Control of CD4 gene expression: connecting signals to outcomes in T cell development

The control of CD4 gene expression is essential for proper T lymphocyte development. Signals transmitted from the T-cell antigen receptor (TCR) during the thymic selection processes are believed to be linked to the regulation of CD4 gene expression during specific stages of T cell development. Thus, a study of the factors that control CD4 gene expression may lead to further insight into the molecular mechanisms that drive thymic selection. In this review, we discuss the work conducted to date to identify and characterize the cis-acting transcriptional control elements in the CD4 locus and the DNA-binding factors that mediate their function. From these studies, it is becoming clear that the molecular mechanisms controlling CD4 gene expression are very complex and differ at each stage of development. Thus, the control of CD4 expression is subject to many different influences as the thymocyte develops.

Differential expression of AMPA-type glutamate receptor subunits during development of the chick optic tectum

Glutamate receptors have been often associated with developmental processes. We used immunohistochemical techniques to evaluate the expression of the AMPA-type glutamate receptor (GluR) subunits in the chick optic tectum (TeO). Chick embryos from the 5th through the 20th embryonic day (E5-E20) and one-day-old (P1) chicks were used. The three types of immunoreactivity evaluated (GluR1, GluR2/3, and GluR4) had different temporal and spatial expression patterns in the several layers of the TeO. The GluR1 subunit first appeared as moderate staining on E7 and then increased on E9. The mature GluR1 pattern included intense staining only in layer 5 of the TeO. The GluR2/3 subunits presented low expression on E5, which became intense on E7. The staining for GluR2/3 changed to very intense on E14 in tectal layer 13. Staining of layer 13 neurons is the most prominent feature of GluR immunoreactivity in the adult TeO. The GluR4 subunit generally presented the lowest expression starting on E7, which was similar to the adult pattern. Some instances of transient expression of GluR subunits were observed in specific cell populations from E9 through E20. These results demonstrate a differential expression of the GluR subunits in the embryonic TeO, adding information about their possible functions in the developmental processes of the visual system.

Visual maps in the adult primate cerebral cortex: some implications for brain development and evolution

In this paper, the topology of cortical visuotopic maps in adult primates is reviewed, with emphasis on recent studies. The observed visuotopic organisation can be summarised with reference to two basic rules. First, adjacent radial columns in the cortex represent partially overlapping regions of the visual field, irrespective of whether these columns are part of the same or different cortical areas. This primary rule is seldom, if ever, violated. Second, adjacent regions of the visual field tend to be represented in adjacent radial columns of a same area. This rule is not as rigid as the first, as many cortical areas form discontinuous, second-order representations of the visual field. A developmental model based on these physiological observations, and on comparative studies of cortical organisation, is then proposed, in order to explain how a combination of molecular specification steps and activity-driven processes can generate the variety of visuotopic organisations observed in adult cortex.

Fluvio-morphological processes of meander bends - Combining conventional field measurements, close-range remote sensing and computational modelling

Meandering rivers have been perceived to evolve rather similarly around the world independently of the location or size of the river. Despite the many consistent processes and characteristics they have also been noted to show complex and unique sets of fluviomorphological processes in which local factors play important role. These complex interactions of flow and morphology affect notably the development of the river. Comprehensive and fundamental field, flume and theoretically based studies of fluviomorphological processes in meandering rivers have been carried out especially during the latter part of the 20th century. However, as these studies have been carried out with traditional field measurements techniques their spatial and temporal resolution is not competitive to the level achievable today. The hypothesis of this study is that, by exploiting e increased spatial and temporal resolution of the data, achieved by combining conventional field measurements with a range of modern technologies, will provide new insights to the spatial patterns of the flow-sediment interaction in meandering streams, which have perceived to show notable variation in space and time. This thesis shows how the modern technologies can be combined to derive very high spatial and temporal resolution data on fluvio-morphological processes over meander bends. The flow structure over the bends is recorded in situ using acoustic Doppler current profiler (ADCP) and the spatial and temporal resolution of the flow data is enhanced using 2D and 3D CFD over various meander bends. The CFD are also exploited to simulate sediment transport. Multi-temporal terrestrial laser scanning (TLS), mobile laser scanning (MLS) and echo sounding data are used to measure the flow-based changes and formations over meander bends and to build the computational models. The spatial patterns of erosion and deposition over meander bends are analysed relative to the measured and modelled flow field and sediment transport. The results are compared with the classic theories of the processes in meander bends. Mainly, the results of this study follow well the existing theories and results of previous studies. However, some new insights regarding to the spatial and temporal patterns of the flow-sediment interaction in a natural sand-bed meander bend are provided. The results of this study show the advantages of the rapid and detailed measurements techniques and the achieved spatial and temporal resolution provided by CFD, unachievable with field measurements. The thesis also discusses the limitations which remain in the measurement and modelling methods and in understanding of fluvial geomorphology of meander bends. Further, the hydro- and morphodynamic models’ sensitivity to user-defined parameters is tested, and the modelling results are assessed against detailed field measurement. The study is implemented in the meandering sub-Arctic Pulmanki River in Finland. The river is unregulated and sand-bed and major morphological changes occur annually on the meander point bars, which are inundated only during the snow-melt-induced spring floods. The outcome of this study applies to sandbed meandering rivers in regions where normally one significant flood event occurs annually, such as Arctic areas with snow-melt induced spring floods, and where the point bars of the meander bends are inundated only during the flood events.

Green aspects study in game development

Context: Game development has become increasingly important in the software industry, but this importance has not affected the way software engineering approaches and methodologies manage the differences they have with game development. Similarly, software engineering does not fully support sustainability practices, causing this element to often not be considered or even known as a requirement for a development lifecycle. Goal: The aim of this thesis is to study the mode in which games are developed, and the involved sustainable aspects and the relevant concerns regarding the migration processes. Method: A quantitative study was conducted, gathering 33 answers of game professionals from four continents, from administrative (25%) and technical oriented positions (75%). Results: Three trends were observed: 1) Agile process models are used, 2) major concerns for mobile development and digital marketing, 3) minor concerns for eco-impact elements and certain development phases such as testing and crunch time development. Conclusion: Traditional Software engineering would require a major change on its processes and models to fit with modern agile development, game development approaches and sustainable requirements.

NFAT transcription factors: from cell cycle to tumor development

The nuclear factor of activated T cells (NFAT) family of transcription factors has been primarily identified in immune cells; however, these proteins have been recently found to be functionally active in several other non-immune cell types. NFAT proteins are activated upon different stimuli that lead to increased intracellular calcium levels. Regardless of their widely known cytokine gene expression properties, NFATs have been shown to regulate other genes related to cell cycle progression, cell differentiation and apoptosis, revealing a broader role for these proteins in normal cell physiology. Several reports have addressed the participation of NFATs in many aspects of malignant cell transformation and tumorigenic processes. In this review, we will discuss the involvement of the different NFAT family members in the regulation of cell cycling, differentiation and tumor formation, and also its implications on oncogenesis. Better understanding the mechanisms by which NFATs regulate cell cycle and tumor-related events should be relevant for the development of rational anti-cancer therapies.

Role of matrix metalloproteinases in the development of airway inflammation and remodeling

Matrix metalloproteinases (MMPs) are a major group of proteases known to regulate extracellular matrix (ECM) turnover and so they have been suggested to be important in the process of lung disease associated with tissue remodeling. This has led to the concept that modulation of airway remodeling including excessive proteolysis damage to the tissue may be of interest for future treatment. Within the MMP family, macrophage elastase (MMP-12) is able to degrade ECM components such as elastin and is involved in tissue remodeling processes in chronic obstructive pulmonary disease including emphysema. Pulmonary fibrosis has an aggressive course and is usually fatal within an average of 3 to 6 years after the onset of symptoms. Pulmonary fibrosis is associated with deposition of ECM components in the lung interstitium. The excessive airway remodeling as a result of an imbalance in the equilibrium of the normal processes of synthesis and degradation of ECM components could justify anti-protease treatments. Indeed, the correlation of the differences in hydroxyproline levels in the lungs of bleomycin-treated mice strongly suggests that a reduced molar pro-MMP-9/TIMP-1 ratio in bronchoalveolar lavage fluid is associated with collagen deposition, beginning as early as the inflammatory events at day 1 after bleomycin administration. Finally, these observations emphasize that effective treatment of these disorders must be started early during the natural history of the disease, prior to the development of extensive lung destruction and fibrosis.

The extracellular matrix provides directional cues for neuronal migration during cerebellar development

Normal central nervous system development relies on accurate intrinsic cellular programs as well as on extrinsic informative cues provided by extracellular molecules. Migration of neuronal progenitors from defined proliferative zones to their final location is a key event during embryonic and postnatal development. Extracellular matrix components play important roles in these processes, and interactions between neurons and extracellular matrix are fundamental for the normal development of the central nervous system. Guidance cues are provided by extracellular factors that orient neuronal migration. During cerebellar development, the extracellular matrix molecules laminin and fibronectin give support to neuronal precursor migration, while other molecules such as reelin, tenascin, and netrin orient their migration. Reelin and tenascin are extracellular matrix components that attract or repel neuronal precursors and axons during development through interaction with membrane receptors, and netrin associates with laminin and heparan sulfate proteoglycans, and binds to the extracellular matrix receptor integrins present on the neuronal surface. Altogether, the dynamic changes in the composition and distribution of extracellular matrix components provide external cues that direct neurons leaving their birthplaces to reach their correct final location. Understanding the molecular mechanisms that orient neurons to reach precisely their final location during development is fundamental to understand how neuronal misplacement leads to neurological diseases and eventually to find ways to treat them.

Development of project cash flow forecasting process

Process management refers to improving the key functions of a company. The main functions of the case company - project management, procurement, finance, and human resource - use their own separate systems. The case company is in the process of changing its software. Different functions will use the same system in the future. This software change causes changes in some of the company’s processes. Project cash flow forecasting process is one of the changing processes. Cash flow forecasting ensures the sufficiency of money and prepares for possible changes in the future. This will help to ensure the company’s viability. The purpose of the research is to describe a new project cash flow forecasting process. In addition, the aim is to analyze the impacts of the process change, with regard to the project control department’s workload and resources through the process measurement, and how the impacts take the department’s future operations into account. The research is based on process management. Processes, their descriptions, and the way the process management uses the information, are discussed in the theory part of this research. The theory part is based on literature and articles. Project cash flow and forecasting-related benefits are also discussed. After this, the project cash flow forecasting as-is and to-be processes are described by utilizing information, obtained from the theoretical part, as well as the know-how of the project control department’s personnel. Written descriptions and cross-functional flowcharts are used for descriptions. Process measurement is based on interviews with the personnel – mainly cost controllers and department managers. The process change and the integration of two processes will allow work time for other things, for example, analysis of costs. In addition to the quality of the cash flow information will improve compared to the as-is process. Analyzing the department’s other main processes, department’s roles, and their responsibilities should be checked and redesigned. This way, there will be an opportunity to achieve the best possible efficiency and cost savings.

Innovation process development and business process integration - a multiple case study

The main objective of this study was to find out the bases for innovation model formulation in an existing organization based on cases. Innovation processes can be analyzed based on their needs and based on their emphasis on the business model development or R&D. The research was conducted in energy sector within one company by utilizing its projects as cases for the study. It is typical for the field of business that development is slow, although the case company has put emphasis on its innovation efforts. Analysis was done by identifying the cases’ needs and comparing them. The results were that because of the variances in the needs of the cases, the applicability of innovation process models varies. It was discovered that by dividing the process into two phases, a uniform model could be composed. This model would fulfill the needs of the cases and potential future projects as well.

Influence of multi-phase phenomena on semibatch crystallization processes of aqueous solutions

Crystal properties, product quality and particle size are determined by the operating conditions in the crystallization process. Thus, in order to obtain desired end-products, the crystallization process should be effectively controlled based on reliable kinetic information, which can be provided by powerful analytical tools such as Raman spectrometry and thermal analysis. The present research work studied various crystallization processes such as reactive crystallization, precipitation with anti-solvent and evaporation crystallization. The goal of the work was to understand more comprehensively the fundamentals, phenomena and utilizations of crystallization, and establish proper methods to control particle size distribution, especially for three phase gas-liquid-solid crystallization systems. As a part of the solid-liquid equilibrium studies in this work, prediction of KCl solubility in a MgCl2-KCl-H2O system was studied theoretically. Additionally, a solubility prediction model by Pitzer thermodynamic model was investigated based on solubility measurements of potassium dihydrogen phosphate with the presence of non-electronic organic substances in aqueous solutions. The prediction model helps to extend literature data and offers an easy and economical way to choose solvent for anti-solvent precipitation. Using experimental and modern analytical methods, precipitation kinetics and mass transfer in reactive crystallization of magnesium carbonate hydrates with magnesium hydroxide slurry and CO2 gas were systematically investigated. The obtained results gave deeper insight into gas-liquid-solid interactions and the mechanisms of this heterogeneous crystallization process. The research approach developed can provide theoretical guidance and act as a useful reference to promote development of gas-liquid reactive crystallization. Gas-liquid mass transfer of absorption in the presence of solid particles in a stirred tank was investigated in order to gain understanding of how different-sized particles interact with gas bubbles. Based on obtained volumetric mass transfer coefficient values, it was found that the influence of the presence of small particles on gas-liquid mass transfer cannot be ignored since there are interactions between bubbles and particles. Raman spectrometry was successfully applied for liquid and solids analysis in semi-batch anti-solvent precipitation and evaporation crystallization. Real-time information such as supersaturation, formation of precipitates and identification of crystal polymorphs could be obtained by Raman spectrometry. The solubility prediction models, monitoring methods for precipitation and empirical model for absorption developed in this study together with the methodologies used gives valuable information for aspects of industrial crystallization. Furthermore, Raman analysis was seen to be a potential controlling method for various crystallization processes.

Roadmap for Service Charging Development

Corporate support functions are increasingly being concentrated into service centers. Service Management principles guide companies in the transition. Service Financial Management is an integral part in supporting the strategic positioning of the service center. The main goal of this thesis is to create a step-by-step plan to improve and automate the service charging processes for the finance service function of the case company. Automating the service transaction data collection for reporting is expected to improve efficiency, reliability and transparency. Interviews with finance service managers are held to define current processes and areas for improvement. These create the basis for the creation of a development roadmap that takes place in two phases. The first phase is to create an environment where automation is possible, and the second phase is the automation of each finance service. Benchmarking interviews are held with the service centers in three other companies to discover best practices. The service charging processes between the studied companies are found incompatible, and suggestions for process automation cannot be inferred. Some implications of Service Financial Management decisions to the strategy of the service center are identified. The bundling of services and charging them inside or outside of the goal-setting frame of the business unit can be used to support the strategic choice and customer acceptance of the service center.

Development of an alternative technology for the oyster mushroom production using liquid inoculum

Pleurotus ostreatus, worldwide known as oyster mushroom, was cultivated in banana straw using inocula produced by two different processes - liquid inoculum and the traditionally used solid inoculum. Different ratios (5, 10, 15, and 20%) were tested. Biological efficiency, yield, productivity, organic matter loss, and moisture of fruiting bodies as well as physical-chemical characteristics of banana straw were studied. Significant differences were observed for cellulose, lignin, and hemicellulose content between one and two harvests for both solid and liquid inocula. It was observed that P. ostreatus growth promoted higher degradation of lignin (80.36%), followed by hemicellulose (78.64%) and cellulose (60.37%). Significant differences between one and two harvests were also observed for the production parameters (biological efficiency and yield) for both kinds of inocula, liquid and solid. However, significant differences in productivity between harvests were observed only for solid inoculum.

Development of prebiotic food products and health benefits

In the current context from the nutritional and epidemiological point of view, it can be seen an occurrence increase of Chronic Non-Communicable Diseases, as well as the inflammatory ones, ordinarily associated to a wrong feed, poor in fibers and rich in fats and simple and refined carbohydrates. This view has evidenced a progressive increase of diseases, highlighting the importance of colonic microbiota as an active mechanism of infectious processes control and modulation of immunologic answer. Therefore, constant the worries related to recovering and maintenance of healthy intestines, stocked with prebiotic nutrients that support the survival of beneficial health agents. This way, researchers and the segment of food industry has encouraged the development of products with prebiotic properties, looking for the health promotion, treatment and diseases prevention, besides the strengthening on the competitive market. This article will embrace the contents about physiologic effects of the main known prebiotic, their potential in relation to fermentatives bacterias, new developed products and used methodologies to the recognition of pre and probiotic functions.

Development of 3D super-resolution tomographic STED microscopy and its application to studies on bone resorption

In this doctoral thesis, a tomographic STED microscopy technique for 3D super-resolution imaging was developed and utilized to observebone remodeling processes. To improve upon existing methods, wehave used a tomographic approach using a commercially available stimulated emission depletion (STED) microscope. A certain region of interest (ROI) was observed at two oblique angles: one at a standard inverted configuration from below (bottom view) and another from the side (side view) via a micro-mirror positioned close to the ROI. The two viewing angles were reconstructed into a final tomogram. The technique, named as tomographic STED microscopy, was able to achieve an axial resolution of approximately 70 nm on microtubule structures in a fixed biological specimen. High resolution imaging of osteoclasts (OCs) that are actively resorbing bone was achieved by creating an optically transparent coating on a microscope coverglass that imitates a fractured bone surface. 2D super-resolution STED microscopy on the bone layer showed approximately 60 nm of lateral resolution on a resorption associated organelle allowing these structures to be imaged with super-resolution microscopy for the first time. The developed tomographic STED microscopy technique was further applied to study resorption mechanisms of OCs cultured on the bone coating. The technique revealed actin cytoskeleton with specific structures, comet-tails, some of which were facing upwards and some others were facing downwards. This, in our opinion, indicated that during bone resorption, an involvement of the actin cytoskeleton in vesicular exocytosis and endocytosis is present. The application of tomographic STED microscopy in bone biology demonstrated that 3D super-resolution techniques can provide new insights into biological 3D nano-structures that are beyond the diffraction-limit when the optical constraints of super-resolution imaging are carefully taken into account.