Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Variation in composition of macro-benthic invertebrates as an indication of water quality status in three bays in Lake Victoria

Knowledge of how biota can be used to monitor ecosystem health and assess impacts by human alterations such as land use and management measures taken at different spatial scales is critical for improving the ecological quality of aquatic ecosystems. This knowledge in Uganda is very limited or unavailable yet it is needed to better understand the relationship between environmental factors at different spatial scales, assemblage structure and taxon richness of aquatic ecosystems. In this study, benthic invertebrate community patterns were sampled between June 2001 and April 2002 and analysed in relation to water quality and catchment land use patterns from three shallow near-shore bays characterized by three major land uses patterns: urban (Murchison Bay); semi-urban (Fielding Bay); rural (Hannington Bay). Variations in density and guild composition of benthic macro-invertebrates communities were evaluated using GIS techniques along an urban-rural gradient of land use and differences in community composition were related to dissolved oxygen and conductivity variation. Based on numerical abundance and tolerance values, Hilsenhoff's Biotic Index ofthe invertebrates was determined in order to evaluate the relative importance of water quality in the three bays. Murchison Bay supported a relatively taxa-poor invertebrate assemblage mainly comprising stenotopic and eurytopic populations of pollution-tolerant groups such as worms and Chironomus sp. with an overall depression in species diversity. On the contrary, the communities in Fielding and Hannington bays were quite similar and supported distinct and diverse assemblages including pollution-intolerant forms such as Ephemeroptera (mayflies), Odonata (dragonflies). The Hilsenhoff Biotic Index in Murchison Bay was 6.53. (indicating poor water quality) compared to 6.34 for Fielding Bay and 5.78 for Hannington Bay (both indicating fair water quality). The characterization of maximum taxa richness balanced among taxa groups with good representation of intolerant individuals in Hannington Bay relative to Fielding and Murchison bays concludes that the bay is the cleanest in terms of water quality. Contrary, the dominance of few taxa with many tolerant iqdividuals present in Murchison Bay indicates that the bay is degraded in terms of water quality. These result are ofimportance when planning conservation and management measures, implementing large-scale biomonitoring programs, and predicting how human alterations (e.g nutrient loading) affect water ecosystems. Therefore, analysis of water quality in relation to macro-invertebrate community composition patterns as bio-indicators can lead to further understanding of their responses to environmental manipulations and perturbations.

The eutrophication in the river Vouga basin: impacts on the quality of water for public supply

The aim of this paper is to make a characterization of water quality problems, in the river Vouga, regarding its use for public water supply. The river Vouga basin is located in a mountainous area, draining to the coastal lagoon of the Ria de Aveiro. Other medium size rivers also contribute to the load of pollution entering the estuarine system of the Ria de Aveiro. Two major impacts of the pollution in the river Vouga basin were identified. One is the eutrophication process of the lower reach of the river, including the Ria de Aveiro; the other is the occasional deterioration in the quality of the water abstracted from the medium reach of river Vouga. The causes of this deterioration are related to the enrichment of the river water with organic material. To improve the river water quality, both urban wastewater and agriculture related sources, must be controlled.

Characterization of water-soluble organic compounds in bioaerosols by liquid chromatography and fluorescence spectroscopy

In the last decades, the effects of the air pollution have been increasing, especially in the case of the human health diseases. In order to overcome this problem, scientists have been studying the components of the air. As a part of water-soluble organic compounds, amino acids are present in the atmospheric environment as components of diverse living organisms which can be responsible for spreading diseases through the air. Liquid chromatography is one technique capable of distinguish the different amino acids from each other. In this work, aiming at separating the amino acids found in the aerosols samples collected in Aveiro, the ability of four columns (Mixed-Mode WAX-1, Mixed-Mode HILIC-1, Luna HILIC and Luna C18) to separate four amino acids (aspartic acid, lysine, glycine and tryptophan) and the way the interaction of the stationary phases of the columns with the analytes is influenced by organic solvent concentration and presence/concentration of the buffer, are being assessed. In the Mixed-Mode WAX-1 column, the chromatograms of the distinct amino acids revealed the separation was not efficient, since the retention times were very similar. In the case of lysine, in the elution with 80% (V/V) MeOH, the peaks appeared during the volume void. In the Mixed-Mode HILIC-1 column, the variation of the organic solvent concentration did not affect the elution of the four studied amino acids. Considering the Luna HILIC column, the retention times of the amino acids were too close to each other to ensure a separation among each other. Lastly, the Luna C18 column revealed to be useful to separate amino acids in a gradient mode, being the variation of the mobile phase composition in the organic solvent concentration (ACN). Luna C18 was the column used to separate the amino acids in the real samples and the mobile phase had acidified water and ACN. The gradient consisted in the following program: 0 – 2 min: 5% (V/V) ACN, 2 – 8 min: 5 – 2 % (V/V) ACN, 8 – 16 min: 2% (V/V) ACN, 16 – 20 min: 2 – 20 % (V/V) ACN, 20 – 35 min: 20 – 35 % (V/V) ACN. The aerosols samples were collected by using three passive samplers placed in two different locations in Aveiro and each sampler had two filters - one faced up and the other faced down. After the sampling, the water-soluble organic compounds was extracted by dissolution in ultra-pure water, sonication bath and filtration. The resulting filtered solutions were diluted in acidified water for the chromatographic separation. The results from liquid chromatography revealed the presence of the amino acids, although it was not possible to identify each one of them individually. The chromatograms and the fluorescence spectra showed the existence of some patterns: the samples that correspond to the up filters had more intense peaks and signals, revealing that the up filters collected more organic matter.

Preparation of environmental monitoring plan pattern for surface water quality in Iran (Case study: Gharehsou River)

Using water quality management programs is a necessary and inevitable way for preservation and sustainable use of water resources. One of the important issues in determining the quality of water in rivers is designing effective quality control networks, so that the measured quality variables in these stations are, as far as possible, indicative of overall changes in water quality. One of the methods to achieve this goal is increasing the number of quality monitoring stations and sampling instances. Since this will dramatically increase the annual cost of monitoring, deciding on which stations and parameters are the most important ones, along with increasing the instances of sampling, in a way that shows maximum change in the system under study can affect the future decision-making processes for optimizing the efficacy of extant monitoring network, removing or adding new stations or parameters and decreasing or increasing sampling instances. This end, the efficiency of multivariate statistical procedures was studied in this thesis. Multivariate statistical procedure, with regard to its features, can be used as a practical and useful method in recognizing and analyzing rivers’ pollution and consequently in understanding, reasoning, controlling, and correct decision-making in water quality management. This research was carried out using multivariate statistical techniques for analyzing the quality of water and monitoring the variables affecting its quality in Gharasou river, in Ardabil province in northwest of Iran. During a year, 28 physical and chemical parameters were sampled in 11 stations. The results of these measurements were analyzed by multivariate procedures such as: Cluster Analysis (CA), Principal Component Analysis (PCA), Factor Analysis (FA), and Discriminant Analysis (DA). Based on the findings from cluster analysis, principal component analysis, and factor analysis the stations were divided into three groups of highly polluted (HP), moderately polluted (MP), and less polluted (LP) stations Thus, this study illustrates the usefulness of multivariate statistical techniques for analysis and interpretation of complex data sets, and in water quality assessment, identification of pollution sources/factors and understanding spatial variations in water quality for effective river water quality management. This study also shows the effectiveness of these techniques for getting better information about the water quality and design of monitoring network for effective management of water resources. Therefore, based on the results, Gharasou river water quality monitoring program was developed and presented.

Seasonal variation of acetylcholinesterase, catalase, glutathione s transferase in different size of Pinctada radiata and metal pollution (Pb, Cd, Ni) in Persian Gulf

There are various tools for monitoring the concentration of pollutants on aquatic ecosystems. Today these studies are based on biological monitoring and biomarkers. The aim of this study was to measure the concentration of the acetylcholinesterase (AChE), glutathione S-transferase and catalase as biomarkers of heavy metal contamination in pearl oyster Pinctada radiata and their mechanism in aquatic ecosystems. Heavy metals lead, cadmium and nickel were measured in soft tissue and studied stations in four seasons. Samples were collected seasonally in Lavan stations, Hendurabi and Nakhilo (in the northern Persian Gulf) from spring 2013 to winter of that year by scuba diving. Pearl oysters are divided according to their shells size; shells separated from soft tissues and were transferred to the laboratory for analysis of heavy metals and enzymes. Moopam standard method for were used for measuring the concentration of heavy metals and for analyzing tissue concentrations of glutathione S-transferase in Clam the method recommended by Habig et al in 1974 were used. For measuring acetylcholinesterase Ellman method were used. Catalase contamination in pearl oyster in the supernatant obtained from the study based on the method homogeate soft tissue of mussels (Abei, 1974) was evaluated. The results showed that the concentration of lead has significant difference in sediments station, the concentration of lead in Lavan is significantly higher than the other two stations, This could be due to the movement of tanker, boats and floating refueling and with a considerable amount of wastewater containing oil and Petroleum into the water, and also due to precipitation and industrial discharges the lead in the region is increasing, land-disposed sewage sludge, has large concentrations of lead. Compare the results of this study with standards related and other similar studies at the regional and international level showed that pollutant concentration of heavy metals in all cases significantly less than all the standards and guide values associated. And also compared to other world research results have been far less than others, Being Less of the conclusion given in this research according that nickel is one of the indicators of oil pollution in the study area and emissions have been relatively low of oil. The concentration of acetylcholinesterase at several stations, in large and small sizes and in the seasons had no significant difference. Variations of catalase, and glutathione S-transferase were almost similar to each other and parameters, station and seasons were significantly different in the concentrations of these enzymes. The effects and interaction between various parameters indicate that following parameters has impact on the concentration of catalase and glutathione S-transferase. Stations; Seasonal changes in antioxidant enzymes related to (assuming a constant in salinity and oxygen) to age, reproductive cycle, availability of food and water temperature. With increasing temperature at warm season, antioxidant enzymes were increase, with increasing temperature and abundance of food in the environment the amount of antioxidant enzymes may increase. The presence of the enzyme concentration may indicate that the higher levels of the enzyme to eliminate ROS activities to be any healthier situation. At the time of gonads maturation and spawning season catalase activity increases. This study also indicates that catalase was significantly higher in the warm season. Due to low pollutants of heavy metals in the study area, a lower level of contaminants were observed in shellfish tissue incidents of international standards and strong correlation between the amount of heavy metal contamination in pearl oyster tissue and enzymes was not observed. Therefore, we can say that the pearl oyster remains in a healthy condition and the amount of enzyme is normal.

Mineral and organic pollution in river Sabor (Northeastern Portugal): ecotoxicological effects on freshwater fauna

Aquatic ecosystems are final collectors of all kinds of pollution as an outcome of anthropogenic inputs, such us untreated industrial and municipal sewage and agricultural pollutants. There are several aquatic ecosystems that are threatened by mineral and organic pollution. In Northeastern Portugal, near Bragança, different watercourses are suffering negative impacts of human activities. It has been developed several studies in the monitoring of environmental impacts in these river basins, namely in Rio Fervença, affected by organic pollution, and in Portelo stream, affected, since 2009, by the collapse and continuous input of mining deposits. In this sense, the present study aimed to continue the monitoring study of ecological status of freshwater ecosystems of Northeastern Portugal, namely the following objectives: a) mineral pollution effects of mining deposits sudden incorporated into Portelo stream; b) organic pollution due to domestic and industrial inputs in River Fervença. Also, since fish are useful experimental models to evaluate toxicological mechanisms of contaminants, c) acute toxicity tests with Cu were conducted in laboratory conditions. During 2015/2016, it was made abiotic and biotic characterization of 16 sampling sites distributed by both Portelo and Fervença rivers, tributaries of main River Sabor (Douro Basin). Several physicochemical parameters were determined and Riparian Quality (QBR Index) and Channel Quality (GQC) Indexes were determined for habitat evaluation. Fish and invertebrate communities were sampled, according to protocols of Water Framework Directive (WFD). Several metrics were determined, with particular emphasis on the Biotic Index IBMWP and the Northern Portuguese Invertebrate Index (IPtIN). Acute toxicity tests were conducted with an Iberian fish species, common barbel (Luciobarbus bocagei) and some plasmatic electrolytes levels were evaluated, to assess their contribution to mitigate osmoregulatory adverse effects of Cu. Also, same electrolytes were measured after changing to clean water, in attempt to assess fish capacity to reverse this situation. Results obtained for both rivers showed a significant level of disturbance that affected decisively water, habitat and biological quality of aquatic ecosystems. Mineral and Organic Pollution in River Sabor (NE Portugal): Ecotoxicological Effects on Freshwater Fauna Due to this change of environmental conditions in Portelo stream (extreme pH values, high conductivity and presence of heavy metals), several biological metrics (e.g. taxonomic richness, abundance, diversity, evenness) confirmed, comparatively with reference sites, a substantial decrease on ecological integrity status. The same pattern was found for Fervença River; however other water parameters, namely the content of most limiting nutrients (e.g. N and P) seemed to have more influence in the composition and structure of macroinvertebrate and fish communities. In fact, despite the operation of the Sewage Treatment Plant of Bragança, Fervença River presented significant levels of disturbance that affected decisively the quality and ecological integrity of the aquatic ecosystem. The synergic effect of domestic and industrial pollution, intensive agriculture, regulation and degradation of aquatic and riparian habitats contributed to the decrease of ecological condition, namely in the downstream zones (after Bragança). The results for acute toxicity, showed that fish can change Na+ and K+ levels face to Cu exposition and, depending of Cu concentration tested, can also return to normal levels, providing some insights to that are believed to occurred in fish population, near the Portelo mines. The low ecological integrity status detected in the lotic ecosystems in NE Portugal as a result of mineral and organic pollution deserves the development of several measures for rehabilitation and improving of water quality. On the other hand, environmental education actions are needed to contribute to improvement of ecological integrity of the river and its conservation.

Effects of an introduced clam (Corbicula) on water quality in the Tennessee River Valley. Presented before the second annual Sanitary Engineering Conference, Vanderbilt University, Nashville, Tenn., May 30-31, 1963.

Mode of access: Internet.

Adsorption of aromatic compound by multi-walled carbon nanotube from sea water

It is global concern that soil and water were contaminated with organic substances such as BTEX (benzene) (B), toluene (T) and xylene (x) .The presence of excessive amounts of BTEX in aqueous surroundings may have a greatly adverse impact on water quality and thus endanger public health and welfare. Carbon nanotubes (CNT) have aroused widespread attention as a new type of adsorptions due to their outstanding ability for the removal of various inorganic and organic pollutants from large volume of wastewater. Due to variety of adsorbent and their ability to adsorb pollutant, it is possible to reduce expenses and completely omit pollutant. In this CNT is used as a new adsorbent for removal pollutant such as benzene, toluene, and xylene. The result in the area of adsorbing benzene, toluene, and xylene is as follows: the changes of pH don’t affect the capacity of adsorption and the greatest amount of adsorption occurs in pH. The greatest amount of adsorption occurs when using 0.01gr CNT oxidized. Comparing CNT with CNT oxidized in term of adsorption capacity, it is proved that the adsorption capacity of CNT oxidized is much more than CNT. The result of comparing the percentage of adsorption of mentioned elements (B, X, T) is as follows; the amount of adsorption of xylene is more than toluene and toluene is more than benzene. It should be mentioned that in this research the percentage of adsorption to measure is between to 70-80.

Evaluation and measurement of chromium in sea water in order to remove it with mineral absorbent kaolin for desalination

Today, the use of heavy metals and chemical products industry expanded. The presence of significant amounts of, pollutants in industrial waste water can lead to serious risks to the environment and human health have heavy metals like chromium is one example of the future of salmon knock pond environment. Chromium is an essential element in the diet, but high doses of this element is very dangerous. Hence the use of chemical methods as a tool for the removal of metals from waste water pond be used. The aim of this study was to investigate the mineral kaolin adsorbents for the removal of chromium is water. Thus, the effect of different concentrations of absorbent micro amounts of chromium absorption and variable temperature, pH and electrolytes were studied. During the investigation of spectroscopic instrument (Varian) UV-VIS are used. Comparison of the absorption mechanism of chromium adsorption by the adsorbent with nano-absorbent kaolin kaolin was investigated. According to the studies done in the same conditions of temperature, pH and shaking rate of chromium absorption by nano kaolin kaolin is much more attractive. Therefore, its use as an adsorbent abundant, cheap, accessible, efficient and effective is proposed.

Application of chitosan loaded with metal oxide nano particles to remove lead present from sea water

Chitosan is a natural polymer obtained by deacetylation of chitin. After cellulose chitin is the second most abundant polysaccharide in nature. It is biologically safe, non-toxic, biocompatible and biodegradable polysaccharide. Chitosan loaded with zinc oxide nanoparticles have gained more attention bio sorbent because of their better stability, low toxicity, simple and mild preparation method and high sorption capacity. Chitosan loaded with zinc oxide nanoparticles have been prepared of chitosan. The physicochemical properties of nanoparticles were characterized by Fourier Transform Infrared (FTIR), Scanning Electron Microscope (SEM) Analysis. Its sorption capacity for lead and cadmium ions studied. Factors such as initial concentration of lead ions, cadmium ions sorbent amount, contact time, pH and temperature were investigated. It is found that chitosan loaded with zinc oxide nanoparticles could sorb lead and cadmium ions effectively, this sorption rate was affected significantly by initial concentration of lead and cadmium ions, sorbent amount, contact time, pH of solution. The maximum of percentage of lead sorption was 98 % with initial concentration 3 mg/l and sorbent amount 0.05 g, pH 11 in 45 min and cadmiumwas90 %with initial concentration 3mg/l and sorbent amount 0.05 g, pH 11 in45 min. Consequently chitosan loaded with zinc oxide nanoparticles demonstrated greater fixation ability for lead ions than cadmium ions.

Investigation on water and sediment quality variation from coast to off shore and its relation to bent hoses biodiversity: case study Bandar tahery

This paper deals with the qualification of water and sediment particularly those of benthos, as well as their interaction results, through careful laboratory researches within 24 experimental sites around the bank of Bandar Taheri, Persian Gulf water of Iranian borders, under 13th phase south Pars project. Samples were carried to the laboratories and careful experimental tests such as physical chemical, heavy metal, nitrate ammoniac, toc and other biologic tests including various type of benthos count were performed. Data gained through Shanon and Dankan statistical analyses were also studied to determine the water, sediment and pollution rate. Resulted information would classify the area as less polluted area which is rather away from critical environmental zone, another word the area could be liable to change to an undesired one while the density rates of principal metals follows the Fe>Mn>Zn>Cu>Pb>Cd>N pattern.

Studying and measuring the amount of detergents in sea-water samples in order to eliminate with adsorbents and inorganic nano-adsorbents for the sake of securing the water for marine nourishment pools

Increasing the amount of detergent industries in world in spite of having abundant benefits; entering a new kind of contamination into environment and attract the attention of environment liable of different countries to itself. Entering detergents into an aqueous solution cause pollution of water sources and environment in respect of appearing e problem and charges like: nutritive phenomenon, decomposition of hard group of detergent and producing foam. After using Detergents, they were poured into rivers, seas and lakes and have destructive effect on environment. A lot of hygiene problems were attributed to the water having detergents more than allowed value. So, it is specified the importance of eliminating detergents from contaminated water and it is application for secondary use. In order to attain to this aim, we can use inorganic nano and micro-caolin. In this study the adsorptive properties of detergent on the micro and nano caolin adsorbents were studied and the effect of various parameters like the amount of adsorptive materials, initial concentration of detergent, speed of stirring, electrolyte, temperature, time and pH were determined. The surface area of micro- and nano-caoline was reported 11.867 and 49.1438 m2 g-1, respectively. That increasing in nano-caoline surface area confirms increasing in capacity and more rate of adsorption. The results gained by this research recommend using micro- and nano-caolin as a plentiful, available and effective adsorbents. Also in comparison, using nano-caoline was recommended in order to have more effectiveness.