Academic literature on the topic 'Optical and molecular fingerprints'

Tandem-repetitive hypervariable minisatellites detected in a DNA fingerprint provide highly informative genetic markers. To identify and localize specific loci represented in a DNA fingerprint, it is necessary to clone individual minisatellites. This thesis is concerned with the characterization of single locus minisatellite probes cloned from DNA fingerprints. Seven single locus human minisatellite probes have been cloned by screening ? libraries with DNA fingerprint probes 33.6 and 33.15. Each locus consists of a minisatellite, with repeat units ranging in length from 9 to 47 base pairs depending on the locus. These autosomal loci are amongst the most variable loci characterized to date. The heterozygosity values of D1S7, D1S8, D5S43, D7S21, D7S22 and D12S11 range from 85% to >99%. Clustering of minisatellites was initially detected at the D12S11 locus. This observation led to the subsequent discovery of minisatellites showing close physical linkage as well as a tendency for minisatellites to be localized in proterminal chromosomal regions. An association of a minisatellite with a dispersed repetitive element was identified when studying the organization of cloned D7S22. This phenomenon was later found to be common amongst minisatellites. Pedigree analysis revealed a high level of instability of the locus detected by D1S7. This manifestation of detectable mutant alleles demonstrated the feasibility of direct estimation of mutation rates at minisatellite loci. The hypervariability of loci detected by minisatellites and their sensitivity in blot hybridizations make minisatellites a powerful tool in genetic analysis. These probes have already proved instrumental in many genetic and clinical studies. The high degree of individual specificity and the relatively simple banding pattern generated make these probes invaluable in forensic medicine. D1S7 and D7S21 were used in the first example of DNA-based identification in a rape and murder enquiry. One minisatellite probe was found to detect two loci, DNF21S1 and DNF21S2, on chromosomes 6 and 16 respectively. The 39 base pair repeat unit of this minisatellite is itself repetitive. The heterozygosity values of DNF21S1 and DNF21S2 are 61% and 16% respectively. Genomic mapping and sequence analyses revealed close similarity between these loci. Human population and pedigree studies showed that some individuals carry two alleles at DNF21S2, some carry one allele, some carry a duplicated allele while some are devoid of this locus. A model of duplication of a large proterminal segment of chromosome 6 DNA containing a minisatellite and transposition into an interstitial region of chromosome 16 in some human individuals is suggested. This is, to my knowledge, the first report of a human DNA polymorphism arising via transposition of DNA. The duplication unit on chromosome 16 is large (>15 kb) and has inserted into a member of a target site family present in 5-10 copies per genome. This sequence family represents a novel class of human repetitive DNA.

Orientador : Prof. Dr. Luciano Silva<br>Coorientador : Profª. Olga Regina Pereira Bellon<br>Tese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa: Curitiba, 28/06/2016<br>Inclui referências : f. 75-82<br>Área de concentração<br>Resumo: Um método para se obter impressões digitais 3D da derme e da epiderme a partir de imagens em alta resolução adquiridas utilizando Tomografia de Coerência Ótica (OCT) é proposto neste trabalho. Este método, resolve limitações das técnicas de reconstrução 3D de impressões digitais que empregam múltiplas câmeras/triangulação ou iluminação estruturada, tais como variações de resolução do centro para as bordas das impressões digitais 3D causadas por erros de reconstrução, sensibilidade a baixa iluminação e contraste insuficiente. Uma técnica de busca e identificação baseados em padrões inovativos, os "mapas KH " (usados para a segmentação de regiões de superfície em imagens de intensidade e de profundidade), extraídos computando as curvaturas Gaussiana (K) e média (H) de uma região de interesse na vizinhança das minúcias (denominada nuvem de minúcia), é apresentada. Grandes bases de mapas KH, uma para cada nuvem de minúcia identificada, podem ser construídos com essa técnica. A estratégia de busca e identificação, em duas etapas, baseia-se primeiro em padrões locais de gradientes (LGP) dos mapas KH, para reduzir o espaço de busca dentro da base, seguidos de uma comparação que utiliza uma medida de similaridade, a correlação cruzada normalizada dos padrões pré-selecionados com o LGP com os que se quer identificar. A acuracidade do método e sua compatibilidade com os métodos correntes, comparável ou superior à dos métodos 2D, é verificada através da identificação biométrica de impressões digitais 3D utilizando duas bases de imagens, uma adquirida através da tecnologia OCT e a outra gentilmente cedida pela Universidade Politécnica de Hong Kong. A base de imagens OCT, a primeira adquirida com essa tecnologia, é composta de imagens coletadas de onze voluntários em duas sessões de escaneamento e contém imagens de dedos de pessoas com diferentes idades, gênero e etnias e contém casos de cicatrizes, calos e alterações, tais como abrasão e arranhões. Uma base de impressões digitais 2D, obtida dos mesmos voluntários através de um leitor regular de impressões digitais, foi adquirida para permitir uma comparação da técnica proposta com os métodos de identificação tradicionais. A aplicabilidade do método proposto à identificação de impressões digitais alteradas, deterioradas acidentalmente ou intencionalmente, é investigada. Nesses casos, a impressão digital 3D extraída da derme e compatível com a da epiderme é empregada. A identificação destas impressões 3D alteradas é testada utilizando a base de imagens adquiridas com OCT. A acuracidade da técnica é comparada com a obtida utilizando os métodos tradicionais 2D usando os gráficos de taxas de Falsa Aceitação e Falsa Rejeição (FAXxFRR) e de Características Cumulativas de Identificação (CMC). Impressões digitais 2D, extraídas a partir das impressões digitais 3D simulando o rolamento do dedo durante a aquisição (rolamento virtual), foram geradas e sua compatibilidade com as bases de imagens 2D foi testada. Um conjunto de medidas de avaliação de qualidade foram aplicados às bases de imagens de impressões digitais 3D e sua correspondência aos escores de identificação foi analisada para determinar aqueles que podem contribuir para melhorar a acuracidade da identificação. Palavras-chave: Impressões digitais 3D. Identificação Biométrica. Tomografia de Coerência Ótica.<br>Abstract: A method to obtain epidermal and dermal 3D fingerprints from high-resolution images acquired using Optical Coherence Tomography (OCT) is proposed. This method addresses limitations of current 3D reconstruction techniques that employ multiple cameras/triangulation or structured illumination such as depth and resolution variations from the center to the borders of the fingerprint caused by reconstruction errors, sensitivity to low illumination and poor contrast. The availability of these 3D fingerprints allowed the creation of new matching methods that benefit from the rich information available in 3D. A 3D fingerprint matching technique based on novel patterns, the KH maps (used to surface region segmentation in range and intensity images), extracted by computing the Gaussian and mean curvatures (SILVA; BELLON; GOTARDO, 2001) from a region of interest around the minutiae, named minutiae clouds is presented. Large databases of KH maps, one for each identified minutiae cloud can be built. The matching strategy, a two-step approach, relies on local gradient patterns (LGP) of the KH maps to narrow the search space, followed by a similarity matching, the normalized cross correlation of patterns being matched. The accuracy and matching compatibility, comparable or improved in relation to the 2D matching methods, is verified through matching 3D fingerprints from two databases one acquired using OCT and a public database gently made available by the Hong Kong Polytechnic University. The OCT database, the first 3D database acquired using Optical Coherence Tomography, to our knowledge, is made of images collected from eleven volunteers in two scanning sessions and contains images of people of different ages, genders and ethnicities and also cases of scars, calluses and alterations as abrasion and scratches. A 2D fingerprint database, scanned from the same volunteers using a regular fingerprint reader was also obtained for comparison with traditional matching methods. We investigate the applicability of our method to the identification of altered fingerprints, damaged unintentionally or accidentally. In these cases, the 3D dermal fingerprint, compatible with the epidermis fingerprint, is employed. Matching with 3D dermal and epidermal fingerprints is tested in the OCT database. Matching accuracy is compared with the obtained using traditional matching 2D methods by using False Acceptance and False rejection rate (FARxFRR) and Cumulative Matching Characteristics (CMC) graphs. Unwrapped fingerprints, 2D fingerprints extracted from 3D fingerprints by virtual unrolling were generated and tested for compatibility with 2D databases. A set of quality evaluation measures were employed to the 3D fingerprint databases and their correspondence to the matching scores was analyzed to identify those that can contribute to improve the matching accuracy. Key-words: 3D Fingerprints. Biometric identification. Optical Coherence Tomography.

Dissertação de Erasmus Mundus para obtenção do grau de mestre em Técnicas Laboratoriais Forenses<br>Aspartic acid is the chemical, amongst amino acids, whose racemization process is considered to be the fastest and the most reliable way to conduct an ageing study in some living-being tissues. Racemization is a natural-occurring event in which L-stereoisomer of aspartic acid is converted into D-stereoisomer in an equilibrium dependent on factors namely pH, environmental conditions and, most critically, on temperature.<br>The main objective of the current study is to assess the influence of temperature on kinetics of aspartic acid racemization and to implement this methodology in fingermarks. The hypothesis is that different starting points of deposition of a biological specimen will give rise to significant differences in L-/D- racemization after the sample has been heated, allowing to determine time since deposition of a fingerprint. In this way, it would be possible to find the time since build a molecular clock for fingerprints, consisting of time since deposition of fingermarks based on racemization degree of aspartic acid.<br>Firstly, a calibration curve was built within the concentrations range expected to be quantified in actual samples both with L-aspartic acid (L-Asp) and D-aspartic acid (D-Asp) separately, Gas Chromatography - Flame Ionization Detector (GC-FID) being the chosen technique and detection mode to set up the calibration experiments. Secondly, L-aspartic acid standards were treated at different temperatures during different time periods and were analyzed by GC-FID with a chiral column, aimed for detecting D- isomer, providing with information about racemization rate of aspartic acid.<br>Eventually a downward trend was observed for L-Asp but not for D-Asp and a pseudo-rate constant could be calculated for the former, demonstrating that temperature degrades this chemical. Fingerprints study was not successful to determine aspartic acid racemization but a simple handling of them and an adequate, sensitive response of the chromatographic system could quantify racemization degree.

Microwave spectroscopy is a gas phase technique typically geared toward measuring the rotational transitions of Molecules. The information contained in this type of spectroscopy pertains to a molecules structure, both geometric and electronic, which give insight into a molecule's chemistry. Typically this type of spectroscopy is high resolution, but narrowband ≤1 MHz in frequency. This is achieved by tuning a cavity, exciting a molecule with electromagnetic radiation in the microwave region, turning the electromagnetic radiation o, and measuring a signal from the molecular relaxation in the form of a free induction decay (FID). The FID is then Fourier transformed to give a frequency of the transition. "Fast passage" is defined as a sweeping of frequencies through a transition at a time much shorter (≤10 s) than the molecular relaxation (≈100 s). Recent advancements in technology have allowed for the creation of these fast frequency sweeps, known as "chirps", which allow for broadband capabilities. This work presents the design, construction, and implementation of one such novel, high-resolution microwave spectrometer with broadband capabilities. The manuscript also provides the theory, technique, and motivations behind building of such an instrument. In this manuscript it is demonstrated that, although a gas phase technique, solids, liquids, and transient species may be studied with the spectrometer with high sensitivity, making it a viable option for many molecules wanting to be rotationally studied. The spectrometer has a relative correct intensity feature that, when coupled with theory, may ease the difficulty in transition assignment and facilitate dynamic chemical studies of the experiment. Molecules studied on this spectrometer have, in turn, been analyzed and assigned using common rotational spectroscopic analysis. Detailed theory on the analysis of these molecules has been provided. Structural parameters such as rotational constants and centrifugal distortion constants have been determined and reported for most molecules in the document. Where possible, comparisons have been made amongst groups of similar molecules to try and get insight into the nature of the bonds those molecules are forming. This has been achieved the the comparisons of nuclear electric quadrupole and nuclear magnetic coupling constants, and the results therein have been determined and reported.

Les activités anthropiques à l'échelle d'un bassin-versant peuvent être très nombreuses (e.g. pratiques agricoles, industries, transport et tourisme). Ces activités engendrent des pressions qui se manifestent par l'apport de polluants vers les cours d'eau (e.g. éléments majeurs, micropolluants organiques, métaux traces). L'identification de ces sources de polluants dans les cours d'eau, et plus particulièrement les sources diffuses, reste un réel défi à ce jour. La matière organique dans sa fraction dissoute (MOD) constitue un mélange complexe de molécules dont la composition et les propriétés physicochimiques dépendent de son origine qu'elle soit naturelle ou anthropique, terrigène ou autochtone, diffuse ou ponctuelle. Du fait de son ubiquité, la MOD présente dans les cours d'eau pourrait ainsi être utilisée comme traceur des activités anthropiques et donc des sources de polluants à l'échelle d'un bassin versant. Dans ce contexte, l'objectif de cette thèse est de mettre en évidence des marqueurs basées sur des propriétés physico-chimiques de la MOD (e.g. distribution en poids moléculaire, aromaticité, famille de composés…) qui soient caractéristiques de sources naturelles (e.g. apports terrigènes, production autochtone) et anthropiques (e.g. rejets de stations de traitement des eaux usées STEU, ruissellement urbain, activités d'agriculture et d'élevage) à l'échelle de bassins versants. Pour cela, une base de données originale a été construite avec plus de 130 échantillons d'eau représentatifs de ces différentes sources et analysés avec un large panel de techniques analytiques (dosage du carbone organique dissous, analyse par spectroscopie UV-Visible et excitation-émission de fluorescence, analyse par chromatographie d'exclusion stérique couplée à la détection UV et fluorescence - HPSEC/UV-fluorescence - , et analyse moléculaire par chromatographie liquide couplée à la spectrométrie de masse haute résolution - LC-HRMS - ). L'exploitation de la base de données a tout d'abord permis d'améliorer la caractérisation de la MOD avec l'identification de nouveaux indicateurs optiques (HPSEC/UV-fluorescence) et moléculaires (LC-HRMS). Un protocole de traitement des données complexes issues de l'analyse LC-HRMS non-ciblée a été développé et validé à l'aide de contrôle qualité afin d'extraire les composés moléculaires les plus pertinents pour différencier les sources de MOD. Ces travaux ont également servi à valider une méthodologie d'échantillonnage spécifique aux sources diffuses terrigènes en lien avec l'occupation des sols. Finalement, l'approche intégrée multi-analytique et multi-sources développée dans le cadre de la thèse a contribué à la construction d'empreintes spécifiques des sources de MOD sélectionnées apriori (naturelles, anthropiques, diffuses, ponctuelles). Les résultats de ces travaux permettent clairement d'envisager la MOD comme traceur de l'origine des masses d'eaux et des pollutions associées dans les cours d'eau<br>Anthropogenic activities at the scale of a watershed can be very numerous (e.g. agricultural practices, industries, transport, and tourism). These activities generate pressures that result in the input of pollutants to the watercourse (e.g. major elements, organic micropollutants, trace metals). The identification of these sources of pollutants in watercourses remains a challenge to date. Organic matter in its dissolved fraction (DOM) constitutes a complex mixture of molecules whose composition and physicochemical properties depend on its origin, whether natural or anthropogenic, terrigenous or autochthonous, diffuse or point source. Because of its ubiquity, the DOM present in the rivers could be used as a tracer of the anthropic activities and thus of the sources of pollutants at the scale of a catchment. In this context, the objective of this thesis is to identify markers based on physico-chemical properties of DOM (that are characteristic of natural (e.g. terrigenous inputs, autochthonous production) and anthropogenic (e.g. wastewater treatment plant discharges, urban runoff, agriculture and livestock activities) sources at the watershed scale. For this purpose, an original database was built with more than 130 water samples representative of these different sources and analyzed with a wide range of analytical techniques (dissolved organic carbon determination, analysis by UV-Visible spectroscopy and fluorescence excitation-emission, analysis by steric exclusion chromatography coupled with UV and fluorescence detection - HPSEC/UV-fluorescence - , and molecular analysis by liquid chromatography coupled with high resolution mass spectrometry - LC-HRMS - ). The exploitation of the database allowed to improve the characterization of DOM with the identification of new optical (HPSEC/UV-fluorescence) and molecular (LC-HRMS) indicators. A protocol for processing complex data from non-targeted LC-HRMS analysis was developed and validated using quality control in order to extract the most relevant molecular compounds to differentiate DOM sources. This work also validated a sampling methodology specific to land-based diffuse sources in relation to land use to build their footprints at the watershed scale. Finally, the integrated multi-analytical and multi-source approach developed in the framework of the thesis allowed the construction of specific fingerprints of the selected sources of DOM (natural, anthropogenic, diffuse, point). The results of this work clearly show that DOM can be considered as a tracer of the origin of the water masses and the associated pollutions in the rivers

Molecular imaging plays an important role for development of systems biomedicine, which non-invasively extracts pictorial information on physiological and pathological activities at the cellular and molecular levels. Optical molecular tomography is an emerging area of molecular imaging. It locates and quantifies a 3D molecular probe distribution in vivo from data measured on the external surface of a small animal around the visible and infrared range. This approach can facilitate or enable preclinical applications such as cancer studies, involving angiogenesis, tumor growth, cell motility, metastasis, and interaction with a micro-environment. The reconstruction of diffuse light sources is the central task of optical molecular tomography, and generally ill-posed and rather complex. The key element of optical molecular tomography includes the geometrical model, tissue properties, photon characteristics, transport model, and reconstruction algorithm. <br /><br />This dissertation focuses mainly on the development optical molecular tomography methods based on bioluminescence/fluorescence probes to solve some well-known challenges in this field. Our main results are as follows. We developed a new algorithm for estimation of optical parameters based on the phase-approximation model.  Our iterative algorithm takes advantage of both the global search ability of the differential evolution algorithm and the ef"ciency of the conjugate gradient method. We published the first paper on multispectral bioluminescence tomography (BLT). The multispectral BLT approach improves the accuracy and stability of the BLT reconstruction even if data are highly noisy. We established a well-posed inverse source model for optical molecular tomography. Based on this model, we proposed a differential evolution-based reconstruction algorithm to determine the source locations and strengths accurately and reliably. Furthermore, to enhance the spatial resolution of fluorescence molecular tomography, we proposed fluorescence micro-tomography to image cells in a tissue scaffold based on Monte Carlo simulation on a massive parallel processing architecture. Each of these methods shows better performance in numerical simulation, phantom experiments, and mouse studies than the conventional methods.<br /><br>Ph. D.

In this Doctorate Thesis project, a small library of four structurally related melamine-bridge bis(porphyrin-ZnII) receptors, was synthesized The coordination properties of these porphyrin derivatives has been investigated by UV-vis spectroscopy for a series of aliphatic diamines of general formula H2N (CH2)n NH2 (n = 4-8). A marked colour variation occours due to a favourable host-guest ditopic interaction. The binding constants, higher than 10e7 M-1, make these receptors excellent candidates for the development of sensor devices for continuous flow analyses, in which the porphyrin derivatives are covalently supported onto appropriate solid materials. These dimeric metalloporphyrin hosts (molecular tweezers), have also been successfully exploited as chirality probes for determination of the absolute configuration (AC) for a wide variety of chiral molecules (diamines, amino esters, amino amides, amino alcohols and secondary monoalcohols) by using circular dichroism spectroscopy, in collaboration with Prof. Nina Berova of Columbia University. The deposition of porphyrin derivatives on different matrices was also investigated. Characterizations of substrates were carried out by scanning electron microscopy (SEM), atomic force microscopy (AFM) and scanning tunneling microscopy. These results show promising potential in the synthesis of highly ordered networks of surface-supported functional materials for sensing and solar energy applications.<br>Il progetto di ricerca di questa Tesi di Dottorato ha riguardato la sintesi, la caratterizzazione e lo studio delle proprietà di ricognizione molecolare di nuovi derivati bis-porfirinici contenenti un ponte triazinico. Studi di spettroscopia UV-vis hanno permesso di determinare l’affinità di tali recettori nei confronti delle diammine lineari di formula generale H2N(CH2)nNH2, con n = 4-8. Le costanti di formazione dei complessi host-guest sono molto grandi, fino a 10e7 M-1, grazie all’effetto ditopico realizzato dai due centri porfirinici. La coordinazione delle diammine al dimero porfirinico è associata ad una variazione marcata del colore e questo fatto ha favorito l’impiego di tali derivati in ambito sensoristico. A tal proposito, è stata messa a punto una procedura per supportare i dimeri porfirinici su materiali polimerici per la costruzione di sensori da utilizzare per l’analisi in flusso continuo. Questi derivati sono stati anche utilizzati come pinze molecolari (tweezers) per la determinazione della configurazione assoluta di molecole chirali (diammine, ammino esteri, ammino ammidi e ammino alcoli, monoalcoli secondari) mediante l’impiego della spettroscopia di dicroismo circolare (CD), in collaborazione con la Prof. Berova della Columbia University. Parallelamente, sono stati realizzati studi di deposizione di derivati porfirinici su superfici in vista di applicazioni di tipo sensoristico e in campo energetico (fotovoltaico). La caratterizzazione dei substrati è stata condotta mediante misure di microscopia elettronica a scansione (SEM), microscopia a forza atomica (AFM) e microscopia a scansione ad effetto tunnel (STM). Questi studi di deposizione hanno dimostrato come, scegliendo le opportune condizioni di deposizione, sia possibile costruire dei sistemi ordinati a lungo raggio, su superfici di diversa natura, rendendo questi sistemi candidati ideali per lo sviluppo di nuovi materiali ad alto contenuto tecnologico.