Functional genes and gene array analysis as tools for monitoring hydrocarbon biodegradation

Bioremediation, which is the exploitation of the intrinsic ability of environmental microbes to degrade and remove harmful compounds from nature, is considered to be an environmentally sustainable and cost-effective means for environmental clean-up. However, a comprehensive understanding of the biodegradation potential of microbial communities and their response to decontamination measures is required for the effective management of bioremediation processes. In this thesis, the potential to use hydrocarbon-degradative genes as indicators of aerobic hydrocarbon biodegradation was investigated. Small-scale functional gene macro- and microarrays targeting aliphatic, monoaromatic and low molecular weight polyaromatic hydrocarbon biodegradation were developed in order to simultaneously monitor the biodegradation of mixtures of hydrocarbons. The validity of the array analysis in monitoring hydrocarbon biodegradation was evaluated in microcosm studies and field-scale bioremediation processes by comparing the hybridization signal intensities to hydrocarbon mineralization, real-time polymerase chain reaction (PCR), dot blot hybridization and both chemical and microbiological monitoring data. The results obtained by real-time PCR, dot blot hybridization and gene array analysis were in good agreement with hydrocarbon biodegradation in laboratory-scale microcosms. Mineralization of several hydrocarbons could be monitored simultaneously using gene array analysis. In the field-scale bioremediation processes, the detection and enumeration of hydrocarbon-degradative genes provided important additional information for process optimization and design. In creosote-contaminated groundwater, gene array analysis demonstrated that the aerobic biodegradation potential that was present at the site, but restrained under the oxygen-limited conditions, could be successfully stimulated with aeration and nutrient infiltration. During ex situ bioremediation of diesel oil- and lubrication oil-contaminated soil, the functional gene array analysis revealed inefficient hydrocarbon biodegradation, caused by poor aeration during composting. The functional gene array specifically detected upper and lower biodegradation pathways required for complete mineralization of hydrocarbons. Bacteria representing 1 % of the microbial community could be detected without prior PCR amplification. Molecular biological monitoring methods based on functional genes provide powerful tools for the development of more efficient remediation processes. The parallel detection of several functional genes using functional gene array analysis is an especially promising tool for monitoring the biodegradation of mixtures of hydrocarbons.

On the maximal rate of (n+1) x n and (n+2) x n complex orthogonal designs

For p x n complex orthogonal designs in k variables, where p is the number of channels uses and n is the number of transmit antennas, the maximal rate L of the design is asymptotically half as n increases. But, for such maximal rate codes, the decoding delay p increases exponentially. To control the delay, if we put the restriction that p = n, i.e., consider only the square designs, then, the rate decreases exponentially as n increases. This necessitates the study of the maximal rate of the designs with restrictions of the form p = n+1, p = n+2, p = n+3 etc. In this paper, we study the maximal rate of complex orthogonal designs with the restrictions p = n+1 and p = n+2. We derive upper and lower bounds for the maximal rate for p = n+1 and p = n+2. Also for the case of p = n+1, we show that if the orthogonal design admit only the variables, their negatives and multiples of these by root-1 and zeros as the entries of the matrix (other complex linear combinations are not allowed), then the maximal rate always equals the lower bound.

Exact solution for the unsteady flow and heat transfer between eccentrically rotating disks

The unsteady heat transfer associated with flow due to eccentrically rotating disks considered by Ramachandra Rao and Kasiviswanathan (1987) is studied via reformulation in terms of cylindrical polar coordinates. The corresponding exact solution of the energy equation is presented when the upper and lower disks are subjected to steady and unsteady temperatures. For an unsteady flow with nonzero mean, the energy equation can be solved by prescribing the temperature on the disk as a sum of steady and oscillatory parts

Circulation and salinity distribution in coastal inlets

The mathematical model developed by Hansen and Rattray based on Pritchard's equations for a coastal-plain estuary has been analysed to study the circulation and salinity distributions in coastal inlets with constant width and depth. Numerical solutions of the basic equations have been obtained without placing any restriction on Rayleigh numbers. A noteworthy contribution of the present analysis is that solutions of equations have been obtained for higher Rayleigh numbers, which was not possible in the earlier model. It is found that the effect of higher Rayleigh numbers is to increase the vertical advection, making the salinities in the upper and lower layers more uniform with a distinct halocline near the mid-depths. Solutions are discussed for some special cases of practical interest.

Spacelike pion form factor from analytic continuation and the onset of perturbative QCD

The factorization theorem for exclusive processes in perturbative QCD predicts the behavior of the pion electromagnetic form factor F(t) at asymptotic spacelike momenta t(= -Q(2)) < 0. We address the question of the onset energy using a suitable mathematical framework of analytic continuation, which uses as input the phase of the form factor below the first inelastic threshold, known with great precision through the Fermi-Watson theorem from pi pi elastic scattering, and the modulus measured from threshold up to 3 GeV by the BABAR Collaboration. The method leads to almost model-independent upper and lower bounds on the spacelike form factor. Further inclusion of the value of the charge radius and the experimental value at -2.45 GeV2 measured at JLab considerably increases the strength of the bounds in the region Q(2) less than or similar to 10 GeV2, excluding the onset of the asymptotic perturbative QCD regime for Q(2) < 7 GeV2. We also compare the bounds with available experimental data and with several theoretical models proposed for the low and intermediate spacelike region.

A unified view of energetic efficiency in active drag reduction, thrust generation and self-propulsion through a loss coefficient with some applications

An analysis of the energy budget for the general case of a body translating in a stationary fluid under the action of an external force is used to define a power loss coefficient. This universal definition of power loss coefficient gives a measure of the energy lost in the wake of the translating body and, in general, is applicable to a variety of flow configurations including active drag reduction, self-propulsion and thrust generation. The utility of the power loss coefficient is demonstrated on a model bluff body flow problem concerning a two-dimensional elliptical cylinder in a uniform cross-flow. The upper and lower boundaries of the elliptic cylinder undergo continuous motion due to a prescribed reflectionally symmetric constant tangential surface velocity. It is shown that a decrease in drag resulting from an increase in the strength of tangential surface velocity leads to an initial reduction and eventual rise in the power loss coefficient. A maximum in energetic efficiency is attained for a drag reducing tangential surface velocity which minimizes the power loss coefficient. The effect of the tangential surface velocity on drag reduction and self-propulsion of both bluff and streamlined bodies is explored through a variation in the thickness ratio (ratio of the minor and major axes) of the elliptical cylinders.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data (sin theta/lambda)(max) = 1.1 angstrom(-1)] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H center dot center dot center dot N and N-H center dot center dot center dot O hydrogen bonds, in which the N3-H3B center dot center dot center dot N1 and N3-H3A center dot center dot center dot O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N center dot center dot center dot H and O center dot center dot center dot H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the pi-electron cloud.

Constraints on the omega pi form factor from analyticity and unitarity

Motivated by the discrepancies noted recently between the theoretical calculations of the electromagnetic omega pi form factor and certain experimental data, we investigate this form factor using analyticity and unitarity in a framework known as the method of unitarity bounds. We use a QCD correlator computed on the spacelike axis by operator product expansion and perturbative QCD as input, and exploit unitarity and the positivity of its spectral function, including the two-pion contribution that can be reliably calculated using high-precision data on the pion form factor. From this information, we derive upper and lower bounds on the modulus of the omega pi form factor in the elastic region. The results provide a significant check on those obtained with standard dispersion relations, confirming the existence of a disagreement with experimental data in the region around 0.6 GeV.

Multiobjective fuzzy optimization for sustainable groundwater management using particle swarm optimization and analytic element method

Groundwater management involves conflicting objectives as maximization of discharge contradicts the criteria of minimum pumping cost and minimum piping cost. In addition, available data contains uncertainties such as market fluctuations, variations in water levels of wells and variations of ground water policies. A fuzzy model is to be evolved to tackle the uncertainties, and a multiobjective optimization is to be conducted to simultaneously satisfy the contradicting objectives. Towards this end, a multiobjective fuzzy optimization model is evolved. To get at the upper and lower bounds of the individual objectives, particle Swarm optimization (PSO) is adopted. The analytic element method (AEM) is employed to obtain the operating potentio metric head. In this study, a multiobjective fuzzy optimization model considering three conflicting objectives is developed using PSO and AEM methods for obtaining a sustainable groundwater management policy. The developed model is applied to a case study, and it is demonstrated that the compromise solution satisfies all the objectives with adequate levels of satisfaction. Sensitivity analysis is carried out by varying the parameters, and it is shown that the effect of any such variation is quite significant. Copyright (c) 2015 John Wiley & Sons, Ltd.

Modified Simplified Rate Equation Model of Flowing Chemical Oxygen-Iodine Laser and its Application

A modified simplified rate equation (RE) model of flowing chemical oxygen-iodine laser (COIL), which is adapted to both the condition of homogeneous broadening and inhomogeneous broadening being of importance and the condition of inhomogeneous broadening being predominant, is presented for performance analyses of a COIL. By using the Voigt profile function and the gain-equal-loss approximation, a gain expression has been deduced from the rate equations of upper and lower level laser species. This gain expression is adapted to the conditions of very low gas pressure up to quite high pressure and can deal with the condition of lasing frequency being not equal to the central one of spectral profile. The expressions of output power and extraction efficiency in a flowing COIL can be obtained by solving the coupling equations of the deduced gain expression and the energy equation which expresses the complete transformation of the energy stored in singlet delta state oxygen into laser energy. By using these expressions, the RotoCOIL experiment is simulated, and obtained results agree well with experiment data. Effects of various adjustable parameters on the performances of COIL are also presented.

Deformation twinning and its effect on crack extension

Deformation twinning near a crack tip is observed in b.c.c. metal Mo based on molecular dynamics simulation at temperature T = 50 K and loading rate (K) over dot(II) = 0.0706 MPa m(1/2)/ps. The defor mation twinning is closely controlled by both the crystal geometry orientation and the stress distribution. The width of the deformation twin band is affected by the distance between the upper and lower crack surfaces. The twin plane and twin direction are (<1(1)over bar>2) and [(1) over bar 11], respectively. The initial crack extension occurs in the deformation twin region near the crack tip. The simulation shows that the extension direction of the crack is changed as the crack propagates over the twinning boundary.

Simulation of the Load-Unload Response Ratio and Critical Sensitivity in the Lattice Solid Model

The Load-Unload Response Ratio (LURR) method is an intermediate-term earthquake prediction approach that has shown considerable promise. It involves calculating the ratio of a specified energy release measure during loading and unloading where loading and unloading periods are determined from the earth tide induced perturbations in the Coulomb Failure Stress on optimally oriented faults. In the lead-up to large earthquakes, high LURR values are frequently observed a few months or years prior to the event. These signals may have a similar origin to the observed accelerating seismic moment release (AMR) prior to many large earthquakes or may be due to critical sensitivity of the crust when a large earthquake is imminent. As a first step towards studying the underlying physical mechanism for the LURR observations, numerical studies are conducted using the particle based lattice solid model (LSM) to determine whether LURR observations can be reproduced. The model is initialized as a heterogeneous 2-D block made up of random-sized particles bonded by elastic-brittle links. The system is subjected to uniaxial compression from rigid driving plates on the upper and lower edges of the model. Experiments are conducted using both strain and stress control to load the plates. A sinusoidal stress perturbation is added to the gradual compressional loading to simulate loading and unloading cycles and LURR is calculated. The results reproduce signals similar to those observed in earthquake prediction practice with a high LURR value followed by a sudden drop prior to macroscopic failure of the sample. The results suggest that LURR provides a good predictor for catastrophic failure in elastic-brittle systems and motivate further research to study the underlying physical mechanisms and statistical properties of high LURR values. The results provide encouragement for earthquake prediction research and the use of advanced simulation models to probe the physics of earthquakes.

The influence of stacks on flow patterns and stratification associated with natural ventilation

We investigate the steady state natural ventilation of an enclosed space in which vent A, located at height hA above the floor, is connected to a vertical stack with a termination at height H, while the second vent, B, at height hB above the floor, connects directly to the exterior. We first examine the flow regimes which develop with a distributed source of heating at the base of the space. If hBhB>hA, then two different flow regimes may develop. Either (i) there is inflow through vent B and outflow through vent A, or (ii) the flow reverses, with inflow down the stack into vent A and outflow through vent B. With inflow through vent A, the internal temperature and ventilation rate depend on the relative height of the two vents, A and B, while with inflow through vent B, they depend on the height of vent B relative to the height of the termination of the stack H. With a point source of heating, a similar transition occurs, with a unique flow regime when vent B is lower than vent A, and two possible regimes with vent B higher than vent A. In general, with a point source of buoyancy, each steady state is characterised by a two-layer density stratification. Depending on the relative heights of the two vents, in the case of outflow through vent A connected to the stack, the interface between these layers may lie above, at the same level as or below vent A, leading to discharge of either pure upper layer, a mixture of upper and lower layer, or pure lower layer fluid. In the case of inflow through vent A connected to the stack, the interface always lies below the outflow vent B. Also, in this case, if the inflow vent A lies above the interface, then the lower layer becomes of intermediate density between the upper layer and the external fluid, whereas if the interface lies above the inflow vent A, then the lower layer is composed purely of external fluid. We develop expressions to predict the transitions between these flow regimes, in terms of the heights and areas of the two vents and the stack, and we successfully test these with new laboratory experiments. We conclude with a discussion of the implications of our results for real buildings.

Modified Simplified Rate Equation Model of Flowing Chemical Oxygen-Iodine Laser and its Application

A modified simplified rate equation (RE) model of flowing chemical oxygen-iodine laser (COIL), which is adapted to both the condition of homogeneous broadening and inhomogeneous broadening being of importance and the condition of inhomogeneous broadening being predominant, is presented for performance analyses of a COIL. By using the Voigt profile function and the gain-equal-loss approximation, a gain expression has been deduced from the rate equations of upper and lower level laser species. This gain expression is adapted to the conditions of very low gas pressure up to quite high pressure and can deal with the condition of lasing frequency being not equal to the central one of spectral profile. The expressions of output power and extraction efficiency in a flowing COIL can be obtained by solving the coupling equations of the deduced gain expression and the energy equation which expresses the complete transformation of the energy stored in singlet delta state oxygen into laser energy. By using these expressions, the RotoCOIL experiment is simulated, and obtained results agree well with experiment data. Effects of various adjustable parameters on the performances of COIL are also presented.

Identification and estimation of size from the beaks of 18 species of cephalopods from the Pacific Ocean

A method of identifying the beaks and estimating body weight and mantle length of 18 species of cephalopods from the Pacific Ocean is presented. Twenty specimens were selected from each of the following cephalopod species: Symplectoteuthis oualaniensis, Dosidicus gigas, Ommastrephes bartramii, S. luminosa, Todarodes pacificus, Nototodarus hawaiiensis, Ornithoteuthis volalilis, Hyaloteuthis pelagica, Onychoteuthis banksii, Pterygioteuthis giardi, Abraliopsis affinis, A. felis, Liocranchia reinhardti, Leachia danae, Histioteuthis heteropsis, H. dofleini, Gonalus onyx, and Loligo opalescens. Dimensions measured on the upper and lower beak are converted to ratios and compared individually among the species using an analysis of variance procedure with Tukey's omega and Duncan's multiple range tests. Significant differences (P =0.05) observed among the species' beak ratio means and structural characteristics are used to construct artificial keys for the upper and lower beaks of the 18 species. Upper and lower beak dimensions are used as independent variables in a linear regression model with mantle length and body weight (log transformed). (PDF file contains 56 pages.)