<p>The goal of this work was to contribute to the fed-batch process optimisation task by deriving parameters that have considerable impact on productivity as well as product quality The chosen parameters were I) the design of the glucose feed profile, II) the choice of induction strategy, with respect to the method of addition, and III) the time of the induction, with respect to the specific glucose consumption rate. </p><p>The present fed-batch experiments using the lacUV5-promoter, for production of b-galactosidase, have shown that a high glucose feed rate gives a specific production rate, q_p, that is twice as high, after induction, compared to a feed rate that is 2.5 times lower. The constant accumulation of lacZ-mRNA indicates that the translational capacity is initially limiting the synthesis machinery, but after four hours of maximum specific production and a corresponding drop in lacZ-mRNA production, the cultivation is likely to be transcription limited. The high feed-rate system resulted in high accumulation of β-galactosidase, corresponding to 40% of total cellular proteins.</p><p>By design of feed profiles in a fed-batch process the detrimental effects of overflow metabolism, giving acetic acid formation, can be avoided. However, the results show that a one-dose addition of isopropyl-β-D-galactopyranoside (IPTG), provokes a non-growth associated production of acetic acid. This response can be alleviated by; lowering the inducer concentration (in this case to below 165 μM), by further reducing the feed rate of glucose or by using alternative induction methods. The use of a stepwise addition or a feed of IPTG thus delayed and reduced the level of acetic acid accumulation. It was also shown that a small change in the time-point of induction lead to large variability, regarding both productivity and acetic acid accumulation, in a fed-batch cultivation, </p><p>In order to further investigate the protein quality two additional proteins were studied in fed-batch cultivations using high and low glucose feed. The aim was to prove the hypothesis that the feed related change in the rate of synthesis of the nascent polypeptide controls the product quality. For the two proteins: Zb-MalE (wt) and Zb-MalE31 (mutant), the transcription rate, in terms of amount of IPTG, and translation rate, in terms of changes in feed rate, influences the percentage of inclusion body formation and degradation of nascent polypeptide. The data show a higher rate of inclusion body formation for the model protein Zb-MalE31 during high feed rate cultivations, as well as at high levels of inducer. Furthermore, the rate of proteolysis was significantly higher for a high feed rate. The high feed rate thus results in a higher rate of synthesis but a lower corresponding quality, for the model proteins studied.</p><p>In the present investigation of fed-batch cultivations using several different expression vectors, it was found that the central alarmone guanosine tetraphosphate (ppGpp) was formed at both high and low feed rates upon induction. It could be shown, however, that by secretion of Zb-MalE to the periplasm, the stringent response could be avoided. This might be due to the decreased burden on the host where the secretion of product further seems to make the cell able to redirect the carbon flux from overflow metabolism, since no acetic acid was produced. The secretion also demonstrates that the growth arrest could be aborted, which is otherwise gained in the P_malKproduction system.</p><p>A novel fed-batch process based on the promoters for the universal stress proteins A and B (P_uspA, P_uspB) was designed to make use of these powerful promoters in an industrial production context. It was concluded that the process had to start from a high specific growth rate and induction was performed once a limiting feed started. This was done to purposely induce the stringent response and/or acetic acid accumulation since this was required for induction. In the suggested system, induction has to be performed and maintained at continuous substrate feeding, whilst avoiding exceeding the cellular capacity, since the stationary phase starvation alone did not lead to production. In conclusion, a new stress induction based production system was achieved resulting in high accumulations of product protein without any detected metabolic side effects.</p>

Titanium (Ti) alloys have been commonly used in the aerospace industry, not only because they have a high strength-to-weight ratio (comparing to the steels) but also their satisfactory corrosion resistance. Furthermore, they can be assembled with the carbon fibre composite parts. However, conventional manufacturing methods cause high material scrap rate and require lots of machining to obtain the final shape and size, which increases both the manufacturing time and cost. In order to improve the efficiency and reduce the cost of Ti parts, Additive Manufacturing (AM) has been developed. Rolled Wire and Arc Additive Manufacturing (rolled WAAM) is one of the AM processes. The main characteristics of this technology is the reduced β grain size to refine the alloy's microstructure. Both the ultimate tensile strength and yield strength of Ti alloy made by rolled WAAM are at least 10% higher than traditional wrought Ti. This project is to investigate the fatigue crack growth rates of the Ti-6Al-4V built by rolled WAAM process in both the longitudinal and transverse orientations to study the effect of rolling on fatigue crack growth rate of WAAM processed Ti. The project was carried out by testing the fatigue crack growth rates for 4 compact tension specimens. The test results of different orientations were compared with each other, and scatters in fatigue life and fatigue crack growth rate were found. Fatigue crack growth rate is lower in the longitudinal specimens. The results are also compared with those of the unrolled WAAM specimens tested in a previous project. It was found that rolling can significantly improve the fatigue crack growth behaviour in WAAM processed Ti, and can reduce the difference between the two orientations, i.e. achieving better isotropic material properties. Recorded scatters may be caused by the process induced residual stresses, error in measurement, and the test machine load range being much higher than the applied loads. More specimens can be tested to validate above observations further.

The goal of wind-waves research is to predict the waves field and its effect on the environment. That environment could be natural or imposed by human endeavour. The mechanism of wind generated waves is described in the present work as a wind-bulk flow interaction rather than as a mechanical process which only transfers the wind energy to the wave. In the light of this description, the generation and growth of surface waves are functions of the physical properties of the interface, density of the bulk flow perturbations and wind shear stress. While the present models for the prediction of surface growth and evolution show some consistence - in some cases - with observations that were conducted in laboratories and in real fields, the work presented in this thesis justifies and explains the inconsistency or contradictions in other cases between the observations and the predictions. Also, physical interpretations for observations, for example wave growth with fetch, are suggested in the present work. To illustrate the physical mechanism responsible for wave generation and growth under the effect of wind action, two approaches are used. The first involves studying the effect of the physical properties of the water surface on atmospheric input into the bulk and thus the effect on the formation and growth of capillary waves. The second involves studying the correlation between the wave formation and growth and the density of the bulk perturbations. Wide ranges of previous data are used to analyse the effect of the physical properties of the water surface on wave generation and growth mechanism for the first approach. Also, a group of experiments using the PIV system (Particle Image Velocimetry) were conducted to study the correlation between the wind speed, bulk flow evolution and wind-waves‟ generation and growth for the second approach. The main physical parameters which are responsible for the generation and growth of capillary waves are determined. The Ohnesorge number is modified to predict the generation and growth of surface waves. In the second part, additional physical parameters of the bulk flow are introduced to illustrate the correlation between the wind generated waves and bulk flow evolution. A new parameter is used to scale the transition of the bulk flow from laminar flow to turbulent flow or the transition of the water surface from an undisturbed surface to a fully disturbed surface. The history of wind-wave research is relatively short. Although there were basic developments in the 18th century, a concentrated effort really began as a result of the military imperative of the Second World War. These developments were however, largely empirical. A theoretical frame work began to develop with the studies of wind-wave generation in the last century. The present work is conducted to fill some gaps in wind generated surface waves research and to introduce new approaches to simplify understanding wind-waves field and its effect on the environment.

<p>Recent technological advances enable us to examine bacterial population dynamics with high temporal resolution with capacity for collecting high throughput data. Precise quantification of bacterial population dynamics can help us to further extend our understanding of how bacteria respond to environmental conditions. Such analysis provides critical information for improving antibiotic treatment protocols and for predictable engineering cellular behavior with synthetic gene circuits. </p><p>A fundamental question in bacterial population dynamics is how fast bacteria are killed in response to antibiotics. Due to their mode of action, β-lactams are more effective against fast-growing bacteria than against slow-growing bacteria. Indeed, it has been recognized that the rate of lysis by β-lactam antibiotics depends on the growth rate of the bacteria, based on previous works. However, past studies examined the growth rate modulation of lysis only during balanced growth and for very limited combinations of bacteria and drugs. Although there is evidence that growth plays key role in determining bacterial response to antibiotics, more comprehensive understanding on how wide range of growth rates affect antibiotic dose response had been overlooked. Instead, bacterial growth has been largely described to be in either growing or non-growing states. </p><p>To examine the general applicability of this growth rate dependence of antibiotic response, I examined how growth rate influences the lysis rate induced by beta-lactams. I found that there is a robust correlation between growth and lysis rates beyond what had been demonstrated in the previous work. Even during unbalanced growth, and regardless of how growth rate was modulated, the robust correlation between growth and lysis rates in bacterial populations were observed. Also, my data suggested a striking versatility of this correlation in different bacterial specie-drug pairs. Thus, my quantification greatly expands previous work by further examining the dependence of lysis rate on growth rate, and extends our understanding of the phenomenon associated with β-lactam antibiotic treatment, and of possible consequences arising from variable lysis rate. My strategy on modulating growth rates and measuring corresponding lysis rates demonstrates a simple and robust method for examining this phenomenon. These results have direct implications in two aspects.</p><p> First, my quantification method allows greater degree of freedom in modulating growth states of bacteria. Indeed, I was able to examine a wide range of growth rates in bacteria that allowed analyses of robust correlation in growth and lysis rates. The simple correlation reported from my work suggests the underlying reasoning for slow or fast lysis of bacterial population that can lead to designing optimal protocols depending on the growth rates of bacterial population. Due to frequent observation of slow-growing cells under conditions such as biofilm of pathogenic bacteria that complicates clinical symptoms and treatments in patients, they have been an important aspect of study for antibiotic tolerance. A quantitative understanding of the robust correlation between growth and lysis rates is critical for designing effective treatment protocols using β-lactams. </p><p> Second, the robust correlation serves as a foundation for predicting dynamics of synthetic gene circuits engineered for practical applications. In my work, I developed a prototype microbial swarmbot, which employs spatial arrangement to control growth dynamics of engineered bacteria. I demonstrated an engineered safeguard strategy to prevent unintended bacterial proliferation with this platform technology. In this work, I adopted several synthetic gene circuits to program collective survival in Escherichia coli: the engineered bacteria could only survive when present at sufficiently high population densities. When encapsulated by permeable membranes, these bacteria can sense the local environment and respond accordingly. The cells inside microbial swarmbots will survive due to their high densities. Those escaping from a capsule, however, will be killed due to a decrease in their densities. In this work, using antibiotics to control growth dynamics of the engineered populations was critical, and optimization of the growth dynamics depended on their environmental conditions that modulated their growth rates.</p><p>Together, my investigation on quantifying and analyzing bacterial growth dynamics demonstrated that understanding of bacterial population dynamics is crucial in addressing antibiotic tolerance in bacteria as well as in using them for engineered functions. By further examining the dependence of lysis rate on growth rate, we extended our understanding of the phenomenon associated with β-lactam antibiotic treatment, and of possible consequences arising from variable lysis rate. This information is important in designing a modular and readily generalizable platform technology as well. Therefore, my work demonstrates quantitative approach towards understanding of bacterial populations, and lays the foundation for engineering integrated and programmable control of hybrid biological-material systems for diverse applications.</p> / Dissertation

The mechanisms that control growth processes in biology tissues have attracted continuous research interest despite their complexity. With the emergence of big data experimental approaches there is an urgent need to develop statistical and computational models to fit the experimental data and that can be used to make predictions to guide future research. In this work we apply statistical methods on growth process of different biological tissues, focusing on development of neuron dendrites and tumor cells. We first examine the neuron cell growth process, which has implications in neural tissue regenerations, by using a computational model with uniform branching probability and a maximum overall length constraint. One crucial outcome is that we can relate the parameter fits from our model to real data from our experimental collaborators, in order to examine the usefulness of our model under different biological conditions. Our methods can now directly compare branching probabilities of different experimental conditions and provide confidence intervals for these population-level measures. In addition, we have obtained analytical results that show that the underlying probability distribution for this process follows a geometrical progression increase at nearby distances and an approximately geometrical series decrease for far away regions, which can be used to estimate the spatial location of the maximum of the probability distribution. This result is important, since we would expect maximum number of dendrites in this region; this estimate is related to the probability of success for finding a neural target at that distance during a blind search. We then examined tumor growth processes which have similar evolutional evolution in the sense that they have an initial rapid growth that eventually becomes limited by the resource constraint. For the tumor cells evolution, we found an exponential growth model best describes the experimental data, based on the accuracy and robustness of models. Furthermore, we incorporated this growth rate model into logistic regression models that predict the growth rate of each patient with biomarkers; this formulation can be very useful for clinical trials. Overall, this study aimed to assess the molecular and clinic pathological determinants of breast cancer (BC) growth rate in vivo.

Few studies have described growth rates of age-0 Atlantic menhaden (Brevoortia tyrannus). Growth rates from tidal freshwater habitats of the Mattaponi and James Rivers, Virginia in 2009 were described and compared using otolith microstructural analyses. Larval tidal freshwater growth rates were significantly faster in the culturally eutrophic James River when compared to those collected from the Mattaponi River (p-value < 0.001). Elevated primary production within tidal freshwater habitats promotes favorable conditions for larval Atlantic menhaden growth. No differences between river habitats for juvenile growth rates were evident. Comparisons of age-0 growth rates to higher salinity habitats indicate that tidal freshwater habitats should be considered essential habitat for age-0 Atlantic menhaden.

The whale shark (Rhincodon typus) has a global distribution in warm to warm temperate oceans, and is a species of high conservation concern currently categorized as Endangered on the International Union for Conservation of Nature (IUCN) Red List. Despite its dire conservation status and concerns about the growing number of ecotourism interactions with this species worldwide, relatively little information is available on key aspects of whale shark biology such as growth rates, reproductive rates, survival rates and breeding habitats. In particular, critical information such as age and growth of whale sharks is needed to improve the management and conservation of this species. Robust knowledge of life history parameters is needed to improve demographic models for whale sharks and enable better evaluation of their vulnerability to fishing pressures and recovery from population declines. Whale sharks are well known to form aggregations in specific locations, with one such site being the South Ari Atoll in the Maldives. My study aimed to expand knowledge of the population dynamics, including age and growth, of whale sharks at the South Ari Atoll by calculating growth parameters and rates from encounters with free-swimming sharks over a decade (April 2006 to May 2016). A total of 1545 encounters with 125 individual sharks were recorded during this time period. To obtain the most accurate information on the sizes of whale sharks, total lengths were estimated by three different measurement methods (visual, laser photogrammetry, and tape), and linear regression was utilized to investigate how these different methods compared to one another. The results showed that visual estimates tended to underestimate sizes of the larger sharks, and laser and tape measurements yielded similar results to one another (R2 = 0.824). New sharks observed at the South Ari Atoll during the study period were significantly smaller than returning sharks, suggesting that young sharks may be recruited to the South Ari Atoll, where they stay and grow until reaching maturity before leaving the area. To the best of my knowledge, my study is the first to infer growth parameters and rates from measurements of free-swimming whale sharks. Estimates of von Bertalanffy growth parameters for combined sexes, calculated from 180 encounters with 44 individual sharks (Males (n=40), Females (n=4), TL=3.16 m – 8.00 m), yielded an L¥ of 19.56 and a k value of 0.021. Analyzing 177 encounters with 40 male sharks (TL=3.16 m - 8.00 m) exclusively provided an L¥ of 18.08 and a k value of 0.023. These values correspond to a male age at maturity of ~25 years and a longevity of ~140 years, exceeding those estimated for whale sharks captured off Taiwan based on analysis of biannual vertebral rings (male maturity =17 years; longevity (combined sexes) = 80.4 years). There have been few growth studies, mainly from vertebral analysis, that have produced wide ranges in L¥ (14 – 20.5) and k values (0.017 – 0.037). These differences underscore the need for additional regional studies to obtain population specific estimates of these key life history parameters.

Seabirds commonly nest colonially on cliffs or inaccessible islands, so that oceanic effects on the quality or quantity of prey fed to chicks more often determine nest success than does terrestrial predation. However, when predators can access nests, impacts can be dramatic. In Kittlitz’s murrelet (KIMU), a rare and recently declining seabird, nests are widely dispersed in poorly accessible areas, growth rates are exceptionally high, and nestling periods are very short. This unique strategy may offset the vulnerability of their ground nests to predators but demands adequate deliveries of high-energy prey. We investigated whether variations in energy content of prey fed to chicks could alter growth rates and resulting duration of exposure to predators, and whether extending predator exposure had important effects on nest success. From 2009‒2016, we measured fish length with cameras, modeled prey energy content from chick energy needs, and measured chick growth rate and nest survival. We monitored an average 17 nests/year (139 total), of which 49% were depredated (almost all by red fox) and 25% survived to fledging. Prey were mainly Pacific sand lance (80%) and capelin (19%), with capelin having 2.3× higher energy per unit length. In a year of slow growth, sand lance energy density needed to increase by 31% from 4.29 to 5.64 kJ/g (within published values), or the proportion of capelin in the diet needed to increase from 5.6% to 27.2%, to achieve maximum chick growth. Adults could supply the energy required for maximum growth by delivering only 1.9 capelin/day versus 5.5 sand lance. Slow growth increased time to fledging by 5 days. This extended exposure to predation could decrease overall nest survival from 14.2% to 13.1%, a relative decrease of 7.7%. With reported breeding propensity of KIMU averaging only 20% and sometimes much lower (range 5 to 45%), even small effects on nest success may be consequential. Although direct predation was the main limitation to nest success, effects of ocean conditions on prey quantity and quality can have overriding effects in some years, and apparently small but substantive indirect effects in other years by mediating exposure to predation. Continued climate warming that adversely affects availability of high-energy fish and allows range expansion of terrestrial predators may have disproportionate effects on species such as KIMU with accessible nests and demands for energy-rich prey.

De acordo com León-Ledesma and Thirlwall (2002), o presente trabalho se propõe a testar a endogeneidade da taxa natural de crescimento para um conjunto amplo de países, no sentido do crescimento de longo prazo ser determinado pela demanda. Econometricamente, a principal hipótese a ser testada é a presença de não linearidade na Lei de Okun, que implica na existência de duas taxas naturais, cada uma correspondendo a um regime de crescimento. Utilizando dados anuais para o período de 1980 a 2007 e dados trimestrais para o intervalo entre 1980 e 2011, os resultados corroboram a hipótese de endogeneidade quando aplicada a metodologia proposta por LLT. Esta evidência se repete ao definir exogenamente os regimes de crescimento pelos métodos de Markov-Switching e threshold autoregressive regression (TAR) para os dados anuais, no entanto, para os dados trimestrais há indicações de endogeneidade e exogeneidade da taxa natural de crescimento. / Following León-Ledesma and Thirlwall (2002), this master\'s thesis aims to examine the sensitivity of the natural growth rate to the actual growth rate for a broad set of countries, based on demand-led growth theory. The main hypothesis being tested is the presence of non-linearities in Okun\'s Law, which means the existence of two natural growth rates, each corresponding to a growth regime. Using annual data over the period 1980-2007 and quarterly data over the period 1980-2011, the results support the idea that natural growth rate is dependent of the actual growth rate when applying LLT\'s methodology. This evidence repeats when establishing exogenously the regimes of growth by using Markov-Switching and threshold autoregressive regression (TAR) for the annual data, however for quarterly data this is less straightforward, having indication of endogenous and exogenous natural growth rate.

Objetivou-seanalisar o crescimento de Anacardium occidentaleL.(Anacardiaceae), Dipteryx alataVogeleParkia platycephalaBenth (Fabaceae), introduzidas em uma área de Cerrado sentido restritoemPorto Nacional, Tocantins. Foram analisados 30 indivíduos de A. occidentale, 16 de D. alatae 34 de P. platycephala, com análises realizadas nos anos de 2006, 2010 e 2016. Foram avaliadas a altura das plantas e o diâmetro dos caules. Esses dados também foram utilizados para o cálculo das taxas de crescimento relativo em altura e em diâmetro. P. platycephala exibiu os maiores incrementos em altura e diâmetro, como também as maiorestaxas de crescimento relativo, mostrando-se a espécie melhor adaptada às condições ambientais da área. A. occidentale e D. alataapresentaram crescimento em altura e diâmetro bem como taxas de crescimento relativo menores, o que dificultou a adaptação dosindivíduos ao ambiente onde foram introduzidos. / Aimed at analyzing the growth of Anacardium occidentaleL.(Anacardiaceae), Dipteryx alataVogel andParkia platycephala Benth (Fabaceae), introduced in a Cerrado stricto sensu area in Porto Nacional, Tocantins. Thirty individuals of A. occidentale, 16 of D. alataand 34 of P. platycephalawere evaluated according to data collected in 2006, 2010 and 2016. Plant height and stem diameter were assessed. These data were also used to determine the relative growth rates of stem height and diameter. P.platycephalaexhibited the greatest increments in height and stem diameter as well as the largest increases in relative growth rates, turning out to be the species that best adapted to the environmental conditions of the area. A. occidentale and D. alata presented lower increments in terms of height, stem diameter and relative growth rates, which hindered the adaptation of individuals to the environment where they were introduced.