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Genetic and Genomic Bases of Evolved Increases in Stickleback Dentition

• Hart, James Clinton
• Advisor(s): Miller, Craig T

Evolution - the great tinkerer - has produced the astounding diversity of form within

and between existing species. It is a fundamental goal of evolutionary biology to understand

the origin of such diversity. What types of genes underlie evolved changes in morphology?

Are certain types of mutations (notably changes within regulatory regions) more likely to be used to produce adaptive changes in form? When distinct populations evolve similar morphological changes, are the underlying genetic bases changes to the same genes, the same genetic pathways, or largely independent? Are changes in form modular, or are their concerted changes to multiple developmentally similar organs? The ever cheapening cost of sequencing, coupled the availability of high-quality reference genomes, allows high-throughput approaches to identifying the loci of evolution. The emergence of a robust genome engineering system, CRISPR/Cas9, allows for efficient and direct testing of a gene's phenotype. Combining both of these techniques with a model system with naturally evolved phenotypic variation, the threespine stickleback, allows for systems-level answers to the many evolutionary questions.

Chapter one outlines the field of evolutionary developmental biology. It proposes two

alternative viewpoints for thinking about the evolution of form. The first is the view of the

`Modern Synthesis', linking Mendelian inheritance with Darwinian natural selection, which

explains evolution as the change in allele frequencies over time. The second views evolution

through the lens of deep homology, focusing on changes to developmental programs over

time, even across related organs within the same animal. It then introduces key concepts

within evolutionary and developmental biology, including cis-regulation of gene expression,

and gene regulatory networks. It then provides examples of evolution reusing similar gene

regulatory networks, including Hox genes, Pax6 dependent eye initiation, and ectodermal

placode development. Teeth use highly conserved signaling pathways, during both their

initiation and replacement. Threespine sticklebacks Gasterosteus aculeatus have repeatedly

adapted following a shift from marine to freshwater environments, with many independently

derived populations sharing common morphological traits, including a gain in tooth number.

The following chapters investigate this gain in tooth number in multiple distinct populations

of sticklebacks.

Chapter two describes the discovery and mapping of a spontaneous stickleback albino

mutation, named casper. casper is a sex-linked recessive mutation that results in oculocutaneous albinism, defective swim bladders, and blood clotting defects. Bulked segregant mapping of casper mutants revealed a strong genetic signal on chromosome 19, the stickleback X chromosome, proximal to the gene Hps5. casper mutants had a unique insertion of a G in the 6th exon on Hps5. As mutants in the human orthologue of Hps5 resulted in similar albino and blood clotting phenotypes, Hps5 is a strong candidate underlying the casper phenotype. Further supporting this model, genome editing of Hps5 phenocopied casper. Lastly, we show that casper is an excellent tool for visualizing the activity of uorescent transgenes at late developmental stages due to the near-translucent nature of the mutant animals.

Chapter three details the fine mapping of a quantitative trail locus (QTL) on chromosome 21 controlling increases in tooth number in a Canadian freshwater stickleback population. Recombinant mapping reduced the QTL-containing region to an 884kb window. Repeated QTL mapping experiments showed the presence of this QTL on multiple, but not all, wild derived chromosomes from the Canadian population. Comparative genome sequencing revealed the perfect correlation with genetic data of ten variants, spanning 4.4kb, all within the 4th intron of the gene Bmp6. Transgenic analysis of this intronic region uncovered its role as a robust tooth enhancer. TALEN induced mutations in Bmp6 revealed required roles for the gene in stickleback tooth development. Finally, comparative RNA-seq between Bmp6 wild-type and mutant dental tissue showed a loss of mouse hair stem cell genes in Bmp6 mutant fish teeth, suggesting deep homology of the regeneration of these two organs.

Chapter four investigates the evolved changes in gene expression that accompany evolved increases in tooth number in two distinct freshwater populations. Independently derived stickleback populations from California and Canada have both evolved increases in tooth number, and previous work suggested that these populations used distinct genetic changes during their shared morphological changes. RNA-seq analysis of dental tissue from both freshwater populations compared to marine revealed a gain in critical regulators of tooth development in both freshwater populations. These evolved changes in gene expression can be partitioned in cis changes (mutations within regulatory elements of a gene) and trans changes (changes to the overall regulatory environment) using phased RNA-seq data from marine-freshwater F1 hybrids. Many genes show evidence for stabilizing selection of expression levels, with cis and trans changes in opposing directions. Most evolved changes in gene expression are due to changes in the trans environment, and these trans changes are more likely to be shared among the high-toothed freshwater populations. Thus, Californian and Canadian sticklebacks have convergently evolved similar trans regulatory environments through distinct cis regulatory changes.

Chapter five identifies candidate genes underlying evolved tooth gain in multiple geographically distinct freshwater populations. Many populations of freshwater sticklebacks have evolved increases in both oral and pharyngeal tooth number. QTL mapping of this evolved gain in pharyngeal tooth number revealed that a 438bp regulatory haplotype of Bmp6 is associated with increased tooth number in five distinct Pacific Northwest populations, though not in the high-toothed California population. QTL mapping of evolved oral tooth gain in California reveals the surprisingly modular nature of evolved changes in dentition. Correlation analysis of gene expression data from 33 separate samples across multiple populations and genotypes revealed Plod2 and Pitx2 as dentally expressed candidate genes underlying evolved tooth gain. CRISPR/Cas9 genome editing of Plod2 resulted in mutants displaying increases in pharyngeal but decreases in oral tooth number. Mutations in Pitx2 are homozygous lethal and show a recessive near-complete loss of dentition across all tooth fields. The pleitropic effects of the coding mutations and the lack of evolved coding changes suggest that modular regulatory changes to Plod2 and Pitx2 underlie increases in tooth number.

Combined, these results make significant contributions to our understanding of the evolutionary genetics underlying an adaptive change in morphology. Modular cis-regulatory alleles appear to play critical roles during the evolution of increased tooth number. Some alleles, such as the regulatory haplotype of Bmp6, are repeatedly used by multiple independently derived freshwater populations, suggesting both that the haplotype is adaptive and that evolution is partially repeatable. The Californian specific use of Plod2 and Pitx2 shows that evolution is not entirely predictable, and that there are many ways to modify teeth. Additionally, the use of high-throughput expression assays and genome sequencing, combined with genome editing with CRISPR/Cas9, allowed for rapid identification and testing of candidate genes underlying evolved changes in morphology. Additional studies could use these approaches to further identify the loci of evolved changes in morphology.

The National School Lunch Program: Ideas, proposals, policies, and politics shaping students' experiences with school lunch in the United States, 1946 - present

• Gosliner, Wendi Anne
• Advisor(s): Keller, Ann

The National School Lunch Program:

Ideas, proposals, policies, and politics shaping students' experiences with school lunch in the United States, 1946 - present

Wendi Anne Gosliner

Doctor of Public Health

University of California, Berkeley

Professor Ann Keller, Chair

On an average school day in 2012, The National School Lunch Program (NSLP) supported the provision of lunch meals to almost 2/3 of school-age youth in the United States. Recent spikes in childhood obesity rates and the emergence of childhood-onset Type 2 diabetes have brought renewed attention to the program's potential to positively impact the health of the nation's youth. The Healthy Hunger Free Kids Act of 2010 began a process of reforming the NSLP, requiring schools to serve foods consistent with updated nutrition standards, representing the most important punctuation to school lunch policy in decades. The three papers comprising this dissertation provide new insights into ways the public health nutrition community can support the success of the new policies, and continue to improve the impact of the school lunch program on children's health and development.

The first paper examines the relationship between fruit and vegetable consumption at school and specific factors in the school setting, such as the amount of time available to eat lunch, the quality and variety of produce options served, and whether students are involved in food service decision-making. This cross sectional study of California 7th and 9th grade students (n=5,439) was conducted in 31 schools in 2010. Multilevel regression models were used to assess relationships between students' responses to survey questions regarding school food behaviors and recorded observations of school food environments. The study found that a longer lunch period was associated with increased odds of a student eating fruits (40%) and vegetables (54%) at school. Fruit quality increased the odds of a student consuming fruit at school (44%). Including a salad bar and involving students in food service decisions increased a student's odds of consuming vegetables at school (48% and 34%, respectively). The findings suggest that institutional factors in schools are positively associated with middle and high school students' consumption of produce items at school.

The second paper explores the original issues and arguments that were presented by advocates, administration officials, and members of Congress in the 1940's, when a National School Lunch program first was being debated in Congress. Political science theory suggests that understanding history can provide insight into current policy debates. The purpose of this paper is to better understand the early framing and arguments that led to the original structure of the NSLP. It was hypothesized that understanding the full complement of issues and arguments debated at the time the program was established would help explain the policies that shape current school lunch environments. This study examined the transcripts of the three Congressional hearings held in 1944-1945, when proposals for establishing ongoing federal support for school lunch programs were first considered in Congress. The study identifies many issues of contention in the early debates, including whether the primary program objective was to serve the Nation's agricultural needs or to support children's health and wellbeing, which federal agency would administer the program, the degree to which federal resources should be used to support school meals, which children would benefit from school lunch programs, whether food and nutrition education should be included, and whether resources would be provided for equipment and training of personnel. The paper shows that the outcome of the early debates continues to shape present policies, and that modern advocates' vision for an optimal school lunch program mirrors the vision of advocates in the 1940's. The paper underscores the importance of understanding the school lunch program's history, in order to more effectively promote and protect children's opportunities to benefit from school meals.

The final paper presents the results of a pilot study of legislative documents from the National School Lunch Program's history (1946 - present), in order to provide a longer-term perspective on the evolution of the program. The purpose of this study is to explore and describe the school lunch policy ideas and proposals that have appeared on the federal decision-making agenda over time, in order to inform future directions for research and advocacy related to school lunch policy. A ProQuest Congressional search utilizing the search terms "school lunch," "school meal," "child nutrition," or "school nutrition" was conducted, and all hearing and bill summaries were reviewed. The findings suggest that Congressional attention to school lunch, in the form of legislative hearings and bills, has shifted over time, with more legislative attention devoted to the program during the period of expansion in the late 1960s through the period of curtailment in the early to mid-1980s. Further, the study shows that the program consistently has suffered from constrained resources, and that periods of investment in the NSLP have been followed by efforts to curtail the program. The study also reveals that after the program's beginning, many issues cycled on and off of the federal decision-making agenda. These issues include: the degree to which the program should be administered at the federal or state level; which students should benefit from school meals; whether nutrition education should be included; what foods and beverages are served; and how the USDA-distributed commodities should be structured. While the school lunch program generally enjoys bi-partisan support, policymakers have not yet exhibited the political will to provide a program consistent with advocates' desires to operate seamlessly within the school system and offer healthy meals to all students. Future efforts to support and improve the program can now be informed with a better understanding of the program's past political successes and failures. Recommendations about ways the public health nutrition community can continue to support and improve the National School Lunch Program, based on the history described, conclude the paper.

Together, these three papers highlight both opportunities and challenges facing the National School Lunch Program. Cast in the light of this historical perspective, advocates for ideas that have failed in the past can see the value of considering whether current approaches are vulnerable to the same politics that trumped them in past political battles. Similarly, program supporters should understand the proposals to dismantle the federal school lunch program, and why they failed, in order to be prepared to defend the program against similar proposals that may be anticipated in the future. Further, these papers show that while the public health nutrition community may perceive the school lunch program to be a stable federal investment, this perceived stability may be more a function of political good fortune than of a strong and secure federal commitment to children's health and nutrition. Yet current projections suggest that investing in the nutritional health of today's youth is especially important, given the costly epidemics of early-onset diet-related chronic diseases now plaguing the nation. We can no longer afford not to provide a robust and effective National School Lunch Program.

The Art of the Archive: Uses of the Past in the German Essay Film

• Hottman, Tara
• Advisor(s): Kaes, Anton

This dissertation tracks the changing conception of the archive in film and media art. It examines filmmakers who reflect upon the historicity of cinema in their work and use the archive as a model for creating their essay films, video essays and installations. The four filmmakers whose work is under examination—Alexander Kluge, Hartmut Bitomsky, Harun Farocki and Hito Steyerl—have each played an instrumental role in the development of the film industry in postwar and contemporary Germany. Considered in a constellation with one another, they cover an important period of German—and global—media history, in which the forms of moving images and their mode of exhibition have diversified. New archival sources and media technology expanded the possibilities for these filmmakers to explore the contents of the German cinematographic archive and to integrate moving images from previous sources into their works. Taking their cue from Walter Benjamin’s concept of history and his practices of citation, these filmmakers use montage to put films from the past into constellation with present-day film and media. Their montages unearth aspects of earlier films that were not visible in their original context and they reveal the shifting configurations between past and present in film history, illustrating the need for a non-linear film historiography.

In these works, film history and the cinematographic archive become a site of potentiality that offers alternative paths for film in the art gallery and museum, and on the Internet. Their works collectively demonstrate how essayistic practices have expanded from the essay film of auteur cinema to the video and digital essay of media artists featured in art installations and on the Internet. The evolution of these essayistic practices testifies to the essay’s continued ability to function as a form that runs against the grain of commercial production. If, as some theorists argue, the bureaucratic documentation of the archive is now the primary force through which biopolitics renders life deathlike, then the archival practices exhibited by these filmmakers not only illustrate how the past might gain a functional, creative use for the present, but they also provide an example for ways in which the archive might be employed against existing forms of control. Their works illustrate the need for increased access to the archive and a democratization of who has the authority to investigate its contents and document its histories today.

Set in Motion: Dance Criticism and the Choreographic Apparatus

• Mattingly, Kate
• Advisor(s): Jackson, Shannon

This dissertation examines the multiple functions of dance criticism in the 20th and 21st centuries in the United States. I foreground institutional interdependencies that shape critics’ practices, as well as criticism’s role in approaches to dance-making, and the necessary and fraught relations between dance criticism and higher education. To challenge the pervasive image of the critic as evaluator and of criticism as definitive, Set in Motion focuses on conditions that produce and endorse certain forms of criticism, and in turn how this writing has gained traction. I employ the concept of a choreographic apparatus to show shifting relations amongst writers, artists, publications, readers, institutions, and audiences. Their interactions generate frameworks that influence dance’s history, canon, and disciplinary formations. I propose a way of situating criticism as a form of writing that intersects with, informs, and influences both history and theory.

Set in Motion expands discourse on writing by examining the continuities and discontinuities in practices over the course of a century. Chapter 1 focuses on articles by John Martin in the New York Times the late 1920s and early 1930s. Chapter 2 analyzes how artists in the 1960s, in particular Yvonne Rainer, took hold of the choreographic apparatus to redirect discourse about their projects. In Chapter 3, I expand my analysis from methodologies to the study of educational institutions. Chapter 4 turns to the question, “where is criticism today?” and investigates how digital technologies in the 21st century inform and inflect our engagements with criticism. Set in Motion contributes to dance studies discourses, disciplinary formation, and histories of professionalization by noticing ways in which criticism and theory function less often as opposing forces and primarily as reciprocal and interconnected partners. By recognizing the ways criticism has functioned as a fulcrum to legitimate and leverage particular approaches to dance, this project highlights artists’ and critics’ modes of production that generate and redesign our definitions of dance writing.

On Stability and Doctor-optimality of Cumulative Offer Process

• Advisor(s): Shannon, Chris

I study the stability and doctor-optimality of doctors' proposing cumulative offer process in the many-to-one matching with contracts. First, I explore some conventional hospital-by-hospital conditions on each hospital's choice function, and show that unilateral substitutability is equivalent to observable substitutability across doctors combined with cumulative offer achievability, each of which is a necessary condition for cumulative offer process to be doctor-optimally stable in a sense that if a hospital does not satisfy the condition, then we could construct some choice functions for other hospitals such that cumulative offer process is not doctor-optimally stable for some doctors' preference profile. Then, I focus on the joint properties of the choice functions for the entire group of hospitals and introduce two joint conditions---independence of proposing order and group cumulative offer achievability---and show that when these conditions are satisfied, cumulative offer process is always doctor-optimally stable. And it is by far the weakest sufficient condition. Moreover, these two conditions are necessary in a sense that if not, then there exists a doctors' preference profile and a proposing order such that cumulative offer process is not doctor-optimally stable. At last, I also introduce doctor's preference monotonicity and show that when cumulative offer process is doctor-optimally stable, this condition guarantees its strategy-proofness.

Compositionality and Modularity for Robot Learning

• Devin, Coline
• Advisor(s): Levine, Sergey ;
• Darrell, Trevor

Humans are remarkably proficient at decomposing and recombiningconcepts they have learned. In contrast, while deep learning-based methods have been shown to fit large datasets and out-perform humans at some tasks, they often fail when presented with conditions even just slightly outside of the distribution they were trained on. In particular, machine learning models fail at compositional generalization, where the model would need to predict how concepts fit together without having seen that exact combination during training. This thesis proposes several learning-based methods that take advantage of the compositional structure of tasks and shows how they perform better than black-box models when presented with novel compositions of previously seen subparts. The first type of method is to directly decompose neural network into separate modules that are trained jointly in varied combinations. The second type of method is to learn representations of tasks and objects that obey arithmetic properties such that tasks representations can be summed or subtracted to indicate their composition or decomposition. We show results in diverse domains including games, simulated environments, and real robots.

The Men You Will Become: Single-Sex Public Education and the Crisis of Black Boys

• Oeur, Freeden
• Advisor(s): Thorne, Barrie

Against a backdrop of massive public school reform, single-sex public schools have become an increasingly popular, but controversial, option for parents and their children. In this dissertation, I demonstrate that single-sex public education today is merely the latest twist in a long-term, historically-situated trajectory of gender- and race-separated schooling in the United States. Drawing on 11 months of intensive fieldwork, over 140 in-depth interviews, and an analysis of documents at two single-sex, nearly all-African American public high schools in the large east coast of "Morgan," I ask: What interventions do single-sex public schools make on behalf of their African American male students? And what impact do those interventions have on the boys' masculinity formation and life chances?

At "Perry High," a grades 7-12 neighborhood public school, officials and community members identified mass incarceration and the lack of caregiving as acute, interrelated crises facing their young African American male students. The administrators desired for their boys to grow to become responsible husbands and fathers, and the boys themselves aspired to be these men. The school, however, lacked the resources and strategies to remove many of the boys off the school-to-prison pipeline. At "Urban Charter," a charter school serving boys in grades 9-11, staff and "consumer" buy-in and a strong formal, academic curriculum enabled the school to remove more of their boys from the school-to-prison pipeline and to place them on a college track. The school also depended on a second hidden curriculum that sought to protect the boys from the perceived degradation of regular public schools, and in particular the threatening specter of the boys who attended those schools. School officials desired for their students to become respectable, middle-class workers in a global economy.

These findings extend knowledge on African American boys and schooling in several ways. I show that single-sex public schools that target this population rely little on beliefs in gender differences between boys and girls, and instead primarily on the unique vulnerabilities of African American boys. I also build on research on caregiving within schools and show how schools frame mass incarceration as a miscarriage of justice requiring certain provisions of care, and how boys desired care from adults. Last, I show how different institutional histories and capacities, particularly between regular public schools and public charters, greatly impact the ability of schools to intervene on behalf of their young Black men and to "save" them.

f-Block Complexes of Chelating Tetraphenolates and their Applications in Catalytic Dinitrogen Functionalization

• Lam, Yu Ting Francis
• Advisor(s): Arnold, Polly

Chapter 1 reports dinuclear actinide (An) complexes supported by the meta-phenyl-bridged tetraphenolate ligand mTP, and their ability to catalyze the N2 reduction reaction (N2RR). The bis-UIV metallacycle [U2(mTP)2] (1.1) possesses a rectangular, ‘letterbox’-shaped cavity between the two UIV cations. When treated with potassium reductant, 1.1 can mediate the reduction of N2 by four electrons; concomitant intramolecular deprotonation of ligand benzylic C–H leads to the formation of a hydrazido [N2H2]2− ligand in K4[U2(μ-η2:η2-N2H2)(mTP−)] (1.3). We also demonstrate that 1.1 can catalyze the selective formation of HN(SiMe3)2, a secondary silylamine, from N2 under ambient conditions, the first catalyst to achieve this transformation. This also represents the first example of a homogeneous f-block N2RR catalyst. A possible reaction mechanism, which was computed via DFT by our collaborator, is discussed.

Chapter 2 extends our investigation in f-block-mediated N2RR to the lanthanides (Ln). The bis-SmIII metallacycle K2[Sm2(mTP)2(THF)2] (2.1) is also capable of catalyzing the N2RR, the first 4f complex to do so. Compared to 1.1, 2.1 catalyzes the formation of the tertiary silylamine N(SiMe3)3 from N2. This suggests that the N2RR catalyzed by 2.1 is mechanistically different to that by 1.1, in that the mTP benzylic C–H is not deprotonated. The bis-SmIII platform complex [Sm2(mTP)I2(THF)6] (2.2) converts to 2.1 under the reaction conditions, further reinforcing the significance of the metallacyclic geometry in this system. Surprisingly, a wider series of dinuclear platform complexes [Ln2(mTP)I2(THF)n] (2.3; Ln = La, Nd, Dy, Lu), [Th2(mTP)Cl4(THF)5(dme)] (2.4) and [U2(mTP)I4(THF)4] (2.5) can also mediate the N2RR, despite showing no evidence of interconversion to metallacyclic complexes. Preliminary characterization data of the reduced N2 species are discussed, including EPR spectroscopy and magnetic susceptibility measurements that suggest the existence of a ligand radical.

Chapter 3 describes a series of An(IV) complexes supported by the pTP ligand, the para-phenyl-bridged counterpart of mTP. In the absence of donor solvents, the mononuclear complexes [An(pTP)] (An = Th 3.1, An = U 3.2) are formed, in contrast to the dinuclear mTP complexes described in Chapter 1. Both 3.1 and 3.2 possess rare η6-AnIV–arene interactions, which were investigated both experimentally, and computationally via DFT by our collaborators. Electronic structure calculations of the reduced analogues [3.1]− and [3.2]−, as well as the isoelectronic Yb counterpart [Yb(pTP)]− (3.15), were able to locate the unpaired electron density in each case and identify potential molecular qubit candidates. Addition of Lewis bases and monoanionic ligands also allowed us to study the effect of axial donor strength.

Chapter 4 investigates the application of the mTP ligand in stabilizing the uranyl(VI) dication, (UO2)2+. The platform complex [(UO2)2(mTP)(THF)3] (4.1) and metallacyclic [Na(15-c-5)(py)]4[(UO2)2(mTP)2] (4.5) were synthesized and fully characterized, locating two uranyl dications in close proximity. The U(VI) to U(IV) reduction of 4.1 can be mediated by the simple f-block halide SmI2(THF)2, but is concomitant with ligand dissociation. Complex 4.1 is also capable of mediating hydrogen atom abstraction reactions from hydrocarbons under visible light irradiation.

Altered Reproductive Function and Amphibian Declines

• Gallipeau, Sherrie
• Advisor(s): Hayes, Tyrone B

Agrochemical exposure is one of the factors that contributes to worldwide amphibian declines. Most studies that examine agrochemicals and amphibian declines focus on toxicity. However, declines are more likely caused by the sub-lethal effects of agrochemical exposure. Past emphases on the lethal effects of agrochemical exposure have overshadowed the contribution of decreased recruitment in amphibian declines. Additionally, studies that examine agrochemicals and reproductive function tend to focus on the effects of single chemical exposures instead of the effects of ecologically relevant mixtures. To address these issues, this dissertation examined the effects of ecologically relevant agrochemical exposures on the stress response and the reproductive endocrinology, morphology, and behaviors of male amphibians in the laboratory and the wild.

Chapter 1 provides a general review of the factors implicated in amphibian declines and provides an overview of the previous research conducted on the effects of agrochemical exposure on recruitment.

Chapter 2 is a field study that examined whether agricultural run-off alters the stress response and reproductive function of male bullfrogs (Lithobates catesbeianus). Bullfrogs were collected upstream and downstream of agricultural activity across three California river systems (Salinas, Sacramento and San Joaquin). Size, primary and secondary sex traits, sperm count, and corticosterone and testosterone levels were examined. Overall, bullfrogs living downstream of agricultural activity (i.e. exposure to agricultural run-off) were small and had elevated testosterone and corticosterone levels. In addition, downstream males from the Salinas and San Joaquin Rivers were also small in size and had elevated testosterone levels. However, only downstream males of the San Joaquin River had elevated corticosterone and exaggerated secondary sex traits. Together, these data suggest that living downstream of agriculture can alter size, hormone levels, and the expression of sexually dimorphic sex traits. Such changes to the reproductive endocrinology and morphology of male amphibians can be detrimental to the reproductive health and long-term reproductive success of amphibian populations.

In Chapter 3, I examined corticosterone, testosterone, and the reproductive clasping behaviors of adult male African clawed frogs (Xenopus laevis) exposed to field collected and simulated agricultural run-off. This experiment implemented a novel eco-relevant experimental design to mimic real-life agrochemical exposures. Male frogs were exposed to field water collected downstream (agricultural run-off) and upstream (negative control) of agricultural activity along the Salinas River, CA. In addition, a pesticide mixture containing the top agrochemicals used in the Monterey County was included to simulate agricultural run-off. Mating behavior was suppressed in males exposed to simulated agricultural run-off but enhanced in males exposed to field collected agricultural run-off. In addition, testosterone levels of clasping males were elevated in comparison to controls. Males immersed in simulated agricultural run-off had significantly lower testosterone levels than control males in 2010. These data suggest that agrochemical exposure (both field collected and simulated) can alter reproductive hormones and clasping behaviors. Altered sex hormones and behaviors in male amphibians may play a role in amphibian declines.

Lastly, this dissertation is summarized in Chapter 4. The applicability of this dissertation as a model for amphibian declines and other reproductive related human health concerns are also introduced.

Using Infectious Disease Modeling to Explain the Distribution of Disease Burden: from Health Economics to Molecular Epidemiology

• Plucinski, Mateusz
• Advisor(s): Getz, Wayne

Infectious disease modeling has an untapped potential to provide insight into how disease burden is distributed in human populations. Here, we apply the techniques of infectious disease modeling to applications ranging from health economics to molecular epidemiology.

The persistence of extreme poverty is increasingly attributed to dynamic interactions between biophysical processes and economics, though there remains a dearth of integrated theoretical frameworks that can inform policy. In Chapter 1, we present a stochastic model of disease-driven poverty traps. Whereas deterministic models can result in poverty traps that can only be broken by substantial external changes to the initial conditions, in the stochastic model there is always some probability that a population will leave or enter a poverty trap. We show that a `safety net', defined as an externally enforced minimum level of health or economic conditions, can guarantee ultimate escape from a poverty trap, even if the safety net is set

within the basin of attraction of the poverty trap, and even if the safety net is only in the form of a public health measure. Whereas the deterministic model implies that small improvements in initial conditions near the poverty-trap equilibrium are futile, the stochastic model suggests that the impact of changes in the location of the safety net on the rate of development may be strongest near the poverty-trap equilibrium.

In Chapter 2, we show that the same feedbacks between health and income explored in the first chapter, when applied to an individual level (rather than population level), can lead to persistent poverty and high levels of disease among certain individuals in a population, even when the population overall has high income and low disease. This suggests that disease-induced poverty might be a compelling mechanistic explanation for the persistence of health and wealth disparities. Using an individual-based network model with community structure, we show that the structure of the disease transmission network is crucial for the formation of clusters of high poverty and high disease, further highlighting the importance of population structure in studying issues of human health, a topic of increasing importance in both infectious disease modeling as well as social epidemiology.

In Chapter 3, we show how network structure could potentially be measured, using standard molecular epidemiology techniques. Using DNA sequence data from pathogens to infer transmission networks has traditionally been done in the context of epidemics and outbreaks. Sequence data could analogously be applied to cases of ubiquitous commensal bacteria; however, instead of inferring chains of transmission to track the spread of a pathogen, sequence data for bacteria circulating in an endemic equilibrium could be used to infer information about host contact networks. We show - using simulated data - that multilocus DNA sequence data, based on multilocus sequence typing schemes (MLST), from isolates of commensal bacteria can be used to infer both local and global properties of the contact networks of the populations being sampled. Specifically, for MLST data simulated from small-world networks, the small world parameter controlling the degree of structure in the contact network can robustly be estimated. Moreover, we show that pairwise distances in the network - degrees of separation - correlate with genetic distances between isolates, so that how far apart two individuals in the network are can be inferred from MLST analysis of their commensal bacteria. This result has important consequences, and we show an example from epidemiology - how this result could be used to test for infectious origins of diseases of unknown etiology.

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Home » For Authors & Researchers » Open Access Theses & Dissertations

Open Access Theses & Dissertations

Theses and dissertations produced by students as part of the completion of their degree requirements often represent unique and interesting scholarship. Universities are increasingly making this work available online, and UC is no exception. Find information related to open access theses and dissertations below.

UC has an open access policy for theses and dissertations, but procedures and specifics vary by campus

Several UC campuses have established policies requiring open access to the electronic theses and dissertations (ETDs) written by their graduate students. As of March 25, 2020, there is now a systemwide Policy on Open Access for Theses and Dissertations , indicating that UC “requires theses or dissertations prepared at the University to be (1) deposited into an open access repository, and (2) freely and openly available to the public, subject to a requested delay of access (’embargo’) obtained by the student.”

In accordance with these policies, campuses must ensure that student ETDs are available open access via eScholarship (UC’s open access repository and publishing platform), at no cost to students. By contrast, ProQuest, the world’s largest commercial publisher of ETDs, charges a $95 fee to make an ETD open access. Institutions worldwide have moved toward open access ETD publication because it dramatically increases the visibility and reach of their graduate research.

Policies and procedures for ETD filing, including how to delay public release of an ETD and how long such a delay can last, vary by campus. Learn more about the requirements and procedures for ETDs at each UC campus:

• UC Berkeley: Dissertation Filing Guidelines (for Doctoral Students) and Thesis Filing Guidelines (for Master’s Students)
• UC Davis: Preparing and Filing Your Thesis or Dissertation
• UC Irvine: Thesis/Dissertation Electronic Submission
• UCLA: File Your Thesis or Dissertation
• UC Merced: Dissertation/Thesis Submission
• UC Riverside: Dissertation and Thesis Submission
• UC San Diego:  Preparing to Graduate
• UCSF: Dissertation and Thesis Guidelines
• UC Santa Barbara:  Filing Your Thesis, Dissertation, or DMA Supporting Document
• UC Santa Cruz: Dissertation and Thesis Guidelines (PDF) from the Graduate Division’s Accessing Forms Online page

Open access can be delayed in certain circumstances

Some campuses allow students to elect an embargo period before the public release of their thesis/dissertation; others require approval from graduate advisors or administrators. Visit your local graduate division’s website (linked above) for more information.

Common copyright concerns of students writing theses and dissertations

Students writing theses/dissertations most commonly have questions about their own copyright ownership or the use of other people’s copyrighted materials in their own work.

You automatically own the copyright in your thesis/dissertation  as soon as you create it, regardless of whether you register it or include a copyright page or copyright notice (see this FAQ from the U.S. Copyright Office for more information). Most students choose not to register their copyrights, though some choose to do so because they value having their copyright ownership officially and publicly recorded. Getting a copyright registered is required before you can sue someone for infringement.

If you decide to register your copyright, you can do so

• directly, through the Copyright Office website , for $35
• by having ProQuest/UMI contact the Copyright Office on your behalf, for $65.

It is common to incorporate 1) writing you have done for journal articles as part of your dissertation, and 2) parts of your dissertation into articles or books . See, for example, these articles from Wiley and Taylor & Francis giving authors tips on how to successfully turn dissertations into articles, or these pages at Sage , Springer , and Elsevier listing reuse in a thesis or dissertation as a common right of authors. Because this is a well-known practice, and often explicitly allowed in publishers’ contracts with authors, it rarely raises copyright concerns. eScholarship , which hosts over 55,000 UC ETDs, has never received a takedown notice from a publisher based on a complaint that the author’s ETD was too similar to the author’s published work.

Incorporating the works of others in your thesis/dissertation – such as quotations or illustrative images – is often allowed by copyright law. This is the case when the original work isn’t protected by copyright, or if the way you’re using the work would be considered fair use. In some circumstances, however, you will need permission from the copyright holder.  For more information, please consult the Berkeley Library’s guide to Copyright and Publishing Your Dissertation .

How to find UC Dissertations and Theses online

All ten UC campuses make their electronic theses and dissertations (ETDs) openly accessible to readers around the world. You can view over 55,000 UC ETDs in eScholarship , UC’s open access repository. View ETDs from each campus:

• Santa Barbara

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Dissertation Writing and Filing

The following guidelines are only for doctoral students. If you are pursuing a master’s degree, please see the Thesis Filing Guide .

Ready to get started?

Research Protocols

Eligibility, fall and spring semesters, summer filing, formatting your manuscript, special page formats, organizing your manuscript, procedure for filing your dissertation, permission to include your own previously published or co-authored material, inclusion of your own publishable papers or article-length essays, copyright & your dissertation, copyright ownership and registration issues, inclusion of third-party content in your dissertation; copyright & fair use issues, publishing your dissertation; embargoes, publication requirement, embargo extensions, changes to a dissertation after filing, diploma, transcript, and certificate of completion, certificate of completion, appendix a: common mistakes, appendix b: mixed media guidelines, definitions and standards, electronic formats and risk categories, appendix c: frequently asked questions.

Filing your doctoral dissertation at the Graduate Division is one of the final steps leading to the award of your graduate degree. Your manuscript is a scholarly presentation of the results of the research you conducted. UC Berkeley upholds the tradition that you have an obligation to make your research available to other scholars. This is done when you submit your dissertation for publishing through the ProQuest online administration system and the Graduate Division forwards your manuscript to the University Library. Your dissertation is subsequently published online in the UC system’s scholarship repository ( eScholarship ) and made available within ProQuest/UMI after your doctoral degree is officially conferred by the Academic Senate.

Your faculty committee supervises the intellectual content of your manuscript and your committee chair will guide you on the arrangement within the text and reference sections of your manuscript. Consult with your committee chair early in the preparation of your manuscript.

The specifications in the following pages were developed in consultation with University Library. These standards assure uniformity in the degree candidates’ manuscripts to be archived in the University Library, and ensure as well the widest possible dissemination of student-authored knowledge.

If your research activities involve human or animal subjects, you must follow the guidelines and obtain an approved protocol  before you begin your research.  Visit our web page for more information  or contact the Committee for the Protection of Human Subjects ( http://cphs.berkeley.edu/  or 642-7461) or the Animal Care and Use Committee ( http://www.acuc.berkeley.edu/  or 642-8855).

In addition to the considerations explained below, your Expected Graduation Term (EGT) must match the term for which you intend to file. EGT can be updated at any time using an eForm available in CalCentral.

To be eligible to file for your degree, you must be registered or on approved Filing Fee status for the semester in which you file. We encourage you to file your dissertation as early in the semester as you can and to come in person to our office to submit your supporting documents. If you cannot come to our office, it is helpful if you have a friend bring your documents. The deadline to file your dissertation in its final form is the last day of the semester for your degree to be awarded as of that semester.

Filing during the summer has a slightly different set of eligibility requirements. If you were fully registered during the immediately preceding Spring semester, and have not used Filing Fee already, you may file your dissertation during the summer with no additional cost or application required. Summer is defined as the period from the day after the Spring semester ends (mid-May) until the last day of the Summer Sessions (mid-August).

International students completing a degree in the Summer should consult Berkeley International Office before finalizing plans, as in some cases lack of Summer enrollment could impact visa status or post-completion employment.

If you have already used Filing Fee previously, or were not registered the preceding Spring semester, you will need to register in at least 1.0 unit in Summer Sessions in order to file.

Dissertations filed during the summer will result in a summer degree conferral.

You must be advanced to candidacy, and in good standing (not lapsed), in order to file.

All manuscripts must be submitted electronically in a traditional PDF format.

• Page Size : The standard for a document’s page size is 8.5 x 11 inches. If compelling reasons exist to use a larger page size, you must contact the Graduate Division for prior approval.
• Basic manuscript text must be a non-italic type font and at a size of 12-point or larger. Whatever typeface and size you choose for the basic text, use it consistently throughout your entire manuscript. For footnotes, figures, captions, tables, charts, and graphs, a font size of 8-point or larger is to be used.
• You may include color in your dissertation, but your basic manuscript text must be black.
• For quotations, words in a foreign language, occasional emphasis, book titles, captions, and footnotes, you may use italics. A font different from that used for your basic manuscript may be used for appendices, charts, drawings, graphs, and tables.
• Pagination:  Your manuscript is composed of preliminary pages and the main body of text and references. Page numbers must be positioned either in the upper right corner, lower right corner, or the bottom center and must be at least ¾ of an inch from the edges. The placement of the page numbers in your document must be consistent throughout.

Be Careful!  If you have any pages that are rotated to a landscape orientation, the page numbers still need to be in a consistent position throughout the document (as if it were printed and bound single-sided).

Do not count or number the title page or the copyright page. All other pages must have numbers. DO NOT SKIP PAGE ” 1 “. The remaining preliminary pages may include a table of contents, a dedication, a list of figures, tables, symbols, illustrations, or photographs, a preface, your introduction, acknowledgments, and curriculum vitae. You must number these preliminary pages using  lower case Roman numerals  beginning with the number “i” and continue in sequence to the end of the preliminary pages (i, ii, iii, iv, v, etc.). Your abstract must have  Arabic numeral  page numbers. Start numbering your abstract with the number “1” and continue in sequence (1, 2, 3, etc.) The main body of your text and your references also use Arabic numerals. Start the numbering of the main body with the number “1” and continue in sequence (1, 2, 3, etc.), numbering consecutively throughout the rest of the text, including illustrative materials, bibliography, and appendices.

Yes! The first page of your abstract and the first page of your main text both start with ‘1’

• Margins:  For the manuscript material, including headers, footers, tables, illustrations, and photographs, all margins must be at least 1 inch from the edges of the paper. Page numbers must be ¾ of an inch from the edge.
• Spacing:  Your manuscript must be single-spaced throughout, including the abstract, dedication, acknowledgments, and introduction.
• Tables, charts, and graphs  may be presented horizontally or vertically and must fit within the required margins. Labels or symbols are preferred rather than colors for identifying lines on a graph.

You may choose to reduce the size of a page to fit within the required margins, but be sure that the resulting page is clear and legible.

• Guidelines for Mixed Media:  please see Appendix B for details.

Certain pages need to be formatted in a very specific way. Links are included here for examples of these pages.

Do not deviate from the wording and spacing in the examples, except for details applicable to you (e.g. name, major, committee, etc.)

• As noted in the above section on pagination, the abstract must be numbered  separately with Arabic numerals starting with ‘1’
• If you have a Designated Emphasis, it must be listed on your abstract.
• IMPORTANT: A physical signature page should no longer be included with your dissertation. Approvals by your committee members will be provided electronically using an eForm.
• The title page does not contain page numbers.
• Do not bold any text on your title page.
• The term and year listed on the title page must be the term of your degree. If you filed during the summer, write  Summer .
• The yellow bubbles in the sample are included for explanatory purposes only. Do not include them in your submission.
• If you have a Designated Emphasis, it must be listed on your title page ( DE Title Page Sample )
• If you are receiving a joint degree, it must be listed on your title page ( Joint Title Page Sample )

The proper organization and page order for your manuscript is as follows:

• Copyright page or a blank page
• Dedication page
• Table of contents
• List of figures, list of tables, list of symbols
• Preface or introduction
• Acknowledgments
• Curriculum Vitae
• Bibliography

Please do not include an approval/signature page.

After you have written your dissertation, formatted it correctly, assembled the pages into the correct organization, and obtained verbal approval from your committee, you are ready to file it with UC Berkeley’s Graduate Division.

• Step 0: Confirm your eligibility to file. Your Expected Graduation Term (EGT) must be current term (i.e. the term in which you expect to file your dissertation). If you need to update your EGT you can use the eForm available in CalCentral. Once your EGT is correct, you will see a number of checklist items (“Tasks”) created for you in CalCentral. You use these checklist items to proceed with filing.
• Step 1: Convert your dissertation into a standard PDF file.
• Step 2:  Upload your PDF to ProQuest/UMI ( http://www.etdadmin.com ) Follow the instructions on the site. NOTE: DO NOT UPLOAD A DRAFT.  Once your dissertation has been submitted, you will not be allowed to make changes. Be sure that it is in its final form!
• Step 3:  When you have successfully submitted the document, a message will be sent to the Graduate Degrees Office to review it on-line.  After Degrees staff has reviewed it you will either receive a message that the manuscript has been accepted or that you need to make further changes. If you need to make more changes, you will need to edit your manuscript, create a new PDF, and resubmit it to ProQuest.  Degrees staff will then need to review it again. An email approval will be sent to you once the manuscript is accepted.
• Step 4: There are two surveys to be completed:the Survey of Earned Doctorates and the Berkeley Doctoral Exit Survey. You will find these surveys as “Tasks”in your CalCentral dashboard (as long as you have a current-term EGT). Follow the instructions to complete the surveys and enter the verification codes. You should see the checklist items complete automatically.
• Review the your committee and email addresses listed — the form will route to each of your committee members for approval.
• If you chose to embargo your dissertation, you will not receive any copies you order from ProQuest until the embargo is lifted.
• Once the form has been filed, you may not make any changes to your embargo selections
• Attach a copy of the approval letter for your study protocol from the Committee for Protection of Human Subjects, or the Animal Care and Use Committee if your research involved human or animal subjects.

A Note on Deadlines

You must upload your electronic dissertation AND submit your final signature eform before 5 p.m. on the last day of the term. Both of these steps must be done before the deadline, regardless of whether your submission has been reviewed and approved. We can not provide a receipt of filing until your dissertation has been reviewed and accepted (which can take up to 4 business days), but you will get credit for the date of first submission.

If you plan use of your own previously published and/or co-authored material in your manuscript, your committee chair must attest that the resulting dissertation represents an original contribution of ideas to the field, even if previously published co – authored articles are included, and that major contributors of those articles have been informed.

Previously published material must be incorporated into a larger argument that binds together the whole dissertation. The common thread linking various parts of the research, represented by individual papers incorporated in the dissertation, must be made explicit, and you must join the papers into a coherent unit. You are required to prepare introductory, transitional, and concluding sections. Previously published material must be acknowledged appropriately, as established for your discipline or as requested in the original publication agreement (e.g. through a note in acknowledgments, a footnote, or the like).

If co-authored material is to be incorporated (whether published or unpublished), all major contributors should be informed of the inclusion in addition to being appropriately credited in the dissertation according to the norms of the field.

If you are incorporating co-authored material in your dissertation, it is your responsibility to inform major contributors. This documentation need not be submitted to the Graduate Division. The eform used by your committee chair to sign off on your dissertation will automatically include text indicating that by signing off they attest to the appropriateness and approval for inclusion of previously published and/or co-authored materials. No addition information or text needs to be added.

Publishable papers and article-length essays arising from your research project are acceptable only if you incorporate that text into a larger argument that binds together the whole dissertation or thesis. Include introductory, transitional, and concluding sections with the papers or essays.

You own copyright in your dissertation. Copyright is automatically created once your work is fixed in a tangible medium (such as saved on your computer hard drive or in cloud storage). Thus, you do not need to register copyright in your dissertation in order to be the copyright holder.

However, registering copyright in your dissertation has certain advantages: First, if your work is registered, you have evidence that you are indeed the author and owner. Second, registration allows greater enforcement of your copyright against an infringer or plagiarist, making available statutory damages set out in Title 17, Section 504 of the U.S. Code, which range from $750 – $150,000 plus attorney fees per copyright infraction. Accordingly, UC Berkeley recommends that you register copyright for your dissertation. You can register copyright through the Copyright Office’s website, www.copyright.gov , for a fee of $35, or through the ProQuest ETDAdmin system when you submit your PDF; doing so through ProQuest costs $55.

You continue to own copyright in your dissertation unless and until you transfer your copyright to another party. By complying with the UC Berkeley Graduate Division’s publishing policies, you are permitting the university to make available a copy of your dissertation online in eScholarship, but you are not transferring your copyright. You grant a similar permission to ProQuest/UMI, the exact terms of which are governed by the agreement with ProQuest you sign in the online submission process. You may request delays (i.e. embargoes) in the release of your dissertation both on eScholarship and in ProQuest. Please see “Publishing Your Dissertation; Embargoes”.

If you are including content in your dissertation not authored or created by you, be sure to consider copyright issues. The University Library can help guide you as you consider these questions. For more detail, please consult the Library’s helpful online guide, entitled Copyright and Publishing Your Dissertation .

To briefly summarize:

• If the content is in the public domain, then you need not get any permission to use the material. For questions about the public domain, see http://copyright.universityofcalifornia.edu/use/public-domain.html.
• If the content you wish to use is subject to a Creative Commons license of some form, you need simply abide by the term of that license. For instance, a CC-BY license means you can use the work without seeking the author’s permission, but must attribute the work to the author. For more on Creative Commons licenses, see https://creativecommons.org/licenses/.
• If the content you wish to use is protected by copyright and no Creative Commons license governs its use, then you must consider whether your use constitutes Fair Use under 17 USC § 107. If your use of the content is a fair use within copyright law, then you need not seek the author’s permission before using it. See http://copyright.universityofcalifornia.edu/use/fair-use.html.
• If your use of the content would exceed fair use under the Copyright Act, then you will need to seek the copyright holder’s permission in order to use the material. Be sure to request the copyright owner’s permission in writing so that you can keep track of permissions granted. Your letter to the copyright holder should make clear that you seek permission to preserve and publish the content in your dissertation through UC Berkeley’s institutional repository, eScholarship, and ProQuest/UMI. For help seeking permission, see http://copyright.universityofcalifornia.edu/use/obtaining-permission.html.

If you have additional questions about copyright and third party content in your dissertation, please contact the University Library .

UC Berkeley’s Graduate Council regulations stipulate that you have an obligation to make your research available to other scholars as part of the degree requirement.  This obligation is consistent with the long-standing principle that doctoral students share their significant scholarly contributions to advance knowledge. This requirement is fulfilled when you submit your dissertation for publishing through the ProQuest online administration system and the Graduate Division forwards your manuscript to the University Library. Your dissertation is subsequently published online in the UC system’s scholarship repository ( eScholarship ) and made available within ProQuest/UMI after your doctoral degree is officially conferred by the Academic Senate.

Making your work available to be read online immediately in eScholarship or ProQuest has many advantages. First, it clearly establishes when your work was created and published, which are powerful resources in preventing or combatting plagiarism. Others will be able to discover your prior publication. Second, it can help support your scholarly profile because people can read and begin citing your work. Citation of your dissertation by others can be offered as evidence of research significance in employment reviews. Further, research available through searches on the Internet can promote contacts that are international in scope and interdisciplinary in reach.

Occasionally, there are circumstances in which you prefer that your dissertation not be published immediately. Such circumstances may include the disclosure of patentable rights in the work before a patent can be granted, similar disclosures detrimental to the rights of the author, or disclosures of facts about persons, institutions, or locations before professional ethics would permit.

The Dean of the Graduate Division may permit the dissertation to be withheld from full-text publication in eScholarship for a specified and limited period of time. An embargo of up to 2 years can be requested at the time of filing. You will need to make an embargo selection both on the Final Signature eForm as well as the ETDAdmin (the ProQuest submission portal). Once you make a selection regarding an embargo, it may not be changed. Discuss the pros and cons of withholding your dissertation with your faculty committee and departmental advisors. For more information, see the memo Advising doctoral candidates on dissertation embargoes and eScholarship repository  (PDF).

Embargoes beyond the initial 2-year option must be requested pursuant to a petition process using the E mbargo Extension Petition Form . Extensions are granted at the discretion of the Graduate Division, and are based on substantiated circumstances of the kind indicated above and with the endorsement of and an explanatory letter from the chair of the dissertation committee (or, if the dissertation chair is unavailable, the current department chair). Be sure to submit the petition form with sufficient time (at least three months) prior to the expiration of your original embargo to ensure adequate processing time prior to your dissertation’s scheduled release. If a renewal request is submitted less than three months from when the original embargo is set to expire, the Graduate Division cannot guarantee that the request will be processed and granted in time to preclude your dissertation from being made publicly available. Please note that it is your responsibility to request an extension beyond the two-year maximum from both the University and separately through ProQuest/UMI if you would like to extend your embargo both on eScholarship and on ProQuest/UMI.

Changes are normally not allowed after a manuscript has been filed.  In exceptional circumstances, changes may be requested by having the chair of your dissertation committee submit a memo to the Associate Dean and sent to Graduate Services: Degrees, 318 Sproul Hall.  The memo must describe in detail the specific changes requested and must justify the reason for the request. Such requests will not be approved for typographical errors, acknowledgments, or other minor revisions. It is your responsibility to ensure that your manuscript is in its final form before submitting it. If such a request is approved, the changes must be made prior to the official awarding of the degree. Once your degree has been awarded, you may not make changes to the manuscript.

After your dissertation is accepted by Graduate Services: Degrees, it is held here until the official awarding of the degree by the Academic Senate has occurred. This occurs approximately two months after the end of the term. After the degree has officially been awarded, the manuscripts transmitted to the University Library and to ProQuest Dissertations Publishing.

Posting the Degree to Your Transcript

Your degree will be posted to your transcript approximately 10 weeks after the conferral date of your degree. You can order a transcript from the Office of the Registrar (https://registrar.berkeley.edu/academic-records/transcripts-diplomas/).

Your diploma will be available from the Office of the Registrar approximately 4 months after the conferral date of your degree. For more information on obtaining your diploma, visit the Registrar’s website.  You can obtain your diploma in person at the Office of the Registrar, 120 Sproul Hall, or submit a form and pay the current mailing fees to have it mailed to you.

Unclaimed diplomas are retained for a period of five (5) years only, after which they are destroyed.

• The most common mistake is following a fellow (or previous) student’s example. Read the current guidelines carefully!
• An incorrect committee — the committee listed on your title page (and on the final signature eform you will submit) must match your currently approved committee. If you have made any changes to your committee since Advancement to Candidacy, you must request an official change from the Graduate Division. Consult your departmental adviser for details.
• Do not use a different name than that which appears in the system (i.e. the name on your transcript and Cal Central Profile ). Students are allowed to use a Lived Name, which can be updated by self-service in CalCentral.
• Page numbers — Read the section on pagination carefully. Many students do not paginate their document correctly.
• Page rotation — some pages may be rotated to a landscape orientation. However, page numbers must appear in the same place throughout the document (as if it were bound like a book).
• If you have an approved designated emphasis, it must be listed on your title page  and  your abstract.
• Do not include the signature/approval page in your dissertation. The abstract must be  unsigned .
• Do not include previous degrees on your title page.
• There should be no bold text on your title page.

In May 2005, the Graduate Council established new guidelines for the inclusion of mixed media content in dissertations. It was considered crucial that the guidelines allow dissertations to remain as accessible as possible and for the longest period possible while balancing the extraordinary academic potential of these new technologies.

The dissertation has three components: a core thesis, essential supporting material, and non-essential supplementary material.

Core Thesis.  The core thesis must be a self-contained, narrative description of the argument, methods, and evidence used in the dissertation project. Despite the ability to present evidence more directly and with greater sophistication using mixed media, the core thesis must provide an accessible textual description of the whole project.

The core thesis must stand alone and be printable on paper, meeting the formatting requirements described in this document. The electronic version of the thesis must be provided in the most stable and universal format available — currently Portable Document Format (PDF) for textual materials. These files may also include embedded visual images in TIFF (.tif) or JPEG (.jpg) format.

Essential Supporting Material.  Essential supporting material is defined as mixed media content that cannot be integrated into the core thesis, i.e., material that cannot be adequately expressed as text. Your faculty committee is responsible for deciding whether this material is essential to the thesis. Essential supporting material does  not include the actual project data. Supporting material is essential if it is necessary for the actual argument of the thesis, and cannot be integrated into a traditional textual narrative.

Essential supporting material  must  be submitted in the most stable and least risky format consistent with its representation (see below), so as to allow the widest accessibility and greatest chance of preservation into the future.

Non-essential Supplementary Material.  Supplementary material includes any supporting content that is useful for understanding the thesis, but is not essential to the argument. This might include, for example, electronic files of the works analyzed in the dissertation (films, musical works, etc.) or additional support for the argument (simulations, samples of experimental situations, etc.).

Supplementary material is to be submitted in the most stable and most accessible format, depending on the relative importance of the material (see below). Any supplemental material must be uploaded to the ProQuest website under the “Supplemental Files” section.

Note . ProQuest and the Library will require any necessary 3rd party software licenses and reprint permission letters for any copyrighted materials included in these electronic files.

The following is a list of file formats in descending order of stability and accessibility. This list is provisional, and will be updated as technologies change. Faculty and students should refer to the Graduate Division website for current information on formats and risk categories.

Category A:

• TIFF (.tif) image files
• WAV (.wav) audio files

Category B:

• JPEG, JPEG 2000 (.jpg) image files
• GIF (.gif) image files

Category C:

• device independent audio files (e.g., AIFF, MIDI, SND, MP3, WMA, QTA)
• note-based digital music composition files (e.g., XMA, SMF, RMID)

Category D:

• other device independent video formats (e.g., QuickTime, AVI, WMV)
• encoded animations (e.g., FLA or SWF Macromedia Flash, SVG)

For detailed guidelines on the use of these media, please refer to the Library of Congress website for digital formats at  http://www.digitalpreservation.gov/formats/index.shtml .

Q1: Can I file my dissertation during the summer?

A1: Yes. There are 2 ways to file during the summer:

• Register for at least 1.0 unit through Berkeley Summer Sessions. With this option, you can file any time before the summer deadline .
• Register the preceding spring semester. As long as you were registered in the spring, and have not used filing fee before, you will be allowed to file during the summer without additional fees or applications.

Q2: If I chose that option, does it matter which session I register in during the summer session?

A2: No. You can register for any of the sessions (at least 1.0 unit). The deadline will always be the last day of the last session.

Q3: If I file during the summer, will I receive a summer degree?

A3: Yes. If you file before the end of the summer sessions, you will receive a summer degree. Remember to write “Summer” on your title page!

Q1: I’ve seen other dissertations from former students that were / that had  __________, should I follow that format?

A1: No. The formatting guidelines can be changed from time to time, so you should always consult the most current guidelines available on our website. This question is most frequently asked in regard to the issue of double vs. single spacing.

Q2: I want to make sure that my dissertation follows the formatting rules. What’s the best way to do this?

A2: If you’ve read and followed the current guidelines available on our website, there shouldn’t be any problems. You can upload your dissertation as soon as it is in its final form. If any changes are necessary, you will be given the opportunity to make them without penalties. If you’ve heard horror stories from other students about formatting changes in their manuscripts, you’ve likely been talking to past students who didn’t follow the directions and had to print out their dissertations on expensive, archival paper. Current students submit their dissertations electronically and, as such, it’s much easier and more painless to make changes!

You are also always welcome to bring sample pages into the Graduate Degrees Office at 318 Sproul Hall to have a staff member look over your manuscript.

Q3:  Does my signature page need to be printed on some special paper?

A3: Signatures are now an eForm process. A physical signature page is no longer required.

Q1: I’m away from Berkeley. Is there any way to file my dissertation remotely?

A1: Yes! The whole process is done remotely.

Q2: Can I have a friend bring my dissertation materials for me?

A2: Yes. Please see the answer above regarding filing remotely.

Q3: I read something about needing to allow 4 days to review my dissertation. So what is the actual deadline?

A3: Two things must happen before the end of the business day on the stated deadline: 1) you must have uploaded your dissertation to the ProQuest website and 2) you must have completed all the checklist items that appear in CalCentral (final signature eform and 2 surveys). Though it is not recommended, you can do both of these things on the very last day.

Q4: So what’s this thing about the 4 days?

A4: As you might expect, the Degrees Office receives hundreds of dissertations near the end of the term (in fact, half of all dissertations are submitted during the final week). This means that it may take several days for us to review your dissertation. Don’t worry. You’ll get credit for the date that you uploaded your dissertation. However, it may take up to 4 business days to review your submission and, if everything is acceptable, provide you a Receipt of Filing.

Q5: Can I do the Final Signature eForm before I upload my dissertation?

A5: Yes. We won’t be able to finalize your filing until everything has been reviewed and approved, but you are welcome to do those in any order.

Q6: What’s a Receipt of Filing? Do I need one?

A6: The Receipt of Filing is an official document that we produce that certifies that you have successfully filed your dissertation on the specified day and that, if all other requirements are met, the date of the degree conferral.

Some students may need the receipt in order to prove to an outside agency that they have officially filed their dissertation. Many students simply keep the receipt as a memento. Picking up your receipt is not required.

Q7: What’s the difference between a Receipt of Filing and a Certificate of Completion?

A7: A Receipt of Filing is automatically produced for all students upon successful filing of their dissertation. However, it only certifies that the dissertation has been accepted. The Certificate of Degree Completion  must be requested. It will state that all requirements  have  been met and notes the date that the degree will be conferred. This is a useful document for students who file early in the semester and need some verification of their degree in advance of its conferral (note: degrees are only conferred twice each year).

Q8: How do I know if I’m eligible for a Certificate of Completion?

A8: In order to be eligible to receive a Certificate of Completion, you must:

• Successfully file your dissertation (your online submission accepted as well as paperwork turned in)
• Have a fully satisfied Academic Progress Report (APR). The APR all the degree requirements as noted by your department. If there are requirements showing as “unmet” but you believe you have completed, please contact your GSAO.
• Pay all of your registration fees. While it may not necessarily hold up the production of your certificate, it is important that all fees are paid before the degree is conferred.

Q9: I’m supposed to bring in my approval letter for research with human subjects or vertebrate animals, but it turns out my research didn’t use this after all. What should I do?

A9: If your research protocol has changed since you advanced to candidacy for your degree, you’ll need to ask you dissertation chair to write a letter to the Graduate Division explaining the change. It would be best to submit this in advance of filing.

Q10: My dissertation uses copyrighted or previously published material. How do I get approval?

A10: The policy on this has recently changed. There is no need to for specific approval to be requested.

Q12: I uploaded my dissertation on the last day. What if I’m told I need to make changes?

A12: This won’t be a problem. If there are formatting issues that need to be resolved, you will be notified and be given the opportunity to make revisions – even if it is a few days after the deadline. As long as your dissertation was originally uploaded before the deadline. Obviously, we won’t be able to provide you a receipt (see Q above on Receipt of Filing) until everything has been finalized.

Q13: I found a typo in dissertation that has already been accepted! What do I do?

A13: Once a dissertation has been submitted and accepted, no further changes will be permitted. Proofread your document carefully. Do not upload a draft. In extreme circumstances, your dissertation chair may write a letter to the Graduate Division requesting additional changes to be made.

Q14: Oh no! A serious emergency has caused me to miss the filing deadline! What do I do? Are extensions ever granted?

A14: In general, no. In exceptional circumstances, the Head Graduate Advisor for your program may write to the Graduate Division requesting an extension. Requests of this type are considered on a case-by-case basis and, if granted, may allow you to file after the deadline. However, even if such an exception is granted you will receive the degree for the subsequent term. Your first step is to consult with your department if an emergency arises.

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Materials science & engineering: dissertations & theses.

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Kresge Engineering Library closed until 2025

The Kresge Engineering Library is temporarily closed due to the Bechtel Engineering Center renovation. We plan to re-open in 2025 when the new Engineering Student Center opens its doors.

Read about the closure here .

Questions? Send us a message and one of our engineering librarians will reach out. 

UC Berkeley Dissertations

UC Berkeley PhD Dissertations

Dissertations and Theses (Dissertation Abstracts)     UCB access only  1861-present 

Index and full text of graduate dissertations and theses from North American and European schools and universities, including the University of California, with full text of most doctoral dissertations from UC Berkeley and elsewhere from 1996 forward. Dissertations published prior to 2009 may not include information about the department from which the degree was granted. 

UC Berkeley Master's Theses

UC Berkeley Digital Collections   2011-present

Selected UC Berkeley master's theses freely available online. For theses published prior to 2020, check UC Library Search for print availability (see "At the Library" below). 

UC Berkeley dissertations may also be found in eScholarship , UC's online open access repository.

Please note that it may take time for a dissertation to appear in one of the above online resources. Embargoes and other issues affect the release timing.

At the Library:

Dissertations: From 2012 onwards, dissertations are only available online. See above links.

Master's theses : From 2020 onwards, theses are only available online. See above links. 

To locate older dissertations, master's theses, and master's projects in print, search UC Library Search by keyword, title or author. For publications prior to 2009 you may also include a specific UC Berkeley department in your search:  berkeley dissertations <department name> . 

Examples:  berkeley dissertations electrical engineering computer sciences  berkeley dissertations mechanical engineering

University of California

Index and full text of graduate dissertations and theses from North American and European schools and universities, including the University of California.

WorldCatDissertations     UCB access only 

Covers all dissertations and theses cataloged in WorldCat, a catalog of materials owned by libraries worldwide. UC Berkeley faculty, staff, and students may use the interlibrary loan request form  for dissertations found in WorldCatDissertations. 

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• Last Updated: Oct 31, 2024 12:00 PM
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Completed Ph.D. Dissertations

Emily Aiken. Targeting Social Protection Programs with Machine Learning and Digital Data. Ph.D. Dissertation. Advisor: Joshua E. Blumenstock. University of California, Berkeley. 2024.

Jeremy Gordon. Embodying the Future: Modeling Visually Guided Planning as Prospective Mental Simulation. Ph.D. dissertation. Advisors: John Chuang, Coye Cheshire, Steven Piantadosi, Giovanni Pezzulo. University of California, Berkeley. 2023.

Daniel Griffin.  Situating Web Searching in Data Engineering: Admissions, Extensions, Repairs, and Ownership . Ph.D. dissertation. Advisors: Deirdre K. Mulligan and Steven Weber. University of California, Berkeley. 2022.

Jonathan Gillick. Creating and Collecting Meaningful Musical Materials with Machine Learning . Ph.D. dissertation. Advisor: David Bamman. University of California, Berkeley. 2022.

Jonas, Anne. 2021. “Blank Slate: Freedom, Connection, and Accountability in U.S. Virtual Schools.” Doctoral dissertation, University of California, Berkeley.

Nitin Kohli.  Leveraging Differential Privacy While Attending to Social and Political Commitments . Ph.D. dissertation. Advisor: Deirdre Mulligan. University of California, Berkeley. 2021.

Doris Jung-Lin Lee. Designing Automated Assistants for Visual Data Exploration . Ph.D. dissertation. Advisor: Aditya G. Parameswaran. University of California, Berkeley. 2021.

Nick Doty. Enacting Privacy in Internet Standards . Ph.D. dissertation. Advisor: Deirdre K. Mulligan. University of California, Berkeley. 2020.

Max T. Curran.  Sensor-Mediated Empathy: A Mixed Methods Investigation of Social Biosensing . Ph.D. dissertation. Advisor: John Chuang. University of California, Berkeley. 2020.

Richmond Y. Wong.  Values by Design Imaginaries: Exploring Values Work in UX Practice . Ph.D. dissertation. Advisor: Deirdre Mulligan. University of California, Berkeley. 2020.

Howell, N. 2020. Emotional Meaning Making with Data. University of California, Berkeley.

Guanghua Chi. Migration and Social Networks: New Insights from Novel Data. Ph.D Dissertation. Advisor: Joshua E. Blumenstock. University of California, Berkeley. 2020.

Sarah Van Wart.  In search of a “fair explanation”: Helping young people to consider the possibilities, limitations, and risks of computer- and data-mediated systems . Ph.D. Dissertation. University of California, Berkeley. 2019.

Niall C. Keleher.  Economic Indicators and Social Networks: New approaches to measuring poverty, prices, and impacts of technology. Ph.D. Dissertation. Advisor: Joshua E. Blumenstock. University of California, Berkeley. 2019.

Sedenberg, Elaine. “Information-intensive innovation: the changing role of the private firm in the research ecosystem through the study of biosensed data.” PhD Diss. University of California, Berkeley, 2019.  https://escholarship.org/uc/item/1s60w39f#main

Nick Merrill.  Mind-Reading and Telepathy for Beginners and Intermediates: What People Think Machines Can Know About the Mind, and Why Their Beliefs Matter . Ph.D. Dissertation. Advisor: John Chuang. University of California, Berkeley. 2018.

Ishita Ghosh. Challenging the dominant narratives of a Digital Financial Inclusion. Ph.D Dissertation. Advisor: Jenna Burrell. University of California, Berkeley. 2018.

Khan, Muhammad Raza (2018). “Machine Learning for the Developing World using Mobile Communication Metadata” PhD dissertation., University of California, Berkeley

Jennifer King. Privacy, Disclosure, and Social Exchange Theory. Ph.D Dissertation. Advisor: Deirdre Mulligan. University of California, Berkeley. 2018.

Sebastian Benthall.  Context, Causality, and Information Flow: Implications for Privacy Engineering, Security, and Data Economics . Ph.D. dissertation. Advisors: John Chuang and Deirdre Mulligan. University of California, Berkeley. 2018.