Photonic applications of biomaterials with special reference to biopolymers and microbes

This thesis Entitled Photonic applications of biomaterials with special reference to biopolymers and microbes. A detailed investigation will be presented in the present thesis related to direct applications of biopolymers into some selected area of photonics and how the growth kinetics of an aerial bacterial colony on solid agar media was studied using laser induced fluorescence technique. This chapter is an overview of the spectrum of biomaterials and their application to Photonics. The chapter discusses a wide range of biomaterials based photonics applications like efficient harvesting of solar energy, lowthreshold lasing, high-density data storage, optical switching, filtering and template for nano s tructures. The most extensively investigated photonics application in biology is Laser induced fluorescence technique. The importance of fluorescence studies in different biological and related fields are also mentioned in this chapter.

Investigation of ultrafast laser-photonic material interactions: Challenges for directly written glass photonics

Currently, direct-write waveguide fabrication is probably the most widely studied application of femtosecond laser micromachining in transparent dielectrics. Devices such as buried waveguides, power splitters, couplers, gratings, and optical amplifiers have all been demonstrated. Waveguide properties depend critically on the sample material properties and writing laser characteristics. In this paper, we discuss the challenges facing researchers using the femtosecond laser direct-write technique with specific emphasis being placed on the suitability of fused silica and phosphate glass as device hosts for different applications.

Room temperature all-silicon photonic crystal nanocavity light emitting diode at sub-bandgap wavelengths

Silicon is now firmly established as a high performance photonic material. Its only weakness is the lack of a native electrically driven light emitter that operates CW at room temperature, exhibits a narrow linewidth in the technologically important 1300-1600 nm wavelength window, is small and operates with low power consumption. Here, an electrically pumped all-silicon nano light source around 1300-1600 nm range is demonstrated at room temperature. Using hydrogen plasma treatment, nano-scale optically active defects are introduced into silicon, which then feed the photonic crystal nanocavity to enhance the electrically driven emission in a device via Purcell effect. A narrow (Δλ=0.5 nm) emission line at 1515 nm wavelength with a power density of 0.4mW/cm2 is observed, which represents the highest spectral power density ever reported from any silicon emitter. A number of possible improvements are also discussed, that make this scheme a very promising light source for optical interconnects and other important silicon photonics applications. © 2012 by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tracking biological invasions in space and time: elucidating the invasive history of the green alga Codium fragile using old DNA

With the advent of 'ancient DNA' studies on preserved material of extant and extinct species, museums and herbaria now represent an important although still underutilized resource in molecular ecology. The ability to obtain sequence data from archived specimens can reveal the recent history of cryptic species and introductions. We have analysed extant and herbarium samples of the highly invasive green alga Codium fragile, many over 100 years old, to identify cryptic accessions of the invasive strain known as C. fragile ssp. tomentosoides, which can be identified by a unique haplotype. Molecular characterization of specimens previously identified as native in various regions shows that the invasive tomentosoides strain has been colonizing new habitats across the world for longer than records indicate, in some cases nearly 100 years before it was noticed. It can now be found in the ranges of all the other native haplotypes detected, several of which correspond to recognized subspecies. Within regions in the southern hemisphere there was a greater diversity of haplotypes than in the northern hemisphere, probably as a result of dispersal by the Antarctic Circumpolar Current. The findings of this study highlight the importance of herbaria in preserving contemporaneous records of invasions as they occur, especially when invasive taxa are cryptic.

Photoacoustic and photothermal deflection studies on certain selected photonic materials“

The emergence of lasers in the early sixties has not only revolutionized the field of optics and communication but also paved new ways in the field of material characterization. Material studies using photothermal techniques possess certain unique characteristics and advantages over conventional methods. The most important aspect of photothennal techniques is their ability to perform noncontact and nondestructive measurement. Photoacoustics, photothermal deflection, thermal lens, photothermal radiometry and photopyroelectric methods are some of the commonly used and powerful techniques for the thermal and optical characterization of materials using lasers. In this thesis the applications of photoacoustic and photothermal deflection techniques for the thermal and optical characterization of different photonic materials, namely, semiconductors, liquid crystals and dye-doped polymers are discussed

Thermo- Optic and Nonlinear-Optical studies on CdSe Quantum Dots for Photonic Applications

In general, linear- optic, thermo- optic and nonlinear- optical studies on CdSe QDs based nano uids and their special applications in solar cells and random lasers have been studied in this thesis. Photo acous- tic and thermal lens studies are the two characterization methods used for thermo- optic studies whereas Z- scan method is used for nonlinear- optical charecterization. In all these cases we have selected CdSe QDs based nano uid as potential photonic material and studied the e ect of metal NPs on its properties. Linear optical studies on these materials have been done using vari- ous characterization methods and photo induced studies is one of them. Thermal lens studies on these materials give information about heat transport properties of these materials and their suitability for applica- tions such as coolant and insulators. Photo acoustic studies shows the e ect of light on the absorption energy levels of the materials. We have also observed that these materials can be used as optical limiters in the eld of nonlinear optics. Special applications of these materials have been studied in the eld of solar cell such as QDSSCs, where CdSe QDs act as the sensitizing materials for light harvesting. Random lasers have many applications in the eld of laser technology, in which CdSe QDs act as scattering media for the gain.

Transformation of malaria parasites by the spontaneous uptake and expression of DNA from human erythrocytes

The uptake and expression of extracellular DNA has been established as a mechanism for horizontal transfer of genes between bacterial species. Such transfer can support acquisition of advantageous elements, including determinants that affect the interactions between infectious organisms and their hosts. Here we show that erythrocyte-stage Plasmodium falciparum malaria parasites spontaneously take up DNA from the host cell cytoplasm into their nuclei. We have exploited this finding to produce levels of reporter expression in P.falciparum that are substantially improved over those obtained by electroporation protocols currently used to transfect malaria parasites. Parasites were transformed to a drug-resistant state when placed into cell culture with erythrocytes containing a plasmid encoding the human dihydrofolate reductase sequence. The findings reported here suggest that the malaria genome may be continually exposed to exogenous DNA from residual nuclear material in host erythrocytes.

Studies on betanin natural dye incorporated ZnO composites at nano and micro scale for photonic device applications

Green energy and Green technology are the most of the quoted terms in the context of modern science and technology. Technology which is close to nature is the necessity of the modern world which is haunted by global warming and climatic alterations. Proper utilization of solar energy is one of the goals of Green Energy Movement. The present thesis deals with the work carried out in the eld of nanotechnology and its possible use in various applications (employing natural dyes) like solar cells. Unlike arti cial dyes, the natural dyes are available, easy to prepare, low in cost, non-toxic, environmentally friendly and fully biodegradable. Looking to the 21st century, the nano/micro sciences will be a chief contributor to scienti c and technological developments. As nanotechnology progresses and complex nanosystems are fabricated, a growing impetus is being given to the development of multi-functional and size-dependent materials. The control of the morphology, from the nano to the micrometer scales, associated with the incorporation of several functionalities can yield entirely new smart hybrid materials. They are special class of materials which provide a new method for the improvement of the environmental stability of the material with interesting optical properties and opening a land of opportunities for applications in the eld of photonics. Zinc oxide (ZnO) is one such multipurpose material that has been explored for applications in sensing, environmental monitoring, and bio-medical systems and communications technology. Understanding the growth mechanism and tailoring their morphology is essential for the use of ZnO crystals as nano/micro electromechanical systems and also as building blocks of other nanosystems.

Estudos moleculares em pacientes com fibrose cística do sul do Brasil

Fibrose Cística (FC) ou mucoviscidose é uma das doenças hereditárias mais comuns em caucasóides, com uma freqüência estimada em um caso em cada 2000 nascimentos sendo a freqüência de indivíduos portadores estimada em 5% em indivíduos. Esta doença caracteriza-se principalmente por infecções e obstrução crônica do aparelho respiratório, insuficiência pancreática exócrina e suas conseqüências nutricionais e por elevados níveis de eletrólitos no suor. A apresentação clínica, a gravidade da doença e a velocidade de progressão da FC variam consideravelmente, incluindo-se entre as manifestações a agenesia congênita de vasos deferentes (ACVD). Dentre as 1006 mutações associadas à FC, a R117H foi descrita em associação com um sítio polimórfico de timidinas no intron 8 do gene CFTR, a qual pode estar relacionada a ACVD. Este trabalho teve como objetivos: ① identificar alterações nas seqüências de nucleotídeos dos exons 3, 4, 5, 7, 9, 11, 12, 19, 20 e 22 do gene CFTR; ② identificar a freqüência de algumas mutações freqüentes no gene CFTR (R347P, R347H, R334W, Q359K, G542X, G551D, R553X, S549N, R1162X, W1282X e N1303K) na amostra e estimar a freqüência destas mutações na população estudada; ③ determinar o genótipo dos pacientes com FC participantes do estudo; ④ estabelecer um protocolo eficiente e rápido para identificar as alterações de politimidinas em pacientes não homozigotos para a mutação ∆F508; ⑤ estabelecer a freqüência dos alelos 5T, 7T e 9T em pacientes com FC do sul do Brasil; ⑥ estabelecer a correlação do polimorfismo politimidinas com manifestações clínicas da doença, como por exemplo, azoospermia Para a identificação das mutações no gene CFTR foram avaliados 100 alelos ou 50 pacientes portadores de FC. No entanto, para a avaliação do polimorfismo de politimidinas foram avaliados 54 pacientes não relacionados. Estes pacientes foram previamente diagnosticados e se encontram em tratamento no Hospital de Clínicas de Porto Alegre. Após extração de DNA destes pacientes, o material foi amplificado por PCR utilizando-se primers específicos para as regiões de interesse. A identificação de alterações nas seqüências de nucleotídios foi possível através da técnica de SSCP. Esta técnica permitiu a detecção de 7 pacientes com alteração no exon 7, 3 pacientes com alterações no exon 11, 2 pacientes com alterações no exon 19 e de 3 pacientes com alterações no exon 20. Nenhum paciente apresentou alteração molecular nos exons 3, 4, 5, 12 e 22. As freqüências das mutações R334W, R1162X e W1282X na amostra estudada foram estabelecidas em 1,0% para cada uma delas. Não foram encontrados pacientes portadores das mutações R347P, R334H, Q359N e S549N na amostra estudada. Com a utilização deste protocolo associado ao do estudo anterior (Streit et al., 1999) foi possível a triagem de mutações em 44,4% do gene da FC O alelo 5T foi encontrado em 2 dos 108 alelos analisados. Já o polimorfismo 7T, o mais comum, foi detectado em 65 alelos, enquanto o polimorfismo 9T estava presente em 41 alelos. O genótipo mais comum estabelecido no presente estudo foi o 7T/9T, encontrado em 39 pacientes (72,2%), seguido do genótipo 7T/7T, encontrado em 12 pacientes (22,2%), e do 5T/7T, encontrado em 2 pacientes (3,7%) e, finalmente, do genótipo 9T/9T, em 1 paciente (1,85%). Os resultados obtidos sugerem que o fenótipo dos pacientes com FC estudados não resulta apenas do genótipo dos mesmos, pois existem pacientes com o mesmo genótipo e expressões fenotípicas diferentes. Fatores epigenéticos assim como ambientais devem influenciar a expressão das alterações moleculares. Entretanto, a identificação do defeito molecular básico é de fundamental importância para a confirmação precoce e precisa do diagnóstico em pacientes suspeitas e para o estudo familiar permitindo que as medidas de tratamento e prevenção sejam implementadas do modo mais eficiente.

Análise molecular de indivíduos com doença de Machado-Joseph

As ataxias espinocerebelares (SCAs) constituem um grupo de doenças neurodegenerativas fatais que apresentam uma grande heterogeneidade clínica. A doença de Machado-Joseph (DMJ), ou ataxia espinocerebelar tipo 3 (SCA3), é causada por uma expansão de uma seqüência repetitiva CAG em um gene, denominado MJD1, localizado no braço longo do cromossomo 14, expansão codificadora de uma seqüência poliglutamínica constituinte da proteína ataxina 3. Indivíduos normais apresentam entre 12 a 41 repetições, enquanto indivíduos afetados apresentam 61 a 84 repetições CAGs neste gene. Este trabalho teve como objetivos principais a padronização de metodologias moleculares para o identificação e a quantificação do número de repetições CAG no gene responsável pela da DMJ. Um grupo de 112 pacientes, pertencentes a 77 famílias, com suspeita clínica de algum tipo de ataxia espinocerebelar foi avaliado no Hospital de Clínicas de Porto Alegre. Após a extração de DNA destes pacientes, este material foi amplificado por PCR utilizando oligonucleotídeos iniciadores específicos para a região de interesse e posterior transferência destes fragmentos (1) para uma membrana de nylon pelo método de Southern blot, visando ao estabelecimento de um protocolo não-radioativo para detectar a presença do alelo normal e/ou mutante; e (2) análise em gel de poliacrilamida para quantificação do número de repetições presentes no alelo mutante. As análises laboratoriais identificaram um total de 77 pacientes com uma expansão CAG no gene da MJD1. Considerando-se apenas indivíduos não relacionados, a freqüência encontrada foi de 61% (47 indivíduos). Os protocolos estabelecidos demonstraram-se bastante eficazes e sensíveis para o diagnóstico da DMJ e quantificação do alelo expandido da respectiva doença.

Ressoador retangular defenda com quatro camadas fotônicas

Recently, planar antennas have attracted interest due to its characteristics as well as the advantages they offer compared to other types of antennas. In the area of mobile communications the need for such antennas has become increasingly intense due to development, which requires antennas that operate in multifrequency and broadband. The microstrip antennas have narrow bandwidth due to losses in the dielectric caused by irradiation. Another limitation is the radiation pattern degradation due to generation of surface waves in the substrate. Some techniques are being developed to minimize this bandwidth limitation, as is the case in the study of type materials PBG - Photonic Band Gap, to compose the dielectric material. The analysis developed in this work were performed with use of the method LTT - Transverse Transmission Line, in the field of Fourier transform that uses a component propagating in the y direction (transerve real direction of propagation z), thus treating the general equations of the fields electric and magnetic fields as a functions of y E and Hy . This work has as main objective the method LTT structures resonator line slot with four layers of material photonic PBG, for obtaining the complex resonant frequency and efficiency of this structure. PBG theory is applied to obtain the relative permittivity for the substrate biases sep compounds photonic material. Numerical-computational results in graph form in two dimensions for all the analysis are presented for the proposed structures that have photonic materials, as substrates

Avaliação da diversidade genética de populações de Pacu (Piaractus mesopotamicus Holmberg, 1887) do Pantanal Matogrossense com o uso de marcadores moleculares do tipo microssatélites

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Os experimentos de Griffith no ensino de Biologia: a transposição didática do conceito de transformação nos livros didáticos

Griffith's experiments regarding bacterial transformation Pneumococcus are regarded as essential when related to DNA/heredity recognition process. The aim of the current study is to assess the didac tic transposition of the concept of bacterial transformation since the Griffith's descriptions until its current approach on didactic books. We realized that the historical context and the relationship between bacterial transformation and DNA recognition as genetic material are poorly explored. The core of our paper is the historical approach of those exper iments. By considering the wide richness of the knowledge that is ranged on Griffith's experiments, we suggest a didactic transposition concerning bacterial transformation in the learning process, involving an integration of contents.

Leptospira interrogans serovar Copenhageni harbors two lexA genes involved in SOS response

Bacteria activate a regulatory network in response to the challenges imposed by DNA damage to genetic material, known as the SOS response. This system is regulated by the RecA recombinase and by the transcriptional repressor lexA. Leptospira interrogans is a pathogen capable of surviving in the environment for weeks, being exposed to a great variety of stress agents and yet retaining its ability to infect the host. This study aims to investigate the behavior of L. interrogans serovar Copenhageni after the stress induced by DNA damage. We show that L. interrogans serovar Copenhageni genome contains two genes encoding putative LexA proteins (lexA1 and lexA2) one of them being potentially acquired by lateral gene transfer. Both genes are induced after DNA damage, but the steady state levels of both LexA proteins drop, probably due to auto-proteolytic activity triggered in this condition. In addition, seven other genes were up-regulated following UV-C irradiation, recA, recN, dinP, and four genes encoding hypothetical proteins. This set of genes is potentially regulated by LexA1, as it showed binding to their promoter regions. All these regions contain degenerated sequences in relation to the previously described SOS box, TTTGN 5CAAA. On the other hand, LexA2 was able to bind to the palindrome TTGTAN 10TACAA, found in its own promoter region, but not in the others. Therefore, the L. interrogans serovar Copenhageni SOS regulon may be even more complex, as a result of LexA1 and LexA2 binding to divergent motifs. New possibilities for DNA damage response in Leptospira are expected, with potential influence in other biological responses such as virulence

Minisatellite marker analysis of Trypanosoma brucei: Reconciliation of clonal, panmictic, and epidemic population genetic structures

The African trypanosome, Trypanosoma brucei, has been shown to undergo genetic exchange in the laboratory, but controversy exists as to the role of genetic exchange in natural populations. Much of the analysis to date has been derived from isoenzyme or randomly amplified polymorphic DNA data with parasite material from a range of hosts and geographical locations. These markers fail to distinguish between the human infective (T. b. rhodesiense) and nonhuman infective (T. b. brucei) “subspecies” so that parasites derived from hosts other than humans potentially contain both subspecies. To overcome some of the inherent problems with the use of such markers and diverse populations, we have analyzed a well-defined population from a discrete geographical location (Busoga, Uganda) using three recently described minisatellite markers. The parasites were primarily isolated from humans and cattle with the latter isolates further characterized by their ability to resist lysis by human serum (equivalent to human infectivity). The minisatellite markers show high levels of polymorphism, and from the data obtained we conclude that T. b. rhodesiense is genetically isolated from T. b. brucei and can be unambiguously identified by its multilocus genotype. Analysis of the genotype frequencies in the separated T. b. brucei and T. b. rhodesiense populations shows the former has an epidemic population structure whereas the latter is clonal. This finding suggests that the strong linkage disequilibrium observed in previous analyses, where human and nonhuman infective trypanosomes were not distinguished, results from the treatment of two genetically isolated populations as a single population.