Genetic engineering of baker's and wine yeasts using formaldehyde hyperresistance-mediating plasmids

Yeast multi-copy vectors carrying the formaldehyde-resistance marker gene SFA have proved to be a valuable tool for research on industrially used strains of Saccharomyces cerevisiae. The genetics of these strains is often poorly understood, and for various reasons it is not possible to simply subject these strains to protocols of genetic engineering that have been established for laboratory strains of S. cerevisiae. We tested our vectors and protocols using 10 randomly picked baker's and wine yeasts all of which could be transformed by a simple protocol with vectors conferring hyperresistance to formaldehyde. The application of formaldehyde as a selecting agent also offers the advantage of its biodegradation to CO2 during fermentation, i.e., the selecting agent will be consumed and therefore its removal during down-stream processing is not necessary. Thus, this vector provides an expression system which is simple to apply and inexpensive to use

Microencapsulation and tissue engineering as an alternative treatment of diabetes

In the 70's, pancreatic islet transplantation arose as an attractive alternative to restore normoglycemia; however, the scarcity of donors and difficulties with allotransplants, even under immunosuppressive treatment, greatly hampered the use of this alternative. Several materials and devices have been developed to circumvent the problem of islet rejection by the recipient, but, so far, none has proved to be totally effective. A major barrier to transpose is the highly organized islet architecture and its physical and chemical setting in the pancreatic parenchyma. In order to tackle this problem, we assembled a multidisciplinary team that has been working towards setting up the Human Pancreatic Islets Unit at the Chemistry Institute of the University of São Paulo, to collect and process pancreas from human donors, upon consent, in order to produce purified, viable and functional islets to be used in transplants. Collaboration with the private enterprise has allowed access to the latest developed biomaterials for islet encapsulation and immunoisolation. Reasoning that the natural islet microenvironment should be mimicked for optimum viability and function, we set out to isolate extracellular matrix components from human pancreas, not only for analytical purposes, but also to be used as supplementary components of encapsulating materials. A protocol was designed to routinely culture different pancreatic tissues (islets, parenchyma and ducts) in the presence of several pancreatic extracellular matrix components and peptide growth factors to enrich the beta cell population in vitro before transplantation into patients. In addition to representing a therapeutic promise, this initiative is an example of productive partnership between the medical and scientific sectors of the university and private enterprises.

Advanced biofuel production: Engineering metabolic pathways for butanol and propane biosynthesis.

Greenhouse gases emitted from energy production and transportation are dramatically changing the climate of Planet Earth. As a consequence, global warming is affecting the living conditions of numerous plant and animal species, including ours. Thus the development of sustainable and renewable liquid fuels is an essential global challenge in order to combat the climate change. In the past decades many technologies have been developed as alternatives to currently used petroleum fuels, such as bioethanol and biodiesel. However, even with gradually increasing production, the market penetration of these first generation biofuels is still relatively small compared to fossil fuels. Researchers have long ago realized that there is a need for advanced biofuels with improved physical and chemical properties compared to bioethanol and with biomass raw materials not competing with food production. Several target molecules have been identified as potential fuel candidates, such as alkanes, fatty acids, long carbon‐chain alcohols and isoprenoids. The current study focuses on the biosynthesis of butanol and propane as possible biofuels. The scope of this research was to investigate novel heterologous metabolic pathways and to identify bottlenecks for alcohol and alkane generation using Escherichia coli as a model host microorganism. The first theme of the work studied the pathways generating butyraldehyde, the common denominator for butanol and propane biosynthesis. Two ways of generating butyraldehyde were described, one via the bacterial fatty acid elongation machinery and the other via partial overexpression of the acetone‐butanol‐ethanol fermentation pathway found in Clostridium acetobutylicum. The second theme of the experimental work studied the reduction of butyraldehyde to butanol catalysed by various bacterial aldehyde‐reductase enzymes, whereas the final part of the work investigated the in vivo kinetics of the cyanobacterial aldehyde deformylating oxygenase (ADO) for the generation of hydrocarbons. The results showed that the novel butanol pathway, based on fatty acid biosynthesis consisting of an acyl‐ACP thioesterase and a carboxylic acid reductase, is tolerant to oxygen, thus being an efficient alternative to the previous Clostridial pathways. It was also shown that butanol can be produced from acetyl‐CoA using acetoacetyl CoA synthase (NphT7) or acetyl‐CoA acetyltransferase (AtoB) enzymes. The study also demonstrated, for the first time, that bacterial biosynthesis of propane is possible. The efficiency of the system is clearly limited by the poor kinetic properties of the ADO enzyme, and for proper function in vivo, the catalytic machinery requires a coupled electron relay system.

Enhancing business-to-business relationship through value co-creation in traditional business sector: A case of building services engineering

This study discusses the significance of having service as a business logic, and more specifically, how value co-creation can be seen as an enhancing phenomenon to business-to-business relationships in traditional business sector. The purpose of this study is to investigate how value cocreation can enhance a business-to-business relationship in the heating, ventilation and airconditioning (HVAC) industry of building services engineering, through three sub-objectives: to identify what is value in the industry, how value is co-created in the industry, and what is value in a business-to-business relationship in the industry. The theoretical part this study consists of academic knowledge and literature related to the concepts of value, value co-creation and business-to-business relationships. In order to research value co-creation and business-to-business relationships in HVAC industry of building services engineering both, metaphorical and conceptual thinking of service dominant (S-D) logic and more managerial approach of service logic (SL), contributed to the theoretical part of the study. The empirical research conducted for this study is based on seven semi-structured interviews, which constituted the holistic, qualitative single case study method chosen for the research. The data was collected in September 2014 from CEOs, managers and owners representing six building services engineering firms. The interviews were analysed with the help of transcriptions, role-ordered matrices and thematic networks. The findings of this study indicate that value in HVAC industry consists of client expertise and supplier expertise. The result of applying client expertise and supplier expertise to the business-to- business relationship is characterized as value-in-reputation, when continuity, interaction, learning and rapport of the business relationship are ensured. As a result, value co-creation in the industry consists of mutual and separate elements, which the client and the supplier apply in the process, in addition to proactive interaction. The findings of this study, together with the final framework, enhance the understanding of the connection existing between value co-creation and business-to-business relationship. The findings suggest that value in the HVAC industry is characterized by both value-in-use and value-inreputation. Value-in-reputation enhances the formation of value-in-use, and consequently, value cocreation enhances the business-to-business relationship. This study thus contributes to the existing knowledge on the concepts of value and value co-creation in business-to-business relationships.

Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate)-based scaffolds for tissue engineering

Development and selection of an ideal scaffold is of importance for tissue engineering. Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) is a biocompatible bioresorbable copolymer that belongs to the polyhydroxyalkanoate family. Because of its good biocompatibility, PHBHHx has been widely used as a cell scaffold for tissue engineering. This review focuses on the utilization of PHBHHx-based scaffolds in tissue engineering. Advances in the preparation, modification, and application of PHBHHx scaffolds are discussed.

Show me your brain! Stories of interdisciplinary knowledge creation in practice. Experiences and observations from Aalto Design Factory, Finland.

This dissertation centres on the themes of knowledge creation, interdisciplinarity and knowledge work. My research approaches interdisciplinary knowledge creation (IKC) as practical situated activity. I argue that by approaching IKC from the practice-based perspective makes it possible to “deconstruct” how knowledge creation actually happens, and demystify its strong intellectual, mentalistic and expertise-based connotations. I have rendered the work of the observed knowledge workers into something ordinary, accessible and routinized. Consequently this has made it possible to grasp the pragmatic challenges as well the concrete drivers of such activity. Thus the effective way of organizing such activities becomes a question of organizing and leading effective everyday practices. To achieve that end, I have conducted ethnographic research of one explicitly interdisciplinary space within higher education, Aalto Design Factory in Helsinki, Finland, where I observed how students from different disciplines collaborated in new product development projects. I argue that IKC is a multi-dimensional construct that intertwines a particular way of doing; a way of experiencing; a way of embodied being; and a way of reflecting on the very doing itself. This places emphasis not only the practices themselves, but also on the way the individual experiences the practices, as this directly affects how the individual practices. My findings suggest that in order to effectively organize and execute knowledge creation activities organizations need to better accept and manage the emergent diversity and complexity inherent in such activities. In order to accomplish this, I highlight the importance of understanding and using a variety of (material) objects, the centrality of mundane everyday practices, the acceptance of contradictions and negotiations well as the role of management that is involved and engaged. To succeed in interdisciplinary knowledge creation is to lead not only by example, but also by being very much present in the very everyday practices that make it happen.

Impact of social vulnerability on the outcomes of predialysis chronic kidney disease patients in an interdisciplinary center

Introduction: Numerous studies examined the associations between socio-demographic, economic and individual factors and chronic kidney disease (CKD) outcomes and observed that the associations were complex and multifactorial. Socioeconomic factors can be evaluated by a model of social vulnerability (SV). Objective: To analyze the impact of SV on the outcomes of predialysis patients. Methods: Demographic, clinical and laboratory data were collected from a cohort of patients with predialysis stage 3 to 5 who were treated by an interdisciplinary team (January 2002 and December 2009) in Minas Gerais, Brazil. Factor, cluster and discriminant analysis were performed in sequence to identify the most important variables and develop a model of SV that allowed for classification of the patients as vulnerable or non-vulnerable. Cox regression was performed to examine the impact of SV on the outcomes of mortality and need for renal replacement therapy (RRT). Results: Of the 209 patients examined, 29.4% were classified as vulnerable. No significance difference was found between the vulnerable and non-vulnerable groups regarding either mortality (log rank: 0.23) or need for RRT (log rank: 0.17). In the Cox regression model, the hazard ratios (HRs) for the unadjusted and adjusted impact of SV on mortality were found to be 1.87 (confidence interval [CI]: 0.64-5.41) and 1.47 (CI: 0.35-6.0), respectively, and the unadjusted and adjusted impact of need for RRT to be 1.85 (CI: 0.71-4.8) and 2.19 (CI: 0.50-9.6), respectively. Conclusion: These findings indicate that SV did not influence the outcomes of patients with predialysis CKD treated in an interdisciplinary center.

A software engineering approach to distributed systems for composite modeling

The goal of this thesis is to define and validate a software engineering approach for the development of a distributed system for the modeling of composite materials, based on the analysis of various existing software development methods. We reviewed the main features of: (1) software engineering methodologies; (2) distributed system characteristics and their effect on software development; (3) composite materials modeling activities and the requirements for the software development. Using the design science as a research methodology, the distributed system for creating models of composite materials is created and evaluated. Empirical experiments which we conducted showed good convergence of modeled and real processes. During the study, we paid attention to the matter of complexity and importance of distributed system and a deep understanding of modern software engineering methods and tools.

Development of Project Logistics in Engineering, Procurement and Construction Projects

The aim of this Master’s Thesis is to develop project logistics functions in large scale en-gineering, procurement and construction projects. The background of the research topic is compounded from two separate subjects; OPAL Program and case study of an actual EPC project. The purpose is to examine Project Logistics process in accordance with OPAL Program as well as logistics process in focus EPC project. Both entities are researched by using the case study research methodology. Logistics process of the focus EPC project is described as well as presented and in addi-tion, logistics related findings and observations are introduced. Significant findings and observations are found from logistics costs as well as shipment volume estimations in the early phase of the focus ECP project. A notable finding is also that because goods were transported as readily assembled as possible it caused expensive oversized cargo deliveries. From findings and observation of the focus EPC project it can be derived that logistics has to be involved in the early sales phase in order to receive more accurate logistics cost esti-mations for project deliveries. It is also noticed that in order to obtain savings in logistics costs, oversized deliveries must be avoided.

Accelerating food safety and quality control: The use of antibody engineering techniques in the detec-tion of low-molecular weight food contaminants

The increased awareness and evolved consumer habits have set more demanding standards for the quality and safety control of food products. The production of foodstuffs which fulfill these standards can be hampered by different low-molecular weight contaminants. Such compounds can consist of, for example residues of antibiotics in animal use or mycotoxins. The extremely small size of the compounds has hindered the development of analytical methods suitable for routine use, and the methods currently in use require expensive instrumentation and qualified personnel to operate them. There is a need for new, cost-efficient and simple assay concepts which can be used for field testing and are capable of processing large sample quantities rapidly. Immunoassays have been considered as the golden standard for such rapid on-site screening methods. The introduction of directed antibody engineering and in vitro display technologies has facilitated the development of novel antibody based methods for the detection of low-molecular weight food contaminants. The primary aim of this study was to generate and engineer antibodies against low-molecular weight compounds found in various foodstuffs. The three antigen groups selected as targets of antibody development cause food safety and quality defects in wide range of products: 1) fluoroquinolones: a family of synthetic broad-spectrum antibacterial drugs used to treat wide range of human and animal infections, 2) deoxynivalenol: type B trichothecene mycotoxin, a widely recognized problem for crops and animal feeds globally, and 3) skatole, or 3-methyindole is one of the two compounds responsible for boar taint, found in the meat of monogastric animals. This study describes the generation and engineering of antibodies with versatile binding properties against low-molecular weight food contaminants, and the consecutive development of immunoassays for the detection of the respective compounds.

Business process re-engineering -menetelmät myyntiprosessin tehokkuuden parantamisessa (Case-yritys)

Tämän Pro Gradu-tutkielman tavoite on tutkia Business Process Re-engineering menetelmiä myyntiprosessien tehostamisessa. Tutkimuksen teoreettinen viiteke-hys rakentuu myynninjohtamisen, myyntiprosessien ja Business Process Mana-gementin ja Business Process Re-enineeringin ympärille. IT-järjestelmät ovat myös oleellinen osa-alue tutkimuksen kannalta ja niiden osuutta kuvataan niin myyntiprosesseissa kuin Business Process Re-engineering -menetelmien yhtey-dessä. Tutkielmassa perehdytään aikaisempaan tutkimusmateriaaliin ja akateemiseen kirjallisuuteen yllämainituilla osa-alueilla. Tavoitteena on löytää aikaisempia tutki-muksia myyntiprosessien tehostamisesta ja BPR:n roolista näissä tapauksissa. Myös myynninjohtamisen vaikutusta tehokkaaseen myyntiprosessiin tutkitaan, kuten myös IT-järjestelmien erilaisia rooleja tehokkaissa myyntiprosesseissa. Tutkielman empiirinen osio on kvalitatiivinen Case-tutkimus eräässä rahoitusalan yrityksessä. Tutkimus tehdään haastattelemalla myyntihenkilöstöä ja esimiehiä. Lisäksi analysoidaan yrityksen myyntiprosessiin liittyvää muuta materiaalia. Case-tutkimuksen tuloksia peilataan aiempaan akateemiseen tutkimukseen ja tuloksista pyritään löytämään ratkaisuja, miten BPR -menetelmillä voidaan tehostaa yrityksen myyntiprosessia.

Applying software performance engineering methods to development of IT device management systems

Ohjelmiston suorituskyky on kokonaisvaltainen asia, johon kaikki ohjelmiston elinkaaren vaiheet vaikuttavat. Suorituskykyongelmat johtavat usein projektien viivästymisiin, kustannusten ylittymisiin sekä joissain tapauksissa projektin täydelliseen epäonnistumiseen. Software performance engineering (SPE) on ohjelmistolähtöinen lähestysmistapa, joka tarjoaa tekniikoita suorituskykyisen ohjelmiston kehittämiseen. Tämä diplomityö tutkii näitä tekniikoita ja valitsee niiden joukosta ne, jotka soveltuvat suorituskykyongelmien ratkaisemiseen kahden IT-laitehallintatuotteen kehityksessä. Työn lopputuloksena on päivitetty versio nykyisestä tuotekehitysprosessista, mikä huomioi sovellusten suorituskykyyn liittyvät haasteet tuotteiden elinkaaren eri vaiheissa.