VictorJuiz/thesis huggingface dataset:
Characterization of N-terminal Myc Ubiquitylation and the Novel Oncogene CUL7
Keywords: Myc
Apoptosis

Myc is an oncogene that is commonly deregulated in human cancers. Mechanistic studies reveal that Myc is a transcription factor that interacts with a protein partner called Max. Heterodimerization and the formation of the Myc:Max complex enables Myc:Max to bind to the E-box and subsequently regulate the activation and repression of Myc target genes. Since regulation of its target genes are essential for Myc to drive transformation, the Myc and Max interaction has been targeted in mouse model studies to determine whether the oncogenic activity of Myc can be inhibited. Surprisingly, these studies reveal that targeting Myc is not only possible but a powerful way to suppress tumour growth. Since a better understanding of how Myc carries out its biological functions makes the possibility of targeting Myc a reality, it is essential to investigate and study the mechanisms of how Myc promotes tumourigenesis. In the first part of this thesis, we investigate the idea that the N-terminal end of Myc may be post-translationally modified and this modification may dictate Myc activities. Indeed we report here that the N-terminal end of Myc can be ubiquitylated as well as acetylated, and that the loss of these modifications results in a decrease in Myc activities. Furthermore, we characterize Mdm2 as a potential E3 ubiquitin ligase that may ubiquitylate the N-terminal end of Myc. In the second part of this thesis, we investigate CUL7 as a novel oncogene that may inhibit Myc-potentiated apoptosis and cooperate with Myc in transformation. Indeed, CUL7 is a novel p53 interacting protein that inhibits Myc potentiated apoptosis through the inhibition of p53. We have also characterized CUL7 to be overexpressed in primary human lung cancers, and a higher level of CUL7 expression associates with short-term survival of lung cancer patients. Through the better understanding of the enzymes that post-translationally modify the N-terminal end of Myc and proteins, such as CUL7, that can cooperate with Myc to drive tumourigenesis, we may begin to devise ways to target and control deregulated Myc in cancer cells.
RNAi Screening of the Kinome to Identify Mediators of proliferation and trastuzumab (Herceptin) resistance in HER2 Breast Cancers
Keywords: RNAi
HER2
high-throughput screen
breast cancer
trastuzumab
Herceptin
drug resistance
siRNA

Breast cancers with overexpression or amplification of the HER2 tyrosine kinase receptor are more aggressive, resistant to chemotherapy, and associated with a worse prognosis. Currently, these breast cancers are treated with the monoclonal antibody trastuzumab (Herceptin®). Unfortunately, not all patients respond to trastuzumab drug therapy; some patients show de novo resistance, while others acquire resistance during treatment. This thesis describes our RNAi studies to identify novel regulators of the HER2 signaling pathway in breast cancer. Three kinome-wide siRNA screens were performed on five HER2 amplified and seven HER2 non-amplified breast cancer cell lines, two normal breast cell lines, as well as two HER2-positive breast cancer cell lines with acquired trastuzumab resistance and their isogenic trastuzumab-sensitive controls. To understand the main kinase drivers of HER2 signaling, we performed a comprehensive screen that selected against growth inhibitors of the non-HER2 amplified breast cancer cell lines. This screen identified the loss of the HER2/HER3 heterodimer as the most prominent selective inhibitor of HER2-amplified breast cancers. In a trastuzumab sensitization screen on five trastuzumab-treated breast cancer cell lines, we identified several siRNA against the PI3K pathway as well as various other signaling pathways that inhibited proliferation. Finally, in a screen for acquired trastuzumab resistance, PKCη and its downstream targets were identified. Loss of PKCη resulted in a decrease in G1/S transition and upregulation of the cyclin dependent kinase inhibitor p27. Initial data suggest that PKCη promotes p27 ubiquitination and degradation. Taken together, these studies provide novel insight into the complex signaling of HER2-positive breast cancers and the mechanisms of resistance to trastuzumab therapy. This work describes how various kinases can modulate cell proliferation, and points to possible novel drug targets for the treatment of HER2-positive breast cancers.
Negative Regulation of Cytokine Singalling in the Myeloid Lineage: Investigating the Role of CBL and SH2B1
Keywords: Hematopoiesis
Erythropoiesis
Cancer biology
Cytokine
Signalling

Negative regulation of cytokine signalling is essential for maintaining hematopoietic homeostasis. We investigated the role of SH2B1 and CBL in the negative regulation of EPO and GM-CSF signaling, respectively. Erythropoiesis is driven by the cytokine erythropoietin (EPO), which mediates its signal by binding to its cognate receptor, the erythropoietin receptor (EPO-R). Murine knock-in studies have demonstrated EPO-R Tyr343 to play an important role in EPO mediated signalling. We have utilized a Cloning of Ligand Target (COLT) screen to identify the adaptor protein SH2B1 as an interactor of EPO-R pTyr343. We have demonstrated that SH2B1 binds to EPO-R via two mechanisms. The amino-terminus of SH2B1 and the membrane proximal region of EPO-R mediate SH2B1 constitutive binding to EPO-R. SH2B1 binds to EPO-R pTyr343 and pTyr 401 in an SH2 domain-dependent manner. SH2B1 displayed dose- and time- dependent Serine/Threonine phosphorylation in response to EPO stimulation. Knockdown of SH2B1 resulted in enhanced activation of Jak2 and EPO-R. These studies demonstrate SH2B1 as a novel negative regulator of EPO signalling. Mutations in the linker region and the RING finger of CBL have been identified in a number of myeloid malignancies, including juvenile myelomonocytic leukemia. We investigated how linker region mutant, CBL-Y371H, and RING finger mutant, CBL-C384R lead to GM-CSF hypersensitivity. Expression of these CBL mutants in the human hematopoietic cell line, TF-1, showed enhanced stimulation induced phosphorylation of GM-CSFR βc. We also demonstrated that the loss of E3 ligase activity of these CBL mutants results in increased expression of JAK2 and LYN kinases. Assessment of the effects of CBL mutants on downstream signalling revealed enhanced phosphorylation of SHP2, CBL and S6. Dasatinib induced inhibition of SRC family kinases abolished the elevated phosphorylation of CBL mutants, and equalized the phosphorylation of GM-CSFR βc in the wild type and CBL mutant cells.
The Role of Osteocyte Apoptosis on Osteoclast Precursor Recruitment
Keywords: osteocyte
osteoclast precursor
apoptosis
recruitment
mechanical disuse

Osteocytes (resident bone cells) are believed to sense loading-induced interstitial fluid flow in bone and transduce the signals to osteoclasts (bone resorption cells) and osteoblasts (bone formation cells) to regulate bone remodeling. Recent studies have shown that bone disuse causes osteocyte apoptosis, which precedes osteoclast activity at the local remodeling site. Although osteoclast precursors are known to travel via the circulation, the specific mechanism by which they are transported to the remodeling site is unclear. We hypothesized that lack of fluid flow induces osteocyte apoptosis. Furthermore, we hypothesized that osteocyte populations containing apoptotic osteocytes secrete cytokines that: 1) promote angiogenesis, and 2) activate the endothelium to promote osteoclast precursor adhesion to the endothelium such that osteoclast precursors can be delivered closer and directly to the remodeling site. In our in vitro studies, we found that lack of oscillatory fluid flow (mimicking mechanical disuse) promotes osteocyte apoptosis. In addition, osteocyte populations containing apoptotic cells promote endothelial cell proliferation, migration, and tubule formation. Inhibition of the potent angiogenic cytokine, vascular endothelial growth factor (VEGF), abrogated osteocyte apoptosis-mediated angiogenesis. Furthermore, we found that osteocyte populations containing apoptotic cells secrete cytokines that promoted osteoclast precursor adhesion. Upon further investigation, we found that apoptotic osteocytes secreted elevated levels of inflammatory cytokine interleukin 6 (IL-6), and its soluble receptor, sIL-6R. We demonstrated that both IL-6 and sIL-6R are required to activate the endothelium to express ICAM-1. Inhibition of ICAM-1 and IL-6 by blocking antibodies abolished apoptotic osteocyte-mediated osteoclast precursor adhesion. Our findings suggest for the first time that osteocytes communicate to endothelial cells directly to mediate angiogenesis and osteoclast precursor adhesion. Results from this study may assist in a better understanding of osteoclast precursor recruitment at the initial onset of bone resorption.
Characterizing the Mechanisms Regulating Myc-induced Transformation
Keywords: Myc
cancer

Many current efforts in cancer research focus on understanding the molecular mechanisms driving oncogenesis and to advance molecular diagnostics and targeted therapeutics. The MYC oncoprotein is estimated to be deregulated in over 50% of human cancers, and its deregulation is often associated with aggressive disease and poor patient outcomes. While the ability of MYC to promote cellular transformation is well established, a better understanding of the mechanisms promoting MYC-mediated tumorigenesis is essential. While MYC has been shown to undergo a number of post-translational modifications (PTMs), our current understanding of biological significance of these modifications is largly limited to two phosphorylation sites located in the N-terminal domain of the protein. Our work, therefore, aimed to further our understanding of how PTMs regulate MYC-dependent transformation. To this end we have identified and characterized three novel human cell line models of MYC-dependent transformation: MCF10A, SH-EP Tet21/N-Myc, and LF1/TERT/LT/ST cells. Using a combination of these novel models and classic systems, we have evaluated point mutants of MYC at key serine/threonine and lysine residues for their ability to influence MYC-dependent transformation. Using a six lysine to arginine substitution mutant, we have identified and chacterized six C-terminal lysines to be important for the negative regulation of MYC activity. We have additionally demonstrated for the first time that MYC can undergo SUMOylation at one of the lysines in this region. We further completed a functional and transcriptional characterization of MYC phosphorylation mutants. We have assigned biological significance to previously identified phosphorylation sites through the characterization of two mutants that have increased transformation potential over wild-type MYC. Expression array analysis identified gene expression changes both common to deregulated MYC and unique to the different gain-of-function phosphorylation mutants. Combined, this work has advanced our understanding of several of the mechanisms that may regulate MYC-induced transformation.
Gianni Celati: Lo sguardo lirico.
Keywords: terapia arte traduzione poesia
solitudine psicoanalisi fotografia documentario cinema

La tesi analizza il lirismo melanconico di Gianni Celati nella sua produzione narrative e documentaristica che spazia in un arco di temporale che va dagli anni Ottanta ai giorni nostri. In queste opere, di ambientazione prevalentemente padana, l’autore utilizza, con notevole maestria, immagini e brevi impressioni altamente evocative, in modo tale da lasciar trasparire le proprie emozioni. Con questa operazione egli aspira a ridurre al minimo l’affiorare della propria soggettività come dimostra il largo impiego di dettagliate descrizioni, in cui abbondano simboli e metafore, riconducibili a oggetti, paesaggi e persone che sono oggetto della sua osservazione. Nel primo capitolo si mostra come, fin dalle prime fasi della sua carriera di scrittore e di studioso, Celati si serve della scrittura come strumento terapeutico, al fine di alleviare l’inquietudine con cui convive da sempre. Del resto, lo conferma la presenza nelle sue opere di modalità espressive tipiche del genere della caricatura. Nell’ambito di questo discorso si fa riferimento al pensiero del filosofo e psicanalista americano James Hillman, come, ad esempio, alla sua idea di poiesis relativa alla tendenza della nostra mente a produrre immagini come avviene nell’atto narrativo e avente su di noi analoghi effetti terapeutici. Alla luce di ciò, sono state esaminate alcune delle traduzioni poetiche compiute da Celati, mettendole in parallelo ad una selezione di sue poesie e racconti. Il secondo capitolo è volto ad indagare le modalità con cui Celati ha trattato il tema tradizionale del viaggio. Si mostra come i suoi vagabondaggi e quelli dei suoi personaggi non siano altro che una metafora della vana ricerca del senso da attribuire alla loro esistenza. Nella trattazione di questo aspetto la narrativa celatiana viene messa a confronto con l’arte di Alberto Giacometti e di Mario Sironi, che hanno trattato i temi della solitudine e dello smarrimento esistenziale. Analogo è il senso di desolazione che affiora dai documentari girati da Celati, servendosi delle immagini per svolgere un’indagine su come percepiamo il modo esterno. Tale approccio è riconducibile all’influsso che la fotografia del suo amico Luigi Ghirri ha esercitato sull’opera celatiana. Quest’ultimo si è a sua volta ispirato a quella di Cesare Zavattini, che costituisce un punto di riferimento fondamentale anche per Celati. Questo aspetto è stato approfondito nell’ultima sezione del secondo ed ultimo capitolo, incentrata sull’analisi del racconto “Non c’è più paradiso”, da cui emerge l’importanza che Celati, come Zavattini, attribuisce all’immaginazione e alla narrazione come componenti essenziali alla nostra esistenza.
Interference Mitigation for Cellular Networks: Fundamental Limits and Applications
Keywords: Interference mitigation
cellular networks
Shannon Capacity
Information Theory

Interference is a key limiting factor in modern communication systems. In a wireless cellular network, the performance of cell-edge users is severely limited by the intercell interference. This thesis studies the use of interference-channel and relay-channel techniques to mitigate intercell interference and to improve the throughput and coverage of cellular networks. The aim of this thesis is to demonstrate the benefit of the proposed interference mitigation schemes through both information theoretical studies and applications in the cellular network. There are three mains results in this thesis: First, it is shown that for the K-user cyclic Gaussian interference channel, where the kth user interferes with only the (k − 1)th user (mod K) in the network, the Etkin-Tse-Wang power splitting strategy achieves the capacity region to within 2 bits in the weak interference regime. For the special 3-user case, this gap can be sharpened to 1 1 2 bits by the time-sharing technique. Second, it is shown that for a two-user Gaussian interference channel with an in-band-reception and out-of-band-transmission relay, generalized hash-and-forward together with Han-Kobayashi information splitting can achieve the capacity region of this channel to within a constant number of bits in a certain weak-relay regime. A generalized-degrees-of-freedom analysis in the high signal-to-noise ratio regime reveals that in the symmetric channel setting, each common relay bit improves the sum rate up to two bits. The third part of this thesis studies an uplink multicell joint processing model in which the base-stations are connected to a centralized processing server via ratelimited digital backhaul links. This thesis proposes a suboptimal achievability scheme employing the Wyner-Ziv compress-and-forward relaying technique and successive-interference-cancellation decoding. The main advantage of the proposed approach is that it results in achievable rate regions that are easily computable, in contrast to previous schemes in which the rate regions can only be characterized by exponential number of rate constraints
Gender Strategies and Sex-ratio Evolution in the Clonal Aquatic Plant: Sagittaria latifolia (Alismataceae)
Keywords: gender
sexual system
evolution
northern range limit
clonality
dioecy
monoecy
subdioecy

Flowering plants display diverse reproductive systems, including a variety of gender strategies and mechanisms of clonal propagation. Here, I investigate gender strategies, sex-ratio evolution, and sexual dimorphism in the North American clonal aquatic, Sagittaria latifolia (Alismataceae), which exhibits three sex phenotypes (hermaphrodites, females, males) and two modal sexual systems (monoecy, dioecy). This provides an outstanding opportunity to examine the costs and benefits of combined versus separate sexes. My research focused on the northern range limit in eastern N. America, and on disjunct populations in western N. America. I developed microsatellite (SSR) markers to investigate population genetic structure at several spatial scales, including the clonal structure of local populations to continental patterns. These analyses provided insights on the roles of historical, ecological and reproductive factors in the evolution and maintenance of sexual system diversity. Phenotypic sex ratios varied near continuously from monoecy through subdioecy (three sex phenotypes) to dioecy. A comparison of phenotypic and genotypic sex ratios in dioecious populations demonstrated close correspondence. The northern range limit was characterized by a decline in female frequency and an increased incidence of subdioecy. I evaluated two hypotheses to explain this pattern: (1) increased sex inconstancy in dioecious populations; (2) hybridization between monoecious and dioecious populations. I found support for both hypotheses, although hybridization appears to be the more common pathway to subdioecy. I parameterized a model predicting female frequency and hermaphrodite sex allocation; observed and predicted values were correlated suggesting that subdioecious populations are closer to equilibrium than expected for a clonal perennial. A comparison of eastern and western populations indicated genetic differentiation between monoecy and dioecy in the east, but in the west, due to habitat isolation, geography plays a more important role in genetic differentiation. Evidence from cpDNA haplotype variation indicated that the western range was established following long-distance colonization from the east involving a genetic bottleneck. The discovery of gynodioecious populations of S. latifolia in the west, and the absence of ecological and genetic differentiation between monoecious and dioecious populations, raise the possibility that dioecy may have evolved autochthonously in the west, and more recently than in the eastern range.
Simulating Vegetation Migration in Response to Climate Change in a Dynamic Vegetation-climate Model
Keywords: seed dispersal
vegetation model
climate change
LPJ-GUESS
refugia
Central America
tropical PFTs

A central issue in climate change research is to identify what species will be most affected by variations in temperature, precipitation or CO2 and via which underlying mechanisms. Dynamic global vegetation models (DGVMs) have been used to address questions of habitat shifts, extinctions and changes in carbon and nutrient cycling. However, DGVMs have been criticized for assuming full migration and using the most generic of plant functional types (PFTs) to describe vegetation cover. My doctoral research addresses both of these concerns. In the first study, I added two new tropical PFTs to an existing regional model (LPJ-GUESS) to improve vegetation representation in Central America. Although there was an improvement in the representation of some biomes such as the pine-oak forests, LPJ-GUESS was still unable to capture the distribution of arid ecosystems. The model representations of fire, soil, and processes unique to desert vegetation are discussed as possible explanations. The remaining three chapters deal with the assumption of full migration, where plants can arrive at any location regardless of distance or physical barriers. Using LPJ-GUESS, I imposed migration limitations by using fat-tailed seed dispersal kernels. I used three temperate tree species with different life history strategies to test the new dispersal functionality. Simulated migration rates for Acer rubrum (141 m year-1) and Pinus rigida (76 m year-1) correspond well to pollen and genetic reconstructed rates. However, migration rates for Tsuga canadensis (85 m year-1) were considerably slower than historical rates. A sensitivity analysis showed that maturation age is the most important parameter for determining rates of spread, but it is the dispersal kernel which determines if there is any long distance dispersal or not. The final study demonstrates how northerly refugia populations could have impacted landscape recolonization following the retreat of the last glacier. Using three species with known refugia (Acer rubrum, Fagus grandifolia, Picea glauca), colonization rates were faster with a northerly refugia population present. The number of refugia locations also had a positive effect on landscape recolonization rates, which was most pronounced when populations were separated. The results from this thesis illustrate the improvements made in vegetation-climate models, giving us increasing confidence in the quality of future climate change predictions.
Integrating Pandemic through Preparedness: Global Security and the Utility of Threat
Keywords: pandemic
global governance
biosecurity
preparedness

Emerging infectious disease has become a paradigmatic way of thinking about disease in recent years. In response to the widely-held view that an emerging pandemic is an imminent, albeit uncertain, event linked to global interconnectedness, pandemic preparedness has been the target of considerable political concern and economic investment. To date, there has been relatively little critical research questioning the broader social and political implications of this seemingly natural undertaking. My research addresses this knowledge gap by exploring pandemic influenza planning as a global approach to the regulation of emerging infectious disease. I investigate how pandemic is framed and the ways in which these framings link to broader political and economic contexts. I undertake a Foucauldian-informed, critical discourse analysis of four key pandemic planning documents produced by the World Health Organization between 1999 and 2009. I ask how infectious disease is constructed in particular ways, and how these constructions can be interpreted in relation to broader global contexts. My findings, which describe a range of discursive strategies in governing pandemic, are four-fold. First, I examine the characterizations of the influenza virus, and their effect of rendering normal and pandemic circumstances as indistinct. I describe how these constructions are implicated in the framing of preparedness as a continuous engagement with the process of emergence. Next, I explore how the delineation and regulation of boundaries simultaneously constitutes bodies and territories as distinct. Third, I describe the discursive construction of a particular kind of global geopolitics which represents vulnerability according to the interconnectedness of states. Finally, the pandemic virus acquires a form of utility that portrays preparedness as having the potential for securing society against a broad range of potential threats. Anticipating the exceptional features of pandemic is to be achieved through the integration of contingency mechanisms into existing systems of preparedness whose objective is continued economic and social functioning. The regulation of circulation central to pandemic preparedness establishes an ongoing engagement in decisions about freedom and constraint in relation to different forms of mobility or circulation. My findings are interpreted in light of their implications for understanding the global regulation of, and intervention into, molecular life.