT-SEM) micrographs and DNA barcodes are provided for both species. The taxonomy of the genus Ultratenuipalpus and the ontogenetic additions of leg setae are discussed. Species of the genus Ultratenuipalpus bear a broad subquadrate propodosoma with many large, flattened, lanceolate to ovate dorsal setae. They also bear some plesiomorphic character states, such as the presence of three pairs of ventral ps setae. Here, we describe Ultratenuipalpus parameekeri Castro, Ochoa & Feres sp. nov. based on adult females, males, and immatures, collected on ferns from Brazil. We also re-describe Ultratenuipalpus meekeri (De Leon), the type species of the genus, based on types and newly collected material from Mexico, and include additional novel data (e.g., dorsal and ventral ornamentation, leg chaetotaxy, and setal measurements) in a standardized form. We include highly detailed images obtained using LT-SEM, accompanied by DNA barcodes, for both species. The ontogenetic additions of leg chaetotaxy are presented and discussed. [ABSTRACT FROM AUTHOR]

Simple Summary: This work aimed to build a molecular marker to detect Spodoptera frugiperda DNA in predators' gut content. The molecular marker developed is highly specific, and it was able to detect S. frugiperda DNA in the gut content of ladybug and earwig predators in field conditions. Our results confirm that generalist predators feed on S. frugiperda in maize fields, and they must be considered in IPM programs for S. frugiperda suppression. Spodoptera frugiperda is a serious pest of maize and other crops worldwide. The integration of control tactics is recommended for S. frugiperda suppression because reports of insecticide and Btplant-resistance are frequent. Biological control agents would be an alternative to improve S. frugiperda control in agricultural areas. We constructed a species-specific molecular marker to detect S. frugiperda DNA in predators' gut content and estimated the predation rates of ladybugs and earwigs on S. frugiperda in maize crops. Predators were sampled in Pirassununga, São Paulo state, Brazil, in 2020 and 2021. Using the species-specific molecular marker in laboratory conditions, we estimated the half-life time to detect S. frugiperda DNA in the gut contents of Hippodamia convergens as 6.16 h and Doru luteipes as 25.72 h. The weekly predation rate of S. frugiperda by predators in maize crop varied from 0 to 42.1% by ladybugs and from 0 to 9.2% by D. luteipes. Predation events on S. frugiperda by predators were more frequent during the maize reproductive stage. Our results confirmed that predators might contribute to S. frugiperda suppression in maize fields. However, further studies of prey–predator interactions and agricultural landscapes are essential for a better understanding of predator dynamics in crops. [ABSTRACT FROM AUTHOR]

Leaf symptoms of chlorosis and blotchy mottling, typically associated with agents of huanglongbing, were found in commercial citrus orchard located in the state of São Paulo, the main citrus producer region in Brazil. Affected trees tested negative for bacteria 'Ca. Liberibacter americanus' and 'Ca. Liberibacter asiaticus'. So, the total DNA was submitted to nested PCR employing the primer pairs P1/Tint followed by R16F2n/R16R2. Genomic fragments of 1.2 kb were amplified, sequenced and analyzed by computer-simulated RFLP, which confirmed the presence of a 16SrVII phytoplasma in symptomatic plants. Collective restriction patterns allowed distinguish the detected phytoplasma from all other members of the 16SrVII group using enzymes BfaI and MseI. In addition, the citrus phytoplasma showed a similarity coefficient lower than 0.97, when compared with all representative strains of subgroups within of the 16SrVII group, characterizing, therefore, a new subgroup. In agreement, the phylogenetic tree displayed that this strain emerges from a distinct branch in relation to those 16SrVII phytoplasmas currently described. Based on these features, the strain identified in the present study may be delineated as a new phytoplasma representative of the novel 16SrVII-G subgroup. Moreover, the results implicate citrus as a new host for a phytoplasma belonging to the group 16SrVII. [ABSTRACT FROM AUTHOR]

Buffaloes (Bubalus bubalis) were introduced to Brazil in 1895. Many authors have used microsatellites for genetic characterization of buffalo, but only some papers include molecular markers in Brazilian populations. Cross-species utility of microsatellites is one of the preferred marker choice criteria. To develop a multiplexed set of microsatellites and characterize Brazilian buffalo 19 cattle microsatellites were tested. Three panels were finally developed with eleven that succeed in amplify and were polymorphic (58%). The average number of alleles was 5.42, with an average observed and expected heterocigozity of 0.441 and 0.695, respectively. Calculated overall exclusion power considering on e parent, two parents available and sample matching were 0.98, 0.9991 and 0.9999999996, respectively. The set has an exclusion power in Brazilian buffalo that allows its use in DNA based traceability and some paternity cases, such as multi-sire breeding scenarios, when one parent is known and could be genotyped. Furthermore, highly informative tested microsatellites could be added to existing panels. [ABSTRACT FROM AUTHOR]

Abstract: Regulations for the use and labeling of genetically modified (GM) products and derived ingredients were implemented in Brazil in 2003. In 2008, GM maize line MON810 was approved for commercialization in Brazil; nevertheless, maize Bt11, Bt176 and MON810 were found in Brazilian market products sold in 2000 and 2001. Nested polymerase chain reaction (PCR) method was employed to monitor the presence of MON810 in 81 maize-derived products (maize flour, corn meal, maize flour flakes and polenta) that are sold in Brazilian markets from 2005 to 2007, after the implementation of genetically modified organism (GMO) labeling regulation. The sensitivity of nested PCR for MON810 detection was 0.1%. CTAB protocol was suitable for the extraction of amplifiable maize DNA from maize flour, corn meal, maize flour flakes, and polenta. MON810 GM maize line was not detected by specific nested PCR in 81 samples of maize-derived food sold in Brazil from 2005 to 2007. This paper reports data concerning the detection of GM maize after publishing Brazilian regulations that stipulate directions for using and labeling of foods and ingredients containing GMOs. [Copyright &y& Elsevier]

Strong phosphine resistance in Tribolium castaneum is due to point mutations in DNA that code for amino acid changes of P45S and/or G131S in the enzyme dihydrolipoamide dehydrogenase (DLD). One allele coding for P45S is the most common in all phosphine-resistant US populations and in one strain from Brazil (TCBR), whereas another allele, G131S, occurs only in Australian beetles. Dose-mortality studies found that the TCBR strain was more resistant to phosphine than US populations. To investigate strong resistance mutations in TCBR, we sequenced cDNA for DLD in TCBR and compared results with a US population from Kansas. The common P45S mutation was detected in both populations, but two additional mutations G131D and V167A were identified only from TCBR. We used a CAPS marker (Cleaved Amplified Polymorphic Sequence) for P45S, herein designated M1, to survey this resistance allele in TCBR. We also developed a marker for the G131D mutation, designated M2. Only two genotypes, R1R1S2S2 (homozygous for resistance at M1, but homozygous susceptible at the M2 site) and R1S1R2S2 (heterozygous for resistance at M1 and M2) existed in TCBR. However, phosphine resistance levels were similar between individuals with the two genotypes. Beetles with strong resistance in TCBR may be homozygous for either the presence of the common P45S allele, or heterozygous for two resistance alleles at a second locus, G131D. The strong resistance phenotype in TCBR may be expressed differently based on previously unknown mutations at the DLD locus, but this will require further research to resolve. [ABSTRACT FROM AUTHOR]

Largemouth Bass (Micropterus salmoides) have been introduced on a global scale for sport fishing but represent a conservation concern given their documented negative impacts on native faunal diversity and abundance. Recent research using molecular data to characterize invasive Largemouth Bass populations elsewhere has demonstrated that populations are typically characterized by limited genetic diversity, or represent a combination of Largemouth Bass and Florida Bass (Micropterus floridanus). To test whether these traits were consistent with invasive populations in Brazil, we generated mitochondrial sequence data from four established populations of Largemouth Bass collected in southern Brazil as well as a local aquaculture facility to confirm species identity and quantify levels of genetic diversity. We identified the exclusive presence of Largemouth Bass in the region and observed limited levels of haplotype (haplotype diversity = 0.0684, SE = 0.038) and nucleotide diversity (0.0003, SE = 0.0002) which suggested the presence of a founder effect associated with introduction. Each of the four populations were dominated by a single haplotype that was identical to one recovered from a nearby aquaculture facility, which identified this facility as a potential introduction source. [ABSTRACT FROM AUTHOR]

Background: Leishmania infantum, the etiological agent of visceral leishmaniasis, is a neglected zoonosis that requires validation and standardization of satisfactory diagnostic methodologies. Thus, the aim of the present study was to evaluate the effectiveness of cathepsin L-like protease as a target for making molecular diagnoses and as a phylogenetic marker enabling to understand the intraspecies variations and evolutionary history of L. infantum in Brazil.Methods: We used 44 isolates of L. infantum. The cathepsin L-like gene fragments were amplified, sequenced, manually aligned and analyzed using inference methods. The sequences generated were used to search and design oligonucleotide primers to be used in reactions specific to the target parasite.Results: The cathepsin L-like gene did not show any intraspecies variability among the isolates analyzed. The pair of primers proposed amplified the target deoxyribonucleic acid (DNA) of L. infantum isolates and were effective for DNA amplification at concentrations of as low as 10- 11 ng/μl. The proposed marker did not present cross-reactions with other hemoparasites. When used for making the diagnosis in a panel of clinical samples from dogs, a positivity rate of 49.03% (102/208) was obtained, versus 14.42% (30/208) for a ribosomal internal transcribed spacer (ITS) marker. In samples from sandflies, the rate was 6.25% and from humans, 14.28%.Conclusions: The results described in this work allow us to infer that CatLeish-PCR is a sensitive and specific marker for use in diagnostic trials of L. infantum and in clinical and epidemiological surveys. [ABSTRACT FROM AUTHOR]

The extraordinary species diversity of the Neotropical freshwater fish fauna is world renown. Yet, despite rich species diversity, taxonomic and genetic resources for its Cerrado ichthyofauna remain poorly developed. We provide a reference library of 149 DNA barcodes for 39 species/lineages of Cerrado headwater stream fishes from the Brazilian Distrito Federal and nearby areas and test the utility of distance‐based criteria, tree‐based criteria and minibarcodes for specimen identification. Mean Kimura 2‐parameter genetic distances within species to orders ranged 1·8–12·1%. However, mean intraspecific v. congeneric‐interspecific distances (0·9–1·3%) overlapped extensively and distance‐based barcoding failed to achieve correct identifications due to c. 4–12·1% error rates and 19·5% ambiguous identifications related to the presence of singletons. Overlap was reduced and best‐match success rates improved drastically to 83·5% when Characidium barcodes representing potential misidentifications or undescribed species were removed. Tree‐based monophyly criteria generally performed similarly to distance methods, correctly differentiating up to c. 85% of species/lineages despite neighbour‐joining and Bayesian tree errors (random lineage‐branching events, long‐branch attraction). Five clusters (Ancistrus aguaboensis, Characidium spp., Eigenmannia trilineata, Hasemania hanseni and Hypostomus sp. 2) exhibited deep intraspecific divergences or para−/polyphyly and multiple Barcode Index Number assignments indicative of putative candidate species needing taxonomic re‐examination. Sliding‐window analyses also indicated that a 200 bp minibarcode region performed just as well at specimen identification as the entire barcode gene. Future DNA barcoding studies of Distrito Federal–Cerrado freshwater fishes will benefit from increased sampling coverage, as well as consideration of minibarcode targets for degraded samples and next‐generation sequencing. [ABSTRACT FROM AUTHOR]

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Multidrug-resistant Salmonella enterica serovar Heidelberg isolates are frequently recovered in the Netherlands from poultry meat imported from South America. Our aim was to retrospectively assess the characteristics of the antimicrobial determinants, gene content and the clonal relatedness of 122 unique S. Heidelberg isolates from chicken meat from Brazil (n = 119) and Argentina (n = 3) that were imported between 2010 and 2015. These isolates were subjected to antimicrobial susceptibility testing, PCR and Illumina HiSeq2500 whole genome sequencing. Draft genomes were assembled to assess the gene content, and the phylogenetic relationships between isolates were determined using single nucleotide polymorphisms. Ciprofloxacin-resistance was identified in 98.4% of the isolates and 83.7% isolates showed resistance to the extended-spectrum cephalosporins cefotaxime and ceftazidime (83.6% and 82.8% respectively). Of the latter, 97.1% exhibited an AmpC phenotype and contained blaCMY-2, whereas the remaining three isolates contained an extended spectrum beta-lactamase. Of the 99 extended-spectrum cephalosporins-resistant isolates harboring CMY-2 plasmids, 56.6% contained the incompatibility group I1 replicon. Phylogenetic cluster analysis showed that all isolates from Brazil clustered together, with 49% occurring in clusters larger than 5 isolates that revealed intra-cluster similarities based on geographical location and/or resistance profiles. The remaining isolates were classified in smaller clusters or as singletons, highlighting the large diversity of S. Heidelberg in the poultry chain in Brazil that was revealed by this study. Considering the potential public health risk associated with multidrug-resistant S. Heidelberg in imported poultry, collaborative whole genome sequencing-based surveillance is needed to monitor the spread, pathogenic properties and epidemiological distribution of these isolates. [ABSTRACT FROM AUTHOR]

The aim of the present study was to detect DNA of Toxoplasma gondii in Crassostrea spp. oysters cultured in the state of Pará, Brazil. A total of 400 oysters were directly collected from a fixed rack system. Gills, gastrointestinal tract (GIT) and intervalvular liquid were separated and grouped into pool samples of 10 animals, resulting in 40 samples each of gills, GIT and intervalvular liquid. DNA extraction was performed using a commercial kit, and T. gondii DNA was detected by nested PCR using the primers Toxo3 and Toxo4, which produced an amplification product of 155 bp of the T. gondii gene B1. Nucleotide sequencing was performed for positive samples, and the obtained sequences were identified by comparison with sequences in GenBank. The DNA of T. gondii was detected in 5.8% (7/120) of the pool samples, of which 7.5% (3/40) was in the GIT, 5% (2/40) in the gills, and 5% (2/40) was in the intervalvular liquid. The obtained sequences presented 100% identity and overlap with T. gondii DNA sequences. This is the report of detection of T. gondii DNA in oysters from genus Crassostrea spp. originating from the state of Pará, eastern Amazon. [ABSTRACT FROM AUTHOR]

Background: Some sexually transmitted infectious agents, such as Chlamydia trachomatis and Herpes simplex, cause local inflammation, and could contribute to Human Papillomavirus (HPV) and cervical lesion progression. Thus, the aim of this study was to determine any association between the presence of microorganisms of gynecological importance, sexual behavior, clinical and demographical variables to the development and progress of cervical lesions.Methods: One hundred and thirty-two women between 14 and 78 years and living at Vitória da Conquista, Bahia, Brazil, were included (62 individuals with cervical lesions and 70 without lesions). They answered a questionnaire to provide data for a socioeconomic and sexual activity profile. Samples of cervical swabs were collected and analyzed by PCR to detect genital microorganisms and HPV. Quantitative PCR was used to detect and quantify Ureaplasma urealyticum and Ureaplasma parvum. Univariate and multiple logistic regression were performed to measure the association with the cervical lesions, and an odds ratio (OR) with 95% confidence intervals (95%CI) were calculated. The Mann-Whitney U test was also used to compare the microorganism load in the case and control groups. The significance level was 5% in all hypotheses tested.Results: Cervical lesions were associated with: women in a stable sexual relationship (OR = 14.21, 95%CI = 3.67-55.018), positive PCR for HPV (OR = 16.81, 95%CI = 4.19-67.42), Trichomonas vaginalis (OR = 8.566, 95%CI = 2.04-35.94) and Gardnerella vaginalis (OR = 6.13, 95%CI = 1.53-24.61), adjusted by age and qPCR for U. parvum. U. parvum load showed a statistical difference between the case and control groups (p-value = 0.002).Conclusion: Variables such as stable relationship, HPV, T. vaginalis, G. vaginalis were associated with cervical lesions in epidemiological studies. U. parvum load was higher in woman with cervical lesions compared with women without lesions. Additional studies are needed to better understand the role of these factors in cervical lesion development. [ABSTRACT FROM AUTHOR]

Objective To compare counts of Aggregatibacter actinomycetemcomitans, Prevotella intermedia, Porphyromonas gingivalis and Fusobacterium nucleatum between crack users and non-users. Materials and methods A cross-sectional study was conducted involving seventy-four crack cocaine users and eighty-one non-users matched for age, gender and tobacco use. Demographic and clinical variables were analysed. Subgingival bacterial samples were collected from four sites with the greatest probing depths and were analysed using real-time polymerase chain reaction. Results No significant difference was found in the prevalence of total counts for each bacterial species analysed between groups. However, crack users had a 1.85 (95% CI: 1.03-3.31), 2.19 (95% CI 1.24-3.88), 2.53 (95% CI 1.27-5.04) and 2.40 (95% CI 1.22-4.75) greater probability of having the higher counts (≥75th percentile) for Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia and Fusobacterium nucleatum, respectively. Conclusion Although some crack users had higher (>75th percentile) bacterial counts for Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia and Fusobacterium nucleatum, total counts did not differ between crack users and non-users, leading to the hypothesis that the higher occurrence of periodontitis on crack users may be related to other non-bacterial factors. [ABSTRACT FROM AUTHOR]

Background: Attention-deficit/hyperactivity disorder (ADHD) symptoms are dimensionally distributed in the population. This study aimed to assess the role of the catechol-O-methyltransferase (COMT) and of the dopamine transporter (DAT1) genes on ADHD symptoms in the general population. Methods: We investigated 4101 individuals from the 1993 Pelotas Birth Cohort Study using the parent version of the Strengths and Difficulties Questionnaire (SDQ) at ages 11 and 15 years. The SDQ hyperactivity/inattention scores were the main outcomes. Results: Linear regression analyses demonstrated that the increasing number of COMT158Val and DAT1 10R alleles significantly predicted increasing SDQ hyperactivity/inattention scores in boys at both 11 and 15 years of age (β coefficient = 0.049, f = 2.189, p = 0.029, R² = 0.012, and β coefficient = 0.064, f = 2.832, p = 0.005, R² = 0.008, respectively). The presence of both COMT158Val and DAT1 10R alleles was also associated with full categorical ADHD diagnosis at 18 years of age in boys (χ² = 4.561, p = 0.033, odds ratio 2.473, 95% confidence interval 1.048-5.838) from this cohort. We did not observe these associations in girls. Limitations: Our analyses of SDQ hyperactivity/inattention scores were not corrected for SDQ scores of conduct problems because these variables were highly correlated. Conclusion: This study demonstrates a role for COMT and DAT1 genes on hyperactivity/inattention symptoms and provides further support for ADHD as the extreme of traits that vary in the population. It also confirms previous evidence for sexual dimorphism on COMT and DAT1 gene expression. [ABSTRACT FROM AUTHOR]

The microhylid frogs belonging to the genusArcovomerhave been reported from lowland Atlantic Rainforest in the Brazilian states of Espírito Santo, Rio de Janeiro, and São Paulo. Here, we use DNA barcoding to assess levels of genetic divergence between apparently isolated populations in Espírito Santo and Rio de Janeiro. Our mtDNA data consisting of cytochrome oxidase subunit I (COI) nucleotide sequences reveals 13.2% uncorrected and 30.4% TIM2 + I + Γ corrected genetic divergences between these two populations. This level of divergence exceeds the suggested 10% uncorrected divergence threshold for elevating amphibian populations to candidate species using this marker, which implies that the Espírito Santo population is a species distinct fromArcovomer passarellii. Calibration of our model-corrected sequence divergence estimates suggests that the time of population divergence falls between 12 and 29 million years ago. [ABSTRACT FROM AUTHOR]

The New World genus Philonome Chambers, 1874 is revised. This genus comprises twelve species, seven of which are described as new: two species, P. nigrescens sp. n. and P. wielgusi sp. n., from the United States; four species, P. albivittata sp. n., P. curvilineata sp. n., P. kawakitai sp. n., and P. lambdagrapha sp. n., from French Guiana; and one species, P. penerivifera sp. n., from Brazil. Lectotypes are designated for Philonome clemensella Chambers, 1874 and P. rivifera Meyrick, 1915. Partially on evidence of their head morphology and particularly from molecular evidence, the genus Philonome, previously associated with Bucculatricidae or Lyonetiidae, is reassigned to Tineidae. A possible systematic position of Philonome within Tineidae is discussed. Eurynome Chambers, 1875, is synonymized with Argyresthia Hübner, 1825 (Argyresthiidae). Photographs of adults and illustrations of genitalia, when available, are provided for all described species of Philonome and two species previously misplaced in Philonome, Argyresthia luteella (Chambers, 1875) and Elachista albella (Chambers, 1877). In addition, DNA barcodes were used for the delimitation of most species. [ABSTRACT FROM AUTHOR]

Here we describe a small mammal community in nonfragmented Atlantic Forest in southern Brazil. A total of 146 individuals were live captured on the ground and in trees (total effort: 5600 trap-nights). Twelve species were identified by morphology, and identification of seven species was confirmed by DNA barcoding. Most species were terrestrial, with Euryoryzomys russatus being the most frequently captured, while the rodent Juliomys pictipes was semiarboreal and the marsupial Marmosa paraguayana was arboreal. With the capture of Trinomys iheringi, we extend the species distribution to the south. Species favored in disturbed environments as Oligoryzomys spp. and Akodon spp. were uncommon, and this small mammal community is typical of a well-conserved forest. [ABSTRACT FROM AUTHOR]

Ceratocystis paradoxa (Anamorph: Thielaviopsis paradoxa) is parasitic on a range of economic and food crops and is the cause of dry basal rot, a limiting disease in oil palm. The objective of this study was to determinate the pathogenic and genetic diversity of Thielaviopsis isolates from oil palms in Colombia, Ecuador and Brazil. A total of 164 strains of Thielaviopsis paradoxa were characterized using pathogenicity tests, random amplified polymorphic DNA ( RAPD) markers and PCR sequencing of the internal transcribed spacer ( ITS) region of 5.8 S ribosomal DNA. Oil palm seedlings were inoculated by injecting the base of stems in the seedling stage with a fungal suspension and severity scores of disease reactions were evaluated. PCR amplification of the ITS region resulted in a 590 base pair (bp) product. Digestion of the PCR product with two restriction enzymes produced three restriction patterns, which according to ITS sequences could be classified as T. paradoxa. Six RAPD primers gave polymorphic bands in T. paradoxa. Population structure analyses of the RAPD data suggested that most of the isolates obtained in this study belonged to a single population. The genetic diversity of the isolates from South America was intermediate, and therefore, T. paradoxa is likely to be predominantly clonal compared with Ceratocystis species. Sporadic sexual reproduction may occur for T. paradoxa but is secondary to clonal reproduction. Data on pathogen diversity will provide information on breeding strategies and population structures. [ABSTRACT FROM AUTHOR]

A novel soybean sudden death syndrome (SDS) pathogen from Argentina and Brazil is formally described herein as Fusarium crassistipitatum based on detailed phenotypic analyses of macro- and microscopic characters and phylogenetic analyses of multilocus DNA sequence data. Fusarium crassistipitatum can be distinguished from the other soybean SDS and bean ( Phaseolus/ Vigna) root rot pathogens (BRR) phenotypically by the production of yellowish colonies on PDA; and tall, stout, and mostly unbranched conidiophores with a thick-walled base, which form multiseptate conidia apically. Phylogenetic species recognition based on genealogical concordance of a six-gene dataset strongly supported the reciprocal monophyly of F. crassistipitatum with respect to the other SDS and BRR pathogens. Isolates of F. crassistipitatum were able to induce typical SDS foliar and root rot symptoms on soybean that were indistinguishable from those caused by three other SDS pathogens (i.e., F. virguliforme, F. brasiliense, and F. tucumaniae) on susceptible cultivars A-6445RG and N-4613RG in a pathogenicity experiment. [ABSTRACT FROM AUTHOR]

The family Phyllostomidae belongs to the most abundant and diverse group of bats in the Neotropics with more morphological traits variation at the family level than any other group within mammals. In this work, we present data of chromosome banding (G, C and Ag-NOR) and Fluorescence In Situ Hybridization (FISH) for representatives of Rhinophylla pumilio Peters, 1865 collected in four states of Brazil (Amazonas, Bahia, Mato Grosso and Pará). Two karyomorphs were found in this species: 2n=34, FN=64 in populations from western Pará and Mato Grosso states and 2n=34, FN=62 from Amazonas, Bahia, and northeastern Pará and Marajó Island (northern). Difference in the Fundamental Number is determined by variation in the size of the Nucleolar Organizer Region (NOR) accompanied with heterochromatin on chromosomes of pair 16 or, alternatively, a pericentric inversion. The C-banding technique detected constitutive heterochromatin in the centromeric regions of all chromosomes and on the distal part of the long arm of pair 15 of specimens from all localities. FISH with a DNA telomeric probe did not show any interstitial sequence, and an 18S rDNA probe and silver staining revealed the presence of NOR in the long arm of the pair 15, associated with heterochromatin, and in the short arm of the pair 16 for all specimens. The intra-specific analysis using chromosome banding did not show any significant difference between the samples. The comparative analyses using G-banding have shown that nearly all chromosomes of R. pumilio were conserved in the chromosome complements of Glossophaga soricina Pallas, 1766, Phyllostomus hastatus Pallas, 1767, Phyllostomus discolor Wagner, 1843 and Mimon crenulatum Geoffroy, 1801, with a single chromosomal pair unique to R. pumilio (pair 15). However, two chromosomes of M. crenulatum are polymorphic for two independent pericentric inversions. The karyotype with 2n=34, NF=62 is probably the ancestral one for the other karyotypes described for R. pumilio. [ABSTRACT FROM AUTHOR]

Blast caused by Magnaporthe grisea ( Pyricularia grisea) is a disease that occurs in many important gramineous plants in Brazil such as rice, wheat, triticale and barley. In 2005, the presence of this disease was reported on black oat ( Avena strigosa) at different locations of Parana state. Due to little information of M. grisea that is infecting this host, this work aimed to characterize it at molecular, sexual and pathogenic level. DNA analysis showed that M. grisea from black oat formed a homogenous and genetic distinct group of its own, different from other hosts, including rice, wheat, triticale and barley. Isolate 15720 was an exception, because it was similar to wheat isolate. There was no sexual compatibility between M. grisea from oat and other tested hosts. In pathogenic terms, isolates of M. grisea from oat infected triticale, wheat, rye, millet, barley, sorghum and rice; cross-inoculation was positive with wheat, triticale, rice and barley. [ABSTRACT FROM AUTHOR]

Background and aims. The application of DNA barcoding as a global standard for fish identification is probing diverse worldwide realms (Nearctic, Australian and the Neotropics) and environments (e.g. marine and freshwater). Comparing the patterns of sequence divergence among conspecific and congeneric taxa between realms can provide valuable information on recent evolutionary histories of lineages as barcode data accumulates. Materials and methods. Herein, we have analyzed over 100 species (around 50%) of the Neotropical fish fauna from the São Francisco River, in southeast Brazil. Our aims were to test the performance of DNA barcoding in this biodiversity-rich region, and to compare patterns of genetic divergence with previous studies. Results. The mean Kimura two-parameter distances within species, genera, families, orders, and classes were 0.5, 10.6, 21.0, 22.7, and 24.4%, respectively, with 100% of the species examined successfully differentiated by barcoding. With the exception of Astyanax bimaculatus lacustris, Piabina argentea, and Bryconamericus stramineus, all other species yield a single, cohesive cluster of barcode sequences. The average 'nearest-neighbor distance' was 11.12%, 21-fold higher than the mean within species distance of around 0.54%. In a few instances, deep lineage divergences among conspecifics (up to 10%) and congenerics (up to 22.9%) taxa were revealed. Conclusions. Reflecting possible cases of cryptic speciation and the deeper phylogeographic history of São Francisco fish fauna, with some higher clades extending back into the late Cretaceous and Cenozoic (90 mya), when much of the diversification of the Neotropical region apparently took place. In addition, barcodes also highlighted misidentifications and helped to document range extensions for known species. [ABSTRACT FROM AUTHOR]

Background and aims: Considering the promising use of DNA barcoding for species identification, the importance of the freshwater fish fauna of the Paraíba do Sul River Basin, and its advanced stage of degradation, the present study evaluated the effectiveness of DNA barcoding to identify the fish species in this basin. Materials and methods: A total of 295 specimens representing 58 species belonging to 40 genera, 17 families, and 5 orders were sequenced. Results: The DNA barcodes discriminated all species analyzed without ambiguity. The results showed a pronounced difference between conspecific and congeneric pair-wise sequence comparisons, demonstrating the existence of a 'barcode gap' for the species analyzed. The nearest-neighbor distance analysis showed only three cases with Kimura two-parameter values lower than a 2% divergence threshold. However, the patterns of divergence observed in each case remained sufficient to discriminate each species, revealing the accuracy of DNA barcoding even cases with relatively low genetic divergence. At the other extreme, three species displayed high genetic sequence divergence among conspecifics. For two cases, Characidium alipioi and Geophagus proximus, barcoding proved effective at flagging possible new species. For another case, Astyanax bimaculatus, the use of DNA barcoding of the comparison of shared freshwater fish fauna between different basins revealed itself as highly useful in disclosing that the previously identified A. bimaculatus 'cluster A' probably represents the species Astyanax altiparanae. Conclusion: The present study is among the first to assess the efficiency of barcoding for the Brazilian freshwater fishes. The results demonstrate the utility of barcoding to identify the fauna from this basin, contribute to an enhanced understanding of the differentiation among species, and to help flag the presence of overlooked species. [ABSTRACT FROM AUTHOR]

Background and aims. We analyzed a small and wide geographically distributed Neotropical freshwater fish, the Piabina argentea from the Upper Paraná Basin, to check the hypothesis that this species is composed of more than one biological unit, since it has a limited dispersion, through the DNA barcode technique. Materials and methods. Partial mitochondrial COI and CytB gene sequences were obtained for 58 specimens drawn from 13 localities. Results. Phylogenetic analysis revealed six major clusters of P. argentea. Kimura-two-parameter (K2P) genetic divergences among these six P. argentea clusters ranged from 2 to 5.6% and from 2.3 to 5.4% for COI and CytB genes, respectively, and these values were on average approximately nine times greater than intra-cluster K2P divergences. The fixation index ( FST) among clusters showed very high values and the haplotype network analysis displayed seven unconnected units. Conclusion. These results reinforce the hypothesis that the widely distributed P. argentea species concept as currently conceived actually represents more than one species (possibly six). These results demonstrate the efficacy of DNA barcoding for the discovery of hidden diversity in Neotropical freshwater fishes, and we conclude that barcoding is a useful tool for alpha taxonomy. [ABSTRACT FROM AUTHOR]

Background: Brazilian Quilombos are Afro-derived communities founded mainly by fugitive slaves between the 16th and 19th centuries; they can be recognized today by ancestral and cultural characteristics. Each of these remnant communities, however, has its own particular history, which includes the migration of non-African derived people. Methods: The present work presents a proposal for the origin of the male founder in Brazilian quilombos based on Y-haplogroup distribution. Y haplogroups, based on 16 binary markers (92R7, SRY2627, SRY4064, SRY10831.1 and .2, M2, M3, M09, M34, M60, M89, M213, M216, P2, P3 and YAP), were analysed for 98 DNA samples from genetically unrelated men from three rural Brazilian Afro-derived communities-- Mocambo, Rio das Rããs and Kalunga--in order to estimate male geographic origin. Results: Data indicated significant differences among these communities. A high frequency of non-African haplogroups was observed in all communities. Conclusions: This observation suggested an admixture process that has occurred over generations and directional mating between European males and African female slaves that must have occurred on farms before the slaves escaped. This means that the admixture occurred before the slaves escaped and the foundation of the quilombo. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Brazilian Amerindians have experienced a drastic population decrease in the past 500 years. Indeed, many native groups from eastern Brazil have vanished. However, their mitochondrial mtDNA haplotypes, still persist in Brazilians, at least 50 million of whom carry Amerindian mitochondrial lineages. Our objective was to test whether, by analyzing extant rural populations from regions anciently occupied by specific Amerindian groups, we could identify potentially authentic mitochondrial lineages, a strategy we have named 'homopatric targeting'. Results: We studied 173 individuals from Queixadinha, a small village located in a territory previously occupied by the now extinct Botocudo Amerindian nation. Pedigree analysis revealed 74 unrelated matrilineages, which were screened for Amerindian mtDNA lineages by restriction fragment length polymorphism. A cosmopolitan control group was composed of 100 individuals from surrounding cities. All Amerindian lineages identified had their hypervariable segment HVSI sequenced, yielding 13 Amerindian haplotypes in Queixadinha, nine of which were not present in available databanks or in the literature. Among these haplotypes, there was a significant excess of haplogroup C (70%) and absence of haplogroup A lineages, which were the most common in the control group. The novelty of the haplotypes and the excess of the C haplogroup suggested that we might indeed have identified Botocudo lineages. To validate our strategy, we studied teeth extracted from 14 ancient skulls of Botocudo Amerindians from the collection of the National Museum of Rio de Janeiro. We recovered mtDNA sequences from all the teeth, identifying only six different haplotypes (a low haplotypic diversity of 0.8352± 0.0617), one of which was present among the lineages observed in the extant individuals studied. Conclusions: These findings validate the technique of homopatric targeting as a useful new strategy to study the peopling and colonization of the New World, especially when direct analysis of genetic material is not possible. [ABSTRACT FROM AUTHOR]

Analyses of mitochondrial 12S and 16S rDNA sequences lead us to propose that the Neotropical hylid genus Phyllodytes is paraphyletic. The level of divergence between the Trinidadian endemic P. auratus and the two Brazilian Phyllodytes included in the analyses (Phyllodytes sp. and P. luteolus) is greater than that of inter-generic distances within the Lophiohylini. The molecular evidence here reported, behavioural differences and restriction to a single host plant in a geographically limited area differentiates Phyllodytes auratus from other supposed Phyllodytes evidencing its unique taxonomic status. We therefore propose a new genus, Phytotriades gen. nov., for Phyllodytes auratus. P. auratus mitochondrial cytochrome b sequences obtained from one locality (seven individuals) contained two haplotypes, one individual differing by a single transition. The other locality (one individual) had the commoner haplotype. The low genetic divergence between the two populations suggests recent isolation at these two localities. [ABSTRACT FROM AUTHOR]

BrazilianFusariumisolates causing soybean sudden death syndrome (SDS) were characterized by comparing them with otherFusariumisolates associated with soybean root rot, as well asF. solanif.sp.glycinesisolates associated with the disease in the USA, using molecular (mitochondrial and nuclear rDNA), morphological, cultural and pathogenic characteristics. On the basis of pathogenicity data, and restriction fragment length polymorphism and sequence analysis of the rDNA internal transcribed spacer (ITS) regions, isolates formed a group distinct from nonSDSF. solaniisolates, as well as otherFusariumspecies. ITS sequence analysis also revealed that Brazilian isolates were distinct from the majority of SDS pathogens from the USA (Fusarium virguliforme) and conformed toFusarium tucumaniae. [ABSTRACT FROM AUTHOR]

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To assess whether the major histocompatibility complex (MHC) profile of patients presenting with primary antiphospholipid syndrome (PAPS) is different from that of patients with secondary antiphospholipid syndrome (SAPS), we studied 123 patients, 34 of whom presented PAPS and 35 SAPS due to systemic lupus erythematosus (SLE), 54 SLE patients without antiphospholipid syndrome (APS), and 166 controls. HLA-DRB1 and DQB1 alleles were typed using amplified DNA hybridized with sequence-specific primers. Compared to controls, PAPS patients exhibited a nonsignificantly increased frequency of DR53-associated alleles, and SAPS patients presented an increased frequency of HLA-DRB1*03 alleles (corrected P = 0.05). In addition, HLA-DRB1*03 alleles were over-represented in SAPS patients presenting anticardiolipin antibody (aCL) (P[sub c] = 0.02), in SLE patients as a whole (P[sub c] < 0.0001), and in SLE patients without APS (P[sub c] = 0.02). The frequency of aCL among SLE patients presenting or not HLA-DRB1*03 alleles was closely similar. A trend to an increase in the frequency of the DQB1*0604 allele (14.3 versus 4.2%, P = 0.03) and of the DQB1*0302 allele (31.4 versus 12.7%, P = 0.01) was observed in SAPS. Taken together, these results indicate that the association of SAPS with HLA-DRB1*03 is due to the association with SLE and is not due to aCL, and suggest that the HLA class II profile of PAPS is different from that of SAPS. [ABSTRACT FROM AUTHOR]

An unidentified shark carcass (minus head, fins and entrails) was landed in Fortaleza, Brazil following its commercial fishery capture off Ceará State in north-eastern Brazil. The absence of key morphological characters precluded traditional identification, necessitating the employment of DNA bar coding techniques. The obtained 639 nts COI sequence fragment perfectly matched six of seven Odontaspis ferox sequences available on the Barcode of Life Data (BOLD) system database, and was 99.2% similar to the seventh. [ABSTRACT FROM AUTHOR]

Background: A significant increase in pertussis incidence occurred in Brazil, from 2011 to 2014, despite high coverage of childhood immunization with whole-cell-pertussis (wP) containing vaccines. This study presents pertussis surveillance data from São Paulo state and discusses the challenges to interpret them considering pertussis cyclic epidemic behavior, the introduction of new diagnostic techniques and new vaccination strategies, and enhanced disease awareness during epidemics.Methods: Observational study including pertussis cases reported to the Surveillance System in São Paulo state, from January 2001 to December 2015. Pertussis cases data were retrieved from the National Notifiable Diseases Information System (SINAN) website and from São Paulo state Epidemiological Surveillance Center (CVE/SP) database. Vaccination coverage and homogeneity data were collected from the Unified Health System Department of Informatics (DATASUS). We presented cases distribution by year, age group and diagnostic criteria and calculated pertussis incidence rates. The proportions of cases among different age groups were compared using chi-square test for trend.Results: Infants less than 1 year of age were the most affected during the whole period, but the proportions of cases in this age group had a significant decreasing trend, with significant increase in the proportions of cases reported among older age groups (1-4, 5-10 and ≥20 years). Cases among infants aged less than 6 months represented ≥90% of all cases in children less than 1 year of age in all but 2 years (2012 and 2015). A non-significant decrease in the proportion of cases among infants aged < 2 months was observed in parallel to a significant increase in the proportion of cases in infants aged 6-11 months.Conclusions: A pertussis outbreak has occurred in a state with universal use of wP vaccine. The disease cyclic behavior has probably had a major role in the increased incidence rates registered in São Paulo state, from 2011 to 2014, as well as in the decreased incidence in 2015. Maternal vaccination cannot explain the drop in the number of cases among all age groups, in 2015, as herd protection is not expected, but may have had an impact on the number of cases in infants aged < 2 months. [ABSTRACT FROM AUTHOR]