The frequency with which individuals do not develop their third molars, or wisdom teeth, is increasing worldwide. This current topic of human evolution is relevant to the research of anthropologists, geneticists, dentists, and other researchers involved in the study of human dentition. Many explanations have been offered to account for the prevalence of molar agenesis including, evolutionary, environmental, and genetic theories. The purpose of this research project is to determine the frequency of third molar agenesis and investigate the relationship between third molar agenesis and maxillomandibular jaw dimensions in a sample of orthodontic patients. This research tests the hypotheses that: H1: Individuals with agenesis of third molars will be significantly different in maxillomandibular dimensions than individuals without agenesis, H2: The agenesis of maxillary third molars is associated with the anteroposterior dimensions of the maxilla, and H3: The agenesis of mandibular third molars is not associated with the anteroposterior dimensions of the mandible. Therefore, the null hypothesis for this research is H0: An individual’s sex and the presence/absence of the third molar are independent. The sample for this research project includes 543 individuals from the University of New Mexico’s Maxwell Museum of Anthropology Orthodontics Case File System. This study examines panoramic radiographs of the dentition for each individual to ascertain whether any of the third molars was congenitally absent, and records the cephalometric measurements for each case for statistical analysis. This study uses descriptive statistics, crosstabulation analysis, chi-square tests, non-parametric Kruskal-Wallis tests, and logistic regression analysis to investigate any associations between third molar agenesis and maxillomandibular jaw dimensions. The results show that Native Americans (9.2%), Hispanics (8.46%), and European Americans (8.37%) have a higher frequency of third molar agenesis than African Americans (0.17%) and Asians (0.17%). This finding is consistent with the published body of work on third molar agenesis, in spite of the small sample sizes for diverse populations. There is a significant difference in the number of molars missing among groups. For the present study, based on crosstabulation analysis, most individuals are missing two molars (34.9%), followed by one absent (31.7%), a lack of four molars (25.3%), and finally a lack of 3 molars (7.9%). Individuals with third molar agenesis are nearly twice as likely to be missing a molar from the mandible (62.8%) than the maxilla (36.9%). This study uses crosstabulation analysis, chi-square analysis, non-parametric Kruskal-Wallis tests, and logistic regression analysis to assess the association between third molar agenesis and measurements of the dental arcade. This study did not find an association between an individual’s maxillomandibular dimensions and third molar agenesis. Therefore, this study did not find support for the hypothesis that individuals with third molar agenesis would have smaller maxillomandibular dimensions than individuals without agenesis. Based on the findings of this study, an association between the size of an individual’s mouth and third molar agenesis does not exist in the sample analyzed. Third molar agenesis is not occurring due to a lack of room in the mouth, but possibly results from heredity. Therefore, it may be more likely that genetic variation influences third molar agenesis, rather than an evolutionary change in diet.

The purpose of this dissertation is to test how growth, reproduction, and immune functioning interact in two populations of adult women residing in vastly different socio-economic and ecological environments, the Kalunga quilombo in Brazil, and the United States of America. The presence of life history trade-offs was tested to determine how the different envirnonments, and socio-ecological contexts of the populations were creating differential risks for health and reproductive outcomes, and life history trade-offs. I hypothesized that the Kalunga people, living in very difficult and harsh conditions, would experience greater amounts of, and more severe, life history trade-offs than the U.S. women. I also hypothesized that in both populations, syndemic interactions between health outcomes, and the larger macro-social conditions, would influence stature, immune functioning, and reproduction. Additionally, these syndemic interactions would perpetuate poor health and reproductive outcomes within the entire Kalunga population, and portions of the U.S. population. I collaborated with the University of Brasilia to collect data adult women from in the Kalunga quilombo in Goiás State, Brazil (n=38) via semi-structured interviews in 2016. In addition, these data were compiled with reproductive, demographic, anthropometric, biological, and socio-economic data collected from adult Kalunga women in 2015 by the University of Brasilia’s Department of Genetics and Morphology. Demographic, anthropometric, biological, and socio-economic data recorded in the National Health and Nutrition Examination Survey (NHANES) 2005-2006 from adult U.S. women was also analyzed. Life history traits were measured through stature (cm), Immunoglobulin E (IgE; kU/l), and reproductive variables (fertility, and reproductive ages) for both populations. My results demonstrated that life history trade-offs impact diverse populations. I found evidence to support life history trade-offs occurred between stature and fertility, and stature and reproductive ages, in both populations. However, my results also indicated that the socio-economic, and ecological, conditions of both populations heavily influenced stature and reproduction in the women. Life history trade-offs were not observable between immune functioning and fertility in the Kalunga population, and not readily evident in the U.S. sample. The positive associations between IgE and fertility in the U.S. women indicate that while life history trade-offs may be suggested, other biocultural variables including: low income, ethnicity, education, and body size, are stronger influences on immune functioning, and fertility, in the U.S. women. Though the Kalunga women had a history of infectious and parasitic diseases, and lived in conditions of poor sanitation and poverty, they had multiple ways of mitigating the stresses of their everyday life. The shared socio-ecological conditions of their community decreased the deprivations they experienced, reduced the disabilities they felt from their health statuses, and was reflected in relative homogeneity of their lived experience. In contrast, the U.S. population was dictated by disparities. Poor health and reproductive outcomes were concentrated disproportionately in low-income, less educated, and/or minority ethnicity status, women. The findings of this dissertation have important implications for applied anthropology and the study of life history theory. My results demonstrate that Western lifestyles must be considered as instigators of life history trade-offs, and life history scholarship in humans must also focus on populations living in these conditions. Additionally, the secular changes resulting in lowered ages of menarche in U.S. women could lead to future poor health outcomes. As the Kalunga transitions into a more Western lifestyle, they are at risk for disparities within their population. It is imperative for applied anthropologists to be engaged in addressing the immune, nutritional, and psychosocial stressors within populations that perpetuate disparities, and instigate and/or exacerbate life history trade-offs.

This project tests the hypothesis that the Langobard migration into the Roman/Byzantine Veneto (northeastern Italy) resulted in significant dietary changes from Late Antiquity (4-5th centuries AD) to the Early Medieval period (6-8th centuries AD). At the end of the Great Germanic Migrations in AD 568, Langobards from Pannonia entered and occupied two-thirds of the Italian peninsula. It is unclear how large these migrations were, as historical documents exaggerate mass movements; however, conservative estimates suggest they made up 8% of the areas they occupied. The degree to which the Langobards influenced economic change and subsistence in this area is poorly understood. Therefore, the goal of this research is to use stable isotope analyses on human remains in conjunction with historical and archaeological data to understand how the migration of the Langobards influenced the population structure and political economy (diet) in the Veneto. A total of 149 individual bone samples from seven sites spanning the 4-8th centuries AD from the Veneto underwent stable carbon and nitrogen isotope analysis. In addition, 60 premolars were sampled for stable carbon, nitrogen, and oxygen isotope analysis to assess migration and dietary changes. Previous paleodietary analyses suggest that the traditional Roman diet consisted of C3 terrestrial plants, such as wheat and barley, and domesticated animals with some contributions from fish. The Langobards consumed a mix of C3 and C4 (millet and sorghum) terrestrial plants and animals. C4 plants such as millet were often considered a low socioeconomic status food source during the Roman Empire. The results indicate that migrating Langobards are not present in the cemetery samples; however, migrating Roman/Byzantines are. This suggests a migration inland from the Byzantine occupied coast for better economic prospects. Byzantine occupied areas in Italy experienced heavy taxations, while the Langobards reduced this burden on the location populations. The dietary analyses show significant differences in diet between local and non-local individuals, with non-local individuals consuming more C3 energy sources (wheat) earlier in life. In terms of overall diet in the Veneto, there appears to be an increase in millet consumption from Late Antiquity to the Early Medieval period. There are no significant differences in socioeconomic status or sex, suggesting that millet became standardized in the Veneto, reflecting a sociocultural change in dietary practices. This research is significant because it fills a geographical and chronological gap in Italian history, during a period of significant migration and economic change.

Protein secretion is a selective and regulated process that is essential in all organisms. In bacteria the preprotein translocase SecA, either free in the cytosol or associated with the SecYEG translocon, recognizes and binds most post-translational secretory proteins containing an N-terminal signal sequence. In Gram-negative bacteria, the molecular chaperone SecB binds many of the preproteins to keep them in a translocation-competent state. Subsequently, SecB delivers the preproteins to the translocon-associated SecA, which binds the signal sequence and also interacts with mature regions of the preprotein. After the preprotein/SecA/SecYEG complex has formed, the energy derived from ATP hydrolysis by SecA coupled with the proton motive force drives the insertion of the preprotein through the translocon pore. During the translocation reaction, the conformation of SecA dramatically changes from an inactive closed form (c-SecA) to one more active and open states. The various crystal structures of SecA have provided many structural details about c-SecA. The recent low resolution crystal structure of a fragment of SecA bound to SecYEG (Zimmer et al., 2008) has provided a starting point for structural analysis of the active and open conformation of SecA. Previous work in our laboratory demonstrated that an N-terminal proteolytic fragment of SecA, SecA64, is an activated form of SecA that with higher affinity signal peptides better than c-SecA (Triplett et al., 2001). To correlate the SecA64 results with full-length SecA, we determined that SecA in the presence of low concentrations of urea has an enhanced ATPase activity similar to translocation level, which is comparable to what was observed with SecA64. Analysis by CD and Trp fluorescence indicates the presence of an intermediate at 2.2 M urea at 22ºC (termed u-SecA). Using limited proteolysis, we determined that u-SecA is in an protease-sensitive conformation that mimics the translocation-active form of SecA. These structural rearrangements occur primarily in the C-terminal one-third of the protein. Next, we sought to understand the signal sequence interactions with c-SecA and translocation-active u-SecA. Using a photoactivatable cross-linking approach along with limited proteolysis, two-dimensional gels, and domain mapping with region-specific antibodies, the signal sequence-binding site was mapped to the interface of NBF II, PPXD, and HSD. The site is the same in both forms of SecA but in our data suggests u-SecA that the binding groove as expanded.

<p>This thesis details the development of a kinetic model of translation which takes into account codon usage. The process of translation involves ribosomes decoding a sequence of codons to produce a protein. Codon usage is important in the kinetics of translation since experiments have shown that codons are processed at different rates. Codons which code for the same amino acid appear with unequal frequencies and certain synonymous codons are preferred by high expression genes. The relationship between translational efficiency and codon adaptation is explored in this thesis.</p> <p>We use a simple physics model called the totally asymmetric exclusion process (TASEP) to emulate the action of ribosomes, and the decoding of mRNA in protein elongation. The simple model is parameterized by an initiation rate that determines how quickly new ribosomes are introduced onto the lattice, and the rate of motion for ribosomes associated with a site on the lattice (codon message). Based on bioinformatics studies, we assign codon speeds so that codons preferred by high expression genes are translated more quickly.</p> <p>The model captures important aspects of translation like ribosome collision and codons of different speeds, and simulating it allows us to see details in dynamics which are inaccessible to experiments. TASEP has non-trivial behaviour when codon rates, and the rate of ribosome binding is varied. Slow codons can cause ribosomes to pause and may lead to a queue. We approximated real genes with its average rate, and with its slowest codons to test the salient features of how codons are used on mRNAs. We found that codon selection is important in determining when queues occur, and the ribosome density on genes. The model also shows that highly expressed genes queue later than low expression genes. The simple model gives us general insights into the translational selection of codons, and the important kinetic parameters.</p> / Master of Science (MSc)

<p>The bending moduli and line tension of bilayer membranes self-assembled from diblock copolymers was calculated using the self-consistent field theory. The limitation of the linear elasticity theory (Helfrich model) was evaluated by calculating fourth- order curvature moduli in high curvature systems. It was found that in highly curved membranes, the fourth-order contributions to the bending energy becomes comparable to the low-order terms. The line tension (γL) of membrane pores was also investigated for mixtures of structurally different diblock copolymers. The line ten- sion was found to depend sensitively on the diblock chain topology. Addition of short hydrophobic copolymers was found to reduce the line tensions to negative values, showing that lipid mixtures may be used as pore stabilizers.</p> / Master of Science (MSc)

<p>Microbeam radiation therapy (MRT) is an experimental radiotherapy concept that has been primarily developed for the treatment of malignant brain tumours. MRT uses high flux synchrotron x-rays delivered as an array of parallel microbeams in high doses of irradiation in fractions of seconds. The aims of this study were to 1) investigate the induction of bystander effects after normal and tumour-bearing rat brains were exposed to MRT and homogenous radiation; 2) validate a brain bystander proteome by detecting protein expression throughout immunohistochemistry: and 3) to investigate whether communication of bystander signals can be produced between animals.</p> <p>Healthy and tumour-bearing Wistar rats were exposed to 17.5, 35, 70 or 350 Gy of MRT or homogenous field of synchrotron radiation to the right brain hemisphere. To study the communication of bystander effects between animals, irradiated rats shared the same cage with non-irradiated rats over a period of 48 hours. After euthanasia of the animals, brains and bladders were dissected, and samples for immunohistochemistry and bystander clonogenic assays were set up.</p> <p>Clonogenic survival of the reporter HPVG cells showed that bystander effects occurred in both the non-irradiated hemisphere and bladder of normal and tumour-bearing rats, while the irradiated hemisphere showed the direct effects of radiation. Moreover, communication of bystander signals was confirmed in the non-irradiated rats.</p> <p>In conclusion, the results suggest that the MRT and homogenous radiation of unilateral normal and tumour-bearing rat brains produce bystander signals that affect the whole organism and that those signals also can be transmitted to non-irradiated animals.</p> / Master of Science (MSc)

<p>The phase behavior of AB diblock copolymers mixed with C homopolymers (AB/C), in which A and C are capable of forming hydrogen-bonds, is examined using self-consistent field theory. The study focuses on the modeling of hydrogen-bonding in polymers. Specifically, we examine two models for the formation of hydrogen-bonds between polymer chains. The first commonly used model assumes a large attractive interaction parameter between the A/C monomers. This model reproduces correct phase transition sequences as compared with experiments, but it fails to correctly describe the change of lamellar spacing induced by the addition of the C homopolymers. The second model is based on the fact that hydrogen-bonding leads to A/C complexation. We show that the interpolymer complexation model predicts correctly the order-order phase transition sequences and the decrease of lamellar spacing for strong hydrogen-bonding. Our analysis demonstrates that hydrogen-bonding of polymers should be modeled by interpolymer complexation.</p> / Master of Science (MSc)

RASSF1A is a tumor suppressor gene which loses its function due to methylation of CpG islands on its promoter region. Detection of methylation leads to early diagnosis of cancer. Zinc finger proteins are capable of detecting a specific DNA sequence and Methyl binding domain can bind to the methyl group on the CpG, using this idea mCpG SEER- Lac system makes use of a split protein, β-lactamase. Lac A attached to the ZFP and Lac B attached to the MBD protein. On binding to the DNA, the Lac A and Lac B come in close proximity with each other causing a reassembly and activation of the enzyme. In the presence of a substrate, the activated β-lactamse enzyme hydrolyzes the β-lactam bond in the substrate and shows a color change from yellow to red in the presence of a methylated cognate DNA. The study suggests that a solution based assay was not as specific in differentiating signal intensities between methylated and non-methylated DNA. It was also not sensitive in measuring dose dependent signals. Zinc finger array could successfully show relatively low signals for non-methylated DNA. The findings of the study show that MBD2 shows higher preference for mCpG than MBD1 in the mCpG SEER-Lac system and oligonucleotides with a 2 bp spacing between methylation and ZF target site shows higher signals than the 3 bp spacing. Due to it’s specificity and sensitivity, it serves as a potential diagnostic tool to detect cancer.

This paper considers the statistical mechanics occupation of the edge of a single helix of DNA by simple polymers. Using Fisher's exact closed form solution for dimers on a two-dimensional lattice, a one-dimensional lattice is created mathematically that is occupied by dimers, monomers, and holes. The free energy, entropy, average occupation, and total charge on the lattice are found through the usual statistical methods. The results demonstrate the charge inversion required for a DNA helix to undergo DNA condensation.