Thesis (Ph.D.)--University of California, San Francisco, 2009. / Source: Dissertation Abstracts International, Volume: 70-10, Section: B, page: 5941. Adviser: Pao-Tien Chuang.

Inferring ancestral gene orders in a phylgenomic tree is an important topic in comparative genomics. In this thesis, three different approaches have been used to infer ancestors, first, using common intervals in a model-free approach and extending it to using common clusters and neighbourhood parameter; second, using double cut and join operation (DCJ); third, using breakpoint distance. A statistically fair comparison between the performance of DCJ and breakpoint criteria ends the thesis. Away from any assumptions or considerations, probabilistic or combinatorial, about specific processes involved in rearranging genomes, we present a new phylogenetic reconstruction method based solely on common intervals. The objective function to be optimized is simply the sum over the tree branches of the symmetric difference between the two sets of intervals associated with the genomes at the two ends of the branch. To achieve this goal, we use dynamic programming optimization to determine the presence of common intervals at the ancestral nodes of the phylogeny. Noticing the drawback that the concept of common intervals suffers from, we introduce the concept of generalized adjacency to find common clusters using a neighborhood parameter that turns out to be closely related to the bandwidth parameter of a graph. Our focus will be on how this parameter affects the characteristics of clusters: how numerous they are, how large they are, how rearranged they are and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. Again, we use dynamic programming optimization to determine the presence of individual edges at the ancestral nodes of the phylogeny. The DCJ (double cut and join) operation introduced by Yancopoulos et al. in 2005 is the most inclusive operation to date as it can generate all the movement rearrangements. One year later, Bergeron et al. restated the DCJ model and produced a simplified (linear) algorithm, which is now the most general existing algorithm to transform one genome into another using genome rearrangements events. Motivated by both, the most inclusive operation, DCJ, and its most general algorithm, we study the small phylogeny problem in the space of multichromosomal genomes under the DCJ metric. This is similar to the existing MGR (multiple genome rearrangements) approach, but it allows, in addition to inversion and reciprocal translocation, operations of transposition and block interchange. Thanks to Tannier et al., the first polynomial solution to the median problem has been found in only one context, namely the case of breakpoint distance on multichromosomal genoms where chromosomes are unconstrained as to linearity or circularity. This motivated us to study the small phylogeny problem using breakpoint median as a third approach, that is different both biologically and computationally from the common intervals and DCJ approaches, and then to compare statistically the performance of both criteria, breakpoint and DCJ. Keywords: phylogenetic tree, genome rearrangment, inversion, reciprocal translocation, transposition, block interchange, common intervals, generalized adjacency, neighborhood parameter, graph bandwidth, multiple genome rearrangement (MGR), double cut and join (DCJ), breakpoint (BP), excess explanatory rate.

The migration of the cranial neural crest is an essential part of cranio-facial development in every vertebrate embryo. The cranial neural crest (CNC) is a transient population of cells that forms the lateral border of the anterior neural plate. In the tailbud stage Xenopus embryo, the neural crest cells delaminate from the neural tube, and undergo a large-scale migration from the dorsal to ventral region of the embryo. The CNC travels along distinct pathways, and populates specific regions of the embryos face. Once the CNC ceases migrating, it differentiates into a variety of tissues that are essential for cranio-facial structure and function. Some of these tissues include bones, muscle, cartilage, and ganglia. The CNC receives a concert of signals from neighboring tissues during and after CNC migration as well as signals transmitted among CNC cells, which act together to determine the fate of each CNC cell. Therefore, the proper migration of the CNC is an essential part of cranio-facial development. What molecules are important for the process of CNC migration? As one might imagine, a milieu of different molecules and interactions are essential for this complicated embryological process to occur. The work presented in this dissertation will focus on the role of a cell adhesion molecule that is important for Xenopus CNC migration. Typically, the amount of cell adhesion decreases within tissues undergoing migration. This behavior is essential to allow fluidity within the tissue as it moves. However, cell adhesions are fundamental for cell migration to occur because the moving cells need a platform on which to mechanically propel themselves. These interactions can occur between the migrating cell and extracellular matrix molecules (ECM), or can happen between cells. The cranial neural crest utilizes both cell-ECM and cell-cell interactions during the process of migration. The amount of cell adhesion mediated by either of these mechanisms will depend on where the cell is located within the CNC. Cells located at the periphery of the CNC tissue, which is surrounded by a matrix of ECM, will have more cell-ECM interactions. Cells located deeper in the CNC tissue, where there is little ECM, will rely more on cell-cell interactions. The work presented in this thesis focuses on a cell-cell adhesion molecule that is part of the cadherin superfamily of molecules. With this in mind, these studies should be descriptive of the environment within the CNC, and to a less degree the environment between the CNC and the surrounding tissues. The work presented in this dissertation will focus on cadherin-11, which is a classical cadherin that is specifically expressed in the cranial neural crest during its migration. How does cadherin-11 function in the CNC during this process? The work presented here suggests that the main role of cadherin-11 in the CNC is to perform as a cell adhesion molecule. However, too much cell adhesion is inhibitory to migration. In this respect, many of the studies described in this work indicate that cadherin-11 mediated cell adhesion is tightly regulated during CNC migration. Here I show that cadherin-11 is extracellularly processed by ADAM metalloproteases, ADAM9 and ADAM13, which removes the adhesive domain of cadherin-11. This extracellular cleavage event occurs throughout CNC migration, and is likely the main mechanism that regulates cadherin-11 mediated cell adhesion. Cleavage of cadherin-11 by ADAMs does not seem to affect its ability to interact with cytoplasmic binding partners, β-catenin and p120-catenin. This observation supports the idea that the “purpose” of cadherin-11 cleavage is to regulate cell adhesion, and not to induce (cell autonomous) signaling events. Additionally, the secreted extracellular domain of cadherin-11 (EC1-3) retains biological activity. This fragment can bind to a number of cell surface molecules in tissue culture including full-length cadherin-11 and specific members of the ADAM family. This observation suggests that EC1-3 may interact with full-length cadherin-11 molecules in vivo, and inhibit cadherin-11 mediated cell adhesion during CNC migration. EC1-3 can rescue CNC migration in embryos that overexpress cadherin-11, further supporting this hypothesis. Many of the above observations have been published in my first-author paper entitled “Extracellular processing of cadherin-11 by ADAM metalloproteases is essential for Xenopus cranial neural crest migration” published in the journal Molecular Biology of the Cell in 2009. Some of the unpublished work in this dissertation further focuses on how EC1-3 effects CNC migration in an ex vivo environment. During these studies, the observation was made that overexpression of EC1-3 in a cranial neural crest explant produces abnormal directional movement. In these experiments, it appeared as though certain regions of the CNC explant were “attracting” other regions of the explant. The preliminary studies described in chapter IV are aimed at answering the question; does EC1-3 attract migrating CNC cells? Here, we generated a Matlab program in order to effectively quantify the amount of directional movement of CNC explants presented with a source of EC1-3. In addition to quantifying cell directionality, this program can also decipher between cells moving with random or directed motion, and measure the velocity of cell migration within certain coordinates. Therefore, this program should be useful other ex vivo studies that require the observation of these features. To conclude, the work presented in this dissertation suggests that the role of cadherin-11 during cranial neural crest migration is predominately based on the adhesive function. In order for CNC migration to proceed, the amount of cadherin-11 mediated cell-cell adhesion is tightly regulated throughout this process. These cell-cell interactions are likely important for “sheet” and “branch” migration where CNC cells maintain a lot of cell-cell cohesion.

The purpose of this study is to understand the evolution and diversification of a complex of basioccipital and pharyngeal structures that are important for feeding in cypriniform fishes with special reference to Catostomidae. Fishes in the family Catostomidae are a diverse group inhabiting temperate lotic and lacustrine waters of North America and East Asia. The palatal organ is a muscular pad that forms the roof of the pharynx in catostomids and some cyprinids and functions in separating food items from inorganic debris during feeding. The basioccipital bone forms the postero-ventral part of the neurocranium and part of the skeletal base of the palatal organ. Palatal organ and basioccipital bone morphology is variable among cypriniform families and statistically significant variation exists among catostomids. Subfamily Cycleptinae has the shortest, narrowest, and thinnest palatal organ of all the subfamilies. Subfamily Ictiobinae has the thickest and widest palatal organ. Generally, the shape and size of the palatal organ in Catostominae is intermediate between the other subfamilies. Catostomids possess a ventral and posterior pharyngeal process of the basioccipital bone that is expanded into a fenestrated lattice of bony struts. The pharyngeal process is not fenestrated in cyprinids; however, its ventral portion is modified in to the masticatory plate for attachment of the chewing pad. Only catostomids and cyprinids possess a chewing pad. The chewing pad is lunate in catostomids and generally ovoid in cyprinids. A synonymy of terms used to describe the palatal organ and chewing pad of Cypriniformes is provided. Phylogenetic analysis of mitochondrial and nuclear genes resolve Catostomidae as a monophyletic group with two major clades. Of the two major clades, one comprises Catostominae and the other includes a basal Cycleptinae sister to Myxocyprininae plus Ictiobinae. The sister group of Catostomidae is uncertain because of low bootstrap support at the base of the cypriniform tree. Ancestral character state reconstruction determines that the palatal organs of Catostomidae and Cyprinidae are not homologous. The ancestor of Catostomidae had a palatal organ, fenestrated pharyngeal process, and was probably a large-bodied fish with an inferior or subterminal mouth that occupied benthic habitats / acase@tulane.edu

<p> Researchers have identified inadequate sleep duration as one of the factors contributing to global obesity. The purpose of this study was to test a hypothesis deduced from a new sleep-duration-based evolutionary theory claiming that sleep extension in response to lengthening night duration in early fall evolved into a behavioral marker of an approaching winter; this adaptive trait was theorized to produce adiposity gain in White men in response to sleep extension. The hypothesis was that White Americans would show a greater increase in the age-adjusted fat mass index per unit of sleep duration compared to that of Black Americans. Data were part of the National Health and Nutrition Examination Survey (NHANES) study between 2005 and 2010. The multiple regression analysis did not support the study hypothesis. The results indicated that habitual sleep duration had no effect on the annual rate of adiposity gain in White men, while in Black men, longer sleep was associated with significantly higher annual rates of adiposity gain. Implications for social change include the case for population-specific antiobesity interventions in Black men, including closer monitoring of sleep duration in order to prevent adverse habitual sleep extension and to improve time budgeting for physical exercise.</p>

<p> I found that in inbred females <i>D. melanogaster,</i> physical condition plays a major role in the amount of polyandry. In some systems there is evidence that the ability to self assess allows inbred females to vary their reproductive behavior to increase promiscuity. I predicted that this may be true in <i>Drosophila melanogaster</i> females, but we found that inbred females behaved less promiscuously in three proxies than outbred females. Inbred females mated with fewer total males, fewer different males, and had longer copulation latency than their outbred conspecifics. However, male mate choice is not predicted in <i>Drosophila melanogaster </i> because males invest less than females, but recently the importance of male preference has been gaining support. How these males are making decisions is an important component to understanding the evolutionary impacts of the male's behaviors. I found that male mate choices are heavily influenced by previous experiences, and the lack of experience causes significant changes in courtship latency and overall preferences.</p>

<p> Comparative and evolutionary cognitive scientists disagree on whether human and nonhuman primate cognition is driven by a general intelligence or more specific, modular mechanisms. Comparative research with chimpanzees is extensive and provides the opportunity to better understand the evolution of human cognition. Little research has been dedicated to individual differences in chimpanzee social and physical cognition. The study of individual differences can be informative in better understanding the generality of primate intelligence. Results supporting a correlation between performances in the social and physical domains would suggest that a domain-general inference system may be responsible. If no relationship is revealed between performances then more compartmentalized, modular mechanisms may be responsible. As a preliminary investigation, I administered four studies focusing on social and physical cognition to a large number of captive chimpanzees. Performance on two tool-using tasks served as indicators of physical intelligence. I administered two social investigations regarding individual variation in social responsiveness and sociability. I did not find a correlation between the social and physical investigations; however strong individual differences in performances were observed. Demographic factors sometimes played a role in the results presented here (e.g. dominance rank and age). While this research does not demonstrate a relationship between sociability and physical intelligence, additional social measures should be utilized in order to measure social cognitive ability in chimpanzees. Focusing on individual differences with a battery of social and physical tasks will be informative regarding the structure of primate intelligence and the underlying cognitive mechanisms that are responsible.</p>

<p> Male katydids produce mating calls through stridulation to attract potential mates. Calls were recorded in the field and analyzed to compare between two related species that occur in overlapping ranges in the northwestern United States. Distinct differences were found between the two species' calls in both dominant frequency and chirp rate. Also, one species interspersed trills amongst the chirps of the call, while the other species' call did not include trills. These distinct call differences can be used for species identification and can be easier to differentiate than physical characteristics. </p><p> The upper limits of sexual selection can be estimated using upper limits on Bateman gradients, which represent how fecundity increases with additional mates. Upper limits on Bateman gradients are expected to be constrained by various factors such as nutrition. These upper limits were estimated using controlled mating experiments with katydids on high and low protein diets (as adults) by measuring how maximum fecundity (fecundity with ideal mates) increased with each mating. Decreases in both maximum fecundity and the potential for sexual selection were expected in males and females due to protein limitation. This would result from decreased potential fecundity in low protein females and decreased value of nuptial gifts given by low protein males. The results did not support our predictions as strongly as hoped, but a decrease in the upper limits of sexual selection was nearly significant in low protein males, evidenced by reduced fecundity gains from remating. Also, spermatophores (the katydid nuptial gift) had a more complicated effect on fecundity than expected. Spermatophore size differed between males' first and second matings, however, larger spermatophores did not always confer more value to females, particularly in second matings. </p><p> Stable isotope analysis was used to examine the lack of significant effects from differences in dietary protein on the upper limits of sexual selection in the previous experiment. Stable isotope ratios were analyzed for three body tissues to infer diet at different life stages by comparison with isotopic values from the foods. Results showed that animals on the low protein diet may have eaten more food to make up for their protein deficit, which would have confounded nutritional effects in the previous study. Sex differences in nutrient processing were present as would be expected if males and females experience different nutritional requirements for reproduction. Nutrient processing in exoskeleton varied across food treatments in males but not in females. This suggests that males experienced greater protein limitation than females and adjusted their nutrient processing accordingly. Further work is underway to determine how much of each type of food was consumed by individuals in different experimental treatments and during different life stages. </p>

<p> The plant hormone auxin plays a major role in shaping plant morphology and development, but the gene networks regulating its synthesis and transport are incompletely known. The maize <i>BARREN INFLORESCENCE 1</i> (<i>BIF1</i>) gene has recently been cloned and shown to play an important role in the early stages of polar auxin transport. Auxin is synthesized in shoot tips and transported basipetally through the plant shoot and acts as a morphogen by facilitating the degradation of transcriptional repressors in a concentration dependent manner. The <i>AUX/IAA</i> gene family encodes transcriptional repressors that regulate a subset of plant developmental responses governed by the transcription of early auxin inducible genes in plants. Although the maize <i>BIF1</i> gene is a member of the <i>AUX/IAA</i> gene family, the co-ortholog(s) of <i> BIF1</i> in <i>Arabidopsis thaliana</i> was not known prior to this research.</p><p> Bayesian phylogenetic reconstruction placed maize <i>BIF1</i> in a clade sister to <i>Arabidopsis thaliana AtIAA15</i>. The <i> BIF1</i> lineage has undergone two gene duplications since the divergence of the early grasses. Molecular evolutionary analyses by maximum likelihood suggest that the <i>BIF1</i> alignment is under strong purifying selection with positive selection acting on a glutamine residue located in a functional region associated with <i>AUX/IAA</i> protein dimerization in one clade of <i>BIF1</i> paralogs, the <i>BIF1-Like2</i> (<i>BIF1L2</i>) clade. A character reconstruction analysis using maximum parsimony estimated an adenine to cytosine transversion at the base of the <i>BIF1L2</i> clade changed a glutamine into an alanine residue in this functional region. Expression of <i>BIF1</i> orthologs is conserved in floral meristems in the eudicot <i>AtIAA15</i> clade containing the taxa <i>Erianthe Guttata, Arabidopsis thaliana, Medicago truncatula</i>, however grass <i>BIF1L2</i> expression has diverged within the PACMAD &ndash; BEP clade, specifically in rice, where <i> BIF1L2</i> expression is reported to have moved into root tissue. These results suggest that <i>BIF1</i> paralogs has changed following a second round of gene duplication in the grasses. Taken together, a change in localized expression in these sequences, and positive selection acting on a glutamine-rich region of the protein-protein binding motif could imply that BARREN INFLORESCENCE1-like2 proteins are probably interacting with a new set or subset of AUXIN RESPONSE FACTOR (ARF) binding partners, and that neofunctionalization has occurred in the <i>BARREN INFLORESCENCE1-like2 </i> clade.</p>

Thesis (Ph.D.)--Indiana University, Dept. of Biology 2009. / Title from home page (viewed on Jul 8, 2010). Source: Dissertation Abstracts International, Volume: 70-10, Section: B, page: 5957. Advisers: Loren H. Rieseberg; Scott D. Michaels.