Imaging Learned Song Representations in Populations of Sensorimotor Neurons Essential to Vocal Communication

Perceiving or producing complex vocalizations such as speech and birdsongs require the coordinated activity of neuronal populations, and these activity patterns can vary over space and time. How learned communication signals are represented by populations of sensorimotor neurons essential to vocal perception and production remains poorly understood. Using a combination of two-photon calcium imaging, intracellular electrophysiological recording and retrograde tracing methods in anesthetized adult male zebra finches (Taeniopygia guttata), I addressed how the bird's own song and its component syllables are represented by the spatiotemporal patterns of activity of two spatially intermingled populations of projection neurons (PNs) in HVC, a sensorimotor area required for song perception and production. These experiments revealed that neighboring PNs can respond at markedly different times to song playback and that different syllables activate spatially intermingled HVC PNs within a small region. Moreover, noise correlation analysis reveals enhanced functional connectivity between PNs that respond most strongly to the same syllable and also provides evidence of a spatial gradient of functional connectivity specific to PNs that project to song motor nucleus (i.e. HVC_RA cells). These findings support a model in which syllabic and temporal features of song are represented by spatially intermingled PNs functionally organized into cell- and syllable-type networks.

A Plasmonic Gold Nanostar Theranostic Probe for In Vivo Tumor Imaging and Photothermal Therapy.

Nanomedicine has attracted increasing attention in recent years, because it offers great promise to provide personalized diagnostics and therapy with improved treatment efficacy and specificity. In this study, we developed a gold nanostar (GNS) probe for multi-modality theranostics including surface-enhanced Raman scattering (SERS) detection, x-ray computed tomography (CT), two-photon luminescence (TPL) imaging, and photothermal therapy (PTT). We performed radiolabeling, as well as CT and optical imaging, to investigate the GNS probe's biodistribution and intratumoral uptake at both macroscopic and microscopic scales. We also characterized the performance of the GNS nanoprobe for in vitro photothermal heating and in vivo photothermal ablation of primary sarcomas in mice. The results showed that 30-nm GNS have higher tumor uptake, as well as deeper penetration into tumor interstitial space compared to 60-nm GNS. In addition, we found that a higher injection dose of GNS can increase the percentage of tumor uptake. We also demonstrated the GNS probe's superior photothermal conversion efficiency with a highly concentrated heating effect due to a tip-enhanced plasmonic effect. In vivo photothermal therapy with a near-infrared (NIR) laser under the maximum permissible exposure (MPE) led to ablation of aggressive tumors containing GNS, but had no effect in the absence of GNS. This multifunctional GNS probe has the potential to be used for in vivo biosensing, preoperative CT imaging, intraoperative detection with optical methods (SERS and TPL), as well as image-guided photothermal therapy.

BDNF-TrkB Signaling in Single-Spine Structural Plasticity

Multiple lines of evidence reveal that activation of the tropomyosin related kinase B (TrkB) receptor is a critical molecular mechanism underlying status epilepticus (SE) induced epilepsy development. However, the cellular consequences of such signaling remain unknown. To this point, localization of SE-induced TrkB activation to CA1 apical dendritic spines provides an anatomic clue pointing to Schaffer collateral-CA1 synaptic plasticity as one potential cellular consequence of TrkB activation. Here, we combine two-photon glutamate uncaging with two photon fluorescence lifetime imaging microscopy (2pFLIM) of fluorescence resonance energy transfer (FRET)-based sensors to specifically investigate the roles of TrkB and its canonical ligand brain derived neurotrophic factor (BDNF) in dendritic spine structural plasticity (sLTP) of CA1 pyramidal neurons in cultured hippocampal slices of rodents. To begin, we demonstrate a critical role for post-synaptic TrkB and post-synaptic BDNF in sLTP. Building on these findings, we develop a novel FRET-based sensor for TrkB activation that can report both BDNF and non-BDNF activation in a specific and reversible manner. Using this sensor, we monitor the spatiotemporal dynamics of TrkB activity during single-spine sLTP. In response to glutamate uncaging, we report a rapid (onset less than 1 minute) and sustained (lasting at least 20 minutes) activation of TrkB in the stimulated spine that depends on N-methyl-D-aspartate receptor (NMDAR)-Ca2+/Calmodulin dependent kinase II (CaMKII) signaling as well as post-synaptically synthesized BDNF. Consistent with these findings, we also demonstrate rapid, glutamate uncaging-evoked, time-locked release of BDNF from single dendritic spines using BDNF fused to superecliptic pHluorin (SEP). Finally, to elucidate the molecular mechanisms by which TrkB activation leads to sLTP, we examined the dependence of Rho GTPase activity - known mediators of sLTP - on BDNF-TrkB signaling. Through the use of previously described FRET-based sensors, we find that the activities of ras-related C3 botulinum toxin substrate 1 (Rac1) and cell division control protein 42 (Cdc42) require BDNF-TrkB signaling. Taken together, these findings reveal a spine-autonomous, autocrine signaling mechanism involving NMDAR-CaMKII dependent BDNF release from stimulated dendritic spines leading to TrkB activation and subsequent activation of the downstream molecules Rac1 and Cdc42 in these same spines that proves critical for sLTP. In conclusion, these results highlight structural plasticity as one cellular consequence of CA1 dendritic spine TrkB activation that may potentially contribute to larger, circuit-level changes underlying SE-induced epilepsy.

Calcium/Calmodulin-Dependent Protein Kinase II Serves as a Biochemical Integrator of Calcium Signals for the Induction of Synaptic Plasticity

Repetitive Ca2+ transients in dendritic spines induce various forms of synaptic plasticity by transmitting information encoded in their frequency and amplitude. CaMKII plays a critical role in decoding these Ca2+ signals to initiate long-lasting synaptic plasticity. However, the properties of CaMKII that mediate Ca2+ decoding in spines remain elusive. Here, I measured CaMKII activity in spines using fast-framing two-photon fluorescence lifetime imaging. Following each repetitive Ca2+ elevations, CaMKII activity increased in a stepwise manner. This signal integration, at the time scale of seconds, critically depended on Thr286 phosphorylation. In the absence of Thr286 phosphorylation, only by increasing the frequency of repetitive Ca2+ elevations could high peak CaMKII activity or plasticity be induced. In addition, I measured the association between CaMKII and Ca2+/CaM during spine plasticity induction. Unlike CaMKII activity, association of Ca2+/CaM to CaMKII plateaued at the first Ca2+ elevation event. This result indicated that integration of Ca2+ signals was initiated by the binding of Ca2+/CaM and amplified by the subsequent increases in Thr286-phosphorylated form of CaMKII. Together, these findings demonstrate that CaMKII functions as a leaky integrator of repetitive Ca2+ signals during the induction of synaptic plasticity, and that Thr286 phosphorylation is critical for defining the frequencies of such integration.

Multiple Dynamic Processes Contribute to the Complex Steady Shear Behavior of Cross-Linked Supramolecular Networks of Semidilute Entangled Polymer Solutions.

Molecular theories of shear thickening and shear thinning in associative polymer networks are typically united in that they involve a single kinetic parameter that describes the network -- a relaxation time that is related to the lifetime of the associative bonds. Here we report the steady-shear behavior of two structurally identical metallo-supramolecular polymer networks, for which single-relaxation parameter models break down in dramatic fashion. The networks are formed by the addition of reversible cross-linkers to semidilute entangled solutions of PVP in DMSO, and they differ only in the lifetime of the reversible cross-links. Shear thickening is observed for cross-linkers that have a slower dissociation rate (17 s(-1)), while shear thinning is observed for samples that have a faster dissociation rate (ca. 1400 s(-1)). The difference in the steady shear behavior of the unentangled vs. entangled regime reveals an unexpected, additional competing relaxation, ascribed to topological disentanglement in the semidilute entangled regime that contributes to the rheological properties.

Photoelectrocatalysis: Principles, nanoemitter applications and routes to bio-inspired systems

An overview on processes that are relevant in light-induced fuel generation, such as water photoelectrolysis or carbon dioxide reduction, is given. Considered processes encompass the photophysics of light absorption, excitation energy transfer to catalytically active sites and interfacial reactions at the catalyst/solution phase boundary. The two major routes envisaged for realization of photoelectrocatalytic systems, e.g. bio-inspired single photon catalysis and multiple photon inorganic or hybrid tandem cells, are outlined. For development of efficient tandem cell structures that are based on non-oxidic semiconductors, stabilization strategies are presented. Physical surface passivation is described using the recently introduced nanoemitter concept which is also applicable in photovoltaic (solid state or electrochemical) solar cells and first results with p-Si and p-InP thin films are presented. Solar-to-hydrogen efficiencies reach 12.1% for homoepitaxial InP thin films covered with Rh nanoislands. In the pursuit to develop biologically inspired systems, enzyme adsorption onto electrochemically nanostructured silicon surfaces is presented and tapping mode atomic force microscopy images of heterodimeric enzymes are shown. An outlook towards future envisaged systems is given. © 2010 The Royal Society of Chemistry.

A PK2/Bv8/PROK2 antagonist suppresses tumorigenic processes by inhibiting angiogenesis in glioma and blocking myeloid cell infiltration in pancreatic cancer.

Infiltration of myeloid cells in the tumor microenvironment is often associated with enhanced angiogenesis and tumor progression, resulting in poor prognosis in many types of cancer. The polypeptide chemokine PK2 (Bv8, PROK2) has been shown to regulate myeloid cell mobilization from the bone marrow, leading to activation of the angiogenic process, as well as accumulation of macrophages and neutrophils in the tumor site. Neutralizing antibodies against PK2 were shown to display potent anti-tumor efficacy, illustrating the potential of PK2-antagonists as therapeutic agents for the treatment of cancer. In this study we demonstrate the anti-tumor activity of a small molecule PK2 antagonist, PKRA7, in the context of glioblastoma and pancreatic cancer xenograft tumor models. For the highly vascularized glioblastoma, PKRA7 was associated with decreased blood vessel density and increased necrotic areas in the tumor mass. Consistent with the anti-angiogenic activity of PKRA7 in vivo, this compound effectively reduced PK2-induced microvascular endothelial cell branching in vitro. For the poorly vascularized pancreatic cancer, the primary anti-tumor effect of PKRA7 appears to be mediated by the blockage of myeloid cell migration/infiltration. At the molecular level, PKRA7 inhibits PK2-induced expression of certain pro-migratory chemokines and chemokine receptors in macrophages. Combining PKRA7 treatment with standard chemotherapeutic agents resulted in enhanced effects in xenograft models for both types of tumor. Taken together, our results indicate that the anti-tumor activity of PKRA7 can be mediated by two distinct mechanisms that are relevant to the pathological features of the specific type of cancer. This small molecule PK2 antagonist holds the promise to be further developed as an effective agent for combinational cancer therapy.

Response decision processes and externalizing behavior problems in adolescents.

Externalizing behavior problems of 124 adolescents were assessed across Grades 7-11. In Grade 9, participants were also assessed across social-cognitive domains after imagining themselves as the object of provocations portrayed in six videotaped vignettes. Participants responded to vignette-based questions representing multiple processes of the response decision step of social information processing. Phase 1 of our investigation supported a two-factor model of the response evaluation process of response decision (response valuation and outcome expectancy). Phase 2 showed significant relations between the set of these response decision processes, as well as response selection, measured in Grade 9 and (a) externalizing behavior in Grade 9 and (b) externalizing behavior in Grades 10-11, even after controlling externalizing behavior in Grades 7-8. These findings suggest that on-line behavioral judgments about aggression play a crucial role in the maintenance and growth of aggressive response tendencies in adolescence.

One sound or two? Object-related negativity indexes echo perception.

The ability to isolate a single sound source among concurrent sources and reverberant energy is necessary for understanding the auditory world. The precedence effect describes a related experimental finding, that when presented with identical sounds from two locations with a short onset asynchrony (on the order of milliseconds), listeners report a single source with a location dominated by the lead sound. Single-cell recordings in multiple animal models have indicated that there are low-level mechanisms that may contribute to the precedence effect, yet psychophysical studies in humans have provided evidence that top-down cognitive processes have a great deal of influence on the perception of simulated echoes. In the present study, event-related potentials evoked by click pairs at and around listeners' echo thresholds indicate that perception of the lead and lag sound as individual sources elicits a negativity between 100 and 250 msec, previously termed the object-related negativity (ORN). Even for physically identical stimuli, the ORN is evident when listeners report hearing, as compared with not hearing, a second sound source. These results define a neural mechanism related to the conscious perception of multiple auditory objects.

Cysteine proteinase-1 and cut protein isoform control dendritic innervation of two distinct sensory fields by a single neuron.

Dendrites often exhibit structural changes in response to local inputs. Although mechanisms that pattern and maintain dendritic arbors are becoming clearer, processes regulating regrowth, during context-dependent plasticity or after injury, remain poorly understood. We found that a class of Drosophila sensory neurons, through complete pruning and regeneration, can elaborate two distinct dendritic trees, innervating independent sensory fields. An expression screen identified Cysteine proteinase-1 (Cp1) as a critical regulator of this process. Unlike known ecdysone effectors, Cp1-mutant ddaC neurons pruned larval dendrites normally but failed to regrow adult dendrites. Cp1 expression was upregulated/concentrated in the nucleus during metamorphosis, controlling production of a truncated Cut homeodomain transcription factor. This truncated Cut, but not the full-length protein, allowed Cp1-mutant ddaC neurons to regenerate higher-order adult dendrites. These results identify a molecular pathway needed for dendrite regrowth after pruning, which allows the same neuron to innervate distinct sensory fields.

Waveguide QED: Many-body bound-state effects in coherent and Fock-state scattering from a two-level system

Strong coupling between a two-level system (TLS) and bosonic modes produces dramatic quantum optics effects. We consider a one-dimensional continuum of bosons coupled to a single localized TLS, a system which may be realized in a variety of plasmonic, photonic, or electronic contexts. We present the exact many-body scattering eigenstate obtained by imposing open boundary conditions. Multiphoton bound states appear in the scattering of two or more photons due to the coupling between the photons and the TLS. Such bound states are shown to have a large effect on scattering of both Fock- and coherent-state wave packets, especially in the intermediate coupling-strength regime. We compare the statistics of the transmitted light with a coherent state having the same mean photon number: as the interaction strength increases, the one-photon probability is suppressed rapidly, and the two- and three-photon probabilities are greatly enhanced due to the many-body bound states. This results in non-Poissonian light. © 2010 The American Physical Society.

Antisense Gene Silencing and Bacteriophages as Novel Disinfection Processes for Engineered Systems

The growth and proliferation of invasive bacteria in engineered systems is an ongoing problem. While there are a variety of physical and chemical processes to remove and inactivate bacterial pathogens, there are many situations in which these tools are no longer effective or appropriate for the treatment of a microbial target. For example, certain strains of bacteria are becoming resistant to commonly used disinfectants, such as chlorine and UV. Additionally, the overuse of antibiotics has contributed to the spread of antibiotic resistance, and there is concern that wastewater treatment processes are contributing to the spread of antibiotic resistant bacteria.

Due to the continually evolving nature of bacteria, it is difficult to develop methods for universal bacterial control in a wide range of engineered systems, as many of our treatment processes are static in nature. Still, invasive bacteria are present in many natural and engineered systems, where the application of broad acting disinfectants is impractical, because their use may inhibit the original desired bioprocesses. Therefore, to better control the growth of treatment resistant bacteria and to address limitations with the current disinfection processes, novel tools that are both specific and adaptable need to be developed and characterized.

In this dissertation, two possible biological disinfection processes were investigated for use in controlling invasive bacteria in engineered systems. First, antisense gene silencing, which is the specific use of oligonucleotides to silence gene expression, was investigated. This work was followed by the investigation of bacteriophages (phages), which are viruses that are specific to bacteria, in engineered systems.


For the antisense gene silencing work, a computational approach was used to quantify the number of off-targets and to determine the effects of off-targets in prokaryotic organisms. For the organisms of Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv the mean number of off-targets was found to be 15.0 + 13.2 and 38.2 + 61.4, respectively, which results in a reduction of greater than 90% of the effective oligonucleotide concentration. It was also demonstrated that there was a high variability in the number of off-targets over the length of a gene, but that on average, there was no general gene location that could be targeted to reduce off-targets. Therefore, this analysis needs to be performed for each gene in question. It was also demonstrated that the thermodynamic binding energy between the oligonucleotide and the mRNA accounted for 83% of the variation in the silencing efficiency, compared to the number of off-targets, which explained 43% of the variance of the silencing efficiency. This suggests that optimizing thermodynamic parameters must be prioritized over minimizing the number of off-targets. In conclusion for the antisense work, these results suggest that off-target hybrids can account for a greater than 90% reduction in the concentration of the silencing oligonucleotides, and that the effective concentration can be increased through the rational design of silencing targets by minimizing off-target hybrids.

Regarding the work with phages, the disinfection rates of bacteria in the presence of phages was determined. The disinfection rates of E. coli K12 MG1655 in the presence of coliphage Ec2 ranged up to 2 h-1, and were dependent on both the initial phage and bacterial concentrations. Increasing initial phage concentrations resulted in increasing disinfection rates, and generally, increasing initial bacterial concentrations resulted in increasing disinfection rates. However, disinfection rates were found to plateau at higher bacterial and phage concentrations. A multiple linear regression model was used to predict the disinfection rates as a function of the initial phage and bacterial concentrations, and this model was able to explain 93% of the variance in the disinfection rates. The disinfection rates were also modeled with a particle aggregation model. The results from these model simulations suggested that at lower phage and bacterial concentrations there are not enough collisions to support active disinfection rates, which therefore, limits the conditions and systems where phage based bacterial disinfection is possible. Additionally, the particle aggregation model over predicted the disinfection rates at higher phage and bacterial concentrations of 108 PFU/mL and 108 CFU/mL, suggesting other interactions were occurring at these higher concentrations. Overall, this work highlights the need for the development of alternative models to more accurately describe the dynamics of this system at a variety of phage and bacterial concentrations. Finally, the minimum required hydraulic residence time was calculated for a continuous stirred-tank reactor and a plug flow reactor (PFR) as a function of both the initial phage and bacterial concentrations, which suggested that phage treatment in a PFR is theoretically possible.

In addition to determining disinfection rates, the long-term bacterial growth inhibition potential was determined for a variety of phages with both Gram-negative and Gram-positive bacteria. It was determined, that on average, phages can be used to inhibit bacterial growth for up to 24 h, and that this effect was concentration dependent for various phages at specific time points. Additionally, it was found that a phage cocktail was no more effective at inhibiting bacterial growth over the long-term than the best performing phage in isolation.

Finally, for an industrial application, the use of phages to inhibit invasive Lactobacilli in ethanol fermentations was investigated. It was demonstrated that phage 8014-B2 can achieve a greater than 3-log inactivation of Lactobacillus plantarum during a 48 h fermentation. Additionally, it was shown that phages can be used to protect final product yields and maintain yeast viability. Through modeling the fermentation system with differential equations it was determined that there was a 10 h window in the beginning of the fermentation run, where the addition of phages can be used to protect final product yields, and after 20 h no additional benefit of the phage addition was observed.

In conclusion, this dissertation improved the current methods for designing antisense gene silencing targets for prokaryotic organisms, and characterized phages from an engineering perspective. First, the current design strategy for antisense targets in prokaryotic organisms was improved through the development of an algorithm that minimized the number of off-targets. For the phage work, a framework was developed to predict the disinfection rates in terms of the initial phage and bacterial concentrations. In addition, the long-term bacterial growth inhibition potential of multiple phages was determined for several bacteria. In regard to the phage application, phages were shown to protect both final product yields and yeast concentrations during fermentation. Taken together, this work suggests that the rational design of phage treatment is possible and further work is needed to expand on this foundation.

Control of radiative processes using tunable plasmonic nanopatch antennas.

The radiative processes associated with fluorophores and other radiating systems can be profoundly modified by their interaction with nanoplasmonic structures. Extreme electromagnetic environments can be created in plasmonic nanostructures or nanocavities, such as within the nanoscale gap region between two plasmonic nanoparticles, where the illuminating optical fields and the density of radiating modes are dramatically enhanced relative to vacuum. Unraveling the various mechanisms present in such coupled systems, and their impact on spontaneous emission and other radiative phenomena, however, requires a suitably reliable and precise means of tuning the plasmon resonance of the nanostructure while simultaneously preserving the electromagnetic characteristics of the enhancement region. Here, we achieve this control using a plasmonic platform consisting of colloidally synthesized nanocubes electromagnetically coupled to a metallic film. Each nanocube resembles a nanoscale patch antenna (or nanopatch) whose plasmon resonance can be changed independent of its local field enhancement. By varying the size of the nanopatch, we tune the plasmonic resonance by ∼ 200 nm, encompassing the excitation, absorption, and emission spectra corresponding to Cy5 fluorophores embedded within the gap region between nanopatch and film. By sweeping the plasmon resonance but keeping the field enhancements roughly fixed, we demonstrate fluorescence enhancements exceeding a factor of 30,000 with detector-limited enhancements of the spontaneous emission rate by a factor of 74. The experiments are supported by finite-element simulations that reveal design rules for optimized fluorescence enhancement or large Purcell factors.

Inhibition-Induced Forgetting Results from Resource Competition between Response Inhibition and Memory Encoding Processes.

UNLABELLED: Response inhibition is a key component of executive control, but its relation to other cognitive processes is not well understood. We recently documented the "inhibition-induced forgetting effect": no-go cues are remembered more poorly than go cues. We attributed this effect to central-resource competition, whereby response inhibition saps attention away from memory encoding. However, this proposal is difficult to test with behavioral means alone. We therefore used fMRI in humans to test two neural predictions of the "common resource hypothesis": (1) brain regions associated with response inhibition should exhibit greater resource demands during encoding of subsequently forgotten than remembered no-go cues; and (2) this higher inhibitory resource demand should lead to memory encoding regions having less resources available during encoding of subsequently forgotten no-go cues. Participants categorized face stimuli by gender in a go/no-go task and, following a delay, performed a surprise recognition memory test for those faces. Replicating previous findings, memory was worse for no-go than for go stimuli. Crucially, forgetting of no-go cues was predicted by high inhibitory resource demand, as quantified by the trial-by-trial ratio of activity in neural "no-go" versus "go" networks. Moreover, this index of inhibitory demand exhibited an inverse trial-by-trial relationship with activity in brain regions responsible for the encoding of no-go cues into memory, notably the ventrolateral prefrontal cortex. This seesaw pattern between the neural resource demand of response inhibition and activity related to memory encoding directly supports the hypothesis that response inhibition temporarily saps attentional resources away from stimulus processing. SIGNIFICANCE STATEMENT: Recent behavioral experiments showed that inhibiting a motor response to a stimulus (a "no-go cue") impairs subsequent memory for that cue. Here, we used fMRI to test whether this "inhibition-induced forgetting effect" is caused by competition for neural resources between the processes of response inhibition and memory encoding. We found that trial-by-trial variations in neural inhibitory resource demand predicted subsequent forgetting of no-go cues and that higher inhibitory demand was furthermore associated with lower concurrent activation in brain regions responsible for successful memory encoding of no-go cues. Thus, motor inhibition and stimulus encoding appear to compete with each other: when more resources have to be devoted to inhibiting action, less are available for encoding sensory stimuli.

Global Rates of Free Hydrogen (H2) Production by Serpentinization and other Abiogenic Processes within Young Ocean Crust

The main conclusion of this dissertation is that global H2 production within young ocean crust (<10 Mya) is higher than currently recognized, in part because current estimates of H2 production accompanying the serpentinization of peridotite may be too low (Chapter 2) and in part because a number of abiogenic H2-producing processes have heretofore gone unquantified (Chapter 3). The importance of free H2 to a range of geochemical processes makes the quantitative understanding of H2 production advanced in this dissertation pertinent to an array of open research questions across the geosciences (e.g. the origin and evolution of life and the oxidation of the Earth’s atmosphere and oceans).

The first component of this dissertation (Chapter 2) examines H2 produced within young ocean crust [e.g. near the mid-ocean ridge (MOR)] by serpentinization. In the presence of water, olivine-rich rocks (peridotites) undergo serpentinization (hydration) at temperatures of up to ~500°C but only produce H2 at temperatures up to ~350°C. A simple analytical model is presented that mechanistically ties the process to seafloor spreading and explicitly accounts for the importance of temperature in H2 formation. The model suggests that H2 production increases with the rate of seafloor spreading and the net thickness of serpentinized peridotite (S-P) in a column of lithosphere. The model is applied globally to the MOR using conservative estimates for the net thickness of lithospheric S-P, our least certain model input. Despite the large uncertainties surrounding the amount of serpentinized peridotite within oceanic crust, conservative model parameters suggest a magnitude of H2 production (~1012 moles H2/y) that is larger than the most widely cited previous estimates (~1011 although previous estimates range from 1010-1012 moles H2/y). Certain model relationships are also consistent with what has been established through field studies, for example that the highest H2 fluxes (moles H2/km2 seafloor) are produced near slower-spreading ridges (<20 mm/y). Other modeled relationships are new and represent testable predictions. Principal among these is that about half of the H2 produced globally is produced off-axis beneath faster-spreading seafloor (>20 mm/y), a region where only one measurement of H2 has been made thus far and is ripe for future investigation.

In the second part of this dissertation (Chapter 3), I construct the first budget for free H2 in young ocean crust that quantifies and compares all currently recognized H2 sources and H2 sinks. First global estimates of budget components are proposed in instances where previous estimate(s) could not be located provided that the literature on that specific budget component was not too sparse to do so. Results suggest that the nine known H2 sources, listed in order of quantitative importance, are: Crystallization (6x1012 moles H2/y or 61% of total H2 production), serpentinization (2x1012 moles H2/y or 21%), magmatic degassing (7x1011 moles H2/y or 7%), lava-seawater interaction (5x1011 moles H2/y or 5%), low-temperature alteration of basalt (5x1011 moles H2/y or 5%), high-temperature alteration of basalt (3x1010 moles H2/y or <1%), catalysis (3x108 moles H2/y or <<1%), radiolysis (2x108 moles H2/y or <<1%), and pyrite formation (3x106 moles H2/y or <<1%). Next we consider two well-known H2 sinks, H2 lost to the ocean and H2 occluded within rock minerals, and our analysis suggests that both are of similar size (both are 6x1011 moles H2/y). Budgeting results suggest a large difference between H2 sources (total production = 1x1013 moles H2/y) and H2 sinks (total losses = 1x1011 moles H2/y). Assuming this large difference represents H2 consumed by microbes (total consumption = 9x1011 moles H2/y), we explore rates of primary production by the chemosynthetic, sub-seafloor biosphere. Although the numbers presented require further examination and future modifications, the analysis suggests that the sub-seafloor H2 budget is similar to the sub-seafloor CH4 budget in the sense that globally significant quantities of both of these reduced gases are produced beneath the seafloor but never escape the seafloor due to microbial consumption.

The third and final component of this dissertation (Chapter 4) explores the self-organization of barchan sand dune fields. In nature, barchan dunes typically exist as members of larger dune fields that display striking, enigmatic structures that cannot be readily explained by examining the dynamics at the scale of single dunes, or by appealing to patterns in external forcing. To explore the possibility that observed structures emerge spontaneously as a collective result of many dunes interacting with each other, we built a numerical model that treats barchans as discrete entities that interact with one another according to simplified rules derived from theoretical and numerical work, and from field observations: Dunes exchange sand through the fluxes that leak from the downwind side of each dune and are captured on their upstream sides; when dunes become sufficiently large, small dunes are born on their downwind sides (“calving”); and when dunes collide directly enough, they merge. Results show that these relatively simple interactions provide potential explanations for a range of field-scale phenomena including isolated patches of dunes and heterogeneous arrangements of similarly sized dunes in denser fields. The results also suggest that (1) dune field characteristics depend on the sand flux fed into the upwind boundary, although (2) moving downwind, the system approaches a common attracting state in which the memory of the upwind conditions vanishes. This work supports the hypothesis that calving exerts a first order control on field-scale phenomena; it prevents individual dunes from growing without bound, as single-dune analyses suggest, and allows the formation of roughly realistic, persistent dune field patterns.