Efficient and cost-effective experimental determination of kinetic constants and data: the success of a Bayesian systematic approach to drug transport, receptor binding, continuous culture and cell transport kinetics

Details about the parameters of kinetic systems are crucial for progress in both medical and industrial research, including drug development, clinical diagnosis and biotechnology applications. Such details must be collected by a series of kinetic experiments and investigations. The correct design of the experiment is essential to collecting data suitable for analysis, modelling and deriving the correct information. We have developed a systematic and iterative Bayesian method and sets of rules for the design of enzyme kinetic experiments. Our method selects the optimum design to collect data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. The rules select features of the design such as the substrate range and the number of measurements. We show here that this method can be directly applied to the study of other important kinetic systems, including drug transport, receptor binding, microbial culture and cell transport kinetics. It is possible to reduce the errors in the estimated parameters and, most importantly, increase the efficiency and cost-effectiveness by reducing the necessary amount of experiments and data points measured. (C) 2003 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

A novel method for the transport and analysis of genetic material from polyps and zooxanthellae of scleractinian corals

We have developed a new simple method for transport, storage, and analysis of genetic material from the corals Agaricia agaricites, Dendrogyra cylindrica, Eusmilia ancora, Meandrina meandrites, Montastrea annularis, Porites astreoides, Porites furcata, Porites porites, and Siderastrea siderea at room temperature. All species yielded sufficient DNA from a single FTA(R) card (19 mug-43 ng) for subsequent PCR amplification of both coral and zooxanthellar DNA. The D1 and D2 variable region of the large Subunit rRNA gene (LSUrDNA) was amplified from the DNA of P. furcata and S. siderea by PCR. Electrophoresis yielded two major DNA bands: an 800-base pair (bp) DNA, which represented the coral ribosomal RNA (rRNA) gene, and a 600-bp DNA, which represented the zooxanthellar srRNA gene. Extraction of DNA from the bands yielded between 290 mug total DNA (S. siderea coral DNA) and 9 mug total DNA (P. furcata zooxanthellar DNA). The ability to transport and store genetic material from scleractinian corals without resort to laboratory facilities in the field allows for the molecular Study of a far wider range and variety of coral sites than have been studied to date. (C) 2003 Elsevier Science B.V. All rights reserved.

Identification of stimulatory and inhibitory inputs to the hypothalamic-pituitary-adrenal axis during hypoglycaemia or transport in ewes

This study used the novel approach of statistical modelling to investigate the control of hypothalamic-pituitary-adrenal (HPA) axis and quantify temporal relationships between hormones. Two experimental paradigms were chosen, insulin-induced hypoglycaemia and 2 h transport, to assess differences in control between noncognitive and cognitive stimuli. Vasopressin and corticotropin-releasing hormone (CRH) were measured in hypophysial portal plasma, and adrenocorticotropin hormone (ACTH) and cortisol in jugular plasma of conscious sheep, and deconvolution analysis was used to calculate secretory rates, before modelling. During hypoglycaemia, the relationship between plasma glucose and vasopressin or CRH was best described by log(10) transforming variables (i.e. a positive power-curve relationship). A negative-feedback relationship with log(10) cortisol concentration 2 h previously was detected. Analysis of the 'transport' stimulus suggested that the strength of the perceived stimulus decreased over time after accounting for cortisol facilitation and negative-feedback. The time course of vasopressin and CRH responses to each stimulus were different However, at the pituitary level, the data suggested that log(10) ACTH secretion rate was related to log(10) vasopressin and CRH concentrations with very similar regression coefficients and an identical ratio of actions (2.3 : 1) for both stimuli. Similar magnitude negative-feedback effects of log(10) cortisol at -110 min (hypoglycaemia) or -40 min (transport) were detected, and both models contained a stimulatory relationship with cortisol at 0 min (facilitation). At adrenal gland level, cortisol secretory rates were related to simultaneously measured untransformed ACTH concentration but the regression coefficient for the hypoglycaemia model was 2.5-fold greater than for transport. No individual sustained maximum cortisol secretion for longer than 20 min during hypoglycaemia and 40 min during transport. These unique models demonstrate that corticosteroid negative-feedback is a significant control mechanism at both the pituitary and hypothalamus. The amplitude of HPA response may be related to stimulus intensity and corticosteroid negative-feedback, while duration depended on feedback alone.

Vibrational energy levels for the electronic ground state of the diazocarbene (CNN) molecule

The vibrational energy levels of diazocarbene (diazomethylene) in its electronic ground state, (X) over tilde (3) Sigma(-) CNN, have been predicted using the variational method. The potential energy surfaces of (X) over tilde (3) A" CNN were determined by employing ab initio single reference coupled cluster with single and double excitations (CCSD), CCSD with perturbative triple excitations [CCSD(T)], multi-reference complete active space self-consistent-field (CASSCF), and internally contracted multi-reference configuration interaction (ICMRCI) methods. The correlation-consistent polarised valence quadruple zeta (cc-pVQZ) basis set was used. Four sets of vibrational energy levels determined from the four distinct analytical potential functions have been compared with the experimental values from the laser-induced fluorescence measurements of Wurfel et al. obtained in 1992. The CCSD, CCSD(T), and CASSCF potentials have not provided satisfactory agreement with the experimental observations. In this light, the importance of both non-dynamic (static) and dynamic correlation effects in describing the ground state of CNN is emphasised. Our best theoretical fundamental frequencies at the cc-pVQZ ICMRCI level of theory, v(1) = 1230, v(2) = 394, and v(3) = 1420 cm(-1) are in excellent agreement with the experimental values of v(1) = 1235, v(2) = 396, and v(3) = 1419cm(-1) and the mean absolute deviation between the 23 calculated and experimental vibrational energy levels is only 7.4 cm(-1). It is shown that the previously suggested observation of the v(3) frequency at about 2847cm(-1) was in fact the first overtone 2v(3).

Theoretical rovibrational line intensities in the electronic ground state of ozone

First-principles calculations of absolute line intensities and rovibrational energies of ozone (O-16(3)) are reported using potential energy and electric dipole moment functions calculated by the internally contracted MRCI approach. The rovibrational energies and eigenfunctions (up to about 8500 cm(-1) and J = 64) were obtained variationally with an exact Hamiltonian in internal valence coordinates. More than 4.8 x 10(6) electric dipole transition matrix elements were calculated for the absolute rovibrational line intensities. They are compared with the values of the HITRAN database. The purely rotational absolute line intensities in the (000) state and the rovibrational intensities for the (001)-(000) band agree to within about 0.3 to 1% for the (0 10)-(000) band to within about 3 to 4%. Excellent agreement with experiment is also achieved for low-lying overtone and combination bands. Inconsistencies are found for the (100)-(000) band overlapping with the antisymmetric stretching fundamental and also for the (002)-(000) antisymmetric stretching overtone. The generated dipole moment function can be used for predicting the absorption intensities in any of the heavier isotopomers, hot bands or the rates of spontaneous emission.

Rovibrational energy levels for the electronic ground state of A1OH

The vibrational-rotational energy levels of aluminum monohydroxide in its electronic ground state, (A) over tilde (1)A' AlOH, have been predicted using the variational method. The potential energy surface of the (X) over tilde (1)A' ground state of AlOH was determined employing the ab initio coupled cluster method with single, double, and perturbative triple excitations [CCSD(T)] and the correlation-consistent polarized valence quadruple zeta (cc-pVQZ) basis set. Low-lying J= 0 and J= 1 vibrational levels are reported. These are analyzed in terms of the quasilinearity of the molecule. Coriolis effects are shown to be significant. We hope that our predictions will be of value in the future when assigning rovibrational transitions in spectroscopic studies. (c) 2006 Elsevier B.V. All rights reserved.

Nitrogen management is essential to prevent tropical oil palm plantations from causing ground-level ozone pollution

More than half the world's rainforest has been lost to agriculture since the Industrial Revolution. Among the most widespread tropical crops is oil palm (Elaeis guineensis): global production now exceeds 35 million tonnes per year. In Malaysia, for example, 13% of land area is now oil palm plantation, compared with 1% in 1974. There are enormous pressures to increase palm oil production for food, domestic products, and, especially, biofuels. Greater use of palm oil for biofuel production is predicated on the assumption that palm oil is an "environmentally friendly'' fuel feedstock. Here we show, using measurements and models, that oil palm plantations in Malaysia directly emit more oxides of nitrogen and volatile organic compounds than rainforest. These compounds lead to the production of ground-level ozone (O-3), an air pollutant that damages human health, plants, and materials, reduces crop productivity, and has effects on the Earth's climate. Our measurements show that, at present, O-3 concentrations do not differ significantly over rainforest and adjacent oil palm plantation landscapes. However, our model calculations predict that if concentrations of oxides of nitrogen in Borneo are allowed to reach those currently seen over rural North America and Europe, ground-level O-3 concentrations will reach 100 parts per billion (10(9)) volume (ppbv) and exceed levels known to be harmful to human health. Our study provides an early warning of the urgent need to develop policies that manage nitrogen emissions if the detrimental effects of palm oil production on air quality and climate are to be avoided.

Spectroscopy of highly excited vibrational states of HCN in its ground electronic state

An experimental technique based on a scheme of vibrationally mediated photodissociation has been developed and applied to the spectroscopic study of highly excited vibrational states in HCN, with energies between 29 000 and 30 000 cm(-1). The technique consists of four sequential steps: in the first one, a high power laser is used to vibrationally excite the sample to an intermediate state, typically (0,0,4), the nu(3) mode being approximately equivalent to the C-H stretching vibration. Then a second laser is used to search for transitions between this intermediate state and highly vibrationally excited states. When one of these transitions is found, HCN molecules are transferred to a highly excited vibrational state. Third, a ultraviolet laser photodissociates the highly excited molecules to produce H and CN radicals in its A (2)Pi electronic state. Finally, a fourth laser (probe) detects the presence of the CN(A) photofragments by means of an A-->B-->X laser induced fluorescence scheme. The spectra obtained with this technique, consisting of several rotationally resolved vibrational bands, have been analyzed. The positions and rotational parameters of the states observed are presented and compared with the results of a state-of-the-art variational calculation. (C) 2004 American Institute of Physics.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcal/mol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively. (C) 2008 American Institute of Physics.

Condensation and moisture transport in cold roofs: effect of roof underlay

Cold pitched roofs, with their form of construction situating insulation on a horizontal ceiling, are intrinsically vulnerable to condensation. This study reports the results derived from using a simulation package (Heat, Air and Moisture modelling tool, or HAM-Tools) to investigate the risk of condensation in cold pitched roofs in housing fitted with a vapour-permeable underlay (VPU) of known characteristics. In order to visualize the effect of the VPUs on moisture transfer, several scenarios were modelled, and compared with the results from a conventional bituminous felt with high resistance (200 MNs/g, Sd = 40 m). The results indicate that ventilation is essential in the roof to reduce condensation. However, a sensitivity analysis proved that reducing the overall tightness of the ceiling and using lower-resistance VPUs would help in controlling condensation formation in the roof. To a large extent, the proposed characteristic performance of the VPU as predicted by manufacturers and some researchers may only be realistic if gaps in the ceiling are sealed completely during construction, which may be practically difficult given current construction practice.