▼ Spider silk is a biomaterial that combines high strength and extensibility. Because of these exceptional material properties, silk could be used for many applications. However, before we can mass-produce spider silk analogs for these applications, we need to better understand the relation between silk molecular structure and its properties. Furthermore, the whole range of properties that can be achieved by silks may not have been gauged yet, as most studies focus on a few selected species. The first part of my research focused on silk plasticity. I found that common house spiders (Achaearanea tepidariorum) change their silk properties in function of their prey type (cricket or pillbug). Silk properties also differ between different regions of the cobweb spun by a common house spider. However, silk properties did not differ for other species (black widows and bridge spiders). Major ampullate silk plasticity increased during spider evolution. Silk plasticity may be mediated by a valve present in the spinning duct of Orbicularia, which allows them to apply shear forces during forcible silking and control their speed during falls. Silk plasticity may have been selected for as spiders make more diverse uses of their major ampullate silk. The second part of my research dealt with supercontraction. Supercontraction refers to the shrinking of silk exposed to high humidities. Several hypotheses on its mechanisms and functions have been proposed, but seldom tested. By measuring supercontraction in many different spider species, with various silk composition, web type and silk uses, I tested three of these hypotheses. GPGXX amino acid motif are likely involved in supercontraction. Furthermore, supercontraction probably allows spiders to better tailor their silk properties, but, contrary to an early idea, it may not help protect webs from water drops. Supercontraction may affect how whole webs function too. Supercontracted webs were found to absorb more kinetic energy and deform more when hit by a projectile (mimicking a flying prey). Thus, another potential function of supercontraction is to improve web performance. To conclude, my research shed light on various aspects of silk material properties by taking an evolutionary approach. This approach may be expanded further in order to better understand silk evolution and estimate the range of silk properties. This study also helps better understand how silk properties and web architecture interact within spider webs. Advisors/Committee Members: Blackledge, Todd A.

▼ Expression and function of protocadherin-17 (pcdh17) in zebrafish retinal development were analyzed in this study. Pcdh17 mRNA (pcdh17) expression pattern was characterized using whole mount in situ hybridization method. Antisense morphlino oligonucleotides (MOs) technique was used to determine pcdh17 function. Moreover, molecular mechanisms underlying pcdh17 expression and function were studied using proteomics. pcdh17 was expressed in developing zebrafish retina during critical stages of its development. Abnormal eye and retinal development was observed in developing zebrafish (49-72 hours post fertilization, hpf) injected with zebrafish pcdh17 specific MOs (pcdh17 morphants). The morphants had significantly smaller eyes and disrupted differentiated retinal cells (e.g. retinal ganglion cells and photoreceptors), due mainly to decreased cell proliferation as well as defects of nonneuronal cell differentiation. Proteomic analysis revealed that several hundred proteins were differentially expressed between wildtype embryos and pcdh17 morphants. A subset of spots showing the biggest differences were identified using Mass Spectrometry. These proteins included phosphoglycerate kinase, beta-actin-like protein, and glial fibrillary acidic protein (GFAP). Most of the identified proteins are involved in basic cellular metabolism and cellular structure, whereas GFAP is a molecule involved in Notch signaling pathway known to play a critical role in vertebrate retinal development. In addition, pcdh17 functions in retina development via regulating certain transcription factors, classical cadherins, homophilic reacting molecules and integrin-dependent adhesion. My research suggests that pcdh17 plays an important role in zebrafish retinal development, likely through involving multiple pathways including Notch-Delta, Wnt pathways. Advisors/Committee Members: Liu, Qin.

▼ Quantitative genetics has provided a proximate tool for making evolutionary predictions based on genetic and environmental sources of variation. Unfortunately, quantitative models have failed to address the evolutionary consequences of development in complex, changeable environments. This type of knowledge can only be achieved by tracking unique genotypes across all possible combinations of changing environmental factors. The first part of my research focuses on the consequences of changing environmental oxygen on zebrafish cardiovascular development. I found that cardiac output at the 48th hour of development in a given oxygen environment was conditional upon oxygen conditions during the first 24 hours of development. These conditional responses varied across genotypes, resulting in interactions between genotype, early, and later environments (G xExE). The second part of my research focused on the consequences of changing oxygen on zebrafish morphology. I found that body shape in zebrafish in a given oxygen environment for days 6-90 was conditional upon oxygen conditions for days 0-6. These conditional responses also varied across genotypes. The third part of my research focused on the consequences of changing oxygen on zebrafish behavior, size, and physiology. I found that size and iv behavior in zebrafish was dictated by oxygen conditions for days 0-30. Physiology, however, was influenced most by oxygen conditions for days 30-90. The fourth part of my research focused on the consequences of changing food rations of zebrafish size and swimming ability. I found that fish raised under all possible combinations of high and low food treatments achieved the same body size at 60 days. Swimming performance, however, was conditional on interactions between feeding treatments. I also detected significant family-level variation for these responses, indicating at least some heritable variation. These studies comprise some of the first quantitative genetic studies to track developmental outcomes across more than one instance of environmental change. My work has shed light on the evolutionary potential in complex, changeable environments as well as provided a tractable tool for partitioning the proximate sources of development across discrete ontogenetic periods. Advisors/Committee Members: Bagatto, Brian.

▼ The modern synthesis of paleontology with evolutionary biology has successfully integrated population ecology into the study of the fossil record. While it may prove impossible to measure and account for the important processes that structure communities through time, the integration of community ecology into paleoecology remains to be done to further the modern synthesis. This dissertation attempts to integrate community ecology into the study of a lacustrine ostracode metacommunity across space today and through the mid Holocene on San Salvador Island, Bahamas. Patterns of community change across space today are investigated by comparing the live/dead agreement in taxonomic composition and rank-abundance of species in seven lakes. This taphonomic study establishes that live/dead agreement of ostracode assemblages is high in all lakes save one. Therefore, sampling of death assemblages, as is common in many paleolimnolgical studies, can be used to investigate changes in alpha and beta diversity of assemblages across time and space. Death assemblages were then sampled from thirty-two lakes on San Salvador to investigate the metacommunity dynamics that explain patterns of beta diversity of communities. I found that beta diversity was most strongly controlled by the local environment in which communities live with the change in communities most strongly correlated with changes in a complex hydrological gradient of: conductivity, dissolved oxygen, and alkalinity. After establishing that the metacommunity dynamics conformed to a species sorting model, I exploited the association between ostracode assemblages and conductivity to create a statistical model that used changes in ostracode assemblages to predict changes in conductivity within individual lakes on San Salvador. This model was then applied to archives of ostracode assemblages from the mid-Holocene to today to create a record of changing conductivity through time in three lakes. The model reveals large, high-frequency fluctuations in conductivity controlled by regional changes in precipitation/evaporation ratios, controlled by similarly high frequency climate oscillations. Finally, I use the metacommunity concept of community ecology as a theoretical tool to explain how changes in communities through time are related to ecosystem dynamics. Ostracodes, as easily-dispersed organisms who respond to changes in their local environment through habitat-tracking, prove to be consistently useful proxies of environmental changes. In this way, neontological principles are successfully applied to the paleoecological record demonstrating the seamless application of community ecology to the fossil record. Advisors/Committee Members: Park, Lisa E.

▼ Lung failure due to chronic bacterial infection is the leading cause of death for patients with cystic fibrosis (CF). It is thought that the chronic nature of these infections is, in part, due to the increased tolerance and recalcitrant behavior of bacteria growing as biofilms. Inhalation of Silver Carbene Complex (SCC) antimicrobial, either encased in L-tyrosine polyphosphate (LTP) particles or in aqueous form, has been proposed as a treatment. Through a coordinated experimental and mathematical modeling effort, this dissertation examines this proposed treatment of lung biofilms. Pseudomonas aeruginosa biofilms grown in a flow-cell apparatus irrigated with an artificial CF sputum medium are analyzed as an in vitro model of CF lung infection. A 2D mathematical model of biofilm growth within the flow-cell is developed. Numerical simulations demonstrate that SCC inactivation by the environment is critical in aqueous SCC, but not SCC-LTP, based treatments. LTP particle degradation rate is shown to be a tunable parameter that can be chosen optimally, based on environmental conditions and bacterial susceptibility. In addition, a 2D model of mushroom-like morphology and cavity formation in Pseudomonas aeruginosa biofilms is developed. Iron-signaling is proposed as a plausible mechanism for cavity formation. Advisors/Committee Members: Young, Gerald.

▼ Reductions in uterine perfusion pressure are thought to be a central component of the pathological pregnancy disease, preeclampsia. Preeclampsia is a hypertensive disorder of pregnancy characterized by vascular dysfunction and end organ underperfusion and is the leading cause of maternal and fetal morbidity and mortality in the United States and throughout the world. Uterine arterial reactivity and structural mechanics during preeclampsia are poorly understood and likely contributed to the pathophysiology of the maternal hypertension and altered fetal growth demonstrated in this disease. The first aim of this dissertation project was to characterize the impact of reductions in uterine perfusion pressure on maternal and fetal pregnancy outcomes. Maternal hypertension and fetal morphometrics have been examined in response to reductions in uterine perfusion pressure. The second aim of this research was to characterize the vascular behavior and structural biophysical mechanics of resistance-caliber uterine arteries in response to reductions in uterine perfusion pressure. Vascular behavior was examined using a pressurized arteriograph where myogenic reactivity, agonist induced vasodilation and vasoconstriction, and passive structural mechanics were assessed. The third aim of this research involved testing the efficacy of a novel L-tyrosine based gene delivery device. L-tyrosine polyphosphate (LTP) nanoparticles have demonstrated promise as a potential intracellular gene delivery device aimed at therapeutic avenues however; the in vivo efficacy of the delivery vehicle has been unknown. We aimed to prove the concept that LTP nanoparticles encapsulated with plasmid DNA would be efficacious as an in vivo gene delivery device in the rat uterus. Chronic reductions in uterine perfusion pressure resulted in maternal hypertension and severe fetal growth restriction in pregnant rats suggesting an integral role of uterine perfusion pressure on maternal and fetal responses to the pathology. Uterine artery reactivity was found to be altered towards a constrictive phenotype in response to chronic reductions in uterine perfusion pressure with increased myogenic reactivity and decreased agonist induced vasodilation. Structural parameters of resistance-caliber uterine arteries were unaltered in response to the pathology while biophysical mechanical properties of the uterine arteries were altered. Distensibility was altered in isolated resistance-caliber uterine arteries isolated from reductions in uterine perfusion pressure gravid rats suggesting a potential contributing factor to the vascular dysfunction described above. Nanoparticles formulated from L-tyrosine polyphosphate successfully delivered plasmid DNA in vivo to the rat uterine tissue. These data suggest that uterine arterial reactivity is altered in response to reductions in uterine perfusion pressure and that LTP nanoparticles encapsulated with plasmid DNA may have potential as a delivery platform for therapies aimed at diseases of the uterus and uterine vasculature. Advisors/Committee Members: Ramirez, Rolando.