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Organisms usually respond to environmental changes by adapting the expression of genes necessary for survival. However, such transcriptional reprogramming requires time and energy, and may also leave the organism ill-adapted when the original environment returns. During my PhD, I studied the dynamics of transcriptional reprogramming and fitness in the model eukaryote Saccharomyces cerevisiae in response to changing carbon environments. In one study, using population and single-cell analyses I found that some wild yeast strains rapidly and uniformly adapt gene expression and growth to changing carbon sources, whereas other strains respond more slowly, resulting in long periods of slow growth (the so-called lag phase) and large differences between individual cells within the population.I exploited this clonal heterogeneity to evolve a set of mutants that demonstrate how the frequency and duration of changes in carbon source can favor the growth of mutants displaying a spectrum of different carbon catabolite repression strategies. At one end of this spectrum are several specialist isolates that display high rates of growth in stable environments, with more stringent catabolite repression and slower transcriptional reprogramming. The other mutants are of a generalist character, displaying slower growth in stable environments, however noisier catabolite repression that allows faster transcriptional reprogramming and shorter lag phases. Whole-genome sequencing of these mutants reveals that mutations in key regulatory genes such as HXK2 and STD1 adjust the regulation and transcriptional noise of metabolic genes, with some mutations leading to alternative gene regulatory strategies that allow stochastic sensing of the environment. Mathematical modeling and experimentation reveals patterns of environmental change that will favor the generalist or specialist phenotypes, as well as regimes of change that will favor a stable co-existence between the two phenotypes.Together, the work presented in this thesis reveals a surprising degree of diversity in the lag phase, within clonal populations and across different yeast isolates. These results further reveal how variable and stable environments favor distinct strategies of transcriptional reprogramming and growth. Future studies will continue to examine the molecular and genetic mechanisms of growth and gene regulation in variable environments.

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Arsenic contamination of groundwater in several parts of the world is the result of natural and/or anthropogenic sources that have a large impact on human health. Millions of people from different countries rely on groundwater containing elevated concentrations of As for drinking purposes. Several removal technologies (oxidation, coagulation flocculation, adsorption, ion exchange and membrane processes) have been applied for the treatment of As rich water. These suggested and applied technologies for the treatment of As contaminated water have various shortcomings, including the need for further treatment of As containing secondary waste, generated from these water treatment processes. In this thesis, forward osmosis (FO) is investigated as a more efficient technique in comparison with pressure driven membrane processes. FO membranes have not been used extensively for As removal from aqueous solutions. Additionally, a chemical reduction of the soluble aqueous As to commercially valuable metallic As is explored. As a result, an integrated approach of two or more techniques is suggested to be more beneficial than a single process. Therefore, membrane processes combined with other processes (especially iron based technologies) are thought to be most sustainable for the removal of arsenic and are investigated in this thesis. At first, the rejection of arsenic by a forward osmosis (FO) membrane, and the effects of relevant physico-chemical factors on the separation have been systematically investigated. MgSO4 and glucose solutions were used as two potential draw solutions for this purpose. More than 98% rejection was observed when the initial As (V) concentration was 500 μg L-1, yielding an As concentration in the permeate below the maximum contamination level (MCL). It was demonstrated that the rejection of As was higher when the membrane active layer faces the feed solution (AL-FS) compared to the rejection when the membrane active layer faces the draw solution (AL-DS). However, for As (III), it was observed that the rejection was low at lower pH (3-12.6% pH 3-7). Therefore, a pretreatment step seems to be obvious to obtain potable water and a simple chemical oxidation technique was applied. After oxidation of As (III), at neutral pH, the rejection increased to 95.7%. Thus, oxidation before FO is suggested as an essential pretreatment for total As removal in the neutral pH range. Secondly, the rejection behavior of As (V) with FO was studied in the presence of several co-existing solutes (nitrate, fluoride, sulfate, phosphate, silicate, bicarbonate and humic acid). Since these solutes are often found in groundwater, the effect of these solutes on As removal was studied. It was observed that silicate shows no significant effect whereas phosphate lowers the As (V) rejection substantially (from 95.5 to 80.5%). The rejection of As (V) in the presence of co-existing solutes follows the sequence humic acid > bicarbonate > nitrate > fluoride > sulfate > phosphate. Additionally, the combined effect of complex formation of arsenic with humic acid and the loose fouling layer helps to enhance the removal efficiency. The increase in pH due to the presence of bicarbonate also helps to increase the rejection. Thus, forward osmosis allowed removing arsenic from water containing various coexisting and competing solutes. Furthermore, a comparison was made with conventional RO membranes. Since previous reports have suggested that RO membranes can remove As below the MCL, it was important to study the removal efficiency of RO. It was observed that some RO membranes can indeed remove As concentration below the MCL. A comparative study was also performed with the FO membrane in an RO module to obtain clear insights. The results suggest that in an FO module the As rejection is higher than in an RO module when the feed water contains a high concentration of As. Finally, the interaction of As (V) with zero valent iron (ZVI) in water was studied under oxic and anoxic conditions. The purpose of this study was to understand the reaction mechanism between As (V) and ZVI and to find a treatment method for As in concentrates with special emphasis to the formation of metallic As. X-ray diffraction and X-ray photoelectron spectroscopic analysis of the ZVI confirmed the core shelled Fe0 structure with an outer coating of iron oxide/hydroxide. From the batch experiment it was clear that the rate of removal of As (V) was very fast for oxic conditions compared to anoxic conditions. While reduction of adsorbed As (V) to As (III) and As (0) was demonstrated by the XPS analysis in anoxic condition, no reduction was observed in oxic condition. Electrons, Fe2+(s) and H(s) formed from Fe0 oxidation were thought to be the reducing agents for such reduction process. Therefore, it was concluded that the inherent oxide/hydroxide layer on the ZVI surface plays an important role and favors the reduction of As (V) indirectly. Thus, the possible mechanism of As (V) reduction in the ZVI-H2O system with formation of As (0) is suggested, which is important in view of arsenic immobilization and avoid secondary As contamination.

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