Polarized fluorescence in an electric field. A model calculation with application to the geometry of the 2-hydroxy-4,4′-diamidinostilbene–DNA complex

Theoretical expressions are derived for the change in the polarized components of the fluorescence, resulting from the orientation of a rigid molecule bearing a chromophore with arbitrary angles for the absorption and transition moments \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _a $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _e $\end{document} with respect to the molecular axis. The break in the symmetry relation H_V = V_H is related to the tilt angle between \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _a $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _e $\end{document}. The theory is applied to a sonicated DNA–2-hydroxy-4,4′-diamidinostilbene complex, in the blue and red emission bands of this peculiar dye. Simultaneous measurements of linear dichroism and fluorescence lead to the determination of an angle of 47° between a fluorescent bound dye and the DNA axis, with no difference for the blue- and red-emitting species, but confirm the presence of nonfluorescent bound dye in a more perpendicular arrangement.     

Construction of Prediction Intervals in Location-Scale Families

Let x₁ ≤x₂ ≤x₃ … ≤x_r be the r smallest observations out of n observations from a location-scale family with density $ \frac{1}{\sigma}f\left({\frac{{x - \mu}}{\sigma}} \right) $ where μ and σ are the location and the scale parameters respectively. The goal is to construct a prediction interval of the form $ \left({\hat \mu + k_1 \hat \sigma,\,\hat \mu + k_2 \hat \sigma} \right) $ for a location-scale invariant function, T(Y) = T(Y₁, …, Y_m), of m future observations from the same distribution. Given any invariant estimators $ \hat \mu $ and $ \hat \sigma $, we have developed a general procedure for how to compute the values of k₁ and k₂. The two attractive features of the procedure are that it does not require any distributional knowledge of the joint distribution of the estimators beyond their first two raw moments and $ \hat \mu $ and $ \hat \sigma $ can be any invariant estimators of μ and σ. Examples with real data have been given and extensive simulation study showing the performance of the procedure is also offered.     

Effects of temperature on microbial ethanol production. III. The influence of the temperature on the relation existing between the specific ethanol formation rate of the yeast Saccharomyces cerevisiae Sc 5 and the ethanol concentration in the culture medium

The ethanol-inhibitory behaviour of the yeast Saccharomyces cerevisiae Sc 5 was found to be characterized by a continual-linear relation between the specific ethanol formation rate and the ethanol concentration. Therefore the simple equation could be applied for it. It is shown that this model is correct only then, if all of the process parameters are in their optimum. Out of the optimum temperature range the characteristics of the function ν = f(P) change in such a way that in regard to the ethanol concentration P twc linear relations exist for each suboptimum temperature: and a non-linear equation is current for each superoptimum temperature: where b_T is also a function of the temperature and always less than 1. Taking as a basis these equations the specific ethanol formation rate of the used strain can be calculated for the whole biokinetic P/T-sphere of ethanol production.     

A kinetic study of the alcoholic fermentation of grape juice

The alcoholic fermentation of grape juice by a wine yeast was studied batchwise at pH 3.6 and 4.05 to develop kinetic equations relating cell concentration, N, to product concentration, P. In the exponential growth phase where A, B, and C are constants, and μ is the specific growth rate. In the stationary phase, where the cell population is constant, was found to apply. This equation, which incorporates a stoichiometric constant, P_m, predicted correctly the operation of a continuous fermentor at pH 3.6 and at 4.05. To study more fully the effect of alcohol concentration on yeast growth, a continuous fermentor was used in which the grape juice feed was supplemented with pure alcohol. At pH 3.6 the specific growth rate varied as, There was no growth inhibition below an alcohol concentration of 2.6 g./100 cc., but inhibition was complete above 6.85 g./100 cc. This is a modified form of the relation suggested by Hinshelwood.¹ The data suggest that growth in batch culture was limited not only by alcohol but also by some other factor, probably a nutritional deficiency.     

On coenzyme Q orientation in membranes: A linear dichroism study of ubiquinones in a model bilayer

Summary A general approach is developed to interpret linear dichroism (LD) spectra of ubiquinones (Q _n) in host bilayers. Information is reported in terms of guest-host mutual orientation and localization. The overall orientational anisotropy of guest ubiquinone molecules is described by a basic set of limiting orientation/localization modes. Assignments of the UV transitions of the ubiquinone chromophore were obtained by the liquid crystal-linear dichroism technique and molecular orbital (CNDO/S) calculations. The LD spectra of Q _n in the bilayers provided by the lyotropic nematic mesophase exhibited by water solutions of potassium laurate and decanol were interpreted on the basis of the above assignments. The resulting experimental evidence showed a multisite distribution in the host bilayer for the aromatic heads of all the investigated Q _n derivatives except Q₀. The orientational distribution suggested by the LD spectra fits the solubilization model recently proposed by G. Lenaz [J. Membrane Biol. (1988) 104:193–209] for ubiquinone in lipid membranes. Within this model Q _n molecules are located in the midplane and their headgroups oscillate transversally across the membrane. Q ₀ instead has a single site location, close to the polar bilayer interface. Experimental evidence that the headgroup carbonyls tend to grasp the polar interface of the host bilayer was also obtained. Orientation and location distributions of Q _n guest molecules are therefore likely to result from the tendency of their aromatic heads to grasp the polar heads of the host bilayer and from the concurrent tendency of their chains to settle into the hydrocarbon host interior.abbreviations AA average absorption - OD, OD optical densities for plane polarized radiations parallel () and perpendicular () to the sample optical axis - OD OD — OD - EPR electron paramagnetic resonance - LC-LD liquid crystal-linear dichroism - LD linear dichroism - LD _r reduced linear dichroism. - MO molecular orbital - N nematic - NMR nuclear magnetic resonance - S _jj order parameters of the directions j of the transition moments of the guest chromophore - S _ii order parameters of the orientational axes i of the guest molecule with respect to the magnetic field - S _ii order parameters of the axes i of the guest molecules with respect to the bilayer axis a - S _a order parameters of the host bilayer axis a with respect to the orienting magnetic field - _j,i deflection angles between the directions j and the axes i - O _i optical factors of the i axis see Eq. (A4)] - Q_n ubiquinone whose isoprenoid chain contains n isoprenoid units Dr. A. Rossi is gratefully acknowledged for the t.e.m. reduction of the spectra. Ubiquinone homologs were kind gifts from Eisai Co., Tokyo, Japan. This work was supported by M.U.R.S.T., and C.N.R. Target Project on Biotechnology and Bioinstrumentation, Rome, Italy.     

Lipid vertical motion and related steric effects in bilayer membranes

We present a theoretical model of a lipid bilayer in its gel state which explicity couples the vertical displacements of the lipid chains to their conformational state. In this model the chains are free to move longitudinally under a potential due to the neighbouring chains. The potential is due to a restoring force with a force constant k and thus acts to keep them in the local plane as defined by their nearest neighbours. It is demonstrated that the force constant k is directly related to the internal bilayer pressure, , and that if a value =33 dynes/cm is assumed then k=17.3 dynes/cm. Steric effects are explicity included by allowing chains to twist into free volume created by the vertical displacement of neighbouring chains. The Hamiltonian is expressed in terms of the projection operators, P _ij , describing the displacement of chain i relative to a neighbour j, and G _ij describing the direction of a twist in chain i. The model is solved both analytically and via Monte Carlo simulations for a one-dimensional system. The possibility of phase-transitions in two-dimensions and the relevance to the bilayer pre-transition is discussed.This work was first presented in poster form at the Canadian Biochemical Society Conference held in Banff, Alberta, Canada, April 29–May 4, 1984Work supported in part by the Natural Sciences and Engineering Research Council of Canada, Le Fonds Formation des Chercheurs et Action a la Recherche du Quebec, and the Advisory Research Council of Queen's University     

Etude par spectroscopie infrarouge de la transformation hélice–chaîne statistique des polypeptides. II. Etude de l'interaction de quelques polypeptides à chaînes latérales polaires avec l'acide trifluoracétique

The various polymer–acid solvation possibilities occuring in the helix–coil transition process of polypeptides with polar side chains were systematically analyzed by infrared spectroscopy. The following samples have been considered: poly-γ-benzyl-L -glutamate (PBLG), alternating poly-γ-benzyl-D ,L -glutamate (PBD-LG), and poly-β-benzyl-L -as-partate (PBLA). The behavior of the amide A, I, II, and νC?O ester absorptions of each polymer dissolved in trifluoroacetic acid–chloroform mixtures was studied in depth. The classical assumptions concerning the interaction between a polypeptide and a proton donor solvent are discussed. This interaction was previously proposed in a theoretical model of helix–coil transition. For PBLG, the spectral characteristics of the cooperative transition are evidenced by the amide bands. These bands also show main chain–acid hydrogen bonding (I) Quantitative analysis of phenomenon (I) was performed in order to localize the “binding sites” of the polymer. In agreement with the theory, only the complexation of peptide units belonging to random coil and terminal helical regions were observed. However, in contrast to the theory in which the association constants KCO and KNH of these residues are generally kept equal, the present results have shown that the main binding site is the carbonyl group (KNH ? 0 or « KCO ). The behavior of the polar side chains of these polypeptides were analyzed during the transition. Similarly to the peptide backbone, they bind the acid by hydrogen bonding (II) Furthermore, this association is more important when the side chains are localized in the coiled regions than in the helical ones. This result suggests, by analogy with the main chain behavior, that the helix–coil transition theory should take into account two more association constants for polar side chains, namely k₁ for the helical regions and k₂ > k₁ for the coiled ones.     

Structural investigations on DNA-protamine complexes.

Protamine·DNA complexes in film and in solution have been investigated by means of infrared linear dichroism, ultraviolet circular dichroism, and laser Raman spectroscopy. At high relative humidity and in solution both infrared linear dichroism and ultraviolet circular dichroism indicate the presence of a modified B form of DNA (designated as B* in our other papers^27,28,46). This modified B form is characterized by a change of the orientation of the \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{OPO} $\end{document} bisector angle by about 4° with respect to the helical axis when compared to the B form of DNA. At decreasing relative humidities the same modified B form is maintained and no structural transitions B → A (or B → C) normally occurring in free DNA were observed. The absence of the A form in these complexes was also confirmed by laser Raman scattering studies of protamine·DNA complexes. On the basis of these results, a model of the protamine·DNA complex is proposed, which suggests that the presence of apolar amino-acid residues, and probably the folding of the polypeptide chain, is responsible for preventing the B-to-A transition; this occurs either by protecting the high-humidity modified B form against dehydration or by steric interference of this protein probably located in one of the DNA grooves.     

Conformational dependence of the vicinal proton coupling constant for the Cα?Cβ bond in peptides

We use the nmr data concerning the C^αH? C^βH fragment in eight peptides with rigid side chains to parametrize a Karplus correlation between the vicinal proton J_αβ coupling constant and the dihedral angle θ. When considering molecules containing the fragment C^αH^α? C^βH^βH^β′, the three-dimensional structure of the model peptides does not need to be known with accurate precision, since each set of J_αβ and J_αβ′ coupling constants is then related to the coefficients of the Karplus equation. A good correlation is observed with the Karplus equation, which is in substantial agreement with the J_αβ coupling constants reported for rigid as well as rotating C^α? C^β bonds in peptides.     

Buoyant densities of natural and synthetic DNA's in CsCl and Cs2SO4 considered as sequence-dependent properties

The buoyant densities of natural and synthetic DNA's can be accurately interrelated if second-neighbor influences are taken into account. We derive the following expressions, based partly on the buoyant densities of six synthetic DNA's, for the buoyant densities ρ (g/cm³) of DNA's having random sequences. In CsCl, and in Cs₂SO₄, . In these equations, H_G is the mole fraction of G : C base pairs in the DNA and the buoyant densities are calculated relative to densities for E. coli DNA of 1.703 and 1.426 (g/cm³) in CsCl and Cs₂SO₄, respectively.     

The parabolic pattern of animal growth: determination of equation parameters and their temperature dependencies

1. Parabolic (power) growth is characteristic of many aquatic poikilothermic animals for certain stages of their development. The parabolic pattern describing growth in weight (or length) under constant ambient conditions can be expressed in the following general form: where Y is growth rate (or specific growth rate), X is animal size, and Ω and τ are coefficients. The constancy of ambient conditions is of cardinal importance in determining τ. The problem of maintaining a constant level of nutrition can be reliably solved only by the presence of food in excess of demand. Data satisfying these requirements have demonstrated that τ does not depend on factors such as temperature, and can be assumed to be independent of ambient conditions. In the growth rate-weight equation, τ ranges between 0.5 and 0.85 for animals representing a variety of taxonomic groups. 2. The coefficient Ω. is affected by ambient conditions (e. g. temperature, amount of food). Its value reflects the ‘level’ of the growth rate-size relationship under given conditions. For a specific time period, Ω can be computed from the following formula: where X₁ and X₂ are the animal sizes (weights, lengths) at time t₁ and t₂, the beginning and end of the time period. The calculated value of Ω corresponds to the average intensity of the ambient factor (F) affecting the growth during the period between the two observations. If the values of the Ω are calculated for wide range of the factor, the relationship between the Ω. and F, Ω=f(F), can be determined. The function can be then incorporated into the parabolic equation of growth, as 3. Dependence of the development rate (1/D, where D is time interval needed to complete a given stage) on temperature (T), and dependence of Ω on T, are both described by sigmoid-shape curves. The broad intermediate part of these curves, a range to which animals are adapted in nature, can be approximated by straight line functions. For two groups, pan-size sockeye salmon (Oncorhynchus nerka) and different species of chironomid larvae, it was shown that an equation combining parabolic growth and linear temperature patterns describes accurately the variability observed in growth rates under experimental and natural conditions.     

Determination of thermodynamic functions from scanning calorimetry data. II. For the system that includes self-dissociation / association process

The basic relations between the molar fractions and the scanning calorimetry data for the system that includes self-dissociation/association process such as are presented, where m_i is the stoichiometric coefficient of the ith state A_i. The relations are described for each state j as where f_j(T) is the molar fraction function of state j and ΔH_j(T) is the difference enthalpy function of the system referred to the state j, which can be obtained by scanning calorimetry; R is the gas constant; and T is the absolute temperature. By these relations, scanning calorimetry data can be deconvoluted in order to determine the thermodynamic functions by means of single and double deconvolution. The concentration dependence of the data is analyzed by a method presented in this paper. The nonlinear least squares fitting method for the determination of the functions is discussed. For an example of the application of this method to the actual scanning calorimetry data, thermodynamic data of multistate thermal transition of Vibrio parahaemolyticus hemolysin are analyzed.     

Conformational characteristics of polyglutamic acid esters: Persistence of orientational correlation along the side chain flanking the α-helical backbone

The side chain conformations of α-helical poly(L -glutamic acid) esters $ \rlap{--}[NHCH(CH_2 CH_2 COOR)CO\rlap{--}]_x $, carrying a homologous series of ester residues such as R = ? (CH₂)_n? with n = 1–3, have been studied in the lyotropic liquid crystalline state (chloroform 20 v/v%) by the deuterium nmr method. In order to study the surface chirality of the molecule, the phenyl groups situated at the terminal of the side chain have been deuterated. From the observed deuterium quadrupolar splittings, the average inclination θ_p of the para-axis of the phenyl group with respect to the α-helical backbone was elucidated. A distinct odd–even oscillation in the quantity such as 〈 cos² θ_p〉 was observed with the number of methylene units n. A rotational isomeric state analysis has indicated that the observed orientational correlation arises from the interdependence of the neighboring bond rotation along the side chain. Preference of the “extended” conformations is also enhanced by the mutual conformational exclusion of neighboring side chains.     

Conformational studies of the capsular polysaccharide produced by Neisseria meningitidis group A

The effect of different cations on the conformational and morphological properties of the capsular polysaccharide produced by Neisseria meningitidis group A was investigated. Circular dichroism studies showed that the presence of Na⁺, or Ca²⁺ ions induced different local conformations of the polysaccharide chain through interactions with the phosphodiester group bridging the saccharide residues in the polymer chain. Atomic force microscopy experiments confirmed that the morphology of the polysaccharide chains was different depending on the nature of the counterion. Ammonium ions were associated with the presence of single polymer chains in an elongated conformation, whereas sodium ions favored the folding of the chains into a globular conformation. The addition of calcium ions produced the aggregation of a limited number of globular polysaccharide chains to form a ‘toroidal-like’ structure.     

Einfluß extracellulärer Konzentrationen auf die spezifische Wachstumsrate von Mikroorganismen

The influence of extracellular concentrations of hydrogen ion and C-substrates on the specific growth rate of different microorganisms is investigated. A general relationship in the form can be used to describe the inhibition effect of H^Plus;- or substrate concentration (c_i) on the growth rate. Different examples are demonstrated and the adequate specific constants K₁ and K₂ calculated.     

Growth characteristics of a thermotolerant strain of lodderomyces elongisporus grown on sucrose

A thermotolerant yeast species of Lodderomyces elongisporus EH 60 was isolated and physiologically characterized. This yeast possesses a high specific growth rate with μ_max = 0.61 h^?1. The dependence of the specific growth rate and cell yield on temperature, dilution rate, sucrose concentration and pH-value is investigated. Sucrose concentrations greater than 10 g/l inhibit the growth velocity. The specific growth rate μ can be calculated by a simple combination equation in the form: . The total optimum values for a sucrose-based continuous growth process with regard to the optimum cell yeild are: Y_S = 0.50 g DM/g S. T_opt. = 38,6 °C and D_opt. = 0,35 h^?1. The function Y_S = f(D, T) is represented by a total model.     

Inhibitory effects of ethanol in alcoholic fermentation

The ethanol tolerance behaviour of the strain Saccharomyces cerevisiae Sc 5 regarding the growth is characterized by a threshold ethanol inhibitory concentration (P₁' = 42.5 g/l) and a linear relationship between the specific growth rate and the ethanol concentration within the limits P₁' < P < P′. The maximum ethanol concentration for growth amounts to P′ = 84 g/l. A general model for the inhibition of growth and alcohol production, respectively, caused by ethanol, is deduced from experimental and bibliographical data: If the inhibitory effects are linear, the exponents b, b' become 1.     

Pigment orientation changes accompanying the light state transition in Synechococcus sp. PCC 6301

Low temperature (77 K) linear dichroism spectroscopy was used to characterize pigment orientation changes accompanying the light state transition in the cyanobacterium, Synechococcus sp. PCC 6301 and those accompanying chromatic acclimation in Porphyridium cruentum in samples stabilized by glutaraldehyde fixation. In light state 2 compared to light state 1 intact cells of Synechococcus showed an increased alignment of allophycocyanin parallel to the cells' long axis whereas the phycobilisomethylakoid membrane fragments exhibited an increased allophycocyanin alignment parallel to the membrane plane. The phycobilisome-thylakoid membrane fragments showed less alignment of a short wave-length chlorophyll a (Chl a) Q_y transition dipole parallel to the membrane plane in state 2 relative to state 1.To aid identification of the observed Chl a orientation changes in Synechococcus, linear dichroism spectra were obtained from phycobilisome-thylakoid membrane fragments isolated from red light-grown (increased number of PS II centres) and green light-grown (increased number of PS I centres) cells of the red alga Porphyridium cruentum. An increased contribution of short wavelength Chl a Q_y transition dipoles parallel to the long axis of the membrane plane was directly correlated with increased levels of PS II centres in red light-grown P. cruentum.Our results indicate that the transition to state 2 in cyanobacteria is accompanied by an increase in the orientation of allophycocyanin and a decrease in the orientation of Chl a associated with PS II with respect to the thylakoid membrane plane.Abbreviations APC - allophycocyanin - Chl a - chlorophyll a - DCMU - 3-(3,4-dichlorophenyl)-1,1-dimethylurea - LD - linear dichroism - LD/A - linear dichroism divided by absorbance - LHC - light-harvesting complex - PBS - phycobilisome - PC - phycocyanin - PS - Photosystem     

The effect of ethanol on continuous culture stability

The stability characteristics of a continuous culture system were studied following the addition of the natural product inhibitor, ethanol. For a steady state culture of Klebsiella (Aerobacter) aerogenes there was a linear dependence of growth rate on ethanol concentration. Following impulse and step addition of the inhibitor, response patterns of the growth rate (μ) and overall metabolism (Q_o2, Q_Co2, Q_AC) were observed. A mathematical model of the transient behavior of a product-limited system is proposed, and analog computer solutions fitted to the experimental data. The transient response of the growth rate could best be described by second or higher order equations, e.g., with values of the second order time constant (T₂) = 5 min, and damping coefficient (ξ) = 0.4.