Modeling of a control induced system for product formation in enzyme kinetics

Double substrate enzyme kinetics has a leading role for product quantification and optimization in different chemical and biochemical sectors. Mathematical approach for controlling these reactions in different stages by suitable parameters adds a new dimension in this interdisciplinary field of research. Applying control theoretic approach in the reversible backward stages of double substrate enzymatic model, time economization with regard to product formation is significant. In this article, we formulate a double substrate mathematical model of enzymatic dynamical reaction system with control measures with a view to observe the effect of changes of these measures with respect to the concentration of substrates, enzyme, complexes and finally product. Here, Pontryagin Minimum Principle is used for observing the effect of control measures in the system dynamics with the help of Hamiltonian. We compare the relevant numerical solutions for the substrates, enzyme, complexes and product concentration profile for a specified time interval with respect to control factors.     

A CNDO/2 localised orbital study of dipole moments of sila- and germa-ethylenes

CNDO/2 calculations have been performed to predict dipole moments for silaethylenes, with either Slater of Burns atomic orbitals, and for germaethylenes with Burns orbitals only. Trends on replacement of two hydrogen atoms at either end of the double bond by fluorine are similar in both sets for the silaethylenes and in accordance with expectation, but an anomalous trend is observed for fluorination of the carbon in germaethylenes.Localised orbitals have been examined to seek an explanation for this anomaly. In all cases the trends are in the unexpected sense for the π orbitals but in the expected sense for the others taken together and for most of these individually. The anomaly with the germaethylenes thus appears to be associated with the relative magnitudes of these opposing trends, where donation of electrons via the π bond to the germanium atom outweighs the accumulation of charge around the fluorine atoms attached to the carbon.     

Precise determination of isotopic ratios for some biologically significant elements by inductively coupled plasma mass spectroscopy

Isotope ratios for copper, iron, lead, lithium, nickel and zinc were measured with an ELAN 5000 ICP-MS instrument. Except for lithium isotopes, ratio relative standard deviations (RSDs) of about 0.1% were achieved with measurement times of 10 min or less per sample on isotope pairs that differed by no more than a factor of 10 in abundance. It was necessary to accumulate several million counts to reduce statistical counting errors, to correct for the dead time in the counting circuitry, and to compensate for a slow drift of apparent ratios with time. Drift compensation was achieved by using a third isotope of the test element, by adding two internal standard elements with isotopes bracketing the mass range of interest, or by frequent recalibration with a standard of known abundances. Attempts to compensate for drift in lithium isotope ratios were not successful and typical RSDs for ⁶Li/⁷Li remained around 0.5%. Copper and zinc ratios were measured in pig feces with ratio precision and drift behavior essentially identical to that seen for synthetic solutions.     

Determination of biuret in urea and mixed fertilizers

A new method has been developed for the determination of biuret in urea, based on the separation of the copper-biuret complex with the aid of an anionexchanger, followed by titration of the bound copper with EDTA. This method may be used directly for the determination of biuret in solutions and in end-products of a urea factory, even with biuret contents down to 0.001%. The well-known photometric method cannot be used for less than 0.1% biuret contents; corrections are needed for the interference of urea, and ammonia and insoluble products have to be removed. Both methods are suitable for the determination of biuret in mixed fertilizers down to 0.5%, provided that cations are first removed on a cation exchanger. However, the photometric determination calls for special precautions with regard to acidity when phosphates are present.     

Action spectra for photoinduced inactivation of bacteriophage T7 sensitized by 8-methoxypsoralen and angelicin

The action spectrum (240-300 nm) for photoinactivation of unsensitized phage T7 and the action spectra (310-380 nm) for photoinactivation of phage T7 sensitized with 8-methoxypsoralen (8-MOP) and angelicin were measured by an automated method. For unsensitized phage T7 the action spectrum is in good agreement with the absorption spectrum. For sensitization with angelicin the action spectrum is similar to the absorption spectrum, but for sensitization with 8-MOP the spectra are different. The agreement between the T7 absorption and action spectra in the far-UV region is due to photodamage of DNA, leading to phage inactivation. The similarity in the action and absorption spectra in the near-UV region for sensitization with angelicin seems to be in accordance with the monofunctional photobinding of angelicin to DNA. The action spectrum for sensitization with 8-MOP has a maximum at about 320 nm and this suggests that, in addition to the monoadducts, the biadducts play a role in the inactivation of phage T7. Taking the number of bound furocoumarin molecules into consideration, the quantum efficiencies were estimated. Furocoumarin increases the quantum efficiency in the near-UV region and the values are similar to those obtained in far-UV light without psoralens.     

Multiplexed identification of different fish species by detection of parvalbumin, a common fish allergen gene: a DNA application of multi-analyte profiling (xMAP™) technology

Fish are a common cause of allergic reactions associated with food consumption, with parvalbumin being the major allergenic protein. Some fish-hypersensitive patients tolerate some fish species while being allergic to others. Reliable detection methods for allergenic fish species in foods are necessary to ensure compliance with food allergen labeling guidelines to protect fish-allergic consumers. The objective of this project was to develop a multi-analyte detection method for the presence of fish in food. Therefore, conserved parvalbumin exon sequences were utilized for the design of universal PCR primers amplifying intron DNA and small regions of exons flanking the enclosed intron from even very distantly related fish species. An assay for the identification of eight fish species was developed using xMAP™ technology with probes targeting species-specific parvalbumin intron regions. Additionally, a universal fish probe was designed targeting a highly conserved exon region located between the intron and the reverse primer region. The universal fish assay showed no cross-reactivity with other species, such as beef, pork, lamb, chicken, turkey, and shrimp. Importantly, with the exception of one notable case with fish in the same subfamily, species-specific detection showed no cross-reactivity with other fish species. Limits of detection for these eight species were experimentally estimated to range from 0.01% to 0.04%, with potential to increase the detection sensitivity. This report introduces a newly developed method for the multiplex identification of at least eight allergenic fish species in food, which could conceivably be extended to detect up to 100 species simultaneously in one sample.     

Automatic multi-sample simultaneous multi-element analysis with a h.f. plasma torch and direct reading spectrometer

The equipment described for automatic multi-sample simultaneous multielement analysis has been in everyday use for practical analysis for four years. Some important points in its design are discussed and reasons are advanced for using a high-powered, free-running oscillator to excite a plasma with two gas streams in addition to the stream carrying the sample aerosol. The frequently-used simple formulae for inductance, appropriate for long coils, were found inadequate; modified formulae, applicable to short coils, which agreed with experimental data, were used. Trace analysis and assay work can alike be performed with good accuracy and precision, and in a convenient way. Some typical results are given, with an indication of the versatility of the equipment.     

Trace analysis of acidic pharmaceutical residues in waters with isotope dilution gas chromatography-mass spectrometry via methylation derivatization

Acidic pharmaceutical residues are pollutants of emerging concern and are generally monitored by HPLC-MS/MS. However, due to the limited separation efficiency of HPLC column and lack of suitable mass transition for confirmation analysis, some interference may not be separated completely and differentiated from ibuprofen, which may cause the results with interference, especially in sample with complex matrix. The objective of this study is to develop a sensitive and reliable method for the determination of acidic pharmaceutical residues in water samples by GC-MS with better resolution by using methylation derivatization and isotope dilution techniques. TMSDM, a mild reagent, was used as the derivatization reagent coupling with the isotope dilution technique, for the first time, to improve the precision and accuracy of the analytical method to determine the pharmaceutical residues in water. The MDLs for the five acidic organic compounds: ibuprofen, gemfibrozil, naproxen, ketoprofen and diclofenac were from 0.7 to 1.1 ng/L, with recoveries ranging from 93 to 110%. Alternative to the HPLC-MS/MS method, the developed GC-MS protocols provides an additional option for the analysis of acidic pharmaceutical residues in water, with better separation efficiency in reducing interferences from complicated sample matrix, for determination of ibuprofen residues.     

Snapshot of degenerative aging of porcine intervertebral disc: a model to unravel the molecular mechanisms

Larger animal models, such as porcine, have been validated as appropriate models of the human disc with respect to biomechanics and biochemistry. They are advantageous for research as the models are relatively straightforward to prepare and easily obtainable for research to perform surgical techniques. The intention of this study was to quantitatively analyze gene expression for collagen and proteoglycan components of the extracellular matrix and for collagenase (MMP-1) in porcine discs of varying ages (Newborn; 2-3weeks, Mature; 6-9 month, Older; 2-3 years). In this study, we observed that the cell number and GAG (glycosaminoglycan) formation dramatically decreased with aging. Also, gene expression in the annulus fibrosus (AF) and nucleus pulposus (NP) cells changed with aging. The level of MMP-1 mRNA increased with age and both type I, II collagens decreased with age. The level of aggrecan mRNA was highest in the mature group and decreased significantly with aging. In the mature group, MMP-1 expression was minimal compared to the newborn group. In AF cells, type II collagen was expressed at a high level in the mature group with a higher level of aggrecan, when aged NP showed a decrease in type II collagen. The model of IVD degeneration in the porcine disc shows many changes in gene expression with age that have been previously documented for human and may serve as a model for studying changes in IVD metabolism with age. We concluded that the porcine model is excellent to test hypotheses related to disc degeneration while permitting time-course study in biologically active systems.     

Including anharmonicity in the calculation of rate constants. 1. The HCN/HNC isomerization reaction

A method for calculating anharmonic vibrational energy levels in asymmetric top and linear systems that is based on second-order perturbation theory in curvilinear coordinates is extended to the bound generalized normal modes at nonstationary points along a reaction path. Explicit formulas for the anharmonicity coefficients, x(ij), and the constant term, E0, are presented, and the necessary modifications for resonance cases are considered. The method is combined with variational transition state theory with semiclassical multidimensional tunneling approximations to calculate thermal rate constants for the HCN/HNC isomerization reaction. Although the results for this system are not very sensitive to the choice of coordinates, we find that the inclusion of anharmonicity leads to a substantial improvement in the vibrational energy levels. We also present detailed comparisons of rate constants computed with and without anharmonicity, with various approximations for incorporating tunneling along the reaction path, and with a more practical approach to calculating the vibrational partition functions needed for larger systems.     

Intensity‐Carrying Modes in Raman and Raman Optical Activity Spectroscopy

We describe a quantum‐chemical approach for the determination of modes with maximum Raman and Raman optical activity (ROA) intensity by maximizing the intensities with respect to the Raman and Raman optical activity intensity, respectively, which is shown to lead to eigenvalue equations. The intensity‐carrying modes are in general hypothetical modes and do not directly correspond to a certain normal mode in the spectrum. However, they provide information about those molecular distortions leading to intense bands in the spectrum. Modes with maximum Raman intensity are presented for propane‐1,3‐dione, propane‐1,3‐dionate, and Λ‐tris(propane‐1,3‐dionato)cobalt(III). Moreover, the mode with highest ROA intensity is examined for this chiral cobalt complex and also for the (chiral) amino acid L ‐tryptophan. The Raman and ROA high‐intensity modes are an optimal starting guess for intensity‐tracking calculations, in which selectively normal modes with high Raman or ROA intensity are converged. We present the first Raman and ROA intensity‐tracking calculations. These reveal a high potential for large molecules, for which the selective calculation of normal modes with high intensity is desirable in view of the large computational effort required for the calculation of Raman and ROA polarizability property tensors.     

Electron-intramolecular-vibration interactions in positively charged phenanthrene-edge-type hydrocarbons

Electron-phonon interactions in positively charged phenanthrene-edge-type hydrocarbons such as phenanthrene, chrysene, and picene are studied. The C-C stretching modes around 1500 cm(-1) and the low-frequency modes around 500 cm(-1) strongly couple to the highest occupied molecular orbitals (HOMO) in phenanthrene-edge-type hydrocarbons. The total electron-phonon coupling constants for the monocations (lHOMO) of 0.251, 0.135, and 0.149 eV for phenanthrene, chrysene, and picene, respectively, are estimated to be larger than those of 0.130, 0.107, and 0.094 eV for anthracene, tetracene, and pentacene, respectively. The phase patterns difference between the HOMO localized on carbon atoms which are located at the molecular edge in acene-edge-type hydrocarbons and the delocalized HOMO in phenanthrene-edge-type hydrocarbons is the main reason for the result. Strengths of orbital interactions between two neighboring carbon atoms in the HOMO become weaker with an increase in molecular size because the electron density on each carbon atom in the HOMO becomes smaller with an increase in molecular size in phenanthrene-edge-type hydrocarbons. On the other hand, the frontier orbitals of acene-edge-type hydrocarbons have somewhat nonbonding characters and thus cannot strongly couple to the totally symmetric vibrational modes compared with the frontier orbitals of phenanthrene-edge-type hydrocarbons. This is the reason why the lHOMO value for phenanthrene-edge-type hydrocarbons decreases with an increase in molecular size more significantly than that for acene-edge-type hydrocarbons, and the reason why the lHOMO value for polyphenanthrene with C2v geometry (0.033 eV) is estimated to be similar to that for polyacene (0.036 eV). The reorganization energies between the neutral molecules and the corresponding monocations for phenanthrene-edge-type hydrocarbons with large molecular size are estimated to be larger than those for acene-edge-type hydrocarbons with large molecular size.     

Mean spherical approximation-mass action law theory of equilibrium and conductance in ionic solutions

An improved Bjerrum theory obtained by combining the mean spherical approximation with the mass action law (MSA&MAL) is used to calculate the fraction of ions unpaired over the full range of states of a primitive model electrolyte. It is combined with a new theory for the electrical conductance of the primitive model under the MSA to yield the conductance of an electrolyte over a wide range of concentrations and Bjerrum parameters with only two parameters A_o and R, the distance of closest approach, adjusted to fit the conductivity data. The theory fits the data for aqueous alkali halides over a wide concentration range with A_o values in good agreement with those deduced by more conventional theories and with reasonable small ion pairing constants deduced from the data. It fits the data for LiBr in octanol without the need for invoking triple ion formation. It leads to reasonable predictions for the conductance curves for 1:1 electrolytes even up to the molar region for solvents with dielectric constant from 10 to 80.     

Effect of antiplasticization on gas sorption and transport. I. Polysulfone

The addition of tricresyl phosphate, N-phenyl-2-naphthylamine, and 4,4′-dichlorodiphenyl sulfone to polysulfone causes changes in thermal and mechanical properties of the glassy mixtures associated with antiplasticization, i.e., reduction in glass transition temperature and increase in stiffness. These changes are also found to be accompanied by reductions in sorption of carbon dioxide and the permeability coefficients for helium, carbon dioxide, and methane at low diluent concentrations with reversal of these trends at higher levels as also occurs for the mechanical properties. Detailed analyses of data for carbon dioxide are given in terms of the dual sorption and mobility models often used for glassy polymers. The mobility for gas transport was found to decrease with diluent addition. The major cause for the decreased sorption is the reduction in glass transition temperature accompanying addition of the diluents. The changes in transport behavior approximately parallel the changes in mechanical behavior. These trends are not even qualitatively correlated with estimates of the excess volume changes associated with addition of the diluents to polysulfone.     

Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains

To establish force-field-based (molecular) modeling capability that will accurately predict condensed-phase thermophysical properties for materials containing aliphatic azide chains, potential parameters for atom types unique to such chains have been developed and added to the COMPASS force field. The development effort identified the need to define four new atom types: one for each of the three azide nitrogen atoms and one for the carbon atom bonded to the azide. Calculations performed with the expanded force field yield (gas-phase) molecular structures and vibrational frequencies for hydrazoic acid, azidomethane, and the anti and gauche forms of azidoethane in good agreement with values determined experimentally and/or through computational quantum mechanics. Liquid densities calculated via molecular dynamics (MD) simulations were also in good agreement with published values for 13 of 15 training set compounds, the exceptions being hydrazoic acid and azidomethane. Of the 13 compounds whose densities are well simulated, nine have experimentally determined heats of vaporization reported in the open literature, and in all of these cases, MD simulated values for this property are in reasonable agreement with the published values. Simulations with the force field also yielded reasonable density estimates for a series of 2-azidoethanamines that have been synthesized and tested for use as hydrazine-alternative fuels.     

Microfluidic Pressure Driven Liquid Chromatography of Biologically Relevant Samples

An overview of the literature regarding the most recent and innovative developments in microfluidic devices for pressure-driven chromatographic separations is given, with a focus on proteomics and metabolomics applications. The applications can be considered as the main driving force for the developments in this research field, since they put high demands on the analytical technology such as for throughput, efficiency, and sensitivity and for the possibilities to interface with mass spectrometry. The developments are evaluated based on the feasibility for use in work flows for the analysis of biologically relevant samples. The literature up to the first half of 2011 is covered. Electrophoretic separations are not within the scope of this review. Several strategies have been described to obtain a retentive phase in microfluidic channels. Open channels with the stationary phase bound to the walls appear to be relatively easy to make. However, the retention in such channels is generally very low for separations of relevant samples. Microfabrication of perfectly ordered topographic structures is the most innovative of the methods discussed for the creation of stationary phases in narrow channels. Several groups work on the improvement of the surface-to-volume ratio in such channels, using different methods, and the developments towards real applications are promising. Channels packed with spherical particles and in situ polymerized monoliths for pressure-driven separations are the most frequently applied. Microfluidic devices with an integrated injection system, a (packed) separation column and a spray tip for coupling to a mass spectrometer are already commercially available, and used in practice in proteomics and metabolomics. Finally, the inherent advantages of microfluidic devices for multidimensional separations have been shown in practice in a number of studies. In these studies, pressure-driven chromatography is coupled (in series or multiplexed) to an electrophoretic separation method. The high peak capacity of such 2-dimensional separations has been shown.

     

Estimation of the electron-collision initiation rate constant for the plasma polymerization and deposition of ethane using a transport-based model

The plasma polymerization and deposition of ethane in a parallel-plate electrode system was predicted using gas-phase transport equations and published gas-phase kinetic rate constants, with the assumption that the deposition rate was limited by the production of monomer free radicals and their diffusion to the deposition surface. The kinetic rate constant for radical initiation by electron collision with ethane was adjusted to bring the modelpredictionsfor mass deposition into line with experimental measurements reported in the literature for 12 combinations of power, gas fowrate, and pressure. Furthermore, the shapes of the predicted deposition profiles were made to closely match the experimental profiles by introducing an adjustable parameter to account for plasma boundary effects and two coefficients to account for nonradical polymerization (constant for all conditions). The best-fit electron-collision initiation constant was compared with theoretical predictions for oxygen and hydrogen in a manner explainable by bond strengths and vibrational degrees of freedom.     

不同腌制剂加工的鸡蛋皮蛋中微量元素含量测定

为了解不同腌制剂对鸡蛋皮蛋中微量元素含量的影响,用原子吸收分光光度法测定了不同腌制剂加工的鸡蛋皮蛋中微量元素含量。结果表明,用PbO为配料加工的鸡蛋皮蛋中Pb含量明显增高,蛋白和蛋黄的Pb含量达到63.34 mg/kg和42.16 mg/kg;用CuSO4为配制加工的鸡蛋皮蛋,蛋白和蛋黄的Cu含量为34.56 mg/kg和24.55 mg/kg;用ZnSO4为配料加工的鸡蛋皮蛋,蛋白和蛋黄的Zn含量为61.94 mg/kg和55.76 mg/kg。可见用含Pb、Cu和Zn的化合物为配料加工的鸡蛋皮蛋,其蛋白和蛋黄中对应元素的含量明显升高。建议有关部门禁止使用PbO为配料加工皮蛋。     

Selective on-line immunoextraction coupled to liquid chromatography for the trace determination of benzidine, congeners and related azo dyes in surface water and industrial effluents.

A new extraction immunosorbent involving antigen-antibody interactions was coupled on-line to liquid chromatography for the selective extraction in aqueous samples of benzidine and congeners, widely used as intermediate compounds in the manufacturing of dyes and pigments. Due to the cross-reactivity of the antibodies for analytes with chemical structures closely related to that of the analyte used for immunization, the immunoextraction sorbent was shown to be able to extract aminoazobenzene and related azo dyes with good recoveries. The on-line coupling was optimized for the trace determination of benzidine, dichlorobenzidine, aminoazobenzene and some azo dyes with detection limits in the range 0.1 to 1 microgram/l. The high selectivity of the immunoextraction was shown by comparing the analysis of an industrial textile effluent obtained using precolumns packed either with a non-selective polymeric sorbent or with the anti-benzidine immunosorbent. In such complex samples, extraction and clean-up are achieved in the same step.     

Comparison of gas chromatographic hyphenated techniques for mercury speciation analysis

In this study, we evaluate advantages and disadvantages of three hyphenated techniques for mercury speciation analysis in different sample matrices using gas chromatography (GC) with mass spectrometry (GC-MS), inductively coupled plasma mass spectrometry (GC-ICP-MS) and pyrolysis atomic fluorescence (GC-pyro-AFS) detection. Aqueous ethylation with NaBEt(4) was required in all cases. All systems were validated with respect to precision, with repeatability and reproducibility <5% RSD, confirmed by the Snedecor F-test. All methods proved to be robust according to a Plackett-Burnham design for 7 factors and 15 experiments, and calculations were carried out using the procedures described by Youden and Steiner. In order to evaluate accuracy, certified reference materials (DORM-2 and DOLT-3) were analyzed after closed-vessel microwave extraction with tetramethylammonium hydroxide (TMAH). No statistically significant differences were found to the certified values (p=0.05). The suitability for water samples analysis with different organic matter and chloride contents was evaluated by recovery experiments in synthetic spiked waters. Absolute detection and quantification limits were in the range of 2-6 pg for GC-pyro-AFS, 1-4 pg for GC-MS, with 0.05-0.21 pg for GC-ICP-MS showing the best limits of detection for the three systems employed. However, all systems are sufficiently sensitive for mercury speciation in environmental samples, with GC-MS and GC-ICP-MS offering isotope analysis capabilities for the use of species-specific isotope dilution analysis, and GC-pyro-AFS being the most cost effective alternative.