VictorJuiz/thesis huggingface dataset:
The chromatin remodeling factor Chd1L in the preimplantation embryo and in ES cells [electronic resource]
Keywords: Genetics

Early embryonic cell types such as the zygote, blastomeres of the preimplantation embryo, and embryonic stem (ES) cells have powerful chromatin remodeling activities that facilitate DNA-dependent processes such as transcription and DNA repair. Chd1l encodes a chromatin remodeling factor and is more highly expressed in the inner cell mass (ICM) compared to the whole blastocyst. Chd1l expression is developmentally regulated during a time course of preimplantation development and is present in ES cells. Intriguing expression patterns suggested Chd1l could be a novel regulator of DNA-dependent processes in early developmental cell types. This dissertation describes research undertaken to address the role of Chd1l in chromatin remodeling in the preimplantation embryo and in ES cells. Reducing Chd1l protein to nearly undetectable levels in ES cells reveals that Chd1l is dispensable for ES cell viability, proliferation, and pluripotent morphology. Global gene expression patterns are unaltered by Chd1l knock-down. Chd1l is also dispensable for expression patterns of lineage markers associated with the formation of the primary germ layers in differentiating embryoid bodies. Zygote-stage embryos injected with Chd1l-MO arrest prior to the morula stage. Knock-down by the MO was confirmed at the transcript levels by microfluidic qPCR, and the arrest phenotype was partially rescued upon co-injection of Chd1l mRNA and Chd1l-MO. ES cells are known to have stringent and unique pathways to repair DNA damage to prevent mutation and genomic instability from arising in the organism. Reduction of Chd1l in ES cells confers resistance to induced DNA damage, a finding that contrasts with another study that used a differentiated cell line. Apoptosis induced by over-expression of Chd1l occurs specifically in ES cells and not in their differentiated counterparts. This switch in the effect of Chd1l over-expression during differentiation suggests that the function of Chd1l is very different in ES cells than in differentiated somatic cells. DNA repair through non-homologous end joining (NHEJ) is particularly critical in the zygote to repair the paternal genome. Differentiated somatic cells, but not ES cells also rely heavily on NHEJ. Biochemical evidence supports the involvement of Chd1l in NHEJ. Deficient DNA repair could underlie the Chd1l arrest phenotype. Therefore, Chd1l functions minimally, or not at all, in regulating gene expression and contributes to the DNA damage response in a developmental stage-specific and/or cell type-specific manner.
Chromosome segregation and structure in Caulobacter crescentus [electronic resource]
Keywords: Developmental Biology.

Bacterial chromosomes are generally ~1000 times longer than the cells in which they reside, and concurrent replication, segregation, and transcription/translation of this crowded mass of DNA poses a challenging organizational problem. At first, it was assumed that DNA is organized randomly inside the cell, much like a bowl of spaghetti. Furthermore, it was argued that segregation of this disordered mass was not carried out by a mitotic machinery as is found in eukaryotes, but rather the by-product of cell growth. Hence, the canonical description of bacterial DNA was that of an unstructured polymer diffusing randomly. Recent advances in cell imaging technology, however, have revealed that the bacterial nucleoid is reliably oriented and highly organized within the cell. Furthermore, the speed of segregation is inconsistent with the old model driven by cell growth. Here, I use a screening approach to identify parS, a 100bp piece of DNA previously found to be anchored to the old cell pole, as the Caulobacter centromere. In direct contrast to other published models, parS segregates ahead of all other sequences, including the origin of replication (Cori), and moving parS away from Cori causes segregation -- but not replication -- to be delayed. The segregation of parS requires the ATPase activity of the ParA protein, and current work is aimed at understanding the molecular details of this process. All of these data point to the presence of an active, mitotic-like machine that drives chromosome segregation in Caulobacter. I also show that the circular Caulobacter chromosome is oriented in relation to the parS anchor site at the old cell pole, so that changing the genomic position of parS causes the entire chromosome to rotate within the cell. Finally, I find that the chromosome is organized into a dense core running down the length of the cell, and I arrive at two possible models for the large-scale structure of this core. Thus, this work forms part of an emerging view of the chromosome as a highly organized structure that is kept in place by simple yet active mechanisms, and whose segregation is insured by a complex dedicated machine.
The ciliated cell transcriptome [electronic resource]
Keywords: Biological Sciences

Multiciliated cells of the respiratory epithelium are unique in that they generate hundreds of modified centrioles called basal bodies per cell. Each basal body anchors a motile cilium at the cell apical surface, and coordinated beating of motile cilia is vital for protecting from airway infection and for respiratory function. We used mice expressing GFP from the promoter of a ciliated cell-specific gene, FOXJ1, to obtain sorted populations of ciliating cells for transcriptional analysis. In addition to successfully identifying candidates found in other proteomics and genomics studies of motile and nonmotile cilia, approximately half of the significantly upregulated genes identified here have not yet been linked to cilia, and of those a third of are currently uncharacterized. We identified several genes associated with human diseases. These include FTO, which has been linked to human obesity, and DYX1C1, which is a candidate gene for developmental dyslexia. Interestingly, FTO localizes to cilia and Dyx1c1-GFP localizes to cilia and centrosomes, establishing novel links between cilia and two genetic diseases with poorly understood cellular and molecular etiology. Finally, we identified a number of transcription factors that are differentially expressed in ciliating mouse tracheal epithelial cells, including the proto-oncogene c-myb. We show that C-myb is expressed specifically in ciliating cells, and that this expression is temporally restricted to early in the differentiation process. These results suggest a role for the leukemogenic transcription factor C-myb in ciliated cell differentiation.
Civilian autonomy in civil war [electronic resource]
Keywords: Political Science.

This study argues that civilians be considered as actors with agency and addresses their varying ability to organize to protect human rights when caught in the cross-fire. Much of the research on civil wars suggests that when civilians are caught between two warring armies, they can do little other than flee for safety or take sides. Yet some civilian communities have gained autonomy, or been able to maintain democratic decision-making power over outcomes for the community within the community, minimizing influence from outside armed groups. What explains this community-level variation? I draw on insights from comparative politics about social capital as well as theories of conflict and cooperation to explain how and when civilians' cohesion and organizational capabilities facilitate institutional solutions at the local level to reduce civil war violence. These solutions can be especially useful when interventions to protect civilians are delayed or rare and where states are weak and cannot evenly provide justice. I employ a multi-method empirical strategy that deals with the issues of reverse causality between the impact of civilians and armed groups as well as possible selection bias of examining only well-known community "cases." Empirical tests use data I collected during fieldwork in Colombia. These include numerous micro-level data sources from both government and private sector organizations, participant observation and numerous interviews with civilians, government officials, and ex-combatants in both rural and urban settings, as well as archival documents. I find that, all other things equal, well-organized communities in Colombia suffer less violence than those that are less organized and that these varying levels of organization are not simply results of historical conflict patterns or armed actor permissiveness. Qualitative case studies deeply explore the mechanisms of how different well-organized communities have actually coped with threats of violence and kept them from resulting in civilian deaths.
Coherent interactions in on-chip photonic-crystal cavities [electronic resource]
Keywords: Materials Science and Engineering

There has been substantial interest in study of coherent interactions in on-chip photonic-crystal microcavities. Such efforts have recently led to realizations of important phenomena, including an all-optical analogue to electromagnetically induced transparency (EIT) and flat-top reflection filters. In this work, we demonstrate EIT-like and flat-top reflection optical resonances in a single on-chip photonic-crystal cavity structure. Most importantly, by tuning the index of refraction and thus the propagation phase in the waveguide between two cavities, we smoothly change the behavior of the structure from EIT-like to flat-top optical resonance. Both resonances are of great significance in applications. EIT-like optical resonance renders an integrated optical system transparent over a very narrow frequency range. The potential for slowing and stopping light on chip in such a system has profound impacts in both fundamental science and optical communications. Flat-top reflection filter, which reflects a narrow range of wavelengths while letting other wavelengths pass through, is a higher-order filter compared to the regular Lorentzian response commonly observed in photonic-crystal resonator filters. This box-like lineshape, featuring a flattened resonance and sharp transition from transmission band to reflection band, is important for achieving low inter-channel cross-talk in wavelength-division multiplexing. In addition, we show an optical analogue to the superradiance effect in photonic-crystal cavities. This work is along the direction of recent substantial interest and progress in mapping coherent effects in atomic systems to on-chip nanophotonics systems. But unlike the previous demonstration in atomic systems where emitters have to be placed within a distance smaller than a wavelength, the two resonators in our system can be separated by a distance much larger than a wavelength. It is enabled by the use of a waveguide to enforce the coherent interaction in a one-dimensional regime. The effect enhances waveguide-resonator coupling, which is essential for low loss device operation, so has broad implications for on-chip photonic integration. Moreover, using laser-pumped thermal differential tuning to align and detune cavity resonances, we experimentally demonstrate structural tuning of the superradiance effect in the system.
Colonial religion and indigenous society in the archaic western Mediterranean, c. 750-400 BCE [electronic resource]
Keywords: Classics

This project examines the long-term responses of indigenous societies in Sicily and Sardinia to colonial religion in the ancient western Mediterranean. It conducts a comparative analysis of religious developments among indigenous, Greek, and Phoenician communities between the 8th and 5th centuries BC. It shows that while indigenous communities near Greek colonies in Sicily integrated Greek-style material culture and practices into their religious lives, those near Phoenician colonies in Sardinia and Sicily showed much less interest in Phoenician material culture and religion. This contrast is then explained in terms of the greater social accessibility and more communal features of Greek polis religion, which made its practices and material culture broadly attractive across cultural divides in a time of rapid social change.
Combinatorial, rational, and bioinformatics approaches to engineering cystine-rich proteins [electronic resource]
Keywords: Bioengineering.

Proteins are the most structurally and functionally diverse class of biological molecules. By exploiting this diversity, nature has evolved proteins for complex biological functions such as molecular recognition and catalysis. The features of proteins that contribute to their structure, stability, and function have been identified through extensive experimental work. However, the principles governing the precise relationships between a protein's sequence, structure, and function remain largely unknown. Here we discuss the application of combinatorial, rational, and bioinformatics techniques for engineering two model cystine-rich proteins: Ecballium elaterium trypsin inhibitor-II (EETI) knottin and epidermal growth factor (EGF). With this multi-faceted engineering approach, we have assessed the sequence plasticity of the structure of EETI and have predicted and experimentally validated a set of sequence criteria that facilitate proper folding of the knottin structure. Using a similar array of protein engineering techniques we have developed EGF variants with modulated receptor binding properties. These EGF variants will serve as useful molecular tools for dissecting the relationship between the sequence of EGF ligand and its affect on receptor activation and signaling properties. Importantly, a handful of the EGF variants were rationally designed to have physicochemical profiles that are promising for their application as protein therapeutics. Finally, the toolkit of engineered cystine-rich proteins developed here can be used to glean future insight into the sequence-structure-function relationships of these two proteins and will inform future protein engineering efforts.
Compliant directional suspensions for climbing with spines and adhesives [electronic resource]
Keywords: Electrical Engineering

Climbing rough vertical surfaces can be useful for applications such as search-and-rescue, surveillance, and the inspection of hard-to-reach locations. In nature, several methods of adhering to vertical surfaces can be observed. Small non-penetrating spines are used effectively by many insects to attach to rough surfaces such as rock, concrete, and similar materials. These structures hook onto surface asperities to provide adhesion. In this thesis, we discuss synthetic arrays of microspines that can be used by robots or humans to attach to rough vertical surfaces. Microspine arrays have the advantages of requiring low preloads, functioning in wet and dusty environments, and supporting loads for extended periods of time without consuming power. Moreover, they can attach to surfaces that are too rough for current synthetic dry adhesives. We discuss the properties of surfaces that make them suitable for use with spines, and present a spine/surface interaction model. We then discuss properties of the spine suspensions necessary for them to be used effectively. The suspensions must permit the spines to conform to the surface, share loads between them, and engage and disengage from the surface. We present spine suspensions that were constructed, and show that they have good measured performance in comparison to ideal designs. We show examples of how spines have been used on climbing robots and in human climbing aids. We also show that the requirements for directional adhesive materials to work on any surfaces are similar to those of spines, and that the principles developed for large spine arrays can be adapted to directional dry adhesives for climbing. We discuss requirements on suspensions for large patches of spines or dry adhesives to enable load-sharing over large areas.
Complicating the ideal of an informed citizenry [electronic resource]
Keywords: Communication

Although theorists agree that having an informed citizenry is necessary for a well-functioning democracy, most individual citizens fall well short of the ideal of being an informed citizen. Scholars and advocates expend special effort to understand how to make citizens more informed and to create programs that promote this goal. Many of these efforts revolve around providing more high quality information to citizens and assume, either directly or indirectly, that these efforts will have positive benefits like educating voters, increasing turnout and reducing bias. Results from three experiments indicate that (1) providing higher quality information than that typically found on a ballot does not increase turnout; (2) providing individuating information does not reduce explicit sexism (but reduces implicit pro-male bias under certain circumstances); and (3) suggestive evidence that deliberative polling causes citizens to report their opinions more accurately. In conclusion, an explanation is offered for these surprising findings and the implications of these findings for researchers and practitioners are considered.
The compulsive construction of heritage [electronic resource] : material culture and identity at the dawn of the 21st Century in northwestern Argentina"
Keywords: Anthropology.

This dissertation is a study of the different social and cultural processes experienced in Quebrada de Humahuaca, northwestern Argentina. Drawing on a combination of archaeological and ethnographical methods, this study follows different practices and experiences in which people and material culture have engaged through discourses of heritage and the uses of the past, resulting from the region's inclusion as part of the World Heritage sites list. By introducing the concept of compulsion, this dissertation explores heritage as a pathological disorder that becomes manifested in people's everyday interaction with material culture producing a myriad of contexts in which notions of the past, modernity, and identity intersect. Heritage, therefore, is identified as one the main factors in the production of material culture and social practices through processes of commodification, reproduction/replication, preservation and sublimation. Understood as a compulsion, heritage is observed as the result of an irresistible impulse in the production and representation of different settings in which heritage is performatively expressed. By discussing heritage as compulsion, this dissertation highlights the tensions between structure and practice, global and local, authentic and inauthentic, and provides an alternative perspective based on an analysis that focuses on the dynamic and mutually constitutive relation involved in the production of material culture and identity. Working in the intersection of archaeology and ethnography, this research focuses on the documentation of the changes expressed in the material culture of Quebrada de Humahuaca, the elaborated production and staging of heritage, and the nuanced notions of ethnicity and subjectivity that are now reconfiguring the character of Argentina as a modern nation. As part of this reconfiguration, the processes of re-centering a previously historically marginal region constitutes itself as a fundamental axis upon which the image of a modern, multicultural and democratic nation is built through a hectic and obsessive production and consumption of cultural difference.
Computational aeroacoustics of complex flows at low Mach number [electronic resource]
Keywords: Mechanical Engineering

Designing quiet mechanical systems requires an understanding of the physics of sound generation. Among various sources of noise, aerodynamic sound is the most difficult component to mitigate. In practical applications, aerodynamic sound is generated by complex flow phenomena such as turbulent wakes and boundary layers, separation, and interaction of turbulent flow with irregular solid bodies. In addition, sound waves experience multiple reflections from solid bodies before they propagate to an observer. Prediction of an acoustic field in such configurations requires a general aeroacoustic framework to operate in complex configurations. A general computational aeroacoustics method is developed to evaluate noise generated by low Mach number flow in complex configurations. This method is a hybrid approach which uses Lighthill's acoustic analogy in conjunction with source-data from an incompressible calculation. Flow-generated sound sources are computed by using either direct numerical simulation (DNS) or large eddy simulation (LES); scattering of sound waves are computed using a boundary element method (BEM). In this approach, commonly-made assumptions about the geometry of scattering objects or frequency content of sound are not present, thus it can be applied to a wider range of aeroacoustic problems, where sound is generated by interaction of complex flows with solid surfaces. This new computational technique is applied to a variety of aeroacoustic problems ranging from sound generated by laminar and turbulent vortex shedding from cylinders to realistic configurations such as noise emitted from a rear-view side mirror and a hydrofoil. The purpose of each test case, in addition to validation of the method, is to explore various physical and technical aspects of the problem of sound generation by unsteady flows. Through these test cases, it is demonstrated that the predicted sound field by this technique is accurate in the frequency range in which the sound sources are resolved by the computational mesh. It is also shown that in computation of sound, acoustic analogies are less sensitive to numerical errors than direct computations. Finally, a discussion on the efficacy of LES and the effect of sub-grid scale dynamics on predicted sound is presented.
Computational modeling of structural heterogeneity in folded proteins [electronic resource]
Keywords: Mechanical Engineering

Proteins are biomolecules that play a key role in a wide diversity of vital functions, such as metabolism and signal transmission. Each protein is a linear chain of amino acids that folds into a flexible three-dimensional structure. Protein's flexibility is widely believed to be essential for its function. Motion of a protein occurs at timescales that span several orders of magnitude. Thermal fluctuations, which occur in picoseconds, are small-amplitude, uncorrelated, harmonic motions of the individual atoms. In contrast, conformational deformations closely related to the protein's function occur in microseconds to milliseconds. These slow deformations are usually large-scale, correlated, anharmonic motions that correspond to transitions between meta-stable states, such as binding and non-binding states. In this dissertation we are mainly interested in modeling structural heterogeneity associated with such slow deformations. This dissertation presents new computational methods to study the flexibility of folded protein in the context of three important biological problems: (a) Loop sampling, (b) Interpretation of electron density maps, and (c) Determination of allosteric pathways. Computational modeling of structural heterogeneity in the folded state of a protein is a challenging problem, mainly because of the high-dimensionality of the protein's conformation space and the very small relative volume of its feasible motion space. Although our methods are specific to each of the three problems, they share the same sample and select approach: they combine efficient sampling algorithms that allow us to represent structural heterogeneity in a folded protein by a collection of sampled conformations and selection algorithms that allow us to reliably pick the sampled conformations that provide a solution to the problem. This dissertation demonstrates the power of geometric computation and efficient sampling to model structural heterogeneity in the folded protein.