Distance-constraint approach to protein folding. I. Statistical analysis of protein conformations in terms of distances between residues

A statistical analysis of protein conformations in terms of the distance between residues, represented by their C atoms, is presented. We consider four factors that contribute to the determination of the distanced _i,i+k between a given pair ofith and(i+k)th residues in the native conformation of a globular protein: (1) the distancek along the chain, (2) the size of the protein, (3) the conformational states of theith to(i+k)th residues, and (4) the amino acid types of the and(i+k)th residues. In order to account for the dependence on the distancek along the chain, the statistics are taken for three ranges, viz., short, medium, and long ranges (k8; 9k20; andk21; respectively). In the statistics of short-range distances, a mean distanceD _k and its standard deviationS _k are calculated for each value ofk, with and without taking into account the conformational states of all residues fromi toi+k (factors 1 and 3). As an Appendix, the relations for converting from the distances between residues into other conformational parameters are discussed. In the statistics of long-range distances, a reduced distanced* _ij (the actual distance divided by the radius of gyration) is used to scale the data so that they become independent of protein size, and then a mean reduced distanceD _l (a, a) and its standard deviation _l (a, a) are calculated for each amino acid pair (a, a) (factors 2 and 4). The effect of the neighboring residues along the chain on the value of the distanced* _ij is explored by a linear regression analysis between the actual reduced distanced* _ij and the mean value over theD _l for all possible pairs of residues in the two segments of the (i–2)th to the (i+2)th and the (j–2)th to the (j+2)th residues. The effect is assessed in terms of the tangentA _l (a, a) of the calculated regression line for each amino acid pair (a, a). In the statistics of medium-range distances, only factors 1 and 4 are considered, to simplify the analysis. The scaled distanced _i,i+k =(d _i,i+k -D _k )/S _k is used to eliminate the dependence onk, the distance along the chain. The propertiesD _m (a, a), _m (a, a) andA _m (a, a) corresponding toD _l (a, a), _l (a, a), andA _l (a, a), and also calculated for each amino acid pair (a, a). The results are interpreted as follows: the smaller values ofD _l (a, a) andD _m (a, a) indicate a preference of the pair (a, a) for a contact (e.g., pairs between hydrophobic amino acids, and pairs of Cys with aromatic amino acids), and the larger values of these quantities indicate a preference for distant mutual location (e.g., pairs between strong hydrophilic amino acids); the smaller values of _l (a, a) and _m (a, a) indicate a strong preference for either contact or noncontact (e.g., pairs between hydrophobic amino acids, and pairs between strong hydrophobic and hydrophilic amino acids, respectively), and the larger values of these quantities indicate the ambivalent/neutral nature of the preference for contact and noncontact (e.g., pairs containing Ser or Thr); the smaller values ofA _l (a, a) andA _m (a, a) indicate that the distance of an (a, a) pair is determined independently of the amino acid character of the neighboring residues along the chain (e.g., some pairs of Cys or Met with other amino acids) and the larger values of these quantities indicare that such amino acid character contributes strongly to the determination of the distance (e.g., pairs containing Ser or Thr, and pairs between amino acids with small side chains). The difference between the statistics for the long- and medium-range distances is also discussed; the former reflect the difference between the hydrophobic and hydrophilic character of the residues, but the latter cannot be easily interpretable only in terms of hydrophobicity and hydrophilicity. The data analyzed here are used in the optimization of an object function to compute protein conformation in a subsequent paper.     

A mathematical theory of the functional dynamics of cortical and thalamic nervous tissue

It is proposed that distinct anatomical regions of cerebral cortex and of thalamic nuclei are functionally two-dimensional. On this view, the third (radial) dimension of cortical and thalamic structures is associated with a redundancy of circuits and functions so that reliable signal processing obtains in the presence of noisy or ambiguous stimuli.A mathematical model of simple cortical and thalamic nervous tissue is consequently developed, comprising two types of neurons (excitatory and inhibitory), homogeneously distributed in planar sheets, and interacting by way of recurrent lateral connexions. Following a discussion of certain anatomical and physiological restrictions on such interactions, numerical solutions of the relevant non-linear integro-differential equations are obtained. The results fall conveniently into three categories, each of which is postulated to correspond to a distinct type of tissue: sensory neo-cortex, archior prefrontal cortex, and thalamus.The different categories of solution are referred to as dynamical modes. The mode appropriate to thalamus involves a variety of non-linear oscillatory phenomena. That appropriate to archior prefrontal cortex is defined by the existence of spatially inhomogeneous stable steady states which retain contour information about prior stimuli. Finally, the mode appropriate to sensory neo-cortex involves active transient responses. It is shown that this particular mode reproduces some of the phenomenology of visual psychophysics, including spatial modulation transfer function determinations, certain metacontrast effects, and the spatial hysteresis phenomenon found in stereopsis.List of Symbols (t) Post-synaptic membrane potential (psp) - Maximum amplitude of psp - t Time - The neuronal membrane time constant - Threshold value of membrane potential - r Absolute refractory period - Synaptic operating delay - v Velocity of propagation of action potentil - x Cartesian coordinate - _jj (x) The probability that cells of class j are connected with cells of class j a distance x away - b _jj The mean synaptic weight of synapses of the jj-th class at x - _jj The space constant for connectivity - _e Surface density of excitatory neurons in a one-dimensional homogeneous and isotropic tissue - _i Surface density of inhibitory neurons in a one-dimensional homogeneous and isotropic tissue - E(x, t) Excitatory Activity, proportion of excitatory cells becoming active per unit time at the instant t, at the point x - I(x, t) Inhibitory Activity, proportion of inhibitory cells becoming active per unit time at the instant t, at the point x - x A small segment of tissue - t A small interval of time - P(x, t) Afferent excitation or inhibition to excitatory neurons - Q(x, t) Afferent excitation or inhibition to inhibitory neurons - N _e (x, t) Mean integrated excitation generated within excitatory neurons at x - N _i (x, t) Mean integrated excitation generated within inhibitory neurons at x - _e [N _e ] Expected proportion of excitatory neurons receiving at least threshold excitation per unit time, as a function of N _e - _i [N _i ] Expected proportion of inhibitory neurons receiving at least threshold excitation per unit time, as a function of N _i - G( _e ) Distribution function of excitatory neuronal thresholds - G( ₁ ) Distribution function of inhibitory neuronal thresholds - ₁ A fixed value of neuronal threshold - h(N _e ; ₁) Proportion per unit time of excitatory neurons at x reaching ₁ with a mean excitation N _e - 1[ ] Heaviside's step-function - R _e (x, t) Number of excitatory neurons which are sensitive at the instant t - R _i (x, t) Number of inhibitory neurons which are sensitive at the instant t - R _e Refractory period of excitatory neurons - r _i Refractory period of inhibitory neurons - E(x, t) Time coarse-grained excitatory activity - I(x, t) Time coarse-grained inhibitory activity - Spatial convolution - Threshold of a neuronal aggregate - v Sensitivity coefficient of response of a neuronal aggregate - E(t) Time coarse-grained spatially localised excitatory activity - I(t)> Time coarse-grained spatially localised inhibitory activity - L ₁,L ₂,L,Q See § 2.2.1, § 2.2.7, § 3.1 - Velocity with which retinal images are moved apart - Stimulus width - E _o, I _o Spatially homogeneous steady states of neuronal activity - k _e ,k _ij S _e S _ij See § 5.1     

The effect of membrane potential on the redox state of cytochromeb 561 in antimycin-inhibited submitochondrial particles

The oxidation of cytochromeb ₅₆₁ by ATP was measured in submitochondrial particles inhibited by antimycin. The redox potential of the bulk (M phase) was controlled by the ratio of fumarate:succinate, and the oxidation of cytochromeb was calculated and expressed as a change in redox potential (E _h) measured in millivolts. The oxidation of cytochromeb ₅₆₁ is an energy-driven reaction affected only by the component of the proton motive force. The oxidation (measured in millivolts) is a function of the phosphate potential, reaching a maximal value of 40 mV at G_ATP<–12 kcal/mole. The maximal measured value of ATP-dependent was 100 mV. Thus only a fraction of the membrane potential effects the redox state of cytochromeb ₅₆₁. In contrast to the ATP-induced oxidation of cytochromeb ₅₆₁, cytochromeb ₅₆₆ is in redox equilibrium with fumarate succinate either in the presence or in the absence of ATP. The selective oxidation ofb ₅₆₁ is explained within the term of theQ cycle as a reflection of on the electron electrochemical potential. The positive electric potential of theC phase causes cytochromeb ₅₆₆ to act as oxidant with respect to cytochromeb ₅₆₁. In the presence of antimycin cytochromeb ₅₆₁ cannot equilibrate with the quinone and undergoes oxidation, while cytochromeb ₅₆₆ reequilibrates with the quinone and thus regains redox equilibrium with the fumarate succinate redox buffer.Abbreviations used: ETP_H, phosphorylating submitochondrial particles; TMPD,N ₁ N ₁ NN-tetramethyl-p-phenylenediamine; FCCP, carbonylcyanidep-trifluoromethoxyphenylhydrazone; Mes, 2-(N-morpholino) ethanesulfonic acid.     

Serological cross-reactivity between products of different Ia loci

Antibody prepared in I-E-subregion-incompatible strains (anti-A _e ^s :E ^/k ) cross-reacts with I-A-subregion controlled A ^b : A ^/b and A ^q A ^q complexes. This cross-reaction defines a new I-region specificity designated Ia.50. The implications of this finding for the genetic origin of the I region and immuneresponse-gene function are discussed.     

Rates of decay for the survival probability of a mutant gene

If qk is the extinction probability of a slightly supercritical branching process with offspring distribution P _kr : r = 0, 1, 2,..., then it is shown that if sup _r r ³ p _kr , < , inf ² _k > 0, and m _k 1, then 1 – q _k 2(m _k –1) _k ^–2, where m _k = _r rp _kr , ² _k = ^k _r r ² p _kr – m _k ². This provides a simple set of sufficient conditions for the validity of a conjecture of Ewens (1969) for the survival probability of a slightly advantageous mutant gene.Research supported in part by NSF grants DMS-8803639 and DMS-9007182     

Inheritance and linkage relationships of glutamate oxaloacetate transaminase isoenzymes in apple

Summary Four zones of enzymatic activity for glutamate oxaloacetate transaminase (GOT) were found in apple tissue. A dimeric gene, GOT-1, determining the fastest migrating zone, was identified. Six alleles were found, including a near null allelle which produced detectable heterodimeric bands but not homodimeric bands. A marked deficit or absence of certain geno-types in all backcrosses and in some crosses between unrelated varieties was attributed to the close linkage (r=0.02±0.005) of GOT-1 with the incompatibility S locus. GOT-1 was also closely linked with the isocitrate dehydrogenase locus IDH-1 (0.03±0.01). Proposed incompatibility genotypes for four cultivars, and the linked GOT-1 alleles are Cox: S ₁ b/S ₂ d, Idared: S ₃ a/S ₄ c, Fiesta: S ₃ a/S ₂ d and Kent: S ₃ a/S ₁ b.The results reported in this paper are part of a PhD Thesis by the first author     

Hydrodynamic characteristics of two-phase inverse fluidized bed

Hydrodynamic characteristics of a new mode of liquid-solid fluidization, termed as inverse fluidization in which low density floating particles are fluidized with downward flow of liquid, are experimentally investigated. The experiments are carried out with low density particles (<534 kg/m³) which allow high liquid throughputs in the system. During the operation, three regimes, namely, packed, semi-fluidization and fully fluidization are encountered. Empirical correlations are proposed to predict the pressure drop in each regime. A computational procedure is developed to simulate the variation of pressure drop with liquid velocity.List of Symbols Ar modified Archimedes number, d _p ³ (– _s)g/² - d _p particle diameter, mm - f friction factor (eq. 2) - g acceleration due to gravity, m/s² - H total bed height, m - H _c height of the column, m - H_f height of fluidized bed, m - H₀ height of initial bed, m - H_p height of the packed bed, m - (p) pressure drop across the bed, N/m² - (p) _f pressure drop across fluidized bed section, N/m² - (p) _p pressure drop across the packed bed section, N/m² - (p) _sf total pressure drop in semifluidization regime, N/m² - Re Reynolds number, d _pU ₁/ - Re_m modified Reynolds number, d _pU ₁/(1– _p) - U ₁ superficial liquid velocity, m/s - U_mf minimum fluidization velocity, m/s - U_osf onset fluidization velocity, m/s Greek Letters _f voidage of fluidized bed - _p voidage of packed bed - liquid viscosity, kg/ms - liquid density, kg/m³ - _s particle density, kg/m³     

Mechanisms of voltage transients during current clamp inNecturus gallbladder

Summary Microelectrode techniques were employed to study the mechanisms of the transepithelial voltage transients (V _ms ) observed during transmural current clamps in the isolatedNecturus gallbladder. The results indicate that: a) part of V _ms is due to a transepithelial resistance change (R _t ), and part to a tissue emf change. b) R _t is entirely caused by changes of the resistance of the paracellular pathway. At all current densities employed, the measured changes are probably due to changes in both fluid conductivity and width of the lateral intercellular spaces. At high currents, in addition to the effects on the lateral spaces, the resistance of other elements of the pathway (probably the limiting junction) drops, regardless of the direction of the current. c) The magnitude and polarity of the R _t -independent transepithelial and cell membrane potential transients indicate that the largest emf change takes place at the basolateral membrane (E _b ), with smaller changes at the luminal membrane (E _a ) and the paracellular (shunt) pathway (E _s ). It is shown that two-thirds of the transient are caused by E _s , and one-third by (E _b –E _a ). E _s can be explained by a diffusion potential generated by a current-dependent NaCl concentration gradient across the tissue. E _a and E _b are caused by [K] changes, mainly at the unstirred layer in contact with the basolateral membrane.     

Analysis of gas exchange in seedlings of Acer saccharum: integration of field and laboratory studies

In the field, photosynthesis of Acer saccharum seedlings was rarely light saturated, even though light saturation occurs at about 100 mol quanta m^-2 s^-1 photosynthetic photon flux density (PPFD). PPFD during more than 75% of the daylight period was 50 mol m^-2 s^-1 or less. At these low PPFD's there is a marked interaction of PPFD with the initial slope (CE) of the CO₂ response. At PPFD-saturation CE was 0.018 mol m^-2 s^-1/(l/l). The apparent quantum efficiency (incident PPFD) at saturating CO₂ was 0.05–0.08 mol/mol. and PPFD-saturated CO₂ exchange was 6–8 mol m^-2 s^-1. The ratio of internal CO₂ concentration to external (C _i /C _a ) was 0.7 to 0.8 except during sunflecks when it decreased to 0.5. The decrease in C _i /C _a during sunflecks was the result of the slow response of stomates to increased PPFD compared to the response of net photosynthesis. An empirical model, which included the above parameters was used to simulate the measured CO₂ exchange rate for portions of two days. Parameter values for the model were determined in experiments separate from the daily time courses being sumulated. Analysis of the field data, partly through the use of simulations, indicate that the elimination of sunflecks would reduce net carbon gain by 5–10%.List of symbols A measured photosynthetic rate under any set of conditions (mol m^-2 s^-1) - A _m (atm) measured photosynthetic rate at saturating PPFD, 350 l/l CO₂ and 21% (v/v) O₂ (mol m^-2 s^-1) - C constant in equation of Smith (1937, 1938) - C _a CO₂ concentration in the air (l/l) - C _i CO₂ concentration in the intercellular air space (l/l) - C _i ^/* C _i corrected for CO₂ compensation point, i.e., C _i -I ^*, (l/l) - CE initial slope of the CO₂ response of photosynthesis (mol m^-2 s^-1/(l/l)) - CEM CE at PPFD saturation - E transpiration rate (mmol m^-2 s^-1) - F predicted photosynthetic rate (mol m^-2 s^-1) - G leaf conductance to H₂O (mol m^-2 s^-1) - I photosynthetic photon flux density (mol m^-2 s^-1) - N number of data points - P _m predicted photosynthetic rate at saturating CO₂ and given PPFD (mol m^-2 s^-1) - P _ml predicted photosynthetic rate at saturating CO₂ and PPFD (mol m^-2 s^-1) - R _d residual respiratory rate (mol m^-2 s^-1) - T _a air temperature (°C) - T _l leaf temperature (°C) - V reaction velocity in equation of Smith (1937, 1938) - V _max saturated reaction velocity in equation of Smith (1937, 1938) - VPA vapor pressure of water in the air (mbar/bar) - VPD vapor pressure difference between leaf and air (mbar/bar) - X substrate concentration in equation of Smith (1937, 1938) - initial slope of the PPFD response of photosynthesis at saturating CO₂ (mol CO₂/mol quanta) - (atm) initial slope of the PPFD response of photosynthesis at 340 l/l CO₂ and 21% (v/v) O₂ (mol CO₂/mol quanta) - I ^* CO₂ compensation point after correction for residual respiration (l/l) - PPFD compensation point (mol m^-2 s^-1)     

Conformational energy of the 5-membered ring. Implication of geometric and energetic properties in the conformational characteristics

In a previous article (8) a geometrical study of the five-membered ring showed that: a) for the case of the 20 symmetrical C₂ and C_s conformations, the pseudorotation formulae for the torsion angles are a geometrical property of the ring; b) geometrical considerations alone are unable to define the puckering amplitude, the bond angle values, and the pathway between two symmetrical conformations. Here we examine how the energy equations enable us to define the deformation amplitude _m, establish the bond angles expressions and check the energy invariability along the pseudorotation circuit. The problem is next developed fully in the case where the bond and torsional energy only are considered: the literal expression¹ of _m is then given as a function of the bond angle which cancels out the bond angle energy. A numerical application is carried out on cyclopentane and the values of the parameters K^t, K¹ and used in the Conformational energy calculations are considered.Notations used 1 _i bond lengths 1 in the case of the regular ring - _i torsional angles - _i bond angles - 3/5 = 108 - 4/5 = 144 - , _{i i} – = complement to the 108 bond angle _i - _T - E Conformational energy of the 5-membered ring - E Conformational energy difference between planar and deformed ring - A _n Coefficients of the energy development in terms of - E _i ^l Bond energy relative to atom i (associated with angle _i) - K _i ^l Bond constant relative to atom i (associated with angle _i) - E _i ^l Torsional energy relative to the i ^th bond (associated with angle _i) - k _i ^l Torsional constant relative to the i ^th bond (associated with angle _i) - _i Angle _i value corresponding to zero bond energy E _i ^l (when the 5 atoms of the ring are identical, _i ) - r _ij Distance between atoms i and j - q _i Charge carried by atom i - e Constant of proportionality including the effective dielectric constant - A _ij, B_ij, d_ij Coefficients dependent on the nature of the atoms i and j and accounted for in the Van der Waals energy and hydrogen bond expressions - S (r _ij) Electrostatic contribution to the hydrogen bond energy - P Pseudorotation phase angle - _m Maximum torsional angle value characterising the deformation amplitudeM     

Stereochemistry and Stereoelectronics of Azines. 13. Conformational Effects on the Quadrupolarity of Azines. An Ab Initio Quantum-Mechanical Study of a Lateral Synthon

The quadrupole moment of formaldazine, H₂C=N-N=CH₂, has been studied for the trans structure (Ð(C-N-N-C) = = 180) and a series of gauche structures ( > 120). Restricted Hartree-Fock theory, second-order Møller-Plesset theory, and quadratic CI theory have been used in conjunction with the basis sets 6-31G^*, 6-31G**, 6-311G** and 6-311++G**. Formaldazine is a quadrupolar molecule with primitive quadrupole moment tensor components of Q _xx = -22.4, Q _yy = -20.4 and Q _zz = -25.6 DÅ at the theoretical level QCISD/6-311++G**. The examination of the theoretical level dependency shows that the reliable computation of a quadrupole moment requires the use of a flexible basis set. A large part of the component Q _zz = -25.6 DÅ is due to the -system and compares, on a per electron basis, with the Q _zz value of benzene. Conformational changes of the azines in the range 120° < < 180 have but a minute effect on the energy and are associated with only minor electronic relaxation. These conformational changes alter the quadrupole moment tensor components less than Q _xx = +0.4, Q _yy = +1.6 and Q _zz = -1.0 DÅ at QCISD/6-311++G**//QCISD/6-31G*. The direction of these changes is explained by consideration of the rotation of the CN--systems and a small reduction of the CN bond polarity in the gauche structures. The Q _zz component of formaldazine is representative of the quadrupole moment tensor component along the direction of the C ₂ axis of the azine bridge as such. Hence, the results of this study suggest that azines can engage in strong quadrupole-quadrupole interactions and can be employed as lateral synthons in crystal engineering. Electronic Supplementary Material available.     

Light-controlled inhibition of hypocotyl growth inSinapis alba L. seedlings

Fluence rate-response curves were determined for the inhibition of hypocotyl growth in 54 h old dark-grownSinapis alba L. seedlings by continuous or hourly 5 min red light irradiation (24 h). In both cases a fluence rate-dependence was observed. More than 90% of the continuous light effect could be substituted for by hourly light pulses if the total fluence of the two different light regimes was the same. Measurements of the far red absorbing form of phytochrome ([P _fr]) and [P _fr]/[P tot] (total phytochrome) showed a strong fluence rate-dependence under continuous and pulsed light which partially paralleled the fluence rate-response curves for the inhibition of the hypocotyl growth.Abbreviations R red - HIR high irradiance response - P _rfr phytochrome in its red, far-red absorbing form - [P _tot]=[P _r]+[P _fr] =k ₁/(k ₁+k ₂): photoequilibrium of phytochrome at wavelength , wherebyk _1,2 rate constants ofP _rP _fr,P _frP _r photoconversion - [P _fr]/[P _tot]     

Dependence of phytochrome dark reactions on the initial photostationary state

Summary Under conditions of continuous irradiation, the P _jr destruction rate constants (k _d ) of phytochrome in hooks and cotyledons of squash (Cucurbita pepo L.) seedlings do not depend on the photostationary state and are the same in both organs. On the other hand, the rate constants of the dark reversion and the first destruction step, plotted as a function of ⁰ , show optimum curves with maxima between ⁰ and 0.5. Similar results were obtained for dark reactions of mustard (Sinapis alba L.)-hook phytochrome in vivo. This indicates a cooperative behaviour of these phytochrome dark reactions.Abbreviations P _r red-absorbing form of phytochrome - P _fr far-red-absorbing form of phytochrome - [P _tot] [P _r ]+[P _fr ] - [P _tot] ([P _fr ]/[P _tot]), photostationary state - ⁰ at t=0, immediately after saturating irradiation     

A dynamic model of a two-synapse feedback loop in the vertebrate retina

The theoretical properties of synapses such as those in the retina which operate on graded potentials are developed using work on tetrodotoxin-treated synapses as a basis. A linearized model of a two-synapse negative feedback loop analogous to the bipolaramacrine feedback loop in the retina possesses a frequency response which developes an increasingly prominent resonance peak at higher input levels and under some circumstances shows instability. Psychophysical studies have shown that the visual system also exhibits this behaviour suggestive of progressive underdamping in a harmonic oscillator. Evidence in favor of the hypothesis that resonance originates in the loop is presented, the conclusions being that the loop functions to tune the retina to a range of temporal frequencies.Symbol Table V millivolts depolarisation relative to resting membrane potential - V _n , V _out pre-synaptic, post-synaptic depolarisation respectively - V _e , V _i reversal potential or e.m.f. of post-synaptic battery of excitatory, inhibitory synapses respectively - V _out (max) maximal post-synaptic depolarisation defined by Eq.(10c) - V ₀ input depolarisation for feedback loop - depolarisation potential normalised with respect to V _out(max) - I milliamperes of depolarising current - I _s post-synaptic membrane current - I _c cable current - I ₀ input depolarising current for feedback loop - I _max maximal physiological value for I ₀ =V _e ·G ₀ - i depolarising current normalised with respect to I_max - e reversal potential normalised with respect to V _e - r _i specific resistivity of internal medium - R _m membrane resistance - C _m membrane capacitance - cable space constant = R _m /2R _i - g ₀ characteristic cable conductance = 2/R _m ·R _i - G conductance of post-synaptic membrane - G _s maximal post-synaptic membrane conductance - g fraction of receptors occupied by transmitter = G/G _s - r the ratio G _s/G ₀ - membrane time constant = R _m·C_m - ₁ time constant of transmitter release in response to presynaptic depolarisation [Eq. (6)] - ₂ time constant of decay of g [Eq. (7a)] - _{2 2}·[1+k·exp(b·v _in)]^–1 - k equilibrium constant for transmitter-receptor interaction [Eq. (7a)] - b constant determining increase in rate of transmitter release with pre-synaptic depolarisation [Eq. (6)] - c concentration of transmitter in synaptic cleft normalised with respect to resting concentration - H _jk (s) linearised transfer function for synaptic transmission from neurone j to neurone k - G(s) H₁₂(s) - H(s) -H₂₁(s) - F(s) linearised closed-loop transfer function - _x 2 times spatial frequency of counterphase grating pattern - the ratio (1+s)/(_x)₂ - a the product (1+r)·k - d density of bipolars per unit area     

Characterization of the MHC class II region in cattle. The number of DQ genes varies between haplotypes

The organization of the major histocompatibility complex (MHC) class II region in cattle was investigated by Southern blot analysis using human probes corresponding to DO, DP, DQ, and DR genes. Exon-specific probes were also employed to facilitate the assessment of the number of different bovine class II genes. The results indicated the presence of single DO and DR genes, at least three DR genes, while the number of DQ genes was found to vary between MHC haplotypes. Four DQ haplotypes, DQ ^{1 1} to DQ ^{2 4}, possessed a single DQ and a single DQ gene whereas both these genes were duplicated in eight other haplotypes, DQ ^{3 5} to DQ ^{9 12}. No firm evidence for the presence of bovine DP genes was obtained. The same human probes were also used to investigate the genetic polymorphism of bovine class II genes. DQ DQ , DR DR , and DO restriction fragment length polymorphisms (RFLPs) were resolved and in particular the DQ restriction fragment patterns were highly polymorphic. Comparison of the present result with the current knowledge of the class II region in other mammalian species suggested that the DO, DP, DQ, DR, and DZ subdivision of the class II region was established already in the ancestor of mammals. The DP genes appear to be the least conserved class II genes among mammalian species and may have been lost in cattle. The degree of polymorphism of different class II genes, as revealed by RFLP analyses, shows striking similarities between species.     

The appearance of competence for phytochrome-mediated anthocyanin synthesis in the cotyledons of Sinapis alba L.

Summary It is demonstrated that phytochrome-mediated anthocyanin synthesis in the epidermal cells of mustard seedling cotyledons takes place only 27 h after sowing onwards (at 25°C). This starting point cannot be shifted by light treatments or by nutrients. The late appearance of competence for P _fr (P _r and P _fr, red- and far-red absorbing forms of phytochrome, respectively) with regard to anthocyanin synthesis is not related to the phytochrome system per se (P _rP _fr) as this is fully functional immediately after sowing of the seed; nor is it related to the primary reaction of phytochrome: P _fr+XP _fr XP _fr X (X, X, two forms of a receptor for P _fr) or to the initial action of P _fr X:P _fr X+KY (K, coupling element, leading to the product Y, which is no longer photoreversible). Rather, the starting point is determined by internal factors only and is thus not accessible to any specific control by external factors. On the other hand, however, the beginning of the initial action of P _fr X (coupling point) can be shifted by light via phytochrome under high irradiance conditions. Moreover, it is shown that there is no phytochrome-independent effect of blue light on photomorphogenesis in the young mustard seedling and that there is no rapid dark reversion of P _fr which can be detected by physiological means, at least duringAbbreviations P _r red-absorbing forms of phytochrome - P _fr far-red-absorbing forms of phytochrome - P ₁ total spectrophotometrically detectable phytochrome - HS Hoagland's nutrient solution - HIR high irradiance response     

Evaluation of sensors for the control of a continuous ethanol fermentation

A method is presented for the evaluation of sensors used in the control of continuous fermentations. Simulations of open-loop response to input disturbance provided a starting point for the choice of sensor type. This was evaluated quantitatively through a sensitivity ratio. It was shown that in the case of ethanol fermentation, there existed three regions where different sensors could be used for the process control depending on the inlet sugar concentration. Sugar sensors were preferable above an inlet sugar concentration of 50 kg/m³, while ethanol sensors were preferable below 25 kg/m³. In the intermediate region, sugar and ethanol sensors demonstrated equally good performance. A controllability study of a continuous ethanol fermentation was also made. A single-stage continuous stirred-tank fermentor was simulated operating at a dilution rate of 0.1 1/h and inlet glucose concentration of 160 kg/m³. The outlet glucose concentration was controlled with a PI controller. Mean square error of the controller input signal during the first five hours after introducing input disturbance was taken as a measure of the controllability. This was studied in the relation to the two key sensor characteristics, sampling time and accuracy.List of Symbols c _p kg/m³ ethanol concentration - c _p kg/m³ fermentor ethanol concentration corresponding to c _si and D - c _s kg/m³ substrate (glucose) concentration - c _s kg/m³ fermentor glucose concentration corresponding to c _si and D - c _si kg/m³ inlet substrate (glucose) concentration - c _si kg/m³ inlet glucose concentration value used for sensitivity evaluation - c _sm kg/m³ glucose concentration — measured value - c _ss kg/m³ glucose concentration setpoint value - c _x kg/m³ biomass concentration - D 1/h dilution rate - D 1/h dilution rate value used for sensitivity evaluation - D _i 1/h dilution rate at ith sampling interval - D ₀ 1/h dilution rate at steady state - K _c m³/kgh controller gain - K _p kg/m³ product inhibition constant - K _s kg/m³ Monod constant - n ₁, n ₂ random numbers - r _p kg/m³ h ethanol production rate - r _s kg/m³ h substrate (glucose) consumption rate - r _x kg/m³ h biomass growth rate - vector of independent variables - y _i ith dependent variable - Y _ps ethanol yield - Y _xs biomass yield - parameter vector - _j jth parameter - _ij sensitivity of y_i with respect to _j - _p sensitivity of fermentor ethanol concentration - _s sensitivity of fermentor glucose concentration - sensitivity ratio - c _p kg/m³ ethanol concentration difference corresponding to a change of c _si by 5% - c _s kg/m³ glucose concentration difference corresponding to a change of c _si by 5% - c _si kg/m³ concentration difference added to c _si - _i kg/m³ error at ith sampling interval - 1/h specific growth rate - _m 1/h maximum specific growth rate - _s kg/m³ standard deviation of monitored glucose concentration - _I h min kg/m³ integral time - _s min sampling period The Swedish Ethanol Foundation and the National Board for Technical Development (NUTEK) are kindly acknowledged for the financial support of this project. The authors wish to thank Peter Warkentin for the linguistic advice.     

Leaf water potential,component potentials and relative water content in a xeric grass,Agropyron dasystachyum (Hook.) Scribn.

Summary Leaf water potential ( _l ), osmotic potential ( _s ), pressure potential ( _p , turgor pressure), relative water content (R) and their interrelationships were determined for a xeric grass (Agropyron dasystachyum) found in the grasslands of Canada. Thermocouple psychrometers were used to measure _l and _s ; _p was obtained by subtraction. _l dropped from near 0 bars to about-28 bars as R went from 90% to 75%. R greater than 90% was not observed, perhaps because of a systematic error in determination of turgid water content. R remained relatively high in A. dasystachyum, even at low _l . The slope of the _l -R relationship was similar to other species which are generally considered to be drought tolerant. _p as high as 14 bars was observed. Most of the decrease in _l was accounted for by a decline in _p . The ability of A. dasystachyum to adjust to fluctuating water stress over the growing season is probably as much related to changes in tissue structure and turgor relationships as to simple changes in osmotic potential.     

Calcium-induced associations of the caseins: Thermodynamic linkage of calcium binding to colloidal stability of casein micelles

The caseins occur in milk as colloidal complexes of protein aggregates, calcium, and inorganic phosphate. As determined by electron microscopy, these particles are spherical and have approximately a 650 Å radius (casein micelles). In the absence of calcium, the protein aggregates themselves (submicelles) have been shown to result from mainly hydrophobic interactions. The fractional concentration of stable colloidal casein micelles can be obtained in a calcium caseinate solution by centrifugation at 1500g. Thus, the amount of stable colloid present with varying Ca²⁺ concentrations can be determined and then analyzed by application of equations derived from Wyman's Thermodynamic Linkage Theory. Ca²⁺-induced colloid stability profiles were obtained experimentally for model micelles consisting of only _s1- (a calcium insoluble casein) and the stabilizing protein -casein, eliminating the complications arising from - and minor casein forms. Two distinct genetic variants _s1-A andB were used. Analysis of _s1-A colloid stability profiles yielded a precipitation (salting-out) constantk ₁, as well as colloid stability (salting-in) parameterk ₂. No variations ofk ₁ ork ₂ were found with increasing amounts of -casein. From the variation of the amount of colloidal casein capable of being stabilized vs. amount of added -casein an association constant of 4 L/g could be calculated for the complexation of _s1-A and -casein. For the _s1-B and -casein micelles, an additional Ca²⁺-dependent colloidal destabilization parameter,k ₃, was added to the existingk ₁ andk ₂ parameters in order to fully describe this more complex system. Furthermore, the value ofk ₃ decreased with increasing concentration of -casein. These results were analyzed with respect to the specific deletion which occurs in _s1-caseinA in order to determine the sites responsible for these Ca²⁺-induced quaternary structural effects.     

Influence of Genotype on Endoreduplication of Giant Chromosomes and Expressivity of Character eyelessin Drosophila melanogaster

In Drosophila melanogaster lines LA (low activity), HA (high activity), andOregon-R (wild type), the effect of genetic background on endoreplication in giant chromosomes of salivary glands, fecundity, and expression of mutation eywas studied. The degree of chromosome polyteny and the number of adult flies in saturated lines ey _L, ey _H, and ey _Or were significantly higher than in the original lines. The degree of chromosome polyteny was correlated with fecundity. The expressivity of the ey character was shown to be far lower in lines ey _L, ey _H, and ey _Or than in the original eyelessline. In the saturated lines, the eye facets were reduced to a similar degree. All the lines studied displayed clear-cut sexual distinctions in this parameter. In the ey _L line, the coefficients of variation for the degree of chromosome polyteny, fecundity, and expressivity of the ey mutation were much lower than in lines eyeless, ey _LAandey _Or.