THE DISTRIBUTION AND FUNCTION OF DENITRIFICATION GENES: EXPLORING AGRICULTURAL MANAGEMENT AND SOIL CHEMICAL IMPLICATIONS

Denitrification is a microbially-mediated process that converts nitrate (NO3-) to dinitrogen (N2) gas and has implications for soil fertility, climate change, and water quality. Using PCR, qPCR, and T-RFLP, the effects of environmental drivers and land management on the abundance and composition of functional genes were investigated. Environmental variables affecting gene abundance were soil type, soil depth, nitrogen concentrations, soil moisture, and pH, although each gene was unique in its spatial distribution and controlling factors. The inclusion of microbial variables, specifically genotype and gene abundance, improved denitrification models and highlights the benefit of including microbial data in modeling denitrification. Along with some evidence of niche selection, I show that nirS is a good predictor of denitrification enzyme activity (DEA) and N2O:N2 ratio, especially in alkaline and wetland soils. nirK was correlated to N2O production and became a stronger predictor of DEA in acidic soils, indicating that nirK and nirS are not ecologically redundant.

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.

Transmission electron tomography: quality assessment and enhancement for three-dimensional imaging of nanostructures

Nanotechnology has revolutionised humanity's capability in building microscopic systems by manipulating materials on a molecular and atomic scale. Nan-osystems are becoming increasingly smaller and more complex from the chemical perspective which increases the demand for microscopic characterisation techniques. Among others, transmission electron microscopy (TEM) is an indispensable tool that is increasingly used to study the structures of nanosystems down to the molecular and atomic scale. However, despite the effectivity of this tool, it can only provide 2-dimensional projection (shadow) images of the 3D structure, leaving the 3-dimensional information hidden which can lead to incomplete or erroneous characterization. One very promising inspection method is Electron Tomography (ET), which is rapidly becoming an important tool to explore the 3D nano-world. ET provides (sub-)nanometer resolution in all three dimensions of the sample under investigation. However, the fidelity of the ET tomogram that is achieved by current ET reconstruction procedures remains a major challenge. This thesis addresses the assessment and advancement of electron tomographic methods to enable high-fidelity three-dimensional investigations. A quality assessment investigation was conducted to provide a quality quantitative analysis of the main established ET reconstruction algorithms and to study the influence of the experimental conditions on the quality of the reconstructed ET tomogram. Regular shaped nanoparticles were used as a ground-truth for this study. It is concluded that the fidelity of the post-reconstruction quantitative analysis and segmentation is limited, mainly by the fidelity of the reconstructed ET tomogram. This motivates the development of an improved tomographic reconstruction process. In this thesis, a novel ET method was proposed, named dictionary learning electron tomography (DLET). DLET is based on the recent mathematical theorem of compressed sensing (CS) which employs the sparsity of ET tomograms to enable accurate reconstruction from undersampled (S)TEM tilt series. DLET learns the sparsifying transform (dictionary) in an adaptive way and reconstructs the tomogram simultaneously from highly undersampled tilt series. In this method, the sparsity is applied on overlapping image patches favouring local structures. Furthermore, the dictionary is adapted to the specific tomogram instance, thereby favouring better sparsity and consequently higher quality reconstructions. The reconstruction algorithm is based on an alternating procedure that learns the sparsifying dictionary and employs it to remove artifacts and noise in one step, and then restores the tomogram data in the other step. Simulation and real ET experiments of several morphologies are performed with a variety of setups. Reconstruction results validate its efficiency in both noiseless and noisy cases and show that it yields an improved reconstruction quality with fast convergence. The proposed method enables the recovery of high-fidelity information without the need to worry about what sparsifying transform to select or whether the images used strictly follow the pre-conditions of a certain transform (e.g. strictly piecewise constant for Total Variation minimisation). This can also avoid artifacts that can be introduced by specific sparsifying transforms (e.g. the staircase artifacts the may result when using Total Variation minimisation). Moreover, this thesis shows how reliable elementally sensitive tomography using EELS is possible with the aid of both appropriate use of Dual electron energy loss spectroscopy (DualEELS) and the DLET compressed sensing algorithm to make the best use of the limited data volume and signal to noise inherent in core-loss electron energy loss spectroscopy (EELS) from nanoparticles of an industrially important material. Taken together, the results presented in this thesis demonstrates how high-fidelity ET reconstructions can be achieved using a compressed sensing approach.

Physicochemical properties of water quality of Imeh, Edegelem and Chokocho communities located along Otamiri-oche River in Etche Ethnic Nationality of Rivers State, Nigeria

Some physiochemical properties of water quality of Otamiri-oche River which runs through Imeh, Edegelem and Chokocho Communities in Etche ethnic nationality of Rivers State, Nigeria were investigated. Samples were collected in triplicate from the three different locations along the river in both rainy and dry seasons. Each sampling points is located 500m away from the successive one, and the samples were taken from the open river at the zone extending beyond the shoreline. Samples were stored in ice packs and immediately taken to the laboratory to investigate some selected physico-chemical characteristics. Also, bacteriological study was carried out on the samples. The laboratory results of the selected physico-chemical parameters when compared with the world health organization (WHO) standard showed that all the selected physico-chemical parameters were within the world health organization (WHO) permissible in both rainy and dry season except pH. For rainy season, the pH values were 5.00±0.00, 5.40 ±0.40, and 5.40± 0.30 for Imeh, Edegelem and Chokocho respectively. For the dry season, the pH values were 5.83± 0.01, 5.56±0.01, 5.90±0.01 for Imeh, Edegelem and Chokocho respectively. Also magnesium hardness exceeded the World Health Organization (WHO) permissible limit in rainy season only. The results of bacteriological study showed that all the sampling locations contained high numbers of coliform bacteria in both rainy and dry seasons. The number of coliform bacteria during rainy season was 25.00±0.00, 25.00±0.00, and 35.00±0.00 for Imeh, Edegelem and Chokocho respectively. Those of dry season were 93.00±3.55, 56.66±4.49, and 35.60±4.17 for Imeh, Edegelem and Chokocho respectively. The difference between the rainy and dry season was tested statistically using the t-test. The results of the statistical analyses showed a significant difference (p<0.05) between the rainy and dry seasons.

SCOR WG 142: Quality Control Procedures for Oxygen and Other Biogeochemical Sensors on Floats and Gliders. Recommendation for oxygen measurements from Argo floats, implementation of in-air-measurement routine to assure highest long-term accuracy

Recommendation for Oxygen Measurements from Argo Floats: Implementation of In-Air-Measurement Routine to Assure Highest Long-term Accuracy As Argo has entered its second decade and chemical/biological sensor technology is improving constantly, the marine biogeochemistry community is starting to embrace the successful Argo float program. An augmentation of the global float observatory, however, has to follow rather stringent constraints regarding sensor characteristics as well as data processing and quality control routines. Owing to the fairly advanced state of oxygen sensor technology and the high scientific value of oceanic oxygen measurements (Gruber et al., 2010), an expansion of the Argo core mission to routine oxygen measurements is perhaps the most mature and promising candidate (Freeland et al., 2010). In this context, SCOR Working Group 142 “Quality Control Procedures for Oxygen and Other Biogeochemical Sensors on Floats and Gliders” (www.scor-int.org/SCOR_WGs_WG142.htm) set out in 2014 to assess the current status of biogeochemical sensor technology with particular emphasis on float-readiness, develop pre- and post-deployment quality control metrics and procedures for oxygen sensors, and to disseminate procedures widely to ensure rapid adoption in the community.

Effects of dredging operations on sediment quality: contaminant mobilization in dredged sediments from the Port of Santos, SP, Brazil

Background, aim, and scope Contaminated sediments are a worldwide problem, and mobilization of contaminants is one of the most critical issues in environmental risk assessment insofar as dredging projects are concerned. The investigation of how toxic compounds are mobilized during dredging operations in the channel of the Port of Santos, Brazil, was conducted in an attempt to assess changes in the bioavailability and toxicity of these contaminants.Materials and methods Bulk sediment samples and their interstitial waters and elutriates were subjected to chemical evaluation and ecotoxicological assessment. Samples were collected from the channel before dredging, from the dredge's hopper, and from the disposal site and its surroundings.Results The results indicate that the bulk sediments from the dredging site are contaminated moderately with As, Pb, and Zn and severely with Hg, and that polycyclic aromatic hydrocarbon (PAH) concentrations are relatively high. Our results also show a 50% increase in PAH concentrations in suspended solids in the water collected from the hopper dredge. This finding is of great concern, since it refers to the dredge overflow water which is pumped back into the ecosystem. Acute toxicity tests on bulk sediment using the amphipod Tiburonella viscana showed no toxicity, while chronic tests with the sea urchin Lytechinus variegatus showed toxicity in the interstitial waters and elutriates. Results are compared with widely used sediment quality guidelines and with a sediment quality assessment scheme based on various lines of evidence.Conclusions The data presented here indicate that the sediments collected in this port show a certain degree of contamination, especially those from the inner part of the channel. The classification established in this study indicated that sediments from the dredged channel are impacted detrimentally and that sea disposal may disperse contaminants. According to this classification, the sediments are inappropriate for disposal at sea. It should be emphasized that the poor quality of fine sediments discharged from the hopper dredge in the overflow process can recontaminate the environment.Recommendations and perspectives These findings will help to underpin improved planning of management strategies for dredging operations and sediment disposal in Brazil and other countries.

Integrated sediment quality assessment in Paranagua Estuarine System, Southern Brazil

Sediment quality from Paranagua Estuarine System (PES), a highly important port and ecological zone, was evaluated by assessing three lines of evidence: (1) sediment physical-chemical characteristics; (2) sediment toxicity (elutriates, sediment-water interface, and whole sediment); and (3) benthic community structure. Results revealed a gradient of increasing degradation of sediments (i.e. higher concentrations of trace metals, higher toxicity, and impoverishment of benthic community structure) towards inner PES. Data integration by principal component analysis (PCA) showed positive correlation between some contaminants (mainly As, Cr, Ni, and Pb) and toxicity in samples collected from stations located in upper estuary and one station placed away from contamination sources. Benthic community structure seems to be affected by both pollution and natural fine characteristics of the sediments, which reinforces the importance of a weight-of-evidence approach to evaluate sediments of PES. (C) 2008 Elsevier B.V. All rights reserved.

Development of site-specific sediment quality guidelines for North and South Atlantic littoral zones: Comparison against national and international sediment quality benchmarks

We aimed to develop site-specific sediment quality guidelines (SQGs) for two estuarine and port zones in Southeastern Brazil (Santos Estuarine System and Paranagua Estuarine System) and three in Southern Spain (Ria of Huelva, Bay of Cadiz, and Bay of Algeciras), and compare these values against national and traditionally used international benchmark values. Site-specific SQGs were derived based on sediment physical-chemical, toxicological, and benthic community data integrated through multivariate analysis. This technique allowed the identification of chemicals of concern and the establishment of effects range correlatively to individual concentrations of contaminants for each site of study. The results revealed that sediments from Santos channel, as well as inner portions of the SES, are considered highly polluted (exceeding SQGs-high) by metals, PAHs and PCBs. High pollution by PAHs and some metals was found in Sao Vicente channel. In PES, sediments from inner portions (proximities of the Ponta do Mix port's terminal and the Port of Paranagua) are highly polluted by metals and PAHs, including one zone inside the limits of an environmental protection area. In Gulf of Cadiz, SQGs exceedences were found in Ria of Huelva (all analysed metals and PAHs), in the surroundings of the Port of CAdiz (Bay of CAdiz) (metals), and in Bay of Algeciras (Ni and PAHs). The site-specific SQGs derived in this study are more restricted than national SQGs applied in Brazil and Spain, as well as international guidelines. This finding confirms the importance of the development of site-specific SQGs to support the characterisation of sediments and dredged material. The use of the same methodology to derive SQGs in Brazilian and Spanish port zones confirmed the applicability of this technique with an international scope and provided a harmonised methodology for site-specific SQGs derivation. (C) 2009 Elsevier B.V. All rights reserved.

A simple approach to integrate the ecotoxicological and chemical data for the establishment of environmental risk levels

O presente trabalho utilizou métodos multivariados e matemáticos para integrar dados químicos e ecotoxicológicos obtidos para o Sistema Estuarino de Santos e para a região próxima à zona de lançamento do emissário submarino de Santos, com a finalidade de estabelecer com maior exatidão os riscos ambientais, e assim identificar áreas prioritárias e orientar programas de controle e políticas públicas. Para ambos os conjuntos de dados, as violações de valores numéricos de qualidade de sedimento tenderam a estar associadas com a ocorrência de toxicidade. Para o estuário, essa tendência foi corroborada pelas correlações entre a toxicidade e as concentrações de HPAs e Cu, enquanto para a região do emissário, pela correlação entre toxicidade e conteúdo de mercúrio no sedimento. Valores normalizados em relação às medias foram calculados para cada amostra, permitindo classificá-las de acordo com a toxicidade e a contaminação. As análises de agrupamento confirmaram os resultados das classificações. Para os dados de sistema estuarino, houve a separação das amostras em três categorias: as estações SSV-2, SSV-3 e SSV-4 encontram-se sob maior risco, seguidas da estação SSV-6. As estações SSV-1 e SSV-5 demonstraram melhores condições. Já em relação ao emissário, as amostras 1 e 2 apresentaram melhores condições, enquanto a estação 5 pareceu apresentar um maior risco, seguida das estações 3 e 4 que tiveram apenas alguns indícios de alteração.

Comparison between benzyladenine and metamitron as chemical thinning agents in Gala, Kanzi, Pink Lady and Red Delicious apple cultivars

Mestrado em Engenharia Agronómica - Instituto Superior de Agronomia - UL

Effects of rainfall on water quality in six sequentially disposed fishponds with continuous water flow

O estudo foi efetuado durante o período de chuva (dezembro-fevereiro) em seis viveiros de produção semi-intensiva de peixes, a fim de avaliar o efeito da chuva na qualidade da água de viveiros que apresentam fluxo contínuo de água, a qual é passada de um viveiro para outro sem tratamento prévio. Foram amostrados oito pontos de coleta nas saídas dos viveiros. O viveiro P1 (próximo à nascente) apresentou as menores concentrações físicas e químicas da água e as maiores no viveiro P4 (considerado um ponto crítico recebendo material alóctone proveniente de outros viveiros e do escoamento do setor de criação de rãs). A disposição seqüencial dos viveiros estudados promoveu aumento nas concentrações dos nutrientes, clorofila-a e condutividade. As chuvas características desta época do ano aumentaram o fluxo de água nos viveiros e conseqüentemente, carreando material particulado e dissolvido de um viveiro para outro e, promovendo um aumento das variáveis limnológicas em direção do P3 ao P6. Os resultados sugerem que a chuva no período de estudo afetou positivamente a qualidade da água dos viveiros estudados, porém, como os sistemas analisados estão dispostos em distribuição seqüencial e escoamento constante da água de viveiros e tanques paralelos sem tratamento prévio, cuidados devem ser averiguados para que o aumento do fluxo de água provocado pelas chuvas não tenha efeito adverso nos viveiros estudados.

Seasonal variations in chemical composition and stable isotopes of farmed and wild Brazilian freshwater fish

This study examined variations in the Fulton condition factor, chemical composition, and stable isotopes of carbon and nitrogen in the Brazilian freshwater fish cachara (Pseudoplatystoma fasciatum), comparing farmed and wild fish in different seasons. Values for energy, protein, moisture, and Fulton's condition factor were higher for farmed than for wild fish in the rainy season, indicating better nutritional quality; however, these differences were not observed in the dry season. Likewise, we found significant enhancement of delta(15)N in farmed fish in the rainy season but not in the dry season, whereas enhancement of delta(13)C was observed in both seasons. The combined measurement of delta(13)C and delta(15)N provided traceability under all conditions. Our findings show that stable isotope analysis of C and N can be used to trace cachara origin, and that seasonal variations need to be considered when applying chemical and isotopic authentication of fish and fish products. (C) 2010 Elsevier Ltd. All rights reserved.

Mechanical and Electrical Properties of Single-walled Carbon Nanotubes Synthesized by Chemical Vapor Deposition

Despite the tremendous application potentials of carbon nanotubes (CNTs) proposed by researchers in the last two decades, efficient experimental techniques and methods are still in need for controllable production of CNTs in large scale, and for conclusive characterizations of their properties in order to apply CNTs in high accuracy engineering. In this dissertation, horizontally well-aligned high quality single-walled carbon nanotubes (SWCNTs) have been successfully synthesized on St-cut quartz substrate by chemical vapor deposition (CVD). Effective radial moduli (Eradial) of these straight SWCNTs have been measured by using well-calibrated tapping mode and contact mode atomic force microscopy (AFM). It was found that the measured Eradial decreased from 57 to 9 GPa as the diameter of the SWCNTs increased from 0.92 to 1.91 nm. The experimental results were consistent with the recently reported theoretical simulation data. The method used in this mechanical property test can be easily applied to measure the mechanical properties of other low-dimension nanostructures, such as nanowires and nanodots. The characterized sample is also an ideal platform for electrochemical tests. The electrochemical activities of redox probes Fe(CN)63-/4-, Ru(NH3)63+, Ru(bpy)32+ and protein cytochrome c have been studied on these pristine thin films by using aligned SWCNTs as working electrodes. A simple and high performance electrochemical sensor was fabricated. Flow sensing capability of the device has been tested for detecting neurotransmitter dopamine at physiological conditions with the presence of Bovine serum albumin. Good sensitivity, fast response, high stability and anti-fouling capability were observed. Therefore, the fabricated sensor showed great potential for sensing applications in complicated solution.

Chemical Composition and Bioactive Compounds in Bananas and Postharvest Alterations

Bananas arise as one of the most popular fruits consumed all around the world. Banana belongs to the genus Musa from the family Musaceae. It is original from tropical regions and presents a strong ability to protect itself from the oxidative stress caused by extreme climatic conditions such as intense sunshine and high temperature. For this protection, bananas increase the production of bioactive compounds with antioxidant activity, which protect the fruit from the oxidative damage. Scientific studies have demonstrated that bananas (both in the pulp and peel) contain different antioxidant compounds, like vitamins (A, B, C and E), β-carotene and phenolic compounds (catechin, epicatechin, lignin, tannins, anthocyanins). Furthermore, banana is also notably rich in minerals, like potassium and phosphorus. The knowledge about the chemical composition and the contents in compounds with biological activity is of high interest given the importance of bananas as a valuable food all over the world. However, because bananas are perishable due to some factors like chemical reactions, including those that result in the production of ethylene, their postharvest conservation in pivotal for the commercialization. The effects of postharvest treatments and storage conditions on the composition of bananas are, therefore, essential. In this way, the present chapter focus on the composition of bananas, including macronutrients, micronutrients and bioactive compounds, as well as the effect of postharvest treatments and storage conditions in the quality of bananas.

INVESTIGATIVE COMPARISON OF TANK AND RECOVERED ASPHALT SAMPLES THROUGH PHYSICAL PERFORMANCE TESTING AND CHEMICAL ANALYSIS

Despite the development of improved performance test protocols by renowned researchers, there are still road networks which experience premature cracking and failure. One area of major concern in asphalt science and technology, especially in cold regions in Canada is thermal (low temperature) cracking. Usually right after winter periods, severe cracks are seen on poorly designed road networks. Quality assurance tests based on improved asphalt performance protocols have been implemented by government agencies to ensure that roads being constructed are at the required standard but asphalt binders that pass these quality assurance tests still crack prematurely. While it would be easy to question the competence of the quality assurance test protocols, it should be noted that performance tests which are being used and were repeated in this study, namely the extended bending beam rheometer (EBBR) test, double edge-notched tension test (DENT), dynamic shear rheometer (DSR) test and X-ray fluorescence (XRF) analysis have all been verified and proven to successfully predict asphalt pavement behaviour in the field. Hence this study looked to probe and test the quality and authenticity of the asphalt binders being used for road paving. This study covered thermal cracking and physical hardening phenomenon by comparing results from testing asphalt binder samples obtained from the storage ‘tank’ prior to paving (tank samples) and recovered samples for the same contracts with aim of explaining why asphalt binders that have passed quality assurance tests are still prone to fail prematurely. The study also attempted to find out if the short testing time and automated procedure of torsion bar experiments can replace the established but tedious procedure of the EBBR. In the end, it was discovered that significant differences in performance and composition exist between tank and recovered samples for the same contracts. Torsion bar experimental data also indicated some promise in predicting physical hardening.