Doctor of Philosophy, University of Akron, 2024, Integrated Bioscience

The scientific reciprocity of environmental geomicrobiology and biotechnology harnessing microbially induced carbonate precipitation (MICP) is epitomized by cave speleothem research; delineating environmental conditions uncovers factors that inform the development of industrial bacteriogenic mineralization processes, with greater control over the end products. Reconciling bacterial metabolism and CaCO3 precipitation has the potential to recontextualize geological precipitation events as microbial byproducts, warranting interdisciplinary investigation. In Wind Cave, South Dakota, I identified a complex weave of speleoclimatic, geochemical, and microbiological dynamics that controls the materialization and polymorphism of CaCO3 secondary deposits known as frostwork. Microclimatic monitoring and analysis suggested an evaporative environment, modelled from detailed temperature, humidity and airflow data. Airflow measurements support a causal link between cave wind directionality and the occurrence of frostwork. Sequential deposition of carbonate phases characterizes bulk frostwork formations according to shifting Mg2+/Ca2+ ratios over the speleothem lifetime, yielding multiaggregate formations consisting of calcite, aragonite, hydromagnesite, dolomite, opal, and smectite. Thin sections showed diagenetic fabrics indicative of oscillating supersaturation conditions in response to surface seasonal climatic changes. Scanning electron microscopy (SEM) analyses identified frostwork's aragonite crystal topography as a microecological niche supporting filamentous Actinomyces bacteria, leaving room for a microbial component to Wind Cave frostwork development. To begin to monitor the impact of factors controlling crystal growth in vitro I developed two parallel techniques for measuring bacteriogenic carbonate precipitation in Escherichia coli cultures, using i) image analysis for agar media, and ii) inductively coupled plasma–optical emission spectroscopy (ICP-OES) ion quantifica (open full item for complete abstract)

Committee: Hazel Barton (Advisor); John Senko (Committee Member); Andreas Pflitsch (Committee Member); Bogdan Onac (Committee Member); Brian Bagatto (Committee Member) Subjects: Biology; Geobiology; Microbiology; Mineralogy

Master of Science, University of Akron, 2024, Chemical Engineering

This research aims to uncover effective nutrient compositions that enable fungi growth in concrete microcracks with carrier-protected fungal spores pre-embedded in concrete, thus facilitating the self-healing of cracks through fungal biomineralization. For fungi to grow, carbon sources are an absolute requirement. Furthermore, the calcite formation by biomineralization in cracks can only occur if calcium and carbonate ions are present or can be generated. On the other hand, adding nutrients that support fungal growth and biomineralization can negatively impact concrete properties. Finding a balance between the quantity of these necessary nutrients for successful crack healing and minimal impact on concrete properties is the primary objective of this study. This objective has been successfully fulfilled by making mortar samples infused with nutrients in a wide range, replicating the nutrient range in the concrete mix to test for concrete properties in a trial-and-error process, and arriving at a composition that balances both sides. Moreover, successful crack healing of lab-scale mortar specimens was achieved by testing the effectiveness of different nutrient compositions and identifying the necessary environmental conditions.

Committee: Lu-Kwang Ju (Advisor); Jie Zheng (Committee Member); Anil Patnaik (Committee Member) Subjects: Chemical Engineering

Master of Science, The Ohio State University, 2020, Earth Sciences

The isotopic composition and mineralogy of modern microbialites provides us with tools useful for interpreting the formation processes and environments of ancient microbialites. Growing in the hypersaline and turbid Storr's Lake on San Salvador Island in The Bahamas today are microbialites with low levels of photosynthesis and high levels of sulfate reduction-in contrast to many of their modern counterparts. Living planktonic, motile microorganisms and suspended algal and bacterial debris create the high turbidity of the shallow lake (<2 m) and rapidly attenuate sunlight in the water column. Within Storr's Lake microbial metabolisms induce precipitation of carbonate within microenvironments of the microbial mats. Both high-Mg calcite (HMC) and aragonite are found within a majority of the microbialites measured leading to the hypothesis that the organomineralization process involves a step where HMC transforms to aragonite. Mineralogy and elemental analysis of a wide sampling of microbialites was undertaken to understand the extent of aragonite within Storr's Lake microbialites. It was found that aragonite occurs at water depths greater than 40 cm within the lake and was present in all but one microbialite measured in this study. New calcium (Ca) stable isotopic analyses from the thermal ionization mass spectrometer using a 42Ca-43Ca double spike provides evidence for exploring the systems fractionating Ca within Storr's Lake water and microbialites. In contrast to geochemical data and previous Mg stable isotopic measurements on the same waters, the Ca stable isotopic value (δ44/40Ca) of water in Storr's Lake is not homogeneous. While the northern sector is primarily influenced by seawater, the southern sector δ44/40Ca is shifted away from seawater to lower values, suggesting internal variability within the lake. In both microbialites measured, δ44/40Ca is strongly correlated to mineralogy and trace elements in the carbonate. To explore the potenti (open full item for complete abstract)

Committee: Elizabeth Griffith PhD (Advisor); Matthew Saltzman PhD (Committee Member); Thomas Darrah PhD (Committee Member) Subjects: Biogeochemistry; Earth; Geobiology; Geochemistry; Geological; Geology; Morphology; Petroleum Geology

Doctor of Philosophy, University of Akron, 2019, Polymer Science

Bone biomineralization is a complex process where the structural type I collagen matrix and interactive non-collagenous proteins (NCPs) interact closely with inorganic calcium and phosphate ions to control the precipitation of nanosized non-stoichiometric hydroxyapatite (HAP, ideal stoichiometry Ca10(PO4)6(OH)2) within the organic structural matrix. This process eventually results in a hierarchical composite material with unique and excellent mechanical properties. Despite their important contributions to dental and orthopedic physiology, pathophysiology, and treatment modalities, mineral-biomacromolecule interactions, especially the roles of NCPs, and their contributions to the various stages of bone biomineralization are still highly debated. This dissertation utilized a two-pronged approach to elucidate the roles of natural and synthetic non-collagenous biomacromolecules in bone biomineralization. The specific objectives of this thesis are: (1) to identify specific NCPs in mineralizing and non-mineralizing tissues of two animal models, to determine whether some NCPs are unique to each type of tissue and thus infer the roles of the NCPs; (2) to systemically investigate the effect of short acidic NCP-mimic oligomer of different well-defined length, oligo(ʟ-glutamic acids), on calcium phosphate precipitation in vitro; and (3) to determine the importance of oligoglutamic acid chain lengths versus the negative charge concentrations in solution, in affecting calcium phosphate precipitation. In the first study of this dissertation, an ex vivo approach was adopted by combining sequential protein extraction with comprehensive protein mapping using proteomics and Western blot. The extraction method enables the separation of various NCPs based on their association in the extracellular matrix phases, i.e., organic collagenous and inorganic mineral phases. The proteomic study provides a complete picture of different NCPs in different tissues and animal species. Subsequently, (open full item for complete abstract)

Committee: Nita Sahai Ph.D. (Advisor); Abraham Joy Ph.D. (Committee Chair); Ali Dhinojwala Ph.D. (Committee Member); Sailaja Paruchuri Ph.D. (Committee Member); Marnie Saunders Ph.D. (Committee Member) Subjects: Analytical Chemistry; Biochemistry; Biomedical Research; Materials Science; Physical Chemistry

Master of Science (M.S.), University of Dayton, 2019, Biology

Biomineralization is a natural phenomenon in which living organisms produce minerals such as bone or shell. This process is widespread across almost all the major phyla, serving various functions in the form of protection, motility, and even digestion. Given the ubiquitous and varied nature of biomineralization, understanding this process poses a challenging task. The bivalve mollusc, Crassostrea virginica, was used as a model organism in this study, as they use biomineralization to create and maintain one of the most important aspects of their existence: shell. Given the fundamental role shell plays, it is necessary to understand how shell formation occurs. Older models of this process suggest a bulk secretion of materials into the extrapallial space; however, this model fails to fully explain how materials are transported to the site of accretion. The research presented here focuses on the potential role of oyster blood, specifically hemolymph, in acting as a transport vector for mineral and organic components. A protein biomarker, the amino acid L-3,4-dihydroxyphenylalanine (L-DOPA), is unique to some proteins involved in rendering the insoluble component of shell organic matrix. Tracking the location and temporal occurrence of these L-DOPA-containing proteins provides insight on how materials are transported for shell formation. An additional component to this study is the characterization of nascent shell after required materials have been transported and incorporated. This research focuses on elucidating the more than decade-old questions concerning shell formation and morphology through the shell deposition process. Three notch-repair studies were conducted to assess short (36 hours), mid (7 days), and long (6 weeks) term changes in materials transport and shell formation. Selected oyster compartments of hemolymph, hemocytes, mantle tissue, and nascent shell were sampled at selected time points to determine the spatial and temporal (open full item for complete abstract)

Committee: Karolyn Hansen (Advisor); Douglas Hansen (Committee Member); Pothitos Pitychoutis (Committee Member); Jayne Robinson (Committee Member) Subjects: Biology; Ecology

Doctor of Philosophy, The Ohio State University, 2019, Earth Sciences

Magnetospirillum magneticum AMB-1 is a member of a phylogenetically diverse group of bacteria characterized by their ability to biomineralize magnetic minerals known collectively as magnetotactic bacteria (MTB). MTB produce chains of membrane-bound intracellular magnetic nanocrystals, collectively known as magnetosomes. The current scientific consensus is that magnetosomes are used by MTB to orient themselves in vertically stratified water columns in order to achieve optimal oxygen concentrations in a process known as magnetoaerotaxis. Biomineralization of magnetosomes is an energy intensive process which accounts for roughly 33% of the cell's metabolic budget. This high metabolic cost seems to contradict with the amount of time MTB cells spend aligned with external magnetic fields. Due to this apparent discrepancy, I examined the potential role the magnetosome may play in bacterial metabolism. Through analysis of comparative growth on a variety of media compositions both magnetic, wild type and non-magnetic, mutant strains of AMB-1, I discovered that cells grown under stress conditions exhibit an inversion of growth dynamics which indicates some advantage for magnetic cells. Non-magnetic, mutant cells display a direct relationship between external magnetic field strength and growth, indicating magnetic field dependence. I believe that this represents a novel magnetosome-dependant mixotrophic metabolism. Due to the ubiquity of MTB and the diversity of sessile eukaryotes which either produce biogenic magnetite or exhibit magnetosensing, this system may be part of a widespread, previously unknown component of global carbon cycling.

Committee: Steven Lower (Advisor); Brian Lower (Committee Member); Ratnasingham Sooryakumar (Committee Member); Ann Cook (Committee Member) Subjects: Biogeochemistry; Geobiology; Geology; Microbiology; Mineralogy

Doctor of Philosophy, University of Akron, 2016, Polymer Science

In the formation of bone, the insoluble collagen matrix and soluble non-collagenous proteins (NCPs) interact with various calcium phosphate (CaP) phases to control the nucleation and growth of nanosized crystals of non-stoichiometric hydroxyapatite (HAP), producing a hierarchical, composite material bearing unique mechanical properties. The mineralization of bone illustrates an exquisite example of how the interactions between biomolecules and inorganic phases well define the nucleation, growth, and structure of composite biomaterials. Despite its critical mechanistic contributions to bone pathology, as well as its general relevance to protein-regulated biomineral formation, bone biomineralization remains poorly understood at the microscopic to atomic levels. This dissertation focuses on molecular simulation methods to understand the microscopic structure-activity relationships at the biomolecule-inorganic interface particularly relevant to bone biomineralization. The primary objectives of this dissertation are: (1) to develop reliable force field parameters for accurate outcomes from the molecular simulations; (2) to apply advanced sampling techniques to overcome the limitations of classical molecular dynamics simulation, which are widely applied in the biomineralization field, for reliably representing the specific issue of the nucleation of ionic solids (such as HAP) and capturing the conformations of biomolecules, water, and inorganic species at the interfaces; (3) to establish the structure-activity relationships of synthetic HAP-binding peptides; (4) to understand the molecular-level mechanisms in various stages of bone mineralization from the form of soluble ion complexes to amorphous and crystalline CaP phases as modulated by osteocalcin (OCN), a model NCP, and (5) to extrapolate the principles learned to general inorganic-biomolecule interfaces. The validity of force field parameters for molecular dynamics simulation of HAP-water/biomolecule interfaces is s (open full item for complete abstract)

Committee: Nita Sahai (Advisor); Mesfin Tsige (Committee Chair); William Landis (Committee Member); Matthew Becker (Committee Member); Jie Zheng (Committee Member) Subjects: Biogeochemistry; Biology; Chemistry; Polymers

PhD, University of Cincinnati, 2003, Engineering : Materials Science

Diatoms, sponges and grasses are all known to produce ornate biogenic silica structures under ambient conditions. Some aspects of the molecular mechanism controlling biosilicification have recently been elucidated. The entrapment of the catalyzing / templating / scaffolding biomacromolecules enables them to be recovered by selective dissolution of biosilica. The proteins extracted from the diatom Cylindrotheca fusiformis (silaffins) and the sponge Tethya aurantia (silicateins) have been shown to precipitate silica from silica precursors in vitro. The identification of synthetic macromolecules that can act as catalysts / templates / scaffolds for silica formation gives exciting possibilities for bioinspired silica synthesis. Herein, the role of various synthetic (bio)macromolecules in silicification is studied. Attempts have also been made to understand the mechanism(s) governing (bio)macromolecule mediated (bio)silicification. Furthermore, the results and the understanding gained from various synthetic systems are used to demonstrate the potential of such bioinspired routes to develop new materials.

Committee: Dr. Stephen J. Clarson (Advisor) Subjects: Engineering, Materials Science

Doctor of Philosophy, Case Western Reserve University, 2011, Macromolecular Science and Engineering

This dissertation covers a wide array of polymer science, from investigating the barrier properties of polymer blends for commercial products and their specifications to using novel approaches to incorporate glassy inorganic materials within a polymer matrix for high density data storage materials to using common materials in new ways to increase the use range of low density clay aerogels to using bioinspired chemistry to develop reinforcement of current materials and bone replacement materials. Chapter 2 discusses the advances in oxygen barrier materials through innovative approaches to modifying the refractive index change induced by biaxial orientation by simple melt blending procedures. Chapter 3 discusses an approach to developing 3D data storage devices by the blending of common optical polymers with inorganic chalcogenide glasses. Chapter 4 discusses the vast mechanical improvement of a polymer/clay aerogel composite material by a simple dip coating procedure. Chapters 5-7 involve the use of biomineralization for various purposes. In Chapter 5 a polyethylene imine/clay aerogel is coated by a silica layer to impart vastly superior mechanical properties, while a layering approach modestly improves mechanical performance. In Chapter 6 a polyacrylic acid/clay aerogel is subjected to CaCO3 deposition, showing the ability to grow large amounts of CaCO3 in relatively short times. Chapter 7 discusses an electrophoretic mineralization approach to collagen hydrogels.

Committee: David Schiraldi (Committee Chair); LaShonda Korley (Committee Member); Gary Wnek (Committee Member); Horst von Recum (Committee Member) Subjects: Polymers

Doctor of Philosophy, Case Western Reserve University, 2008, Macromolecular Science

Polyelectrolyte multilayer formation is achieved by alternate adsorption of oppositely charged polymers in a layer-by-layer (LbL) fashion from dilute polyelectrolyte solutions. This dissertation examines the formation, growth, structure, and morphology of polyelectrolyte multilayers by utilizing molecular dynamics (MD) simulations and polyelectrolyte spin assembly (PSA) experiments employing a spin-coating radial flow. Application of multilayers as substrates for biomineralization of hydroxyapatite (HA) and silica is also examined. MD simulations of assembly of flexible polyelectrolytes into multilayers were performed at a charged planar surface from dilute polyelectrolyte solutions. These simulations show that multilayer growth proceeds through surface overcharging, chain intermixing, and a linear increase in polymer surface coverage at each deposition step. The strong electrostatic attraction between oppositely charged polyelectrolytes at each deposition step is a driving force behind the multilayer growth. Polymer surface coverage and multilayer structure are each strongly influenced by the charge fraction of polyelectrolytes, as well as the strength of electrostatic and short-range interactions. Experimental results from PSA elucidated the synergistic effect of the spin-speed and the solution ionic strength on the growth and morphology of multilayers. The growth rate and polymer surface coverage of multilayers shows a non-monotonic dependence on solution ionic strength, first increasing and then decreasing as the solution ionic strength is increased. This is a manifestation of two competing mechanisms responsible for multilayer formation in agreement with Flory-like theory of multilayer formation from polyelectrolyte solutions under flow. At low salt concentrations, the electrostatic interactions control the multilayer assembly process while, at high salt concentrations, the multilayer assembly it is dominated by shear flow. For applications of multilayers in bi (open full item for complete abstract)

Committee: Patrick Mather (Advisor) Subjects: Chemistry, Polymer

Doctor of Philosophy (Ph.D.), Bowling Green State University, 2013, Photochemical Sciences

This dissertation reflects efforts to the combine biomineralization research and rational peptide design using the coiled-coil peptide motif and calcium hydrogen phosphate dihydrate (CaHPO4 x 2H2O), commonly known as brushite. Coiled-coils were designed to alter the complete growth pathway of brushite beginning with an amorphous precursor and resulting in a modified crystalline state. Both the designed chemical character and the secondary structure of the coiled-coil peptides were found to be important factors in controlling the growth pathway of brushite and the morphology of the final crystalline state. The impact of peptide secondary structure on the growth of brushite was studied by comparing the effects of a well structured coiled-coil peptide (AQQ5E) to a structurally disordered analog with nearly identical chemical properties (RCA5E) on the final crystal morphology. Typically, brushite crystals formed in the absence of growth modifying agents display {100}, {010}, {10-2} and {10-1} crystal faces. However, in the presence of AQQ5E the growth of the {10-2} faces were selectively inhibited in the final crystal product. Conversely, crystals grown in the presence of RCA5E adopted a wide variety of morphologies without a preferred means of crystal modification. Computational analysis demonstrated how the two peptides may interact with the different crystal faces of brushite and provided insight for explaining this behavior. In another study, a series of coiled-coil peptides with similar secondary structure yet increasing acidic amino acid content were used to determine the impact of designed peptides on amorphous-to-crystalline transition of brushite leading up to the final crystalline state. In the absence of peptides, the amorphous-to-crystalline transition of brushite occurred rapidly with the final crystalline state being achieved within several hours. However, the addition of acidic peptides prolonged this process over several days and allowed for th (open full item for complete abstract)

Committee: Michael Ogawa (Advisor); George Bullerjahn (Committee Member); Marshall Wilson (Committee Member); John Farver (Committee Member) Subjects: Chemistry