The role of splicing factors and small nuclear RNAs in spliceosomal formation

Protein coding genes are comprised of protein-coding exons and non-protein-coding introns. The process of splicing involves removal of the introns and joining of the exons to form a mature messenger RNA, which subsequently undergoes translation into polypeptide. The spliceosome is a large, RNA/protein assembly of five small nuclear RNAs as well as over 300 proteins, which catalyzes intron removal and exon ligation. The selection of specific exons for inclusion in the mature messenger RNA is spatiotemporally regulated and results in production of an enormous diversity of polypeptides from a single gene locus. This phenomenon, known as alternative splicing, is regulated, in part, by protein splicing factors, which target the spliceosome to exon/intron boundaries. The first part of my dissertation (Chapters II and III) focuses on the discovery and characterization of the 45 kilodalton FK506 binding protein (FKBP45), which I discovered in the silk moth, Bombyx mori, as a U1 small nuclear RNA binding protein. This protein family binds the immunosuppressants FK506 and rapamycin and contains peptidyl-prolyl cis-trans isomerase activity, which converts polypeptides from cis to trans about a proline residue. This is the first time that an FKBP has been identified in the spliceosome. The second section of my dissertation (Chapters IV, V, VI and VII) is an investigation of the potential role of small nuclear RNA sequence variants in the control of splicing. I identified 46 copies of small nuclear RNAs in the 6X whole genome shotgun of the Bombyx mori p50T strain. These variants may play a role in differential binding of specific proteins that mediate alternative splicing. Along these lines, further investigation of U2 snRNA sequence variants in Bombyx mori demonstrated that some U2 snRNAs preferentially assemble into high molecular weight spliceosomal complexes over others. Expression of snRNA variants may represent another mechanism by which the cell is able to fine tune the splicing process.

Design and performance assessment of aortic heart valve for tissue engineering

Current artificial heart valves are classified as mechanical and bioprosthetic. An appealing pathway that promises to overcome the shortcomings of commercially available heart valves is offered by the interdisciplinary approach of cardiovascular tissue engineering. However, the mechanical properties of the Tissue Engineering Heart Valves (TEHV) are limited and generally fail in the long-term use. To meet this performance challenge novel biodegradable triblock copolymer poly(ethylene oxide)-polypropylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO or F108) crosslinked to Silk Fibroin (F108-SilkC) to be used as tri-leaflet heart valve material was investigated. ^ Synthesis of ten polymers with varying concentration and thickness (55 µm, 75 µm and 100 µm) was achieved via a covalent crosslinking scheme using bifunctional polyethylene glycol diglycidyl ether (PEGDE). Static and fatigue testing were used to assess mechanical properties of films, and hydrodynamic testing was performed to determine performance under a simulated left ventricular flow regime. The crosslinked copolymer (F108-Silk C) showed greater flexibility and resilience, but inferior ultimate tensile strength, by increasing concentration of PEGDE. Concentration molar ratio of 80:1 (F108: Silk) and thickness of 75 µm showed longer fatigue life for both tension-tension and bending fatigue tests. Four valves out of twelve designed satisfactorily complied with minimum performance requirement ISO 5840, 2005. ^ In conclusion, it was demonstrated that the applicability of a degradable polymer in conjugation with silk fibroin for tissue engineering cardiovascular use, specifically for aortic valve leaflet design, met the performance demands. Thinner thicknesses (t<75 µm) in conjunction with stiffness lower than 320 MPa (80:1, F108: Silk) are essential for the correct functionality of proposed heart valve biomaterial F108-SilkC. Fatigue tests were demonstrated to be a useful tool to characterize biomaterials that undergo cyclic loading. ^

Mixed spatial and nonspatial problems in location based services

With hundreds of millions of users reporting locations and embracing mobile technologies, Location Based Services (LBSs) are raising new challenges. In this dissertation, we address three emerging problems in location services, where geolocation data plays a central role. First, to handle the unprecedented growth of generated geolocation data, existing location services rely on geospatial database systems. However, their inability to leverage combined geographical and textual information in analytical queries (e.g. spatial similarity joins) remains an open problem. To address this, we introduce SpsJoin, a framework for computing spatial set-similarity joins. SpsJoin handles combined similarity queries that involve textual and spatial constraints simultaneously. LBSs use this system to tackle different types of problems, such as deduplication, geolocation enhancement and record linkage. We define the spatial set-similarity join problem in a general case and propose an algorithm for its efficient computation. Our solution utilizes parallel computing with MapReduce to handle scalability issues in large geospatial databases. Second, applications that use geolocation data are seldom concerned with ensuring the privacy of participating users. To motivate participation and address privacy concerns, we propose iSafe, a privacy preserving algorithm for computing safety snapshots of co-located mobile devices as well as geosocial network users. iSafe combines geolocation data extracted from crime datasets and geosocial networks such as Yelp. In order to enhance iSafe's ability to compute safety recommendations, even when crime information is incomplete or sparse, we need to identify relationships between Yelp venues and crime indices at their locations. To achieve this, we use SpsJoin on two datasets (Yelp venues and geolocated businesses) to find venues that have not been reviewed and to further compute the crime indices of their locations. Our results show a statistically significant dependence between location crime indices and Yelp features. Third, review centered LBSs (e.g., Yelp) are increasingly becoming targets of malicious campaigns that aim to bias the public image of represented businesses. Although Yelp actively attempts to detect and filter fraudulent reviews, our experiments showed that Yelp is still vulnerable. Fraudulent LBS information also impacts the ability of iSafe to provide correct safety values. We take steps toward addressing this problem by proposing SpiDeR, an algorithm that takes advantage of the richness of information available in Yelp to detect abnormal review patterns. We propose a fake venue detection solution that applies SpsJoin on Yelp and U.S. housing datasets. We validate the proposed solutions using ground truth data extracted by our experiments and reviews filtered by Yelp.

The Role of Splicing Factors and Small Nuclear RNAS in Spliceosomal Formation

Protein coding genes are comprised of protein-coding exons and non-protein-coding introns. The process of splicing involves removal of the introns and joining of the exons to form a mature messenger RNA, which subsequently undergoes translation into polypeptide. The spliceosome is a large, RNA/protein assembly of five small nuclear RNAs as well as over 300 proteins, which catalyzes intron removal and exon ligation. The selection of specific exons for inclusion in the mature messenger RNA is spatio-temporally regulated and results in production of an enormous diversity of polypeptides from a single gene locus. This phenomenon, known as alternative splicing, is regulated, in part, by protein splicing factors, which target the spliceosome to exon/intron boundaries. The first part of my dissertation (Chapters II and III) focuses on the discovery and characterization of the 45 kilodalton FK506 binding protein (FKBP45), which I discovered in the silk moth, Bombyx mori, as a U1 small nuclear RNA binding protein. This protein family binds the immunosuppressants FK506 and rapamycin and contains peptidyl-prolyl cis-trans isomerase activity, which converts polypeptides from cis to trans about a proline residue. This is the first time that an FKBP has been identified in the spliceosome. The second section of my dissertation (Chapters IV, V, VI and VII) is an investigation of the potential role of small nuclear RNA sequence variants in the control of splicing. I identified 46 copies of small nuclear RNAs in the 6X whole genome shotgun of the Bombyx mori p50T strain. These variants may play a role in differential binding of specific proteins that mediate alternative splicing. Along these lines, further investigation of U2 snRNA sequence variants in Bombyx mori demonstrated that some U2 snRNAs preferentially assemble into high molecular weight spliceosomal complexes over others. Expression of snRNA variants may represent another mechanism by which the cell is able to fine tune the splicing process.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Fatores de virulência, resistência ao estresse osmótico e susceptibilidade de isolados de Candida tropicalis oriundos de ambiente costeiro do nordeste brasileiro

Several studies have been developed regarding health risks associated with the recreational use of beaches contaminated with domestic sewage. These wastes contain various microorganisms, including Candida tropicalis, etiologic agent of both superficial infections such as systemic, as well as indicator of fecal contamination for the environment. In this context, the objective of this study was to characterize C. tropicalis isolates from the sandy beach of Ponta Negra, Natal, Rio Grande do Norte, Brazil, regarding the expression of in vitro virulence factors, adaptation to osmotic stress and susceptibility to antifungal drugs. We analyzed 62 environmental isolates of C. tropicalis and observed a great variation between them for the various virulence factors evaluated. In general, environmental isolates were more adherent to CEBH than C. tropicalis ATCC13803 reference strain, besides the fact they were also highly biofilm producers. In relation to morphogenesis, most isolates presented wrinkled phenotype in Spider medium (34 isolates, 54.8 %). When assessing enzyme activity, most isolates had higher proteinase production than C. tropicalis ATCC13803 reference strain. In addition, 35 isolates (56.4 %) had high hemolytic activity (hemolysis index > 55). With regard to C. tropicalis resistance to osmotic stress, 85.4% of the isolates were able to grow in a liquid medium containing 15% sodium chloride, corroborating to high survival capacity described for this yeast at marine environment. Finally, with regard to sensitivity to antifungal drugs, it was observed high resistance to the azoles tested, with the occurrence of the "Low-high" phenomenon and similar effect to the paradoxical growth which occurs to the echinocandins. For the three azoles tested we verified that 15 strains were resistant (24.2 %). Some strains were also resistant to amphotericin B (14 isolates, 22.6 %), while all of them were sensitive for the echinocandins tested. Therefore, our results demonstrate that C. tropicalis isolated from the sand of northeast of Brazil can fully express virulence attributes and showed a high persistence capacity on the coastal environment, in addition of being significantly resistant to most applied antifungals in current clinical practice. This constitutes a potential health risk to visitors of this environment, especially immunocompromised individuals and those with extreme age range.

Polymer Process Partitioning: Extruding Plastic Pipe

When plastic pipe is solidified, it proceeds through a long cooling chamber. Inside this chamber, inside the hollow extrudate, the plastic is molten, and this inner surface solidifies last. Sag, the flow due to the self-weight of the molten plastic, then happens in this cooling chamber, and sometimes, thickened regions (called knuckles) arise in the lower quadrants, especially of large diameter thickwalled pipes. To compensate for sag, engineers normally shift the die centerpiece downward. This thesis focuses on the consequences of this decentering. Specifically, when the molten polymer is viscoelastic, as is normally the case, a downward lateral force is exerted on the mandrel. Die eccentricity also affects the downstream axial force on the mandrel. These forces govern how rigidly the mandrel must be attached (normally, on a spider die). We attack this flow problem in eccentric cylindrical coordinates, using the Oldroyd 8-constant constitutive model framework. Specifically, we revise the method of Jones (1964), called polymer process partitioning. We estimate both axial and lateral forces. We develop a corresponding map to help plastics engineers predict the extrudate shape, including extrudate knuckles. From the mass balance over the postdie region, we then predict the shape of the extrudate entering the cooling chamber. We further include expressions for the stresses in the extruded polymer melt. We include detailed dimensional worked examples to show process engineers how to use our results to design pipe dies, and especially to suppress extrudate knuckling.

Teaching Empowerment Through Sport: An Analysis of Fast and Female

This project is about Fast and Female, a community-based girls’ sport organization, that focuses on empowering girls through sport. In this thesis I produce a discourse analysis from interviews with six expert sportswomen and a textual analysis of the organization’s online content – including its social media pages. I ground my analysis in poststructural theory as explained by Chris Weedon (1997) and in literature that helps contextualize and better define empowerment (Collins, 2000; Cruikshank, 1999; Hains, 2012; Sharma, 2008; Simon, 1994) and neoliberalism (Silk & Andrews, 2012). My analysis in this project suggests that Fast and Female develops a community through online and in-person interaction. This community is focused on girls’ sport and empowerment, but, as the organization is situated in a neoliberal context, organizers must take extra consideration in order for the organization to develop a girls’ sport culture that is truly representative of the desires and needs of the participants rather than implicit neoliberal values. It is important to note that Fast and Female does not identify as a feminist organization. Through this thesis I argue that Fast and Female teaches girls that sport is empowering – but, while the organization draws on “empowerment,” a term often used by feminists, it promotes a notion of empowerment that teaches female athletes how to exist within current mainstream and sporting cultures, rather than encouraging them to be empowered female citizens who learn to question and challenge social inequity. I conclude my thesis with suggestions for Fast and Female to encourage empowerment in spite of the current neoliberal situation. I also offer a goal-setting workbook that I developed to encourage girls to set goals while thinking about their communities rather than just themselves.

Financial media, globalisation, and China’s economic integration: comparing narrative construction of the Economist and Caijing

In June 2015, legal frameworks of the Asian Infrastructural Investment Bank were signed by its 57 founding members. Proposed and initiated by China, this multilateral development bank is considered to be an Asian counterpart to break the monopoly of the World Bank and the International Monetary Fund. In October 2015, China’s Central Bank announced a benchmark interest rate cut to combat the economic slowdown. The easing policy coincides with the European Central Bank’s announcement of doubts over US Fed’s commitment to raise interest rates. Global stock markets responded positively to China’s move, with the exception of the indexes from Wall Street (Bland, 2015; Elliott, 2015). In the meantime, China’s ‘One Belt, One Road’ (or New Silk Road Economic Belt) became atopic of discourse in relation to its growing global economy, as China pledged $40 billion to trade and infrastructure projects (Bermingham, 2015). The foreign policy aims to reinforce the economic belt from western China through Central Asia towards Europe, as well as to construct maritime trading routes from coastal China through the South China Sea (Summers, 2015). In 2012, The Economist launched a new China section, to reveal the complexity of the‘meteoric rise’ of China. John Micklethwait, who was then the chief editor of the magazine, said that China’s emergence as a global power justified giving it a section of its own(Roush, 2012). In July 2015, Hu Shuli, the former chief editor of Caijing, announced the launch of a think tank and financial data service division called Caixin Insight Group, which encompasses the new Caixin China Purchasing Managers Index (PMI). Incooperation with with Markit Group, a principal global provider of PMI, the index soon became a widely cited economic indicator. One anecdote from November’s Caixin shows how much has changed: in a high-profile dialogue between Hu Shuli and Kevin Rudd, Hu insisted on asking questions in English; interestingly, the former Prime Minister of Australia insisted on replying in Chinese. These recent developments point to one thing: the economic ascent of China and its increasing influence on the power play between economics and politics in world markets. China has begun to take a more active role in rule making and enforcement under neoliberal frameworks. However, due to the country’s size and the scale of its economy in comparison to other countries, China’s version of globalisation has unique characteristics. The ‘Capitalist-socialist’ paradox is vital to China’s market-oriented transformation. In order to comprehend how such unique features are articulated and understood, there are several questions worth investigating in the realms of media and communication studies,such as how China’s neoliberal restructuring is portrayed and perceived by different types of interested parties, and how these portrayals are de-contextualised and re-contextualised in global or Anglo-American narratives. Therefore, based on a combination of the themes of globalisation, financial media and China’s economic integration, this thesis attempts to explore how financial media construct the narratives of China’s economic globalisation through the deployment of comparative and multi-disciplinary approaches. Two outstanding elite financial magazines, Britain’s The Economist, which has a global readership and influence, and Caijing, China’s leading financial magazine, are chosen as case studies to exemplify differing media discourses, representing, respectively, Anglo-American and Chinese socio-economic and political backgrounds, as well as their own journalistic cultures. This thesis tries to answer the questions of how and why China’s neoliberal restructuring is constructed from a globally-oriented perspective. The construction primarily involves people who are influential in business and policymaking. Hence, the analysis falls into the paradigm of elite-elite communication, which is an important but relatively less developed perspective in studying China and its globalisation. The comparing of characteristics of narrative construction are the result of the textual analysis of articles published over a ten-year period (mid-1998 to mid-2008). The corpus of samples come from the two media outlets’ coverage of three selected events:China becoming a member of the World Trade Organization, its outward direct investment, and the listing of stocks of Chinese companies in overseas exchanges, which are mutually exclusive in sample collection and collectively exhaustive in the inclusion of articles regarding China’s economic globalisation. The findings help to understand that, despite language, socio-economic and political differences, elite financial media with globally-oriented readerships share similar methods of and approaches to agenda setting, the evaluation of news prominence, the selection of frame, and the advocacy of deeply rooted neoliberal ideas. The comparison of their distinctive features reflects the different phases of building up the sense of identity in their readers as global elites, as well as the different economic interests that are aligned with the corresponding readerships. However, textual analysis is only relevant in terms of exploring how the narratives are constructed and the elements they include; textual analysis alone prevents us from seeing the obstacles and the constrains of the journalistic practices of construction. Therefore, this thesis provides a brief discussion of interviews with practitioners from the two media, in order to understand how similar or different narratives are manifested and perceived, how the concept of neoliberalism deviates from and is justified in the Chinese context, and how and for what purpose deviations arise from Western to Chinese contexts. The thesis also contributes to defining financial media in the domain of elite communication. The relevant and closely interlocking concepts of globalisation, elitism and neoliberalism are discussed, and are used as a theoretical bedrock in the analysis of texts and contexts. It is important to address the agenda-setting and ideological role of elite financial media, because of its narrative formula of infusing business facts with opinions,which is important in constructing the global elite identity as well as influencing neoliberal policy-making. On the other hand, ‘journalistic professionalism’ has been redefined, in that the elite identity is shared by the content producer, reader and the actors in the news stories emerging from the much-compressed news cycle. The professionalism of elite financial media requires a dual definition, that of being professional in the understanding of business facts and statistics, and that of being professional in the making sense of stories by deploying economic logic.

The European Union Foreign Policy in the Caucasus and Central Asia: The Limitations of the Opening towards the East

This article intends to study the evolution of the European Union foreign policy in the Southern Caucasus and Central Area throughout the Post-Cold War era. The aim is to analyze Brussels’ fundamental interests and limitations in the area, the strategies it has implemented in the last few years, and the extent to which the EU has been able to undermine the regional hegemons’ traditional supremacy. As will be highlighted, the Community’s chronic weaknesses, the local determination to preserve sovereignty and an increasing international geopolitical competition undermine any European aspiration to become a pre-eminent actor at the heart of the Eurasian continent in the near future.

Latina Super-heroines: Hot Tamales in Tights vs. Women Warriors, Wrestlers and Guerrilla Fighters of La Raza

The year 1977 saw the making of the first Latino superhero by a Latino artist. From the 1980s onwards it is also possible to find Latina super-heroines, whose number and complexity has kept increasing ever since. Yet, the representations of spandexed Latinas are still few. For that reason, the goal of this paper is, firstly, to gather a great number of Latina super-heroines and, secondly, to analyze the role that they have played in the history of American literature and art. More specifically, it aims at comparing the spandexed Latinas created by non-Latino/a artists and mainstream comic enterprises with the Latina super-heroines devised by Latino/a artists. The conclusion is that whereas the former tend to conceive heroines within the constraints of the logic of Girl Power, the latter choose to imbue their works with a more daring political content and to align their heroines with the ideologies of Feminism and Postcolonialism.

Thermobonded Fabrics

In 2009 Avella created a series of innovative fabrics for the Yves St Laurent (YSL) collection, deploying techniques from vehicle engineering to generate new materials for a range of garments. Studying the bonding of layers of material in ceramic plate thermobonding technology, Avella conducted a series of experiments with textiles such as flannel, silk and synthetics, and material such as leather, layered with polyamide foam and textile substrate to create new, textured and insulating fabrics with beautiful surfaces and interesting forms. The lightweight properties of the foam enabled the maximum insulation/weight ratio, and the panel moulding technology brought new forms of draping prêt-a-porter fashion design. Exclusive to YSL, this technique was patented and then shown at the Premiere Vision textiles trade fair in 2010. Much documented in specialist journals this innovation also breached the trade-culture barrier and was reported and documented in mainstream newspapers (New York Herald Tribune). Avella’s background in textile workshop studio experimentation at the RCA brought to YSL textiles research for manufacture, the innovative collaboration between fashion couture and engineering laboratory experiments from vehicle design.

Tooth Mobility, Periodontal Ligament Space, and the Alveolus During Periodontal Health, Disease, and Disuse

Thesis (Ph.D.)--University of Washington, 2016-07

A internacionalização do Ensino Superior em Moçambique

International Conference Of Silk, Sugar and Spices: new directions in East-West Cooperation ISCAP 11-12-12 november 2015

Creative industries in Macau innovation and tradition at USJ

International Conference Of Silk, Sugar and Spices: new directions in East-West CooperationISCAP 11-12-13 November 2015