Resolution and uniqueness of estimated parameters of a model of thin filament regulation in solution

The estimation of chemical kinetic rate constants for any non-trivial model is complex due to the nonlinear effects of second order chemical reactions. We developed an algorithm to accomplish this goal based on the Damped Least Squares (DLS) inversion method and then tested the effectiveness of this method on the McKillop–Geeves (MG) model of thin filament regulation. The kinetics of MG model is defined by a set of nonlinear ordinary differential equations (ODEs) that predict the evolution of troponin–tropomyosin–actin and actin–myosin states. The values of the rate constants are estimated by integrating these ODEs numerically and fitting them to a series of stopped-flow pyrene fluorescence transients of myosin-S1 fragment binding to regulated actin in solution. The accuracy and robustness of the estimated rate constants are evaluated for DLS and two other methods, namely quasi-Newton (QN) and simulated annealing (SA). The comparison of these methods revealed that SA provides the best estimates of the model parameters because of its global optimization scheme. However it converges slowly and does quantify the uniqueness of the estimated parameters. On the other hand the QN method converges rapidly but only if the initial guess of the parameters is close to the optimum values, otherwise it diverges. Overall, the DLS method proves to be the most convenient method. It converges fast and was able to provide excellent estimates of kinetic parameters. Furthermore, DLS provides the model resolution matrix, which quantifies the interdependence of model parameters thereby evaluating the uniqueness of their estimated values. This property is essential for estimating of the dependence of the model parameters on experimental conditions (e.g. Ca²⁺ concentration) when it is assessed from noisy experimental data such as pyrene fluorescence from stopped-flow transients. The advantages of the DLS method observed in this study should be further examined in other physicochemical systems to firmly establish the observed effectiveness of DSL vs. the other parameter estimation methods.     

Diffuse reflection and polarization modulation FT-IR spectrometry of surface species

Summary Two techniques for measuring the infrared spectra of adsorbed species on surfaces of different types are described. Diffuse reflectance spectra of species adsorbed on powdered substrates with a high surface area can be measured with an exceptionally high signal-to-noise ratio. The technique is illustrated by the adsorption of carbon monoxide on rhodium supported on alumina at metal loadings between 0.1 and 10%. Some doubt is cast on previous band assignments for adsorbed CO molecules. Grazing incidence reflection-absorption spectrometry can be used to measure the spectra of molecules on flat metallic substrates of very low surface area. Attempts to develop a technique for observing the intermolecular vibration between the adsorbate and the substrate using a unique triple modulation approach are discussed.

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FT-IR-Spektrometrie mit diffuser Reflexions- und Polari-sations-Modulation von Adsorbaten an Oberflächen

Zusammenfassung Zwei Techniken zur Messung von Infrarot-Spektren von Adsorbaten verschiedener Art werden beschrieben. Diffuse Reflexionsspektren von Adsorbaten an pulverförmigen Substraten mit einer großen Oberfläche können mit einem außerordentlich großen Signal-zu-RauschVerhältnis gemessen werden. Als Beispiel dient die Adsorption von Kohlenstoffmonoxid an Rhodium auf Aluminiumoxid bei Metallgehalten von 0,1 bis 10%. Einige Zweifel an früheren Bandzuweisungen für adsorbierte CO-Moleküle werden geäußert. Reflexions-Absorptions-Spektrometrie mit streifendem Einfall kann zur Messung der Spektren von Molekülen an flachen metallischen Substraten mit sehr geringer Oberfläche benutzt werden. Versuche zur Entwicklung einer Technik für die Beobachtung der intermolekularen Schwingungen zwischen dem Adsorbaten und dem Substrat mittels einer einzigartigen Dreifach-Modulationstechnik werden diskutiert.

     

Targeted Metabolomics for Biomarker Discovery

Metabolomics is a truly interdisciplinary field of science, which combines analytical chemistry, platform technology, mass spectrometry, and NMR spectroscopy with sophisticated data analysis. Applied to biomarker discovery, it includes aspects of pathobiochemistry, systems biology/medicine, and molecular diagnostics and requires bioinformatics and multivariate statistics. While successfully established in the screening of inborn errors in neonates, metabolomics is now widely used in the characterization and diagnostic research of an ever increasing number of diseases. In this Review we highlight important technical prerequisites as well as recent developments in metabolomics and metabolomics data analysis with special emphasis on their utility in biomarker identification and qualification, as well as targeted metabolomics by employing high‐throughput mass spectrometry.     

Compressibility measurements of quasi-one-dimensional quantum wires

We report measurements of the compressibility of a one-dimensional quantum wire, defined in the upper well of a GaAs/AlGaAs double quantum well heterostructure. A wire defined simultaneously in the lower well probes the ability of the upper wire to screen the electric field from a biased surface gate. The technique is sensitive enough to resolve spin splitting of the subbands in the presence of an in-plane magnetic field. We measure a compressibility signal due to the 0.7 structure and study its evolution with increasing temperature and magnetic field. We see no evidence of the formation of the quasibound state predicted by the Kondo model, instead our data are consistent with theories which predict that the 0.7 structure arises as a result of spontaneous spin polarization.     

Continuous and pulsed ultrasound-assisted extractions of antioxidants from pomegranate peel

There is a great demand for developing efficient extraction methods in order to reduce extraction time and increase the yield and activity of functional antioxidants. The yields, activities, and extraction kinetics of antioxidants from dry peel of pomegranate marc were studied using ultrasound-assisted extraction in continuous and pulsed modes and the results were compared with conventional extraction (CE) at a temperature of 25±2°C and water/peel ratio of 50/1, w/w. The studied factors were intensity level and treatment time for continuous ultrasound-assisted extraction (CUAE), and intensity level, number of pulse repetition, and pulse duration and interval for pulsed ultrasound-assisted extraction (PUAE). The results showed that all factors significantly affected the antioxidant yield, but only treatment time had a significant effect on the antioxidant activity. Compared to CE, PUAE at intensity level of 59.2 W/cm(2), and the 5 and 5s of pulse duration and interval increased the antioxidant yield by 22% and reduced the extraction time by 87%. Similarly, CUAE at the same intensity level increased the antioxidant yield by 24% and reduced the extraction time by 90%. Since PUAE had 50% energy saving compared to CUAE, we recommend using PUAE for the extraction with antioxidant yield of 14.5% and DPPH scavenging activity of 5.8 g/g. A second-order kinetic model was successfully developed for describing the mechanism of ultrasound-assisted extractions under PUAE and CUAE. This research clearly demonstrated the superiority of PUAE for producing antioxidants from peel of pomegranate marc.