VictorJuiz/thesis huggingface dataset:
Fluorophores for single-molecule imaging in living cells [electronic resource] : characterizing and optimizing DCDHF photophysics
Keywords: Chemistry

The number of reports per year on single-molecule imaging experiments has grown roughly exponentially since the first successful efforts to optically detect a single molecule were completed over two decades ago. Single-molecule spectroscopy has developed into a field that includes a wealth of experiments at room temperature and inside living cells. The fast growth of single-molecule biophysics has resulted from its benefits in probing heterogeneous populations, one molecule at a time, as well as from advances in microscopes and detectors. There is a need for new fluorophores that can be used for single-molecule imaging in biological media, because imaging in cells and in organisms require emitters that are bright and photostable, red-shifted to avoid pumping cellular autofluorescence, and chemically and photophysically tunable. To this end, we have designed and characterized fluorescent probes based on a class of nonlinear-optical chromophores termed DCDHFs. This dissertation describes various physical and optical studies on these emitters, from sensing local environment to photoactivation. Chapter 1 is a general introduction to fluorescence and single-molecule spectroscopy and imaging. Single-molecule experiments in living cells are discussed and probes used for such experiments are summarized and compared. Chapter 2 explores the basic photophysics of the DCDHF fluorophores and some general methods of measuring relevant spectroscopic parameters, including photostability. Chapter 3 discusses the various approaches we have taken to modify particular properties by changing the fluorophore's structure. We have redesigned the DCDHF fluorophore into a photoactivatable fluorogen--a chromophore that is nonfluorescent until converted to a fluorescent form using light--described in Chapter 4. Finally, a different, chemical route to fluorescence activation is presented in Chapter 5. The remainder of the Dissertation is the Appendix and a full Bibliography. The Appendix includes a table of photophysical parameter for DCDHF fluorophore, various protocols used in the experiments discussed, MatLab codes, and NMR spectra.
Force space studies of elastomeric anisotropic fibrillar adhesives [electronic resource]
Keywords: Applied Physics

Previous research into the climbing ability of the gecko lizard has revealed an adhesive system fundamentally different from existing synthetic adhesives. Instead of using a soft material, the gecko uses a complex system of hairs of beta-keratin, a material that is not tacky. This unique architecture affords the adhesive characteristics that make it well suited for climbing. Borrowing themes from the gecko, we developed a synthetic adhesive possessing similar properties using molded arrays of micron-scale silicone pillars. These arrays demonstrate the gecko property of frictional adhesion where increased shear stress at the interface leads to increased normal load capacity. To distinguish between intrinsic and emergent behavior, we also isolated single pillars to test on a dual-axis force-sensing cantilever capable of micro-Newton resolution. We observed that gecko-like properties were observed for tapered pillars but not for pillars of uniform cross-section. Most synthetic adhesive architectures use a uniform cross-section beam but the results presented here suggest such a design does not capture gecko-like behavior. These results point to ways to optimize the type of adhesion demonstrated by the synthetic dry adhesives and to create adhesives tailored for climbing or static applications.
Francisella tularensis host-pathogen relationships [electronic resource] : dissecting bacterial interactions with the Drosophila innate immune system
Keywords: Microbiology and Immunology

The survival of a bacterial pathogen within a host depends upon its ability to outmaneuver the host immune response. Thus mutant pathogens provide a useful tool for dissecting host-pathogen relationships as the strategies the microbe has evolved to counteract immunity reveal a host's immune mechanisms. In this study, we examined the pathogen Francisella tularensis subspecies novicida and identified new bacterial virulence factors that interact with different parts of the Drosophila melanogaster innate immune system. We performed a genome-wide screen to identify F. novicida genes required for growth and survival within the fly and identified a set of 149 negatively selected mutants. Among these, we identified a class of genes including the transcription factor oxyR, and the DNA repair proteins uvrB, recB, and ruvC that help F novicida resist oxidative stress. We determined that these bacterial genes are virulence factors that allow F. novicida to counteract the fly melanization immune response. We then performed a second in vivo screen to identify an additional subset of bacterial genes that interact specifically with the imd signaling pathway. Most of these mutants have decreased resistance to the antimicrobial peptide polymyxin B. Characterization of a mutation in the putative transglutaminase FTN_0989 produced a curious result that could not easily be explained using known Drosophila immune responses. By using an unbiased genetic screen, these studies provide a new view of the Drosophila immune response from the perspective of a pathogen. We show that two branches of the fly's immunity are important for fighting F. novicida infections in a model host: melanization and an imd-regulated immune response, and identify bacterial genes that specifically counteract these host responses. Our work suggests that there may be more to learn about the fly immune system as not all of the phenotypes we observe can be readily explained by its interactions with known immune responses.
From gender-based violence to women's violence in Haiti [electronic resource]
Keywords: Law.

This dissertation explores the conditions, incentives, and rationale that induce women victims of sexual violence to join armed groups and to become involved in community violence. Drawing on in-depth interviews, participant observation and focus group discussions collected during over one year of fieldwork in Haiti, the findings presented in this study reflect an attempt to deepen the understanding of women's decision-making processes, the interplay between gender-based women and women's violence, and, ultimately, the extent to which female aggression, committed in a context of armed violence, should be interpreted as a survival strategy or a deliberate choice for retaliation. Based on the empirical evidence collected, the three major factors that motivate women and girls to engage in criminal and community violence included their need to protect themselves and their families, their resentment toward state negligence and denial of their plight, and their dysfunctional desire to attain personal and social respect through retaliation. Important implications for legal and policy interventions may be derived from such an analysis. If women's violence is to be understood as a survival strategy within the coercive context of armed violence, the current Haitian legislation that provides solely for girls' and women's prosecution for the offense of association with armed groups, is at the very least inadequate. Conversely, according to international humanitarian and human rights legal norms, specific programs, along the lines of those implemented in other countries affected by armed conflict, should be effectively designed to dispel women's anger and resentment towards forms of community reconciliation as well as to adequately reintegrate them into society.
From state street to Bilski [electronic resource] : patent protection in the financial industry
Keywords: Law.

Abstract: In the last few years a renewed interest in the validity of patenting business methods has emerged. The issues appeared to have been settled in 1998 with the State Street decision. However, recently the Federal Circuit, following the more restrictive approach toward the patent system adopted by the Supreme Court, has questioned the soundness of the policy of extending patent protection to this type of subject matter. This new scenario occurred explicitly in In re Bilski when the Federal Circuit decided to rehear the case en banc and reconsider the conclusions previously reached in State Street. In so doing, the court significantly restricted the ability of inventors to obtain patents in certain fields. Indeed, to secure a patent on a process, it is no longer sufficient to show that an invention produces "a useful, concrete and tangible result." Now, an applicant also needs to demonstrate that her invention is either tied to a machine or transforms an article into a different state or thing. In June 2009, the Supreme Court decided to granted certiorari on In re Bilski, and the resulting decision is expected to shed light on the proper way to deal with the many questions that this case raises. Ultimately, the issues under consideration revolve around the empirical question of whether the patent system in the specific sector is "doing its job" or, in other words, whether that patent system is fostering the creation of additional business methods. To answer this question, I conducted a two parts empirical investigation of financial methods, as a subset of business methods. Specifically, I studied the innovative types of securities that emerged between 1980 and 2007. Then, I analyzed the patent applications submitted and the patents issued for different types of securities after 1998. Finally, I conducted structured interviews with market participants about the production and consumption of financial methods. The collected results indicate that after 2004 creators of new types of securities have shown less interest in the patent system. Nevertheless, the rate of innovation in this field has remained constant. The structured interviews revile that market participants are ambivalent about the benefits that both the financial market and their companies can derive from having exclusive rights on their inventions. They also provide a description of the financial market and of its dynamics that does not fit well with the patents system's mechanisms. Thus, serious doubts emerge that in the ten years between State Street and In re Bilski patent protection had any impact on innovation in the financial industry.
A frozen field of dreams, science, strategy, and the Antarctic in Norway, Sweden, and the British Empire, 1912-1952 [electronic resource]
Keywords: History.

The dissertation examines how actors in Norway, Sweden, and the British Empire conceived the Antarctic as a space for science during the years 1912 to 1952. Instead of tracing a narrative of enlightenment, how science became the dominant form of activity in the Antarctic, I examine a series of episodes with particular attention to why particular kinds of science held sway within specific political, cultural, and economic contexts. Concerned more with how Antarctic science was planned and justified than how it was executed in the field, the project draws upon recent scholarship in geography and geopolitics, as well as the history of exploration. The six case studies involve an aborted Anglo-Swedish Antarctic expedition in 1912; Britain's interwar Antarctic whaling research program; debates among whaling magnates and their associates over the relationship between Antarctic science and whaling in interwar Norway; the culture of polar exploration that emerged at Cambridge (and to some extent Oxford) between the world wars; the approach to polar exploration and quantitative glaciology pioneered by the Swedish geographer Hans Ahlmann; and the complicated history of the Norwegian-British-Swedish Antarctic Expedition (1949-52). I conclude with an epilogue arguing that the rise of international science in the Antarctic during the 1950s reflected the geopolitical dynamics of the Cold War, rather than the triumph of science over politics.
Functional analyses of HPH1and HPH2 revealed roles in post-translational protein translocation and nutrient translocation and nutrient signaling [electronic resource]
Keywords: Biology.
Academic theses.

Calcineurin is a Ca2+/calmodulin-dependent serine/threonine protein phosphatase conserved from yeast to mammals required for cell survival during environmental stress in yeast. It dephosphorylates several proteins located in different cellular compartments. Hph1 is a substrate of calcineurin that together with Hph2, its homolog, is also required for cellular adaptation to environmental stress. Hph1 and Hph2 are novel proteins of unknown function. Hph1 and Hph2 are tail-anchored integral ER-membrane proteins and have no identifiable homologs of in other organisms, except closely related yeast species. The goal of this work was to identify proteins that interact with Hph1 and Hph2 to help us identify their biological function. We show that Hph1 and Hph2 interact with the post-translational translocation machinery and are required for Vph1 stability, suggesting that they function in post-translational translocation at the ER. We have found several additional phenotypes for cells lacking HPH1 and HPH2 that overlap with the phenotypes observed for cells that have defects in vacuolar acidification. Hph1, but not Hph2, interacts with Vam6, a guanine-nucleotide-exchange factor, that regulates homotypic vacuolar fusion (through Ypt7) and TORC1 activation (through Gtr1). Interestingly, hph1[Delta] hph2[Delta] cells are resistant to rapamycin, further suggesting a role for these proteins in nutrient signaling. Structure-function analyses revealed that the coiled-coil motif is required for proper Hph1 localization and function, whereas the transmembrane domain is dispensable. This study has advanced our understanding of Hph1 and calcineurin function in regulating the cell's response to environmental stress and paves the way for a mechanistic understanding of Hph1 and Hph2 function in yeast.
Functional analysis of YneA, an SOS-induced inhibitor of cell division in Bacillus subtilis [electronic resource]
Keywords: Biological Sciences

In both prokaryotic and eukaryotic organisms, the coordination of cell division with DNA replication, segregation, and repair is critical for ensuring that each daughter cell receives an intact copy of the genome. In Bacillus subtilis, DNA damage triggers the SOS response, which activates a host of repair pathways, as well as an inhibitor of cell division, YneA. The mechanism by which YneA inhibits cell division and the processes involved in shutting off YneA activity remain unclear. In this work, we show that YneA is induced under a variety of DNA stress conditions, including replication initiation blocks. We observed that YneA is exported, does not stably associate with the cell wall, and is rapidly proteolyzed. Our results also suggest that YneA may be active prior to signal peptide cleavage. We have isolated mutations that indicate that protein-protein interactions mediated by the transmembrane domain might be required for YneA activity. One possible YneA target may be DivIB, a divisome component that we identified in a screen for suppressors of yneA overexpression.
Functional trait mediation of plant-animal interactions [electronic resource] : effects of defaunation on plant functional diversity in a neotropical forest
Keywords: Biological Sciences

This dissertation examines how terrestrial vertebrates, as seed dispersers, seed predators and herbivores, influence plant functional trait composition in tropical forests and thereby diversity. I conducted this work in the Barro Colorado National Monument (BCNM) in Central Panama, where a long term mammal exclosure experiment has been ongoing, and in neighboring Parque Nacional Soberanía, which together with the BCNM forms a defaunation gradient driven by hunting. Seedling communities showed shifts toward higher seed mass in response to exclosure, but no changes in leaf traits or wood density. In contrast, the sapling community did show significant shifts toward higher specific leaf area and lower leaf toughness in response to herbivore exclosure, primarily due to an increased dominance of species with those traits, and secondarily due to differences in the species present in each treatment type. Finally, I tested a model of the seed size responses to changes in mammal abundance by measuring vertebrate seed predation rates in a protected and hunted forest. I found that in Central Panama, in contrast to the model, seed mass does not correlate well with either body size of the seed predator, or vertebrate seed predation rates. This work suggests that terrestrial vertebrates play an underappreciated role in maintaining plant diversity and composition and that pan-tropical levels of unsustainable hunting may indirectly lead to losses of plant biodiversity.
Functionally relevant solvation dynamics in the protein interior
Keywords: Chemistry.

Functionally relevant solvation dynamics in the protein interior Stanford University, 2010. The role of solvent in the kinetics and thermodynamics of charge transfer reactions in simple solvents is well studied. However, biologically relevant systems often involve chemical reactions not in simple aqueous environments, but within a protein interior that constitutes an organized solvent environment. The role of the protein environment during catalysis and charge transfer reactions continues to be debated. To determine the role of the protein environment during charge transfer reactions, experiments presented in this dissertation were designed to measure the time-resolved response of a protein environment to sudden electronic perturbation. Specifically, time-resolved fluorescence measurements were used to determine the solvation response of a chromophore bound in the protein interior. An unnatural amino acid containing a fluorescent side chain, aladan, was synthetically incorporated into seven sites of a small globular protein, GB1, in order to determine the degree of solvation in different regions of a single protein. In all regions, the solvation dynamics showed an ultra-fast solvation response on the subpicosecond timescale. However, in addition to the subpicosecond dynamics, buried sites also showed relatively long solvation behavior over nanoseconds. mPlum, a variant of the red-fluorescent protein DsRed, was produced by a directed evolution experiment in the Roger Tsien lab. Ultra-fast fluorescence upconversion experiments measured a solvation response in mPlum. Examining the comprehensive library of mutants generated by the directed evolution experiment identified a single hydrogen bond between glutamic acid 16 and the chromophore to be the origin of the solvation process. The possibility of localizing a solvation response to a single interaction is only possible in an organized solvent system like a protein interior. The catalytic relevance of solvation dynamics was studied with a light-driven reaction analog for isomerisation of [delta]5-3-ketosteroids in ketosteroid isomerase. The light-driven analog consists of a photoacid bound to the active site of ketosteroid isomerase. In the ground state, the photoacid electrostatically resembles the reaction intermediate. In the excited state, the photoacid resembles the starting material. The solvation response recorded from the fluorescing photoacid shows a dramatically reduced solvation capacity and slower dynamics than observed with the same fluorophore in solution. Solvation within the protein occurs on the nanosecond timescale compared to picoseconds in solution. The active site of ketosteroid isomerase does show dynamic electrostatic behavior during the simulated reaction; however, the response is among the slowest recorded. The resistance to electrostatic perturbation suggests an electrostatically preorganized environment which does not significantly reorganize during catalysis.
Funding innovation in young firms [electronic resource] : the case of minimally invasive surgical devices
Keywords: Management Science and Engineering.

This dissertation explores the impact of different types of investors on invention and innovation in new firms. While prior work has focused primarily on one type of investor, venture capitalists, and has investigated a few long-term outcomes such as exit events, I compare a variety of investor types and consider more immediate innovation-related goals. Drawing from agency and resource dependence theories, I develop and test hypotheses linking different investor types to invention and innovation in new firms. To do this, I construct a novel longitudinal dataset of 198 U.S.-based minimally invasive surgical device firms between 1986 and 2007. The findings indicate that investor type matters for both invention and innovation. Technology-focused investors promote invention while commercially-focused investors are more beneficial to innovation. I also find that although some investors (VCs) help innovation, other investors (the government's SBIR program) hurt it. This difference can be traced to investors' use of monitoring to tailor resources to the specific needs of new firms. These findings suggest that monitoring can be mutually beneficial to both parties as it allows investors to focus their efforts and new firms to receive needed resources at opportune times. My findings also suggest that new firms should be cautious, as there is a potential dark side to the relationships they form with investors: obtaining resources from some investors may prevent new firms from accomplishing their goals.