Para a execução da etapa inicial da identificação médico-legal de restos humanos (antropometria e exame dos arcos dentários), faz-se necessária uma limpeza prévia da ossada, para a remoção de tecidos moles putrefeitos. Os casos não identificados por esses métodos tradicionais, poderão ser submetidos ao exame de DNA. No entanto, apesar do grande avanço da biologia molecular, utilizando a amplificação de DNA pela PCR, algumas limitações que afetam a habilidade de se obter DNA em restos humanos, permanecem. Dessa forma, o objetivo deste trabalho foi fornecer subsídios morfológicos para os analistas forenses, com ênfase na prática médico-legal, visando uma utilização mais eficiente do DNA obtido de osso compacto de restos humanos em decomposição ou já esqueletizados, sem tecidos moles aderidos. Foi realizado o estudo da microestrutura do tecido ósseo compacto femoral, de restos humanos em decomposição, ainda com tecidos moles, que foram limpos pela fervura em água (n = 7) e ossadas já esqueletizadas pela decomposição natural, que não foram fervidas (n = 8). Destes, seis ossadas foram provenientes de cemitério público regular, após 3 anos de inumação, 1 ossada proveniente da região amazônica, e 1 ossada de origem desconhecida. Estas duas ultimas, apresentado-se porosas ou quebradiças. As análises morfológicas de cortes histológicos foram coradas com hematoxilina e eosina e o DNA amplificado pela PCR para os loci CSF1PO, TPOX, TH01, F13A0, FESFPS, vWA, D16S539, D7S820, D13S317 e amelogenina. Os resultados da análise desses dois grupos foram comparados com os de cadáveres frescos (n = 5) do Serviço de Verificação de Óbitos da Capital. A fervura dos ossos, do modo como é realizada no Instituto Médico Legal de São Paulo, pode aumentar a eosinofilia da matriz óssea e, em alguns casos, pode promover a desagregação dos ósteons. Tal procedimento pode remover células, mas pode também remover possíveis inibidores da PCR, favorecendo a análise do DNA obtido destas amostras. O fator limitante para a obtenção e análise de DNA, em amostras de ossos limpos por fervura, é a quantidade exígua de células. Ossos não submetidos à fervura, após inumação por três anos ou há mais tempo em contato com a terra, podem apresentar alterações da microestrutura. No entanto, a presença de hemácias preservadas e núcleos de osteócitos nestas amostras, indica melhor preservação de células em relação às amostras de ossos fervidos. O fator limitante para a análise de DNA nestas amostras é a presença sugestiva de inibidores da reação de amplificação pela PCR. Restos humanos, sem tecidos moles, macroscópicamente não preservados (porosos e quebradiços), e não submetidos à fervura, apresentam alterações de perda de matriz mineralizada; no entanto, nestas amostras ainda é possível encontrar células preservadas. Os resultados obtidos no neste trabalho permitem traçar algumas estratégias para uma melhor utilização nos protocolos de extração e análise do DNA em osso compacto de restos humanos. / To the first essential step to forensic identification of human remains (anthropological study of race, sex, age, etc) it is necessary a previous cleaning of the bones, to remove decomposing soft tissues. Medico-legal inconclusive or non identified cases, by using these traditional methods, could be subjected to DNA analysis. However, in spite of advances in human identification techniques, specially by PCR amplified DNA, some limitations that affect the ability to obtain DNA in human remains still persist. Therefore, the aim of this study was to provide additional support from morphological analysis, to help forensic analysts personnel to utilise more efficiently the DNA, extracted from compact bones of human remains in decomposition or already skeletonized corpse, it means without soft tissues, with special emphasis in the legal-medicine practice. Femoral compact bones were obtained from: 7 human remains found on the ground, in different degree of decomposition which were cleaned by boiling to remove soft tissues; also studied were collections of bones from 8 corpses having undergone natural decomposition: 6 human remains exhumed after 3 years from a common public cemetery in São Paulo City; 1 case from amazon region and 1 case with no information, both cases remained from long time (more than 3 years) in contact with soil. All eight cases, were not boiled as no soft tissue were adhered. As a control, five cadavers 12 to 16 hours post mortem were also used. The compact bones histological sections were stained by haematoxilin and eosin and the loci CSF1PO, TPOX, TH01, F13A01,FESFPS, vWA, D16S539, D7S820, D13S317 and amelogenin were amplified by PCR.The procedure for boiling the human remains utilised in the Legal Medicine Institute of São Paulo would have increased the eosinophily of bone matrix and, in some cases, promoted the desaggregation of the osteons. In addition these procedures would have removed the cells, but in some cases would have removed possible inhibitors of the PCR, favouring in this way the analysis of DNA obtained from these samples. The limiting factor to obtain successful analysis in bones submitted to boiling seem to be the low quantity of nuclei present in these samples. For the other hand, in bones not cleaned by boiling, the presence of preserved red cells and oscteocyte nuclei inside the lacunae indicates better preservation of cells in relation to those bones cleaned by boiling. The limiting factor to obtain successful DNA analysis in bones exhumed or in contact of soil, is the suggestive presence of inhibitors of PCR. Porous and brittle bones from human remains, without soft tissues that are not processed by boiling, present alterations through loss of mineralised matrix, although it is still possible to found preserved cells in these samples. The results presented in this work clarify concerns about viability of DNA for identification analysis. They also help to establish better strategies for optimisation of DNA extraction and analysis in compact bones of human remains.

INTRODUÇÃO: A determinação do genótipo RHD fetal no plasma materno é um teste de diagnóstico pré-natal não invasivo oferecido a gestantes RhD negativo que apresentam potencial de sensibilização e/ou Doença Hemolítica Perinatal. Atualmente, este exame é realizado de rotina em diversos países, mas não no Brasil. A Clínica Obstétrica do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP) oferece atendimento terciário a gestantes RhD negativo, com monitorização dos títulos de anticorpos irregulares, administração da imunoglobulina anti-D e/ou terapêutica fetal, quando necessários. OBJETIVO: Avaliar a acurácia do teste semiautomatizado para determinação do genótipo RHD fetal no plasma materno. METODOLOGIA: Foram coletadas prospectivamente amostras de sangue de 220 gestantes RhD negativo, com idade gestacional entre 8-28 semanas. O plasma foi obtido em no máximo 2 horas após a coleta, e uma alíquota de 1 mL foi submetida à extração de ácidos nucléicos no equipamento automatizado MagNA Pure Compact (Roche), empregando o kit Large Volume. O DNA extraído foi submetido a PCR em tempo real (Step One Plus - Applied Biosystems), usando o protocolo do grupo SAFE, que tem como alvos os éxons 5 e 7 do gene RHD. RESULTADOS: Ocorreu exclusão de 35 amostras devido a problemas pré-analíticos, aborto ou desconhecimento do fenótipo do recém-nascido. Entre as 185 amostras analisadas, 130 (70,2%) foram genotipadas como RHD+ e 55 (29,8%) RHD-. Os resultados obtidos foram comparados com a fenotipagem do cordão umbilical, e houve concordância completa (100%). Sete amostras exibiram amplificação exclusiva para o éxon 7. Essas amostras foram submetidas aos protocolos em PCR convencional, e PCR em tempo real específico para o pseudogene RHD. Ambos os ensaios apresentaram os mesmos resultados: cinco positivos e dois negativos. Nesses mesmos 7 casos, após extração da camada de leucócitos materna, os protocolos foram repetidos, e o resultado confirmou que cinco mães eram RHD. As duas amostras com resultado negativo foram submetidas ao protocolo Multiplex, envolvendo os éxons 3-9 do gene RHD, com resultados negativos, confirmando que as mães são verdadeiramente RHD- portanto o sinal do éxon 7 é provindo dos fetos que são D variantes. CONCLUSÃO: O método para a determinação do RHD fetal no plasma materno descrito demonstrou ser rápido, de fácil execução, alta precisão e reprodutível, além de indicar possíveis variantes RHD em nossa população / BACKGROUND: Fetal RHD genotype determination in maternal plasma is a noninvasive prenatal diagnostic test performed in RhD negative pregnant women at risk of alloimmunization and/or Hemolytic Disease of Fetus and Newborn. Currently, this test is routinely performed in many countries but not in Brazil. The Department of Obstetrics at Hospital das Clínicas, São Paulo University Medical School provides tertiary antenatal care for RhD negative pregnant women including anti-D immunoglobulin administration, antibody levels monitoring and intrauterine treatment if necessary. AIMS: To validate the accuracy of a semi-automated test for fetal RHD genotype determination in maternal plasma. METHODS: Two-hundred and twenty blood samples were prospectively collected between 8 and 28 weeks of gestational age. Plasma processing was performed within 2 hours after blood collection, and nucleic acids were extracted from 1mL aliquots with an automated extraction platform (MagNA Pure Compact Roche) and the Large Volume kit. RHD gene exons 5 and 7 were amplified with real-time PCR (Step One Plus - Applied Biosystems) using the SAFE group protocol. RESULTS: Thirty-five samples were excluded due to pre-analytical problems, miscarriage and missing follow-up. In the remaining 185 samples, 130 (70.2%) were genotyped as RhD+ and 55 (29.8%) RhD-. Comparison with umbilical cord blood group phenotype showed 100% concordance. Seven samples showed amplification for exon 7 only. These were further investigated with conventional and real-time PCR with an specific protocol for RHD? pseudogene: 5 were positive and 2, negative. In these 7 cases, maternal buffy-coat DNA analysis also confirmed that 5 women were RHD?. In the remaining 2 cases, a multiplex protocol directed at RHD gene exons 3-9 confirmed that both mothers were truly RhD negative so exon 7 signal comes from the fetuses, further found to harbor D variants. CONCLUSION: The present study demonstrates that fetal RHD determination in maternal plasma is a fast, easy-to-perform and reproducible technique with high accuracy in our population. Moreover, it helps in the identification of possible RHD variants in our population

A síndrome de Noonan (SN) é uma doença de herança autossômica, relativamente frequente na população e que apresenta heterogeneidade genética. Caracteriza-se por dismorfismos faciais, baixa estatura, pescoço curto/alado, alterações cardíacas, deformidades esternais e criptorquia. A SN apresenta sobreposição dos achados clínicos com outras síndromes mais raras, denominadas síndromes Noonan-like (SNL): síndrome cardio-facio-cutânea (CFC), síndrome de Costello (SC), neurofibromatose-síndrome de Noonan (NFSN), síndrome de Noonan com manchas lentiginosas/síndrome de LEOPARD (SL), síndrome de Noonan-like com perda de cabelos anágenos (SNL-PCA) e síndrome de Noonan-like com leucemia mielomonocítica juvenil (SNL-LMMJ). As SN e SNL decorrem de mutações em genes pertencentes à via de sinalização RAS/MAPK alguns dos quais são protooncogenes, o que tem despertado o interesse na caracterização do risco de desenvolvimento de neoplasias nessas síndromes. Os objetivos deste estudo visam o sequencimento conjunto dos genes PTPN11, SOS1, RAF1, KRAS, SHOC2, BRAF e HRAS em pacientes com diagnóstico clínico das SN e SNL a fim de: determinar a frequência de mutação; estabelecer uma correlação genótipo-fenótipo; estabelecer um fluxograma para o estudo molecular a partir dos hotspots; e avaliar se a variabilidade fenotípica apresentada nos pacientes com SN pode ser explicada pela presença de mutações em mais de um gene da via RAS/MAPK. Foram avaliados 194 probandos - 152 com SN e 42 com SNL (19 CFC, 15 NFNS, 4 CS e 4 LS). Mutações foram identificadas em 99 pacientes 80 com SN (53%); 19 com SNL. Apenas um paciente com SN apresentou mutação em dois genes da via RAS/MAPK (PTPN11 e SOS1). O estudo molecular na SN mostrou, assim como na literatura, um maior envolvimento do gene PTPN11 (34%), seguido dos genes SOS1 (12%) e RAF1 (7%). A comparação dos achados clínicos, levando em consideração as alterações gênicas, também confirma as correlações já descritas na literatura; entre elas observamos que pacientes com SN e mutação no gene: PTPN11, apresentaram maior frequência de estenose pulmonar valvar (EPV) e baixa estatura; SOS1, apresentaram maior frequência de EPV; RAF1, apresentaram maior frequência de miocardiopatia hipertrófica, e menor frequência de EPV e déficit intelectual; SHOC2, apresentaram anormalidades de cabelo. Na nossa casuística também foram observados alguns achados raros: craniosinostose, tumor expansivo em fossa posterior e a primeira descrição de um tumor sólido (schwanomatose) em um paciente com mutação no gene KRAS. A partir deste estudo foi possível estabelecer um fluxograma para investigação molecular devido à correlação genótipo-fenótipo, que embora não seja totalmente precisa, explica parte da grande variabilidade clínica observada em especial quanto ao tipo de cardiopatia. A presença de mutações em diferentes genes da via RAS/MAPK não é frequente, além de não agravar o fenótipo e não explicar a variabilidade fenotípica observada. Embora um grande avanço no conhecimento sobre SN e SNL tenha sido alcançado, vários aspectos precisam ser melhor elucidados, como: caracterização precisa da propensão ao desenvolvimento de neoplasias, estudos que permitam avaliar as consequências biológicas das mutações, identificação de outros genes responsáveis, assim como outros fatores genéticos e/ou ambientais que possam explicar a variabilidade clínica inter e intrafamilial / Noonan syndrome (NS) is a relatively common, autosomal dominant disease that presents a marked genetic heterogeneity. It is characterized by facial dysmorphisms, short stature, webbed/short neck, cardiac abnormalities, esternal anomalies and cryptorchidism. NS shows clinical overlap of some of its findings with other rarer syndromes, known as Noonan-like syndromes (NLS): cardio-facio-cutaneous syndrome (CFC), Costello syndrome (CS), neurofibromatosis-Noonan syndrome (NFNS), Noonan syndrome with lentiginous stains/LEOPARD syndrome (LS), Noonan-like syndrome with loose anagen hair (NLS-LAH) and Noonan-like syndrome with juvenile myelomonocytic leukemia (NLS-JMML). NS and NLS are related to mutations in genes belonging of RAS-MAPK signaling pathway. Some of these genes are classified as proto-oncogenes. This fact also arouses the interest in the characterization of the risk for cancer development in this group of patients. The objectives of this study are to sequence the genes associated with NS and NLS (PTPN11, SOS1, RAF1, KRAS, SHOC2, HRAS and BRAF) in patients that fulfilled clinical diagnostic criteria for NS or NLS to: determine the frequency of the mutations; establish a genotype-phenotype correlation; estabilish a flowchart for molecular study from the hotspots; and evaluate when the phenotypic variability presented in NS patients can be explained by the presence of mutations in more than one gene of the RAS/MAPK pathway. This study evaluated 194 probands 152 with NS e 42 with NLS (19 CFC, 15 NFSN, 4 SC e 4 SL). Mutations were identified in 99 patients 80 with NS (53%), 19 with NLS. Only one patient presented mutation in two different genes of the RAS/MAPK pathway (PTPN11 and SOS1). The molecular analysis showed a predominance of mutations in the PTPN11 gene (34%), followed by the SOS1 (12%) and RAF1 (7%) genes in patients with NS, in accordance with the literature. Patients with NS and mutation in the: PTPN11 gene, presented a higher frequency of valvular pulmonary stenosis (VPS) and short stature; SOS1 gene, showed a higher frequency of VPS; RAF1 gene, showed a higher frequency of hypertrophic cardiomyopathy and lower frequency of VPS and intellectual deficit; and SHOC2 gene, showed more hair abnormalities. This genotype-phenotype correlations is also concordant with the literature. In our study, we also observed some rare finds in some patients: craniosynostosis, expansive tumor in the posterior fossa and the first description of a solid tumor (schwanomatose) in a patient with NS and KRAS gene mutation. Based on this genotype-phenotype correlation, we have proposed a flowchart for molecular investigation. The presence of mutation in more them one gene of the RAS/MAPK pathway was not frequent; additionally, it did not aggravate the phenotype and could not explain the phenotypic variability observed. Although a great advance in the knowledge about SN and SNL has been achieved, several aspects remain to be clarified, as the exact risk for cancer development, functional studies to assess the biological consequences of the mutations and the identification of other genes, as well as other genetic and/or environmental factors that influence the interand intrafamilial clinical variability

With the completion of the human genome sequencing project, attention is currently shifting toward understanding how genetic variation, such as single nucleotide polymorphism (SNP), leads to disease. To identify, understand, and control biological mechanisms of living organisms, the enormous amounts of accumulated sequence information must be coupled to faster, cheaper, and more powerful technologies for DNA, RNA, and protein analysis. One approach is the miniaturization of analytical methods through the application of microfluidics, which involves the manipulation of fluids in micrometer-sized channels. Advances in microfluidic chip technology are expected to play a major role in the development of cost-effective and rapid DNA analysis methods. This thesis presents microfluidic approaches for different DNA genotyping assays. The overall goal is to combine the potential of the microfluidic lab-on-a-chip concept with biochemistry to develop and improve current methods for SNP genotyping. Three genotyping assays using miniaturized microfluidic approaches are addressed. The first two assays are based on primer extension by DNA polymerase. A microfluidic device consisting of a flow-through filter chamber for handling beads with nanoliter liquid volumes was used in these studies. The first assay involved an allelespecific extension strategy. The microfluidic approach took advantage of the different reaction kinetics of matched and mismatched configurations at the 3’-ends of a primer/template complex. The second assay consisted of adapting pyrosequencing technology, a bioluminometric DNA sequencing assay based on sequencing-bysynthesis, to a microfluidic flow-through platform. Base-by-base sequencing was performed in a microfluidic device to obtain accurate SNP scoring data on nanoliter volumes. This thesis also presents the applications of monolayer of beads immobilized by microcontact printing for chip-based DNA analysis. Single-base incorporation could be detected with pyrosequencing chemistry on these monolayers. The third assay developed is based on a hybridization technology termed Dynamic Allele-Specific Hybridization (DASH). In this approach, monolayered beads containing DNA duplexes were randomly immobilized on the surface of a microheater chip. DNA melting-curve analysis was performed by dynamically heating the chip while simultaneously monitoring the DNA denaturation profile to determine the genotype. Multiplexing based on single-bead analysis was achieved at heating rates more than 20 times faster than conventional DASH provides. / QC 20101008

Within the realm of biosensing, DNA analysis has become an indispensable research tool in medicine, enabling the investigation of relationships among genes, proteins, and drugs. Conventional DNA microarray technology uses multiple lasers and complex optics, resulting in expensive and bulky systems which are not suitable for point-of-care medical diagnostics. The immobilization of DNA probes across the microarray substrate also results in substantial spatial variation. To mitigate the above shortcomings, this thesis presents a set of techniques developed for the CMOS image sensor for point-of-care spectrally-multiplexed fluorescent DNA sensing and other fluorescence biosensing applications. First, a CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. The CPG exploits the absorption property of a polysilicon gate to form an optical filter, thus the sensor does not require an external color filter. A prototype has been fabricated in a standard 0.35μm digital CMOS technology and demonstrates intensity measurements of blue (450nm), green (520nm), and red (620nm) illumination. Second, a wide dynamic range CMOS multi-color image sensor is presented. An analysis is performed for the wide dynamic-range, asynchronous self-reset with residue readout architecture where photon shot noise is taken into consideration. A prototype was fabricated in a standard 0.35μm CMOS process and is validated in color light sensing. The readout circuit achieves a measured dynamic range of 82dB with a peak SNR of 46.2dB. Third, a low-power CMOS image sensor VLSI architecture for use with comparator based ADCs is presented. By eliminating the in-pixel source follower, power consumption is reduced, compared to the conventional active pixel sensor. A 64×64 prototype with a 10μm pixel pitch has been fabricated in a 0.35μm standard CMOS technology and validated experimentally. Fourth, a spectrally-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem has been quantitatively modeled and validated in the detection of marker gene sequences for spinal muscular atropy disease and the E. coli bacteria. Spectral multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limit of 240nM and 210nM of target concentration at a sample volume of 10μL for the green and red transduction channels, respectively.

Within the realm of biosensing, DNA analysis has become an indispensable research tool in medicine, enabling the investigation of relationships among genes, proteins, and drugs. Conventional DNA microarray technology uses multiple lasers and complex optics, resulting in expensive and bulky systems which are not suitable for point-of-care medical diagnostics. The immobilization of DNA probes across the microarray substrate also results in substantial spatial variation. To mitigate the above shortcomings, this thesis presents a set of techniques developed for the CMOS image sensor for point-of-care spectrally-multiplexed fluorescent DNA sensing and other fluorescence biosensing applications. First, a CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. The CPG exploits the absorption property of a polysilicon gate to form an optical filter, thus the sensor does not require an external color filter. A prototype has been fabricated in a standard 0.35μm digital CMOS technology and demonstrates intensity measurements of blue (450nm), green (520nm), and red (620nm) illumination. Second, a wide dynamic range CMOS multi-color image sensor is presented. An analysis is performed for the wide dynamic-range, asynchronous self-reset with residue readout architecture where photon shot noise is taken into consideration. A prototype was fabricated in a standard 0.35μm CMOS process and is validated in color light sensing. The readout circuit achieves a measured dynamic range of 82dB with a peak SNR of 46.2dB. Third, a low-power CMOS image sensor VLSI architecture for use with comparator based ADCs is presented. By eliminating the in-pixel source follower, power consumption is reduced, compared to the conventional active pixel sensor. A 64×64 prototype with a 10μm pixel pitch has been fabricated in a 0.35μm standard CMOS technology and validated experimentally. Fourth, a spectrally-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem has been quantitatively modeled and validated in the detection of marker gene sequences for spinal muscular atropy disease and the E. coli bacteria. Spectral multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limit of 240nM and 210nM of target concentration at a sample volume of 10μL for the green and red transduction channels, respectively.

Human hair profiling is an integral part of a forensic investigation but it is one of the most technically difficult subjects in forensic science. This thesis describes the research and development of a novel approach for the rapid identification of unknown human and other related keratin fibres found at a crime scene. The work presented here is developed systematically and considers sample collection, sample preparation, analysis and interpretation of spectral data for the profiling of hair fibres encountered in criminal cases. Spectral comparison of fibres was facilitated with the use of chemometrics methods such as PCA, SIMCA and Fuzzy Clustering, and the less common approach of multi-criteria decision making methodology (MCDM). The aim of the thesis was to investigate the potential of some vibrational spectroscopy techniques for matching and discrimination of single keratin hair fibres in the context of forensic evidence. The first objective (chapter 3) of the thesis was to evaluate the use of Raman and FT-IR micro-spectroscopy techniques for the forensic sampling of hair fibres and to propose the preferred technique for future forensic hair comparisons. The selection of the preferred technique was based on criteria such as spectral quality, ease of use, rapid analysis and universal application to different hair samples. FT-IR micro-spectroscopy was found to be the most appropriate technique for hair analysis because it enabled the rapid collection of spectra from a wide variety of hair fibres. Raman micro-spectroscopy, on the other hand, was hindered with fluorescence problems and did not allow the collection of spectra from pigmented fibres. This objective has therefore shown that FT-IR micro-spectroscopy is the preferable spectroscopic technique for forensic analysis of hair fibres, whilst Raman spectroscopy is the least preferred. The second objective (chapter 3) was to investigate, through a series of experiments, the effect of chemical treatment on the micro-environment of human hair fibres. The effect of bleaching agents on the hair fibres was studied with some detail at different treatment times and the results indicate a significant change in the chemical environment of the secondary structure of the hair fibre along with changes in the C-C backbone structure. One of the most important outcomes of this research was the behaviour of the fÑ-helix during chemical treatment. The hydrogen bonding in the fÑ-helix provides for the stable structure of the fibre and therefore any disruption to the fÑ-helix will inevitably damage the molecular structure of the fibre. The results highlighted the behaviour of the fÑ-helix, which undergoes a significant decrease in content during oxidation, and is partly converted to a random-coil structure, whilst the fÒ-sheet component of the secondary structure remains unaffected. The reported investigations show that the combination of FT-IR and Raman micro-spectroscopy can provide an insight and understanding into the complex chemical properties and reactions within a treated hair fibre. Importantly, this work demonstrates that with the aid of chemometrics, it is possible to investigate simultaneously FT-IR and Raman micro-spectroscopic information from oxidised hair fibres collected from one subject and treated at different times. The discrimination and matching of hair fibres on the basis of treatment has potential forensic applications. The third objective (chapter 4) attempted to expand the forensic application of FT-IR micro-spectroscopy to other keratin fibres. Animal fibres are commonly encountered in crime scenes and it thus becomes important to establish the origin of those fibres. The aim of this work was to establish the forensic applications of FT-IR micro-spectroscopy to animal fibres and to investigate any fundamental molecular differences between these fibres. The results established a discrimination between fibres consisting predominantly of fÑ-helix and those containing mainly a fÒ-sheet structure. More importantly, it was demonstrated through curve-fitting and chemometrics, that each keratin fibre contains a characteristic secondary structure arrangement. The work presented here is the first detailed FT-IR micro-spectroscopic study, utilising chemometrics as well as MCDM methods, for a wide range of keratin fibres, which are commonly, found as forensic evidence. Furthermore, it was demonstrated with the aid of the rank ordering MCDM methods PROMETHEE and GAIA, that it is possible to rank and discriminate keratin fibres according to their molecular characteristics obtained from direct measurements together with information sourced from the literature. The final objective (chapter 5) of the thesis was to propose an alternative method for the discrimination and matching of single scalp human hair fibres through the use of FT-IR micro-spectroscopy and chemometrics. The work successfully demonstrated, through a number of case scenarios, the application of the technique for the identification of variables such as gender and race for an unknown single hair fibre. In addition, it was also illustrated that known hair fibres (from the suspect or victim) can be readily matched to the unknown hair fibres found at the crime scene. This is the first time that a substantial, systematic FT-IR study of forensic hair identification has been presented. The research has shown that it is possible to model and correlate individual¡¦s characteristics with hair properties at molecular level with the use of chemometrics methods. A number of different, important forensic variables of immediate use to police in a crime scene investigation such as gender, race, treatment, black and white hair fibres were investigated. Blind samples were successfully applied both to validate available experimental data and extend the current database of experimental determinations. Protocols were posed for the application of this methodology in the future. The proposed FT-IR methodology presented in this thesis has provided an alternative approach to the characterisation of single scalp human hair fibres. The technique enables the rapid collection of spectra, followed by the objective analytical capabilities of chemometrics to successfully discriminate animal fibres, human hair fibres from different sources, treated from untreated hair fibres, as well as black and white hair fibres, on the basis of their molecular structure. The results can be readily produced and explained in the courts of law. Although the proposed relatively fast FT-IR technique is not aimed at displacing the two slower existing methods of hair analysis, namely comparative optical microscopy and DNA analysis, it has given a new dimension to the characterisation of hair fibres at a molecular level, providing a powerful tool for forensic investigations.

Para a execução da etapa inicial da identificação médico-legal de restos humanos (antropometria e exame dos arcos dentários), faz-se necessária uma limpeza prévia da ossada, para a remoção de tecidos moles putrefeitos. Os casos não identificados por esses métodos tradicionais, poderão ser submetidos ao exame de DNA. No entanto, apesar do grande avanço da biologia molecular, utilizando a amplificação de DNA pela PCR, algumas limitações que afetam a habilidade de se obter DNA em restos humanos, permanecem. Dessa forma, o objetivo deste trabalho foi fornecer subsídios morfológicos para os analistas forenses, com ênfase na prática médico-legal, visando uma utilização mais eficiente do DNA obtido de osso compacto de restos humanos em decomposição ou já esqueletizados, sem tecidos moles aderidos. Foi realizado o estudo da microestrutura do tecido ósseo compacto femoral, de restos humanos em decomposição, ainda com tecidos moles, que foram limpos pela fervura em água (n = 7) e ossadas já esqueletizadas pela decomposição natural, que não foram fervidas (n = 8). Destes, seis ossadas foram provenientes de cemitério público regular, após 3 anos de inumação, 1 ossada proveniente da região amazônica, e 1 ossada de origem desconhecida. Estas duas ultimas, apresentado-se porosas ou quebradiças. As análises morfológicas de cortes histológicos foram coradas com hematoxilina e eosina e o DNA amplificado pela PCR para os loci CSF1PO, TPOX, TH01, F13A0, FESFPS, vWA, D16S539, D7S820, D13S317 e amelogenina. Os resultados da análise desses dois grupos foram comparados com os de cadáveres frescos (n = 5) do Serviço de Verificação de Óbitos da Capital. A fervura dos ossos, do modo como é realizada no Instituto Médico Legal de São Paulo, pode aumentar a eosinofilia da matriz óssea e, em alguns casos, pode promover a desagregação dos ósteons. Tal procedimento pode remover células, mas pode também remover possíveis inibidores da PCR, favorecendo a análise do DNA obtido destas amostras. O fator limitante para a obtenção e análise de DNA, em amostras de ossos limpos por fervura, é a quantidade exígua de células. Ossos não submetidos à fervura, após inumação por três anos ou há mais tempo em contato com a terra, podem apresentar alterações da microestrutura. No entanto, a presença de hemácias preservadas e núcleos de osteócitos nestas amostras, indica melhor preservação de células em relação às amostras de ossos fervidos. O fator limitante para a análise de DNA nestas amostras é a presença sugestiva de inibidores da reação de amplificação pela PCR. Restos humanos, sem tecidos moles, macroscópicamente não preservados (porosos e quebradiços), e não submetidos à fervura, apresentam alterações de perda de matriz mineralizada; no entanto, nestas amostras ainda é possível encontrar células preservadas. Os resultados obtidos no neste trabalho permitem traçar algumas estratégias para uma melhor utilização nos protocolos de extração e análise do DNA em osso compacto de restos humanos. / To the first essential step to forensic identification of human remains (anthropological study of race, sex, age, etc) it is necessary a previous cleaning of the bones, to remove decomposing soft tissues. Medico-legal inconclusive or non identified cases, by using these traditional methods, could be subjected to DNA analysis. However, in spite of advances in human identification techniques, specially by PCR amplified DNA, some limitations that affect the ability to obtain DNA in human remains still persist. Therefore, the aim of this study was to provide additional support from morphological analysis, to help forensic analysts personnel to utilise more efficiently the DNA, extracted from compact bones of human remains in decomposition or already skeletonized corpse, it means without soft tissues, with special emphasis in the legal-medicine practice. Femoral compact bones were obtained from: 7 human remains found on the ground, in different degree of decomposition which were cleaned by boiling to remove soft tissues; also studied were collections of bones from 8 corpses having undergone natural decomposition: 6 human remains exhumed after 3 years from a common public cemetery in São Paulo City; 1 case from amazon region and 1 case with no information, both cases remained from long time (more than 3 years) in contact with soil. All eight cases, were not boiled as no soft tissue were adhered. As a control, five cadavers 12 to 16 hours post mortem were also used. The compact bones histological sections were stained by haematoxilin and eosin and the loci CSF1PO, TPOX, TH01, F13A01,FESFPS, vWA, D16S539, D7S820, D13S317 and amelogenin were amplified by PCR.The procedure for boiling the human remains utilised in the Legal Medicine Institute of São Paulo would have increased the eosinophily of bone matrix and, in some cases, promoted the desaggregation of the osteons. In addition these procedures would have removed the cells, but in some cases would have removed possible inhibitors of the PCR, favouring in this way the analysis of DNA obtained from these samples. The limiting factor to obtain successful analysis in bones submitted to boiling seem to be the low quantity of nuclei present in these samples. For the other hand, in bones not cleaned by boiling, the presence of preserved red cells and oscteocyte nuclei inside the lacunae indicates better preservation of cells in relation to those bones cleaned by boiling. The limiting factor to obtain successful DNA analysis in bones exhumed or in contact of soil, is the suggestive presence of inhibitors of PCR. Porous and brittle bones from human remains, without soft tissues that are not processed by boiling, present alterations through loss of mineralised matrix, although it is still possible to found preserved cells in these samples. The results presented in this work clarify concerns about viability of DNA for identification analysis. They also help to establish better strategies for optimisation of DNA extraction and analysis in compact bones of human remains.

Neste estudo, foi avaliada a relação entre polimorfismos dos genes da leptina (LEP) e receptores da leptina (LEPR) e parâmetros antropométricos, leptinemia glicemia e lipídeos séricos, em indivíduos da população brasileira. Foram incluídos 238 indivíduos com idade entre 30 e 80 anos. Foram medidos o índice de massa corporal (IMC), a cintura abdominal (CA) e a razão cintura quadril (RCQ). Amostras de sangue periférico foram obtidas para análise do perfil bioquímico e extração de DNA. Os polimorfismos de nuleotideo único (SNPs) LEP G-2548A e LEPR Lys109Arg, Gln223Arg e Lys656Asn foram detectados por PCR-RFLP. Os SNPs LEPR Lys109Arg e Gln223Arg foram associados com obesidade e com IMC e CA aumentados (p<0.05). Estes polimorfismos também foram associados com leptina e glicose elevada (p<0,05). O perfil lipídico sérico foi influenciado pelo polimorfismo LEPR Lys109Arg (p<0.05). A relação entre os SNPs LEPR Lys109Arg e Gln223Arg e o perfil lipídico foi modificada pelo gênero. Os haplótipos LEP G-2548/ LEPR Lys109Arg foram relacionados com diferenças no IMC de obesos. Os haplotipos LEPR Lys109Arg/Gln223Arg foram associados com diferenças na CA e glicemia e lipídeos séricos. Em conclusão, os polimorfismos LEPR Lys109Arg e Gln223Arg estão associados com obesidade e alterações de leptina, glicose e lipídeos circulantes de forma dependente do gênero. / We have assessed the relationship between polymorphisms of the leptin (LEP) and the leptin receptor (LEPR) genes and anthropometric parameters, plasma leptin and glucose and serum lipids in individuals of the Brazilian population. We included 238 individuais with 30 to 80 years. Body mass index (BMI), abdominal circumference (AC) and waist-to-hip ratio (WHR) were measured. Peripheral blood samples were collected for analysis of the biochemical profile and DNA extraction. The single nucleotide polymorphisms (SNP) LEP G-2548A and LEPR Lys109Arg, Gln223Arg and Lys656Asn were detected by PCR-RFLP. The SNPs LEPR Lys109Arg and Gln223Arg were associated with obesity and with increased BMI and AC (p <0.05). These polymorphisms were also associated with increase leptin and glucose (p<0,05). The serum lipid profile was influenced by the LEPR Lys 1 09Arg (p<0.05). The relationship between the SNPs LEPR Lys 1 09Arg and Gln223Arg and the lipid profile was modified by gender. The haplotypes LEP G-2548A1 LEPR Lys109Arg were related with differences on BMI in obese group. The haplotypes LEPR Lys109Arg/Gln223Arg were associated with differences on AC, glucose and serum lipids. In conclusion, the LEPR Lys109Arg and Gln223Arg polymorphisms are associated with obesity and alterations in blood leptin, glucose and lipids in a gender-dependent manner.

Indiana University-Purdue University Indianapolis (IUPUI) / Analyses of tobacco products and their usage are well-researched and have implications in analytical chemistry, forensic science, toxicology, and medicine. As such, analytical methods must be developed to extract compounds of interest from tobacco products and biological specimens in order to determine tobacco exposure. In 2009, R.J. Reynolds Tobacco Co. released a line of dissolvable tobacco products that are marketed as a smoking alternative. The dissolvables were extracted and prepared by ultrasonic extractions, derivatization, and headspace solid phase microextraction (SPME) with analysis by gas chromatography-mass spectrometry (GC-MS). The results show that the compounds present are nicotine, flavoring compounds, humectants and binders. Humectant concentrations vary among different tobacco types depending on the intended use. Humectants were quantified in various tobacco types by GC and “splitting” the column flow between a flame ionization detector (FID) and an MS using a microfluidic splitter in order to gain advantage from the MS’s selectivity. The results demonstrated excellent correlation between FID and MS and show that MS provides a higher level of selectivity and ensures peak purity. Chemometrics was also used to distinguish products by tobacco type. Hair is a common type of evidence in forensic investigations, and it is often subjected to mitochondrial DNA (mtDNA) analysis. Preliminary data was gathered on potential “lifestyle” markers for smoking status as well as any indications of subject age, gender, or race by investigating the organic “waste” produced during a mtDNA extraction procedure. The normally discarded organic fractions were analyzed by GC-MS and various lipids and fatty acids were detected. At this point, a total vaporization-SPME (TV-SPME) method was theorized, developed, and optimized for the specific determination of nicotine and its metabolite, cotinine. The theory of TV-SPME is to completely vaporize an organic extract which will eliminate the partitioning between the sample and the headspace, thereby simplifying the thermodynamic equilibrium. Parameters such as sample volume, incubation temperature, and extraction time were optimized to achieve the maximum analyte signal. Response surface methodology (RSM) is a statistical model that is very useful in predicting and determining optimum values for variables to ensure the ideal response. RSM was used to optimize the technique of TV-SPME for the analysis of nicotine and cotinine. Lastly, quantitation of nicotine and cotinine in human hair typically requires large sample sizes and extensive extraction procedures. Hence, a method using small sample sizes and a simple alkaline digestion followed by TV-SPME-GC-MS has been developed. Hair samples were collected from anonymous volunteers and nicotine and cotinine were identified and quantitated in the hair of tobacco users.