Weakly electric fish produce and detect electric fields and use their electrosensory modality in a number of behaviours including navigation and communication. They can modulate their electric discharge in frequency and amplitude to produce electrocommunication signals in variable patterns during social interactions. In one model neuroethological species, Apteronotus leptorhynchus, the most commonly produced communication signal is the ‘small chirp’ – a brief 10-30ms modulation. Individuals tend to produce these signals at high rates during agonistic interactions. In this thesis I will explore the social value of chirps, and to a lesser extent other communication behaviours, in A. leptorhynchus using a variety of experimental designs involving different staged social contexts. I use time series analysis methods to explore the patterns of chirps produced and accompanying aggressive behaviours. I first characterize electrocommunication and chirping in pairs of free swimming fish and correlate signal production with aggressive displays. Bursts of echoed, or reciprocated, chirps tend to be produced in the intervals separating aggressive attacks. Behavioural analysis shows that fish respond to conspecific chirps with echoed chirps and decreased aggression in social contexts outside the range in which previous modelling and electrophysiological data predicted that chirps could be encoded effectively. I then characterize the chirping and aggressive responses to playbacks simulating intruders with different chirping styles to test whether alternative chirp patterns differentially influence conspecific behaviour. In response to simulated intruders producing chirps that echo the real fish’s chirps with a short latency, less aggressive fish tend to produce more of their chirps in bursts than more aggressive fish. For randomly chirping intruders, the response of fish depends on the rate of chirps delivered. Fish respond less aggressively, with fewer chirps, and echo the stimulus chirps at a higher rate when high rates of random chirps are delivered than when responding to simulated intruders with low rates of randomly delivered chirps. Further, across all playback scenarios, fish that produce chirps in response to the playbacks are more aggressive than those that do not chirp. Finally, to better understand the electrosensory inputs during these interactions, I characterize changes in the electric image received by a restrained fish during movements of a free-swimming conspecific and correlate these with chirp production. When one fish is restrained, bursts of chirps tend to be associated with approach behaviours. Communication signals often function to promote individual assessment of potential rivals during agonistic encounters and bursty, antiphonal chirp exchanges may facilitate these assessments and deter potentially costly physical escalations.

During embryogenesis and post-embryonic patterning, active transport of the phytohormone auxin, reflected in the expression of the Arabidopsis PIN family of auxin efflux mediators, generates local auxin distributions that are crucial for correct organ and tissue specification. Polar auxin transport routes have also long been postulated to regulate vein formation in the leaf. The molecular identification of PIN proteins has made it possible to investigate this hypothesis further by visualizing auxin transport routes in developing leaves. In Arabidopsis leaf primordia, PIN1 is expressed before the earliest known markers of vascular identity, in domains that are gradually restricted to sites of vein formation. PIN1 polarity indicates that auxin is directed towards distinct “convergence points” (CPs) in the marginal epidermis, from which it defines the sites of major vein formation. Within incipient veins, PIN1 polarity indicates drainage of auxin into preexisting veins, such that veins connected at both ends display two divergent polarities. Local auxin application triggers the formation of ectopic CPs and new veins, demonstrating the sufficiency of auxin as a vein-specifying signal. However, not all PIN1-labeled auxin transport routes differentiate as veins: Minor veins are initially unstable, suggesting local competition for auxin transport. Expression of ATHB8, a marker of vascular cell selection, correlates with enhanced PIN1 expression domain (PED) stability and vascular differentiation. Auxin application and auxin transport inhibition reveal that both CP formation in the epidermis and subepidermal PED dynamics are auxin-dependent and self-organizing. Furthermore, normal auxin perception through the ARF-Aux/IAA signaling pathway is required for the restriction of PIN1-mediated auxin transport to narrow subepidermal domains. ARF-Aux/IAA signaling is known to control auxin transport through the regulation of PIN1 dynamics, but the mechanism of this regulation is unclear. It is here shown that two redundantly acting AUXIN RESPONSE FACTOR (ARF) transcription factors, ARF5/MONOPTEROS (MP) and ARF7/NPH4, jointly regulate both PIN1 expression and localization during lateral root patterning in Arabidopsis, in part through the direct transcriptional activation of PIN1 by MP. Taken together, these results indicate that feedback between PIN-mediated auxin transport and ARF-Aux/IAA signaling regulates the patterning of root and shoot organs.

During embryogenesis and post-embryonic patterning, active transport of the phytohormone auxin, reflected in the expression of the Arabidopsis PIN family of auxin efflux mediators, generates local auxin distributions that are crucial for correct organ and tissue specification. Polar auxin transport routes have also long been postulated to regulate vein formation in the leaf. The molecular identification of PIN proteins has made it possible to investigate this hypothesis further by visualizing auxin transport routes in developing leaves. In Arabidopsis leaf primordia, PIN1 is expressed before the earliest known markers of vascular identity, in domains that are gradually restricted to sites of vein formation. PIN1 polarity indicates that auxin is directed towards distinct “convergence points” (CPs) in the marginal epidermis, from which it defines the sites of major vein formation. Within incipient veins, PIN1 polarity indicates drainage of auxin into preexisting veins, such that veins connected at both ends display two divergent polarities. Local auxin application triggers the formation of ectopic CPs and new veins, demonstrating the sufficiency of auxin as a vein-specifying signal. However, not all PIN1-labeled auxin transport routes differentiate as veins: Minor veins are initially unstable, suggesting local competition for auxin transport. Expression of ATHB8, a marker of vascular cell selection, correlates with enhanced PIN1 expression domain (PED) stability and vascular differentiation. Auxin application and auxin transport inhibition reveal that both CP formation in the epidermis and subepidermal PED dynamics are auxin-dependent and self-organizing. Furthermore, normal auxin perception through the ARF-Aux/IAA signaling pathway is required for the restriction of PIN1-mediated auxin transport to narrow subepidermal domains. ARF-Aux/IAA signaling is known to control auxin transport through the regulation of PIN1 dynamics, but the mechanism of this regulation is unclear. It is here shown that two redundantly acting AUXIN RESPONSE FACTOR (ARF) transcription factors, ARF5/MONOPTEROS (MP) and ARF7/NPH4, jointly regulate both PIN1 expression and localization during lateral root patterning in Arabidopsis, in part through the direct transcriptional activation of PIN1 by MP. Taken together, these results indicate that feedback between PIN-mediated auxin transport and ARF-Aux/IAA signaling regulates the patterning of root and shoot organs.

Weakly electric fish produce and detect electric fields and use their electrosensory modality in a number of behaviours including navigation and communication. They can modulate their electric discharge in frequency and amplitude to produce electrocommunication signals in variable patterns during social interactions. In one model neuroethological species, Apteronotus leptorhynchus, the most commonly produced communication signal is the ‘small chirp’ – a brief 10-30ms modulation. Individuals tend to produce these signals at high rates during agonistic interactions. In this thesis I will explore the social value of chirps, and to a lesser extent other communication behaviours, in A. leptorhynchus using a variety of experimental designs involving different staged social contexts. I use time series analysis methods to explore the patterns of chirps produced and accompanying aggressive behaviours. I first characterize electrocommunication and chirping in pairs of free swimming fish and correlate signal production with aggressive displays. Bursts of echoed, or reciprocated, chirps tend to be produced in the intervals separating aggressive attacks. Behavioural analysis shows that fish respond to conspecific chirps with echoed chirps and decreased aggression in social contexts outside the range in which previous modelling and electrophysiological data predicted that chirps could be encoded effectively. I then characterize the chirping and aggressive responses to playbacks simulating intruders with different chirping styles to test whether alternative chirp patterns differentially influence conspecific behaviour. In response to simulated intruders producing chirps that echo the real fish’s chirps with a short latency, less aggressive fish tend to produce more of their chirps in bursts than more aggressive fish. For randomly chirping intruders, the response of fish depends on the rate of chirps delivered. Fish respond less aggressively, with fewer chirps, and echo the stimulus chirps at a higher rate when high rates of random chirps are delivered than when responding to simulated intruders with low rates of randomly delivered chirps. Further, across all playback scenarios, fish that produce chirps in response to the playbacks are more aggressive than those that do not chirp. Finally, to better understand the electrosensory inputs during these interactions, I characterize changes in the electric image received by a restrained fish during movements of a free-swimming conspecific and correlate these with chirp production. When one fish is restrained, bursts of chirps tend to be associated with approach behaviours. Communication signals often function to promote individual assessment of potential rivals during agonistic encounters and bursty, antiphonal chirp exchanges may facilitate these assessments and deter potentially costly physical escalations.

Compared to 'conventional' materials made from metal, glass, or ceramics, protein-based materials have unique mechanical properties. Furthermore, the morphology, mechanical properties, and functionality of protein-based materials may be optimized via sequence engineering for use in a variety of applications, including textile materials, biosensors, and tissue engineering scaffolds. The development of recombinant DNA technology has enabled the production and engineering of protein-based materials ex vivo . However, harsh production conditions can compromise the mechanical properties of protein-based materials and diminish their ability to incorporate functional proteins. Developing a new generation of protein-based materials is crucial to (i) improve materials assembly conditions, (ii) create novel mechanical properties, and (iii) expand the capacity to carry functional protein/peptide sequences. This thesis describes development of novel protein-based materials using Ultrabithorax, a member of the Hox family of proteins that regulate developmental pathways in Drosophila melanogaster . The experiments presented (i) establish the conditions required for the assembly of Ubx-based materials, (ii) generate a wide range of Ubx morphologies, (iii) examine the mechanical properties of Ubx fibers, (iv) incorporate protein functions to Ubx-based materials via gene fusion, (v) pattern protein functions within the Ubx materials, and (vi) examine the biocompatibility of Ubx materials in vitro . Ubx-based materials assemble at mild conditions compatible with protein folding and activity, which enables Ubx chimeric materials to retain the function of appended proteins in spatial patterns determined by materials assembly. Ubx-based materials also display mechanical properties comparable to existing protein-based materials and demonstrate good biocompatibility with living cells in vitro . Taken together, this research demonstrates the unique features and future potential of novel Ubx-based materials.

<p>Evolution can be studied at many levels, from phenotypic to molecular, and from a variety of disciplines. An integrative approach can help provide a more complete understanding of the complexities of evolutionary change. This dissertation examines the ecology, genetics, and molecular mechanisms of the evolution of floral anthocyanin pigmentation in four species of <em>Mimulus</em> native to central Chile. Anthocyanins, which create red and purple colors in many plants, are a valuable model for studying evolutionary processes. They are ecologically important and highly variable both within and between species, and the underlying biosynthetic pathway is well characterized. The focus of this dissertation is dramatic diversification in anthocyanin coloration, in four taxa that are closely related to the genomic model system <em>M. guttatus</em>. I posed three primary questions: (1) Is floral diversification associated with pollinator divergence? (2) What is the genetic basis of the floral diversification? (3) What is the molecular mechanism of the increased production of anthocyanin pigment? The first question was addressed by evaluating patterns of pollinator visitation in natural populations of all four study taxa. The second question was explored using segregation analysis for a series of inter- and intraspecific crosses. One trait, increased petal anthocyanins in <em>M. cupreus</em>, was further dissected at the molecular level, using candidate gene testing and quantitative gene expression analysis. Pollinator studies showed little effect of flower color on pollinator behavior, implying that pollinator preference probably did not drive pigment evolution in this group. However, segregation analyses revealed that petal anthocyanin pigmentation has evolved three times independently in the study taxa, suggesting an adaptive origin. In addition to pollinator attraction, anthocyanins and their biochemical precursors protect against a variety of environmental stressors, and selection may have acted on these additional functions. Molecular analysis of petal anthocyanins in <em>M. cupreus</em> revealed that this single-locus trait maps to a transcription factor, <em>McAn1</em>, which is differentially expressed in high- versus low-pigmented flowers. Expression of the anthocyanin structural genes is tightly correlated with <em>McAn1</em> expression. The results suggest that <em>M. cupreus</em> pigmentation evolved by a mutation cis to <em>McAn1</em> that alters the intensity of anthocyanin biosynthesis.</p> / Dissertation

As devices and new technologies continue to shrink, nanocrystalline multi-metal compounds are becoming increasingly important for high efficiency and multifunctionality. However, synthetic methods to make desirable nanocrystalline multi-metallics are not yet matured. In response to this deficiency, we have developed several solution-based methods to synthesize nanocrystalline binary alloy and intermetallic compounds. This dissertation describes the processes we have developed, as well as our investigations into the use of lithographically patterned surfaces for template-directed self-assembly of solution dispersible colloids. We used a modified polyol process to synthesize nanocrystalline intermetallics of late transition and main-group metals in the M-Sn, Pt-M’, and Co-Sb systems. These compounds are known to have interesting physical properties and as nanocrystalline materials they may be useful for magnetic, thermoelectric, and catalytic applications. While the polyol method is quite general, it is limited to metals that are somewhat easy to reduce. Accordingly, we focused our synthetic efforts on intermetallics comprised of highly electropositive metals. We find that we can react single-metal nanoparticles with zero-valent organometallic Zinc reagents in hot, coordinating amine solvents via a thermal decomposition process to form several intermetallics in the M’’-Zn system. Characterization of the single-metal intermediates and final intermetallic products shows a general retention of morphology throughout the reaction, and changes in optical properties are also observed. Following this principle of conversion chemistry, we can employ the high reactivity of nanocrystals to reversibly convert between intermetallic phases within the Pt-Sn system, where PtSn2 ↔ PtSn ↔ Pt3Sn. Our conversion chemistry occurs in solution at temperatures below 300 °C and within 1 hour, highlighting the high reactivity of our nanocrystalline materials compared to the bulk. Some evidence of the generality for this process is also presented. Our nanocrystalline powders are dispersible in solution, and as such are amenable to solution-based processing techniques developed for colloidal dispersions. Accordingly, we have investigated the use of lithographically patterned surfaces to control the self-assembly of colloidal particles. We find that we can rapidly crystallize 2-dimensional building blocks, as well as use epitaxial templates to direct the formation of interesting superlattice structures comprised of a bidisperse population of particles.

The aim of this study was to investigate the viability of patterning by immobilization, photocatalytic removal, and re-immobilization steps of the enzyme on photocatalytically active thin films for biosensor fabrication purposes. For this aim, TiO2-SiO2-Au sol-gel colloids were synthesized and deposited on glass substrates as thin films by dip coating. Cysteamine linker was assembled on gold nanoparticles to functionalize thin films with amine groups for immobilization of model enzyme invertase. Effect of immobilization temperature, enzyme concentration of the immobilization solution and immobilization period on invertase immobilization were investigated. The immobilized invertase activity was found independent from the immobilization temperature in the range tested (4oC-room temperature). The optimum enzyme concentration and period for immobilization was determined as 10&micro / g/ml and 12 hours respectively. The resulting invertase immobilized thin films showed high storage stability retaining more that 50% of their initial activity after 9 weeks of storage. Photocatalytic enzyme removal and re-immobilization studies were carried out by irradiating the invertase immobilized thin films with blacklight. Upon 30 minutes of irradiation, immobilized invertase was completely and irreversibly inactivated. Initial immobilized invertase activity (before the irradiation) was attained when invertase was re-immobilized on thin films that were irradiated for 5 hours. Thus it was inferred that with sufficient exposure, enzymes can be completely removed from the surfaces which makes the re-immobilization possible. The possibility of enzyme removal with photocatalytic activity and re-immobilization can pave the way to new patterning techniques to produce multi-enzyme electrode arrays.

Zeolites are crystalline aluminosilicates which have highly ordered pore structures and high surface area. Also the tailorable surface properties, high ion-exchange capability, high chemical, thermal, and mechanical strength make these particles an important candidate for various application such as sensors, catalysis, dielectric materials, separation, and membrane technologies. Although zeolites have these unique properties, applications where zeolites are integrated into devices according to their application areas, are limited due to the powder form of the material. The purpose of the current study was to investigate the effect of zeolite nanoparticles on conductometric biosensor performance and cell viability measurements. Firstly, zeolite attachment on silicon surfaces was investigated by attaching silicalite and zeolite A nanoparticles onto the silicon substrates by direct attachment methodology in a closely packed monolayer form with perfect orientation and full coverage without using any chemical linker. Furthermore, the ability to pattern these zeolite crystals on silicon substrates with electron beam lithography and photolithography techniques was investigated. With the combination of electron beam lithography and direct attachment methodology, zeolite patterns were produced with feature sizes as small as a single silicalite nanoparticle thick line, that is approximately 500 nm. This approach has the ability of patterning very small features on silicon substrate, but the drawback is the long patterning time and lack of electron beam stability during long pattern formation process. Accordingly, it is almost impossible to form large patterns with electron beam lithography systems. Afterwards, to have full control on surfaces with differentiated areas on solid substrates, patterns of one type of zeolite crystals was formed on the monolayer of another type of zeolite layer with electron beam lithography for the first time. The same closed packed and highly oriented silicalite patterns were successfully formed on zeolite A monolayers and vice versa. Then photolithography technique was combined with direct attachment methodology to overcome the problem of the lack of total patterned area. With this technique, it was possible to pattern the whole silicon wafer in a couple of seconds, however the feature size of the zeolite patterns was limited with the infrastructures of the mask fabricated for photolithography studies. In this particular study, zeolite lines patterns with a minimum of 5 &micro / m thickness were prepared and the total patterned area was kept constant at 1 cm2. Similar to what was obtained by electron beam lithography study, zeolite A patterns were formed on silicalite monolayers with the minimum feature size of 5 &micro / m and vice versa. In the second part of the study, zeolite films were prepared on the transducers of conductometric biosensors using dip coating technique and named as Zeolite Coated Transducers (ZCT). Electrodes prepared using a mixture of zeolite and enzyme solution and then subjected to casting using glutaraldehyde were called Zeolite Membrane Transducers (ZMT). The operational and storage stabilities were determined to be in an acceptable range using ZCTs for conductometric urea biosensors. It was observed that using electrodes fabricated by the ZCT technique enhanced the biosensor signals up to two times and showed a rapid response after the addition of urea to the medium when it was compared with Standard Membrane Transducers (SMT). This enhancement can be explained by the lack of GA layer on top of the film, which acts as a diffusion barrier and inhibits the activity of the enzyme. On the second part of this conductometric biosensor study, effect of zeolite modification with methyl viologen (MV) and silver nanoparticles (Ag+ and Ag0), as well as the effect of changing Si/Al ratio was investigated with three different zeolite Beta particles which have Si/Al ratios of 40, 50, and 60. There were no significant effect of MV modification on ZMTs and there was no response observed with Ag+ and Ag0 modified zeolites. However, it was observed that conductometric responses increased with increasing Si/Al ratio for ZMTs. This behavior can be due to an increased hydrophobicity and/or the increasing acidic strength with the increasing Si/Al ratio within the zeolite crystals. Also ZCTs showed higher responses with respect to both SMTs and ZMTs. When compared with SMTs and ZMTs, ZCTs had higher reproducibility due to the controlled thickness of zeolite thin film by dip coating, and the controlled amount of enzyme adsorbed on this film. In the third part of the study, effect of zeolites on cell proliferation with MG63 osteoblast cells and NIH3T3 fibroblast cells were investigated. For that purpose, zeolite A, silicalite, and calcined forms of these zeolites were patterned with photolithography technique onto silicon wafers. Three different patterns prepared for this particular study, which has 0.125cm2, 0.08825cm2, and 0.04167cm2 zeolite patterned areas on 1 cm2 samples. In that way, not only the zeolite type and effect of calcination of zeolites, but also the effect of zeolite amount on MG63 osteoblast cells and NIH3T3 fibroblast cells were investigated. Silicalite coated samples were observed to have higher amount of cells than zeolite A coated samples after 24, 48, and 72 hours of incubation. This may be referred to the hydrophilic/hydrophobic properties, surface charge, and/or particle size of zeolites. Also it is observed that higher zeolite amount on samples resulted in an increase in the number of cells attached to the samples. There was also a significant increase in the number of cells upon using calcined silicalite samples. Accordingly, it can be hypothesized that zeolite pores result in an enhancement of protein adsorption and proliferation, even if this only occurs at the pore openings. On the other hand, there was no positive effect of calcining zeolite A. This result was expected since there is no structure directing agent used in synthesis procedure of zeolite A, which again supports the fact that pores might have some role in cell attachment.

As devices and new technologies continue to shrink, nanocrystalline multi-metal compounds are becoming increasingly important for high efficiency and multifunctionality. However, synthetic methods to make desirable nanocrystalline multi-metallics are not yet matured. In response to this deficiency, we have developed several solution-based methods to synthesize nanocrystalline binary alloy and intermetallic compounds. This dissertation describes the processes we have developed, as well as our investigations into the use of lithographically patterned surfaces for template-directed self-assembly of solution dispersible colloids. We used a modified polyol process to synthesize nanocrystalline intermetallics of late transition and main-group metals in the M-Sn, Pt-M', and Co-Sb systems. These compounds are known to have interesting physical properties and as nanocrystalline materials they may be useful for magnetic, thermoelectric, and catalytic applications. While the polyol method is quite general, it is limited to metals that are somewhat easy to reduce. Accordingly, we focused our synthetic efforts on intermetallics comprised of highly electropositive metals. We find that we can react single-metal nanoparticles with zero-valent organometallic Zinc reagents in hot, coordinating amine solvents via a thermal decomposition process to form several intermetallics in the M''-Zn system. Characterization of the single-metal intermediates and final intermetallic products shows a general retention of morphology throughout the reaction, and changes in optical properties are also observed. Following this principle of conversion chemistry, we can employ the high reactivity of nanocrystals to reversibly convert between intermetallic phases within the Pt-Sn system, where PtSn2 ↔ PtSn ↔ Pt3Sn. Our conversion chemistry occurs in solution at temperatures below 300 °C and within 1 hour, highlighting the high reactivity of our nanocrystalline materials compared to the bulk. Some evidence of the generality for this process is also presented. Our nanocrystalline powders are dispersible in solution, and as such are amenable to solution-based processing techniques developed for colloidal dispersions. Accordingly, we have investigated the use of lithographically patterned surfaces to control the self-assembly of colloidal particles. We find that we can rapidly crystallize 2-dimensional building blocks, as well as use epitaxial templates to direct the formation of interesting superlattice structures comprised of a bidisperse population of particles.