Several nanomaterials systems, both inorganic and organic in nature, have been extensively investigated by a number of characterization techniques including atomic force microscopy (AFM), electron microscopy, Fourier transform infrared spectroscopy (FTIR), and energy dispersive x-ray spectroscopy (EDX). The first system consists of boron nitride nanotubes (BNNTs) synthesized via two different methods. The first method, silica-assisted catalytic chemical vapour deposition (SA-CVD), produced boron nitride nanotubes with different morphologies depending on the synthesis temperature. The second method, growth vapour trapping chemical vapour deposition (GVT-CVD), produced multiwall boron nitride nanotubes (MWBNNTs). The bending modulus of individual MWBNNTs was determined using an AFM three-point bending technique, and was found to be diameter-dependent due to the presence of shear effects. The second type of nanomaterial investigated is the biomineralized calcareous shell of the serpulid Hydroides dianthus. This material was found to be an inorganic-organic composite material composed of two different morphologies of CaCO3, collagen, and carboxylated and sulphated polysaccharides. The organic components were demonstrated to mediate the mineralization of CaCO3 in vitro. The final system studied is the proteinaceous cement of the barnacle Amphibalanus amphitrite. The secondary structure of the protein components was investigated via FTIR, revealing the presence of β-sheet conformation, and nanoscale rod-shaped structures within the cement were identified as β-sheet containing amyloid fibrils via chemical staining. These rod-shaped structures exhibited a stiffer nature compared with other structures in the adhesive, as measured by AFM nanoindentation.

The discovery of deep-sea chemosynthesis-based ecosystems including hydrothermal vents and cold seeps has greatly expanded our view of life on Earth. Nevertheless, for many benthic organisms in these ecosystems, little is known about where they come from, how scattered populations are connected by larval dispersal, and how they adapt to the local environments. Mussels of Bathymodiolus platifrons (Bivalvia: Mytilidae) are one of the dominant and foundation species in deep-sea chemosynthesis-based ecosystems. They are known to have a wide geographic distribution, and are also one of the few deep-sea species capable of living in both hydrothermal vents [in Okinawa Trough (OT)] and methane seeps [in the South China Sea (SCS) and Sagami Bay (SB)]. Previous population genetics studies of B. platifrons mostly relied on one to several genes, which suffered from the lack of sensitivity required to resolve their fine-scale genetic structure, and were unable to reveal their adaptation to the local environments. With the repaid development of molecular techniques, it is now possible to address their demographic mechanisms and local adaptation from a genome-wide perspective. Therefore, in the first part of my thesis, I aimed to generate genome-wide single nucleotide polymorphisms (SNPs) for B. platifrons via a combination of genome survey sequencing and the type IIB endonuclease restriction-site associated DNA (2b-RAD) approach, assess the potential use of SNPs in detecting fine-scale population genetic structure and signatures of diversifying selection, as well as their cross-species application in other bathymodioline mussels. Genome survey sequencing was conducted for one individual of B. platifrons. De novo assembly resulted in 781 720 sequences with a scaffold N50 of 2.9 kb. Using these sequences as a reference, 9307 genome-wide SNPs were identified from 28 B. platifrons individuals collected from a methane seep in the SCS and a hydrothermal vent in the middle OT (M-OT), with nine outlier SNPs showed significant evidence of diversifying selection. The small FST value (0.0126) estimated based on the neutral SNPs indicated high genetic connectivity between the two populations. However, the permutation test detected significant differences (P < 0.00001), indicating the two populations having clearly detectable genetic differentiation. The Bayesian clustering analyses and principle component analyses (PCA) performed based on either the neutral or outlier SNPs also showed that the two populations were genetically differentiated. This initial study successfully demonstrated the applicability of combining genome sequencing and 2b-RAD in population genomics studies of B. platifrons. Besides, using the survey genome of B. platifrons as a reference, a total of 10 199, 6429, and 3811 single nucleotide variants (SNVs) were detected from three bathymodioline mussels Bathymodiolus japonicus, Bathymodiolus aduloides, and Idas sp. These results highlighted the potential of cross-species and cross-genus applications of the B. platifrons genome for SNV/SNP identification among different bathymodioline lineages, which can be further used in various evolutionary and genetic studies. To have a deeper understanding of how individuals of B. platifrons are connected among and adapt to their habitats, in the second part of my thesis, I used both mitochondrial genes and genome-wide SNPs to conduct a more comprehensive population genetics/genomics study of B. platifrons. Three mitochondrial genes (i.e. atp6, cox1, and nad4) and 6398 SNPs generated by 2b-RAD were obtained from 110 B. platifrons individuals from six representative locations along their known distribution range in the Northwestern Pacific. The small FST values based on both types of genetic markers all revealed high genetic connectivity of B. platifrons, which may have been driven by the strong ocean currents (i.e. Kuroshio Current, North Pacific Intermediate Water). However, when using SNP datasets rather than mitochondrial genes, individuals in the SCS were identified as a distinct genetic group, indicating the Luzon Strait may serve as a dispersal barrier that limits their larval exchange between the SCS and the open area in the Northwestern Pacific. Moreover, a genetic subdivision of B. platifrons in the southern OT (S-OT) from those in M-OT and SB was observed when using 125 outlier SNPs for data analyses. The outlier-associated proteins were found to be involved in various biological processes, such as DNA and protein metabolism, transcription and translation, and response to stimulus, indicating local adaptation of B. platifrons even they are confronted with extensive gene flow in the OT-SB region. Furthermore, by using SNP datasets, populations in S-OT were revealed to be the source of gene flow to those in the SCS, M-OT, and SB. Overall, these results offered novel perspectives on the potential forces that may have led to the genetic differentiation and local adaptation of B. platifrons, which can serve as an example for other deep-sea species with high dispersal potential, and contribute to the designation of marine protected areas and conservation of deep-sea chemosynthesis-based ecosystems. Molluscan shell formation is one of the most common and abundant biomineralization processes in metazoans. Although composed of less than 5 wt% of the molluscan shells, shell matrix proteins (SMPs) are known to play multiple key roles during shell formation, such as providing a gel-like micro-environment to favour mineral precipitation, promoting crystal nucleation, as well as guiding and inhibiting crystal growth. To date, all studies on SMPs have focused on molluscs in terrestrial and shallow-water ecosystems with no reports for those living in the deep ocean. Herein, the third part of my thesis was to study the shell proteomes of B. platifrons and its shallow-water relative Modiolus philippinarum with the aim to bridge such knowledge gaps in biomineralization studies. A total of 94 and 55 SMPs were identified from the shell matrices of B. platifrons and M. philippinarum, respectively, with 31 SMPs shared between two species. These SMPs can be assigned into six broad categories, comprising calcium binding, polysaccharide interaction, enzyme, extracellular matrix-related proteins, immunity-related proteins, and those with uncharacterized functions. Many of them, such as tyrosinases, carbonic anhydrases, collagens, chitin-related proteins, peroxidases, as well as proteinase and proteinase inhibitor domain-containing proteins, have been widely found in molluscan shell matrices and other metazoan calcified tissues (e.g. exoskeletons of corals, tubes of tubeworms), whereas some others, such as cystatins, were found for the first time in molluscan shell matrices, and ferric-chelate reductase-like proteins and heme-binding proteins were to be detected for the first time in metazoan calcified tissues. This is the first report of the shell proteome of deep-sea molluscs, which will support various follow-up studies to better understand the functions of these SMPs, especially in relation to environmental adaptation. Overall, my population genetics/genomics studies have improved our understanding of the population dynamics, genetic connectivity, fine-scale genetic structure, and local adaptation of B. platifrons in the Northwestern Pacific, and my proteomics study has shed light on the biomineralization processes of molluscs in the deep ocean.

El hierro es un elemento fundamental para la vida, siendo imprescindible en procesos vitales como el transporte de oxígeno, la transferencia de electrones, reacciones enzimáticas, metabolismo aeróbico, la fotosíntesis o la fijación de nitrógeno. Dada la relevancia de este elemento en rutas metabólicas centrales para el desarrollo de la vida, no nos tiene que sorprender el gran número de enfermedades que están asociadas a problemas relacionados con el metabolismo del hierro. Las especies patológicas con hierro que aparecen en el marco de algunas enfermedades son materiales nanométricos cuya caracterización presenta grandes dificultades. El conocimiento en detalle de estas especies puede tener gran relevancia en situaciones tan diferentes como la mejora de técnicas de diagnóstico de la malaria o el tratamiento de enfermedades neurodegenerativas. / Iron is a fundamental element for life, being essential in vital processes such as oxygen transport, electron transfer, enzymatic reactions, aerobic metabolism, photosynthesis or nitrogen fixation. Given the relevance of this element in metabolic routes central to life development, it is unsurprising that a great number of pathologies are linked to iron metabolism problems. Iron pathological species that appear in the frame of some diseases are nanometric materials, whose characterization presents huge difficulties. Detailed knowledge of these species may have great relevance in different problems such as the improvement of malaria diagnostic techniques or the treatment of neurodegenerative diseases.

O processo de biomineralização óssea é a deposição de cristais de fosfato de cálcio, na forma de hidroxiapatita formando o tecido ósseo. São mediados pelas vesículas da matriz (MVs) que são liberadas no local específico do início da biomineralização. As MVs contêm altas concentrações de íons Ca2+ e fosfato inorgânico (Pi), proporcionando um microambiente adequado para a formação inicial e propagação dos cristais de hidroxiapatita. Para que isso ocorra corretamente são necessárias diversas proteínas/enzimas, bem como microambientes com condições específicas. Neste trabalho uma atenção especial foi dada a duas proteínas presentes nas MVs: Anexina V (AnxA5) e a nucleotídeo pirofosfatase/fosfodiesterase-1 (NPP1). A Anexina V é responsável pela formação de um canal de cálcio por meio da associação desta proteína tanto com a face externa quanto interna da membrana das MVs. A NPP1 possui a função principal de hidrolisar adenosina trifosfato (ATP), formando adenosina monofosfato (AMP) e pirofosfato (PPi). Assim, experimentos de expressão de Anexina V e NPP1 foram realizados com o intuito de iniciar os estudos de interação entre as duas proteínas, por meio de reconstituição em lipossomos. A expressão de Anexina V foi realizada em células E. coli BL21(DE3) e induzida por isopropil -D-1-tiogalactopiranosídeo (IPTG); para purificação, três procedimentos foram necessários, utilizando coluna de níquel, coluna Desalting e coluna de troca iônica (Mono-Q). Experimentos de dicroísmo circular foram realizados com amostras de Anexina V após purificação e mostraram que todas as amostras apresentavam estruturas em -hélice. Pelo método da gota pendente foi estudada a interação de Anexina V com íons Ca2+ (10 mM) em monocamadas constituídas por dipalmitoil fosfatidilcolina (DPPC) e de uma mistura de composição lipídica 9:1 de DPPC e dipalmitoil fosfatidilserina (DPPS). Os dados obtidos mostraram alta afinidade de Anexina V por monocamadas constituídas de (9:1) DPPC:DPPS na presença de íons Ca2+. A expressão de NPP1 foi realizada com transfecção por meio de eletroporação do DNA recombinante em células COS-1, e seleção com antibiótico G418 após 24 horas de cultivo. Amostras de fração de membrana controle e NPP1 recombinante foram preparadas após 60 horas de cultivo celular e foi observada atividade catalítica na amostra de fração de membrana da NPP1. Todas as amostras de expressão, tanto de Anexina V e NPP1, foram analisadas por eletroforese em gel de poliacrilamida. A padronização da Anexina V foi obtida com sucesso, porém com relação à NPP1, experimentos ainda devem ser realizados a fim de padronizar a obtenção desta proteína recombinante em quantidade suficiente para continuar os estudos. / The bone biomineralization process is the deposition of calcium phosphate crystals in the form of hydroxyapatite forming the bone tissue. They are mediated by matrix vesicles (MVs) that are released at the specific site of the onset of biomineralization. MVs contain high concentrations of Ca2+ ions and inorganic phosphate (Pi), providing a suitable microenvironment for the initial formation and propagation of hydroxyapatite crystals. To occur properly, several proteins/enzymes are needed, as well as microenvironments with very particular conditions. In this work, special attention should be given to two proteins present in the MVs: Annexin V (AnxA5) and nucleotide pyrophosphatase/ phosphodiesterase (NPP1). Annexin V is responsible for the formation of a calcium channel through the association of this protein with both the outer and the inner face of the MVs membrane. NPP1 has the main function of hydrolyzing adenosine triphosphate (ATP), adenosine monophosphate (AMP) and pyrophosphate (PPi).Thus, experiments of expression of Annexin V and NPP1 were performed with the aim of initiating the interaction studies between the two proteins, through reconstitution in liposomes. Annexin V expression was performed in E.coli BL21 (DE3) and the cells were induced by isopropyl -D-1-thiogalactopyranoside (IPTG); for purification, three procedures were required using a nickel column, a Desalting column and an ion exchange column (Mono-Q). Circular dichroism experiments were performed with Annexin V samples after purification and showed that all samples contain -helix structures. Using the pendant drop method, the interaction of Annexin V with (10 mM) Ca2+ ions was studied in monolayers composed of dipalmitoyl-phosphatidyl-choline (DPPC) and a mixture of lipid composition 9:1 DPPC and dipalmitoyl-phosphatidyl-serine (DPPS). Data showed high affinity of Annexin V by monolayers constituted of (9: 1) DPPC:DPPS in the presence of Ca2+ ions. NPP1 expression was performed with transfection by electroporation of the recombinant DNA into COS-1 cells and selection with G418 antibiotic after 24 hours of culture. Samples of the control membrane fraction and recombinant NPP1 were prepared and the activity of the membrane fraction of NPP1 was observed in the samples. All expression samples, both AnxA5 and NPP1, were analyzed by polyacrylamide gel electrophoresis. The standardization of Annexin V has been obtained with success, but regarding NPP1, experiments have yet to be performed to standardize the production of this recombinant protein and to obtain enough quantity to continue the study.

Muitos organismos vivos, tal como seus constituintes, são formados por sistemas químicos complexos que envolvem a interação entre compostos orgânicos e inorgânicos ligados química e/ou fisicamente. Nestes sistemas as matrizes orgânicas são geralmente compostas por macromoléculas como polissacarídeos e proteínas. Essas moléculas têm o papel de direcionar a nucleação e o crescimento da porção inorgânica. O uso de superfícies metálicas adequadas recobertas por este tipo de filme híbrido tem potencial aplicação em implantes de substituição óssea, no qual são requeridas superfícies quimicamente inertes, mas que ao mesmo tempo estimulem processos de calcificação. Nesta tese estudou-se o crescimento de CaCO3 sobre superfícies metálicas de alumínio e aço inox recobertas por matrizes orgânicas compostas por diferentes poliânions e pelo policátion quitosana, na forma de filmes montados camada-a-camada (do inglês LbL), na presença ou não de fosfolipídeos (filmes Langmuir-Blodgett), formando um meio confinado para o crescimento do mineral. Diferentes técnicas foram utilizadas: microscopia eletrônica, microscopia de força atômica, espectroscopias de reflexão nas regiões do Uv-vis, e do infravermelho, Raman, espalhamento e difração de raios-X. Estudou-se a influência de diferentes grupos carregados dos fosfolipídeos e dos poliânions, tal como sua conformação, no crescimento de CaCO3. O tipo de interação entre o poliânion e a quitosana leva ao crescimento de matrizes poliméricas com diferenças em suas espessuras e capacidade de retenção de líquido, modificando as condições de supersaturação local e influenciando no tipo de estrutura de CaCO3. Puderam ser identificados dois polimorfos formados sobre os filmes orgânicos de poli(ácido acrílico) e quitosana, sugerindo que existem dois diferentes sítios onde a nucleação pode ser iniciada: a partir da solução de CaCl2 aprisionada na matriz polimérica e o outro a partir dos íons cálcio ligados como contra-íons aos grupos negativamente carregados do poliânion. Na presença do pré-recobrimento LB, a natureza da cabeça polar do fosfolipídeo direciona o tipo de ligação e crescimento da matriz polimérica, que levam ao crescimento de partículas de CaCO3 com morfologia e tamanho variados, explicados em termos da presença de ambientes com diferenças de concentrações locais de Ca2+. Além disso, verificou-se que a rugosidade superficial dos suportes metálicos pode favorecer a formação do polimorfo de CaCO3 cineticamente mais estável, mostrando que o processo de cristalização sobre estes suportes é um processo governado por difusão. A hidrofilicidade dos suportes é aumentada pela presença da matriz orgânica e pela presença de CaCO3 sobre as matrizes. O crescimento de CaCO3 em meios confinados tridimensionais, formados por membranas de policarbonato modificadas com filme finos de polieletrólitos, também foi estudado. Este tipo de molde leva à formação de estruturas cilíndricas que seguem a morfologia dos poros da membrana. A presença de poli(ácido acrílico) leva a formação de estruturas cilíndricas ocas, enquanto que cilindros completamente preenchidos foram formados nos poros contendo quitosana na última camada. Estes resultados foram explicados com base em diferenças na etapa de nucleação: na presença de PAA a nucleação de CaCO3 deve iniciar-se a partir dos íons Ca2+ ligados ao poliânion que, por sua vez, está ligado diretamente às paredes do molde; já na presença que quitosana, com maior capacidade de retenção de liquido e sem interação específica com Ca2+ a nucleação e seqüente cristalização devem ocorrer por todo o poro da membrana. As estruturas formadas são em sua maioria monocristais de calcita hexagonal orientadas na direção cristalográfica <2 -2 1>. / Some living organisms as well as their constituents are formed by complex chemical systems which involves the interaction among organic and inorganic compounds bounded physically or chemically. In these systems the organic matrices are usually composed by macromolecules like polysaccharides and proteins. These molecules have an important hole in tailoring the nucleation and the sequent growth of the inorganic portion. Metallic surfaces coated with these hybrid films have potential application as implants for bone substitution for which the surfaces must be chemically inert but at the same time they should stimulate calcification processes. In this present thesis we studied the growth of CaCO3 over aluminium and stainless steal surfaces coated with layer-by-layer films composed by different polyanions and chitosan as polycation, in the presence or not of phospholipids (Langmuir-Blodgett films). These organic matrices formed a confined medium within which CaCO3 particles were growth. Different techniques were applied in order to understand these systems: electronic microscopy, atomic force microscopy, UV-Vis and infrared reflection spectroscopy, Raman, and X-ray scattering and diffraction. We studied the influence of the different charged groups of the phospholipids and the polyanion as well as their conformation on CaCO3 growth. The type of interaction between the polycation and the polyanions tailors the growth of the organic matrices, forming films with different thickness and different water retention abilities which change the local supersaturation conditions changing the structure of the CaCO3 formed. Two types of CaCO3 polymorphs were growth over poly(acrylic acid) (PAA) and chitosan films suggesting that there are two sites where the nucleation can be started: the CaCl2 solution retained in the gel-like organic films and the Ca2+ ions bounded to the negative groups of the polyanion. In the presence of the LB pre-coating, the nature of the phospholipid polar head tailors the binding and the growth of the polymeric matrices leading to the formation of CaCO3 particles with difference in their sizes and morphologies. This result was explained in basis of the differences in the Ca2+ local concentrations in each situation. Moreover, it was observed that the surface roughness of the supports can favour the formation of vaterite, the kinetically most stable CaCO3 polymorph, showing that the crystallization may be guided by diffusion processes. The hidrophilicity of the supports was improved by the presence of both organic and hybrid films. The growth of CaCO3 in tridimentional confined mediums was done using LbL modified polycarbonate membranes as template. This template leads to the formation of cylindrical CaCO3 particles following the morphology of the membrane pores. CaCO3 tube-like structures were formed in presence of PAA, while rod-like structures were formed in presence of chitosan in the top LbL layer. These results were explained on basis of the difference in the nucleation stages: in the presence of PAA the nucleation starts on the Ca2+ ions bounded to the polyanion that is linked to the walls of the template; in the presence of chitosan that presents higher water retention ability and has no specific interaction with Ca2+ ions, the nucleation and sequent crystallization should occur through the entire pore of the membrane. The electron diffraction patterns showed that the CaCO3 structures are single crystals of the calcite polymorph oriented in < 2 -2 1> crystallographic direction.

Molecular self-assembly is the process of molecules able to associate into more ordered structures. Examples of self-assembling molecules is a class of ultrashort amphiphilic peptides with a distinct sequence motif, which consist of only three to seven amino acids. These peptides can self-assemble to form nanofibrous scaffolds, such as in form of hydrogels, organogels or aerogels, due to their amphiphilic structure which contains a dominant hydrophobic tail and a polar head group. Interestingly, these peptide scaffolds offer a remarkably similar fiber topography to that one found in collagen which is a dominant part of the extracellular matrix. The resemblance to collagen fibers brings a potential benefit in using these peptide scaffolds together with native human cells. Specifically, they can maintain high water content over 99 % weight per volume and are suitable for tissue engineering and regenerative medicine applications. Over the last decade, they have shown promising therapeutic potential in treating several diseases thanks to their high activity, target specificity, low toxicity, and minimal nonspecific and drug-drug interactions. This dissertation describes how to characterize and use ultrashort amphiphilic peptides for tissue engineering and biomedicine. The first chapter offers an overview of already reported self-assembling ultrashort peptides and their applications. As a proof-of-concept, ultrashort peptide scaffolds were used for osteogenic differentiation. Peptide nanoparticles were embedded into 5 peptide hydrogels with the goal to tune the stiffness of the peptide gels. Furthermore, the peptide scaffold was used for the generation of gold and silver nanoparticles after UV irradiation, which allowed the production of nanoparticles in the absence of any additional reducing agent. The mechanism of the generation of these nanoparticles was then investigated. The last chapter describes how tetrameric peptide solutions were utilized for 3D bioprinting applications. Compared to earlier reported self-assembling ultrashort peptide compounds, these tetrapeptides can form hydrogels at an extremely low concentration of 0.1% w/v in a relatively short time under physiological conditions. These promising findings suggest that the peptide solutions are promising bioinks for use in 3D bioprinting.

No description available.

No description available.

Organisms have evolved a remarkable ability to mineralize complex skeletons and functional biomaterials. These structures are nucleated and grown in close associaiton with macromolecular assemblages of proteins and polysaccharides that are implicated in regulating all stagees of mineralization. Because of this intimate association of organic with inorgaic components, many studies have investigated the effects of particular organic species on mineral morphology, phase, and growth rate. However, the diversity and species-specific nature of the organic assemblages associated with biominerals across a wide variety of taxa, has limited our understanding of how organisms use biomolecules to regulate skeletal formation. It is clear that a mechanistic picture of biomolecular controls on mineralization requires molecular-level investigations of the interplay between organic and inorganic components at all stages of crystallizaiton. This dissertation presents the findings from theoretical and experimental studies of the physical mechanisms that underlie biomolecule controls on mineral formation. Molecular dynamics simulations probe the effects of acidic molecules on the hydration of alkaline earth cations. After first calculating baseline hydration properties for magnesium, calcium, strontium, and barium, I determine the effects of carboxylate-containing molecules on cation hydration state as well as the kinetics and thermodynamics of water exchange. Experimental work utilizes self-assembled monolayers as proxies for matrix macromolecules in order to understand their effects on CaCO3 nucleation kinetics and thermodynamics. Estimates of nucleation rates and barriers are made from optical microscopy data and correlated with measurements of crystal – substrate rupture force from dynamic force microscopy. These investigations show that an important function of biomolecules in directing mineralization lies in their ability to modulate cation hydration. Both chemical functionality and molecular conformation are influential in regulating the kinetics and thermodynamics of mineral nucleation, and these effects may be predicted by the strength of interaction between organic and inorganic components. These findings contribute to a mechanistic understanding of how organic matrices act to regulate biomineral formation. They demonstrate a plausible physical basis for how carboxyl-rich biomolecules accelerate the kinetics of biomineral growth and suggest roles for organic species in the nucleation and pre-nucleation stages of mineralization. / Ph. D.

Calcified skeletons are produced within complex assemblages of proteins and polysaccharides whose roles in mineralization are not well understood. Researchers have long postulated that living organisms utilize the macromolecules of organic matrices to actively guide the formation of crystal structures. The timing and placement of the subsequent minerals that form are most easily controlled during nucleation; however, a physical and chemical picture of how organic functional group chemistry influences the initial stages of nucleation is not yet established. These processes are further complicated by the realization that carbonate biominerals can form by an amorphous to crystalline transformation process, which has prompted the question of how chemical signatures are recorded during mineralization. Investigations of mineralization processes such as the kinetics of nucleation and the transformation of amorphous calcium carbonate (ACC) to crystalline products are critical to building a better understanding of biomineral formation. Only from that fundamental basis can one begin to decipher changes in climate and seawater chemistry over geologic time and by recent anthropogenic effects. This dissertation presents the findings from experimental studies of the thermodynamics and kinetics of multiple mineral formation processes, including nucleation and transformation from an amorphous phase. The kinetics of calcite nucleation onto a suite of high-purity polysaccharide (PS) substrates were quantified under controlled conditions. Nucleation rates were measured as a function of 1) supersaturation extending above and below ACC solubility and 2) ionic strength extending to seawater salinity. These conditions decipher the chemical interactions between the PS substrate, calcite crystal, and solution. These investigations show the energy barrier to calcite formation is regulated by competing interfacial energies between the substrate, crystal, and liquid. The energy barriers to nucleation are PS-specific by a systematic relationship to PS charge density and substrate structure that is rooted in minimization of the competing substrate-crystal and substrate-liquid interfacial energies. The data also suggest ionic strength regulates nucleation barriers through substrate-liquid and crystal-liquid interfacial energetics. In a second experimental study, stable isotope labeling was used to directly probe the transformation pathway. Four processes were considered: dissolution-reprecipitation, solid-state, or combinations of these end member processes. Isotope measurements of calcite crystals that transform from ACC have signatures that are best explained by dissolution-reprecipitation. The extent of isotopic mixing correlates with the amount of ACC transferred and the time to transformation, suggesting the calcite crystals are recording the changing local solution environment during the transformation. These investigations into different mineralization mechanisms build a framework for how functional group chemistries of organic molecules regulate mineralization and the resulting isotopic and elemental signatures in the calcite. This may provide useful insights to interpreting chemical signatures of carbonate biominerals in fossil record and understanding ocean chemistry changes throughout geologic time. / Ph. D.