Pressure induced structural changes and gas diffusion pathways in monomeric fluorescent proteins

Fluorescent proteins (FPs) are extremely valuable biochemical markers which have found a wide range of applications in cellular and molecular biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for in vivo applications in mammalian cell imaging. Fluorescent proteins consist of a chromophore caged in the beta-barrel protein scaffold. The photophysical properties of an FP is determined by its chromophore structure and its interactions with the protein barrel. Application of hydrostatic pressure on FPs results in the modification of the chromophore environment which allows a systematic study of the role of the protein-chromophore interactions on photophysical properties of FPs. Using Molecular Dynamics (MD) computer simulations, I investigated the pressure induced structural changes in the monomeric variants mCherry, mStrawberry, and Citrine. The results explain the molecular basis for experimentally observed pressure responses among FP variants. It is found that the barrel flexibility, hydrogen bonding interactions and chromophore planarity of the FPs can be correlated to their contrasting photophysical properties at vaious pressures. I also investigated the oxygen diffusion pathways in mOrange and mOrange2 which exhibit marked differences in oxygen sensitivities as well as photostability. Such computational identifications of structural changes and oxygen diffusion pathways are important in guiding mutagenesis efforts to design fluorescent proteins with improved photophysical properties.

Structural flexibility and oxygen diffusion pathways in monomeric fluorescent proteins

Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions result in improved photostabilities. Therefore, understanding oxygen diffusion pathways in FPs is important for both photostabilites and maturation of the chromophores. We used molecular dynamics calculations to investigate the protein barrel fluctuations in mCherry, which is one of the most useful monomeric mFruit variants, and its GFP homolog citrine. We employed implicit ligand sampling and locally enhanced sampling to determine oxygen pathways from the bulk solvent into the mCherry chromophore in the interior of the protein. The pathway contains several oxygen hosting pockets, which were identified by the amino acid residues that form the pocket. We calculated the free-energy of an oxygen molecule at points along the path. We also investigated an RFP variant known to be significantly less photostable than mCherry and find much easier oxygen access in this variant. We showed that oxygen pathways can be blocked or altered, and barrel fluctuations can be reduced by strategic amino acid substitutions. The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins.

State Political Parties in American Politics: Innovation and Integration in the Party System

What role do state party organizations play in twenty-first century American politics? What is the nature of the relationship between the state and national party organizations in contemporary elections? These questions frame the three studies presented in this dissertation. More specifically, I examine the organizational development of the state party organizations and the strategic interactions and connections between the state and national party organizations in contemporary elections.

In the first empirical chapter, I argue that the Internet Age represents a significant transitional period for state party organizations. Using data collected from surveys of state party leaders, this chapter reevaluates and updates existing theories of party organizational strength and demonstrates the importance of new indicators of party technological capacity to our understanding of party organizational development in the early twenty-first century. In the second chapter, I ask whether the national parties utilize different strategies in deciding how to allocate resources to state parties through fund transfers and through the 50-state-strategy party-building programs that both the Democratic and Republican National Committees advertised during the 2010 elections. Analyzing data collected from my 2011 state party survey and party-fund-transfer data collected from the Federal Election Commission, I find that the national parties considered a combination of state and national electoral concerns in directing assistance to the state parties through their 50-state strategies, as opposed to the strict battleground-state strategy that explains party fund transfers. In my last chapter, I examine the relationships between platforms issued by Democratic and Republican state and national parties and the strategic considerations that explain why state platforms vary in their degree of similarity to the national platform. I analyze an extensive platform dataset, using cluster analysis and document similarity measures to compare platform content across the 1952 to 2014 period. The analysis shows that, as a group, Democratic and Republican state platforms exhibit greater intra-party homogeneity and inter-party heterogeneity starting in the early 1990s, and state-national platform similarity is higher in states that are key players in presidential elections, among other factors. Together, these three studies demonstrate the significance of the state party organizations and the state-national party partnership in contemporary politics.

Institutions, Innovation, and Grassroots Change: Alternatives to Transnational Governance in the Global South

Transnational governance has been advanced as a viable option for regulating commodities produced in emerging economies—where incapable or unwilling states may undersupply institutions requisite for overseeing supply chains consistent with the quality, safety, environmental, or social standards demanded by the global marketplace. Producers from these jurisdictions, otherwise left with few venues for securing market access and price premiums, ostensibly benefit from whatever pathways transnational actors offer to minimize barriers to entry—including voluntary certification for compliance with a panoply of public and private rules, such as those promulgated by NGOs like the Fair Trade Federation or multinational retailers like Wal-Mart. Yet, such transnational “sustainability” governance may neither be effective nor desirable. Regulatory schemes, like third-party certification, often privilege the interests of primary architects and beneficiaries—private business associations, governments, NGOs, and consumers in the global North—over regulatory targets—producers in the global South. Rather than engaging with the international marketplace via imported and externally-driven schemes, some producer groups are instead challenging existing rules and innovating homegrown institutions. These alternatives to commercialization adopt some institutional characteristics of their transnational counterparts yet deliver benefits in a manner more aligned with the needs of producers. Drawing on original empirical cases from Nicaragua and Mexico, this dissertation examines the role of domestic institutional alternatives to transnational governance in enhancing market access, environmental quality and rural livelihoods within producer communities. Unlike the more technocratic and expert-driven approaches characteristic of mainstream governance efforts, these local regulatory institutions build upon the social capital, indigenous identity, “ancestral” knowledge, and human assets of producer communities as new sources of power and legitimacy in governing agricultural commodities.

Improving innovation and performance of Social Enterprises: Knowing what they know

Social Enterprises (SEs) are normally micro and small businesses that trade to tackle social problems, and to improve communities, people’s life chances, and the environment. Thus, their importance to society and economies is increasing. However, there is still a need for more understanding of how these organisations operate, perform, innovate and scale-up. This knowledge is crucial to design and provide accurate strategies to enhance the sector and increase its impact and coverage. Obtaining this understanding is the main driver of this paper, which follows the theoretical lens of the Knowledge-based View (KBV) theory to develop and assess empirically a novel model for knowledge management capabilities (KMCs) development that improves performance of SEs. The empirical assessment consisted of a quantitative study with 432 owners and senior members of SEs in UK, underpinned by 21 interviews. The findings demonstrate how particular organisational characteristics of SEs, the external conditions in which they operate, and informal knowledge management activities, have created overall improvements in their performance of up to 20%, based on a year-to-year comparison, including innovation and creation of social and environmental value. These findings elucidate new perspectives that can contribute not only to SEs and SE supporters, but also to other firms.

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

Customer needs in innovation and R&D strategy development

Tutkimuksen kohteena oleva yritys avasi innovaatiokeskuksen 2015 vuoden loppupuolella. Tutkimuksen tavoite on tutkia keinoja löytää asiakastarpeita innovaatiokeskuksessa sekä selvittää, kuinka asiakastarpeet sisällytetään innovaatio- ja tuotekehitysstrategiaan. Kattava prosessi asiakastarvekartoituksesta esitellään ja prosessi säädetään yritykselle sopivaksi asiakkaille tehdyn kyselyn tulosten mukaan. Lisäksi yrityksen tuotepäälliköille järjestettiin haastattelu, jotta heidän näkemyksiään asiakastarvekartoituksen kehittämisestä ja tarpeiden lisäämisestä strategiaan päästiin myös hyödyntämään. Asiakastarpeiden kartoittamiseen soveltuvaksi menetelmäksi löydettiin ryhmätyömalliin perustuva menetelmä, jossa tarpeita kerätään innovaatiokeskuksessa. Lisäksi tietokoneita hyödyntävä GDSS-kokous auttaa välttämään useita yleisiä kokousten ongelmia. Tutkimuksen mukaan asiakastarpeiden suuret kehityslinjat ja kaikista tärkeimmät tarpeet voidaan lisätä strategiaan hyödyntämällä innovaatiokenttiä, skenaarioita ja roadmappeja sekä asiakastarvetaulukkoja.

External linkages, innovation and the small and medium sized enterprise: the role and effectiveness of public technology policy in Portugal.

Doutoramento em Economia.

Pressure Induced Structural Changes and Gas Diffusion Pathways in Monomeric Fluorescent Proteins

Fluorescent proteins (FPs) are extremely valuable biochemical markers which have found a wide range of applications in cellular and molecular biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for in vivo applications in mammalian cell imaging. Fluorescent proteins consist of a chromophore caged in the beta-barrel protein scaffold. The photophysical properties of an FP is determined by its chromophore structure and its interactions with the protein barrel. Application of hydrostatic pressure on FPs results in the modification of the chromophore environment which allows a systematic study of the role of the protein-chromophore interactions on photophysical properties of FPs. Using Molecular Dynamics (MD) computer simulations, I investigated the pressure induced structural changes in the monomeric variants mCherry, mStrawberry, and Citrine. The results explain the molecular basis for experimentally observed pressure responses among FP variants. It is found that the barrel flexibility, hydrogen bonding interactions and chromophore planarity of the FPs can be correlated to their contrasting photophysical properties at vaious pressures. I also investigated the oxygen diffusion pathways in mOrange and mOrange2 which exhibit marked differences in oxygen sensitivities as well as photostability. Such computational identifications of structural changes and oxygen diffusion pathways are important in guiding mutagenesis efforts to design fluorescent proteins with improved photophysical properties.

Enterprise longevity in Colombian companies From a perspective of innovation and corporate social responsibility as a strategy

Hoy en día la Innovación y la Responsabilidad Social Empresarial son una herramienta clave para la perdurabilidad de una empresa a través del tiempo. Este es el caso de las organizaciones colombianas donde las decisiones de gerencia son enfocadas en el desarrollo de plataformas que soportan practicas sociales y éticas ya que estas incentivan a los trabajadores ofreciéndoles a sus clientes un mejor servicio y son necesarias para generar una estrategia de reputación, ganar fidelidad y credibilidad por parte de los consumidores. Crepes & Waffles es uno de los restaurantes colombianos más exitosos y que ha logrado mantenerse en el tiempo aún así en tiempos turbulentos. Su éxito se debe al uso de RSE en su estrategia, ellos crean innovación de valor en cada uno de sus platos al hacerlos diferentes, en el servicio al cliente y en los servicios y el buen trato que se le ofrece a los trabajadores. Por otro lado, Procolombia es una organización que promueve las exportaciones no tradicionales, la inversión extranjera y la marca país. Ellos al igual que Crepes & Waffles también se enfocan en la RSE y crea innovación de valor en sus procesos de orientar a las empresas a través de conferencias, seminarios, entrenamientos entre otras.

Computer and laboratory simulation in the teaching of neonatal nursing: innovation and impact on learning

Objectives: to evaluate the cognitive learning of nursing students in neonatal clinical evaluation from a blended course with the use of computer and laboratory simulation; to compare the cognitive learning of students in a control and experimental group testing the laboratory simulation; and to assess the extracurricular blended course offered on the clinical assessment of preterm infants, according to the students. Method: a quasi-experimental study with 14 Portuguese students, containing pretest, midterm test and post-test. The technologies offered in the course were serious game e-Baby, instructional software of semiology and semiotechnique, and laboratory simulation. Data collection tools developed for this study were used for the course evaluation and characterization of the students. Nonparametric statistics were used: Mann-Whitney and Wilcoxon. Results: the use of validated digital technologies and laboratory simulation demonstrated a statistically significant difference (p = 0.001) in the learning of the participants. The course was evaluated as very satisfactory for them. The laboratory simulation alone did not represent a significant difference in the learning. Conclusions: the cognitive learning of participants increased significantly. The use of technology can be partly responsible for the course success, showing it to be an important teaching tool for innovation and motivation of learning in healthcare.

System innovation and life cycle thinking in packaging value chain: the circularity of plastics.

Compared to other, plastic materials have registered a strong acceleration in production and consumption during the last years. Despite the existence of waste management systems, plastic_based materials are still a pervasive presence in the environment, with negative consequences on marine ecosystem and human health. The recycling is still challenging due to the growing complexity of product design, the so-called overpackaging, the insufficient and inadequate recycling infrastructure, the weak market of recycled plastics and the high cost of waste treatment and disposal. The Circular economy package, the European Strategy for plastics in a circular economy and the recent European Green Deal include very ambitious programmes to rethink the entire plastic value chain. As regards packaging, all plastic packaging will have to be 100% recyclable (or reusable) and 55% recycled by 2030. Regions are consequently called upon to set up a robust plan able to fit the European objectives. It takes on greater importance in Emilia Romagna where the Packaging valley is located. This thesis supports the definition of a strategy aimed to establish an after-use plastics economy in the region. The PhD work has set the basis and the instruments to establish the so-called Circularity Strategy with the aim to turn about 92.000t of plastic waste into profitable secondary resources. System innovation, life cycle thinking and participative backcasting method have allowed to deeply analyse the current system, orientate the problem and explore sustainable solutions through a broad stakeholder participation. A material flow analysis, accompanied by a barrier analysis, has supported the identification of the gaps between the present situation and the 2030 scenario. Eco-design for and from recycling (and a mass _based recycling rate (based on the effective amount of plastic wastes turned into secondary plastics), valorized by a value_based indicator, are the key-points of the action plan.