Orientador: Fausto Foresti / Coorientador: José Carlos Pansonato Alves / Banca: Diogo Teruo Hashimoto / Banca: Vanessa Paes da Cruz / Resumo: No presente estudo, foram analisadas citogeneticamente cinco espécies de peixes pertencentes ao gênero Trichomycterus: T. diabolus, T. iheringi, T. zonatus, Trichomycterus cf. mimonha e Trichomycterus sp., provenientes de diferentes bacias hidrográficas brasileiras. Foram utilizadas as técnicas de citogenética clássica (coloração com Giemsa, localização das RONs pela marcação com nitrato de Prata e bandamento C) e cito-moleculares (Hibridação Fluorescente in situ - FISH com sondas de DNAr 5S e 18S e o snDNA U2). Todas as espécies apresentaram número diploide de 2n=54 cromossomos com variações em sua fórmula cariotípica. Trichomycterus diabolus, T. iheringi, T. zonatus e Trichomycterus cf. mimonha apresentaram seu cariótipo com 34m + 12sm + 8st e Trichomycterus sp. apresentou 36m + 10sm + 8st, além da ocorrência de cromossomos supranumerários. As espécies também revelaram diferenças em relação ao tamanho dos dois primeiros pares cromossômicos do cariótipo, onde Trichomycterus sp. e T. diabolus apresentaram o primeiro e segundo metacêntrico de tamanho semelhante e maiores em relação aos demais cromossomos, enquanto em T. zonatus, Trichomycterus cf. mimonha e T. iheringi apenas o primeiro metacêntrico foi considerado o maior par. O bandamento C evidenciou blocos heterocromáticos instersticiais nos pares 2, 3, 7, 8, 19 e 23 de T. iheringi e no par 18 de T. diabolus, sendo que as demais espécies apresentaram blocos centroméricos de diferentes tamanhos espalhados por quase todo o cariótipo. As RONs foram identificadas em apenas um par cromossômico e foram coincidentes com a hibridação fluorescente in situ realizada com a sonda para DNAr 18S, com exceção de T. zonatus e Trichomycterus sp. que apresentaram marcações centroméricas no primeiro par e em um pequeno metacêntrico, respectivamente. A hibridação com a sonda para DNAr 5S revelou resultados mais diversos, sendo detectado um par para... / Abstract: In the present study five species of fish from the genus Trichomycterus were analyzed cytogenetically, including T. diabolus, T. iheringi, T. zonatus, Trichomycterus cf. mimonha and Trichomycterus sp., collected at different Brazilian basins. The analyses involved classical (Giemsa conventional staining, localization of NORs for silver nitrate marking and C-banding) and molecular cytogenetic techniques (fluorescent in situ hybridization with ribosomal 5S and 18S, and U2 snDNA probes). All species showed diploid number of 2n = 54 chromosomes with variations in karyotype formula. Trichomycterus diabolus, T. iheringi, T. zonatus and Trichomycterus cf. mimonha presented their karyotype with 34m + 12sm + 8st and Trichomycterus sp. presented 36m + 10sm + 8st, besides the occurrence of supernumerary chromosomes. The species also reveals differences in relation to the size of the first two chromosome pairs of the karyotype, where Trichomycterus sp. and T. diabolus presented the first and second metacentric with similar size and larger than the other chromosomes, while in T. zonatus, Trichomycterus cf. mimonha and T. iheringi only the first metacentric was considered the largest pair. The constitutive heterochromatin showed interstitial blocks in pairs 2, 3, 7, 8, 19 and 23 in T. iheringi and the par 18 in T. diabolus and the other species presented centromeric blocks with different sizes spread throughout the greater part of the karyotype. NORs were identified in only one chromosome pair and were coincident with the fluorescent in situ hybridization using probes of 18S rDNA, except for T. zonatus and Trichomycterus sp. that showed additional centromeric signals on the first pair and other small metacentric, respectively. FISH using the probes of 5S rDNA was differentially distributed in the different species, with one chromosome pairs detected in T. diabolus, two pairs in T. iheringi, T. zonatus and three ... / Mestre

Orientador: Paulo Eduardo Martins Ribolla / Banca: Sandra Aparecida Drigo Linde / Banca: Deilson Elgui de Oliveira / Resumo: O câncer de mama é a forma mais comum de câncer e a segundo causa mais comum de morte por uma doença neoplásica afetando mulheres. Há uma série de fatores de risco reconhecidos para o desenvolvimento do câncer de mama incluindo fatores hereditários, hormonais, reprodutivos e história menstrual, idade, falta de exercício, álcool, radiação, doença benigna da mama, e obesidade. Embora aproximadamente 10% a 30% dos casos de câncer de mama sejam atribuídos a fatores hereditários, apenas 5% a 10% dos casos são identificados com um componente hereditário forte, e apenas uma pequena fração desses (4% a 5%) são explicados por mutações em genes de alta penetrância em uma herança autossômica dominante. Grande parte dos casos de câncer de mama hereditário são atribuídos a mutações germinativas nos genes de alta penetrância BRCA1 e BRCA2, responsáveis pela Síndrome de Câncer de Mama o Ovário Hereditários. Vários estudos têm identificado outros genes de susceptibilidade para o câncer de mama com alta penetrância, mas alguns casos de forte indício para uma síndrome hereditária como causa dos tumores de mama o resultado é negativo para mutações nestes genes. Recentemente, outros genes e marcadores polimórficos comuns também foram associados com aumento pequeno ou moderado no risco para câncer de mama. O sequenciamento de nova geração (NGS) permite analisar múltiplos genes simultaneamente em testes no formato de painéis, a um custo reduzido em comparação com o sequenciamento pela metodologia de Sanger. No entanto, informações clínicas relevantes sobre as variantes encontradas nestes testes estendidos não mantiveram o mesmo ritmo da tecnologia de sequenciamento. Faltam informações importantes como a penetrância das variantes genéticas (em particular, de variantes missense) e o manejo clínico adequado dos portadores destas mutações. O objetivo do presente estudo foi avaliar a ocorrência de... / Abstract: Breast cancer is the most common form of cancer and the second most common cause of death from a neoplastic disease affecting women. There are a number of recognized risk factors for the development of breast cancer including hereditary factors, hormonal, reproductive and menstrual history, age, lack of exercise, alcohol, radiation, benign breast disease, and obesity. Although approximately 10% to 30% of breast cancer cases are attributed to hereditary factors, only 5% to 10% of cases are identified with a strong genetic component, and only a small fraction of these (4% to 5%) are explained by mutations in high penetrance genes in an autosomal dominant inheritance. Most cases of hereditary breast cancer are attributed to germline mutations in high penetrance genes BRCA1 and BRCA2 that are responsible for Breast Cancer Ovary Syndrome the hereditary. Several studies have identified other susceptibility genes for breast cancer with high penetrance, but some cases of strong evidence for a hereditary syndrome as a cause of breast tumors the result is negative for mutations in these genes. Recently, other genes and common polymorphic markers were also associated with small or moderate increase in risk for breast cancer. The next generation sequencing (NGS) allows the analysis of multiple genes simultaneously in tests on panels format whit a reduced cost compared to sequencing by the Sanger methodology. However, relevant clinical information about variants found in these extended tests have not kept the same pace of sequencing technology. Important information such as penetrance genetic variants (in particular, missense variants) and the appropriate clinical management of carriers of these mutations are not availabe. The aim of this study was to evaluate the occurrence of genetic changes in 17 breast cancer predisposition genes in Brazilian risk patients, suitable for genetic testing. Genetic testing included analysis of the DNA of patients using... / Mestre

Made available in DSpace on 2016-09-27T13:39:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-07-20. Added 1 bitstream(s) on 2016-09-27T13:45:06Z : No. of bitstreams: 1 000868528.pdf: 1329679 bytes, checksum: cfad7bfc51dbbb09d097d17b2827ff26 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O câncer de mama é a forma mais comum de câncer e a segundo causa mais comum de morte por uma doença neoplásica afetando mulheres. Há uma série de fatores de risco reconhecidos para o desenvolvimento do câncer de mama incluindo fatores hereditários, hormonais, reprodutivos e história menstrual, idade, falta de exercício, álcool, radiação, doença benigna da mama, e obesidade. Embora aproximadamente 10% a 30% dos casos de câncer de mama sejam atribuídos a fatores hereditários, apenas 5% a 10% dos casos são identificados com um componente hereditário forte, e apenas uma pequena fração desses (4% a 5%) são explicados por mutações em genes de alta penetrância em uma herança autossômica dominante. Grande parte dos casos de câncer de mama hereditário são atribuídos a mutações germinativas nos genes de alta penetrância BRCA1 e BRCA2, responsáveis pela Síndrome de Câncer de Mama o Ovário Hereditários. Vários estudos têm identificado outros genes de susceptibilidade para o câncer de mama com alta penetrância, mas alguns casos de forte indício para uma síndrome hereditária como causa dos tumores de mama o resultado é negativo para mutações nestes genes. Recentemente, outros genes e marcadores polimórficos comuns também foram associados com aumento pequeno ou moderado no risco para câncer de mama. O sequenciamento de nova geração (NGS) permite analisar múltiplos genes simultaneamente em testes no formato de painéis, a um custo reduzido em comparação com o sequenciamento pela metodologia de Sanger. No entanto, informações clínicas relevantes sobre as variantes encontradas nestes testes estendidos não mantiveram o mesmo ritmo da tecnologia de sequenciamento. Faltam informações importantes como a penetrância das variantes genéticas (em particular, de variantes missense) e o manejo clínico adequado dos portadores destas mutações. O objetivo do presente estudo foi avaliar a ocorrência de... / Breast cancer is the most common form of cancer and the second most common cause of death from a neoplastic disease affecting women. There are a number of recognized risk factors for the development of breast cancer including hereditary factors, hormonal, reproductive and menstrual history, age, lack of exercise, alcohol, radiation, benign breast disease, and obesity. Although approximately 10% to 30% of breast cancer cases are attributed to hereditary factors, only 5% to 10% of cases are identified with a strong genetic component, and only a small fraction of these (4% to 5%) are explained by mutations in high penetrance genes in an autosomal dominant inheritance. Most cases of hereditary breast cancer are attributed to germline mutations in high penetrance genes BRCA1 and BRCA2 that are responsible for Breast Cancer Ovary Syndrome the hereditary. Several studies have identified other susceptibility genes for breast cancer with high penetrance, but some cases of strong evidence for a hereditary syndrome as a cause of breast tumors the result is negative for mutations in these genes. Recently, other genes and common polymorphic markers were also associated with small or moderate increase in risk for breast cancer. The next generation sequencing (NGS) allows the analysis of multiple genes simultaneously in tests on panels format whit a reduced cost compared to sequencing by the Sanger methodology. However, relevant clinical information about variants found in these extended tests have not kept the same pace of sequencing technology. Important information such as penetrance genetic variants (in particular, missense variants) and the appropriate clinical management of carriers of these mutations are not availabe. The aim of this study was to evaluate the occurrence of genetic changes in 17 breast cancer predisposition genes in Brazilian risk patients, suitable for genetic testing. Genetic testing included analysis of the DNA of patients using...

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The growing markets for analytical techniques in areas such as pathogen detection, clinical analysis, forensic investigation, environmental analysis and food analysis require the development of devices with simultaneous high performance, speed, simplicity and low cost. Analysis of deoxyribonucleic acid (DNA) has been enhanced by use of the polymerase chain reaction (PCR) technique, which is now a widely used tool for in vitro amplification of nucleic acids. In this work, a miniaturised PCR system comprising a microfluidic PCR chip, novel heating method and fluorescence detection unit was developed. PCR chip with reactants were shunted along three temperature zones in a fine polycarbonate chip. The polycarbonate PCR chip was fabricated using milling and thermal fusion binding for sealing of the cover. Thermal-cycling within the microfluidic chip was achieved by programmable shunting of the chip between three double side temperature zones with different temperatures to accomplish the denaturation, annealing and elongation steps necessary for PCR amplification. This thermal-cycling model potentially improves PCR efficacy because it increases the ramping rates for heating and cooling the PCR mixture. The detection unit comprises a photo-detector and Light Emitting Diode (LED) as the source of excitation. The detection limit of the system was determined on the PCR chip using Fluorescein isothiocyanate (FITC) as a fluorophore dye. The detection limit achieved was 7.8 pg ml-1 or (19.7 pmol) of FITC. The chromosomal DNA used in this work was extracted from non-pathogenic K-12 subtype of Escherichia coli (E. coli). The investigations showed that the system was capable of performing PCR amplification with different annealing temperature ranging from 54 to 68 °C, targeting three different sizes of PCR products of 250, 552 and 1500 bp. The prototype thermal-cycler and PCR chip were used successfully to amplify the three sizes and the results were compared with same fragments amplified on a conventional PCR .thermal-cycler machine. The method used for comparison was gel electrophoresis. In addition, a fluorescence detection system was employed for detecting of PCR products using SYBR Green I fluorescent dye. The whole system allows for developments of low cost, easy to use and portable instruments.

A diversidade da seqüência do DNA de oito populações de Octopus cf. vulgaris da costa brasileira e de uma população de Octopus vulgaris proveniente de Portugal foi investigada pelo uso do gene Citocromo oxidase subunidade I (COI) do DNA mitocondrial. Aproximadamente 600 pb do gene COImt foram amplificados por meio dos primers LCO1490 e HCO2198, purificados e seqüenciados. As seqüências foram alinhadas pelo método Clustal W. A árvore filogenética gerada pelo alinhamento das seqüências do COImt revelou dois conjuntos principais, formando clados monofiléticos sustentados por bootstraps superiores a 93%. Um clado contendo os indivíduos provenientes das regiões Sudeste e Sul, similares aos haplótipos de Portugal, que são classificados como Octopus vulgaris, e outro conjunto formado pelos indivíduos coletados em várias localidades das regiões Norte e Nordeste. O nível de diferenciação genética encontrado sugere a presença de duas espécies de Octopus. Quanto à estruturação populacional, os resultados encontrados pelo uso do DNA nuclear e do DNA mitocondrial indicam que as populações estão estruturadas geneticamente. / The diversity of the sequence of the DNA of eight vulgaris populations of Octopus cf. vulgaris of the Brazilian coast and a population of Octopus vulgaris proceeding from Portugal was investigated by the use of the mitochondrial Cytochrome c oxidase subunit I (COI) gene. Approximately 600 bp of the mitochondrial COI gene were amplified by means of primers LCO1490 and HCO2198, purified and sequenced. The sequences were lined up by the ClustalW method. The phylogenetic tree generated by the alignment of the sequences of the COI revealed two main sets, forming monophyletic supported by bootstraps 93%. A clade containing the individuals proceeding from the Southeastern and South regions similar to the haplotypes of Portugal, which are classified as Octopus vulgaris, and another set formed by the individuals collected in several places of the North and Northeast regions. The level of the found genetic differentiation suggests the presence of two species of Octopus. As far as the population structure is concerned, the results found by the use of the nuclear DNA and the mitochondrial DNA indicates that the populations are genetically structured.

Y-chromosome testing has become more prevalent in recent years as a means of identifying forensic samples using STRs or identifying biomarkers for disease or determining geographic origins of populations. Additionally, Y-chromosome analysis is especially useful in paternity testing as the Y chromosome is inherited paternally and the male-specific region of the Y chromosome does not undergo any recombination events, allowing the genotypic data of both the father and son to be identical. Though in most cases a father-son pair will have the same Y-allelic data, random mutations like allele insertions and deletions can occur, which can interfere and result in incorrect conclusions in regards to paternity testing, forensic analysis, or genealogy. Though the exact mechanism of Y loci mutability is unknown, postulations of factors that can cause mutations have been studied, as well as attempts to determine mutation rate specific to each locus. A multi-generational pedigree consisting of 9 males was analyzed using two different methodologies: capillary electrophoresis and next-generation sequencing. The samples were amplified using either a ForenSeq™ Signature DNA Prep Kit (Verogen, San Diego, CA) or a YFiler™ Plus PCR Amplification Kit (Thermo Fisher Scientific, Waltham, MA). Between the two methods, five Y-STR loci were identified as being discordant between a father-son pair. Next-generation sequencing identified an allele insertion at DYS385a/b, resulting in a potential tri-allelic locus, but was disproved after comparison with the capillary electrophoresis data of the sample. The capillary electrophoresis data identified four discordances between father-son pairs, one of which was an allele mutation with a gain of a repeat at DYS458. At DYS 389II, an allele insertion was identified, but was contradicted after comparison with the next-generation sequencing data. There was a potential null allele at DYS518 and either an OL variant allele or a 2 base pair deletion at DYS481. Following peak height ratio, stutter, and comparative analysis between the genotypic data of the two analysis methods, two of these discordances were proven to be errors, one was a definitive mutational event, and the other two could neither be confirmed nor denied due to differences in loci tested in each kit.

Despite the many advancements to forensic DNA analysis adopted by crime laboratories across the country, the most common method for the differential extraction of sexual assault samples has remained relatively unchanged since forensic deoxyribonucleic acid (DNA) typing was discovered in 1985. As the quantity and quality of extracted DNA has significant implications on the success of subsequent analysis methods, the development and optimization of effective extraction procedures is vital to progressing the field of forensic DNA analysis. The graduate students and faculty at the Boston University School of Medicine have been developing a differential extraction process that utilizes a multi-enzymatic approach to preferentially lyse and wash the cell types within temperature controlled environments. The overall procedure is less labor-intensive and time-consuming than the conventional method. Through the extraction process, the inhibitory nature of each enzyme on the amplification process is avoided, circumventing the need for an additional purification step. A single centrifugation step is required in order to pellet the sperm while the cumbersome wash steps are replaced with selective digestion in order to remove the residual epithelial cell DNA from the sperm fraction. The three enzyme used (EA1, Benzonase®, and Acrosolv) operate optimally at distinct temperatures which allows for controlled and sequential activation to achieve desired lysis and digestion outcomes. The enzymatic reactions are conducted within a DNA extraction lab thermal cycler to obtain rapid and accurate temperature changes. This novel temperature controlled differential extraction protocol has been developed and optimized for extraction of primarily liquid mixed samples in 0.2 milliliter (mL) tubes. The epithelial cell lysis and sperm cell lysis stages of the extraction contained a final reaction volume of 100 microliters (µL). Slight modifications to this 100 direct-lysis differential extraction method resulted in a similarly efficient method with a high male DNA yield (74-100%) and minimal female carryover among varying ratios of epithelial cells to sperm cells. This sensitive technique provided nearly complete profiles (14/16 loci) of the male contributor in mixed samples containing ~15,200 female epithelial cells and ~500 sperm, with complete profiles observed in mixed samples containing ~1000 sperm. This modified extraction protocol better accommodates sample sizes that may be encountered in forensic casework testing while providing a more concentrated sperm fraction, possibly eliminating the need for an additional concentration step in some dilute samples. The ease of implementation and the rapid processing time of 2-3 hours make it a great candidate for use in forensic DNA laboratories and may help alleviate backlogs of sexual assault kit. However, further work is needed to alter the composition of the sperm lysis buffer to make it compatible with currently used amplification kits. Until such time, caution must be taken in the kit selection used for amplification of extracts produced with this method. This study also demonstrated a sensitivity of the GlobalFiler® PCR Amplification Kit to inhibition by the buffers used in this extraction protocol, particularly the Orange+ Buffer. This inhibition has dramatic effects on the profile quality of the amplified sperm fractions, with extensive allelic drop-out observed even when the Orange+ Buffer concentration was scaled from 1.0X to 0.2X. Amplification using the AmpFℓSTR® Identifiler® Plus PCR Amplification Kit showed marginal recovery in the profile quality. Other expanded-loci STR amplification kits may also demonstrate resistance to this inhibition.

The following is a comparison study of the Globalfiler™ PCR Amplification Kit analyzed on an ABI 3130 Genetic Analyzer Capillary Electrophoresis (CE) versus the ForenSeq™ DNA Signature Prep Kit analyzed on the MiSeq FGx™ System. The MiSeq FGx™ System measures results by Allele Read Count (ARC), while the CE measures results as Relative Fluorescent Units (RFU). Mixture samples were prepared in ratios of 1:1, 1:4, and 1:10 in replicates of four using a female major contributor and a male minor contributor, intended to represent some commonly seen mixture samples ratios in forensic cases [48]. Both systems performed equally well for the 1:1 mixture while the MiSeq FGx™ System had improved accuracy and precision for the 1:4 mixture compared to CE (4.033 + 1.506 ARC and 4.678 + 2.093 RFU, respectively). The MiSeq FGx™ System showed increased variation in the 1:10 mixture compared to CE (10.347 + 5.184 ARC and 9.311 + 3.363 RFU, respectively). Over the four replicates, the MiSeq FGx™ System had a total of 15 out of 528 possible alleles (2.84%) dropout compared to a total of 13 out of 384 possible alleles (3.39%) dropout on CE. The additional loci analyzed by the MiSeq FGx™ System results in a lower percentage of alleles lost due to dropout compared to CE. Isoalleles in sequence data may reveal the presence of minor contributor alleles that would otherwise be masked by the major contributor in length-based STR analysis. The presence of isoalleles are most helpful in mixture ratios greater than 1:1, where it is easier to assign alleles to a specific contributor. In certain cases, deconvolution of loci with shared alleles may not be improved by sequencing if intra-contributor isoalleles are present. Unless using known reference profiles, it is difficult to accurately assign alleles to contributors when intra-contributor isoalleles are present. Additionally, the sequencing data from the MiSeq FGx™ System provided information to aid the separation of stutter from true alleles. Previous studies report a significant increase in the amount of alleles present at some loci due to differences by nucleotide sequence, which may improve the discriminating power of those loci [31,52,53,54]. With all its potential, there is still much room for sequencing technology to improve before it becomes a standard analysis method in forensic laboratories.

The communal breeding system of the smooth-billed ani (Crotophaga ani) was studied at two wildlife refuges in southwest Puerto Rico. Groups ranged in size from 2 to 9 adults, and communal clutches ranged in size from 11 to more than 25 eggs. Microsatellite DNA loci were isolated and used to examine the mating system and the extent of reproductive skew in individual groups. Loci were also screened in guira cuckoos (Guira guira) to examine the relationships suggested by Quinn et al. (1994). In the four focal smooth-billed ani groups, I found suggestions of monogamy, polygamy, and incidents of intraspecific brood parasitism. In all groups, incubated clutch size and microsatellite data indicate that subordinate females are gaining some reproductive success. At one nest, evidence suggested a decrease in the intensity of reproductive skew between successive nests. Although the data are limited, they suggest that alternative strategies to monogamy may be more prevalent than previously believed, and that reproductive skew may be affected by the availability of limiting resources within the breeding season. / Thesis / Master of Science (MS)