A hallmark of cancerous transformation is altered chromosome structure. Inappropriate regulation of chromatin structure inhibits normal cell function, and may represent the origin of transformation. A handful of important studies have indicated that chromatin structure in the human genome is dynamic and regulatory, but the role of chromatin structure in cancer progression has not been addressed. In our initial studies, we have analyzed chromatin structure of patients with different grades and stages of adenocarcinoma as compared to matched normal tissue using microarray-based nucleosome distribution and chromosomal sensitivity assays. We report that low-grade lung adenocarcinoma displays widespread nucleosome alterations compared to matched normal tissue at over half of 886 genes studied, and that these changes are consistent between patients. Additionally, we determined many changes in early colorectal adenocarcinoma, and the alterations are consistent between patients and concordant with the lung adenocarcinoma alterations. Genes with nucleosome distribution changes are enriched for the phosphoinositide 3-kinase (PI3K) cascade, a key oncoregulatory pathway. Together these results suggest an early, shared regulatory mechanism of transformation. We have also measured substantial disruptions in chromosomal sensitivity in a high-grade and high-stage tumor, linking aggressive tumors with high-order nuclear architecture alterations. From this initial study, we have developed a model in which early adenocarcinoma is linked to changes in nucleosome distributions, whereas aggressive tumors are linked to high-order chromosomal changes. This work has laid the foundation for comprehensive studies on the role of chromatin structure in cancer progression. As such, we have developed a new approach to generate ultra high-resolution, genome-wide nucleosome distribution maps at the transcription start site using deep sequencing, which we call mTSS-seq. Building on the published microarray-based nucleosome distribution mapping of select loci in adenocarcinoma patients, we have provided the first measurements of genome-wide nucleosome distribution using mTSS-seq. We have confirmed that nucleosome distribution is an early, widespread transformation event in lung and colon adenocarcinoma. These findings guide a shift in our perspective from chromatin structural alterations as terminal states to transient events of clinical importance. These altered nucleosome architectures are consistent between patients indicating that they may serve as important early adenocarcinoma markers. We present evidence that the nucleosome alterations are driven by and may influence cis and trans acting factors - the underlying DNA sequence and transcription factor binding. Our study reveals at unprecedented breadth and depth that DNA-directed nucleosome redistributions are a widespread feature early in the progression of cancer, which has allowed us to propose a hierarchical model for genome regulation through chromatin structure. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2014. / April 9, 2014. / Cancer, Chromatin, Genome, Nuclease, Nucleosome / Includes bibliographical references. / Jonathan H. Dennis, Professor Directing Dissertation; Myra M. Hurt, University Representative; Brian P. Chadwick, Committee Member; Hengli Tang, Committee Member.

Restoration is increasingly implemented to reestablish habitat structure and function following natural and anthropogenic physical disturbances, but scientific knowledge of the effectiveness of methods lags behind demand for guidelines. On coral reefs, recovery is largely dependent on coral reestablishment, and substratum stability is critical to the survival of coral fragments and recruits. Concrete is often used to immobilize or replace loose rubble, but its ecological performance, in terms of fostering coral recruitment, has not been rigorously evaluated, and attempts to restore coral reefs have generally fallen short of returning degraded habitat to pre-disturbance conditions. Fragments of erect branching sponges are known to mediate natural reef recovery by facilitating coral rubble consolidation, yet such natural processes have been largely overlooked in reef restoration practice. Effectively harnessing the recovery abilities of sponges to restore and repopulate damaged coral reefs requires basic ecological information (e.g., rates of growth, fragment attachment, and wound healing) that is currently in short supply for the majority of Caribbean reef sponge species. However, observation of injury and recovery following natural disturbances and experimental wounding suggests that sponge growth form, skeletal composition, and investment in chemical defense in large part determine susceptibility to injury, which appears to be inversely related to recovery ability. If these factors operate under less stressful conditions, they could aid in the selection of sponge species that might most effectively be used to rehabilitate damaged reefs. Through the use of observational studies and field experiments this dissertation focused on: 1) the potential of using fragments of Caribbean coral reef sponges to aid the rejuvenation of coral reefs; and 2) the influence of growth form, skeletal composition, and investment in chemical defense on patterns and rates of: a) size change; b) fragment reattachment; and c) wound healing. The results of this research suggest that employing organisms that jump start successional pathways and facilitate recovery can significantly improve restoration outcomes; however, best practices require techniques be tailored to each system. Furthermore, patterns and rates of size change, fragment attachment, and wound healing among growth forms, and within growth forms among species differing in their composition of skeletal elements, support the resistance vs. recovery hypothesis, and suggest that these traits, in addition to influencing the ecology and evolution of reef sponges, can aid selection of sponge species that might most easily be restored following disturbance or that might most effectively be used to rehabilitate degraded coral reefs. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2014. / April 1, 2014. / Coral reef, Growth Rates, Reattachment, Restoration, Sponges, Wound Healing / Includes bibliographical references. / Janie Wulff, Professor Directing Dissertation; Bill Parker, University Representative; Don Levitan, Committee Member; Tom Miller, Committee Member; Alice Winn, Committee Member.

DNA replication in eukaryotic cells follows a temporal order that is consistent from cell cycle to cell cycle and is correlated with the spatial organization of DNA in the nucleus. This "replication-timing program" is conserved in evolution, shares dynamic relationships with cell-type-specific properties of chromatin in multicellular organisms, and is disrupted in many human diseases including cancer. Despite these intriguing associations, over 50 years of research has yet to uncover any biological significance for a replication-timing program and little is known about how the program is determined. This dissertation combined various approaches designed primarily to determine whether any determinants of replication timing are encoded in the DNA sequence and to understand the nature of such putative regulatory elements. The collective work demonstrates the existence of DNA elements that sufficiently direct human-specific replication timing in a mouse background, and a neural-specific switch in replication timing at an otherwise constitutive locus in the mouse genome. Minor differences in DNA sequence such as single nucleotide polymorphism or small insertions or deletions had no detectable effect on replication timing, while rearrangements of large chromosome segments or site-specific insertion of certain bacterial artificial chromosomes exhibited a dominant regulatory effect on replication timing in ectopic contexts. In addition, perturbations to replication timing that were associated with genetic rearrangement and cancer were shown to align with changes that occur during normal development and with topologically-associating chromosome domains, demonstrating that stable structural subunits underlie the regulation of replication timing. Further dissection of DNA fragments sufficient to direct replication timing should help to uncover the trans factors responsible for executing the replication-timing program and will hopefully provide insight into the significance of replication timing for cell function and disease. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2014. / June 10, 2014. / Cell differentiation, Chromatin organization, Chromosome domains, Chromosome engineering, DNA replication timing, Embryonic stem cells / Includes bibliographical references. / David M. Gilbert, Professor Directing Dissertation; David M. Lind, University Representative; Karen M. McGinnis, Committee Member; Fanxiu Zhu, Committee Member; Brian P. Chadwick, Committee Member.

Understanding how organisms adapt to their environments is one of the fundamental goals of biology. However, delineating the exact relationships between genotypes, phenotypes, and fitness can be difficult in natural systems. Studying phenotypes that have both simple underlying genetics and direct effects on the survival of an organism can make the connections more clear. The evolutionary patterns of snake venoms and the complete lack of alternative mechanisms of feeding and defense in venomous species makes them an ideal system for studying molecular adaptation and predator-prey coevolution. In chapter one, I investigate the venom-gland transcriptomes of Agkistrodon piscivorus and Agkistrodon contortrix, congeners that have different ecological niches from each other and previously characterized species. Using these congeners as a model system, I will explore the roles of mutational process and selection in venom evolution. I test the hypothesis that A. piscivorus will show higher divergence and strength of selection in toxin gene expression patterns and more gene-family expansion than A. contortrix, due the acquisition of an entirely novel dietary item (fish). Given current knowledge of the evolutionary arms race between venom composition and prey's resistance (Gibbs et al. 2013), A. piscivorus is likely to have toxin gene paralogs that are under strong selection to adapt to a new diet. The test of this hypothesis will provide a direct view of molecular evolution and selection due to novel adaptation in an ecologically critically phenotype. The extraordinarily broad diet of A. piscivorus lends itself to the study of local adaptation, as the most common prey items are unlikely to be found across the entire range of the species. I will investigate the role of expression variation by conducting a detailed analysis of population-level adaptation across the range of a dietary generalist, A. piscivorus. I will test for both ontogenetic and geographic differences in A. piscivorus, focusing on the role of toxin expression variation between life stages and populations. Specifically, I test the hypothesis that A. piscivorus' has population variation in venom composition tied to geographically-based prey availability, given the breath of diet in this species and the strength of selection on venom. / A Thesis submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2014. / July 1, 2014. / Adaptation, Agkistrodon contortrix, Agkistrodon piscivorus, Proteomics, Transcriptomes, Venom / Includes bibliographical references. / Darin R. Rokyta, Professor Co-Directing Thesis; Don Levitan, Professor Co-Directing Thesis; Scott Steppan, Committee Member.

Biocompatible coatings are often used to improve fixation between implants and tissues. Polyelectrolyte multilayer (PEMU) coatings built layer by layer with alternating pairs of polyelectrolytes can be tuned to improve cell interactions with surfaces. In Chapter 2, we show that human mesenchymal stem cells (hMSCs) induced with bone differentiation medium (BDM) to become osteoblasts, biomineralize crosslinked PEMUs built with the polycation poly(allylamine hydrochloride) (PAH) and the polyanion poly(acrylic acid) (PAA). Degrees of hMSC osteoblast differentiation and surface biomineralization reflect differences in extracellular matrix (ECM) deposited and organized by the cells on the smooth PAH-terminated PEMUs (PAH-PEMUs) and microstructured PAA-terminated PEMUs (PAA-PEMUs). BDM-induced hMSCs expressed higher levels of the early osteoblast differentiation marker alkaline phosphatase (ALP) sooner and assembled a less fibrillar collagen I organization on PAA-PEMUs than on PAH-PEMUs. Although cells on both types of PEMUs eventually expressed similar levels of the later stage osteoblast differentiation markers bone sialoprotein (BSP), osteonectin, and osteopontin, the cells organized a more amorphous Collagen I and denser BSP localization on PAA-PEMUs than on PAH-PEMUs. These ECM properties correlated with greater biomineralization on the PAA-PEMUs than on PAH-PEMUs. To further investigate ECM effects on hMSC behavior and differentiation, we developed a novel model for deposition and decellularization of cell secreted ECM on tissue culture plastic (TCP) and PEMU surfaces. The microenvironment presented by extracellular matrix (ECM) influences cell adhesion, proliferation and differentiation. Chapter 3 describes development of a cold EDTA-PBS protocol to remove intact cells from ECM deposited by cultured human bone marrow mesenchymal stems cells (hMSCs), osteogenic hMSCs, and two smooth muscle cell (SMC) lines, with minimal ECM damage and contamination. The decellularized ECM deposited by uninduced hMSCs enhanced naïve hMSC proliferation, stemness, and cell motility. Decellularized ECM deposited by osteogenic hMSCs early in the differentiation process stimulated naïve hMSCs osteogenesis and substrate biomineralization in the absence of added differentiation factors, but this osteogenic induction potential was lost by later differentiation stages. Both smooth muscle cell line decellularized ECMs induced naïve hMSC myofibroblast differentiation, but each ECM type induced naïve hMSC development into distinct SMC phenotypes. Chapter 4 describes our characterization of decellularized ECMs deposited by deposited by several cell types on PAH-PAA PEMUs. ECMs deposited on PAA-terminated PEMUs by hMSCs that were induced to become osteogenic with dexamethasone-containing bone differentiation medium (BDM) for 3, 8, and 15 days were decellularized. The ECM deposited for 3 days induced osteogenesis of naïve hMSCs and substrate biomineralization in the absence of the dexamethasone differentiation factor. This osteogenic induction potential was lower for ECM deposited for 8 and 15 days. ECMs deposited by human hTERT-immortalized myometrial smooth muscle cells (myomSMCs) induced naïve hMSCs to become myoblastic with 'synthetic' smooth muscle cell phenotypic characteristics. Overall, this research demonstrates the biocompatibility of PAH-PAA PEMUs, especially for biomineralization by osteogenic hMSCs. The protocol for decellularization of ECM deposited by cells on surfaces including PEMUs described here provides a potentially useful method for constructing biomaterial-ECM scaffolds and highlights the importance of ECM microenvironments on stem cell behavior. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2014. / March 31, 2014. / Differentiation, Extracellular matrix, Mesenchymal stem cell, Modulus, Osteoblast, Polyelectrolyte multilayer / Includes bibliographical references. / Thomas C. S. Keller, III, Professor Directing Dissertation; Joseph B. Schlenoff, University Representative; David M. Gilbert, Committee Member; Wu-Min Deng, Committee Member; Laura R. Keller, Committee Member.

When cells encounter DNA replication stress, the S-phase checkpoint is activated to facilitate cell cycle arrest and DNA repair. An important aspect of the checkpoint is the transcriptional response, but the details governing this response are poorly understood. Intragenic transcription initiates within the coding region of a gene, thereby producing shorter mRNAs and proteins. However, the role of intragenic transcription in the functional regulation of genes remains largely unknown. Previous work has shown that the spindle is stabilized during replication stress to prevent chromosome segregation errors, but the mechanism for the stabilization remains unclear. When yeast cells were treated with hydroxyurea (HU) to block DNA synthesis and induce replication stress, we found that Ase1, a highly conserved spindle midzone protein, appeared as two short protein isoforms in addition to the full length protein. We further demonstrated that the short protein isoforms result from intragenic transcription of ASE1, which depends on the S-phase checkpoint kinase Rad53. Blocking the generation of short Ase1 isoforms leads to increased HU sensitivity and a destabilized S-phase spindle, a likely consequence of altered spindle dynamics and collapse. The short Ase1 protein isoforms induced during replication stress act dominant negatively to maintain a stable spindle structure during HU arrest, likely by regulating microtubule motor protein activity. It is well documented that the transcription of some genes exhibit Rad53-dependent changes during DNA replication stress. We suspect that more genes are subjected to Rad53-dependent transcriptional regulation in response to DNA replication stress. For this purpose, we used both a tiling microarray and RNA-sequencing to systematically identify Rad53-dependent transcription in cell cycle control. As a result we identified a large number of genes whose transcription is regulated in response to HU treatment and depends on Rad53. Furthermore, we provide insight into the mechanism responsible for mitotic gene repression with evidence that supports the role of the transcriptional repressor Yox1 in Rad53-dependent transcriptional regulation. Together, our results reveal a unique mechanism that down-regulates gene function by intragenic transcription. Additionally, our systematic identification of differential gene expression in response to DNA replication stress using RNA-sequencing was successful in identifying potential Rad53-depedendent transcription targets. / A Dissertation submitted to the Department of Biomedical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2014. / March 10, 2014. / Includes bibliographical references. / Yanchang Wang, Professor Directing Dissertation; Wu-Min Deng, University Representative; Hong-Guo Yu, Committee Member; Yoichi Kato, Committee Member; Akash Gunjan, Committee Member; Jamila Horabin, Committee Member.

Macro histone H2A (macroH2A) is a variant of core histone H2A that differs primarily by an extensive carboxy-terminal tail of unknown function that makes up two-thirds of the protein's mass. The histone variant is distributed throughout the nucleus, but in female mammalian cells, it has been found to be associated with the inactive X chromosome (Xi) in a local accumulation referred to as a macrochromatin body. The association of macroH2A with facultative heterochromatin of the Xi is suggestive of a role for the variant in gene silencing. MacroH2A1 was the first form of macroH2A discovered and is encoded by the H2AFY gene. Two splice isoforms exist due to two alternate versions of exon-6, giving rise to macroH2A1.1 and macroH2A1.2. A second form of macroH2A encoded by H2AFY2 gene, known as macroH2A2, shares 80% amino acid identity with macroH2A1 and also accumulates at Xi, suggesting the possibility of functional redundancy between the two proteins. In order to further investigate macroH2A, we have generated knockouts of macroH2A1 and targeted a single allele of macroH2A2 in a human female telomerase immortalized retinal pigment epithelial cell line (RPE1). Targeted clones were generated by exchanging exon-2 of one or both alleles with a promoter-trap construct containing a promoterless neomycin selection cassette flanked by arms of homology designed to the intronic sequences immediately adjacent to exon-2. The selection cassette contains a splice-acceptor, internal ribosome entry site and polyadenylation signal, which when exchanged with exon-2 results in the inclusion of the neomycin coding sequence in the resulting truncated messenger RNA and its subsequent translation, allowing for correct targeting to be selected for through neomycin resistance. To enhance targeting, Zinc Finger Nucleases (ZFNs) were engineered to create a double strand break at or close to exon-2. In order to target the genes, cells were co-nucleofected with the targeting construct and ZFNs before seeding cells in media containing neomycin. Single cell clones were screened for correct targeting and loss of macroH2A assessed by Western blotting. In order to explore the impact of macroH2A1 loss, RNA was extracted from a macroH2A1 knockout as well as parental RPE1 and changes to the transcriptome assessed by massively paralleled sequencing of complementary DNA (RNAseq). Genes that showed a significant change in expression between the wildtype and knockout cells were selected for further study. Quantitative Chromatin Immunoprecipitation (qChIP) was performed on an affected gene to evaluate any local chromatin changes due to macroH2A1 loss. Additionally, to examine the possibility that macroH2A1 splice isoforms fulfill different roles, full-length MYC-tagged expression constructs for macroH2A1.1 and macroH2A1.2 were reintroduced into cells and rescue of wild-type expression assessed for genes that displayed altered expression in response to macroH2A1 loss. / A Thesis submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Master of Science. / Spring Semester, 2014. / March 31, 2014. / Gene Targeting, Histone Variant, Inactive X, MacroH2A, Transcription activator-like effector nucleases, Zinc Finger Nucleases / Includes bibliographical references. / Brian Chadwick, Professor Directing Thesis; Jonathan Dennis, Committee Member; Karen McGinnis, Committee Member.

The maize genome is highly complex and repetitive, with almost 85% of the genome encoding transposable elements (TE). The movement of TE can have deleterious effects on a genome. In maize, one model for transcriptional gene silencing (TGS) relies heavily on a pathway termed RNA dependent DNA Methylation (RdDM). The current model dictates that RdDM establishes a silent state at TE and other repetitive regions of the genome. It employs two plant specific DNA dependent RNA polymerases, (Pol IV and V). Transcription by Pol IV is modeled to result in the generation of 24 nucleotide (24nt) small interfering RNA (siRNA). While Pol V transcription is modeled to generate a scaffold transcript, required for the targeting of chromatin remodelers and de novo methyl transferases to regions of the genome for regulation and silencing. Current maize data supports this model; however, large gaps in our understanding of this pathway exist. Three transgenic constructs were used to test the necessity of three RNA polymerases in RNA mediated TGS. BTG-s, is regulated through a MOP1, RMR1, and RMR2 dependent pathway. A forward genetic screen was used to identify additional proteins required for silencing of BTG-s. Through this screen Tgr1 was identified as a regulator of BTG silencing. Mapping of tgr1-1 indicated a 12 Mbp window on chromosome 1. Complementation experiments confirmed tgr1-1 is an allele of GRMZM2G007681, which encodes the largest subunit of Pol IV. Consistent with the current model for Pol IV, tgr1-1 mutants are deficient in 24nt siRNA biosynthesis. Identification of Tgr1 as a subunit of Pol IV agrees with previous reports that determined that BTG silencing is mediated by an RNA-dependent silencing pathway. Mutants affecting additional RNA polymerases that are part of the RdDM pathway—--Pol IV (Mop2-1 and mop3-1), Pol V (Mop2-1) and an RNA dependent RNA polymerase (mop1-1)—--were used in conjunction with inverted repeat transgenes complementary to two maize loci to ascertain the requirements for these RNA polymerases in the establishment of silencing at endogenous loci. The a1 locus requires functional MOP2, but is not dependent on the function of MOP1 or MOP3 to establish silencing. A second transgene complementary to the enhancer of the b1 locus does not require functional MOP1, MOP2, or MOP3 to establish silencing of the b1 enhancer. This indicates that Pol V is required at some, but not all genomic loci for silencing to be established. Thus the genetic requirements for establishment of silencing at three genetic loci vary with respect to these three RNA polymerases. / A Thesis submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Master of Science. / Spring Semester, 2014. / April 8, 2014. / Includes bibliographical references. / Karen McGinnis, Professor Directing Thesis; George Bates, Committee Member; Jonathan Dennis, Committee Member.

Hepatitis C virus (HCV) is an enveloped RNA virus that often manifests into chronic infections of the liver, which represents a threat to human health due to the morbidity it presents within infected patients. The virus is especially persistent as current antiviral treatments have difficulty in restricting the infections, allowing most new cases of viral hepatitis to develop into persistent infections. It has emerged as a major causative agent of liver diseases, resulting in cirrhosis, liver failure, and hepatocellular carcinoma as the disease progresses with time. There is no prophylactic vaccine currently available to protect against HCV, nor is there an effective therapy capable of generating a sustained virologic response. HCV has shown the capability of developing resistance to antiviral compounds that target specific viral enzymes necessary for replication. HCV is found as quasispecies within an individual due to its error prone RNA-dependent RNA polymerase. The genetic heterogeneity of HCV allows it to be capable of escaping the effect of compounds that specifically target viral proteins. Several cellular cofactors have been identified recently that permit HCV to be infectious. The interactions of these cofactors with viral proteins shed light on the life cycle of HCV and warrant further study as potential cellular targets to restrict viral infectivity. One such cofactor is cyclophilin A (CyPA) which has peptidylproline isomerase (PPIase) activity. HCV strains with a reduced dependency on CyPA for replication were selected in a CyPA-knockdown cell line. Sequencing of these isolates revealed mutations within a dipeptide motif of domain 2 of NS5A for all clones (D316E and/or Y317N). Analysis of these phenotypes upon insertion into the full-length viral genome revealed the double mutant, termed DEYN, to most efficiently restore the infectivity of the virus in CyPA-knockdown cells to that of control cells. We have hypothesized several possible mechanisms for the reduced dependency on CyPA of DEYN virus. These mutations could potentially affect viral replication via the PPIase activity of CyPA which catalyzes the cis-trans isomerization of proline residues. Presumably, HCV requires CyPA as a host cofactor to isomerize one or more proline residues within NS5A, converting it from a non-functional, unfolded protein into a functional, folded conformer. The work described here identifies structural differences between wt and mutant NS5A sequences, identifies CyPA binding sites within domain II and LCS II, and describes critical determinants within CyPA and NS5A that permit their interactions. Furthermore, this work identified AphiPXW and [AP]LPP as CyPA binding motifs among the 7 genotypes tested. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctorate of Philosophy. / Summer Semester, 2011. / June 14, 2011. / Includes bibliographical references. / Hengli Tang, Professor Directing Dissertation; Kenneth Roux, Professor Co-Directing Dissertation; Timothy Logan, University Representative; Fanxiu Zhu, Committee Member.

As vertebrates attain a larger body size, the relative growth of various body parts results in differential rates of growth across the organism and may result in substantial impacts on mechanical performance. To deal with this problem, shape changes often accompany somatic growth, and the nature of these changes is thought to reflect a tight relationship between the morphological form of an organism's anatomy and its function within a given environment. In this context, the feeding anatomy of vertebrates is a consummate form-function relationship. An extreme example of a taxon that undergoes ontogenetic dietary shifts is the American alligator, Alligator mississippiensis, which traverses a 5000-fold increase in mass during its lifetime. As a consequence, this species must cope with changes in its feeding functional morphology (i.e., size and shape of dental and musculoskeletal attributes) while exploiting varying ecological feeding niches. Hatchlings start out as insectivorous neonates but abandon that feeding niche as larger body size allows them access to a wider range of prey items, first frogs and fish and other small, compliant prey before finally reaching the adult ecomorphology where they access more robust quarry. Absolute body size and bite-force positive allometry play an important role in these transitions. Therefore, to understand the nature of the anatomical changes that underpin these factors and thus facilitate dietary niche transitions, I dissected a growth series of wild A. mississippiensis. I standardized the topology, attachment points, and naming scheme for the jaw adductor musculature and quantified the growth of the cranial skeleton, jaw adductor muscle system, and dental form throughout ontogeny. I derived mathematical models of bite-force and hold-force generation based on these data, and tested them against additional developmental series of known bite-force A. mississippiensis. I developed and implemented a novel technique to identify the aerobic capacity of the jaw adductor muscles, called Muscle Oxidative Inference Analysis (MOIA). Finally, dental pressures were quantified using bite forces and dental morphology. These data demonstrate that after hatching, larger body size (25 cm snout-vent length, SVL) initially allows A. mississippiensis access to increasingly larger, compliant prey. At 45 cm SVL positive allometry in the post-orbital growth of the skull and M. Pterygoideus ventralis muscles in addition to substantial changes in the aerobic capacity of some jaw adductor muscles facilitates access elusive terrestrial prey such as birds and small mammals. By 75 cm SVL, subtle changes in dental form along with bite-force positive allometry make it possible for this taxon to generate tooth pressures that can fracture and mechanically fail the bony carapaces of turtles. Finally, large adult body size (150+ cm SVL) and continued positive allometry in the musculoskeletal attributes of its jaw adductor system and further augmented oxidative capacity of its adductor muscles allow A. mississippiensis to secure large game mammals such as deer, boar, and cattle. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2010. / March 26, 2010. / Includes bibliographical references. / Gregory Erickson, Professor Directing Dissertation; William Parker, University Representative; P. Bryant Chase, Committee Member; Brian Inouye, Committee Member; Emily DuVal, Committee Member; Patrick Hollis, Committee Member.