New synthetic advances in the control of nanoparticle size and shape along with the development of new surface modifications facilitates the growing use of nanomaterials in biomedical applications. Of particular interest are functional and biocompatible nanomaterials for sensing, imaging, and drug delivery. The goal of this research is to tailor the function of nanomaterials for biomedical applications by improving the biocompatibility of the systems. Our work demonstrates both a bottom up and a post synthetic approach for incorporating stability, stealth, and biocompatibility to metal based nanoparticle systems. Two main nanomaterial projects are the focus of this dissertation. We first investigated the development of a green synthetic procedure to produce gold nanoparticles for biological imaging and sensing. The size and morphology of gold nanoparticles directly impact their optical properties, which are important for their function as imaging agents or their use in sensor systems. In this project, a synthetic route based on the natural process of biomineralization was developed, where a designed protein scaffold initiates the nucleation and subsequent growth of gold ions. To gain insight into controlling the size and morphology of the synthesized nanoparticles, interactions between the gold ions and the protein surface were studied along with the effect of ionic strength on interactions and then subsequent crystal growth. We are able to control the size and morphology of the gold nanoparticles by altering the concentration or identity of protein scaffold, salt, or reducing agent. The second project involves the design and optimization of metal organic framework nanoparticles for an external stimulus triggered drug delivery system. This work demonstrates the advantages of using surface coatings for improved stability and functionalization. We show that the addition of a polyethylene glycol surface coating improved the colloidal stability and biocompatibility of the system. The nanoparticle was shown to successfully encapsulate a variety of small molecule cargo. This is the first report of photo-triggered degradation and subsequent release of the loaded cargo as a mechanism of stimuli-controlled drug delivery. Each of the aforementioned projects demonstrates the design, synthesis, and optimization of metal-based systems for use in biomedical applications. / Ph. D.

Regeneration, the replacement of lost or damaged body parts, and biomineralisation, the biologically controlled formation of minerals, are important and widespread abilities in the animal kingdom. Both phenomena have a complex evolutionary history; thus their study benefits from investigations in diverse animals. Spirobranchus (formerly Pomatoceros) lamarcki is a small tube-dwelling polychaete worm of the serpulid family. Serpulids have evolved a novel head appendage, the operculum, which functions as a defensive tube plug and regenerates readily when lost. In S. lamarcki, the end of the operculum is reinforced by a calcareous plate; thus, the operculum is a good system in which to study both regeneration and biomineralisation. This thesis explores several aspects of these important processes in the adult operculum. First, a time course of normal regeneration is established. Next, cell proliferation patterns are described, suggesting a combination of proliferation-dependent and proliferation-independent elements in opercular regeneration. The formation of the calcareous opercular plate is examined using both microscopic observations of whole opercular plates and X-ray diffraction analysis of isolated plate mineral, revealing a large shift in mineralogy over the course of regeneration. Histochemical study of alkaline phosphatase enzyme activity indicates the importance of these enzymes in the operculum, although their precise functions are as yet unclear. Finally, a preliminary survey of three opercular transcriptomic datasets is presented, with a broad sampling of gene families with regeneration- or biomineralisation-related roles in other animals. The opercular transcriptome constitutes the first biomineralisation transcriptome from any annelid, and one of the first transcriptomic datasets related to annelid regeneration. Many of the candidate genes examined here display interesting behaviour and suggest targets for further investigation. The work presented here establishes the S. lamarcki operculum as a promising model system in the field of evolutionary developmental biology.

Call number: LD2668 .T4 1985 E46 / Master of Science

The applications of calcium-isotope measurements in marine carbonates are explored in several different contexts within this thesis. As a record of global ion fluxes, seawater calcium-isotope ratios can be used as tracers for large weathering imbalances, which develop as a feedback system in response to intervals of climate change. This approach provides valuable constraints on the complex climatic and oceanographic phenomena known as the Oceanic Anoxic Events. Over much longer timescales, the calcium-isotope ratio of seawater is influenced by steady-state processes that reflect the evolution of seawater chemistry. To understand these influences, the modern calcium-isotope budget is assessed quantitatively using a compilation of marine carbonate samples, revealing several distinctive components of the carbonate burial sink that can affect the steady-state balance of the calcium cycle. Changes in the major ion composition of seawater and in the organisms that contribute to sedimentary carbonate burial are shown to contribute significantly to the geological record of seawater calcium-isotope ratios. The importance of skeletal carbonate in the calcium cycle leads to another application of calcium isotopes towards understanding biomineralization. This large and complex topic is approached with calcium-isotope data from two unique growth experiments that constrain some of the mechanisms by which biogenic aragonite acquires its geochemical signatures. This range of topics presents a diverse, but by no means exclusive, sample of the topics that are accessible for investigation through calcium-isotope analysis. The potential of this isotopic tool is demonstrated by the breadth of environments and timescales represented in this work.

Le processus de biominéralisation confère aux organismes qui le développent une valeur adaptative. La coquille carbonatée des mollusques intègre les fonctions de protection biomécanique à différentes échelles. La coquille résulte de l'association de composés inorganiques et d'une matrice organique protéique, médiatrice du contrôle biologique de la minéralisation. L'analyse du protéome de la coquille chez 4 espèces de bivalves met en évidence deux patrons fonctionnels et leur degré de conservation phylogénétique : l'un lié au contrôle de la minéralisation stricto sensu ; l'autre à la protection immune. L'étude de populations vivant à l'état naturel en mer Baltique, dont les eaux présentent localement de fortes variations ioniques montre que le protéome intègre également l'impact de conditions environnementales limitantes. L'anthropocène impose un rythme adaptatif pressant aux organismes et la modification acido-basique des eaux océaniques est susceptible d'impacter sensiblement les organismes calcifiants. La signature de mécanismes adaptatifs du contrôle biologique de la biominéralisation se traduit dans le protéome de la coquille. Les implications sont particulièrement signifiantes dans un contexte d'intérêt de développement aquacole grandissant. / In this study, the SMPs from four commercially important and divergent bivalve species crassostrea gigas (pacific oyster), Mya truncata (soft shell clam), Mytilus edulis (blue mussel) and Pecten maximus (king scallop) were extracted and analysed using standardized extraction protocol and proteomic pipeline. This enables us to identify critical elements of basic biomineralization tool kit for calcification process irrespective of their shell morphology, mineralogy and microstructure. In addition, it enables the identification of SMPs that are specific to calcite and aragonite mineralogies. The signifiant numbers of SMPs found species-specific were hypothesized as adaptation to their modus vivendi. In fact, the latter proteins possess immunity-related functions and fit into specific pathway, phenoloxidase, suggesting their role in defense against pathogen. The comparative study of shell proteome of mussels living in full marine condition, North Sea and the Iow saline Baltic Sea showed the modulation of the SMPs that constitute the basic biomineralization tool kit. Higher modulation of chitin related proteins and non-modulated protein such as carbonic anhydrase, EGF and fibronectin domain containing proteins points out the impaired scaffold and mineral nucleation process in Baltic mussel. The modulation of immunity related proteins denote the influence of biotic components. These investigations show the functional diversity of SMPs and their roles beyond shell formation in the bivalvesand put forth the idea that shell is dynamic, endowed with both biochemical and mechanical protection.

Dentre os diversos processos de formação de mineral em organismos vivos, a formação do tecido ósseo é um exemplo particular, uma vez que fosfatos de cálcio, na forma de hidroxiapatita, são produzidos em meio a fibrilas de colágeno na matriz extracelular de células osteogênicas; processo este regulado por um complexo enzimático. A fosfatase alcalina tecido não-específico (TNAP) desempenha um papel fundamental na histogênese óssea, responsável principalmente pela produção de fosfato inorgânico necessário para a formação dos minerais. Diversas abordagens experimentais permitem a reconstituição desta enzima em sistemas miméticos de membrana celular, dentre os quais, os filmes Langmuir-Blodgett (LB), que possibilitam a formação de materiais com propriedades osteoindutoras. No presente estudo, foi investigada a imobilização desta enzima em filmes LB sobre suportes de Ti. O ácido dimiristoil fosfatídico foi o fosfolipídeo utilizado na confecção dos filmes LB, obtendo um regime de deposição linear de massa em função do número de camadas depositadas em subfases de CaCl2. A TNAP foi imobilizada nos filmes através de duas metodologias: a partir da adsorção física da enzima aos filmes LB pré-transferidos a um suporte sólido, ou ainda por meio da construção do filme a partir de uma monocamada mista de DMPA/Ca2+/TNAP. Em ambas as metodologias adotadas, foi obtida uma diminuição drástica da atividade fosfohidrolítica da forma imobilizada da enzima, em relação à sua atividade obtida em meio homogêneo. Ao expor suportes de Ti modificados com os filmes LB em uma solução contendo íons Ca2+ e ATP como fonte de fosfato inorgânico, foi observada a formação de uma maior quantidade de mineral para as amostras contendo a TNAP imobilizada; atribuída a uma maior supersaturação local de íons fosfato devido a maior hidrólise de ATP na presença da enzima, demonstrando a capacidade desta em conferir à superfície modificada uma maior capacidade na indução de formação de mineral. Após este ensaio de mineralização in vitro, foi obtida uma maior hidrofilicidade das superfícies recobertas com os filmes LB na presença da TNAP, tornando estas superfícies modificadas mais bioativas. A presença dos filmes LB mistos de lipídeo/TNAP nas superfícies permitiram a adesão, proliferação e recobrimento homogêneo de células osteogênicas, que posteriormente promoveram o extravasamento de fibrilas proteicas e a formação de nódulos de mineralização. Estes resultados são importantes na confecção de materiais que acelerem o processo de osteoindução. / Among all the processes of mineral formation in living organisms, the osseous tissue formation is a particular example, since that calcium phosphates as hydroxyapatite are produced among collagen fibrils at the extracellular matrix of osteogenic cells, being this process regulated by an enzymatic complex. The tissue nonspecific alkaline phosphatase (TNAP) plays a central role on the osseous histogenesis, responsible mainly for the inorganic phosphate production necessary for mineral formation. Various experimental approaches allows this enzyme reconstitution in cellular membrane mimetic systems, among which, the Langmuir-Blodgett films (LB), that allows the formation of materials with osteoinductive properties. With that in mind, the immobilization of that enzyme in titanium supports modified with LB films was investigated. The dimyristoyl phosphatidic acid was the phospholipid used in the LB film construction, obtaining a linear deposition-layer numbers relation in CaCl2 subphases. The TNAP was immobilized at the films through two main methodologies: from the physical adsorption of the enzyme to the LB film pre-constructed on a solid support, or through the film construction from the mixed DMPA/Ca2+/TNAP monolayer. At both the adopted methodologies, it was obtained a diminishment at the phosphohidrolytic activity of the immobilized enzyme, comparing to its activity at homogeneous media. Exposing the Ti supports with the LB films in a solution containing Ca2+ ions and ATP as a phosphate source, it was observed a higeher mineral formation to the samples containing the immobilized TNAP, possibly due to a higher phosphate ions supersaturation from the higher ATP hydrolysis at the presence of the enzyme, demonstrating the capacity of the TNAP in promoting a higher mineral formation induction to the modified surface. After this in vitro mineralization assay, it was obtained surfaces more hydrophilic at presence of the LB films containing TNAP, making those modified surfaces more bioactive. The mixed LB films presence at the surfaces allowed the adhesion, proliferation and homogeneous covering of osteogenic cells, that posteriorly promoted the production of proteic fibrils and mineralization nodules. Those results are important in order to construct materials more osteointegrative.

Conchas do molusco Physa sp., um gastrópode (caracol) comum de aquários de água doce, serviram como modelo para o estudo de alguns aspectos envolvidos na biomineralização. A concha calcária é constituída por cristais de carbonato de cálcio depositados em associação com uma matriz orgânica. Os componentes cristalinos e a matriz, foram estudados por microscopia eletrônica de transmissão e de varredura, e caracterizados por métodos espectroscópicos e analíticos. A constituição cristalina, em geral, assemelha-se àquela existente na maioria dos moluscos, enquanto a camada nacarada, interna da concha, apresenta comparativamente maiores variações. A matriz orgânica consta de um componente insolúvel, essencialmente constituído por polissacarídeos, enxofre e fósforo; e outro componente solúvel, com predominância de serina, glicina, ácido aspártico e ácido glutâmico. A análise feita por ativação de nêutrons demonstrou maior concentração de cálcio, sódio e estrôncio; estes elementos estão geralmente relacionados à presença de aragonita, em outras conchas de moluscos. O estudo qualitativo da fase cristalina foi realizado por difração eletrônica e por espectroscopia de infravermelho. Para análise quantitativa, usou-se a difração de raios-X, sendo os dados refinados pelo método de Rietveld. Os resultados obtidos demonstram a existência de dois polimorfos do carbonato de cálcio, aragonita e calcita, na concha da Physa. A caracterização qualitativa dos componentes inorgânico e orgânico do material estudado, mostrou semelhanças com relação a outros gêneros de moluscos. Experimentos de cristalização do carbonato de cálcio in vitro produziram aragonita e vaterita em presença de ácido aspártico ou glutâmico. Sob ação de glicina, serina ou quitina, houve formação de calcita. Em presença da matriz orgânica insolúvel, houve cristalização de calcita, enquanto a matriz solúvel induziu a cristalização da aragonita. Analisou-se quantitativamente todas as fases cristalinas obtidas nestes experimentos e estudou-se a morfologia dos cristais formados através da MEV e por MO luz. O resultado comparativo das investigações usando a concha natural, e dos cristais sintetizados, permitiu confirmar o papel fundamental da matriz orgânica no processo de cristalização do carbonato de cálcio. / Shells of Physa sp., a common freshwater gastropod snail, were used as a model for mineralization studies of calcium carbonate. The shell is a biomineral that consists of organized crystalline deposits associated to an organic matrix, both of which were studied by transmission and scanning electron microscopy; they were further characterized by means of pectroscopic and analytical methods. As a whole, its structural organization does not differ greatly from that found in other mollusc shells, except for the innermost, nacreous layer, that lines the shell. The organic matrix in Physa was found to consist of an insoluble fraction, essentially containing a polysaccharide, sulphur and phosphor. In addition, another (soluble) fraction is present, in which serine, glycine, aspartic acid and glutamic acid residues prevail. Neutronic activation analysis demonstrates a high concentration of calcium, sodium and strontium, elements known to be related to the presence of aragonite in other molluscan shells. A qualitative study of the crystalline phase was obtained through use of electron diffraction and FTIR spectroscopy. For quantitative analysis X-ray diffraction was used, as refined by the Rietveld method. Results obtained demonstrate the existence of two calcium carbonate polymorphs, aragonite and calcite in the shell of Physa, Qualitative evaluation of both organic and inorganic material from Physa showed similarities to those found in other mollusk shells. In vitro experiments performed at similar-to-natural conditions, on crystallization of calcium carbonate, did also crystallize aragonite and vaterite, provided aspartic acid or glutamic acid were present; whereas calcite was formed in solutions containing glycine, serine or chitin. Aragonite did crystallize when the soluble organic matrix was added to the solution. All these crystalline phases obtained were quantitatively evaluated, their morphologies being studied through light and electron microscopies. A comparative study of the natural crystals from the shell, and those obtained in laboratory experiments, stresses the fundamental role of the organic matrix on calcium carbonate crystallization

A indústria da construção civil é conhecida como umas das atividades econômicas que causam os maiores impactos ambientais desde o processo de extração da matéria prima até a produção dos produtos, incluindo o transporte e manutenção do ambiente construído. A produção de um dos seus principais componentes, o cimento, é o maior contribuinte para a emissão de gases de efeito estufa, principalmente devido a queima de combustíveis fósseis. Por este motivo, pesquisas na área de biotecnologia sustentável são conduzidas para diminuir e até mitigar os efeitos danosos provocados pelos fatores que compõem a construção civil. Dentre estas pesquisas destacam-se as que se baseiam na Biomimética, que é uma ciência que busca na Natureza as soluções tecnológicas para os problemas que os desenvolvimentos humanos geralmente apresentam: a geração de resíduos poluentes, uso de produtos químicos tóxicos e processos que operam com energia e pressão elevadas. Com base nos conceitos biomiméticos, este trabalho se propôs a estudar a biomineralização, que é um processo que ocorre na Natureza a milhares de anos e é responsável pela formação de muitas estruturas biomineralizadas tanto no ambiente terrestre como aquático. A biomineralização é um fenômeno provocado pela ação de diversas espécies de microrganismos que durante o processo de obtenção de energia reciclam minerais presentes no solo e na água e os precipitam na forma de sais inorgânicos. Este material precipitado age como agente ligante de partículas como no caso de formações geológicas (estromatólitos) ou exoesqueletos de animais marinhos, por exemplo. Neste estudo foi avaliado a biomineralização por biodeposição de carbonato de cálcio precipitado na presença da espécie de bactéria ureolítica (Bacillus subtilis) em ensaios em escala laboratorial utilizando corpos de prova de areia, argamassa e concreto. Os corpos de prova em areia e argamassa foram observados em MEV e EDS permitindo a identificação de células de microrganismos, formação de biofilme e provável formação de cristais de carbonato de cálcio na região de biofilme. Os corpos de prova de concreto foram utilizados para avaliar as consequências da biodeposição na absorção de água por capilaridade do material. Resultados indicam redução de 20% na absorção de água por capilaridade. Com os resultados obtidos é possível concluir que a técnica de biodeposição pode ser uma alternativa ao tratamento superficial de estruturas de concreto, contudo requer estudos posteriores de aplicação técnica e viabilidade econômica. / The construction industry has been known as one of the economic activities that cause the major environment impacts since the process of raw material extraction until the products manufacturing including transport and maintenance of the built environment. The production of one of the main compounds, the cement, is the largest contributor to the greenhouse gas emissions, mainly due to burn fossil fuels. For this reason, researches in sustainable biotechnological area are conducted to minimize and even mitigate the damaging effects either promoted by construction industry factors. Among these ones, it stands out researches based on Biomimetic, which is a science that seeks in Nature the technological solutions for problems that human’s development usually presents: the generation of pollutant residues, the use of toxic chemicals and process that operates in high pressure and energy. Based on biomimetic concepts this research proposes to study the biomineralization, which is a process that has occurred in the Nature for thousands of years and it is responsible for the formation of many structures either in soil and water environments. The biomineralization is a phenomenon caused by several specimens of microorganisms that during the process of obtaining energy, they recycle minerals presents at soil and water inducing precipitation as inorganic salts. This precipitated material works as a binder of particles similar to geologic formations (stromatolites) or exoskeleton of sea animal for example. In this study the biomineralization was evaluated through biodeposition of precipitated calcium carbonate by specimen of ureolytic bacteria (Bacillus subtilis). Essays were held using samples made by sand, mortar and concrete. The samples made by sand and mortar were observed at MEV and EDS, allowing the identification of microorganism cells, biofilm formation and probable formation of calcium carbonate crystals at biofilm region. The concrete samples were used to evaluate the consequences of biodeposition on water absorption by capillarity of the material. The results show reduction of 20% on water absorption by capillarity. According the results achieved it possible to conclude that the biodeposition technique can be an alternative to superficial treatment for concrete structures. However, it will be required more studies to evaluate technical application and economical availability.

In the future the demand for ethanol is expected to increase greatly due to the rising energy requirements in the world. Lignocellulosic materials are a suitable and potentially cheap feedstock for sustainable production of fuel ethanol, since vast quantities of agricultural and forest residues are available in many countries. However, there are several problems involved in the utilization of lignocellulosic raw materials as sugar source. The most common way of releasing the simple sugars in the material is by dilute acid hydrolysis. This procedure is relatively simple and cheap, but in addition to the sugars it creates inhibitory compounds. These inhibitors make it very hard for the yeast to ferment the hydrolyzate and detoxification is often necessary. One way to overcome this problem is to encapsulate the yeast. Encapsulation is an attractive method since it improves the cells stability and inhibitor tolerance, increases the biomass amount inside the reactor, and decreases the cost of cell recovery, recycling and downstream processing. However, the method does not yet permit long-term cultivation since the capsules used so far are not robust enough. Therefore more studies have to be conducted in order to find methods which produce mechanically robust capsules. The main goal of this paper is to find a suitable method to produce robust capsules using different concentration of the chemicals at different pH and also implementing some modifications such as addition of cross-linkers in preparation procedure. In this paper comparison of three different encapsulation techniques were studied based on the mechanical robustness of the capsules. The three different techniques were calcium mineralized alginate-chitosan capsules, alginate capsules coated with 2% chitosan (2% AC) and genipin crosslinked alginate-chitosan (GCAC) capsules. The results indicate that GCAC capsules are most robust and were good enough for prolonged use since most of the capsules were not deformed in mechanical strength test. There were slight differences in the diameter and membrane thickness before and after swelling. No negative influence was observed on the yeast growth when applying the cross-linker. The results of this study will hopefully add valuable information and helps in further studies using other cross-linkers to prepare robust capsules. / Program: Industrial Biotechnology

Biomineralization refers to the production of mineralized tissues by organisms. The fine control which organisms can exert over this process produces crystals with morphologies and properties contrasting to that of non-biogenic crystals and specifically altered to suit the required functional need. A key model system of biomineralization are a unicellular marine algae, coccolithophores, which produce calcium carbonate scales known as coccoliths. These coccoliths are comprised of arrangements of single crystals of calcite interlocked to form a plate-shaped structure. Coccoliths are developed intracellularly in a specialised compartment called the coccolith vesicle, before being extruded to the cell surface. In this work, two vital components of the coccolith biomineralization process are investigated - a soluble polysaccharide thought to act as a habit modifier and an insoluble organic scaffold known as a baseplate that provides the surface for nucleation and growth of the crystals. Whilst both these elements are thought to play a key part in the biomineralization process, the role of each is not fully understood. To investigate the effect of coccolith-associated polysaccharides (CAPs) on nucleation and polymorph selection, two systems that promote different polymorphs of calcium carbonate were utilised. In both systems, the intracrystalline polysaccharide fraction extracted from one species, Gephyrocapsa oceanica, was able to promote calcite nucleation in vitro, even under conditions favouring the kinetically-privileged polymorphs of calcium carbonate: vaterite and aragonite. As this property is not observed with CAPs extracted from its 'sister species', Emiliania huxleyi, the in vivo function of CAPs may differ between the two species. Both cryo-transmission electron microscopy (cryoTEM) and scanning electron microscopy (SEM) were used to determine the mechanism of calcite growth in the presence of G. oceanica CAPs, showing its impact on the forming amorphous calcium carbonate (ACC), decreasing the size of the particles and producing irregular, angular particles. Using cryo-electron tomography (cryoET), it was possible to create a 3D representation of the structure of the baseplate from the coccolithophore Pleurochrysis carterae, revealing its two-sided organisation. Examination of several stages of the coccolith growth process demonstrated the interlocking nature of the calcite crystals that make up the coccolith and the progression of the crystal morphologies over time, and the interaction of these crystals with the baseplate rim. Additionally, the effect of inhibiting carbonic anhydrase (CA), an enzyme involved in the regulation of carbonate species, revealed that inhibition of CA can affect coccolithogenesis as well as cell proliferation.