Biochemical biomarkers in samples processed by different methods in Environmental Specimen Banks

In the last decades the creation of new Environmental Specimen Banks (ESB) is increasing due to the necessity of knowing the effects of pollutants in both the environment and human populations. ESBs analyze and store samples in order to understand the effects of chemicals, emerging substances and the environmental changes in biota. For a correct analysis of the effect induced by these variables, there is a need to add biological endpoints, such as biomarkers, to the endpoints based on chemical approaches which have being used until now. It is essential to adapt ESB´s sampling strategies in order to enable scientists to apply new biological methods. The present study was performed to obtain biochemical endpoints from samples stored in the BBEBB (Biscay Bay Environmental Biospecimen Bank) of the Marine Station of Plentzia (PIE - UPV/EHU). The main objective of the present work was to study the variability caused in biochemical biomarkers by different processing methods in mussels (Mytilus galloprovincialis) from two localities (Plentzia and Arriluze) with different pollution history. It can be concluded that the selected biomarkers (glutathione S-transferase and acetylcholinesterase) can be accurately measured in samples stored for years in the ESBs. The results also allowed the discrimination of both sampling sites. However, in a further step, the threshold levels and baseline values should be characterized for a correct interpretation of the results in relation to the assessment of the ecosystem health status.

National Status and Trends Bioeffects Program: field methods

Environmental quality indicators provide resource managers with information useful to assess coastal condition and scientifically defensible decisions. Since 1984, the National Oceanic and Atmospheric Administration (NOAA), through its National Status and Trends (NS&T) Program, has provided environmental monitoring data on chemical, physical, and biological indicators of coastal environments. The program has two major monitoring components to meet its goals. The Bioeffects Assessments Program evaluates the health of bays, estuaries, and the coastal zone around the nation using the Sediment Quality Triad technique that includes measuring sediment contaminant concentrations, sediment toxicity and benthic community structure. The Mussel Watch Program is responsible for temporal coastal monitoring of contaminant concentrations by quantifying chemicals in bivalve mollusks. The NS&T Program is committed to providing the highest quality data to meet its statutory and scientific responsibilities. Data, metadata and information products are managed within the guidance protocols and standards set forth by NOAA’s Integrated Ocean Observing System (IOOS) and the National Monitoring Network, as recommended by the 2004 Ocean Action Plan. Thus, to meet these data requirements, quality assurance protocols have been an integral part of the NS&T Program since its inception. Documentation of sampling and analytical methods is an essential part of quality assurance practices. A step-by–step summary of the Bioeffects Program’s field standard operation procedures (SOP) are presented in this manual.

Assessment of some physico-chemical parameters of River Ogun (Abeokuta, Ogun State, southwestern Nigeria) in comparison with national and international standards

This study assessed the physico-chemical quality of River Ogun, Abeokuta, Ogun state, Southwestern Nigeria. Four locations were chosen spatially along the water course to reflect a consideration of all possible human activities that are capable of changing the quality of river water. The water samples were collected monthly for seven consecutive months (December 2011 – June 2012) at the four sampling stations. pH, air temperature (℃), water temperature (℃), conductivity (µs/cm) and total dissolved solids (mg/L) were conducted in-situ with the use of HANNA Combo pH and EC multi meter Hi 98129 and Mercury-in-glass thermometer while dissolved oxygen (mg/L), nitrate (mg/L), phosphate (mg/L), alkalinity (mg/L) and hardness (mg/L) were determined ex-situ using standard methods. Results showed that dissolved oxygen, hydrogen ion concentration, total hardness and nitrate were above the maximum permissible limit of National Administration for Food, Drugs and Control (NAFDAC), Standard Organization of Nigeria (SON), Federal Environmental Protection Agency (FEPA), United States Environmental Protection Agency (USEPA), European Union (EU) and World Health Organization (WHO) for drinking water during certain months of the study period. Results also showed that water temperature and conductivity were within the permissible limits of all the standards excluding FEPA. However, total dissolved solids and alkalinity were within the permissible limits of all the standards. Adejuwon and Adelakun, (2012) also reported similar findings on Rivers Lala, Yobo and Agodo in Ewekoro local government area of Ogun state, Nigeria. Since most of the parameters measured were above the maximum permissible limits of the national and international standards, it can be concluded that the water is unfit for domestic uses, drinking and aquacultural purposes and therefore needs to be treated if it is to be used at all. The low dissolved oxygen values for the first four months was too low i.e. < 5 mg/L. This is most likely as a result of the amount of effluents discharged into the river. To prevent mass extinction of aquatic organisms due to anoxic conditions, proper regulations should be implemented to reduce the organic load the river receives.

Deposition of diamond-like carbon films by photon-enhanced chemical vapour deposition of methane using a windowless hydrogen lamp

Thin films of diamond-like carbon (DLC) have been deposited using a novel photon-enhanced chemical vapour deposition (photo-CVD) method. This low energy method may be a way to produce better interfaces in electronic devices by reducing damage due to ion bombardment. Methane requires high energy photons for photolysis to take place and these are not transmitted in most photo-CVD methods owing to the presence of a window between the lamp and the deposition environment. In our photo-CVD system there is no window and all the high energy photons are transmitted into the reaction gas. Initial work has proved promising and this paper presents recent results. Films have been characterized by measuring electron energy loss spectra, by ellipsometry and by fabricating and testing diode structures. Results indicate that the films are of a largely amorphous nature and are semiconducting. Diode structures have on/off current ratios of up to 106.

Methods of sensory evaluation of quality and application of statistical methods in sensory evaluation problems with special reference to fishery products

The quality of raw and processed fishery products depend on several factors like physiological conditions at the time of capture, morphological differences, rigor mortis, species, rate of icing and subsequent storage conditions. Sensory evaluation is still the most reliable method for evaluation of the freshness of raw processed fishery products. Sophisticated methods like Intelectron fish tester, cell fragility technique and chemical and bacteriological methods like estimation of trimethylamine, hypoxanthine, carbonyl compounds, volatile acid and total bacterial count have no doubt been developed for accessing the spoilage in fish products.

Methods of harvesting and preservation of the diatom Chaetoceros calcitrans

Diatom culture and larval feeding experiments were conducted to test the viability and acceptability of preserved algal concentrates. C. calcitrans is characterised by the presence of setae which keep them suspended in cultures and make autoflocculation very difficult. Flocculation was induced by the addition of a floc-forming chemical. Using the optimum conditions, it was possible to harvest the algae within 1-h settling time and with about 84% recovery. The viability of frozen Chaetoceros was determined by actual cell reproduction. Preliminary feeding experiments showed that Chaetoceros can be successfully used as a substitute for fresh diatoms as feed for Penaeus monodon larvae. Simple freezing techniques, with or without the use of protectants has been found convenient for preserving algal concentrates in small volumes for both feeding and culture purposes.

Chemical Constituents from the Leaves and Stems of Schisandra rubriflora

Six new nortriterpenoids, schirubridilactones A-F (1-6). as well as 14 known compounds, were isolated from the leaves and stems of Schisandra rubriflora. The Structures of 1-6 were elucidated oil the basis of spectroscopic methods including HSQC, HMBC, H-1-H-1 COSY, and ROESY NMR experiments. The relative stereochemistry of I was confirmed through single-crystal X-ray analysis. In addition, compounds 1-6 showed anti-HIV-1 activity with EC50 values in the range 14.3-80.8 mu g/mL and Selectivity indices in the range 2.2-9.0.

Direct chemical vapor deposition of large-area carbon thin films on gallium nitride for transparent electrodes: A first attempt

Direct formation of large-area carbon thin films on gallium nitride by chemical vapor deposition without metallic catalysts is demonstrated. A high flow of ammonia is used to stabilize the surface of the GaN (0001)/sapphire substrate during the deposition at 950°C. Various characterization methods verify that the synthesized thin films are largely sp 2 bonded, macroscopically uniform, and electrically conducting. The carbon thin films possess optical transparencies comparable to that of exfoliated graphene. This paper offers a viable route toward the use of carbon-based materials for future transparent electrodes in III-nitride optoelectronics, such as GaN-based light emitting diodes and laser diodes. © 1988-2012 IEEE.

On representing chemical environments

We review some recently published methods to represent atomic neighbourhood environments, and analyse their relative merits in terms of their faithfulness and suitability for fitting potential energy surfaces. The crucial properties that such representations (sometimes called descriptors) must have are differentiability with respect to moving the atoms, and invariance to the basic symmetries of physics: rotation, reflection, translation, and permutation of atoms of the same species. We demonstrate that certain widely used descriptors that initially look quite different are specific cases of a general approach, in which a finite set of basis functions with increasing angular wave numbers are used to expand the atomic neighbourhood density function. Using the example system of small clusters, we quantitatively show that this expansion needs to be carried to higher and higher wave numbers as the number of neighbours increases in order to obtain a faithful representation, and that variants of the descriptors converge at very different rates. We also propose an altogether new approach, called Smooth Overlap of Atomic Positions (SOAP), that sidesteps these difficulties by directly defining the similarity between any two neighbourhood environments, and show that it is still closely connected to the invariant descriptors. We test the performance of the various representations by fitting models to the potential energy surface of small silicon clusters and the bulk crystal.

Alternative methods for surface texturing

Surface texturing has a great potential to improve tribological performance. First, possible texturing methods were identified and classified according to their physical principles. In sequence, some alternative texturing methods are presented. Some of them are already currently used either in industry or in laboratory, and innovations or simplifications are described for them. Others are innovative techniques. Some were explored only tentatively, where basic ideas and simple experimental investigations were developed to check their validity. Others were explored in more detail, so that their practical applicability could be identified. The first texturing method was photochemical texturing using a simple and cheap apparatus. Masking with inkjet printing before chemical etching was also successful to texture metallic samples. A new method involving electrochemical texturing, without the need to previously mask the samples to be textured have been studied in terms of voltage, current, mechanical configuration of the apparatus and electrolyte flushing. Another method aims to generate randomly distributed circular pockets on steel surfaces and involves dispersion of small acid droplets in oil. The final method involves the selective formation of hard areas on a steel surface by locallised diffusion, which should then develop into a texture during wear.

Simulations of thermal upgrading methods for oil shale reservoirs

This paper analyzes reaction and thermal front development in porous reservoirs with reacting flows, such as those encountered in shale oil extraction. A set of dimensionless parameters and a 3D code are developed in order to investigate the important physical and chemical variables of such reservoirs when heated by in situ methods. This contribution builds on a 1D model developed for the precursor study to this work. Theory necessary for this study is presented, namely shale decomposition chemical mechanisms, governing equations for multiphase flow in porous media and necessary closure models. Plotting the ratio of the thermal wave speed to the fluid speed allows one to infer that the reaction wave front ends where this ratio is at a minimum. The reaction front follows the thermal front closely, thus allowing assumptions to be made about the extent of decomposition solely by looking at thermal wave progression. Furthermore, this sensitivity analysis showed that a certain minimum permeability is required in order to ensure the formation of a traveling thermal wave. It was found that by studying the non-dimensional governing parameters of the system one can ascribe characteristic values for these parameters for given initial and boundary conditions. This allows one to roughly predict the performance of a particular method on a particular reservoir given approximate values for initial and boundary conditions. Channelling and flow blockage due to carbon residue buildup impeded each method's performance. Blockage was found to be a result of imbalanced heating. Copyright 2012, Society of Petroleum Engineers.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Mechanical and chemical bonding properties of ground state BeH2

The crystal structure, mechanical properties and electronic structure of ground state BeH2 are calculated employing the first-principles methods based on the density functional theory. Our calculated structural parameters at equilibrium volume are well consistent with experimental results. Elastic constants, which well obey the mechanical stability criteria, are firstly theoretically acquired. The bulk modulus B, Shear modulus G, Young's modulus E, and Poisson's ratio upsilon are deduced from the elastic constants. The bonding nature in BeH2 is fully interpreted by combining characteristics in band structure, density of states, and charge distribution. The ionicity in the Be-H bond is mainly featured by charge transfer from Be 2s to H 1s atomic orbitals while its covalency is dominated by the hybridization of H 1s and Be 2p states. The Bader analysis of BeH2 and MgH2 are performed to describe the ionic/covalent character quantitatively and we find that about 1.61 (1.6) electrons transfer from each Be (Mg) atom to H atoms.

Chemical trends of defect formation in Si quantum dots: The case of group-III and group-V dopants

Using first-principles methods, we have systematically calculated the defect formation energies and transition energy levels of group-III and group-V impurities doped in H passivated Si quantum dots (QDs) as functions of the QD size. The general chemical trends found in the QDs are similar to that found in bulk Si. We show that defect formation energy and transition energy level increase when the size of the QD decreases; thus, doping in small Si QDs becomes more difficult. B-Si has the lowest acceptor transition energy level, and it is more stable near the surface than at the center of the H passivated Si QD. On the other hand, P-Si has the smallest donor ionization energy, and it prefers to stay at the interior of the H passivated Si QD. We explained the general chemical trends and the dependence on the QD size in terms of the atomic chemical potentials and quantum confinement effects.