The Role of Recharge and Evapotranspiration as Hydraulic Drivers of Ion Concentrations in Shallow Groundwater on Everglades Tree Islands, Florida (USA)

Recently, evapotranspiration has been hypothesized to promote the secondary formation of calcium carbonate year-round on tree islands in the Everglades by influencing groundwater ions concentrations. However, the role of recharge and evapotranspiration as drivers of shallow groundwater ion accumulation has not been investigated. The goal of this study is to develop a hydrologic model that predicts the chloride concentrations of shallow tree island groundwater and to determine the influence of overlying biomass and underlying geologic material on these concentrations. Groundwater and surface water levels and chloride concentrations were monitored on eight constructed tree islands at the Loxahatchee Impoundment Landscape Assessment (LILA) from 2007 to 2010. The tree islands at LILA were constructed predominately of peat, or of peat and limestone, and were planted with saplings of native tree species in 2006 and 2007. The model predicted low shallow groundwater chloride concentrations when inputs of regional groundwater and evapotranspiration-to-recharge rates were elevated, while low evapotranspiration-to-recharge rates resulted in a substantial increase of the chloride concentrations of the shallow groundwater. Modeling results indicated that evapotranspiration typically exceeded recharge on the older tree islands and those with a limestone lithology, which resulted in greater inputs of regional groundwater. A sensitivity analysis indicated the shallow groundwater chloride concentrations were most sensitive to alterations in specific yield during the wet season and hydraulic conductivity in the dry season. In conclusion, the inputs of rainfall, underlying hydrologic properties of tree islands sediments and forest structure may explain the variation in ion concentration seen across Everglades tree islands.

The sources of Luke's passion-narrative /

Published also as thesis, University of Chicago.

Determinação seletiva de tributilestanho na presença de Sn(IV) em amostras ambientais usando HG-ICP OES e Saccharomyces cerevisiae como material sorvente

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Sources of hydrochemical variability and implications associated with CSG water extraction

Coal Seam Gas (CSG) production is achieved by extracting groundwater to depressurize coal seam aquifers in order to promote methane gas desorption from coal micropores. CSG waters are characteristically alkaline, have a neutral pH (~7), are of the Na-HCO3-Cl type, and exhibit brackish salinity. In 2004, a CSG exploration company carried out a gas flow test in an exploration well located in Maramarua (Waikato Region, New Zealand). This resulted in 33 water samples exhibiting noteworthy chemical variations induced by pumping. This research identifies the main causes of hydrochemical variations in CSG water, makes recommendations to manage this effect, and discusses potential environmental implications. Hydrochemical variations were studied using Factor Analysis and this was supported with hydrochemical modelling and a laboratory experiment. This reveals carbon dioxide (CO2) degassing as the principal source of hydrochemical variability (about 33%). Factor Analysis also shows that major ion variations could also reflect changes in hydrochemical composition induced by different pumping regimes. Subsequent chloride, calcium, and TDS variations could be a consequence of analytical errors potentially committed during laboratory determinations. CSG water chemical variations due to degassing during pumping can be minimized with good completion and production techniques; variations due to sample degassing can be controlled by taking precautions during sampling, transit, storage and analysis. In addition, the degassing effect observed in CSG waters can lead to an underestimation of their potential environmental effect. Calcium precipitation due to exposure to normal atmospheric pressure results in a 23% increase in SAR values from Maramarua CSG water samples.

Competition between polyphosphate and glycogen accumulating organisms in enhanced biological phosphorus removal systems with acetate and propionate as carbon sources

Enhanced biological phosphorus removal (EBPR) is a widely used process for achieving phosphorus removal from wastewater. A potential reason for EBPR failure is the undesirable growth of glycogen accumulating organisms (GAOs), which can compete for carbon sources with the bacterial group responsible for phosphorus removal from wastewater: the polyphosphate accumulating organisms (PAOs). This study investigates the impact of carbon source on EBPR performance and the competition between PAOs and GAOs. Two sequencing batch reactors (SBRs) were operated during a 4-6 month period and fed with a media containing acetate or propionate, respectively, as the sole carbon source. It was found that the acetate fed SBR rarely achieved a high level of phosphorus removal, and that a large portion of the microbial community was comprised of Candidatus Competibacter phosphatis, a known GAO. The propionate fed SBR, however, achieved stable phosphorus removal throughout the study, apart from one brief disturbance. The bacterial community of the propionate fed SBR was dominated by Candidatus Accumulibacter phosphatis, a known PAO, and did not contain Competibacter In a separate experiment, another SBR was seeded with a mixture of PAOs and a group of alphaproteobacterial GAOs, both enriched with propionate as the sole carbon source. Stable EBPR was achieved and the PAO population increased while the GAOs appeared to be out-competed. The results of this paper suggest that propionate may provide PAOs with a selective advantage over GAOs in the PAO-GAO competition, particularly through the minimisation of Competibacter Propionate may be a more suitable substrate than acetate for enhancing phosphorus removal in EBPR systems. (c) 2005 Elsevier B.V. All rights reserved.

Development of Microfluidic Devices with the Use of Nanotechnology to Aid in the Analysis of Biological Systems Including Membrane Protein Separation, Single Cell Analysis, and Genetic Markers

Computation technology has dramatically changed the world around us; you can hardly find an area where cell phones have not saturated the market, yet there is a significant lack of breakthroughs in the development to integrate the computer with biological environments. This is largely the result of the incompatibility of the materials used in both environments; biological environments and experiments tend to need aqueous environments. To help aid in these development chemists, engineers, physicists and biologists have begun to develop microfluidics to help bridge this divide. Unfortunately, the microfluidic devices required large external support equipment to run the device. This thesis presents a series of several microfluidic methods that can help integrate engineering and biology by exploiting nanotechnology to help push the field of microfluidics back to its intended purpose, small integrated biological and electrical devices. I demonstrate this goal by developing different methods and devices to (1) separate membrane bound proteins with the use of microfluidics, (2) use optical technology to make fiber optic cables into protein sensors, (3) generate new fluidic devices using semiconductor material to manipulate single cells, and (4) develop a new genetic microfluidic based diagnostic assay that works with current PCR methodology to provide faster and cheaper results. All of these methods and systems can be used as components to build a self-contained biomedical device.

Astringency and other oral sensations : biological sources of individual variation and association with food and beverage behaviour

Orosensory perception strongly influences liking and consumption of foods and beverages. This thesis examines the influence of biological sources of individual variation on the perception of prototypical orosensory stimuli, food liking, self-reported alcohol liking and consumption, and indices of health. Two orosensory indices were examined: propylthiouracil (PROP) responsiveness, a genetically-mediated index of individual variation associated with enhanced responsiveness to orosensory stimuli often expressed as PROP taster status (PTS); and thermal taster status (TTS), a recently reported index of orosensory responsiveness. Taster status in PTS and/or TTS confers greater responsiveness to most orosensory stimuli. Gender, age, ethnicity, and fungiform papillae (FP) density were not associated with orosensory responsiveness to tastants, an astringent, and a flavour. Unlike PROP responsiveness, FP density was not associated with TTS. Both PROP responsiveness and TTS were associated with increased responsiveness to orosensory stimuli, including temperature and astringency. For PROP, this association did not hold when stimuli were presented at cold or warm temperatures, which are ecologically valid since most foods and beverages are not consumed at ambient temperature. Thermal tasters (TTs), who perceive 'phantom' taste sensations with lingual thermal stimulation, were more responsive to stimuli at both temperatures than thermal non-tasters (TnTs). While PTS, TIS, and gender affected self-reported liking and consumption of some alcoholic beverages, gender associated with the greatest number of beverage types and consumption parameters, with males generally liking and consuming alcoholic beverages more than females. Age and gender were the best predictors of alcoholic beverageAiking and consumption. As expected, .. liking of bitter and fatty foods and cream was inversely related to PROP responsiveness. TTS did not associate with body mass index or waist circumference, and contrary to previous studies, neither did PROP responsiveness. Taken together, TnTs' greater liking of cooked fruits and vegetables and high alcohol, and astringent alcoholic beverages than TTs suggests differences between TTS groups may be driven by perceived temperature and texture. Neither an interaction between PTS and TTS nor a TTS effect on PROP responsiveness was observed, suggesting these two indices of individual variation exert their influences on orosensory perception independently.

Structure-activity relationship of mastoparan analogs: effects of the number and positioning of Lys residues on secondary structure, interaction with membrane-mimetic systems and biological activity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Econometric analysis of stuctural systems with permanent and transitory shocks

This paper considers the implications of the permanent/transitory decomposition of shocks for identification of structural models in the general case where the model might contain more than one permanent structural shock. It provides a simple and intuitive generalization of the influential work of Blanchard and Quah [1989. The dynamic effects of aggregate demand and supply disturbances. The American Economic Review 79, 655–673], and shows that structural equations with known permanent shocks cannot contain error correction terms, thereby freeing up the latter to be used as instruments in estimating their parameters. The approach is illustrated by a re-examination of the identification schemes used by Wickens and Motto [2001. Estimating shocks and impulse response functions. Journal of Applied Econometrics 16, 371–387], Shapiro and Watson [1988. Sources of business cycle fluctuations. NBER Macroeconomics Annual 3, 111–148], King et al. [1991. Stochastic trends and economic fluctuations. American Economic Review 81, 819–840], Gali [1992. How well does the ISLM model fit postwar US data? Quarterly Journal of Economics 107, 709–735; 1999. Technology, employment, and the business cycle: Do technology shocks explain aggregate fluctuations? American Economic Review 89, 249–271] and Fisher [2006. The dynamic effects of neutral and investment-specific technology shocks. Journal of Political Economy 114, 413–451].

Emerging water treatment technologies for decentralised systems : an overview of selected systems suited for application in towns and settlements in remote and very remote regions of Australia and vulnerable and lagging rural regions in Sri Lanka

The primary purpose of this paper is to overview a selection of advanced water treatment technology systems that are suited for application in towns and settlements in remote and very remote regions of Australia and vulnerable and lagging rural regions in Sri Lanka. This recognises that sanitation and water treatment are inextricably linked and both are needed to reduce risks to environment and population health from contaminated water sources. For both Australia and Sri Lanka only a small fraction of the settlements in rural and remote regions are connected to water treatment facilities and town water supplies. In Australia’s remote/very remote regions raw water is drawn from underground sources and rainwater capture. Most settlements in rural Sri Lanka rely on rivers, reservoirs, wells, springs or carted water. Furthermore, Sri Lanka has more than 25,000 hand pumped tube wells which saved the communities during recent droughts. Decentralised water supply systems offer the opportunity to provide safe drinking water to these remote/very remote and rural regions where centralised systems are not feasible due to socio-cultural, economic, political, technological reasons. These systems reduce health risks from contaminated water supplies. In remote areas centralized systems fail due to low population density and less affordability. Globally, a new generation of advanced water treatment technologies are positioned to make a major impact on the provision of safe potable water in remote/very remote regions in Australia and rural regions in Sri Lanka. Some of these systems were developed for higher income countries. However, with careful selection and further research they can be tailored to match local socio-economic conditions and technical capacity. As such, they can equally be used to provide decentralised water supply in communities in developed and developing countries such as Australia and Sri Lanka.

On the Role of Delays in Biological Systems : Analysis and Design

This work quantifies the nature of delays in genetic regulatory networks and their effect on system dynamics. It is known that a time lag can emerge from a sequence of biochemical reactions. Applying this modeling framework to the protein production processes, delay distributions are derived in a stochastic (probability density function) and deterministic setting (impulse function), whilst being shown to be equivalent under different assumptions. The dependence of the distribution properties on rate constants, gene length, and time-varying temperatures is investigated. Overall, the distribution of the delay in the context of protein production processes is shown to be highly dependent on the size of the genes and mRNA strands as well as the reaction rates. Results suggest longer genes have delay distributions with a smaller relative variance, and hence, less uncertainty in the completion times, however, they lead to larger delays. On the other hand large uncertainties may actually play a positive role, as broader distributions can lead to larger stability regions when this formalization of the protein production delays is incorporated into a feedback system.

Furthermore, evidence suggests that delays may play a role as an explicit design into existing controlling mechanisms. Accordingly, the reccurring dual-feedback motif is also investigated with delays incorporated into the feedback channels. The dual-delayed feedback is shown to have stabilizing effects through a control theoretic approach. Lastly, a distributed delay based controller design method is proposed as a potential design tool. In a preliminary study, the dual-delayed feedback system re-emerges as an effective controller design.

Unanticipated biological changes and global warming

Evidence of global warming is now unequivocal, and studies suggest that it has started to influence natural systems of the planet, including the oceans. However, in the marine environment, it is well-known that species and ecosystems can also be influenced by natural sources of large-scale hydro-climatological variability. The North Atlantic Oscillation (NAO) was negatively correlated with the mean abundance of one of the subarctic key species Calanus finmarchicus in the North Sea. This correlation was thought to have broken down in 1996, however, the timing has never been tested statistically. The present study revisits this unanticipated change and reveals that the correlation did not break down in 1996 as originally proposed but earlier, at the time of an abrupt ecosystem shift in the North Sea in the 1980s. Furthermore, the analyses demonstrate that the correlation between the NAO and C. finmarchicus abundance is modulated by the thermal regime of the North Sea, which in turn covaries positively with global temperature anomalies. This study thereby provides evidence that global climate change is likely to alter some empirical relationships found in the past between species abundance or the ecosystem state and large-scale natural sources of hydro-climatological variability. A theory is proposed to explain how this might happen. These unanticipated changes, also called ‘surprises’ in climatic research, are a direct consequence of the complexity of both climatic and biological systems. In this period of rapid climate change, it is therefore hazardous to integrate meteo-oceanic indices such as the NAO in models used in the management of living resources, as it has been sometimes attempted in the past.

Performance analysis of switch-and-stay combining in two-way relay systems with analog network coding and time-division broadcast protocols

In this paper, weconsider switch-and-stay combining (SSC) in two-way relay systems with two amplify-and-forward relays, one of which is activated to assist the information exchange between the two sources. The system operates in either analog network coding (ANC) protocol where the communication is only achieved with the help of the active relay or timedivision broadcast (TDBC) protocol where the direct link between two sources can be utilized to exploit more diversity gain. In both cases, we study the outage probability and bit error rate (BER) for Rayleigh fading channels. In particular, we derive closed-form lower bounds for the outage probability and the average BER, which remain tight for different fading conditions. We also present asymptotic analysis for both the outage probability and the average BER at high signalto-noise ratio. It is shown that SSC can achieve the full diversity order in two-way relay systems for both ANC and TDBC protocols with proper switching thresholds. Copyright © 2014 John Wiley & Sons, Ltd.

(Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions – a review

The use of buffers to maintain the pH within a desired range is a very common practice in chemical, biochemical and biological studies. Among them, zwitterionic N-substituted aminosulfonic acids, usually known as Good’s buffers, although widely used, can complex metals and interact with biological systems. The present work reviews, discusses and updates the metal complexation characteristics of thirty one commercially available buffers. In addition, their impact on biological systems is also presented. The influences of these buffers on the results obtained in biological, biochemical and environmental studies, with special focus on their interaction with metal ions, are highlighted and critically reviewed. Using chemical speciation simulations, based on the current knowledge of the metal–buffer stability constants, a proposal of the most adequate buffer to employ for a given metal ion is presented.

Design and study of self-assembled functional organic and hybrid systems for biological applications

The focus of self-assembly as a strategy for the synthesis has been confined largely to molecules, because of the importance of manipulating the structure of matter at the molecular scale. We have investigated the influence of temperature and pH, in addition to the concentration of the capping agent used for the formation of the nano-bio conjugates. For example, the formation of the narrower size distribution of the nanoparticles was observed with the increase in the concentration of the protein, which supports the fact that γ-globulin acts both as a controller of nucleation as well as stabiliser. As analyzed through various photophysical, biophysical and microscopic techniques such as TEM, AFM, C-AFM, SEM, DLS, OPM, CD and FTIR, we observed that the initial photoactivation of γ-globulin at pH 12 for 3 h resulted in small protein fibres of ca. Further irradiation for 24 h, led to the formation of selfassembled long fibres of the protein of ca. 5-6 nm and observation of surface plasmon resonance band at around 520 nm with the concomitant quenching of luminescence intensity at 680 nm. The observation of light triggered self-assembly of the protein and its effect on controlling the fate of the anchored nanoparticles can be compared with the naturally occurring process such as photomorphogenesis.Furthermore,our approach offers a way to understand the role played by the self-assembly of the protein in ordering and knock out of the metal nanoparticles and also in the design of nano-biohybrid materials for medicinal and optoelectronic applications. Investigation of the potential applications of NIR absorbing and water soluble squaraine dyes 1-3 for protein labeling and anti-amyloid agents forms the subject matter of the third chapter of the thesis. The study of their interactions with various proteins revealed that 1-3 showed unique interactions towards serum albumins as well as lysozyme. 69%, 71% and 49% in the absorption spectra as well as significant quenching in the fluorescence intensity of the dyes 1-3, respectively. Half-reciprocal analysis of the absorption data and isothermal titration calorimetric (ITC) analysis of the titration experiments gave a 1:1 stoichiometry for the complexes formed between the lysozyme and squaraine dyes with association constants (Kass) in the range 104-105 M-1. We have determined the changes in the free energy (ΔG) for the complex formation and the values are found to be -30.78, -32.31 and -28.58 kJmol-1, respectively for the dyes 1, 2 and 3. Furthermore, we have observed a strong induced CD (ICD) signal corresponding to the squaraine chromophore in the case of the halogenated squaraine dyes 2 and 3 at 636 and 637 nm confirming the complex formation in these cases. To understand the nature of interaction of the squaraine dyes 1-3 with lysozyme, we have investigated the interaction of dyes 1-3 with different amino acids. These results indicated that the dyes 1-3 showed significant interactions with cysteine and glutamic acid which are present in the side chains of lysozyme. In addition the temperature dependent studies have revealed that the interaction of the dye and the lysozyme are irreversible. Furthermore, we have investigated the interactions of these NIR dyes 1-3 with β- amyloid fibres derived from lysozyme to evaluate their potential as inhibitors of this biologically important protein aggregation. These β-amyloid fibrils were insoluble protein aggregates that have been associated with a range of neurodegenerative diseases, including Huntington, Alzheimer’s, Parkinson’s, and Creutzfeldt-Jakob diseases. We have synthesized amyloid fibres from lysozyme through its incubation in acidic solution below pH 4 and by allowing to form amyloid fibres at elevated temperature. To quantify the binding affinities of the squaraine dyes 1-3 with β-amyloids, we have carried out the isothermal titration calorimetric (ITC) measurements. The association constants were determined and are found to be 1.2 × 105, 3.6× 105 and 3.2 × 105 M-1 for the dyes, 1-3, respectively. To gain more insights into the amyloid inhibiting nature of the squaraine dyes under investigations, we have carried out thioflavin assay, CD, isothermal titration calorimetry and microscopic analysis. The addition of the dyes 1-3 (5μM) led to the complete quenching in the apparent thioflavin fluorescence, thereby indicating the destabilization of β-amyloid fibres in the presence of the squaraine dyes. Further, the inhibition of the amyloid fibres by the squaraine dyes 1-3, has been evidenced though the DLS, TEM AFM and SAED, wherein we observed the complete destabilization of the amyloid fibre and transformation of the fibre into spherical particles of ca. These results demonstrate the fact that the squaraine dyes 1-3 can act as protein labeling agents as well as the inhibitors of the protein amyloidogenesis. The last chapter of the thesis describes the synthesis and investigation of selfassembly as well as bio-imaging aspects of a few novel tetraphenylethene conjugates 4-6.Expectedly, these conjugates showed significant solvatochromism and exhibited a hypsochromic shift (negative solvatochromism) as the solvent polarity increased, and these observations were justified though theoretical studies employing the B3LYP/6-31g method. We have investigated the self-assembly properties of these D-A conjugates though variation in the percentage of water in acetonitrile solution due to the formation of nanoaggregates. Further the contour map of the observed fluorescence intensity as a function of the fluorescence excitation and emission wavelength confirmed the formation of J-type aggregates in these cases. To have a better understanding of the type of self-assemblies formed from the TPE conjugates 4-6, we have carried out the morphological analysis through various microscopic techniques such as DLS, SEM and TEM. 70%, we observed rod shape architectures having ~ 780 nm in diameter and ~ 12 μM in length as evidenced through TEM and SEM analysis. We have made similar observations with the dodecyl conjugate 5 at ca. 70% and 50% water/acetonitrile mixtures, the aggregates formed from 4 and 5 were found to be highly crystalline and such structures were transformed to amorphous nature as the water fraction was increased to 99%. To evaluate the potential of the conjugate as bio-imaging agents, we have carried out their in vitro cytotoxicity and cellular uptake studies though MTT assay, flow cytometric and confocal laser scanning microscopic techniques. Thus nanoparticle of these conjugates which exhibited efficient emission, large stoke shift, good stability, biocompatibility and excellent cellular imaging properties can have potential applications for tracking cells as well as in cell-based therapies. In summary we have synthesized novel functional organic chromophores and have studied systematic investigation of self-assembly of these synthetic and biological building blocks under a variety of conditions. The investigation of interaction of water soluble NIR squaraine dyes with lysozyme indicates that these dyes can act as the protein labeling agents and the efficiency of inhibition of β-amyloid indicate, thereby their potential as anti-amyloid agents.