<p> This study used fine-scale phylogeography of populations of side-blotched lizard, <i>Uta stansburiana</i> to determine concordance with previously identified phylogeographic patterns in the Transverse Mountain Range of Southern California. Mitochondrial DNA analysis revealed clade distributions that both agreed and conflicted with previously identified clade breaks. This study revealed two new distinct clade breaks that transect the San Gabriel Mountains and detected haplotype mixtures in populations sampled between the San Gabriel and San Bernardino Mountains. Genetic landscape GIS analyses identified areas of genetic divergence and diversity for this species. This combined analysis enabled the discovery of a suture zone between the San Gabriel and San Bernardino Mountains that represents a phylogenetic crossroads with high levels of diversity and divergence and complex phylogeographic structure. My results suggest the importance of the use of fine-scale phylogeographic analysis in the discovery of new clade boundaries within a geologically complex and hyper-diverse region.</p>

<p> Signaling theory originated in evolutionary biology and explains the mechanisms behind the honest communication of information between organisms. Communication scholars are increasingly turning to signaling theory as a way to test evolutionary explanations for human behavior. The present study tests if receiver-dependent costly signals can be used to predict the moment of aggressive behavior in video game environments. High status (but not high trait aggression) male subjects were fastest to engage in combat against a low voice pitch male opponent - but only when subject skill was high. This result underscores the importance of video game skill as a variable of interest as well as the need for video games researchers to tease out when real-world behaviors map to video game contexts.</p>

<p>Much of plant growth is directly or indirectly regulated by the plant hormone auxin. Although some genes involved in the auxin pathway have been characterized, there are still gaps in our knowledge of this genetic pathway. Recently, the orthologous maize genes <i>BARREN STALK2</i> (<i> BA2</i>) and rice gene <i>LAX PANICLE2</i> (<i>LAX2</i>) have been cloned and characterized. Maize <i>ba2</i> and rice <i> lax2</i> mutant plants both show significant flaws in axillary meristem (AM) initiation, suggesting a role in auxin regulation. In support of this hypothesis, <i>LAX2</i> interacts with the auxin regulating <i> LAX PANICLE1</i> (<i>LAX1</i>) protein. My research reconstructs the evolutionary history of the <i>BA2</i>/<i>LAX2</i> lineage and tests for conservation of <i>BA2</i>/<i>LAX2</i> mRNA expression in diverse grasses. My results indicate that the <i> BA2</i>/<i>LAX2</i> gene family&mdash;comprising <i>BA2 </i>/<i>LAX2</i>, <i>BA2</i>/<i>LAX2-Like1</i> (<i>BA2</i>/<i>LAX2L1</i>), and <i>BA2</i>/<i> LAX2-Like2</i> (<i>BA2</i>/<i>LAX2L2</i>)&mdash;is restricted to monocots, and shows evidence of two independent gene duplication events. During its evolution, the <i>BA2</i>/<i>LAX2</i> gene family appears to have gained a PDZ Protein Binding motif, which may allow it to interact with other proteins besides <i>BA1</i>/<i> LAX1</i>. My expression analyses show that <i>BA2</i>/<i> LAX2</i> genes are expressed during multiple stages of inflorescence development, and this expression is conserved across multiple grass species. A unique floral expression pattern appears to have evolved at the base of the Joinvilleaceae lineage. My study further supports the hypothesis that <i> BA2</i>/<i>LAX2</i> genes are functioning in multiple AM pathways. </p>

Thesis (Ph. D.)--University of Chicago, Dept. of Organismal Biology and Anatomy. / Includes bibliographical references. Also available on the Internet.

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

The characteristics of space and the movement of agents are intrinsic elements which are fundamental to any class of biological problems. From the diffusion properties of small and macromolecules in the cytoplasm, to the migration patterns of populations in a macroecological perspective, it is now clear that a full understanding of the different phenomena requires further insights not only on how the different elements interact, but on the different ways they are distributed in space, according to the proper spatial scales for each problem. This work analyzes three different classes of biological problems, focusing on the role played by space in understanding the phenomena from a theoretical perspective. First, we investigate the clustering of mechanosensitive channels on bacterial membranes and how their spatial distribution can lead to collective behaviour, significantly altering their functions. Second, we study protein production, trying to understand how particular properties on ribosomes' diffusion are linked with specific features of the translation process. Finally, on a very different scale, we explore spatial patterns' formation on a coevolutionary problem, where the interaction between two species is site-dependent. We approach these problems with different analytical and numerical techniques, revealing new biological aspects and providing novel views on current discussions in each field. We believe our results reinforce the importance of theoretical approaches to Biology and how space can significantly change many of these models.

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

Thesis (Ph. D.)--Ohio State University, 2003. / Title from first page of PDF file. Document formatted into pages; contains xiv, 131 p.; also includes graphics. Includes abstract and vita. Advisor: David L. Haury, College of Education. Includes bibliographical references (p. 97-104).