Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / This paper presents a method for generating estimates of temporal changes in the surrounding area of a highway located in the Amazon, using the technique Cellular Automata and explanatory variables, only attributes of the land. The proposed model uses vector images (obtained from the National Institute for Space Research in Brazil), which are converted to grid type files â raster image, representing a series of spatial changes in the region of study. With this proposition, it is expected to assist decision makers in order to meet the requests of CONAMA Resolution 01, relating to environmental impacts, more specifically, as regards the construction of models which consider scenarios with and without the project, and that the process of construction / rehabilitation of roads can be made in view of the legal norms in order to minimize potential environmental and social impacts. The model generated from the CAs showed promise in generating future estimates of deforestation and a good quantitative and qualitative indicators to support the decision making process to consider future deforestation being caused by construction and / or paving of road in the Amazon. / Este trabalho apresenta um mÃtodo para a estimativa de mudanÃas espaÃo temporais no entorno de uma rodovia localizada na AmazÃnia, utilizando para tanto a tÃcnica AutÃmatos Celulares adaptada em ambiente SIG, onde as variÃveis explicativas do modelo serÃo somente os atributos do terreno. O modelo proposto usa imagens vetoriais (obtidas junto ao Instituto Nacional de Pesquisas Espaciais) que posteriormente sÃo convertidas para arquivos tipo grid â em formato raster, com a sÃrie histÃrica das mudanÃas espaciais na regiÃo objeto de estudo. Espera-se auxiliar os tomadores de decisÃo no atendimento das solicitaÃÃes da resoluÃÃo CONAMA 01/86 relativas à concepÃÃo de modelos que considerem cenÃrios com e sem o empreendimento, e que os processos de construÃÃo/recuperaÃÃo de rodovias possam ser realizados atendendo Ãs normas legais, visando minimizar os potenciais impactos sÃcio ambientais. O modelo gerado a partir dos ACs mostrou-se promissor na geraÃÃo de estimativas futuras de desmatamento e um bom indicador quantitativo e qualitativo para suporte no processo de tomada de decisÃo que pondere o desmatamento futuro a ser causado pela construÃÃo e/ou pavimentaÃÃo de uma rodovia na AmazÃnia.

Many past events go unmarked and unremembered, and eventually lose their significance. One such area is the Wonderboom fort, tree and the Nature Reserve. The research investigates how the landscape design can strengthen the existing spirit of place. The place’s identity - that of a refuge – is intangible and unconscious, but can be made tangible through a narrative that engaged with the cultural and biophysical history of the site (the tangible world) by means of didactics and semiotics. This will provide a learning experience with added meaning that gives added identity of place. Furthermore, specific design principles are investigated namely: better access, heightened awareness, and heightened interest created through complexity and coherence in design. Complexity and coherence will generate interest in the user to engage with the physical/conscious experience, engaging and learning about the physical aspects of the site’s nature and culture. The unconscious experience will be guided through semiotics – the use of symbols that give meaning and add identity to place and user. The design intervention will be a landscape which tells the story of the place and unveils the heritage and history of the site in such a way that visitors will have an engaging and informative experience of the past events. The site can be the northern link and gateway into the city of Pretoria, a destination for local and international tourism, and a green corridor for people to experience the city in a different way. The design approach ties in with the Burra Charter approach, namely “changing as much as necessary but as little as possible” but also with the Ename charter stating that Heritage sites should be presented to the public and the public should be educated to ensure their protection. Hampton Adams rightfully says that: 'Only by looking at the past, can we plan the future.' / Dissertation (ML(Prof))--University of Pretoria, 2011. / Architecture / unrestricted

When estimating economic value associated with changes in water quality, recreation demand models typically depend upon either (i) biophysical measures of water quality as collected by natural scientists or (ii) the perception of water quality by recreationists. Models based upon biophysical metrics (such as oxygen concentration, pollutant concentrations, Secchi depth measurements, etc.) operate on the assumption that people can perceive and respond to these metrics, or respond to factors that are, indeed, correlated with the biophysical measure. Economists have often estimated willingness-to-pay (WTP) measures associated with unit changes in biophysical measures without examining the degree to which the measures are truly correlated with perceptions. Recreation demand models that are based upon respondents’ perceptions of water quality necessarily assume that perceptions correlate well with the measures used by scientists to evaluate water quality. Again, WTP for unit changes in perceptions have been estimated without examining the relationship to the underlying biophysical measures. The relationship between biophysical metrics and perceptions is rarely addressed, yet it has profound implications for water quality management and policy. Consider a federal or state agency wishing to manage the quality of its waters in an economically efficient way. Through mandated water quality monitoring regulations, an agency may have many years of biophysical measurements, but these measures are in no way linked to people’s perceptions of water quality and, thus, to WTP. Using biophysical measures of water quality and recreation use data recently collected in Utah, this study links technical measures of water quality at a water body to survey respondents’ perceptions of water quality at the same site. This approach is akin to estimating an ecological production function wherein biophysical measures are “inputs” to water quality perceptions (the output). Truncated Negative Binomial models of water-based recreation are used to estimate welfare effects of changes in water quality as measured through (i) unit changes in biophysical measures, (ii) unit changes in perceptions, and (iii) unit changes in biophysical as they change perceptions through the ecological production function.

No / Growing three dimensional (3D) cells is an emerging research in tissue engineering. Biophysical properties of the 3D cells regulate the cells growth, drug diffusion dynamics and gene expressions. Scaffold based or scaffoldless techniques for 3D cell cultures are rarely being compared in terms of the physical features of the microtissues produced. The biophysical properties of the microtissues cultured using scaffold based microencapsulation by flicking and scaffoldless liquid crystal (LC) based techniques were characterized. Flicking technique produced high yield and highly reproducible microtissues of keratinocyte cell lines in alginate microcapsules at approximately 350 ± 12 pieces per culture. However, microtissues grown on the LC substrates yielded at lower quantity of 58 ± 21 pieces per culture. The sizes of the microtissues produced using alginate microcapsules and LC substrates were 250 ± 25 μm and 141 ± 70 μm, respectively. In both techniques, cells remodeled into microtissues via different growth phases and showed good integrity of cells in field-emission scanning microscopy (FE-SEM). Microencapsulation packed the cells in alginate scaffolds of polysaccharides with limited spaces for motility. Whereas, LC substrates allowed the cells to migrate and self-stacking into multilayered structures as revealed by the nuclei stainings. The cells cultured using both techniques were found viable based on the live and dead cell stainings. Stained histological sections showed that both techniques produced cell models that closely replicate the intrinsic physiological conditions. Alginate microcapsulation and LC based techniques produced microtissues containing similar bio-macromolecules but they did not alter the main absorption bands of microtissues as revealed by the Fourier transform infrared spectroscopy. Cell growth, structural organization, morphology and surface structures for 3D microtissues cultured using both techniques appeared to be different and might be suitable for different applications. / (Science Fund Vot No.: 0201-01-13-SF0104 or S024) awarded by Malaysia Ministry of Science and Technology (MOSTI) and IGSP Grant Vot No. U679 awarded by Universiti Tun Hussein Onn Malaysia.

Eukaryotic cell chemotaxis, or directed cell migration in response to a chemoeffector gradient, plays a central role in many important biological process such as wound healing, cancer metastasis, and embryogenesis. In vivo, cells migrate on fibrous ECM, but chemotaxis studies are typically conducted on flat substrates which fail to recapitulate ECM or 3D gel environments with heterogeneous and poorly defined biophysical properties. To address these challenges, this thesis focused on developing a microfluidic assay device which utilizes a reductionist approach to study single cell chemotaxis on aligned, suspended ECM-mimicking nanofibers. The device is comprised of a network of microfluidic mixing channels which produce a temporally invariant, linear chemical gradient over nanofiber scaffolds in an observation channel. The microfluidic device design was guided by a numerical model and validated with experimental testing. This device was used to study mouse embryonic fibroblast NIH/3T3 response to platelet derived growth factor (PDGF) on flat polystyrene and suspended, polystyrene nanofibers with small (15 μm), and large (25 μm) spacing. Cell aspect ratio is lowest for flat polystyrene (spread morphology) and highest for large-spaced fibers (spindle morphology). Cells migrating on fibers begin to show a chemotaxis response to a PDGF gradient 10 times shallower than that required for chemotaxis response on a flat substrate. Furthermore, cells with spindle morphology maintain a robust and strong response over a broad range of chemoattractant concentration. These cells also had a 45% increase in speed and 26% increase in persistence over cells on flat polystyrene. The findings of this thesis suggest that 2D substrates may not be sufficient for studying physiologically relevant chemotaxis. / Master of Science

No / Paleoanthropological studies often center on teeth, not only because these elements are commonly preserved in the fossil record, but because they apparently contain a wealth of information with regard to development, phylogeny, and function. However, despite a plethora of studies, somefundamental problems are still unresolved. For example, while it is recognized that the 3-dimensional arrangement of enamel prisms may hold important information with regard to phylogeny (von Koenigswald and Sander, 1997) and function (Rensberger, 2000), many paleoanthropological studies have thus far relied on investigating enamel microanatomy as a 2-dimensional structure (e.g., Dean et al., 2001 C Dean, M.G Leakey, D Reid, F Schrenk, G.T Schwartz, C Stringer and A Walker, Growth processes in teeth distinguish modern humans from Homo erectus an earlier hominins, Nature 414 (2001), pp. 628¿631. Full Text via CrossRef | View Record in Scopus | Cited By in Scopus (120)Dean et al., 2001). This is mainly due to difficulties in visualizing and quantifying the 3-D structure of prisms. In order to overcome these limitations a computer model was developed (Jiang et al., 2003) which attempted to simulate the effects of biophysical processes governing enamel formation in modern humans (adapted from Osborn, 1970). Here we extend our model and present preliminary data on inter-specific variation in prism arrangement among primates. Furthermore, during our work torecreate the 3D microstructure of prismatic enamel it became increasingly clear that there are not only limitations with previous dental growth studies, but that these studies are based on fundamentally different concepts regarding evolutionary processes from those assumed in our approach. These limitations and differences will be highlighted also.

Bacteria in nature predominantly grow as biofilms on living and non-living surfaces. The development of biofilms on non-living surfaces is significantly affected by the surface micro/nano topography. The main goal of this dissertation is to study the interaction between microorganisms and nanopatterned surfaces. In order to engineer the surface with well-defined and repeatable nanoscale structures, a new, versatile and scalable nanofabrication method, termed Spun-Wrapped Aligned Nanofiber lithography (SWAN lithography) was developed. This technique enables high throughput fabrication of micro/nano-scale structures on planar and highly non-planar 3D objects with lateral feature size ranging from sub-50 nm to a few microns, which is difficult to achieve by any other method at present. This nanolithography technique was then utilized to fabricate nanostructured electrode surfaces to investigate the role of surface nanostructure size (i.e. 115 nm and 300 nm high) in current production of microbial fuel cells (MFCs). Through comparing the S. oneidensis attachment density and current density (normalized by surface area), we demonstrated the effect of the surface feature size which is independent of the effect on the surface area. In order to better understand the mechanism of microorganism adhesion on nanostructured surfaces, we developed a biophysical model that calculates the total energy of adhered cells as a function of nanostructure size and spacing. Using this model, we predict the attachment density trend for Candida albicans on nanofiber-textured surfaces. The model can be applied at the population level to design surface nanostructures that reduce cell attachment on medical catheters. The biophysical model was also utilized to study the motion of a single Candida albicans yeast cell and to identify the optimal attachment location on nanofiber coated surfaces, thus leading to a better understanding of the cell-substrate interaction upon attachment. / Ph. D. / Formation of surface associated multicellular communities of microorganisms known as biofilms is of concern in medical settings as well as in industries such as oil refineries and marine engineering. It has been shown that micro/nanoscale surface features can highly regulate the process of biofilm formation and the attached cell activities. In this dissertation, we study the interaction between surface nanoscale structures and bacterial adhesion by experiments and biophysical modelling. We develop the Spun-Wrapped Aligned Nanofiber (SWAN) lithography, a versatile, scalable, and high throughput technique for masterless nanopatterning of hard materials. Using this technique, we demonstrate high fidelity whole surface single step nanopatterning of bulk and thin film surfaces of regularly and irregularly shaped 3D objects. SWAN lithography is used to texturize the electrode surface of microbial fuel cells (MFCs), which are envisioned as an alternative sustainable energy source. Compared to the non-patterned electrodes, the electrodes with 115 nm surface patterns facilitate larger biofilm coverage and 40% higher current production. We also develop a biophysical model to optimally texturize the surface of central venous and uretic medical catheters to prevent biofilm formation by fungal pathogen, Candida albicans. We show that the surface structures that result the highest cell total energy retained the least C. albicans. Furthermore, the adhesion behaviour of a single yeast cell is also experimentally studied in conjunction with the developed model.

Structure determination of macromolecular protein assemblies remains a challenge for well-established experimental methods. In this thesis, an emerging structural technique, ion mobility-mass spectrometry (IM-MS) is explored. An assessment of collision cross section (CCS) measurement accuracy using travelling-wave IM (TWIMS) instrumentation was carried out (Chapter 3). Through the collation of a protein complex CCS database and the development of a calibration framework for TWIMS, significant improvements to CCS measurement accuracy have been achieved. Next, the advantages and limitations of using IM-MS to generate restraints for structure characterisation were explored. Computational tools designed to exploit IM-MS data for structural modelling were developed and tested on a training set of systems (Chapter 4). These include two heteromeric protein complexes, and an oligomeric intermediate involved in beta-2-microglobulin aggregation. Further structural information can be attained by using gas-phase dissociation techniques, such as collision-induced dissociation (CID). The effects of charge state on CCS and the gas-phase dissociation pathway of complexes were investigated (Chapter 5). This highlighted the possibility of using CID in conjunction with supercharging to manipulate dissociation pathways to achieve more useful structural information. Finally, the gas-phase structures of globular and intrinsically disordered protein complexes were probed by IM-MS and molecular dynamics (MD) simulations (Chapter 6). Experimental observations were recapitulated remarkably closely by simulations, including gas-phase structural collapse and the ejection of monomer subunits when the energy of the system was increased sufficiently. Overall, this research has contributed to the IM-MS field by providing the framework for improved CCS measurements of large protein complexes and the use of restraints from IM-MS for structural modelling. Significantly, IM-MS has been used in combination with charge manipulation, CID and MD simulations to reveal further insights into the gas-phase structures, stabilities and dissociation pathways of multimeric protein complexes.

Advances in genetics and fluorescent protein chemistry have enabled us to fuse fluorescent probes directly to biomolecules in stably growing organisms; making it easier to image the precise position and movement of cells in three dimensions. Fluorescent stains and dyes can be employed in a similar fashion to visualize nano-scale fluctuations in active cellular structures without fixation. While informative and exciting on a qualitatively level, microscopy truly becomes powerful when we can extract meaningful quantitative information. To accomplish this, custom MATLAB (Mathworks, Natick, MA) image analysis algorithms were developed to specifically measure the biophysical parameters related to pathogenesis and function in microbes and mammalian cells. These parameters can then be exploited in the development of biophysical models to validate current measurements, and make critical predictions about the system's behavior, often addressing quantities inaccessible by experimental methods. The following research chapters of this dissertation thoroughly describe how these techniques were developed and applied to study the biophysical mechanisms of bacterial and cellular invasion.

Investigating the structures of membrane proteins and their interactions with lipids remains challenging for well-established biophysical techniques. In this thesis the use of mass spectrometry (MS) and ion mobility (IM) spectrometry were explored for the interrogation of membrane proteins, their stoichiometry, stability and interactions with lipids. The techniques used were also applied to the identification of drug metabolites. In the first two chapters reviews of both mass spectrometry methods, and membrane protein biogenesis and membrane protein-lipid interactions are presented. The first challenge for studying membrane proteins by MS was to optimise solution conditions. A detergent screening strategy was developed for this purpose (Chapter 3). The various detergent environments studied revealed dramatic differences in mass spectral quality permitting investigation of membrane protein-lipid interactions. Changes were observed in the electrospray charging of membrane proteins and trends were established from an extensive collection of membrane proteins ejected from a wide variety of detergent environments. The physicochemical principles behind the MS of membrane proteins were deduced and are presented (Chapter 4). The results of these experiments led to a deeper understanding of the ionisation processes and the influence of detergent micelles on both charge state and release mechanisms. Experiments from a range of different micelles also allowed the influence of charge and its effects on the preservation of native-like membrane protein conformations to be monitored by IM-MS. By resolving lipid-protein interactions, and by monitoring the effects of lipid binding on the unfolding of three diverse membrane protein complexes, substantial differences in the selectivity of membrane proteins for different lipids were revealed (Chapter 5). Interestingly lipids that stabilised membrane proteins in the gas-phase were found to induce modifications in structure or function thus providing an approach to assess direct lipid contributions, and to rank order lipids based on their ability to modulate membrane proteins. Using the MS approaches developed here also enabled study of the diversity of oligomeric states of the mechanosensitive channel of large conductance (MscL) (Chapter 6). Results revealed that the oligomeric state of MscL is sensitive to deletions in its C-terminal domain and to its detergent-lipid environment. Additionally, a case study with GlakoSmithKline (GSK) was undertaken using IM-MS technology but in this case applied to the identification of drug metabolites (Chapter 7). The results showed that IM-MS and molecular modelling could inform on the identity of different drug metabolites and highlights the potential of this approach in understanding the structure of various drug metabolites.