RNA polymerase II (Pol II) is responsible for the transcription of all protein-coding and some non-coding genes in eukaryotes. Its largest subunit, Rpb1, contains a unique C-terminal domain (CTD) which consists of repeats of the heptad YSPTSPS. It acts as a binding platform for proteins that control the different stages of transcription and their recruitment is regulated mainly by differential phosphorylation of residues contained within the CTD. Previous studies could unveil proteins containing a CTD-interacting domain (CID) as important players that specifically bind to certain phosphorylation types of the CTD. More precisely, they were shown to be important for the last step of transcription, termination. Despite extensive research over the past 30 years, the exact mechanism of how these proteins facilitate the dislodgement of Pol II from the DNA template, still remains unknown. The work presented here contains detailed studies of the CID-containing protein Seb1 from the fission yeast Schizosaccharomyces pombe, revealing an unexpectedly broad role of this protein in transcription termination. In addition to a CID, Seb1 also contains an RNA recognition motif (RRM) which allows direct binding to RNA. Here, I present high-resolution crystal structures of both domains of Seb1. While the CID has a very conserved fold, the RNA binding regions contains an unusual arrangement of a canonical RRM intertwined with a second domain that are both important for RNA binding. Structure-based mutations were introduced and a combination of in vitro and genome-wide in vivo studies uncover Seb1 as an essential player in transcription termination. Importantly, both domains are required to promote the full function of Seb1. Despite its homology to the well-studied budding yeast protein Nrd1, the role of Seb1 in fission yeast is quite different. This thesis therefore provides important insight into the mechanisms that underlie eukaryotic transcription termination.

Esta tese apresenta resultados sobre a estrutura, relações de escala e cinemática para 48 galáxias em 22 grupos compactos de Hickson, sendo que a apresentação de mapas de velocidades, monocromáticos (na linha H alpha) e de dispersão de velocidades são feitos pela primeira vez para 35 galáxias em 12 dos grupos. A partir dos mapas de velocidades e imagens óticas, foi possível obter os parâmetros cinemáticos, morfológicos e as curvas de rotação das galáxias da presente amostra. Usando as velocidades máximas de rotação para cada galáxia (derivadas das curvas de rotação) e as luminosidades óticas, infravermelhas, as massas estelares e bariônicas, foram estudadas as diferentes relações de Tuly-Fisher (TF) para as galáxias dos grupos compactos. Comparando esses resultados com os apresentados por uma amostra de galáxias de campo, foi encontrado que as galáxias de grupos compactos seguem a relação de TF definida pelas galáxias em ambientes menos densos, no entanto algumas galáxias de baixa massa apresentam altas luminosidades para as suas velocidades de rotação. Surtos de formação estelar e atividade nuclear parecem ser os principais fatores que fazem com que as galáxias de baixas massas dos grupos compactos não estejam na relação de TF definida pelas galáxias do campo. Este resultado indica que as velocidades máximas de rotação não são alteradas em galáxias em interação e portato não há um stripping de massa significativo nas galáxias de grupos compactos, dentro de R(25). O uso das curvas de rotação para estudar a distribuição de massas nestas galáxias revelou que estas curvas apresentam um alto grau de assimetria, a qual seria produzida em eventos de interação galáxia-galáxia. Esses eventos, além de perturbar as curvas de rotação, conseguem expulsar parte do gás neutro das galáxias ao meio intra grupo. Usando dados ultravioleta, nesta tese foram encontradas vários sistemas estelares jovens no meio intergaláctico de grupos compactos. Esses sistemas podem se converter em galáxias satélites ou simplesmente serem dissolvidos, enriquecendo o meio intragrupo. / This thesis presents results on the kinematics, scaling relations and structures of 48 galaxies in 22 compact groups. For 35 galaxies in 12 compact groups, velocity fields, monochromatic maps (derived from H alpha observations) and velocity dispersion maps are presented for the first time. By using these data, it was possible to determine the kinematic and morphological parameters, the rotation curves and to derive the Tully-Fisher relation for the galaxies in dense environments. By using the maximum rotational velocity for each galaxy (derived from its rotation curve) and its optical and near-infrared luminosity and mass, the different Tully-Fisher relations for galaxies in compact groups were derived. Comparing these results with the results displayed by galaxies in less dense environments, it was found that galaxies in compact groups agrees with the Tully-Fisher relation defined by non-interacting galaxies. However, some of the low-mass galaxies are off the Tully-Fisher relation, having too high luminosities for their maximum rotational velocities. This scenario can be explained by a burst of star formation and/or by nuclear activity. We conclude that the maximum rotational velocities of compact groups galaxies are not affected during galaxy-galaxy interactions which implies that there is no significant mass stripping in galaxies of compact groups inside their optical radius. The mass distribution of galaxies in compact groups indicates that the rotation curves of these galaxies are highly asymmetric. The asymmetry could be produced by interactions between galaxies. These interactions, besides affecting the shape of the rotation curve, can eject some neutral gas from the disk of the interacting galaxies into the intragroup medium. By using ultraviolet data, we find several young star-forming regions in the intragroup medium of compact groups. It is still an open question wether these young stellar systems can survive and become new members of the group or if they will fall back onto their parent galaxies.

abstract: This dissertation examines six different models in the field of econophysics using interacting particle systems as the basis of exploration. In each model examined, the underlying structure is a graph G = (V , E ), where each x ∈ V represents an individual who is characterized by the number of coins in her possession at time t. At each time step t, an edge (x, y) ∈ E is chosen at random, resulting in an exchange of coins between individuals x and y according to the rules of the model. Random variables ξt, and ξt(x) keep track of the current configuration and number of coins individual x has at time t respectively. Of particular interest is the distribution of coins in the long run. Considered first are the uniform reshuffling model, immediate exchange model and model with saving propensity. For each of these models, the number of coins an individual can have is nonnegative and the total number of coins in the system is conserved for all time. It is shown here that the distribution of coins converges to the exponential distribution, gamma distribution and a pseudo gamma distribution respectively. The next two models introduce debt, however, the total number of coins again remains fixed. It is shown here that when there is an individual debt limit, the number of coins per individual converges to a shifted exponential distribution. Alternatively, when a collective debt limit is imposed on the whole population, a heuristic argument is given supporting the conjecture that the distribution of coins converges to an asymmetric Laplace distribution. The final model considered focuses on the effect of cooperation on a population. Unlike the previous models discussed here, the total number of coins in the system at any given time is not bounded and the process evolves in continuous time rather than in discrete time. For this model, death of an individual will occur if they run out of coins. It is shown here that the survival probability for the population is impacted by the level of cooperation along with how productive the population is as whole. / Dissertation/Thesis / Doctoral Dissertation Mathematics 2019

Thirty-eight preschool children (20 male and 18 females) w ere filmed in a seated dyadic interaction with an adult experimenter. Frame- by-frame film analysis was done for head and arms of subjects and head, arms, and legs of experimenter for expe rimenter and subjects approach and withdrawal movements. Chi- square analysis were pe rformed for the data both between and within zones with the following cells: approach-approach (A-A), experimenter and subject approach each other; approach-withdrawal (A-W), experimenter approaches and subject withdraws; withdrawal-approach (W -A), experimenter withdraws and subject approaches; withdrawal-withdrawal (W - W), both subject and experimenter withdraw. The most frequent and significant movements for each zone and body part were A-Wand W -A. It was found that in the 3 foot zone the A-W cells (of the 2 X 2 contingency table) were the most frequent dyadic movements. For the 2 and 1 foot zones the W -A cells were the most frequent. For all three one-foot zones the W-W and A-A were respectively the least frequent dyadic interactional patterns. The intimate zone of personal space was found to be larger than the 18 inches previously identified for adults; it was found to be over 24 inches. Modifications for personal space and equilibrium theories to accommodate present findings are advanced.

<p>In this thesis we present a model of the interacting agents on the financial market. The agents are represented by a non-Euclidean random graph, where each agent communicate with another with probability p, and the interaction according to the Ising Model. We investigate properties of the model by direct calculations for small graph sizes, and by perfect simulation for larger graph sizes. We also present a model for asset price variation by using the magnetization of the Ising model.</p>

<p>The Signalosome is a term used to define a putative signalling complex, which assembles near the plasma membrane in response to external signals received at cell surface receptors and then migrates towards downstream effectors. It is proposed to regulate the level of intracellular Ca2+ and subsequent downstream signalling events. To date it has been defined to consist of BTK, BLNK, BCAP, VAV, PLCγ2 and PI3K1-4 in B-Cells.</p><p>This work entailed initiating a new proteomic approach to investigate the nature and extent of Bruton’s tyrosine kinase, Btk, involvement in the signalosome – inherently, the aim was to study multiple interactions of Btk with other molecules. By transfecting host cells with a Btk gene-transfer plasmid, virus particles were produced that were used to up-regulate and analyse the expression of Btk in three haematopoietic cell lines: B-cells, Pre-B-cells and a myeloid cancer cell. The construction of a new gene-transfer vector was successfully carried out by plasmid sub-cloning and it was subsequently found to effectively transfect the host cells and produce virus particles. The recombinant virus particles were employed with success in transducing three haematopoietic cell lines and with immunopurification and subsequent gel separation protein signalosome complexes were obtained ready for analysis by mass spectrometrical fingerprinting (to be carried out as a joint effort in Mount Sinai Hospital in Toronto, Canada).</p>

The Signalosome is a term used to define a putative signalling complex, which assembles near the plasma membrane in response to external signals received at cell surface receptors and then migrates towards downstream effectors. It is proposed to regulate the level of intracellular Ca2+ and subsequent downstream signalling events. To date it has been defined to consist of BTK, BLNK, BCAP, VAV, PLCγ2 and PI3K1-4 in B-Cells. This work entailed initiating a new proteomic approach to investigate the nature and extent of Bruton’s tyrosine kinase, Btk, involvement in the signalosome – inherently, the aim was to study multiple interactions of Btk with other molecules. By transfecting host cells with a Btk gene-transfer plasmid, virus particles were produced that were used to up-regulate and analyse the expression of Btk in three haematopoietic cell lines: B-cells, Pre-B-cells and a myeloid cancer cell. The construction of a new gene-transfer vector was successfully carried out by plasmid sub-cloning and it was subsequently found to effectively transfect the host cells and produce virus particles. The recombinant virus particles were employed with success in transducing three haematopoietic cell lines and with immunopurification and subsequent gel separation protein signalosome complexes were obtained ready for analysis by mass spectrometrical fingerprinting (to be carried out as a joint effort in Mount Sinai Hospital in Toronto, Canada).

This thesis is study about how public spaces can be transformed through performance within them.More specifically, this study involves two public venues: The Museum of Science and Industry (MOSI), Tampa, FL and The University of South Florida (USF), Tampa, FL in that within these public venues, not only do performances take place, but they transform the space they are performed in and the spaces in-between the public spaces into performance spaces.

This thesis is concerned with certain properties of stochastic growth models. A stochastic growth model is a model of infection spread, through a population of individuals, that incorporates an element of randomness. The models we consider are variations on the contact process, the simplest stochastic growth model with a recurrent infection. Three main examples are considered. The first example is a version of the contact process on the complete graph that incorporates dynamic monogamous partnerships. To our knowledge, this is the first rigorous study of a stochastic spatial model of infection spread that incorporates some form of social dynamics. The second example is a non-monotonic variation on the contact process, taking place on the one-dimensional lattice, in which there is a random incubation time for the infection. Some techniques exist for studying non-monotonic particle systems, specifically models of competing populations [38] [12]. However, ours is the first rigorous study of a non-monotonic stochastic spatial model of infection spread. The third example is an additive two-stage contact process, together with a general duality theory for multi-type additive growth models. The two-stage contact process is first introduced in \cite{krone}, and several open questions are posed, most of which we have answered. There are many examples of additive growth models in the literature [26] [16] [29] [49], and most include a proof of existence of a dual process, although up to this point no general duality theory existed. In each case there are three main goals. The first is to identify a phase transition with a sharp threshold or ``critical value'' of the transmission rate, or a critical surface if there are multiple parameters. The second is to characterize either the invariant measures if the population is infinite, or to characterize the metastable behaviour and the time to extinction of the disease, if the population is finite. The final goal is to determine the asymptotic behaviour of the model, in terms of the invariant measures or the metastable states. In every model considered, we identify the phase transition. In the first and third examples we show the threshold is sharp, and in the first example we calculate the critical value as a rational function of the parameters. In the second example we cannot establish sharpness due to the lack of monotonicity. However, we show there is a phase transition within a range of transmission rates that is uniformly bounded away from zero and infinity, with respect to the incubation time. For the partnership model, we show that below the critical value, the disease dies out within C log N time for some C>0, where N is the population size. Moreover we show that above the critical value, there is a unique metastable proportion of infectious individuals that persists for at least e^{\gamma N}$ time for some $\gamma>0$. For the incubation time model, we use a block construction, with a carefully chosen good event to circumvent the lack of monotonicity, in order to show the existence of a phase transition. This technique also guarantees the existence of a non-trivial invariant measure. Due to the lack of additivity, the identification of all the invariant measures is not feasible. However, we are able to show the following is true. By rescaling time so that the average incubation period is constant, we obtain a limiting process as the incubation time tends to infinity, with a sharp phase transition and a well-defined critical value. We can then show that as the incubation time approaches infinity (or zero), the location of the phase transition in the original model converges to the critical value of the limiting process (respectively, the contact process). For the two-stage contact process, we can show that there are at most two extremal invariant measures: the trivial one, and a non-trivial upper invariant measure that appears above the critical value. This is achieved using known techniques for the contact process. We can show complete convergence, from any initial configuration, to a combination of these measures that is given by the survival probability. This, and some additional results, are in response to the questions posed by Krone in his original paper \cite{krone} on the model. We then generalize these ideas to develop a theory of additive growth models. In particular, we show that any additive growth model, having any number of types and interactions, will always have a dual process that is also an additive growth model. Under the additional technical condition that the model preserves positive correlations, we can then harness existing techniques to conclude existence of at most two extremal invariant measures, as well as complete convergence. / Graduate

Despite of enormous progress in experimental nanophysics theoretical studies of low-dimensional electron systems still remains a challenging task. Indeed, most of the structures are strongly correlated, so that an effective perturbative treatment is impossible due to the lack of a small parameter. The problem can be partly solved within the dynamical mean-field theory (DMFT) paradigm, nevertheless the correlations in physically relevant high-temperature superconductors are of purely non-local nature. The recently developed dual fermion approximation, combining field-theoretical diagram technique and numerical methods, allows for explicit account of spatial correlations. The approximation was shown to be of fastest convergence compared with standard DMFT extensions, and along with renormalization group is used here to study Fermi condensation on a triangular lattice near van Hove singularities. The still debated phenomenon of Fermi condensation is believed to be a precursor to strongly correlated low-temperature instability and is found in this thesis to be robust even at high temperature, making its experimental verification feasible. Unlike homogeneous ferromagnetic ordering a variety of non-collinear ground state configurations emerge as a result of competition among exchange, anisotropy, and dipole-dipole interaction. These particle-like states, e.g. magnetic soliton, skyrmion, domain wall, form a spatially localized clot of magnetic energy. Consistent study of spin, which essentially is a quantum mechanical entity, led to the emergence of spintronics (spin-based electronics) and magnonics (photonics with spin waves), in the meanwhile topologically protected magnetic solitons and skyrmions might potentially be applied for data processing and information storage in next generation of electronic technology (rapidly advancing solitonics and skyrmionics). An ability to easily create, address, and manipulate such structures is among the prerequisite forming a basis of "-onics" technology. It is shown here that spins on a kagome lattice, interacting via Heisenberg exchange and Dzyaloshinskii-Moriya coupling, allow the formation of topologically protected edge states through which a skyrmion can propagate. Not only can chemical methods be used to design novel functionality, but also geometric structuring. It is demonstrated that for graphene sandwiched between two insulating media external circularly-polarized light serves as an effective magnetic field. The direct practical implication permits to control light polarization and induce spin-waves propagating on the surface of e.g. a topological insulator. The newly discovered Dirac materials, graphene and three-dimensional topological insulators, are not easy to handle. In fact, the quasiparticle band function is gapless preventing them from being used in integrated circuits, nevertheless the problem is shown here to be partially relaxed by placing a vacancy on top of it.