VictorJuiz/thesis huggingface dataset:
The Impacts of Natural Episodic Hypoxia on Escape Performance in Juvenile Sebastes mystinus

The physical characteristics of an ecosystem provide the framework for its biological structure, and changes to this framework can have widespread ecological impacts. While it is well documented that the kelp forest in Monterey Bay experiences frequent low oxygen (hypoxic) episodes, little is known about how these episodes affect kelp forest organisms. To answer this question, specimens of Sebastes mystinus (blue rockfish) were collected from the wild and C-start escape responses—burst swimming to evade predation—were elicited in the laboratory using a dropped weight method. Trials were performed both in normoxic conditions and discrete low oxygen levels spanning levels measured in the field. Each C-start escape was recorded at high speed with a digital video camera and analyzed in ImageJ to quantify swimming performance and responsiveness, both indicators of ability to escape predators and thus of fitness. As oxygen levels declined, fewer individuals responded to the startle stimulus, indicating lower escape performance in hypoxia. Significant changes to escape response duration and final escape velocity were also observed with changes in dissolved oxygen concentration, possibly representing strategies for mediating physiological stress in hypoxia and conserving energy. Physiological stress could motivate S. mystinus and other kelp-associated species to avoid hypoxic areas, a distributional shift that could alter the structure of the kelp forest ecosystem and interactions among its associated species. Exploring the impacts of hypoxia on kelp forest organisms is crucial to understanding how these ecosystems will change in response to changes in the physical environment.

Keywords:  Department of Biology
Biology
Marine Ecology
Hypoxia
Kelp Forest
Rockfish
Thesis
Advisor: Micheli Fiorenza
Denny Mark
The Influence of ENSO on Migrations and Vertical Movements of Blue Marlin (Makaira nigricans) in the Equatorial Pacific South of Hawaii

Upwelling in the equatorial Pacific changes in intensity according to the ENSO (El Niño Southern Oscillation) phase. The cold phase of the cycle (La Niña) is associated with intense upwelling that brings cold and oxygen-depleted water closer to the surface. The warm phase with reduced upwelling, El Niño, deepens the mixed layer and brings warmer waters closer to the surface. In this thesis, I hypothesize that low oxygen concentration and temperature associated with La Niña conditions form an oceanographic boundary that precludes blue marlin migrations due to limitations of their circulatory and cardiac physiology. The purpose of this study is to determine how ENSO events in the equatorial Pacific Ocean affect the long-range movements and depth distributions of blue marlin (Makaira nigricans). I use pop-up satellite telemetry data from tag deployments in 2009-2012, during which a moderate El Niño, a strong La Niña, a weak La Niña, and a normal year occurred. To examine the impacts of ENSO variability on blue marlin movements I compare World Ocean Atlas and shipboard in situ data sets in the geographic region from 30oN-20oS and 175oW-115oW to analyze diving behavior in relation to physical oceanographic conditions during this period. For blue marlin tagged in this region, temperature and depth distributions revealed a preference for a warmer subset (>24oC) of the available thermal habitat and a bimodal diving behavior consistent with previous studies of this species. Blue marlin spent 85.25% of their time in surface waters warmer than 25.5oC and 14.75% in those less than 25.5oC. The ENSO phase and related changes in sea surface temperatures and upwelling strength affected not only the probability of trans-equatorial blue marlin migrations, but also their longitudinal location along the equator. Blue marlin traversed regions of cold surface water coupled with downwelling, warm surface water combined with upwelling, but not cold surface water in concert with upwelling. These results suggest that sea surface temperature is the limiting factor for blue marlin migrations across upwelling regions of the equatorial Pacific south of Hawaii. These findings will inform future efforts to conserve blue marlin populations and their ability to exchange genetic information across oceanographic boundaries.

Keywords:  Department of Biology
Biology
Marine Biology
Thesis
Advisor: Block Barbara
Somero George
The Neural Mechanism of Social Ascent: A Novel Role for Isotocin and Arginine Vasotocin in Behavior Modulation during Social Flux

In vertebrates, social status not only impacts reproductive success, but also regulates physiology across the reproductive axis. While lower social status represses aggressive behavior and limits mating opportunities, a dynamic social environment can allow subordinate individuals to “ascend” to dominance. The hormonal, physiological, and behavioral changes that accompany the social ascent process are well understood, but little is known about the mechanisms by which the brain translates the sensory information associated with social opportunity into changes along the reproductive axis. While previous studies have implicated broad regions of the brain in social ascent, none have convincingly identified the neuronal populations involved. Here, we determined the specific brain nuclei and neuronal populations activated upon the perception of social opportunity in the African cichlid fish Astatotilapia burtoni. In the wild, male burtoni exist in one of two social states, dominant (D) or nondominant (ND), and ND males can ascend to dominance in response to a dynamic social environment. This natural social structure allows for reliable, reproducible manipulation of social status in the laboratory. By allowing males to ascend socially and measuring consequent neuronal activity via immediate early gene expression, we determined that multiple discrete regions of the preoptic area of the hypothalamus are activated during social ascent. Furthermore, three candidate peptidergic populations (Gonadotropin Releasing Hormone 1, Arginine Vasotocin, Isotocin) show increased activity in ascending as compared to stable dominant and non-dominant males. We observe Isotocin receptor expression in regions of the brain responsible for both sensory processing and overall arousal, suggesting that Isotocin may play a role in modulating the brain’s response to both visual and olfactory cues during social flux. Finally, we find that Gonadotropin Releasing Hormone 1 neurons, the so- called “gateway to the reproductive axis” express neither Isotocin nor Arginine Vasotocin receptors, suggesting that at least a portion of this mechanism exists external to the hypothalamic-pituitary-gonadal axis.

Keywords:  Department of Biology
Biology
Neurobiology
Social Behavior
Neuropeptide
Isotocin
Arginine Vasotocin
Social Ascent
Thesis
Advisor: Fernald Russell
Sapolsky Robert
The persistence of stoicism in New Father masculinity: A case study of first time parents in Sweden

Studies have demonstrated Swedish fathers are conscious of the importance of sex roles, and aspire to a gender-equal, childcare-oriented model of manhood. Among gender traits not well examined is stoicism, or reluctance to communicate openly about personal stress and anxiety. The aim of this study is to locate stoicism as a gendered trait in Swedish definitions of fatherhood-masculinity through an examination of individual ideologies, and the infrastructure and practices of parental leave in Sweden. The data come from semi-structured, in-depth interviews with 20 fathers, 4 mothers, and 4 professionals who work with parents. Interview data were analyzed using a grounded qualitative approach. Evidence suggests fathers have stoic dispositions by default, but they are not analytical about stoicism like they are for other gender traits. Fathers seem to value stoicism but also avoid acknowledging it, suggesting a potential incongruity with idealized Swedish father masculinity. I suggest practical barriers to fathers developing emotional openness due to the nature of public resources available for fathers on leave.

Keywords: Parental leave
Sweden
fatherhood
masculinity
Thesis
Advisor: Wotipka Christine Min
The Polar Bear in the Room: The Role of Institutions in the Changing Arctic

This thesis focuses on the role of international institutions in the Arctic. Specifically, it examines the two main governance structures in the Arctic—the Arctic Council and the United Nations Law of the Seas Treaty (UNCLOS)—in light of the changing Arctic environment. It evaluates to what extent these two governance structures have been effective at keeping the peace in the Arctic, and whether this cooperation is likely to continue in the future. While the Arctic—and its institutions—are frequently cited as a model for geopolitical cooperation, this thesis finds that predictions that this cooperation will continue are overly optimistic. This conclusion is based on two overall findings. The first is that the Arctic Council, the preeminent forum for cooperation in the Arctic, is unlikely to adapt to upcoming issues, as it is limited by its primarily environmental mandate. The second argument concerns the role of UNCLOS, and finds that, despite its effectiveness in bringing states to the negotiation table for some territorial disputes, it has generally been unable to mandate long-term solutions. By showing the limitations of the Arctic Council and UNCLOS in regards to their ability to provide cooperative governance, this thesis questions the existing literature about the Arctic and raises the question of what other structures—perhaps economic or security related—are needed to ensure that the Arctic remains a peaceful sphere of cooperation in the future. As such, it is valuable for policymakers or academics that have to deal with the Arctic in particular, and for international cooperation literature more generally.

Keywords: Arctic
institutions
international law
cooperation
United Nations Convention on the Law of the Sea
Arctic Council
Center for International Security and Cooperation
Thesis
Advisor: Schultz Kenneth
Slayton David
The Role of Neat1 in p53-mediated cell-cycle arrest, apoptosis and senescence

Mutations of p53 in over half of all human cancers indicate p53’s critical role as a tumor suppressor. In response to cellular stress, p53 transcriptionally activates a set of target genes to induce cell-cycle arrest and apoptosis. While most known p53 target genes are protein-coding, we have recently discovered that p53 activates transcription of the noncoding RNA Neat1. Neat1 plays a structural role in the formation of paraspeckles, nuclear compartments that regulate gene expression via nuclear retention of mRNA. The role of paraspeckles in cellular functions is not fully understood, and the potential role of Neat1 in tumor suppression mechanisms has not been studied previously. This project illuminates the roles of Neat1 in p53-mediated cell-cycle arrest, apoptosis and senescence. Our data suggest that Neat1 is not necessary for p53-mediated cell-cycle arrest or apoptosis as Neat1-/- mouse embryonic fibroblasts (MEFs) retain the capacity to undergo both G1 cell-cycle arrest and apoptosis in response to DNA damage, although apoptosis is delayed in the absence of Neat1. We additionally show that Neat1 is not necessary for p53 function in senescence as Neat1-/- MEFs retain the ability to senesce. Since Neat1-/- MEFs could upregulate compensatory mechanisms to compensate for the lack of Neat1, we further tested Neat1’s function in cell-cycle arrest using Neat1 overexpression. We found that Neat1 is sufficient for p53-mediated cell-cycle arrest, as Neat1 overexpression was able to induce cell-cycle arrest in p53-/- MEFs. Seeming inconsistency between Neat1 overexpression results and Neat1-/- results is likely due to compensation for the absence of Neat1 in the Neat1-/- MEFs or redundancy of Neat1’s role in p53-mediated cell-cycle arrest. Because Neat1 acts downstream of p53 to promote cell-cycle arrest, further understanding of Neat1’s role in p53-mediated cell-cycle arrest, apoptosis and tumor suppression could suggest Neat1 as a novel target for cancer therapies.

Keywords:  Department of Biology
Biology
p53 tumor suppressor
Radiation Oncology
Stanford
Thesis
Advisor: Attardi Laura D.
Cyert Martha
The role of neuronal activity in oligodendroglial cell lineage dynamics and myelination in the healthy and demyelinated mammalian brain

Mature oligodendrocytes from oligodendrocyte precursor cells (OPCs) have been shown to cause myelination of the central nervous system. In this study, we use optogenetic stimulation of the premotor cortex in awake, behaving mice to demonstrate that neuronal activity causes a robust proliferative response in OPCs and promotes subsequent oligodendrogenesis. Behaviorally relevant activity also increases myelination within the deep layers of the premotor cortex and subcortical fibers entering the corpus callosum. Interestingly, this neuronal activity–regulated oligodendrogenesis and myelination is correlated with improved motor function of the corresponding limb. Inhibition of oligodendrocyte differentiation blocks this improvement in behavior.

Keywords:  Department of Biology
Biology
Thesis
Advisor: Monje-Deisseroth Michelle
McConnell Sue
The Role of the GABA Antagonist, Pentylenetetrazole, on Augmenting Cognition

Previous studies have shown that pentylenetetrazole (PTZ), a GABA antagonist, can ameliorate cognitive defects in both Down Syndrome mice model and arrhythmic hamsters. Starting with the observation that entrained hamsters perform poorly on hippocampal-dependent memory tests in the morning, and well in the afternoon, we sought to see if PTZ improves cognitive performance in normal, entrained animals at both times. To answer this question we performed both an acute injection study and a long-term chronic injection study. Chronic injections of PTZ had no effect on memory test performance in entrained animals, but did increase their exploratory behavior during the tests. Animals treated with acute injections of PTZ or vehicle performed better than control animals in the morning, but worse than controls in the afternoon. However, animals treated with PTZ performed significantly better than Veh animals in the morning. These results suggest that PTZ can rescue a defect, but not augment normal cognition. Further, PTZ may modulate a stress response in acutely injected animals.

Keywords:  Department of Biology
Biology
Circadian Rhythms
Learning and Memory
Neurobiology
Thesis
Advisor: Heller H. Craig
Fernald Russell
The roles of Arabidopsis chaperone J3 and the Xanthomonas type III effector XopX in plant immunity

Xanthomonas euvesicatoria (Xcv) is the causal agent of bacterial spot disease in pepper and tomato plants. Xcv uses its type III secretion (T3S) system to translocate effector proteins into the cytoplasm of plant cells. Although the function of each T3S effector is not well understood, it is known that they are required to collectively suppress innate immune signaling in plants.  In this thesis, I focused on one effector protein, XopX, which has been found to be a major contributor towards Xcv virulence. Using the yeast two-hybrid system and in vitro affinity protein purification, the Mudgett laboratory discovered that XopX physically associates with the Arabidopsis thaliana J-domain protein, J3. Given this finding, I hypothesize that XopX may be directly targeting J3 to alter its function during Xcv infection to promote pathogenesis. Here I studied the role of J3 in plant pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI) by utilizing the heterologous Pseudomonas syringae pathovar tomato (Pst)-Arabidopsis thaliana pathosystem. Arabidopsis j3 mutants were less susceptible to Pst infection than wild-type Arabidopsis lines in PTI assays. By contrast, J3 did not appear to play a significant role in ETI. Studies examining the role of XopX in bacterial virulence in Arabidopsis revealed that both wild-type and j3 mutant leaves were equally more resistant to Pst expressing XopX compared to infection with Pst alone. This suggests that XopX may be triggering Arabidopsis immune responses, possibly in a J3-dependent manner, or that XopX may be interfering with Pst virulence mechanisms during infection. In conclusion, my research identifies J3 as a negative regulator of PTI in Arabidopsis. It is unclear if XopX is directly interfering with J3 function; however, my preliminary findings suggest that J3 is required for XopX-induced resistance in Arabidopsis.

Keywords:  Department of Biology
Biology
Plant Bacterial Pathogen
Thesis
Advisor: Mudgett Mary Beth
Jones Patricia
The Structural and Functional Role of Calcium Ions at the Globular Domain of C1Q-Like Proteins

Elucidation of the molecular mechanisms that regulate synapse formation, maintenance, and homeostasis is required to understand neuron communication and how they contribute to the formation of neural networks and higher cognitive functions. Recent work has shown that C1q-like (C1QLs) are secreted proteins expressed in neurons in specific regions of the brain, and they act as ligands to the postsynaptic brain-specific angiogenesis inhibitor 3 (BAI3) adhesion GPCRs. Although these two proteins have been implicated in synapse development, fundamental questions regarding the calcium-binding properties of C1QL remain unanswered, and little is known about their downstream signaling with BAI3. As such, there is great merit in illuminating their integral roles in synapse regulation.
The globular domain of C1QL (gC1q) binds to thrombospondin repeat domains of BAI3 in a calcium-dependent manner. We generate mutants of calcium sites at the trimer interface of C1QL3. Using X-ray crystallography, we provide high-resolution structures of C1QL3 and its mutants to show changes in structure and ion capacity, which may be relevant for BAI3 receptor binding. We examine folding and stability using circular dichroism (CD) spectroscopy and test calcium affinity using isothermal titration calorimetry (ITC) to narrow down the important calcium sites involved in BAI3 interactions. Together, the results suggest that C1QL and BAI3 mediate synapse homeostasis in the presence of calcium ions bound at specific sites. This research describes the calcium binding properties of the first known ligand to BAI3 and can be applied to the broader regulation of synapses in the brain through the interaction of these two proteins.

Keywords:  Department of Biology
Stanford
Molecular
Structural
Neuroscience
Biology
Thesis
Advisor: Brunger Axel
Jones Patricia
Theater and prestige [electronic resource] : the development of the playhouse in Shakespeare's time

Early modern playhouses did not exist independently of one another: they constituted a theatrical milieu, and to understand one theater we must understand its relation to other theaters. From the Elizabethan period through the Jacobean and Caroline periods, different theatrical venues occupied different niches in London's playgoing culture and increasingly came to cater to different audiences. This affected the kinds of plays that playwrights wrote and also influenced how playwrights defined themselves as authors. As venues became increasingly differentiated according to their audience and repertoire, literary prestige started to influence the kinds of plays that authors produced. Theatrical venues, authorship, and prestige determined the style of many plays, led to the creation of new genres, and ultimately determined how people conceived of the theater as an institution. We can gain important new insights into early modern drama by looking at how Londoners imagined their array of theatrical venues.

Keywords: English.
Advisor: Hoxby Blair
Orgel Stephen primary advisor. Thesis advisor
Lupic Ivan advisor. Thesis advisor
Theme and variation [electronic resource] : essayistic lineages in four 20th century Spanish-American and German novels

My dissertation offers a revisionist account of a novelistic tendency generally called "essayism, " in terms of its development vis-à-vis the realist novel and twentieth century literary experiments, within two distinct literary traditions: those of Europe and of Latin America. It explores the insights that essayistic theory can provide into the comparative writing of authority in these contexts, and argues for a more diversified approach than is currently taken to essayistic aesthetics in the study of fiction and other hybrid genres— despite the essay's unmanageable diversity of forms and the impossibly broad set of claims for its uniqueness. My case studies focus on the disjuncture between the much-discussed twentieth-century European essay-novel and its Latin American counterpart, which develops in dialogue with an influential body of essayistic work and tradition. The essayistic novel as seen in this broadened context is symptomatic of an ongoing quarrel between the moral claims of fictional and non-fictional writing.

Keywords: Comparative Literature.
Advisor: Gumbrecht Hans Ulrich primary advisor. Thesis advisor
Berman Russell A.
Hoyos Ayala Héctor advisor. Thesis advisor
Theoretical and experimental evolution studies of adaptation under diploidy and epistasis [electronic resource]

The dynamics of adaptive evolution is explored in the context of diploidy and epistasis. In the first chapter I model the dynamics of adaptation in the framework of Fisher's geometric model for diploids and find that balancing selection due to heterozygote advantage naturally emerges during adaptation. In the second chapter I explore patterns of divergence and adaptation emerging in a model incorporating functional linkage between genes. Finally, in the third chapter I describe an evolutionary experiment where a populations of a diploid yeast strain adapt to glucose-limited continuous cultures by overdominant mutations, result that supports the predictions of the model from chapter 1.

Keywords: Biology.
Advisor: Petrov Dmitri Alex
Feldman Marcus W. advisor. Thesis advisor
Fisher Daniel advisor. Thesis advisor
Fraser Hunter B. advisor. Thesis advisor
Sherlock Gavin advisor. Thesis advisor
Theory and applications of sparsity for radar sensing of ionospheric plasma [electronic resource]

In order to enable flexible high-resolution measurements of ionospheric plasma phenomena, a sparsity-based radar waveform inversion technique is formulated and found to eliminate processing artifacts caused by the standard matched filter approach. Taking direction from the theory of compressed sensing, sparsity of the radar target scene is employed as prior knowledge to successfully perform the inversion. The result is cleaner data that limits self-interference of range-spread targets and enables differentiation in crowded and variable environments. Though the approach has been applied to ionospheric radar, it is generally applicable and especially relevant for radar target scenes with multiple or distributed scatterers. As a basis for the technique, a discrete radar model that captures signal sparsity in a delay-frequency dictionary is developed. This model is shown to have a strong connection to existing methods, resulting in an intuitive interpretation of the inversion technique as an iterative thresholding matched filter. An explicit formulation of the discrete model's representation of arbitrary distributed scatterers is derived, and it shows that sparsity is reasonably preserved in the discrete representation. Building on top of the model, waveform inversion is implemented using modern convex optimization techniques tailored for efficient computation and quick convergence. Finally, the real-world flexibility and effectiveness of the inversion technique is demonstrated by the elimination of filtering artifacts from meteor observations made with a variety of standard radar waveforms.

Keywords: Aeronautics and Astronautics.
Advisor: Close Sigrid
Erickson Philip
Kochenderfer Mykel J.