Search

Ligula intestinalis is a cestode parasite that affects freshwater fish in different countries of the world. The current study aims to reveal the phylogenetic, genetic and haplotype diversity of mt-CO1 gene sequences sent to the NCBI database from different countries by using in-silico analysis. The 105 mt-CO1 (371 bp) gene sequences of L. intestinalis obtained from NCBI were used for bioinformatics analyses. Sequences were subjected to phylogenetic and haplotype analysis. As a result of the haplotype analysis of L. intestinalis, 38 haplotypes were obtained from 13 different countries. Hap24 constituted 44.76% of the obtained haplotype network. Changes in nucleotides between haplotypes occurred at 1-84 different points. China and Turkey have highest fixation index (Fst) values of 0.59761, while the lowest (-0.10526) was found between Russia and Turkey. This study provides a baseline for future studies on extensive scale on the epidemiology, ecological aspects, distribution pattern, transmission dynamics and population dispersion of L. intestinalis worldwide. Resumo Ligula intestinalis é um parasita cestódeo que acomete peixes de água doce em diversos países do mundo. O presente estudo visa revelar a diversidade filogenética, genética e de haplótipos das sequências do gene mt-CO1 enviadas ao banco de dados do NCBI de diferentes países, por meio de análise in-silico. As sequências gênicas de 105 mt-CO1 (371 pb) de L. intestinalis obtidas do NCBI foram utilizadas para análises bioinformáticas. As sequências foram submetidas a análise filogenética e de haplótipos. Como resultado da análise de haplótipos de L. intestinalis, 38 haplótipos foram obtidos de 13 países diferentes. Hap24 constituiu 44,76% da rede de haplótipos obtida. Mudanças nos nucleotídeos entre os haplótipos ocorreram em 1-84 pontos diferentes. A China e a Turquia apresentam os maiores valores do índice de fixação (Fst), 0,59761, enquanto o menor (-0,10526) foi encontrado entre a Rússia e a Turquia. Este estudo fornece uma linha de base para futuros estudos em larga escala sobre epidemiologia, aspectos ecológicos, padrão de distribuição, dinâmica de transmissão e dispersão populacional de L. intestinalis em todo o mundo.

Copy number variations (CNV) are an important source of genetic variation. CNV has been increasingly studied and frequently associated with diseases and productive traits in livestock animals. However, CNV-based genome-wide association studies (GWAS) in Santa Inês sheep, one of the principal sheep breeds in Brazil, have not yet been reported. Thus, the aim of this study was to investigate the association between CNV and growth, efficiency and carcass traits in sheep. The Illumina OvineSNP50 BeadChip array was used to detect CNV in 491 Santa Inês individuals. Then, CNV-based GWAS was performed with a linear mixed model approach considering a genomic relationship matrix, for ten traits: (1) growth: body weight at three (W3) and six (W6) months of age; (2) efficiency: residual feed intake (RFI) and feed efficiency (FE) and (3) carcass: external carcass length (ECL), leg length (LL), carcass yield (CY), commercial cuts weight (CCW), loin eye area (LEA) and subcutaneous fat thickness (SFT). We identified 1,167 autosomal CNV in 438 sheep, with 294 non-redundant CNV, ranging from 21.8 to 861.9 kb, merged into 216 distinct copy number variation regions (CNVRs). One significant CNV segment (p

Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N - and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved ‘high-coverage’ and ‘high-accuracy’ glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics., This analysis presents the results of a community-based evaluation of existing software for large-scale glycopeptide data analysis.

Purpose To identify novel genes associated with intellectual disability (ID) in four unrelated families. Methods Here, through exome sequencing and international collaboration, we report eight individuals from four unrelated families of diverse geographic origin with biallelic loss-of-function variants in UBE4A. Results Eight evaluated individuals presented with syndromic intellectual disability and global developmental delay. Other clinical features included hypotonia, short stature, seizures, and behavior disorder. Characteristic features were appreciated in some individuals but not all; in some cases, features became more apparent with age. We demonstrated that UBE4A loss-of-function variants reduced RNA expression and protein levels in clinical samples. Mice generated to mimic patient-specific Ube4a loss-of-function variant exhibited muscular and neurological/behavioral abnormalities, some of which are suggestive of the clinical abnormalities seen in the affected individuals. Conclusion These data indicate that biallelic loss-of-function variants in UBE4A cause a novel intellectual disability syndrome, suggesting that UBE4A enzyme activity is required for normal development and neurological function.

he aims of this study were to investigate the genetic variability and the genotype × environment interaction for quality and yield traits in common bean (Phaseolus vulgaris L.), to evaluate the degree of informativeness of the evaluations of grain quality in only one environment, to estimate genetic parameters for grain quality traits, and to select lines with superior grain quality. We evaluated 81 carioca common bean lines in preliminary line trials in several environments for nutritional, technological, and commercial quality and selected the 20 superior lines, which were evaluated in validation trials in nine environments. Individual and combined ANOVAs were performed for all the traits. Correlations were estimated between Fe and Zn concentrations and yield; adaptability and phenotypic stability were analyzed; and superior genotypes were selected based on the Mulamba & Mock index. It is possible to increase the Fe, Zn, and crude protein concentrations and reduce cooking time; however, increasing crude fiber is a challenge. Preliminary evaluation of the quality traits in only one environment was effective and sufficient for selection of genotypes superior in Fe concentration, crude fiber, crude protein, and cooking time; and genetic gains can be obtained from selection for these traits. Genetic and phenotypic correlations were observed between Fe and Zn concentrations. The lines CNFC 16627, CNFC 16518, CNFC 16602, CNFC 16615, and CNFC 16520 are superior based on the selection index and are recommended for breeding for grain quality in carioca common bean. Made available in DSpace on 2021-09-10T15:05:59Z (GMT). No. of bitstreams: 1 cs.pdf: 249903 bytes, checksum: ef9f181f778db91831b3f000202db229 (MD5) Previous issue date: 2021

INTRODUCTION: The treatment of human and animal sporotrichosis is often performed with antifungal agents; however, the emergence of antifungal-resistant strains of Sporothrix species has been reported. We aimed to discuss the ability of Sporothrix species in developing resistance to the conventional antifungals and mechanisms for this. METHODOLOGY: Published data on databases (PubMed, Science Direct, Google Scholar) were investigated using a combination of keywords from 2008 to 2019 by the StArt tool. RESULTS: The minimal inhibitory concentrations values based on the Clinical and Laboratory Standards Institute (CLSI) from eight references were classified according to the epidemiological cutoff values in wild-type or non-wild-type strains. In this way, non-wild-type S. schenckii and, mainly, S. brasiliensis isolates were recognized on itraconazole, amphotericin B, terbinafine, and voriconazole, which are strains that deserve more attention toward antifungal control, with a probable risk of mutation to antifungal resistance. Among the few reviewed studied on antifungal resistance, the melanin production capacity (DHN-melanin, L-DOPA melanin, and pyomelanin), the low genetic diversity due to the abnormal number of chromosomes, and the mutation in cytochrome P450 are some of the factors for developing resistance mechanism. CONCLUSIONS: The emergence of Sporothrix species with in vitro antifungal resistance was evidenced and the possible mechanisms for resistance development may be due to the melanin production capacity, genetic diversity and mutations in cytochrome P450. Further studies should be carried out targeting gene expression for the development of antifungal resistance on Sporothrix species in order to prospect new therapeutic targets for human and veterinary use.

Size grading is a common management practice in fish farming to minimize growth variability. Such practice has not been established for pirarucu Arapaima gigas. Therefore, the present study assessed the effect of size grading on the growth of pirarucu. Juvenile pirarucu were divided into three groups: ungraded fish (U: mean initial weight 1.12 kg), small fish (S: mean initial weight 0.81 kg), and large fish (L: mean initial weight 1.36 kg), and reared for 129 days (phase I) and 158 additional days (phase II), consecutively. No significant difference was observed in the final length, specific growth rate, biomass, survival and feed conversion rate between fish groups. Ungraded fish presented a greater decrease in the coefficient of variation for weight in phase I than in phase II. Size sorting resulted in significantly higher growth after 287 days of farming in the L-graded fish (9.49 kg, final weight), followed by the ungraded group (8.80 kg) and S-graded group (8.01 kg). However, the mean weight of pooled S- and L-graded fish was similar to the ungraded fish group in phase I and phase II, indicating that grading did not improve the general performance of pirarucu in captivity. Made available in DSpace on 2020-03-17T00:37:39Z (GMT). No. of bitstreams: 1 CNPASA2020lajar.pdf: 787820 bytes, checksum: b928c656748c056eddc119958a51f226 (MD5) Previous issue date: 2020

BACKGROUND Erythema nodosum leprosum (ENL) is an acute and systemic inflammatory reaction of leprosy characterised by painful nodules and involvement of various organs. Thalidomide is an immunomodulatory and anti-inflammatory drug currently used to treat this condition. Cereblon (CRBN) protein is the primary target of thalidomide, and it has been pointed out as necessary for the efficacy of this drug in others therapeutics settings. OBJECTIVES In this study, we aimed to evaluate the influence of CRBN gene variants on the dose of thalidomide as well as its adverse effects during treatment of ENL. METHODS A total of 103 ENL patients in treatment with thalidomide were included in this study. DNA samples were obtained from saliva and molecular analysis of CRBN gene were performed to investigate the variants rs1620675, rs1672770 and rs4183. Different genotypes of CRBN variants were evaluated in relation to their influence on the dose of thalidomide and on the occurrence of adverse effects. FINDINGS No association was found between CRBN variants and thalidomide dose variation. However, the genotypes of rs1672770 showed association with gastrointestinal effects (p = 0.040). Moreover, the haplotype DEL/C/T (rs4183/rs1672770/rs1620675) was also associated with gastrointestinal adverse effects (p = 0.015). MAIN CONCLUSIONS Our results show that CRBN variants affect the treatment of ENH with thalidomide, especially on the adverse effects related to the drug.

Genealogical data comprised 45,711 animals born between 1901 and 2016, with 48,127 animals in the pedigree file. Population structure was analyzed in terms of pedigree completeness, individual inbreeding coefficient (F), generation interval (L), rate of inbreeding (ΔF), effective population size (Ne), effective number of founders (ff), and effective number of ancestors (fa). The herd initially consisted of 13 bulls and 14 cows, and there were variations in the number of selected bulls and cows throughout the analyzed period, with 2,575 bulls, 13,691 cows, and 45,711 births recorded at the end of 2016. In total, 48.81% of the cows had only one progeny. Most dams (47.59%) were between three and seven years old, with a mean L in the population of 7.9 years. According to the results, 52.75% of the cows, 44.92% of the bulls, and 63.71% of the calves of the Guzerat breed in the northern region of Brazil showed some degree of inbreeding, with small-magnitude coefficients (0.56, 0.83, and 0.71% for cows, bulls, and calves, respectively). This fluctuation did not hinder the genetic evolution of the herd in the region. The effective population size does not seem to compromise the maintenance of genetic variability in the breed.

Oligogenic inheritance of autism spectrum disorder (ASD) has been supported by several studies. However, little is known about how the risk variants interact and converge on causative neurobiological pathways. We identified in an ASD proband deleterious compound heterozygous missense variants in the Reelin (RELN) gene, and a de novo splicing variant in the Cav3.2 calcium channel (CACNA1H) gene. Here, by using iPSC-derived neural progenitor cells (NPCs) and a heterologous expression system, we show that the variant in Cav3.2 leads to increased calcium influx into cells, which overactivates mTORC1 pathway and, consequently, further exacerbates the impairment of Reelin signaling. Also, we show that Cav3.2/mTORC1 overactivation induces proliferation of NPCs and that both mutant Cav3.2 and Reelin cause abnormal migration of these cells. Finally, analysis of the sequencing data from two ASD cohorts—a Brazilian cohort of 861 samples, 291 with ASD; the MSSNG cohort of 11,181 samples, 5,102 with ASD—revealed that the co-occurrence of risk variants in both alleles of Reelin pathway genes and in one allele of calcium channel genes confer significant liability for ASD. Our results support the notion that genes with co-occurring deleterious variants tend to have interconnected pathways underlying oligogenic forms of ASD.

Whole-genome sequence analyses have significantly contributed to the understanding of virulence and evolution of the Mycobacterium tuberculosis complex (MTBC), the causative pathogens of tuberculosis. Most MTBC evolutionary studies are focused on single nucleotide polymorphisms and deletions, but rare studies have evaluated gene content, whereas none has comprehensively evaluated pseudogenes. Accordingly, we describe an extensive study focused on quantifying and predicting possible functions of MTBC and Mycobacterium canettii pseudogenes. Using NCBI’s PGAP-detected pseudogenes, we analysed 25 837 pseudogenes from 158 MTBC and M. canetii strains and combined transcriptomics and proteomics of M. tuberculosis H37Rv to gain insights about pseudogenes' expression. Our results indicate significant variability concerning rate and conservancy of in silico predicted pseudogenes among different ecotypes and lineages of tuberculous mycobacteria and pseudogenization of important virulence factors and genes of the metabolism and antimicrobial resistance/tolerance. We show that in silico predicted pseudogenes contribute considerably to MTBC genetic diversity at the population level. Moreover, the transcription machinery of M. tuberculosis can fully transcribe most pseudogenes, indicating intact promoters and recent pseudogene evolutionary emergence. Proteomics of M. tuberculosis and close evaluation of mutational lesions driving pseudogenization suggest that few in silico predicted pseudogenes are likely capable of neofunctionalization, nonsense mutation reversal, or phase variation, contradicting the classical definition of pseudogenes. Such findings indicate that genome annotation should be accompanied by proteomics and protein function assays to improve its accuracy. While indels and insertion sequences are the main drivers of the observed mutational lesions in these species, population bottlenecks and genetic drift are likely the evolutionary processes acting on pseudogenes' emergence over time. Our findings unveil a new perspective on MTBC’s evolution and genetic diversity.

BackgroundPotential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs.ResultsThe systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR ConclusionHere we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.

Orientador: Clarice Weis Arns Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas Resumo: Os membros da família Paramyxoviridae, subfamília Pneumovirinae são vírus envelopados, não-segmentados dotados de genoma de RNA de fita simples com sentido negativo. O vírus Respiratório sincicial humano (hRSV) é o agente viral melhor caracterizado neste grupo, associado à doença do trato respiratório inferior. Recentemente foi identificado um novo patógeno humano pertencente à subfamília Pneumovirinae, o metapneumovírus humano (hMPV), o qual possui similaridades com o hRSV, na sua organização genômica, estrutura viral, antigenicidade e sintomas clínicos. Na primeira parte do presente trabalho o objetivo foi analisar a variabilidade genética dos isolados de hRSV circulantes na região de Campinas, no período de Abril a Setembro de 2004, comparando as seqüências previamente obtidas do gene que codifica as proteínas F e G do vírus com seqüências parciais e completas de gene homólogo de isolados identificados em outros países. A análise filogenética permitiu classificar os isolados de hRSV como pertencentes aos subgrupos A e B. Os isolados pertencentes ao subgrupo A se distribuíram em três genótipos: GA2, GA5 e SSA1. O genótipo SSA1 foi identificado pela primeira vez no sul da África, e existem poucos relatos do mesmo na literatura. As seqüências analisadas dos isolados do subgrupo B foram identificadas em 3 genótipos distintos dentro desse subgrupo, notadamente GB3 (SAB3) e BA (BAIII). Das amostras analisadas no presente estudo, duas foram identificadas como pertencentes ao genótipo BA, os isolados apresentaram a duplicação dos 60nt na posição 781-840 do gene. Na segunda parte da tese o objetivo foi identificar a presença e caracterizar molecularmente o hMPV por seqüenciamento parcial do gene que codifica para a proteína F de amostras coletadas de crianças em dois hospitais universitários na região de Campinas, São Paulo, Brasil. Com base nas seqüências de nucleotídeos do gene F do hMPV, foi identificada a presença do subgrupo B/genótipo B1 em nosso trabalho, semelhante ao que foi relatado em 2004 na Austrália. Nossas amostras apresentaram duas amostras variantes neste mesmo genótipo, com base nas seqüências de nucleotídeos Abstract: The members of the Paramyxoviridae are enveloped, non-segmented viruses, with negative-sense single stranded genomes. Respiratory syncytial virus (hRSV) is the best characterized agent viral of this group, associated with respiratory diseases in lower respiratory tract. Recently, a new human pathogen belonging to the subfamily Pneumovirinae was identified, the human metapneumovirus (hMPV), which is structurally similar to the hRSV, in genomic organization, viral structure, antigenicity and clinical symptoms. In the first part of the present work the objective is to analyze the genetic variability hRSV isolates circulating in the region of Campinas, in the period April and September 2004, comparing previously obtained sequences from the F and G protein gene of such strains with other partial and complete gene sequences from the homologous genes from isolates identified in other countries. The phylogenetic analysis conducted here allowed us to allocate the isolates belonging to groups A and B. The isolates belonging to the group A showed three clusters, GA2, GA5 and SAA1. The genotype SSA1 was previously identified in South Africa, and there are few reports of such genotype it in the literature. Analyzed sequences belonging to group B were identified in three distinct clusters, GB3 (SAB3) and BA (BAIII). Of the analyzed sequences in the present study, two were identified as belonging to genotype BA the isolates showed 60 nucleotide (nt) duplication at positions 781-840 the gene. In the second part of the thesis the objective was to identify the presence and molecular characterization of hMPV by partially sequencing of the F protein gene in samples collected from children of two university hospitals in the region of Campinas, São Paulo state, Brazil. Based on nucleotide sequences of hMPV F gene, we identified the presence of subgroup B/genotype B1 in our work, similarly to reports in 2004 in Australia. Our samples showed to variants in the same genotype, based on nucleotides sequences Mestrado Ciências Básicas Mestre em Clínica Médica

Orientadores: Luiz Francisco Lembo Duarte, Vera Nisaka Solferini Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: A riqueza de espécies, abundância, proporção de jovens, crescimento corporal, seleção de microhabitat, diversidade genotípica, variabilidade e estrutura genética de anêmonas-do-mar da região entremarés foram estudados no período de agosto de 2005 a julho de 2006. Cinco espécies foram encontradas e tiveram as suas populações acompanhadas em duas praias do município de São Sebastião, SP: Bunodosoma caissarum, Bunodosoma cangicum, Anthopleura cascaia, Actinia bermudensis e Phyllactis flosculifera. Destas, as mais abundantes foram Bunodosoma caissarum, Bunodosoma cangicum e Anthopleura cascaia. Estas três espécies mostraram oscilações muito grandes em seus tamanhos populacionais, padrão não esperado considerando a longevidade de anêmonas-do-mar. As espécies B. caissarum e B. cangicum mostraram um padrão de recrutamento aparentemente contínuo e pequeno enquanto A. bermudensis e A. cascaia apresentaram um maior número de jovens principalmente na primavera. Não foi verificado um padrão claro de crescimento corporal das espécies estudadas, devido, possivelmente, à variação no número de indivíduos amostrados em cada mês, ou a uma taxa de crescimento muito pequena para ser detectada no período de um ano. Os microhabitats ocupados pelas espécies foram significativamente relacionados às suas preferências, mostrando que a localização espacial não acontece aleatoriamente. Bunodosoma caissarum, B. cangicum e Phyllactis flosculifera foram as espécies escolhidas para as análises genéticas. Cada uma delas teve duas populações amostradas, e as populações de B. caissarum foram também organizadas localmente em subgrupos. As três espécies apresentaram altos valores de diversidade genética e todas as populações apresentaram déficits de heterozigotos. Os valores de diferenciação genética encontrados para B. caissarum (? = 0.039) são significativos, considerando que a espécie apresenta larva planctônica e as populações amostradas estavam separadas por apenas 13 km. Além disso, foi encontrada evidência de estruturação microgeográfica para esta espécie. Bunodosoma cangicum apresentou valores baixos de estruturação genética (? = 0.021) e P. flosculifera valores moderados (? = 0.080). Phyllactis flosculifera e B. cangicum apresentam populações distantes (1000 km e 1300 km, respectivamente) geneticamente conectadas, o que sugere que ambas as espécies tenham larvas com capacidade de dispersão em grandes distâncias. Todos os indivíduos das populações estudadas das três espécies apresentaram genótipos únicos, o que sugere que nenhuma delas tenha reprodução assexuada Abstract: We studied the richness of species, abundance, proportion of juveniles, growth, microhabitat selection, genotypic diversity, genetic variability and structure of intertidal sea anemones between August 2005 and July 2006. Five species were found and their populations were studied in São Sebastião, SP: Bunodosoma caissarum, B. cangicum, Anthopleura cascaia, Actinia bermudensis and Phyllactis flosculifera. The most abundant ones were Bunodosoma caissarum, B. cangicum and Anthopleura cascaia. These three species showed important oscillations in their populations sizes, a pattern that was not expected considering the long life of sea anemones. Bunodosoma caissarum and B. cangicum showed small and continuous recruitment, while A. bermudensis and A. Cascaia presented a bigger number of juveniles mainly in the spring. A clear pattern of growth was not observed for any of the species studied, probably due to the variation in populations¿ size during the study or it could have been caused by a growth rate too small to be detected in one year time. The microhabitats occupied by all five species were related to their preferences, indicating that the spatial distribution found was not at random. Bunodosoma caissarum, B. cangicum and P. flosculifera were also genetically analyzed. Each one of them had two populations sampled, and the ones of B. caissarum were sampled in subgroups following spatial distribution in situ. All the species showed high levels of genetic diversity and all the populations presented a deficit of heterozygotes. The values of genetic differentiation found for B. caissarum (? = 0.039) are significant given the long-lived planktonic larva of the species and the small distance between the samples (13 km) and we also found evidence of microgeographic structuring in this species. Bunodosoma cangicum showed low levels of genetic structuring (? = 0.021) while P. flosculifera presented a moderate value of structuring (? = 0.080). Phyllactis flosculifera and B. cangicum present distant populations (1000 km and 1300 km apart, respectively) genetically connected suggesting that both species have larvae capable of good dispersal distances. All of the individuals of the three species showed unique genotypes, suggesting that none of them have asexual reproduction Mestrado Ecologia Mestre em Ecologia

Background The influence of linkage disequilibrium (LD), epistasis, and inbreeding on genotypic variance continues to be an important area of investigation in genetics and evolution. Although the current knowledge about biological pathways and gene networks indicates that epistasis is important in determining quantitative traits, the empirical evidence for a range of species and traits is that the genotypic variance is most additive. This has been confirmed by some recent theoretical studies. However, because these investigations assumed linkage equilibrium, considered only additive effects, or used simplified assumptions for two- and higher-order epistatic effects, the objective of this investigation was to provide additional information about the impact of LD and epistasis on genetic variances in noninbred and inbred populations, using a simulated dataset. Results In general, the most important component of the genotypic variance was additive variance. Because of positive LD values, after 10 generations of random crosses there was generally a decrease in all genetic variances and covariances, especially the nonepistatic variances. Thus, the epistatic variance/genotypic variance ratio is inversely proportional to the LD level. Increasing inbreeding increased the magnitude of the additive, additive x additive, additive x dominance, and dominance x additive variances, and decreased the dominance and dominance x dominance variances. Except for duplicate epistasis with 100% interacting genes, the epistatic variance/genotypic variance ratio was proportional to the inbreeding level. In general, the additive x additive variance was the most important component of the epistatic variance. Concerning the genetic covariances, in general, they showed lower magnitudes relative to the genetic variances and positive and negative signs. The epistatic variance/genotypic variance ratio was maximized under duplicate and dominant epistasis and minimized assuming recessive and complementary epistasis. Increasing the percentage of epistatic genes from 30 to 100% increased the epistatic variance/genotypic variance ratio by a rate of 1.3 to 12.6, especially in inbred populations. The epistatic variance/genotypic variance ratio was maximized in the noninbred and inbred populations with intermediate LD and an average allelic frequency of the dominant genes of 0.3 and in the noninbred and inbred populations with low LD and an average allelic frequency of 0.5. Conclusions Additive variance is in general the most important component of genotypic variance. LD and inbreeding have a significant effect on the magnitude of the genetic variances and covariances. In general, the additive x additive variance is the most important component of epistatic variance. The maximization of the epistatic variance/genotypic variance ratio depends on the LD level, degree of inbreeding, epistasis type, percentage of interacting genes, and average allelic frequency.

Orientador: Vera Nisaka Solferini Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: A leguminosa Crotalaria pallida é considerada uma espécie invasora na região Neotropical e em outras regiões ao redor do mundo. Acredita-se que ela seja nativa da África, porém sua história evolutiva é desconhecida devido à carência de dados sobre sua introdução e de estudos genéticos e filogeográficos com a planta. No presente trabalho buscou-se avaliar a variabilidade e estruturação genética de populações de C. pallida e inferir os processos históricos evolutivos que explicam o padrão de distribuição atual da espécie. A origem da espécie na região Neotropical foi discutida com relação às hipóteses de "eventos naturais antigos de dispersão a longa distância" e de "introdução recente mediada pelo homem". Foram analisadas amostras de 25 pontos de ocorrência distribuídos na região tropical, incluindo onze pontos localizados no Brasil, sete na África, cinco em outros países da América Latina, um na Índia e um na Austrália. Os dados de sequências de duas regiões intergênicas, uma nuclear (ITS) e uma plastidial (rpl32-trnL), foram utilizados em análises de diversidade, filogeográficas e de estrutura populacional. Os padrões de diversidade e estruturação geográfica encontrados para as duas regiões sequenciadas foram semelhantes. Cada marcador apresentou apenas quatro haplótipos com poucos passos mutacionais de diferença entre eles. A região Neotropical (Hd: 0,1139 - ITS e 0,0982 - rpl32-trnL) não apresentou haplótipos exclusivos e, os dois haplótipos de cada marcador encontrados na região são compartilhados com amostras africanas. Todos os indivíduos brasileiros analisados são monomórficos para os marcadores estudados, indicando uma origem comum das populações do país. O baixo polimorfismo encontrado, provavelmente está associado à biologia da espécie e/ou a história demográfica das populações da região de distribuição nativa, além de ser um padrão comumente registrado em espécies invasoras. Os índices de diversidade genética maiores na África (Hd: 0,5111 - ITS e 0,6667 - rpl32-trnL) e a ausência e haplótipos exclusivos nos neotrópicos sugerem que C. pallida tem origem africana e foi introduzida recentemente na região Neotropical, o que concorda com a hipótese de introdução mediada pelo homem. A importância da variabilidade genética para o estabelecimento e propagação de uma espécie invasora é um assunto intensamente debatido e o alto potencial invasor de C. pallida, a despeito da baixa diversidade genética, contribui na delimitação das características que são de fato relevantes durante o processo de invasão Abstract: The herbaceous legume Crotalaria pallida is considered an invasive species in the Neotropics and others regions across the world. This species is presumably native from Africa, nevertheless its evolutionary history is unknown due to the lack of information about its introduction and of genetical and phylogeographical studies with the plant. The present study sought to investigate the genetic variability and structuring of C. pallida populations and to understand the evolutionary processes that led to the current distribution pattern of the species. The origin of the plant in the Neotropics was discussed contrasting the hypothesis of "early natural events of long distance dispersion" and "recently introduction by humans". We analyzed samples of 25 sites spread around the Tropical region, comprising: eleven sites in Brazil, seven in Africa, five in others Latin America countries, one in India and one in Australia. The DNA sequence data of two intergenic regions, one nuclear (ITS) and one plastidial (rpL32-trnL), was evaluated through diversity indices, phylogeographical and population structure analyses. The patterns of diversity and geographic structure for the two DNA regions were similar. Each marker exhibited only four haplotypes with a few mutational differences between them. The Neotropical region (Hd: 0,1139 - ITS and 0,0982 - rpl32-trnL) does not hold exclusive haplotypes and the two haplotypes of each marker found in this region are shared with African samples. All Brazilians individuals analyzed are monomorphic for both markers, indicating a common origin of the populations in this country. The low polymorphism is probably associated to organism biology and/or to demographic history of native populations; besides, it is a frequent pattern in invasive species. The higher diversity indices in Africa (Hd: 0,5111 - ITS and 0,6667 - rpl32-trnL) and absence of exclusive haplotypes in the Neotropics suggest that C. pallida has an African origin and was recently introduced in the Neotropical region, what supports the hypothesis of introduction by humans. The importance of genetic variability for the establishment and spread of an invasive species is intensely debated and the high invader potential of C. pallida, despite its low genetic diversity, contributes to the delimitation of truly relevant characteristics for the invasion process Mestrado Genética Animal e Evolução Mestra em Genética e Biologia Molecular CAPES FAPESP

Orientador: Luciana Bolsoni Lourenço Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: Recentes análises filogenéticas e citogenéticas têm revelado grande diversidade dentre leiuperídeos do grupo Physalaemus cuvieri. O parafiletismo de P. cuvieri em relação a Physalaemus ephippifer foi inferido com base na análise de sequências de DNA, e linhagens reconhecidas dentre indivíduos de P. cuvieri parecem representar espécies ainda não descritas. A espécie Physalaemus ephippifer ocorre na foz do Rio Amazonas no Brasil e possivelmente na Guiana, mas sua correta distribuição geográfica permanece desconhecida. Análises citogenéticas de indivíduos de P. ephippifer da localidade-tipo (Belém-PA) revelaram um interessante heteromorfismo entre os homólogos do par cromossômico 8 de fêmeas, caracterizando a presença de um sistema de determinação sexual cromossômico ZZ/ZW. Os cromossomos Z e W apresentam uma NOR distal no braço longo, adjacente a uma banda heterocromática terminal, e o cromossomo W difere do Z por apresentar um segmento terminal no braço curto que inclui uma NOR e uma banda heterocromática. As NORs de P. ephippifer se mostraram co-localizadas, em experimentos de hibridação in situ, com as sequências de DNA repetitivo Pep194. Com o objetivo de contribuir para a investigação da diversidade genética e citogenética de populações amazônicas de Physalaemus do grupo P. cuvieri, analisamos as relações filogenéticas e os cariótipos de indivíduos de P. ephippifer de Santa Isabel-PA e exemplares coletados em localidades do Pará (Monte Alegre, Óbidos, Alenquer, Curuá, Parauapebas e Prainha) e de Roraima (Viruá), cuja identificação taxonômica é incerta. Para tanto, as preparações cromossômicas obtidas de machos a partir de suspensões de células do intestino e testículo foram submetidas à coloração convencional por Giemsa, bandamento C, coloração com DAPI, impregnação por prata e experimentos de hibridação in situ com sondas de DNA repetitivo Pep194 e DNA ribossomal 28S. Além disso, utilizamos uma sonda, chamada de Zqter, produzida a partir de um segmento microdissecado da região terminal do braço longo do cromossomo Z de P. ephippifer. As relações filogenéticas foram inferidas com base em sequências de DNA mitocondrial dos genes 12S, RNAt-val e 16S, utilizando o critério de máxima parcimônia. Os cariótipos dos indivíduos de Physalaemus sp. em análise foram semelhantes entre si, porém três citótipos foram reconhecidos devido ao padrão diferencial na distribuição das NORs no par 8. Os cariótipos dos espécimes de Monte Alegre, Óbidos, Alenquer, Prainha e Curuá (Citótipo I) e Parque Nacional do Viruá (Citótipo II) mostraram uma NOR pericentromérica no braço curto do par 8, porém apenas o Citótipo I foi portador de uma NOR terminal no braço longo desse mesmo par. O exemplar de Parauapebas (Citótipo III) mostrou duas NORs no braço longo dos cromossomos do par 8. Nas inferências filogenéticas, os exemplares de Physalaemus sp. portadores dos Citótipos I e II foram recuperados no mesmo clado (Clado A). Neste clado, foi possível observar uma subestruturação que acompanha a variação cariotípica detectada, no entanto a distância genética entre os dois grupos em questão, inferida com base em sequências parciais do gene 16S, foi baixa (0,1%). É provável, portanto, que os dois citótipos representem uma variação intraespecífica. O exemplar de Parauapebas incluído nas análises filogenéticas (Clado B) apresentou-se como grupo-irmão de um clado que incluiu P. ephippifer (Clado C) e o clado correspondente a uma das linhagens de P. cuvieri (Clado D, equivalente à Linhagem 1 de P. cuvieri, que agrupa indivíduos do norte e do nordeste do Brasil). A alta distância genética do Clado A em relação aos Clados B-D, inferida com base em segmento do gene 16S, sugere que o Clado A possa representar uma espécie ainda não descrita. Nas metáfases de indivíduos de Viruá, Alenquer e Curuá a sonda Zqter foi detectada na região pericentromérica do braço curto do par 8, adjacente às NORs detectadas pela sonda Pep194, sugerindo que esta região é homeóloga a região terminal ao braço longo do Z de P. ephippifer. As homelogias encontradas sugerem um possível evento de inversão cromossômica durante diferenciação desses cariótipos. A sonda Pep194 detectou, além das NORs dos cromossomos Z e W de P. ephippifer e da NOR pericentromérica de Physalaemus sp., as NORs dos cromossomos 8 e 9 de indivíduos de P. cuvieri de Urbano Santos-MA e os cromossomos 8 e 11 de indivíduos de P. cuvieri de Palestina-SP. Em contraste, essa sonda não detectou a NOR pericentromérica do cromossomo 9 de P. centralis, uma espécie mais distantemente relacionada filogeneticamente a P. cuvieri e P. ephippifer Abstract: Recent phylogenetic and cytogenetic analyses have revealed high diversity among leiuperids of the Physalaemus cuvieri group. The paraphyly of P. cuvieri with respect to Physalaemus ephippifer was inferred based on the analysis of DNA sequences, and genetic lineages that included individuals at first identified as P. cuvieri may represent undescribed species. P. ephippifer occurs at the mouth of the Amazon River in Brazil and possibly in Guyana, but its geographical distribution is unclear. Cytogenetic analyses of individuals of P. ephippifer from the type locality (Belém-PA) revealed an interesting heteromorphism between the homologous chromosomes of pair 8 in females, which characterized the presence of a chromosomal sex determination system ZZ/ZW. The Z and W chromosomes have a distal NOR in the long arm, adjacent to a terminal heterochromatic band, and the W chromosome differs from Z chromosome by a terminal segment in the short arm that comprises a NOR and a heterochromatic band. The NORs of P. ephippifer are shown co-located with DNA repetitive Pep194 in in situ hybridization experiments. Aiming to contribute to the investigation of the genetic and cytogenetic diversity of Amazonian populations belonging to P. cuvieri group, we analyzed the phylogenetic relationships and the karyotypes of individuals of P. ephippifer from Santa Isabel-PA and specimens collected from seven localities in the states of Pará (Monte Alegre, Óbidos, Alenquer, Curuá, Parauapebas and Prainha) and Roraima (Viruá), for which the taxonomic identification is uncertain. Chromosome preparations obtained from male individuals were subjected to conventional staining with Giemsa, C-banding, DAPI staining, silver impregnation and in situ hybridization with probes for the repetitive DNA Pep194 and ribosomal DNA 28S. In addition, we used a probe, named Zqter probe, produced from a segment microdissected from the terminal region of the long arm of the Z chromosome of P. ephippifer. Phylogenetic relationships were inferred based on mitochondrial DNA sequences of 12S, tRNA-val and 16S genes, using the criterion of maximum parsimony. The karyotypes of the individuals of Physalaemus sp. analyzed were similar, but three cytotypes were recognized with differential distribution of NORs in pair 8. Individuals from Monte Alegre, Óbidos, Alenquer, Prainha and Curuá (Cytotype I) showed a pericentromeric NOR in the short arm of pair 8 and a terminal NORin the long arm. In the male karyotypes of Viruá (Cytotype II), the NOR was located in the pericentromeric region of the short arm of pair 8. The individuals from Parauapebas (Cytotype III) showed two NORs in the long arm of chromosome pair 8. In the phylogenetic inferences, the specimens of Physalaemus sp. with Cytotypes I and II were nested in the same clade (Clade A). This clade showed a substructure that reflected the two karyotypic groups detected. The genetic distance between these two groups, however, inferred from partial sequences of the 16S gene, was low 0,1 %. It is likely, therefore, that the two cytotypes represent an intraspecific variation. The exemplar of Parauapebas included in the phylogenetic analysis (Clade B) was the sister group of a clade that included P. ephippifer (Clade C) and the clade corresponding to one of the lineages of P. cuvieri (Clade D, equivalent to Lineage 1 of P. cuvieri, which groups individuals of northern and northeastern Brazil). The high genetic distance between Clade A and clades B-D, inferred from 16S gene segment, suggests that Clade A may represent an undescribed species. In metaphases of individuals from Viruá, Alenquer and Curuá, the Zqter probe was detected in the pericentromeric region of the short arm of pair 8, adjacent to the NOR detected by the probe Pep194, suggesting that this region is homeologous with the terminal region of the long arm of the Z chromosome of P. ephippifer. The inferred homeologies suggest a possible event of chromosomal inversion along the differentiation of these karyotypes. The Pep194 probe detected, beyond the NORs of the Z and W chromosomes of P. ephippifer and the pericentromeric NOR of chromosomes 8 of the cytotypes of Physalaemus sp., the NORs of chromosomes 8 and 9 of individuals of P. cuvieri from Urbano Santos-MA and chromosomes 8 and 11 of individuals P. cuvieri from Palestina-SP. In contrast, this probe did not detect the pericentromeric NOR of chromosome 9 of P. centralis, which is distantly related phylogenetically to P. cuvieri and P. ephippifer Doutorado Biologia Celular Doutora em Biologia Celular e Estrutural

Orientadores: Maria Imaculada Zucchi, Ricardo Ribeiro Rodrigues Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: A degradação ecológica e o desflorestamento são processos que se iniciaram há muito tempo e cuja história confunde-se com a da agricultura. A Mata Atlântica é a segunda maior floresta tropical em ocorrência e importância na América do Sul, possuindo grande diversidade biológica e altos níveis de endemismo. A ocupação desordenada da Mata Atlântica causou sua redução a 11,26% de sua área original, com distribuição de forma fragmentada pelo território brasileiro. A destruição da Mata Atlântica tem resultado na eliminação de muitas populações e, potencialmente, na erosão da diversidade genética de diversas espécies. Essa combinação de alto endemismo e forte ameaça de extinção, faz com que a Mata Atlântica seja considerada um hotspot para a conservação. Nas últimas décadas a recuperação de ecossistemas degradados recebeu a atenção da comunidade científica, dando origem ao campo do conhecimento chamado Ecologia da Restauração, que se dedica aos estudos teóricos dos princípios, práticas, resultados e conseqüências de projetos de restauração. O estudo e monitoramento de áreas de restauração florestal é essencial para melhorar as técnicas de restauração em ecossistemas tropicais e subtropicais. Para que uma determinada espécie se perpetue em uma área em processo de restauração, é preciso que a mesma desenvolva todo o seu ciclo de vida e que gerem descendentes capazes de se desenvolver a ponto de substituir as árvores mães quando as mesmas entrarem em senescência. Por isso há a necessidade de se estudar a variabilidade genética de populações arbóreas dentro de áreas de floresta restaurada, assim como a ocorrência e efetividade do fluxo gênico entre estas áreas e os fragmentos de seu entorno. Neste trabalho, estudamos a variabilidade genética de Myroxylon peruiferum L. f., em duas diferentes áreas de restauração florestal e em duas áreas de remanescentes naturais de Floresta Estacional Semidecidual. Nossos resultados indicam que as restaurações florestais de Cosmópolis e Iracemápolis conservam diversidades genéticas HE e alélicas semelhantes às de remanescentes naturais. A principal diferença entre áreas naturais e restauradas foi a menor riqueza de alelos endêmicos nestas últimas o que é um efeito de amostragem que favorece a perda de alelos raros. A área de restauração florestal mais antiga em Cosmópolis apresentou uma estruturação genética espacial compatível com a de áreas naturais. O mesmo não ocorreu com a restauração mais recente de Iracemápolis. Observou-se a ocorrência de estruturação genética local nas áreas naturais e na área de restauração mais antiga e indícios de fluxo gênico entre os áreas nativas e restauradas. Um estudo adicional do efeito de amostragem sobre as freqüências alélicas demonstrou o fenômeno de perda de alelos com baixa freqüência em eventos de amostragem. O mesmo trabalho indicou que uma amostra de cerca de 30 indivíduos é capaz de representar adequadamente alelos com freqüências acima de 0,05; sendo este um bom número a se considerar na seleção de matrizes para fornecimento de mudas para restauração florestal Abstract: Ecological degradation and deforestation are processes that started long ago and whose history is intertwined with that of agriculture. Atlantic Forest is the second largest rainforest in occurrence and importance in South America, having great biological diversity and high levels of endemism. Disordered occupation of Atlantic Forest caused its reduction to 11.26% of the original area, with distribution in forest fragments poorly conected across the Brazilian territory. Destruction of the Atlantic Forest has resulted in the elimination of many populations and potentially the erosion of genetic diversity of several species. This combination of high endemism and strong threat of extinction causes the Atlantic Forest to be considered a hotspot for conservation. In the last decades recovery of degraded ecosystems has received attention from the scientific community giving birth to an new area of knowledge called the Restoration Ecology. The study and monitoring of areas of forest restoration is essential to improve restoration techniques in tropical and subtropical ecosystems. For a given species to perpetuate itself in an area undergoing a restoration process, it needs to develop its whole life cycle and generates progeny capable of developing to the point of replacing mothers trees when they die. Therefore there is a need to study the genetic variability of tree populations within areas of restored forest, as well as the occurrence and effectiveness of gene flow between these areas and surrounding fragments. We studied the genetic variability of Myroxylon peruiferum L. f., in two different areas of forest restoration and in two areas of natural remnants of semideciduous forest. Our results indicates that restorations in Cosmopolis and Iracemápolis conserve genetic and allelic diversity HE similar to that of natural remnants. The main difference between natural and restored areas was the lowest richness of endemic alleles which is the result of a sampling effect that favors the loss of rare alleles. The area of older forest restoration in Cosmopolis presented a spatial genetic structure consistent with natural areas. This did not occur with the newer restoration in Iracemápolis. We observed the occurrence of local genetic structure in natural areas and in the area of older restoration and evidence of gene flow between native and restored areas. An additional study about the effect of sampling size on allele frequencies showed the phenomenon of loss of low frequency alleles in sampling events. The same study found that a sample of about 30 individuals are able to adequately represent alleles with frequencies above 0.05; this is a good number to consider in selecting matrix trees to supply seedlings for forest restoration Doutorado Genética Vegetal e Melhoramento Doutor em Genética e Biologia Molecular

SUMMARY OBJECTIVE: This study was to assess the genetic association of copy number variations in two genes (PRKAB2 and PPM1K) located in two regions (tetralogy of Fallot and ventricular septal defect) in a Chinese Han population. METHODS: A total of 200 congenital heart disease patients (100 tetralogy of Fallot patients and 100 ventricular septal defect patients) and 100 congenital heart defect-free controls were recruited, and quantitative real-time PCR analysis was used to replicate the association of two copy number variations with congenital heart defects in a Chinese Han population. RESULTS: One deletion at PRKAB2 and one duplication at PPM1K were found in two of the tetralogy of Fallot patients, respectively; while all these regions were duplicated in both ventricular septal defect patients and in the 100 congenital heart defects-free controls. CONCLUSIONS: We replicated the copy number variations at the disease-candidate genes of PRKAB2 and PPM1K with tetralogy of Fallot in a Chinese Han population, and in patients with ventricular septal defect mutations in these two genes were not found. These results indicate the same molecular population genetics exist in these two genes with different ethnicity. This shows that these two genes are possibly specific pf tetralogy of Fallot candidates.

Introduction: The chromosomal region 15q11-13 contains a group of genes essential for normal neurodevelopment and alterations in this region result in different syndromes. Among the most frequent alterations, there are chromosomal deletions and duplications. Duplications of chromosome region 15q11q13 occur as a supernumerary chromosome 15, and may occur as interstitial duplications. The main clinical manifestations are intellectual impairment, problems with vision, hearing, teething and in bones and joints. Currently, there are few cases reported in the literature about this genetic condition, which justifies the relevance of this study. Objective: To report a case of duplication in the chromosomal region 15q11q13 and describe the clinical manifestations. Methodology: This is a case report of a qualitative nature. Case report: J.V.A.S., male, eight years old, attended at the Associação de Pais e Amigos dos Excepcionais (APAE), in Anápolis, Goiás, Brazil, in 2017, diagnosed with neuropsychomotor developmental delay (ADNPM) and macrocrania. No complications during childbirth. The patient had head support at six months, sat up at nine months, walked and talked at one year and ten months. He attends school and has good interaction, but has learning difficulties. In 2018, the CGH – ARRAY (aCGH) revealed the presence of a duplication in 15q11.2q13.1 of approximately 6.1Mb classified as pathogenic. Results and discussion: Due to the rarity of this syndrome, we did not find a satisfactory number of articles that specifically addressed this duplication. Conclusion: It is necessary to carry out more studies, in the long term and through satisfactory samples, in order to elucidate the main aspects involved in this pathology. Introducción: La región cromosómica 15q11-13 contiene un grupo de genes esenciales para el normal neurodesarrollo y las alteraciones en esta región dan lugar a diferentes síndromes. Entre las alteraciones más frecuentes se encuentran las deleciones y duplicaciones cromosómicas. Las duplicaciones de la región cromosómica 15q11q13 ocurren como un cromosoma 15 supernumerario y pueden ocurrir como duplicaciones intersticiales. Las principales manifestaciones clínicas son deterioro intelectual, problemas de visión, audición, dentición y en huesos y articulaciones. Actualmente, existen pocos casos reportados en la literatura sobre esta condición genética, lo que justifica la relevancia de este estudio. Objetivo: Reportar un caso de duplicación en la región cromosómica 15q11q13 y describir las manifestaciones clínicas. Metodología: Se trata de un reporte de caso de carácter cualitativo. Caso clínico: J.V.A.S., masculino, ocho años, atendido en la Associação de Pais e Amigos dos Excepcionais (APAE), en Anápolis, Goiás, Brasil, en 2017, diagnosticado con retraso del desarrollo neuropsicomotor (ADNPM) y macrocráneo. Sin complicaciones durante el parto. El paciente tenía soporte para la cabeza a los seis meses, se sentó a los nueve meses, caminó y habló al año y diez meses. Asiste a la escuela y tiene una buena interacción, pero tiene dificultades de aprendizaje. En 2018, el CGH – ARRAY (aCGH) reveló la presencia de una duplicación en 15q11.2q13.1 de aproximadamente 6,1 Mb clasificada como patógena. Resultados y Discusión: Debido a la rareza de este síndrome, no encontramos un número satisfactorio de artículos que traten específicamente esta duplicación. Conclusión: Es necesario realizar más estudios, a largo plazo y mediante muestras satisfactorias, para dilucidar los principales aspectos involucrados en esta patología. Introdução: A região cromossômica 15q11-13 contém um grupo de genes fundamentais para o neurodesenvolvimento normal e alterações nessa região resulta em síndromes diversas. Dentre as alterações mais frequentes, há deleções e duplicações cromossômicas. As duplicações da região cromossômica 15q11q13 ocorrem como um cromossomo supranumerário 15, podendo ocorrer como duplicações intersticiais. As principais manifestações clínicas são o comprometimento intelectual, problemas de visão, audição, dentição e em ossos e articulações. Atualmente, existem poucos casos relatados na literatura sobre essa condição genética, o que justifica a relevância deste estudo. Objetivo: Relatar um caso de duplicação na região cromossômica 15q11q13 e descrever as manifestações clínicas. Metodologia: Trata-se de um relato de caso de natureza qualitativa. Relato de caso: J.V.A.S., sexo masculino, oito anos, atendido na Associação de Pais e Amigos dos Excepcionais (APAE), em Anápolis – Goiás, Brasil, em 2017, diagnosticado com atraso do desenvolvimento neuropsicomotor (ADNPM) e macrocrania. Sem intercorrências no parto. O paciente teve sustento cefálico aos seis meses, sentou-se com nove meses, andou e falou com um ano e dez meses. Frequenta escola e tem boa interação, porém tem dificuldade de aprendizagem. Em 2018, o CGH – ARRAY (aCGH) revelou a presença de uma duplicação em 15q11.2q13.1 de aproximadamente 6,1Mb classificada como patogênica. Resultados e discussão: Devido à raridade dessa síndrome, não foi encontrado um número satisfatório de artigos que tratasse especificamente dessa duplicação. Conclusão: Faz-se necessária a realização de mais estudos, a longo prazo e por meio de amostras satisfatórias, a fim de elucidar os principais aspectos envolvidos nessa patologia.

Made available in DSpace on 2019-10-06T16:48:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-12-01 HLA-G/E/F genes exhibit immunomodulatory properties and are expressed in placenta. Little attention has been devoted to the study of these genes in sub-Saharan African populations, which are yet the most diverse. To fill this gap, we evaluated the complete gene variability, approximately 5.1 kb for HLA-G (n = 149), 7.7 kb for HLA-E (n = 150) and 6.2 kb for HLA-F (n = 152) in the remote Beninese Toffin population, using massive parallel sequencing. Overall, 96, 37 and 68 variable sites were detected along the entire HLA-G, -E and -F, respectively, arranged into region-specific haplotypes; i.e., promoter haplotypes (16, 19, and 15 respectively), coding haplotypes (19, 15, and 29 respectively), 3’ untranslated region (3′UTR) haplotypes (12, 7 and 2, respectively) and extended haplotypes (33, 31 and 32 respectively). All promoter/coding/3'UTR haplotypes followed the patterns already described in worldwide populations. HLA-E was the most conserved, exhibiting mainly two full-length encoded-molecules (E*01:01 and E*01:03), followed by HLA-F, three full-length proteins (F*01:01, F*01:02 and F*01:03) and HLA-G, four proteins: three full-length (G*01:01, G*01:03 and G*01:04) and one truncated (G*01:05N). Although HLA-G/E/F alleles in the Toffin population were the most frequently observed worldwide, the frequencies of the coding haplotypes were closely similar to those described for other African populations (Guinea-Conakry and Burkina-Faso), when compared to non-African ones (Brazilian), indicating that variable sites along these genes were present in Africa before human dispersion. Laboratório de Biologia Molecular Universidade de São Paulo Programa de Imunologia Básica e Aplicada (IBA) Faculdade de Medicina de Ribeirão Preto (FMRP-USP) Laboratório de Biologia Molecular Universidade de São Paulo Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto (FMRP-USP) Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE) Faculté des Sciences de la Santé UMR 216 MERIT IRD Faculté de Pharmacie de Paris Université Paris Descartes Sorbonne Paris Cité Université d'Abomey-Calavi Département de Zoologie Faculté des Sciences et Techniques Université d'Abomey-Calavi Commissariat à l'Energie Atomique et aux Energies Alternatives Direction de la Recherche Fondamentale Institut de Biologie François Jacob Service de Recherches en Hémato-Immunologie Hôpital Saint-Louis Université Paris-Diderot Sorbonne Paris-Cité UMR_E5 Institut Universitaire d'Hématologie Hôpital Saint-Louis Departamento de Química Faculdade de Filosofia Ciências e Letras de Ribeirão Preto Universidade de São Paulo Laboratoire de Biologie et Physiologie Cellulaire Université d'Abomey-Calavi São Paulo State University (UNESP) Molecular Genetics and Bioinformatics Laboratory Experimental Research Unit (UNIPEX) School of Medicine São Paulo State University (UNESP) Department of Pathology School of Medicine São Paulo State University (UNESP) Molecular Genetics and Bioinformatics Laboratory Experimental Research Unit (UNIPEX) School of Medicine São Paulo State University (UNESP) Department of Pathology School of Medicine

Orientadores: Anete Pereira de Souza, Antonio Augusto Franco Garcia Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: As pastagens cultivadas constituem a forma mais econômica de fornecer alimentação abundante e de qualidade aos animais. As gramíneas do gênero Brachiaria representam as forrageiras mais utilizadas no Brasil, dentre as quais a espécie B. humidicola caracteriza-se por ser tolerante à solos úmidos, à cigarrinha-das-pastagens, principal praga das pastagens, e apresentar elevada produção. O conhecimento da extensão da variabilidade genética contida dentro dos bancos de germoplasma pode auxiliar no planejamento de estratégias para maximizar os ganhos genéticos em programas de melhoramento. Além disso, a construção de mapas de ligação é uma importante fonte de informações a respeito da estrutura do genoma e da genética de características de interesse agronômico. Nesse contexto, foram isolados e caracterizados marcadores microssatélites para a espécie como ferramenta para o estudo da diversidade genética de acessos do banco de germoplasma de B. humidicola e a construção de um mapa genético e posterior mapeamento do modo de reprodução por apomixia do tipo aposporia Foram desenvolvidos 154 marcadores microssatélites para a espécie. Os resultados da análise do banco de germoplasma revelaram quatro grupos de acessos que apresentam diferenças significativas entre si, além do único acesso sexual, o qual ficou isolado dos demais acessos, mostrando-se bem distante geneticamente. Esses dados fornecem importantes subsídios para o programa de melhoramento da espécie, orientando cruzamentos e futuras coletas de acessos. O mapa genético desenvolvido conta com 124 marcas em dose-única (geradas a partir de 79 locos microssatélites polimórficos na população de mapeamento) distribuídas em 38 grupos de ligação, com uma cobertura de 1.543,8cM do genoma hexaplóide (2n=6x=36) da espécie, com uma densidade de 12,3cM. O modo de reprodução por aposporia foi mapeado em um único grupo de ligação, de acordo com o esperado, por provavelmente estar associada a uma região genômica específica associada à aposporia (ASGR). Com base no perfil de amplificação dos locos microssatélite e em dados sobre o comportamento meiótico de 45 desses híbridos, pode-se sugerir que os genótipos hexaplóides desta espécie tenham origem autoalopoliplóide, corroborando alguns estudos citogenéticos e moleculares para a espécie Abstract: Cultivated pastures are the most economic way to produce quality feed in abundance to the animal herd. Grasses from the genus Brachiaria are the ones most plants for pastures in Brazil. Among those, the species B. humidicola is the most adapted to poor drained soils, is tolerant to spittlebugs, the major pest of the tropical forage grasses and is very productive. The knowledge about extension of the genetic variability in the germplasm banks can help to plan out strategies to maximize the gains in breeding programs. The construction of genetic maps is an important source of information about the genome structure and the genetics of characteristics that are important to agronomic studies. Based on this, microsatellite loci have been isolated and characterized for this species as a tool to study genetic diversity in the germplasm bank and the construction of a linkage map and apospory mapping. In total, 154 microsatellite loci were developed for this species. The results obtained from the germplasm analysis show that the germplasm is divided into four major groups and the only sexual accession was keep separated, showing its high divergence from the other accessions. These data are important to the breeding program of the species to define crosses and for future collections. The genetic map developed is formed by 124 single-dose markers (generated from 79 polymorphic SSR loci in the mapping population) distributed in 38 linkage groups, covering 1.543,8cM of the hexaploid genome (2n=6x=36) of the species, with a density of 12,3cM. The reproductive mode hrough apospory has been mapped in only one linkage group, as expected, as it is probably linked to an apospory-specific genomic region (ASGR), described in other grasses. Based on the amplification pattern of the microsatellite loci and in meiotic behaviour data of 45 hybrids from the mapping population, an autoallopolyploid origin can be suggested for the hexaploid genotypes of this species, corroborating some molecular and cytogenetics studies in B. humidicola Doutorado Doutor em Genética e Biologia Molecular

Orientadores: Clarice Weis Arns, Fernando Rosado Spilki Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas Resumo: O vírus da doença de Newcastle (VDN) é o agente causador de uma das mais importantes doenças em aves e representa uma ameaça para a indústria avícola. O VDN é um membro da família Paramyxoviridae, subfamília Paramyxovirinae, gênero Avulavirus. São vírus envelopados, não segmentados dotados de genoma RNA de fita simples sentido negativo, associado à doença do trato respiratório, digestivo e nervoso das aves. O Controle da DN se baseia em biossegurança, uso de vacinas e detecção precoce de lotes infectados. No presente estudo, examinamos dez vacinas vivas comercializadas no Brasil quanto à sua estabilidade térmica (ET), virulência e imunogenicidade. Em outra etapa do trabalho, investigou-se a soroprevalência perante o VDN em regiões de produção avícola voltada à exportação ou não de produtos aviários, seguido da detecção do VDN em aves migratórias. Os estudos são complementados pela análise filogenética de VDN isolado de aves comerciais, dos resultados alcançados, cumpre ressaltar: i) os testes de ET revelam elevada estabilidade para as vacinas utilizadas no país, mesmo após dois anos de sua fabricação; ii) o grau de proteção conferido por vacinas vivas contra a DN não depende da virulência residual conforme testes de inoculação intracerebral; iii) a soroprevalência contra VDN em aves nas regiões produtoras e exportadoras, foi de 39,1% e foram isoladas 77 amostras virais, sempre com perfil não-patogênico; iv) sorologia realizada em uma segunda oportunidade detectou-se uma soroprevalência de 28,8% e isolamento de 15 amostras virais que também foram caracterizadas como não-patogênicas; v) observou-se numa soropositividade de 41,7 a 84,3% dependendo da região e isolamento de 12 VDN na região Nordeste, caracterizados como não-patogênicas, indicando que nas áreas não exportadoras circulam vírus de baixa patogenicidade; vi) o genoma dos vírus isolados e das vacinas vivas, atesta que os vírus circulantes em aves comerciais são de provável origem vacinal e pertencem à classe II sendo 71,8% do genótipo II ou La Sota-like e 28,2% do genótipo I ou Ulster-like; vii) por último, a caracterização biológica dos isolados de aves migratórias mostram que há circulação de vírus de baixa e alta patogenicidade em nosso território. Portanto, este conjunto de trabalhos evidencia o status do Brasil como país livre da Doença de Newcastle em aves comerciais Abstract: Newcastle disease virus (NDV) is the agent that causes one of the most important diseases in birds and represents a threat to industrial aviculture. NDV is a member of the Paramyxoviridae family, Paramyxovirinae subfamily, Avulavirus genus. In the present study, live vaccines commercialized in Brazil were examined in regard to their thermostability (TS), virulence and immunogenicity. In another stage of this work, soroprevalence was investigated, with viral isolation and characterization carried out in poultry production regions focused on production for exportation or domestic commercialization, followed by the detection of the virus in migratory birds. The studies were complemented by phylogenic analysis carried out on the isolates from the commercial birds. From the results obtained, it is important to underscore that i) the tests of TS revealed a high stability of the vaccines used in Brazil, even two years after their manufacture; ii) the level of protection given by live vaccines against NDV does not depend on residual virulence, as confirmed by tests of intracerebral inoculation iii) soroprevalence against NDV in regions with production for exportation was 39.1% and it was possible to isolate 77 samples, always with a non-pathogenic profile; iv) on a second opportunity, a soroprevalence of 28.8% was detected, with isolation of 15 samples, also classified as non-pathogenic; v) in the Brazilian Northeast, a seropositivity of 41.7 to 84.3% was observed depend of region, with isolation of 12 NDVs, characterized as non-pathogenic, indicating that virus of low pathogenicity circulates in those areas that do not export; vi) the genome of the isolated virus and vaccine implies that the circulating virus in commercial birds probably originates from the vaccine and belongs to class II, being 71.8% from genotype II or La Sota-like and 28.2% from genotype I or Ulster-like; vii) finally, the biological characterization of isolates from migratory birds showed that there is circulation of virus of low and high pathogenicity in Brazil. However, this set of studies agrees with the status of Brazil as being a country free of Newcastle disease in commercial birds Doutorado Ciências Básicas Doutor em Clínica Médica

Orientadores: Vera Nisaka Solferini, John Wakeley Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: A estrutura populacional é um dos principais fatores moldando os padrões de variabilidade genética no tempo e no espaço. Devido às flutuações climáticas que ocorreram durante o período Quaternário, muitas espécies podem ter sofrido redução e fragmentação populacional, ficando restritas a "refúgios" durante períodos glaciais e se expandindo novamente durante os interglaciais. Isto tem sido utilizado para explicar alguns padrões encontrados nas espécies atualmente. O presente trabalho consistiu no desenvolvimento e estudo de modelos para auxiliar na compreensão das conseqüências genéticas de mudanças cíclicas na estruturação e tamanho populacionais, como as que teriam ocorrido ao longo das flutuações climáticas do Quaternário. A redução populacional é capaz de causar redução do tamanho efetivo populacional, do tempo médio de coalescência e da variabilidade genética, ao passo que um aumento na subdivisão populacional pode ter o efeito oposto. Para investigar estes efeitos opostos, foram estudados dois modelos, ambos com alternância de duas fases correspondendo aos períodos glaciais e interglaciais. Em ambos os modelos permitiram-se mudanças na estrutura populacional, além de mudanças no tamanho populacional, de uma maneira cíclica. No primeiro modelo, fases totalmente panmíticas alternaram-se com fases totalmente estruturadas. A partir deste modelo, obteve-se uma expressão para a esperança do tempo de coalescência de duas seqüências e, a partir desta, uma expressão para a esperança do número de sítios polimórficos. Tanto o aumento do número de demes quanto da duração das fases estrutura das causaram um aumento do tempo de coalescência e dos níveis de variabilidade genética. Os resultados obtidos foram comparados com os que seriam esperados para uma população panrnítica de tamanho constante. Verificou-se que a estruturação pode superar o efeito da redução populacional durante os períodos glaciais. Especificamente, o número médio de sítios polimórficos pode ser maior no modelo proposto, mesmo quando o támanho populacional é muito reduzido durante as fases estruturadas. No segundo modelo, permitiu-se subdivisão populacional de acordo com o modelo de finitas ilhas em ambas as fases, com migração. O tamanho populacional, a taxa de migração e o número de demes variaram entre as fases. Para este modelo, além de uma expressão para a o tempo médio de coalescência, obteve-se também uma expressão para a distribuição dos tempos de coalescência de duas seqüências. As distribuições observadas foram muito diferentes do que seria esperado para uma população panrnítica de tamanho constante. Um tamanho populacional reduzido durante os períodos glaciais causou descontinuidades e picos múltiplos na distribuição dos tempos de coalescência, bem como uma redução dos tempo médios. O aumento da estrutura populacional, através da redução da taxa de migração, aumentou os tempos médios e atenuou os picos da distribuição. O tempo médio de coalescência, em geral, também aumentou em decorrência de um maior número de demes durante os períodos glaciais. Os resultados encontrados ajudam na compreensão das conseqüências genéticas de ciclos glaciais e, em especial, da importância da estrutura populacional na manutenção da variabilidade genética. Além' disso, oferecem uma possível explicação para padrões genéticos observados em muitas espécies em que genealogias gênicas muito longas são econtradas, com o ancestral comum mais recente antecedendo em muito ao último período glacial Abstract: Population structure is one of the major factors shaping the pattems of genetic variation across time and space. Due to the climatic fluctuations of the Qua terna ry, several species may have suffered population reduction and fragmentation, becoming restricted to refugia during glacial periods and expanding again during interglacials. This has been used to explain some patterns currently observed in several species. The present work consisted in the development and study of models to help understand the genetic consequences of cyclic changes in population structure and size, such as the ones that may have occurred throughout the climatic fluctuations of the Quatemary. Population reduction may cause reduction in population effective size, mean coalescence time and genetic variation; whereas an increase in population subdivision may have the opposite effect. In order to investigate these two opposite effects, two models were studied, both with two alternating phases, corresponding to the glacial and interglacial periods. Both models included changes in population structure, besides those in population size, in a cyclic manner. In the first model, completely panrnictic phases were alternated with completely structured ones. Based on this model, an expression was derived for the expectation of coalescence times of two sequences and, from this, an expression for the expectation of the number of segregating sites. Both an increase in the number of demes and in the duration of the structured phases caused an increase in coalescence times and levels of genetic variation. The results obtained were compared to what would be expected for a panrnictic population of constant size. It was verified that population structure may outhweigh the effect of population reduction during glacial periods. Specifically, the mean number of segregating sites can be greater in the proposed model, even when population size is quite reduced during the structured phases. In the second mode!, population subdivision was allowed in both phases' - according the finite island model with migration. Population size, migration rate and number of demes varied between phases. For this model, besides an expression for the mean coalescence time, an expression for the distribution of coalescence times was also obtained. The distributions observed were quite different from what would be expected for a panrnictic population of constant size. Population reduction during glacial periods caused discontinuities and multiple peaks in the distribution of coalescence times, as well as a reduction in the expected times. An increase in population structure, through reducing migration rates, increased the mean times and attenuated the peaks of the distribution. Mean coalescence times, in general, also increased with a greater number of demes during glacial periods. The results obtained help understand the genetic consequences of glacial cycles, and, especially, point to the importance of population structure for the maintenance of genetic varlation. Besides, they offer a potential explanation for the genetic pattems observed in several species, for which long gene genealogies are observed, with the most recent ancestor predating by far the last glacial period Doutorado Genética Animal e Evolução Doutor em Genética e Biologia Molecular

Orientadores: Carmen Silvia Passos Lima, Maria de Lourdes Setsuko Ayrizono Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas Resumo: O desenvolvimento de câncer colorretal (CCR) é resultado de uma complexa interação de variáveis, incluindo elementos externos, como a exposição a agentes ambientais e dietéticos, e fatores internos, de natureza somática ou hereditária. Não está estabelecido se genótipos de polimorfismos de baixa penetrância em genes relacionados com o metabolismo do ácido fólico, como o metilenotetrahidrofolato redutase (MTHFR C677T e MTHFR A1298C), o metionina sintase (MTR A2756G), o metionina sintase redutase (MTRR A66G) e o timidilato sintase (TS 2R3R), estão associados com o risco de ocorrência da doença ou com suas manifestações clínicas. Portanto, o objetivo deste estudo foi verificar se esses polimorfismos gênicos influenciam o risco de ocorrência do adenocarcinoma colorretal esporádico (ACRE) e suas manifestações clínicas e biológicas em pacientes da região sudeste do Brasil. Foram avaliados 113 pacientes com ACRE e 188 controles, considerando os aspectos clínicos como a idade, o sexo, a raça, a localização, o grau de diferenciação do tumor, o estágio e os genótipos de cada gene. Os genótipos dos polimorfismos dos genes MTHFR, MTR, MTRR e TS foram avaliados por meio da reação em cadeia da polimerase (PCR) seguida ou não por digestão enzimática. O significado estatístico das diferenças entre grupos foi calculado por meio do teste da probabilidade exata de Fisher ou qui-quadrado. As determinações dos riscos de ocorrência do ACRE, a que pacientes e controles foram submetidos, foram obtidas por meio das razões das chances (ORs) e calculadas considerando um intervalo de confiança de 95%. Portadores dos genótipos MTRR 66AG+GG, do MTHFR 1298AC+CC+677CT+TT, do MTHFR 677CT+TT+MTR 2756AG+GG, do MTHFR 1298AC+CC + 677CT+TT + MTR 2756AG+GG e MTHFR 1298AC+CC + 677CT+TT + MTRR 66AG+GG apresentaram riscos 1,99, 3,26, 2,22, 10,92 e 14,88 vezes maiores, respectivamente, de desenvolver ACRE do que os outros. Além disso, os indivíduos com o genótipo MTHFR 677CT+TT e os genótipos MTR 2756AG+GG tiveram um risco de 2,12 e 1,42 vezes maior de desenvolver ACRE com idade menor do que 50 anos. Afro-Brasileiros com o genótipo GG do polimorfismo MTRR A66G tiveram risco 1,98 vezes maior de desenvolver ACRE, e indivíduos com o genótipo MTR 2756AG+GG e os genótipos MTHFR 677CT+TT estiveram sob risco 2,11 e risco 1,62 vezes maiores de ocorrência de tumores indiferenciados e avançados, respectivamente, do que os demais. Portadores dos genótipos MTHFR 1298AC+CC e MTHFR 1298AC+CC + MTRR 66AG+GG estiveram sob riscos 1,42 e 3,07 vezes maiores de tumor no reto, respectivamente, enquanto que portadores dos genótipos MTHFR 677CT+TT e MTHFR 677CT+TT + TS 2R3R+3R3R estiveram sob riscos 1,55 e 5,39 vezes maiores de tumor de cólon, respectivamente, do que portadores dos genótipos selvagens. Estes dados sugerem que polimorfismos dos genes MTHFR, MTR, MTRR e TS, que codificam enzimas que participam do metabolismo do ácido fólico, especialmente em combinação, têm papéis consistentes para o risco de desenvolver ACRE em indivíduos da região sudeste do Brasil Abstract: The development of colorectal cancer (CRC) is the result of a complex interaction of variables, including external factors such as exposure to environmental agents and dietary factors and internal factors, whether somatic or hereditary. Is not been established genotypes with low penetrance polymorphisms in genes related to metabolism of folic acid such as methylenetetrahydrofolate reductase (MTHFR C677T and A1298C), methionine synthase (MTR A2756G), methionine synthase reductase (MTRR A66G) and thymidylate synthase (TS 2R3R), are associated with the risk of the disease or its clinical manifestations. Therefore, the aim of this study was to determine whether these genetic polymorphisms influence the risk of sporadic colorectal adenocarcinoma (SCA) and their clinical and biological manifestations in patients from southeast Brazil. For this, we analyzed 113 patients with SCA and 188 controls, considering the clinical aspects such as age, sex, race, location, stage, degree of tumor differentiation and the genotypes of each gene described above. The genotypes of the polymorphisms of the MTHFR, MTR, MTRR and TS were assessed by polymerase chain reaction (PCR) and enzyme digestion. The statistical significance of differences between groups was calculated using the probability test of Fisher's exact or chi-square. Determination of the risks of SCA, the patients and controls were submitted, was obtained through the odds ratios (ORs) and calculated assuming a range of 95%. Carriers of the MTRR 66AG + GG, the MTHFR 1298AC+CC + 677CT+TT, the MTHFR 677CT+TT + MTR 2756AG+GG, the MTHFR 1298AC+CC + 677CT+TT + MTR 2756AG+GG, and the MTHFR 1298AC+CC + 677CT+TT + MTRR 66AG+GG genotypes had a 1.99, a 3.26, a 2.22, a 10.92 and a 14.88-fold increased risks for SCA than others, respectively. In addition, individuals with the MTHFR 677CT+TT and the MTR 2756AG+GG genotypes had a 2.12 and a 1.42-fold increased risks for SCA diagnosed under 50 years. African-Brazilians with the MTRR 66GG genotype had a 1.98-fold increased risk for SCA, and individuals with the MTR 2756AG+GG and the MTHFR 677CT+TT genotypes were under a 2.11 and a 1.62-fold increased risks for undifferentiated and advanced tumors, respectively, than others. Carriers of the MTHFR 1298AC+CC and the MTHFR 1298AC+CC + MTRR 66AG+GG genotypes had a 1.42 and a 3.07-fold increased risks for rectal tumor, respectively, while carriers of the MTHFR 677CT+TT and the MTHFR 677CT+TT + TS 2R3R+3R3R genotypes had a 1.55 and a 5.39-fold increased risks for colon tumor, respectively, than carriers of the wild genotypes. This data suggest that polymorphisms of genes MTHFR, MTR, MTRR and TS, which encode folate-dependent enzymes, particularly in combination, have consistent roles for SCA risk in southeastern Brazil Doutorado Fisiopatologia Cirúrgica Doutor em Ciências

Orientadores: João Aristeu da Rosa, Carlos Eduardo Almeida Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: Triatoma sherlocki, espécie primeiramente coletada por Cerqueira, 1975, tem distribuição registrada na região do município de Gentio do Ouro, Centro Norte do Estado da Bahia, Brasil. Populações intradomiciliares dessa espécie foram encontradas em um assentamento de garimpo em Gentio do Ouro, conhecido como Encantado. Em sua localidade tipo (Santo Inácio) invasões domiciliares são frequentes, mas não foi constatado qualquer indício de domiciliação, portanto informações sobre a sua biologia e aspectos epidemiológicos quanto à transmissão de Trypanosoma cruzi se fazem necessárias. O objetivo central deste trabalho foi verificar se o fator genético poderia estar envolvido no processo de domiciliação de T. sherlocki e se as populações provenientes de ambientes antropizados poderiam apresentar identidade genética. Coletas em ambientes estritamente silvestres e em áreas antropizados nas localidades Santo Inácio e Encantado foram efetuadas entre 2008 e 2009. A análise da variabilidade genética das populações coletadas de T. sherlocki foi verificada por meio de sequenciamento de um fragmento do gene mitocondrial Citocromo B e a estrutura genética foi avaliada utilizando Análise de Variância Molecular (AMOVA). Exemplares de T. sherlocki foram coletados em nove localidades, duas antrópicas, denominadas "Encantado 1" e "Santo Inácio 1", e as demais estritamente silvestres denominadas "Encantado 2", "Santo Inácio 2", "Gentio do Ouro 1", "Gentio do Ouro 2", "Gentio do Ouro 3", "Gentio do Ouro 4" e "Gentio do Ouro 5". Somente na localidade de "Encantado 1" existem registros de capturas de ninfas e adultos no intradomicílo. Em Santo Inácio 1, segundo a Secretaria de Saúde de Gentio do Ouro, casos de invasões esporádicas são frequentes apenas por exemplares adultos. Foram obtidas 292 sequências de 565 pares de bases do fragmento do gene mitocondrial Cit B e 63 haplótipos foram encontrados. Os valores de diversidade haplotípica variaram de 0.602 para a localidade "Gentio do Ouro 4" até 0.820 para a localidade "Gentio do Ouro 2". Os resultados obtidos por AMOVA demonstraram que o agrupamento de populações por distância geográfica variou mais entre os grupos (11.13%) do que entre populações dentro dos grupos (2.83%). As análises baseadas em agrupamentos ecológicos, isto é, silvestres versus antrópicos, variaram em 13.39% entre as populações dentro desses grupos, portanto, sem estruturação genética para esses agrupamentos. Esses resultados não suportam a hipótese de dispersão passiva para a formação de colônias intradomiciliares em Encantado 1 a partir de Santo Inácio 1 e sugerem que a colonização das habitações em Encantado 1 ocorre a partir de focos silvestres adjacentes. Como as populações de Encantado 1 e 2 apresentaram relativo grau de diferenciação genética quando comparadas às demais, a possibilidade do fator genético estar envolvido na colonização dos domicílios em Encantado deve ser considerada. As análises de populações de T. juazeirensis e de T. melanica, membros do complexo T. brasiliensis, foram conduzidas com a mesma abordagem utilizada para o estudo da estrutura genética de T. sherlocki. A variação entre as populações T. sherlocki e T. melanica são compatíveis com a diferenciação intraespecífica, ao passo que para T. juazeirensis encontrou-se alta diferenciação genética entre populações da Localidade Tipo (Juazeiro) em relação às populações da região Centro Norte do Estado da Bahia, indicando um possível processo de isolamento reprodutivo Abstract: Triatoma sherlocki, a specie first collected by Cerqueira, 1975, it is registered in the municipality of Gentio do Ouro region North Central from Bahia State, Brazil. Household population of T. sherlocki were found in a small artisan quarry-mining community in the municipality of Gentio do Ouro, known as Encantado. From the type locality (Santo Inácio) home invasions are common, but did not report any evidence of domestication, therefore information about its biology and epidemiology aspects in relation to the transmission of Chagas disease are needed. The main objective of this study was to determine if the genetic factor might be involved in the process of domestication of this specie and if the populations from anthropized environments could present genetic identity. Collected from wild strictly and anthropized environmental in the localities Santo Inácio and Encantado were performed between 2008 and 2009. The analysis of genetic variability of populations collected was verified by sequencing of fragment of the mitochondrial gene Cytochrome B and the genetic structure was evaluated by using analysis molecular variance (AMOVA). Specimens of the T. sherlocki were collected in nine locations, two anthropogenics, denominated "Encantado 1" and "Santo Inácio 1", and the others wild strictly denominated "Encantado 2", "Santo Inácio 2", "Gentio do Ouro 1", "Gentio do Ouro 2", "Gentio do Ouro 3", "Gentio do Ouro 4" and "Gentio do Ouro 5". Only in the Encantado 1 locality were collected nymphs and adults in households. In Santo Inácio 1 according the Health Secretary from Gentio do Ouro, Bahia, sporadic invasions are frequent and only adults were collected in households. 292 sequences of 565 bases pairs of the fragment mitochondrial gene Cyt B were obtained and 63 haplotypes were founded. Haplotype diversity values ranged from 0.602 in the "Gentio do Ouro 4" locality to 0.820 in the "Gentio do Ouro 2" locality. The results of AMOVA showed that the population grouping based on geographical distance resulted in a greater variation between groups (11.13%) than among populations within groups (2.83%). When performed the analysis based on groupings ecologic, ie, localities wild strictly vs. anthropized localities, where specimens household are observed, there was no significance for the variation between groups, which showed 13.39% of variation among populations within groups. These results rule out the hypothesis of passive spread to formation of household colonies in Encantado 1 from Santo Inácio 1, suggesting that colonizations of houses in Encantado 1 occurs from adjacent foci wild. As the populations Encantado 1 and 2 presented relative degree of genetic differentiation when compared to other populations, the possibility that the genetic factor is involved in the colonization of houses in Encantado should be considered. Analysis of populations of T. juazeirensis and T. melanica, others members of the Triatoma brasiliensis complex that occur in the Bahia State, was also conducted with the same approach for the inferences about the genetic structure of T. sherlocki. The variation between T. sherlocki and T. melanica populations are consistent with intraspecific differentiation, whereas T. juazeirensis found a high genetic differentiation between populations from the Type Locality (Juazeiro) in relation to the populations of the North Central region of Bahia State, indicating a possible process of reproductive isolation Doutorado Parasitologia Doutor em Parasitologia

The inflammasome is a cytoplasmic multiprotein complex responsible for the activation of inflammatory caspases (caspase-1, -4, and -5) in response to pathogen- and/or damage-associated molecular patterns or to homeostasis-altering molecular pathways, and for the consequent release of the pro-inflammatory cytokines interleukin (IL)-1ß and IL-18. Taking in account the complexity of inflammasome activation and that several regulatory steps are involved in maintaining its physiologic role in homeostasis and innate immune response, it does not surprise that several genetic variants in inflammasome components have been associated with common pathologies in the general population, such as autoimmune disorders, cardiovascular diseases, obesity and associated metabolic syndrome, neurodegenerative diseases, and cancer. Moreover, the susceptibility to infectious agents and/or to develop severe complications during infections also has been related to inflammasome genetics. In this work, we revised genetic association studies about polymorphisms of main inflammasome genes in sterile as well as infectious diseases, trying to depict the genetic contribution of inflammasome in disease pathogenesis.

Avian coronavirus (AvCoV) infects a range of tissues in chickens and several other avian species. Although the viruscan be isolated in chicken embryos, only a few strains of the 6 genotypes/33 lineages can grow in cell lines, with theBeaudette strain (GI-1 lineage) being the most used for in vitro studies. Considering the differences between celllines and chicken embryos as habitats for AvCoV, this study aimed to assess the diversity of the genes coding forthe nonstructural protein 3 (nsp3) and spike envelope protein (S) after serial passages in BHK-21 and Vero cells.After 14 passages of an embryo-adapted Beaudette strain, the virus loads fluctuated in both cell lines, with the highestloads being 8.72 log genome copies/µL for Vero and 6.36 log genome copies/µL for BHK-21 cells. No polymorphismswere found for nsp3; regarding S, not only aa substitutions (Vero: 8th passage A150S, and 14th S150A; BHK-21: 4thS53F, 8th F53Y, and 8th S95R), but also minor variants could be detected on chromatograms with fluctuating intensities.As the regions of these aa substitutions are within the receptor-binding domain of S, it can be speculated that differencesin cell receptors between Vero and BHK-21 cells and the speed of cell death led to the selection of different dominantstrains, while the stability of nsp3 supports its function as a protease involved in AvCoV replication. In conclusion,AvCoV quasispecies evolution is influenced by the biological model under consideration, and a gradual transition isseen for minor and major variants. O Coronavírus aviário AvCoV infecta uma variedade de tecidos de galinhas e de outras espécies aviárias. Apesarde este vírus poder ser isolado em ovos embrionados de galinha, apenas alguns dos 6 genótipos / 33 linhagenspodem crescer em cultivo celular, sendo a cepa Beuadette (linhagem GI-11) a mais utilizada para estudos in vitro.Considerando as diferentes linhagens celulares e ovos embrionados como habitats para o AvCoV, este estudo tevepor objetivo estudar a diversidade de genes que codificam para a proteína não-estrutural 3 (nsp3) e espícula (S)após passagens seriadas em células BHK-21 e VERO. Após 14 passagens, de uma amostra Beuadette adaptada aovos embrionados, os títulos virais variaram em ambas as células, com os maiores títulos sendo de 8,72 log cópiasgenômicas/µL para Vero e 6,36 cópias genômicas/µL para BHK-21. Nenhum polimorfismo foi encontrando paransp3. Considerando a proteína S, não somente foram encontradas substituições de aminoácidos (Vero: 8apassagemA150S e 14apassagem S150A; BHK-21: 4apassagem S53F, 8apassagem F53Y e S95R), mas também, variantessubconsensuais foram detectadas pelos cromatogramas com intensidades flutuantes. Uma vez que as regiões destesaa se encontram no domínio de ligação de receptor de S, pode-se especular que diferenças em receptores celularesentre Vero e BHK-21, além da velocidade da morte celular, levaram à seleção de diferentes cepas dominantes,enquanto que a estabilidade de nsp3 concorda com sua função como protease com papel na replicação de AvCoV.Como conclusão, a evolução de quase-espécies de AvCoV é influenciada pelo modelo biológico sob consideraçãoe uma transição gradual é vista para variantes dominantes e subdominantes.&nbsp

Mangalarga Marchador (MM) is the most numerous horse breed in Brazil. The aim of this study was to analyze the genetic structure of the MM horses population of Brazil based on pedigree analysis and identify factors that may affect its genetic variability. Pedigree data from 1906 to 2015 was used and the inbreeding and probability of gene origin parameters were obtained, considering the total population (TP, n = 514,282) and a reference population (RP, n = 172,508) from 2005 to 2015. The generation interval was 10.43 in the TP and 9.48 in the RP. The inbreeding coefficient (F) was 1.02% in the TP and 1.10% in the RP. The effective population size was 1,471 for the TP and 959 for the RP. The effective number of ancestors, founders, and founder genomes were 1,038, 1,062, and 150 in the TP, and 198, 225, and 133 in the RP, respectively. The numbers of founders that exhibit 50% of the current gene pool of the breed represented 7.94% of the total founders of the TP and 19.09% of the RP. The analysis of probability of gene origin alert for a small loss of genetic diversity in the recent population. However, the Mangalarga Marchador population does not exhibit relevant factors that may seriously affect your genetic variability and that would impair the evolution of the breed in Brazil.

A Dieta Mediterrânica é caracterizada pela abundância de nutrimentos e substâncias com atividade antioxidante e anti-inflamatória, tendo sido implicada na prevenção do envelhecimento celular e de várias doenças crónicas. O conhecimento sobre a influência global desses nutrimentos na fisiologia celular e humana é crucial para uma melhor compreensão acerca dos benefícios da adesão à Dieta Mediterrânica na saúde e doença. Nesse sentido, as tecnologias “ómicas” são ferramentas analíticas muito atrativas uma vez que fornecem informação molecular funcionalmente inter-relacionada, facultando um nível de conhecimento amplo e integrado sobre a ação desses nutrimentos. Contudo, a aplicação dessa abordagem metodológica ao estudo dos benefícios da adesão à Dieta Mediterrânica é presentemente limitada, em parte devido à sua complexidade científica e sofisticação tecnológica. O presente trabalho estabelece a perspetiva histórica dos principais avanços científicos e tecnológicos subjacentes à Genómica Nutricional. Adicionalmente, analisa a contribuição desta área emergente das Ciências da Nutrição para a elucidação dos mecanismos de ação da Dieta Mediterrânica e para a evolução da nutrição personalizada. The Mediterranean Diet is characterised by the abundance of nutrients and substances with antioxidant and anti-inflammatory activity and has been implicated in the prevention of cellular aging and several chronic diseases. Knowledge about the global influence of these nutrients on cell and human physiology is crucial for a better understanding of the benefits of adherence to Mediterranean Diet in health and disease. In this sense, “omic” technologies are very attractive analytical tools since they generate functionally interrelated molecular information, providing a broad and integrated level of knowledge about the action of these nutrients. Nevertheless, the current application of this methodological approach to the study of the benefits of adherence to the Mediterranean Diet is currently limited, in part because of its scientific complexity and technological sophistication. The present work establishes the historical perspective of the main scientific and technological advances underlying Nutritional Genomics. In addition, it analyses the contribution of this emerging field from Nutritional Sciences to the elucidation of the mechanisms of action of Mediterranean Diet and evolution of personalised nutrition.

The objective of this study was to assess the genetic diversity among accessions of Paspalum notatum based on morphological marker traits and identify those morphological traits that contribute most to the variability among accessions. Fifty-three accessions were evaluated for the following traits: length, width, color, and pubescence of sheath; length, width, insertion angle, color of midrib, and pubescence of leaves; number, length, and angle of racemes; length of flowering stems; and plant growth habit (erect or prostrate). Multivariate analysis of the quantitative morphological data based on the Mahalanobis distance and UPGMA method grouped the accessions into 19 heterogeneous clusters. The relative contribution of each trait to cluster formation was obtained using the Singh method. Qualitative morphological traits were used to construct a dendrogram based on Jaccard's similarity, generating 13 clusters. Based on the morphological traits investigated, there is high genetic variation among accessions of P. notatum, demonstrating that these accessions have a good potential for a breeding program. Length of racemes, width of sheath, length of flowering stems, and length of leaves were found to contribute most to the variability among accessions. A number of traits contributed to a lesser degree. The set of characters used are representative of the vast phenotypic plasticity observed in P. notatum, a diversity which is likely to be related to the species apomictic form of reproduction and the origin of the accessions.

Auriculocondylar syndrome, mainly characterized by micrognathia, small mandibular condyle, and question mark ears, is a rare disease segregating in an autosomal dominant pattern in the majority of the families reported in the literature. So far, pathogenic variants in PLCB4, GNAI3, and EDN1 have been associated with this syndrome. It is caused by a developmental abnormality of the first and second pharyngeal arches and it is associated with great inter- and intra-familial clinical variability, with some patients not presenting the typical phenotype of the syndrome. Moreover, only a few patients of each molecular subtype of Auriculocondylar syndrome have been reported and sequenced. Therefore, the spectrum of clinical and genetic variability is still not defined. In order to address these questions, we searched for alterations in PLCB4, GNAI3, and EDN1 in patients with typical Auriculocondylar syndrome (n = 3), Pierre Robin sequence-plus (n = 3), micrognathia with additional craniofacial malformations (n = 4), or non-specific auricular dysplasia (n = 1), which could represent subtypes of Auriculocondylar syndrome. We found novel pathogenic variants in PLCB4 only in two of three index patients with typical Auriculocondylar syndrome. We also performed a detailed comparative analysis of the patients presented in this study with those previously published, which showed that the pattern of auricular abnormality and full cheeks were associated with molecularly characterized individuals with Auriculocondylar syndrome. Finally, our data contribute to a better definition of a set of parameters for clinical classification that may be used as a guidance for geneticists ordering molecular testing for Auriculocondylar syndrome. © 2017 Wiley Periodicals, Inc.

Aims Fungal diseases are among the main factors limiting high yields of soybean crop. Colletotrichum isolates from soybean plants with anthracnose symptoms were studied from different regions and time periods in Brazil using molecular, morphological and pathogenic analyses. Methods and Results Bayesian phylogenetic inference of GAPDH, HIS3 and ITS-5.8S rDNA sequences, the morphologies of colony and conidia and inoculation tests on seeds and seedlings were performed. All isolates were clustered only with Colletotrichum truncatum species in three well-separated clusters. Intraspecific genetic diversity revealed 27 distinct haplotypes in 51 fungal isolates; some of which were identical to C. truncatum sequences from other regions around the world, while others were related to alternative hosts. Conidia were falcate, hyaline, unicellular and aseptate, with variable dimensions, formed in acervuli. Despite being pathogenic to seedlings by both inoculation methods, variation was observed in the aggressiveness of the tested isolates, which was not correlated to genetic variation. Conclusion The identification of C. truncatum in the sampled isolates evidenced it being the only causal agent of soybean anthracnose in Brazil until 2007, with relevant genetic, morphological and pathogenic variability as well as a broad geographical origin. The wide distribution of the predominant C. truncatum haplotype indicated the existence of a highly efficient mechanism of pathogen dispersal over long distances, reinforcing the role of seeds as the primary source of disease inoculum. Significance and Impact of the Study The characterization and distribution of Colletotrichum species in soybean-producing regions in Brazil is fundamental for understanding the disease epidemiology and for ensuring effective control strategies against anthracnose. This article is protected by copyright. All rights reserved.

Jatropha is a potential oilseed crop, which requires mitigating factors such as the low genetic variability of the species. The solution runs through the research of Brazilian germplasm. Attention should be given to the germplasm of jatropha the north of Minas Gerais, because this is the oldest national collection and because this region may be a regions of jatropha diversity due to selection pressure arising from environmental adversities. Therefore, the objective of this study was to investigate the genetic diversity of 48 accessions of collection from Empresa de Pesquisa Agropecuária de Minas Gerais (EPAMIG), using SSR and ISSR markers. The results showed low genetic diversity, but some individuals stood out as J. mollissima (48), J. podagrica (47), Mexican accessions (42, 43, 44 and 45) and some national accessions (28, 29, 41 and 46). Therefore, aiming to increase the genetic variability and improve the effectiveness of jatropha breeding programs, it is suggested to explore such as parental accessions to generate commercial hybrids. This fact implies the possibility to support future production of jatropha, since this culture may be an important source of income, especially for small farmers living in semiarid regions of Brazil.

Unravelling the details of range expansion and ecological dominance shifts of insect pests has been challenging due to the lack of basic knowledge about population structure, gene flow, and most importantly, how natural selection is affecting the adaptive process. Piezodous guildinii is an emerging pest of soybean in the southern region of the United States, and increasingly important in Brazil in recent years. However, the reasons P. guildinii is gradually becoming more of a problem are questions still mostly unanswered. Here, we have genotyped P. guildinii samples and discovered 1,337 loci containing 4,083 variant sites SNPs that were used to estimate genetic structure and to identify gene candidates under natural selection. Our results revealed the existence of a significant genetic structure separating populations according to their broad geographic origin, i.e., U.S. and Brazil, supported by AMOVA (FGT = 0.26), STRUCTURE, PCA, and FST analyses. High levels of gene flow or coancestry within groups (i.e., within countries) can be inferred from the data, and no spatial pattern was apparent at the finer scale in Brazil. Samples from different seasons show more heterogeneous compositions suggesting mixed ancestry and a more complex dynamic. Lastly, we were able to detect and successfully annotated 123 GBS loci (10.5%) under positive selection. The gene ontology (GO) analysis implicated candidate genes under selection with genome reorganization, neuropeptides, and energy mobilization. We discuss how these findings could be related to recent outbreaks and suggest how new efforts directed to better understand P. guildinii population dynamics.

During the last years, Brazilian government control programs have detected an increase of Salmonella Heidelberg in poultry slaughterhouses a condition that poses a threat to human health However, the reasons remain unclear. Differences in genetic virulence profiles may be a possible justification. In addition, effective control of Salmonella is related to an efficient epidemiological surveillance system through genotyping techniques. In this context, the aim of this study was the detection of 24 virulence-associated genes in 126 S. Heidelberg isolates. We classified the isolates into 56 different genetic profiles. None of the isolates presented all the virulence genes. The prevalence of these genes was high in all tested samples as the lowest number of genes detected in one isolate was 10/24. The lpfA and csgA (fimbriae), invA and sivH (TTSS), and msgA and tolC (intracellular survival) genes were present in 100% of the isolates analyzed. Genes encoding effector proteins were detected in the majority of SH isolates. No single isolate had the sefA gene. The pefA gene was found in only four isolates. We have also performed a screening of genes associated with iron metabolism: 88.9% of isolates had the iroN geneand 79.4% the sitC gene . Although all the isolates belong to the same serotype, several genotypic profiles were observed. These findings suggest that there is a diversity of S. Heidelberg isolates in poultry products. The fact that a single predominant profile was not found in this study indicates the presence of variable sources of contamination caused by SH. The detection of genetic profiles of Salmonella strains can be used to determine the virulence patterns of SH isolates.

The cajuí Anacardium spp., which is similar to the caju Anacardium Ocidentale L., is a species adapted to edaphic-climatic conditions of the biome Cerratinga (Cerrado e Caatinga). Its fruit is composed of one swollen stalk (pedicel) which is formed by nutritional reserves rich in vitamin C and drupe (cashew nut). It is also rich in protein and lipids, but with smaller size. This paper focuses on investigating the applicability of the biplot graphical analysis in the process of selective breeding of cajuí population. The cajuí working population in Embrapa Meio Norte comprises of 11 genotypes collected in areas of natural habitat in the state of Piaui. The experiment was designed in randomized complete blocks with two plants per plot and four replications. A graphical analysis (biplot) was used to study the relationships between variables and behavior of the experimental genotypes. This was implemented to principal component analysis based on singular value decomposition biplot. The total variable weight can be predicted from length of peduncle, basal and apical diameter of peduncle, and variables of easy mensuration. Genotypes M40A, M23, M14, and M17 are similar to each other and they have high amounts of brown, apical and basal diameter of the peduncle, total weight, and peduncle length. They are considered as candidates selected for consumption in natura and industrial processing. The graphical analysis (biplot) showed robustness in the presentation of relationships between variables considered and the indication of the selection candidate genotypes in the population studied. Made available in DSpace on 2019-12-09T18:16:59Z (GMT). No. of bitstreams: 1 ART19049.pdf: 486166 bytes, checksum: 2f2a75b10f93ffaf655e6decb28e7e58 (MD5) Previous issue date: 2019

The occurrence of genotype by environment interaction (G x E), which is defined as the differential response of genotypes to environmental variation, is frequently reported in maize cultures, making it challenging to recommend cultivars. Methods allowing to study the potential nonlinear pattern of genotype responses to environmental variation allied to prior beliefs on unknown parameters are interesting to evaluate the phenotypic adaptability and stability of genotypes. In this context, the present study aimed to assess the adaptability and stability of maize hybrids, by using the Bayesian segmented regression model, and evaluate the efficacy of using informative and minimally informative prior distributions for the selection of cultivars. Randomized complete-block design experiments were carried out to study the yield (kg/ha) of 25 maize hybrids, in 22 different environments, in Northeastern Brazil. The Bayesian segmented regression model fitted using informative prior distributions presented lower credibility intervals and Deviance Criterium of Information values, compared to those obtained by fitting using minimally informative distributions. Therefore, the model using informative prior distributions was considered for the adaptability and stability evaluation of maize genotypes. Once most northeastern farmers in Brazil have limited capital, the genotype P4285HX should be considered for planting, due to its high yield performance and adaptability to unfavorable environments.

Ceratocystis fimbriata Ellis & Halsted recently was recorded causing seed and seedling blight on Carapa guianensis Aubl. (andiroba), a tree species native to the Amazon Rainforest and prized for its valuable timber and medicinal seed oil. C. fimbriata more commonly causes wilt type diseases in woody hosts, especially on non-native host trees. However, on andiroba the disease occurs on seedlings and seeds, affecting the species regeneration. We studied 73 isolates of C. fimbriata on andiroba from three regions of the Amazon Basin to see if they represented natural or introduced populations. Analysis of ITS rDNA sequences and phylogenetic analysis of mating type genes revealed new haplotypes of C. fimbriata from the Latin American Clade that were closely related to other Brazilian populations of the fungus. In mating experiments, andiroba isolates were inter-fertile with tester strains of C. fimbriata from Brazil and elsewhere, confirming that they belong to a single biological species. Using microsatellite markers, 14 genotypes and populations with intermediate levels of genetic variability were found, suggesting that the fungus is indigenous to the Amazon Basin. Inoculation tests indicated that the andiroba isolates are host-specialized on andiroba, supporting the proposition of the special form C. fimbriata f. sp. carapa. Made available in DSpace on 2019-03-20T00:43:38Z (GMT). No. of bitstreams: 1 26788.pdf: 3260751 bytes, checksum: e216b037faec9a95d9551042e8f53907 (MD5) Previous issue date: 2019

Orientador: Marcus Aloizio Martinez de Aguiar Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: Interações interespecíficas influenciam propriedades básicas populacionais e determinam dinâmicas ecológicas e evolutivas das espécies interagentes. Interações tradicionalmente consideradas mutualistas não necessariamente resultam em benefício líquido para as espécies interagentes, e de forma geral, apresentam variação em sua magnitude e sinal. Essa variação é resultado de três aspectos fundamentais: custos e benefícios associados à interação; variação espacial e temporal na interação; e contexto da comunidade. Uma consequência evolutiva de interações é que elas podem levar à mudanças recíprocas em características das espécies, processo conhecido como coevolução. O interesse central desta tese consiste em investigar mecanismos que promovem diversidade biológica em sistemas coevolutivos envolvendo poucas espécies para as quais a interação varia em magnitude e sinal. Exploramos como a estrutura espacial de um par de espécies interagentes influencia o processo coevolutivo em um cenário de comunidades ligadas por fluxo gênico. Encontramos que comunidades centrais tem um papel fundamental em promover diversidade alélica e que polimorfismos são esperados para uma ampla variedade de condições, inclusive quando mutualismos são prevalentes na paisagem. Estudamos como parceiros de interação que exercem pressões seletivas distintas determinam a evolução de características fenotípicas da planta com que interagem. Encontramos que conflito na direção de seleção entre parceiros de interação promove coexistência e uma maior diversidade fenotípica em plantas. Ainda, conflito na relação entre os benefícios adquiridos por cada parceiro definem as espécies que persistem na comunidade. Finalmente, investigamos estratégias de defesa em mutualismos de proteção entre formigas e suas plantas hospedeiras. Mais especificamente como custos e benefícios associados à interação entre formigas e plantas definem seu investimento na interação, determinando estratégias de defesa e influenciando a coexistência entre estratégias e a dinâmica do mutualismo. Interações competitivas entre formigas que adotam a mesma estratégia, bem como alto custo associado à defesa em plantas, levam à coexistência entre estratégias tanto de formigas quanto de plantas. Os resultados apresentados mostram como a importância do contexto da comunidade, a direção da seleção e a relação entre custos e benefícios da interação determinam padrões de diversidade em sistemas coevolutivos com poucas espécies. As abordagens apresentadas podem ser estendidas para incluir outros tipos de interação e utilizadas para compreender maneiras pelas quais sistemas com poucas espécies podem ser vistos como subconjuntos que formam sistemas ricos em espécies Abstract: Interspecific interactions influence basic properties of populations and determine ecological and evolutionary dynamics of interacting species. Interactions traditionally considered as mutualisms not necessarily result in net benefit for the interacting species, and in general, present variation in magnitude and sign. Such variation is the outcome of three fundamental aspects: costs and benefits associated with the interaction; spatial and temporal variation in interaction; and community context. An evolutionary consequence of interespecific interaction is that it can lead to reciprocal changes in traits of interacting species, a process known as coevolution. The main interest of this thesis is to investigate mechanisms promoting biological diversity in coevolutionary systems involving few species for which the interaction varies in sign and magnitude. We explored how spatial structure of a pair of interacting species influences the coevolutionary process in a scenario where communities are linked by gene flow. We found that central communities play a fundamental role in promoting alelic diversity and that polymorphisms are expected for a broad range of conditions, even when mutualisms are prevalent across the landscape. We studied how interaction partners exerting contrasting selective pressures determine the evolution of the phenotypic traits of the plants they interact with. We found that conflict in the direction of selection between interaction partners promote coexistence and a greater phenotypic diversity in plants. In addition, trade-offs between benefits acquired from each partner determine species that thrive in the community. Finally, we investigated defensive strategies in protective mutualisms between ants and its host plants. More specifically, how costs and benefits associated with the interaction between ants and plants define its investiment in the interaction, establishing defensive strategies and influencing coexistence between strategies and mutualism dynamics. Competitive interactions between ants that adopt the same strategy as well as high costs associated with defense in plants lead to coexistence between strategies in both ants and plants. The results show how community context, interaction costs and benefits and direction of selection determine coevolutonary patterns in coevolutionary system with few species. The frameworks presented can be extended to include other types of interaction and used to comprehend how systems with few species might be understood as building blocks of species rich systems Doutorado Ecologia Doutora em Ecologia CAPES 0

Anopheles cruzii is the main vector of human and simian malaria in the Brazilian Atlantic Forest. This biome, which is an important hotspot of malaria transmission, has suffered fragmentation and deforestation as a result of urban expansion. Fragmentation and deforestation occur continually in the south of the city of Sao Paulo, Brazil, and findings of An. cruzii in the peridomicile have consequently become more frequent in this part of the city. Although An. cruzii is of considerable epidemiological importance, the impact of urbanization on the microevolution of this species in this malaria-endemic region has not been investigated to date. In this study, we investigated temporal variation in wing shape and size in An. cruzii populations collected in sylvatic, peri-urban and urban areas over a three-year period. Our results show a slight but significant phenotypic variation in all three populations over the study period. Time was a more powerful driver for wing variation than geographic distance. Temporal wing-shape variation appears to be positively associated with urbanization, suggesting that anthropogenic changes in the environment may be a strong driver for wing-shape variation in An. cruzii. Further studies using genetic markers are needed to assess genetic differentiation in these populations.

Orientadores: André Olmos Simões, Anete Pereira Souza Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: A diversidade genética é um dos três níveis de organização da biodiversidade, sendo a força motriz por trás do surgimento e adaptação das espécies a diferentes habitats. A interação entre a variabilidade genética presente no seio de uma população e elementos do ambiente onde esta ocorre eventualmente se traduzirá sob a forma de uma estrutura genética espacial, i.e., a distribuição espacial não-aleatória dos genótipos. Informações acerca da estrutura genética espacial de uma população constituem uma valiosa ferramenta para o estudo de populações e também da história evolutiva de uma espécie. O objetivo do presente trabalho foi investigar como a estrutura genética de uma população está organizada através de diferentes escalas espaciais, e de que maneira essas escalas relacionam-se entre si. Para tanto, escolhemos como modelo de estudo o bambu lenhoso Merostachys neesii Rupr. (Poaceae: Bambusideae), uma espécie endêmica da Mata Atlântica cujo ciclo de vida e características da história de vida as tornam um excelente modelo para estudos sobre estrutura genética espacial. No primeiro capítulo, descrevemos os marcadores moleculares utilizados nas análises genéticas dos capítulos subsequentes. No segundo capítulo, analisamos a estrutura genética espacial de uma população de M. neesii localizada na Floresta Ombrófila Densa Montana no Parque Estadual da Serra do Mar (PESM), SP, e discutimos quais processos podem estar por trás da geração desses padrões em diferentes escalas. No terceiro capítulo, estendemos nossa análise da estrutura genética espacial à escala do interior das moitas e discutimos como os processos ecológicos que determinam a estrutura genética espacial em maiores escalas podem afetar também a organização interna das moitas de bambu. As análises revelaram a existência de uma acentuada estrutura genética espacial em fina escala, em que o grau de parentesco entre indivíduos é significativo até um limite de 11m de distância. Esse padrão pode ser explicado pela ausência de adaptações à dispersão a longa distância em espécies de bambu, um fenômeno que leva à agregação espacial de genótipos aparentados. Também foi observada a existência de duas subpopulações cujo padrão de distribuição possivelmente está ligado à ocorrência de assimetrias na distribuição de condições e recursos ao longo da paisagem. Nossos resultados demonstram que os processos ligados à estruturação genética espacial repercutem igualmente na organização interna das moitas de bambu: em mais da metade dos casos, as moitas analisadas não constituem um indivíduo único, mas contêm uma coleção de genótipos intimamente aparentados. Esse padrão também pode ser compreendido como resultado da limitação de dispersão e pode estar relacionado a uma estratégia evolutiva mais ampla deste grupo de plantas. Nosso estudo revelou que diversas forças podem atuar simultaneamente determinando a estrutura genética espacial de uma população em diferentes escalas espaciais: enquanto a limitação da dispersão constitui o fenômeno determinante em escalas de alguns centímetros até poucos metros, a heterogeneidade ambiental parece ser o fator governando a distribuição de grupos genéticos mais amplos Abstract: Genetic diversity is one of the three levels of biodiversity and constitutes the driving force behind the emergence and adaptation of species to their habitats. The interaction between the genetic variability present within a population and elements from the environment where it occurs will eventually be translated into a spatial genetic structure; i.e., the nonrandom distribution of genotypes in space. Information about a population¿s spatial genetic structure represents a valuable tool to better understand population dynamics and the evolutionary history of a species. The aim of this study was to investigate how the genetic structure of a population is organized across different spatial scales and how these scales relate to each other. We chose as a study model the woody bamboo Merostachys neesii (Poaceae: Bambusideae), a species endemic to the Atlantic Forest whose life cycle, reproductive traits, clonal habit and organization in clumps renders an excellent model to test hypothesis about genetic structure in different spatial scales. In the first chapter, we describe the molecular markers used in the genetic analyses of the subsequent chapters. In the second chapter, we analyse the spatial genetic structure of a M. neesii population localized in a portion of Montane Atlantic Forest at Serra do Mar State Park ¿ SP, Brazil, and discuss which process may be behind the generation of such patterns in different scales. In the third chapter, we extend our analysis of spatial genetic structure to the interior of the clumps and discuss how ecological process that determine genetic structure in broader scales may also affect the internal organization of bamboo clumps. Our analysis revealed the existence of a strong fine-scale spatial genetic structure, in which kinship levels between individuals are significant up to a 11m distance threshold. This pattern may be explained by the absence of adaptations to seed dispersal in bamboo species, which leads to the spatial aggregation of related genotypes. We also observed the occurrence of two broader subpopulations whose distribution across the plot is most likely related to assymmetries in the distribution of conditions and resources across the landscape. At last, our results demonstrate that the processes related to spatial genetic structuring in broader scales also affect the internal structure of bamboo clumps: in more than half the cases, analysed clumps did not constitute a single individual, but rather a collection of closely related genotypes. This pattern may also be explained as a result of the limited dispersal typical of bamboo species and may be related to a broader evolutionary strategy present in this group of plants. Our study revealed that several forces may act simultaneously to determine the genetic structure of a population in different spatial scales: while limited dispersal is the main determinant phenomenon in the scale of a few centimeter up to a few meters, environmental heterogeneity seems to be the factor governing the distribution of broader genetic groups in this population Mestrado Biologia Vegetal Mestre em Biologia Vegetal CAPES CNPQ 403710/2012-0 FAPESP 03/12595-7, 12/51872-9

Background Plasmodium vivax parasites are the predominant cause of malaria infections in the Brazilian Amazon. Infected individuals are treated with primaquine, which can induce haemolytic anaemia in glucose-6-phosphate dehydrogenase (G6PD)-deficient individuals and may lead to severe and fatal complications. This X-linked disorder is distributed globally and is caused by allelic variants with a geographical distribution that closely reflects populations exposed historically to endemic malaria. In Brazil, few studies have reported the frequency of G6PD deficiency (G6PDd) present in malaria-endemic areas. This is particularly important, as G6PDd screening is not currently performed before primaquine treatment. The aim of this study was to determine the prevalence of G6PDd in the region of Alto do Juruá, in the Western Brazilian Amazon, an area characterized by a high prevalence of P. vivax infection. Methods Five-hundred and sixteen male volunteers were screened for G6PDd using the fluorescence spot test (Beutler test) and CareStart™ G6PD Biosensor system. Demographic and clinical-epidemiological data were acquired through an individual interview. To assess the genetic basis of G6PDd, 24 SNPs were genotyped using the Kompetitive Allele Specific PCR assay. Results Twenty-three (4.5%) individuals were G6PDd. No association was found between G6PDd and the number of malaria cases. An increased risk of reported haemolysis symptoms and blood transfusions was evident among the G6PDd individuals. Twenty-two individuals had the G6PDd A(−) variant and one the G6PD A(+) variant. The Mediterranean variant was not present. Apart from one polymorphism, almost all SNPs were monomorphic or with low frequencies (0–0.04%). No differences were detected among ethnic groups. Conclusions The data indicates that ~1/23 males from the Alto do Juruá could be G6PD deficient and at risk of haemolytic anaemia if treated with primaquine. G6PD A(−) is the most frequent deficiency allele in this population. These results concur with reported G6PDd in other regions in Brazil. Routine G6PDd screening to personalize primaquine administration should be considered, particularly as complete treatment of patients with vivax malaria using chloroquine and primaquine, is crucial for malaria elimination. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-1889-6) contains supplementary material, which is available to authorized users.