VictorJuiz/thesis huggingface dataset:
Structural insight into the photochemistry of split green fluorescent proteins [electronic resource]

Previous studies in the Boxer lab characterized two variants of split green fluorescent protein (GFP), which appeared to behave distinctly with respect to interaction with their complementary peptides in the presence of light. Truncated green fluorescent protein (GFP) with its 11th β-strand removed (i.e. the strand 11 system) can recover the absorbance and fluorescence properties of the whole protein when refolded in the presence of synthetic strand 11 peptide. When refolded on its own, the same truncated protein is no longer receptive to binding exogenous strand 11; however, light irradiation generates a species which is capable of binding the complementary peptide. Meanwhile, the truncated GFP with its 10th β-strand removed (i.e. the strand 10 system) can readily bind to synthetic strand 10 peptide to recover the absorbance and the fluorescence of the whole protein. It was found that strand 10 spontaneously dissociates from this bound complex very slowly, and this process is greatly accelerated by light irradiation. In short, the strand 11 system undergoes photoassociation, and the strand 10 system undergoes photodissociation, but the origin of this difference was unclear despite extensive characterization of the two species. Our work attempted to reconcile the apparent differences in the photophysical properties of the two systems by directly investigating the structure of the strand 11 system at atomic level resolution using two techniques: solution state NMR and X-ray crystallography. Although we fell short of obtaining a full NMR structure, we were able to assign backbone chemical shifts for most of the residues in two variants of the strand 11 system, and probed the solvent accessibility of different residues by hydrogen-deuterium exchange. In the process of preparing this protein for crystallography, we found that the attached N-terminal His-tag, which is generally assumed to have negligible impact on the properties of the fused protein, was necessary to preserve the stability and spectral properties of the truncated protein. In the crystal structure of this construct, we found that the N-terminal His-tag and several neighboring residues play a highly unusual structural and functional role in stabilizing the truncated GFP by substituting as a surrogate β-strand in the groove vacated by the native strand. This finding provides serves to reconcile many of the apparent differences between the peptide binding and photodissociation properties of split proteins involving β-strands 10 and 11. We show that these truncated GFPs can bind other non-native sequences, and this promiscuity invites the possibility for rational design of sequences optimized for strand binding and photodissociation, both useful for optogenetic applications.

Keywords: Chemistry.
Advisor: Boxer Steven G. (Steven George)
Lin Michael Z. advisor. Thesis advisor
Moerner W. E. (William Esco)
Structure and function of glia in the lung [electronic resource]

Non-myelinating Schwann cells (NMSCs) are the most abundant cells in the peripheral nervous system. Most of the nerve supply to visceral organs is autonomic, unmyelinated and ensheathed by NMSCs. In the brain, glia play important functional roles in neurotransmission, response to injury and maintenance of the blood brain barrier. Similarly, enteric glia are known to have analogous roles to those of glia in the brain. In contrast to this, very little is known about the function of NMSCs in other visceral organs. We reviewed the literature and present a review of known anatomy, morphology, development, and function of visceral NMSCs. We focused our research on the lung. Like the gut, the lung forms a barrier between airborne pathogens and the bloodstream, and autonomic lung innervation is known to affect pulmonary inflammation and lung function. We defined transgenic tools to study lung glia, and investigated their morphology and anatomy using these tools. We detail the relationship between non-myelinating Schwann cells and pulmonary nerves in the airways and vasculature. To validate existing transgenic mouse tools useful for studying lung glial function, we focused on the glial fibrillary acidic protein promoter, which is a cognate marker of astrocytes that is expressed by enteric glia and non-myelinating Schwann cells. We describe the morphology of non-myelinating Schwann cells in the lung and verify that they express glial fibrillary acidic protein (GFAP) and S100, a classic glial marker. Next, to study the role of pulmonary NMSCs in inflammation, we used two models of acute lung inflammation, bacterial pneumonia and lipopolysaccharide; and one model of chronic inflammation, asthma. For the acute models, we report an improved technique for intratracheal instillation that decreased the variability. We found that, contrary to astrocytes in the brain and enteric glia, NMSCs in the lung do not upregulate GFAP after acute or chronic lung injury nor do they change morphology. We next aimed to do transcriptional profiling of lung glia in the presence and absence of lung inflammation. We took advantage of mice expressing green fluorescent protein under a GFAP promoter. Lungs from mice treated with either LPS or saline were dissociated enzymatically and separated using fluorescence activated cell sorting to obtain a pure population of lung NMSCs. We are currently constructing libraries to submit for RNA sequencing. Together, these results are the first characterization of the identity and function of NMSCs in the lung. Furthermore, we describe and validate tools that will be useful to anyone interested in studying NMSCs in other organs.

Advisor: Buckmaster Paul S. primary advisor. Thesis advisor
Buckwalter Marion
Desai Tushar
Palmer Theo advisor. Thesis advisor
Zuchero J. advisor. Thesis advisor
Structure of soil microbial communities associated with willow (genus:Salix) species and genotypes across abiotic stress gradients [electronic resource]

Microbes that associate with plants form taxonomically and functionally diverse communities. These microbial communities are shaped by many different aspects of plant identity, such as phylogeny, taxonomy and functional group. However, plant-associated microbial communities are also shaped by abiotic environment and a plant's response to abiotic environment. This dissertation explores how plant habitat specialization, species, and genotype shape soil and root microbial communities across hydrologic and abiotic stress gradients in field settings. In chapter 2, ectomycorrhizal communities associated with seven willow species across a hydrologic gradient respond primarily to soil moisture, organic matter and pH; communities were not strongly differentiated across willow species. In chapter 3, I utilized a field experiment to test how water availability, willow habitat specialization and willow species influence soil microbial communities underneath a willow plant. Microbial communities were most dissimilar in contrasting water availability treatments. Both plant habitat specialization and species identity influenced microbial community composition, but the degree and direction depended on the abiotic environment and microbial group. In chapter 4, I tested the influence of willow genotype and wind exposure, which alters soil moisture and nutrients, on root associated fungal and bacterial community structure. Microbial community composition differed by wind exposure and seven of the ten willow genotypes hosted different microbial communities, but again direction depended on the wind exposure and genotype. In conclusion, these three studies show that the turnover in plant microbiome communities will be dependent on plant traits, species, and genotype as environmental conditions change.

Keywords: Biology.
Advisor: Peay Kabir
Dirzo Rodolfo advisor. Thesis advisor
Fukami Tadashi
Structure sensitive interpretation [electronic resource] : a case study in Tagalog

How are indefinite or definites interpreted in languages which lack definite or indefinite articles? Previous works which have addressed this question have observed that cross-linguistically indefinite and definite readings of bare noun phrases are at least partly determined by the broader syntactic structure of their containing clause. However, these analyses often do not consider the reasoning that interlocutors engage in when calculating the meanings of bare noun phrases. In this dissertation, I explore the issue of noun phrase interpretation in article-less languages using a case study in the Philippine language Tagalog. Compared to English, Tagalog demonstrates very different strategies of expressing (in)definiteness. Tagalog uses a complex interaction of case marking, voice affixes and word order in order to signal a nominal as definite or indefinite. I argue that this system sheds light on how we should understand the compositional semantics and pragmatic reasoning underlying definiteness. I argue for a particular compositional semantics for Tagalog which captures the observed patterns of definite and indefinite readings of bare noun phrases. I give an account for the cross-linguistically common observation that bare NPs which are syntactically local to their selecting verb are interpreted as indefinites, while bare NPs in other syntactic positions are not subject to this restriction. The account deals with the conventional meanings of definite and indefinite expressions, however, in order to consider the entire empirical picture, I also consider meanings which arise as non-conventionalized pragmatic enrichments. I discuss how interlocutors calculate conversational implicatures in a language which lacks articles. I argue for a model of pragmatic competition which assumes that interlocutors take the broader grammatical structure of an utterance into consideration when calculating a conversational implicature. If pragmatic alternatives are ruled out by the morphosyntactic and lexical idiosyncrasies of the interlocutors' language, conversational implicatures can fail to emerge.

Keywords: Linguistics.
Advisor: Condoravdi Cleo A.
Gribanova Vera advisor. Thesis advisor
Kiparsky Paul advisor. Thesis advisor
Potts Christopher
Studies in secure computation [electronic resource] : post-quantum, attribute-based and multi-party

The invention of the first public-key cryptosystem four decades ago fired up the development of myriads of secure solutions for protecting data in a large variety of scenarios such as data retrieval, transmission and processing. This dissertation brings together several results on secure computations. We study post-quantum key agreement from generic lattices, attribute-based encryption, and privacy preserving multi-party computations with applications to machine learning. We provide the first instantiation and implementation of a key agreement protocol based on hard problems in random lattices. We show numerous optimizations of the protocol that make it efficient and practical. Next, we build a new lattice-based encryption scheme that lets anyone translate a ciphertext encrypted under a public key x into a ciphertext encrypted under the public key (f(x), f) of the same plaintext for any arithmetic circuit f. We showthat this scheme gives an Attribute-Based Encryption with short keys. Third, we develop systems for privacy preserving data-mining. We design and implement a protocol for computing linear regression model on user data without revealing any other information about the data.

Advisor: Boneh Dan
Charikar Moses advisor. Thesis advisor
Reingold Omer advisor. Thesis advisor
Studies of actomyosin-ring-independent cytokinesis in budding yeast [electronic resource]

In the budding yeast Saccharomyces cerevisiae, cytokinesis is achieved through the coordinated action of constriction of the contractile actomyosin ring (CAR), ingression of the plasma membrane, and formation of the septal cell wall. Formation of the CAR depends on Myo1, the sole type II myosin, but myo1∆ cells lacking the CAR are viable, indicating that the CAR is not essential for cytokinesis. Although most myo1∆ cells form disoriented and/or disorganized cleavage furrows and primary septa (PS), in some cells these structures are nearly normal. Among the proteins that are involved in the assembly, function, and/or coordination of the CAR and PS-formation machinery are those in the complex containing Cyk3, Hof1, and Inn1. To further investigate the mechanisms underlying the CAR-independent processes of cytokinesis, I focused on elucidating the roles of this protein complex and of the interactions among Cyk3, Hof1, Inn1, and other interacting proteins. First, I found (Chapter 2) that a direct Cyk3-Hof1 interaction plays an important role in regulating the function of Cyk3 (and probably also that of Hof1) in PS formation during cytokinesis. Second, I found (Chapter 3) that four additional Cyk3-interacting proteins are involved in the function of the Cyk3-Hof1-Inn1 complex and the formation of normal septa during cytokinesis. The work presented here furthers our understanding of the CAR-independent aspects of yeast cytokinesis, and it may shed light on similar pathways in other cell types that form cleavage furrows in the absence of a CAR.

Keywords: Genetics.
Advisor: Pringle John
Bassik Michael advisor. Thesis advisor
Fuller Margaret
Stearns Tim advisor. Thesis advisor
A study of Fermi surfaces in strongly interacting quantum field theories via holoraphy [electronic resource]

The motivation for this work is to obtain a holographic description of strongly interacting quantum field theories that exhibit Fermi surface behavior at low energies. A first step towards this is to determine the contexts in which Fermi surfaces are manifest holographically - that is, which theories of gravity with holographic duals contain low energy degrees of freedom that exist at nonzero momentum. The spectral weight is an important field theoretic quantity that acts as a spectral weight diagnostic:it directly counts the number of degrees of freedom at a given frequency and momentum. Calculating a nonzero value for the spectral weight at low energy and over a finite range of momenta is a signature of a Fermi surface. In what follows, I introduce the calculation of the low energy spectral weight in three holographic theories: the semi-local quantum liquid, the D3/D5 brane system and the holographic superfluid. In the semi-local quantum liquid theories, we discover nonzero low energy spectral weight over a finite range of momenta, and attribute this Fermi surface behavior to the charges existing behind the black hole horizon. Contrary to our expectations, we also obtain nonzero spectral weight in the holographic superfluid case, complete with a bulk instability indicating that the theory is not in the true ground state. We offer an interpretation of these findings, and present interesting questions that arise regarding the connection between the bulk and boundary charge distributions.

Keywords: Physics.
Advisor: Hartnoll Sean
Kachru Shamit
Senatore Leonardo
A study of monotopic-integrated proteins [electronic resource]

The biological roles of integral membrane proteins are fundamentally related to their topologies. Bitopic and polytopic proteins have soluble domains on both sides of lipid membranes by adopting transmembrane domains (TMDs) and transfer information and solutes between aqueous compartments. Monotopic integral proteins (MIPs), in contrast, have all soluble domains facing one side of the membrane and organize membrane surfaces to facilitate biochemical reactions and biological processes. Although MIPs are critical to many cellular processes, detailed biochemical analyses required for their identification leave their structures under studied. One main factor that hinders systematic MIP study is that they are difficult to distinguish from TMD-containing proteins by primary sequence analysis and require biochemical assays on a protein-to-protein basis in a bilayer membrane. We exploited lipid droplets (LDs), which are monolayer-encased organelles that cannot accommodate bitopic or polytopic proteins, to unambiguously identify MIPs. Chapter 2 presents a method that uses chaotrope treatments, quantitative proteomics, and mixture modeling to identify integral membrane proteins in LD membranes, which would exclude bitopic and polytopic proteins, and thus, all be MIPs. We identified, 87 MIPs, which include proteins predicted to contain TMDs. We used a combination of biochemical solvent accessibility assays and coarse-grained molecular dynamics to identify a subset of the predicted TMDs in our dataset that adopt interfacial amphipathic helices. These results expand the set of definitive MIPs and suggest the importance of interfacial amphipathic helix motifs for anchoring MIPs to biological membranes. UBXD8 is a MIP that traffics from the endoplasmic reticulum (ER) to LDs. Although the trafficking mechanism from the ER to LD is unknown, the targeting of this protein to ER membranes was recently demonstrated to be critical for its localization to LDs. Farnesylated-Pex19 post-translationally delivers UBXD8 to Pex3, its ER membrane receptor. To determine which other LD proteins require farnesylated-Pex19 for LD localization, we combined chaotrope stripping with quantitative proteomics and identified four MIPs absent from LDs purified from cells expressing a farnesylation mutant but present in LDs purified from wild-type cells. This work expands our basic understanding of membrane biology by elucidating the identities and membrane topologies of MIPs. Furthermore, we identified novel MIPs dependent on Pex19 for trafficking to the ER membrane and subsequently to LDs. The methods presented herein can be applied to further detailed studies of MIPs and their biological functions.

Keywords: Biochemistry.
Advisor: Kopito Ron Rieger
Brandman Onn advisor. Thesis advisor
Elias Joshua
Straight Aaron
Study of nanoscale magnetization dynamics and reversal following ultrafast optical excitation by resonant X-ray diffraction [electronic resource]

In 1996, femtosecond (fs) optical laser pulse was first discovered by as one of the novel methods to quench the magnetization[1]. While the fs optical laser pulses typically induces demagnetization, they are also discovered to be able to cause all-optical switching (AOS) of magnetic domains in the transition metal-rare earth (TM-RE) alloy GdFeCo[2, 3, 4, 5, 6]. This phenomenon not only opened door for fascinating non-equilibrium magnetism research but also brought forth the possibility of optical control of magnetism in future magnetic recording technologies. In this thesis, we take an microscopic approach to study the optically-induced magnetization dynamics by utilizing x-ray diffraction technique. We are able to address some important physics questions and technological relevancy regarding the phenomenon. The technological potential of AOS has recently increased with the discovery of the same effect in other materials, including RE-free magnetic multilayers[7, 8]. However, to be technologically competitive for the bit density requirement of future storage device, AOS must further restrict its optically-switched magnetic areas to sizes well below the diffraction limit. By deploying gold plasmonic antenna structure on the surface of ferrimagnetic TbFeCo alloy, we demonstrate reproducible and robust all-optical switching of magnetic domains of 53 nm size. The nanoscale magnetic reversal is imaged both around and beneath plasmonic antennas using x-ray resonant holographic imaging technique. Furthermore, our results also demonstrate the importance of the sample chemical nanostructure on the magnetic switching. The microscopic dynamics of magnetization following an fs optical excitation is also studied in the similar material GdFeCo. Based on theoretical predictions[9, 10], we searched for magnetic solitons generated from spin wave condensation in the far-from-equilibrium condition induced by fs optical excitation. By studying the resonant x-ray diffraction pattern, we present evidence of such soliton feature formation in magnetization dynamics experimentally. We also relate the microscopic magnetization picture to the bulk magnetization response of the sample.

Keywords: Physics.
Advisor: Stöhr Joachim primary advisor. Thesis advisor
Kasevich Mark A. advisor. Thesis advisor
Reis David A.
Subjects in transition [electronic resource] : (counter)culture as critique of Spanish democracy (1976-1986)

Since the onset of the ongoing economic and political crisis in Spain, there has been increased scrutiny on the period of consolidation of Spanish democracy, known as the Transition. My project contributes to this dialogue that problematizes the dominant memory of the Spanish Transition, which having been shaped most notably by the hegemonic "end of history" narrative, remembers the process and resulting political culture as a triumph of Western liberal democracy. However, beyond being a critique of the Transition, this project unearths a social critique contemporary to the historical moment (1976-1986) found in the period's (counter)cultural production. I argue that as reform took precedence over rupture with the Franco regime, political contestation was displaced into culture primarily through cinema, music, and the boom of underground media texts and comics. My analysis of the production and consumption of these more immediate forms of cultural expression in the urban centers and peripheries of Barcelona, Madrid, and Bilbao demonstrates how this culture constituted a necessary part of subject formation for a new generation unable or unwilling to speak the language of negotiation and consensus. In doing so, I assert that beyond the transformation of social mores through the well-documented hedonism and individualism of the late 1970s to mid 1980s youth culture in Spain, what remains relevant today is how, in the absence of a more participatory democracy, subjects during the Transition tackled the aesthetic problem of inserting art into everyday life as a form of agency. To conclude, I explore how—given the current state of uncertainty of Spain's constitutional and cultural consensus, as well as of Western liberal democratic consensus in general—the specter of the Transition and a new perspective on its counterculture may inform the rethinking of political subjectivity and representation in the present.

Keywords: Iberian and Latin American Cultures.
Advisor: Resina Joan Ramon primary advisor. Thesis advisor
Barletta Vincent advisor. Thesis advisor
Rocha Marília Librandi advisor. Thesis advisor