Measurement of protein by spectrophotometry at 205 nm

A method is described for the measurement of protein concentration by using the peptide bond absorption at 205 nm. ?₂₀₅ is estimated, allowing for the absorption due to Trp and Tyr residues, by measuring the absorbance at 280 nm as well as at 205 nm. The estimated ?₂₀₅ is compared with the actual ?₂₀₅ for a number of proteins, the mean error being less than 2%. This is about three times better than using an average ?₂₀₅^{1 mg/ml} of 31 and approaches the range of experimental error inherent in any method of protein estimation.     

Purification, properties, and kinetic observations on the isoenzymes of NADP isocitrate dehydrogenase of maize.

A successful method for the purification of NADP isocitrate dehydrogenase from a plant source, Zea mays, is reported. Two mitochondrial isoenzymes were found and purified to homogeneity by a course of acetone fractionation, bulk exchange on DEAE-cellulose, cellulose hydroxylapatite column chromatography, and continuous elution electrophoresis. The mitochondrial isoenzymes are very similar with respect to kinetic properties, response to solvent perturbation, and temperature dependence of the pH/V relationship of isocitrate dehydrogenation. The Michaelis constant for isocitrate is identical for both isoenzymes. The enzymes have a molecular weight of 81,000 as estimated by permeation chromatography and an isoelectric point of 5.5 as extrapolated from gel-electrophoretic mobilities. Detectable differences are confined to differences in electrophoretic mobilities and heat denaturation. In D₂O the rate of the overall reaction from isocitrate to α-ketoglutarate and CO₂ was about 3.6 times slower than the same reaction in H₂O. Both the forward and reverse reactions, in which isocitrate is dehydrogenated or generated from oxalosuccinate, were observed to decrease by this amount in D₂O. The decarboxylation of oxalosuccinate was found to decrease by only about 25% in D₂O relative to the velocity of the reaction in H₂O. Thus the slow step in the overall reaction must be the initial dehydrogenation step rather than the decarboxylation of oxalosuccinate. The pK of the overall reaction did not change in D₂O as compared to H₂O.     

Simultaneous Determination of Glass Transition Temperatures of Several Polymers

Aims

A simple and easy optical method is proposed for the determination of glass transition temperature (T_g) of polymers.

Methods & Results

T_g was determined using the technique of microsphere imaging to monitor the variation of the refractive index of polymer microsphere as a function of temperature. It was demonstrated that the method can eliminate most thermal lag and has sensitivity about six fold higher than the conventional method in T_g determination. So the determined T_g is more accurate and varies less with cooling/heating rate than that obtained by conventional methods. The most attractive character of the method is that it can simultaneously determine the T_g of several polymers in a single experiment, so it can greatly save experimental time and heating energy.

Conclusion

The method is not only applicable for polymer microspheres, but also for the materials with arbitrary shapes. Therefore, it is expected to be broadly applied to different fundamental researches and practical applications of polymers.     

Electron Microscopy of Retinal Photoreceptors : The Use of Chromation Following Formaldehyde Fixation as a Complementary Technique to Osmium Tetroxide Fixation

The fine structure of the cone and rod outer segments of the toad was studied under the electron microscope after fixation in osmium tetroxide and fixation in formaldehyde followed by chromation. In the OsO₄-fixed specimens, the rod outer segment appears to be built of a stack of lobulated flattened sacs, each of which is made of two membranes of about 40 A separated by an innerspace of about 30 A. The distance between the rod sacs is about 50 A. The sacs in the cone outer segment are originated by the folding of a continuous membrane. The thickness of the membranes and width of the spaces between the cone sacs is the same as in rod, but the sac innerspace is slightly narrower in the cone (~ 20 A). After fixation in formaldehyde and chromation, two different dense lines (l₁ and l₂) separated by spaces of less density appear. One of the lines, l₁, has a thickness of 70 A and is less dense than the other, l₂, which is 30 A thick. The correlation of the patterns obtained with both fixatives is considered and two possible interpretations are given. The possibility that l₂ is related to a soluble phospholipid component is discussed. It is suggested that the outer segments have a paracrystallin organization similar to that found in myelin.     

Reliable prediction of adsorption isotherms via genetic algorithm molecular simulation

Conventional molecular simulation techniques such as grand canonical Monte Carlo (GCMC) strictly rely on purely random search inside the simulation box for predicting the adsorption isotherms. This blind search is usually extremely time demanding for providing a faithful approximation of the real isotherm and in some cases may lead to non-optimal solutions. A novel approach is presented in this article which does not use any of the classical steps of the standard GCMC method, such as displacement, insertation, and removal. The new approach is based on the well-known genetic algorithm to find the optimal configuration for adsorption of any adsorbate on a structured adsorbent under prevailing pressure and temperature. The proposed approach considers the molecular simulation problem as a global optimization challenge. A detailed flow chart of our so-called genetic algorithm molecular simulation (GAMS) method is presented, which is entirely different from traditions molecular simulation approaches. Three real case studies (for adsorption of CO₂ and H₂ over various zeolites) are borrowed from literature to clearly illustrate the superior performances of the proposed method over the standard GCMC technique. For the present method, the average absolute values of percentage errors are around 11% (RHO-H₂), 5% (CHA-CO₂), and 16% (BEA-CO₂), while they were about 70%, 15%, and 40% for the standard GCMC technique, respectively.     

Diagnostics of a nonequilibrium nitrogen plasma from the emission spectra of the second positive system of N2

A method is proposed for determining the electron density N _e and the electric field E in the non-equilibrium nitrogen plasma of a low-pressure discharge from the spectra of the second positive system of N₂. The method is based on measuring the specific energy deposition in the plasma and the distribution of nitrogen molecules over the vibrational levels of the C ³Π _u state, as well as on modeling this distribution for a given energy deposition. The fitting parameters of the model are the values of N _e and E. A kinetic model of the processes governing the steady-state density of the C ³Π _u nitrogen molecules is developed. The testing of this method showed it to be quite reliable. The method is of particular interest for diagnosing electrodeless discharges and provides detailed information on the processes occurring in the discharge plasma. Preliminary data are obtained on the plasma parameters in a cavity microwave discharge and an electrode microwave discharge. In particular, it is found that the electric field in an electrode microwave discharge in nitrogen is lower than that in a hydrogen discharge. This effect is shown to be produced by stepwise and associative processes with the participation of excited particles in nitrogen.     

Separation of acetanilide and its hydroxylated metabolites and quantitative determination of "acetanilide 4-hydroxylase activity" by high-pressure liquid chromatography.

A simple and very sensitive method for the separation of 4-hydroxyacetanilide, 3-hydroxyacetanilide, 2-hydroxyacetanilide, and acetanilide was developed with the use of high-pressure liquid chromagraphy. Each of these phenolic derivatives can be separated completely from acetanilide and from one another. A simple assay for “acetanilide 4-hydroxylase activity” is thus described. The limit of sensitivity for cytochrome P-450-mediated acetanilide 4-hydroxylase activity is estimated to be 1.0 pmol/min/mg microsomal protein, thereby allowing this assay to be useful in detecting monooxygenase activity in “low level” nonhepatic tissues. Hepatic acetanilide 4-hydroxylase activity is induced about fourfold in $\text{C57BL}\text{6N}$ mice by 3-methylcholanthrene. Although acetanilide 2-hydroxylase activity is about seven times lower than the 4-hydroxylase activity, the 2-hydroxylase is also induced about three- or fourfold in $\text{C57BL}\text{6N}$ mice by 3-methylcholanthrene. The “2-hydroxylase activity” cannot, however, be strictly quantitated under the conditions described herein. The K_m values of both the 3-methylcholanthrene-induced and control 4-hydroxylase activity are about 0.55 mm; V_max values for 3-methylcholanthrene-treated and control mice, respectively, are 4.9 ± 1.1 and 1.1 ± 0.31 nmol/min/mg microsomal protein. The 4-hydroxylase in the liver of both 3-methylcholanthrene-treated and control mice appears to represent two or more catalytic activities, i.e., two or more forms of P-450 having widely differing affinities for the substrate acetanilide.     

Helical channels in crystals of gramicidin A and of a cesium--gramicidin A complex: an x-ray diffraction study.

X-ray crystallographic studies of gramicidin A crystallized from methanol (P2₁) and ethanol (P2₁2₁2₁), and of a Cs⁺ gramicidin A complex crystallized from methanol (P222₁, P2₁2₁2 or P2₁2₁2₁) are reported here. The asymmetric unit consists of two molecules of gramicidin A in the native crystals and four molecules in the cesium complex crystal. Patterson analyses show that gramicidin A in these crystals forms a cylindrical helical channel. In the two types of native gramicidin crystals, the diameter of this channel is about 5 å and its length is about 32 å. Cesium ions are bound inside this channel in crystals of the cesium-gramicidin A complex. The channel in this complex is considerably shorter (26 Å) and wider (6·8Å) than in the native forms. The Patterson maps of these three crystal forms are compatible with either the single-stranded β-helix (Urry, 1971) or the double-stranded parallel or anti-parallel, β-helix (Veatch et al., 1974).     

Steady-state kinetics of ADP-arsenate and ATP-synthesis in Rhodospirillum rubrum chromatophores

(1) Rates of ATP synthesis and ADP-arsenate synthesis catalyzed by Rhodospirillum rubrum chromatophores were determined with the firefly luciferase method and by a coupled enzyme assay involving hexokinase and glucose-6-phosphate dehydrogenase. (2) V_m for ADP-arsenate synthesis was about 2-times lower than V_m for ATP-synthesis. With saturating [ADP], K(As_i) was about 20% higher than K(P_i). With saturating [anion], K(ADP) was during arsenylation about 20% lower than during phosphorylation. (3) Plots of $\text{1}\text{v}$ vs. $\text{1}\text{[}\text{substrate}\text{]}$ were non-linear at low concentrations of the fixed substrate. The non-linearity was such as to suggest a positive cooperativity between sites binding the variable substrate, resulting in an increased $\text{V}{}_{\mathrm{<mtext>m</mtext>}}\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ ratio. High concentrations of the fixed substrate cause a similar increase in $\text{V}{}_{\mathrm{<mtext>m</mtext>}}\text{K}{}_{\mathrm{<mtext>m</mtext>}}$, but abolish the cooperativity of the sites binding the variable substrate. (4) Low concentrations of inorganic arsenate (As_i) stimulate ATP synthesis supported by low concentrations of P_i and ADP about 2-fold. (5) At high ADP concentrations, the apparent K_i of As_i for inhibition of ATP-synthesis was 2–3-times higher than the apparent K_m of As_i for arsenylation; the apparent K_i of P_i for inhibition of ADP-arsenate synthesis was about 40% lower than the apparent K_m of P_i for ATP synthesis. (6) The results are discussed in terms of a model in which P_i and As_i compete for binding to a catalytic as well as an allosteric site. The interaction between these sites is modulated by the ADP concentration. At high ADP concentrations, interaction between these sites occurs only when they are occupied with different species of anion.     

Exploring structural homology of proteins.

A method for systematically comparing the folding of the three-dimensional structures of proteins has been developed. A search function, plotted in terms of three Eulerian angles, represents the number of sequentially equivalenced amino acids. For each orientation one protein structure is rotated about its center of mass with respect to the other and probabilities are calculated which estimate the degree of structural parallelism. The structurally equivalent residues with highest probabilities are then selected for the best common topology. It was observed that, when structures containing about 150 residues were compared, the random background had a mean value of around 14 residues and the standard deviation was approximately nine residues. The method has been shown to be successful in determining the similarity of the NAD binding domains of lactate dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase, and in comparing the heme binding fold of cytochrome b₅ with the globins.Application of the method to compare hen egg white lysozyme and T4 phage lysozyme led to a single significant peak of 62 residues. The structural homology indicated by this peak showed that the substrate, as bound to hen egg white lysozyme, has a corresponding binding site in the large cleft of the phage lysozyme. The predicted binding site of N-acetyl glucosamine at position C compares well with an N-acetyl glucosamine center observed to bind to crystalline phage lysozyme (B. W. Matthews, personal communication).Some results for the comparison of the two Fe-S cage binding domains of ferredoxin are also presented.     

The results of an assessment of the ecological state of zoobenthos communities according to the difference of evenness index (D E′ )

The difference of the evenness index (D _E′ ) is offered for an assessment of the ecological state of zoobenthos communities. The index is deduced on the basis of the Shannon indexes calculated according to abundance and biomass data and differentiates between these informational estimations (Shannon diversity) of evenness of species in any given community. Conclusions made by Pianka about the predomination of organisms with r and K life strategy in communities impacted and unimpacted by ecological stress, as well as the ABC-curves method suggested by Warwick, were used as the basis of the functioning mechanism for the suggested index. The examples of index applicability are demonstrated by an assessment of materials collected in freshwater, estuarine, and marine waterbodies during one-time surveys and long-term monitoring observations. The results are compared with zoobenthos assessments made on the basis of some other indexes. Conclusions concerning the efficiency of the D _E′ have been made and some of its advantages over other indexes are shown.     

Studies on glutathione-S-arene oxidase transferase. A sensitive assay and partial purification of the enzyme from sheep liver

A sensitive assay has been devised for glutathione-S-arene oxidase transferase using as substrates naphthalene-1,2-oxide or styrene oxide along with [³⁵S]glutathione. Activity of the order of 2–3 nmoles of conjugate formed during a 5-min incubation can be detected. This yields about 2000 cpm above a blank of about 1500 cpm. Transferase activity was found mainly in liver and kidney but was also present in most other tissues of rats. Glutathione-S-arene oxide transferase has been purified 70- to 80-fold from sheep liver 100,000 g supernatants using the conventional procedures. After electrofocusing, enzyme activity separated into two major peaks and two or three minor peaks, ranging in isoelectric point from pH 6.5 to 7.5. Activities assayed with naphthalene-1,2-oxide or styrene oxide as substrates were found to almost parallel each other in all the peaks.The sheep liver transferase required neither metal ions nor cofactors such as FAD, pyridoxal-phosphate and thiamine pyrophosphate. The molecular weight of the transferase has been estimated to be about 40,000.K_m values for glutathione, naphthalene-1,2-oxide, and styrene oxide are 1.6, 0.11, and 0.13 mm, respectively. K_m values for glutathione decreased with increasing pH, whereas the K_m values for naphthalene-1,2-oxide were independent of pH in the range of 6.5–8.     

Analysis of metabolism by mathematical programming techniques

A method is presented for analyzing metabolic interactions by procedures based on mathematical programming techniques. In the procedures described it is assumed that the organism has (through natural selection) maximized (within the constraints imposed on it by its genetic constitution) its fitness to the environment. A practical experimental procedure is described through which the constraints imposed on reaction rates can be observed and from which the metabolic objective function which, it is presumed, metabolism has optimized can be calculated. A method for testing the validity of the objective function is given. Discussion is carried out in terms of a two-dimensional example but the procedures are valid for any number of dimensions. The results of the procedures are expressed by statements of the sort: the metabolic interactions of the cell are such that Q is maximized where Q = a₁x₁ + a₂x₂ + ... + a_nx_n, where a₁, ..., a_n are constants and x₁, ..., x_n are reaction rates. Some possible uses of metabolic objective functions are given.     

Reexamination of the interaction between ferredoxin:NADP reductase and NADP

A comparison was made of graphical and subtractive methods for the determination of the dissociation constant of a complex between ferredoxin:NADP reductase and NADP. The subtractive method gave K_d values near 10 μm which are consistent with recently determined values for K_m,NADP in assays of NADP photoreduction by chloroplast membranes. The graphical method gave values which were considerably higher. The difference between the two methods is due to the failure of the graphical method to correct for the amount of each component present in the complex at the low NADP/ flavoprotein ratios necessary for binding studies. A second NADP binding site of much lower affinity (K_d approx 1 mm) was also detected.     

A Two-Stage System for the Large-Scale Cultivation of Biomass: a Design and Operation Analysis Based on a Simple Steady-State Model Tuned on Laboratory Measurements

The optimal design and operation at large scale of a continuous fermentation process including a biological reactor/photobioreactor and a gravity settler with partial recycle and purge of the biomass are addressed. The proposed method is developed with reference to microalgae (Scenedesmus obliquus) cultivation, but it can be applied to any fermentation process as well as to activated sludge wastewater treatment. A procedure is developed to predict the effect of process variables, mainly the recycle ratio (R), the solid retention time (θ _c ), the reactor residence time (θ), and the ratio between feed and purge flow rates (F _I /F _W ). It includes a simple steady-state model of the two units coupled in the process and the experimental measurement of basic kinetic data, in both the bioreactor and the settler, for the tuning of model parameters. The bioreactor is assumed as perfectly mixed, and a rigorous gravity-flux approach is used for the settler. The process model is solved in terms of dimensionless variables, and plots are given to allow sensitivity analyses and optimization of operating conditions. A discussion about washout is presented, and a simple method is outlined for the calculation of the minimum values of residence time (θ _min ) and recycle ratio (R _min ) and of the maximum allowed recycle ratio (R _{max,operating} ) and biomass purge rate (F _Wmax ). In particular, it is shown that the system is sensitive to the concentration of biomass lost from the top of the settler (C _X ^S ). The proposed method can be useful for the design and analysis of large-scale processes of this type.     

Gate Length Variation Effect on Performance of Gate-First Self-Aligned In0.53Ga0.47As MOSFET

A multi-gate n-type In_0.53Ga_0.47As MOSFET is fabricated using gate-first self-aligned method and air-bridge technology. The devices with different gate lengths were fabricated with the Al₂O₃ oxide layer with the thickness of 8 nm. In this letter, impact of gate length variation on device parameter such as threshold voltage, high and low voltage transconductance, subthreshold swing and off current are investigated at room temperature. Scaling the gate length revealed good enhancement in all investigated parameters but the negative shift in threshold voltage was observed for shorter gate lengths. The high drain current of 1.13 A/mm and maximum extrinsic transconductance of 678 mS/mm with the field effect mobility of 364 cm²/Vs are achieved for the gate length and width of 0.2 µm and 30µm, respectively. The source/drain overlap length for the device is approximately extracted about 51 nm with the leakage current in order of 10⁻⁸ A. The results of RF measurement for cut-off and maximum oscillation frequency for devices with different gate lengths are compared.     

A sensitive technique for the rapid measurement of carbon dioxide concentrations

A method has been developed to measure concentrations of CO₂ in gases rapidly. A gas sample is injected into a flowing carrier gas that passes through an infrared CO₂ analyzer. A strip chart recorded peak response is obtained which is proportional to the CO₂ concentration. A resolution of better than 2 microliters of CO₂ per liter of gas was obtained. Seven to 10 seconds were required for sample analysis once the sample was obtained. Sorghum bicolor plant respiration was determined at different temperatures by measuring CO₂ using this system and by using a conventional system. The correlation between techniques was 0.996, and about the same variation occurred within each method. This technique greatly increased the efficiency of the infrared CO₂ analyzer in our laboratory for use in plant respiration and photosynthetic studies.     

Analysis of phospholipase C (Bacillus cereus) action toward mixed micelles of phospholipid and surfactant.

The action of phospholipase C (Bacillus cereus) toward mixed micelles of phosphatidylcholine and the nonionic surfactant Triton X-100 is analyzed according to the “surfaceas-cofactor” kinetic scheme recently proposed for characterizing the action of lipolytic enzymes [Deems, R. A., Eaton, B. R., and Dennis, E. A. (1975) J. Biol. Chem.250, 9013–9020]. According to this scheme, the enzyme first associates with the surface or mixed micelles, where the dissociation constant is K_s^A. The enzyme, now part of the mixed micelle surface, then binds the substrate phospholipid molecule in its active site and this binding is related to the Michaelis constant, K_m^B. The surface, or mixed micelles in this scheme, behaves kinetically as a cofactor in that, under initial rate conditions, the surface properties of the mixed micelles are virtually unchanged after catalysis. For phospholipase C with egg phosphatidylcholine as substrate, it was found that at pH 6.4 (the pH optimum for the enzyme) and 40 °C, V is about 2 × 10³ μmol min^?1 (mg of protein)^?1. K_s^A is about 2 mm and K_m^B is 1 to 2 × 10^?10 mol cm^?2. The kinetic constants for phospholipase C are compared with those previously reported for phospholipase A₂ and the membrane-bound enzyme phosphatidylserine decarboxylase determined under similar conditions.     

Hydrocarbons,sterols and tocopherols in the seeds of six Adansonia species

The composition of the unsaponifiable matter of the lipids of six Adansonia species (A. grandidieri, A. za, A. fony, A. madagascariensis, A. digitata and A. suarezensis) was investigated. The total unsaponifiable content, its general composition and the identity of the components of the hydrocarbon, sterol and tocopherol fractions are presented. The unsaponifiable content in oil ranges from 0.4 to 1.1% (hexane method) and from 0.6 to 2.2% (diethyl ether method). In two species (A. grandidieri and A. suarezensis) the major components are 4-demethylsterols (23–42%) tocopherols (37-10%) and hydrocarbons (15–17%). In both species examined, eight 4-demethylsterols occur in the sterol fraction with sitosterol (81–88%) being predominant. Among the four tocopherols present, γ-tocopherol (68–98%) is the major compound. Each Adansonia species shows a characteristic gas liquid chromatography pattern for the hydrocarbon fraction. Squalene is the major component for five species (40–75%). Iso-, anteiso- and other branched hydrocarbons were not identified but were present in small amounts in comparison with n-alkanes. The dominance of odd- over even-carbon number chain length of n-alkanes was not observed in any species. The results show that C₂₂, C₂₅, C₂₆, C₂₇, C₂₈ and C₂₉ are the most frequent major constituents.     

A partial characterization of the cyclic nucleotide phosphodiesterases of Drosophila melanogaster

The cyclic nucleotide phosphodiesterases in crude homogenate, soluble material, and particulate preparations of adult Drosophila melanogaster flies, hydrolyze cyclic AMP with nonlinear kinetics. Cyclic GMP is hydrolyzed by the phosphodiesterases in crude homogenate and soluble material with linear kinetics. Physical separation techniques of gel filtration, velocity sedimentation, and ion-exchange chromatography reveal that Drosophila soluble fraction contains two major forms of cyclic nucleotide phosphodiesterase. Form I hydrolyzes both cyclic AMP and cyclic GMP. Inhibition experiments suggest that the hydrolysis of both cyclic nucleotides by Form I occurs at a single active site. The K_m's for hydrolysis of both substrates are about 4 μm. This form has a molecular weight of about 168,000 as estimated by gel nitration. Form II cyclic nucleotide phosphodiesterase is specific for cyclic AMP as substrate. Gel filtration indicates that this form has a molecular weight of about 68,000. The K_m for cyclic AMP is about 2 μm.