Sensitivity Profiles of Diversity Indices

The author previously described special sensitivity measures for diversity indices. These measures make possible on analytical treatment of the index sensitivity. In the article a detailed analysis of sensitivity properties of the Hurlbert indices is presented. In the first step the abundances n_k were sequenced in an increasing order. Plotting the sensitivity against n_k or log n_k, essential sensitivity properties can be observed. For example, one can study the sensitivities to changes in the dominant and subdominant abundances, the site of the “nearly neutral” abundance and the site of local sensitivity maxima in the domain of the relatively rare categories. The observations are supported by mathematical reasoning.     

Contributions of binding and catalytic rate constants to evolutionary modifications inKm of NADH for muscle-type (M4) lactate dehydrogenases

Summary The apparent Michaelis constant (K _m) of NADH for muscle-type (M₄ isozyme) lactate dehydrogenases (LDHs) is highest, at any given temperature of measurement, for LDHs of cold-adapted vertebrates (Table 1). However, these interspecific differences in theK _m of NADH are not due to variations in LDH-NADH binding affinity. Rather, theK _m differences result entirely from interspecific variation in the substrate turnover constant (k _cat) (Fig. 1; Table 2). This follows from the fact that theK _m of NADH is equal tok _cat divided by the on constant for NADH binding to LDH,k ₁, so that interspecific differences ink _cat, combined with identical values fork ₁ among different LDH reactions, make the magnitude of theK _m of NADH a function of substrate turnover number. The temperature dependence of theK _m of NADH for a single LDH homologue is the net result of temperature dependence of bothk _cat andk ₁ (Figs. 3 and 4). Temperature independentK _m values can result from simultaneous, and algebraically offsetting, increases ink _cat andk ₁ with rising temperature. Salt-induced changes in theK _m of NADH also may be due to simultaneous perturbation of bothk _cat andk ₁ (Table 3). These findings are discussed from the standpoint of the evolution of LDH kinetic properties, particularly the interspecific conservation of catalytic and regulatory functions, in differently-adapted species.     

A Simple Procedure for Constructing Experiment Designs with Incomplete Blocks of Sizes 2 and 3

In order to maximize control of heterogeneity within complete blocks, an experimenter could use incomplete blocks of size k = 2 or 3. In certain situations, incomplete blocks of this nature would eliminate the need for such spatial types of analyses as nearest neighbor. The intrablock efficiency factors for such designs are relatively low. However, with recovery of interblock information, FEDERER and SPEED (1987) have presented measures of design efficiency factors which demonstrate that efficiency factors approach unity for certain ratios of the intrablock and interblock variance components. Hence with recovery of interblock information, even incomplete block designs with k = 2 or 3 have relatively high efficiency factors. The reduction in the intrablock error variance over the complete block error variance in many situations will provide designs with high efficiency. A simple procedure for constructing incomplete blocks of sizes 2 and 3 is presented. It is shown how to obtain additional zero-one association confounding arrangements when v = 4 t, t an integer, and for v = pk, k ≤ p. It is indicated how to do the statistical analysis for these designs.     

A Model for the Unusual Kinetics of Thermal Denaturation of Rubredoxin

The thermal denaturation of the simple, redox-active iron protein rubredoxin is characterized by a slow, irreversible decay of the characteristic red color of the iron center at elevated temperatures in the presence of oxygen at pH 7.8. The denaturation rate is essentially constant and the time period for complete bleaching is nearly independent of protein concentration. These two characteristics of the kinetics can be fit by a simple self-catalyzed kinetics model consisting of the combination of a first-order decay and catalysis by some product of that decay, i.e., dP/dt=k ₁[A]+(k ₂[P][A])/(K _m+[A]), where A is native rubredoxin, P, is unspecified product, k ₁ is a first-order rate constant, and k ₂ and K _m are the catalytic constants. In order for the second term to be of this simple form over the full course of a decay, the model must include the condition that the reaction is effectively irreversible. This model has properties which suggest other biological roles in regulation (changes in k ₁ or k ₂ can dramatically modulate the kinetics), in timing (titer-independent fixed reaction time), and in self-activation reactions. At one extreme (k₁ k₂) the kinetics becomes exponential, but at the other extreme (k₂ k₁) they show a dramatic and rapid terminal increase after a lag period. Some obvious possible roles in the kinetics of programmed cell death, prion disease, and protease autoactivation are discussed.     

A Simple Construction Procedure for Eesolvable Incomplete Block Designs for any Number of Treatments

A simple, straightforward procedure, which requires no special tables or generators, is presented for constructing resolvable incomplete block designs for v=pk, v=p²k, …, treatments, for k≥p, in incomplete blocks of size k. Also, it is shown, how to obtain incomplete block designs for any v in blocks of size k and k+1. The procedure allows construction of balanced incomplete block designs for p = k a prime number. For p = n not a prime number, incomplete block designs can be obtained by the procedure, but are not balanced. However, for p_s being the smallest prime factor of n, p_s + 1 for v = n², p_s²+ p_s + 1 for v = n³, …, arrangements can be obtained for which the occurrence of any treatment pair in the blocks is either zero or one. This is called a zero-one concurrence design. Procedures are described for obtaining additional zero-one concurrence arrangements. It is shown that the efficiency of these designs is maximum. Both intra-block and inter-block analyses are described.     

A Note on Estimation of Several Missing Values in Two Way Classified Data with Many Observations Per Cell

In this paper an attempt has been made to reduce the computational complexities involved in estimation of several missing values. As a result it has been shown that one can estimate m missing values by developing only k (≤m) linear equations, where m and k are respectively the number of missing values and missing cells. The procedure is also illustrated with the help of a numerical example.     

A discrete branching process model for the spread of HIV via steady sexual partnerships

The transmission of HIV in a monogamous heterosexual population structured by the ordinal number of the current partnership is considered. The sexual carreer of a man (woman) is thought to be a succession of k(m) partnerships, and a multitype Galton-Watson process is defined, in which the objects are infections and the types are related to the ordinal number of the partnership during which a person has acquired the infection. Contrary to multitype models in which the types are not age-related in some sense, this process contains at least two singular types, namely infections acquired in the last partnership of a man or a woman. The criticality parameter of this branching process is the epidemic threshold parameter R₀. In the case k=m an epidemic is impossible, however large k may be, if the difference between the ordinal numbers of the partners in a pair is never > 1. When the frequency of pairs in which this difference is 2 increases, then R₀ increases. This is demonstrated for the cases k=m=3 and k=4,m=3. The formulae obtained show also the joint influence of the mixing pattern and of variable infectivity. The result for the case of uniform mixing implies that a formula of May and Anderson (1987) is an approximation for k and m large.Mathematics Subject Classification (2000): 92D (primary), 60J (secondary)     

Kinetic analysis of local structure formations in protein folding

The protein folding process is described by a cluster model based on the assumption that local structures or clusters are formed at an early stage in different regions of the polypeptide chain. Possible local structural elements in a globular protein are helices, bends, and hydrophobic cores whose formation is presumably determined by the interaction with the environment. Thus the tendency of local structure formation is expressed by a surface free energy of the cluster, which is assigned to the interface between the cluster and its environment. The probability of finding the chain of N residues with k clusters and m residues in the cluster is represented by a cluster distribution map. The cluster model exhibits a distinct two-state-like equilibrium transition, which can be seen on this map as well-separated native and denatured populations at the midpoint of the transition. The native population is localized at k ≈ 1 and m ≈ N, while the position of the denatured population can vary significantly depending on the surface free energy of the cluster. If the surface free energy is strong, the denatured population is localized near k = 0 and m = 0. On the other hand, if the surface free energy is weak, the denatured population is localized at high k and m values. The dynamics of the cluster model are treated as a stochastic process involving the transition from a state (k,m) to one of its six neighbors. The transition probability for each transition is determined by the free energy difference between two states; thus no activation process is assumed. However, the conversion of the two macrostates, native and denatured populations, involves the free energy activation due to the cooperative interaction of the macrosystem. The dynamics are analyzed by following the time evolution of the population profile on the cluster distribution map. Kinetic schemes are proposed to describe the multistep mechanism of protein folding and unfolding.     

Belowground inter‐ramet water transport capacity in Populus euphratica,a Central Asian desert phreatophyte

• Populus euphratica Oliv. is a widespread phreatophytic tree species that forms riparian forests in (hyper‐)arid regions of Central Asia. Its recruitment strongly relies on vegetative propagation from ‘root suckers’ that emerge from underground root spacers. The water transport through the spacers, although decisive for emerging ramets, has only rarely been quantified, but is crucial for the vegetative regeneration of the forests.
• In root spacers with different diameters collected from a mature poplar forest in northwest China, we calculated the hydraulic conductivity (k_c) from anatomical investigations on the basis of a modified Hagen‐Poiseuille equation and measured it (k_m) with a perfusion solution in the laboratory. The k_m values were compared with the water use by young and mature P. euphratica trees determined in previous studies.
• We obtained a significant correlation between k_m and k_c (which, however, was higher by at least one order of magnitude). Due to the extensive occurrence of tyloses, particularly in older conduits and thicker spacers, and because the conduit area did not increase with spacer diameter, neither k_c nor k_m increased with an increase in spacer diameter. The water supply through the spacers would be sufficient to meet the water demand even of mature trees.
• Our results provide a mechanistic explanation for the observed occurrence of P. euphratica clones across large areas and, provided that they are also valid for stands with larger distances to the water table, for the sustained growth and vegetative reproduction of P. euphratica stands growing at larger distances from the groundwater.

     

Enzymic and Structural Studies on Drosophila Alcohol Dehydrogenase and Other Short-Chain Dehydrogenases/Reductases

Enzymic and structural studies on Drosophila alcohol dehydrogenases and other short-chain dehydrogenases/reductases (SDRs) are presented. Like alcohol dehydrogenases from other Drosophila species, the enzyme from D. simulans is more active on secondary than on primary alcohols, although ethanol is its only known physiological substrate. Several secondary alcohols were used to determine the kinetic parameters k_cat and K_m. The results of these experiments indicate that the substrate-binding region of the enzyme allows optimal binding of a short ethyl side-chain in a small binding pocket, and of a propyl or butyl side-chain in large binding pocket, with stereospecificity for R(−) alcohols. At a high concentration of R(−) alcohols substrate activation occurs. The k_cat and K_m values determined under these conditions are about two-fold, and two orders of magnitude, respectively, higher than those at low substrate concentrations. Sequence alignment of several SDRs of known, and unknown three-dimensional structures, indicate the presence of several conserved residues in addition to those involved in the catalyzed reactions. Structural roles of these conserved residues could be derived from observations made on superpositioned structures of several SDRs with known structures. Several residues are conserved in tetrameric SDRs, but not in dimeric ones. Two halohydrin-halide-lyases show significant homology with SDRs in the catalytic domains of these enzymes, but they do not have the structural features required for binding NAD⁺. Probably these lyases descend from an SDR, which has lost the capability to bind NAD⁺, but the enzyme reaction mechanisms may still be similar. Received: 23 May 2000 / Accepted: 4 January 2001     

Effect of cytoplasmic acidification on the membrane potential of T-lymphocytes: Role of trace metals

Summary The effect of lowering intracellular pH on the membrane potential (E _m ) of rat thymic lymphocytes was studied using the potential-sensitive dyebis-oxonol. Cells were acid loaded by addition of the electroneutral K⁺/H⁺ exchanging ionophore nigericin. Acidification to pH 6.3 in Na⁺-free solution resulted in a biphasic change inE _m : an early transient hyperpolarization followed by a sustained depolarization. These changes were associated with a rise in cytosolic free Ca²⁺ ([Ca²⁺] _i ). The hyperpolarization was eliminated when the change in [Ca²⁺] _i was prevented using BAPTA, an intracellular Ca²⁺ chelator. Moreover, a similar hyperpolarization was elicited by elevation of [Ca²⁺] _i at physiological pH _i using ionomycin, suggesting involvement of Ca²⁺-activated K⁺ channels. In contrast, the depolarization phase could not be mimicked by raising [Ca²⁺] _i with ionomycin. However, intracellular BAPTA effectively inhibited the acidificationinduced depolarization. Inhibition was also obtained by extracellular addition of EGTA or dithiothreitol, even when the external free Ca²⁺ concentration remained unaltered. These observations suggested a possible role of contaminating trace metals. Cytosolic acidification is envisaged to induce intracellular accumulation of one or more trace metals, which induces the observed changes inE _m . Accordingly, similar changes inE _m can be induced without acidification by the addition of small amounts of Cu²⁺ to the medium. The ionic basis of theE _m changes induced by acidification and the significance of these observations are discussed.     

Leaf hydraulic conductance and mesophyll conductance are not closely related within a single species

Stomata represent one resistor in a series of resistances for carbon and water exchange between the leaf and the atmosphere; the remaining resistors occurring within the leaf, commonly represented as mesophyll conductance to CO₂, g_m, and leaf hydraulic conductance, k_Leaf. Recent studies have proposed that g_m and k_Leaf may be coordinated across species because of shared pathways. We assessed the correlation between g_m and k_Leaf within cotton, under growth CO₂ partial pressure and irradiance treatments and also with short‐term variation in irradiance and humidity. g_m was estimated using two isotopic techniques that allowed partitioning of total g_m (Δ¹³C‐g_m) into cell wall plus plasma membrane conductance (Δ¹⁸O‐g_m) and chloroplast membrane conductance (g_cm). A weak correlation was found between Δ¹³C‐g_m and k_Leaf only when measured under growth conditions. However, Δ¹⁸O‐g_m was related to k_Leaf under both short‐term environmental variation and growth conditions. Partitioning g_m showed that g_cm was not affected by short‐term changes in irradiance or correlated with k_Leaf, but was strongly reduced at high growth CO₂ partial pressure. Thus, simultaneous measurements of g_m, k_Leaf and g_cm suggest independent regulation of carbon and water transport across the chloroplast membrane with limited coordinated regulation across the cell wall and plasma membrane.     

Time-resolving luminescence techniques for possible detection of forest decline

Summary Needles from spruces at different environmental and physiological conditions were analyzed by long term delayed luminescence in the seconds-range (LDL) using a novel set-up with on-line computer and a specially written computer program. Upon red light induction, the LDL-kinetics showed a super-position of three exponentially decaying components (fast, medium and slow) with reaction constants ofk _f =5–15 s^–1,k _m =0.8–1.8 s–1 andk _s =0.13–0.23 s^–1,k _s -values are fairly independent of the individual tree and quite stable throughout the whole year. They are also independent of the status and localization, i.e. the physiological situation of the individual tree. However,k _m -andk _f -values as well as the related amplitudesA _m andA _f exhibit a general, significant seasonal variation and obviously are correlated with the damage class or the environmental situation of the individual tree. Therefore, the measurement of long term delayed luminescence might offer a valuable piece of information in search of an early detection of forest decline.Abbreviations SDL short term delayed luminescence (lasting from ms to µs), LDL long term delayed luminescence (lasting from s to min) - OTC Open Top Chamber     

Collagenase induced changes in the circular dichroism spectrum of collagen

The maximum at 220 nm in the circular dichroism spectrum of native collagen solution changed to a negative value after heat denaturation or collagenase hydrolysis. The enzyme induced rate of CD change at 220 nm was shown to be first order in collagen concentration. The specific rate constant k is actually a combined rate constant k_fast and k_slow in which the ratio k_f/k_s is 4.1. The initial rates were linear with respect to enzyme concentration, and the K_m was found to be 5.5 × 10^?7 M. The rate of ultraviolet hyperchromicity at 220 nm on collagen hydrolysis was determined. The k_fast was the same as that obtained by CD. The k_f/k_s ratio was 4.6. Both methods may be readily used to assay for collagenase activity.     

The metal ion requirements of Arabidopsis thaliana Glx2-2 for catalytic activity

In an effort to better understand the structure, metal content, the nature of the metal centers, and enzyme activity of Arabidopsis thaliana Glx2-2, the enzyme was overexpressed, purified, and characterized using metal analyses, kinetics, and UV–vis, EPR, and ¹H NMR spectroscopies. Glx2-2-containing fractions that were purple, yellow, or colorless were separated during purification, and the differently colored fractions were found to contain different amounts of Fe and Zn(II). Spectroscopic analyses of the discrete fractions provided evidence for Fe(II), Fe(III), Fe(III)–Zn(II), and antiferromagnetically coupled Fe(II)–Fe(III) centers distributed among the discrete Glx2-2-containing fractions. The individual steady-state kinetic constants varied among the fractionated species, depending on the number and type of metal ion present. Intriguingly, however, the catalytic efficiency constant, k _cat/K _m, was invariant among the fractions. The value of k _cat/K _m governs the catalytic rate at low, physiological substrate concentrations. We suggest that the independence of k _cat/K _m on the precise makeup of the active-site metal center is evolutionarily related to the lack of selectivity for either Fe versus Zn(II) or Fe(II) versus Fe(III), in one or more metal binding sites.     

Penicillin acylase mutants with altered site-directed activity from Kluyvera citrophila

Summary Oligonucleotide-directed mutagenesis has been used to obtain specific changes in the penicillin acylase gene from Kluyvera citrophila. Wild-type and mutant proteins were purified and the kinetic constants for different substrates were determined. Mutations in Met168 highly decreased the specificity constant of the enzyme for penicillin G, penicillin V and phenylacetyl-4-aminobenzoic acid and the catalytic constant k _cat for phenylacetyl-4-aminobenzoic acid. Likewise, the phenylmethylsulphonyl-fluoride sensitivity was significantly decreased. It is concluded that the 168 residue is involved in binding by interaction with the acid moiety of the substrate. A putative penicillin-binding domain was located in penicillin acylase by sequence homology with other penicillin-recognizing enzymes. Lys374 and His481, the conserved amino acid residues that are essential for catalysis in these enzymes, can be changed in penicillin acylase with no changes to the k _cat and phenylmethylsulphonyl fluoride reactivity, but change the K _m.The likelihood of the existence of this proposed penicillin binding site is discussed. The reported results might be used to alter the substrate specificity of penicillin acylase in order to hydrolyse substrates of industrial significance other than penicillins. Offprint requests to: I. Prieto     

Kinetic behavior of heterogeneous populations in completely mixed reactors

The kinetic behavior of heterogeneous microbial populations was studied in a continuous flow completely mixed reactor operated at various dilution rates. Glucose was used as the growth-limiting nutrient. The physiological growth parameters for cells harvested from continuous flow reactors were determined using batch experiments. It, was found that the growth parameters, maximum growth rate (μ_m), saturation constant (k_s), and cell yield (Y) vary for each dilution rate, and cannot be considered as precise constants in depicting the kinetic behavior of heterogeneous populations. In addition, it was found that the yield coefficients obtained from batch experiments were always lower than those obtained from continuous flow experiments. Levels of substrate and biological solids calculated for different dilution rates using growth constants from batch experiments did not agree with the experimental values observed in steady-state experiments. However, when the yield values from, the continuous flow experiments were used in conjunction with batch values for μ_m and k_s the theoretical and experimental dilute-out curves agreed fairly closely (within the range needed for engineering prediction) until the culture began to wash out of the unit. In general, the data substantiated the use of the single phase relationship between growth rate and substrate concentration described by the Monod equation, μ = μ_mS/(k_s + s).     

Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family

The nearly 50,000 known Nudix proteins have a diverse array of functions, of which the most extensively studied is the catalyzed hydrolysis of aberrant nucleotide triphosphates. The functions of 171 Nudix proteins have been characterized to some degree, although physiological relevance of the assayed activities has not always been conclusively demonstrated. We investigated substrate specificity for eight structurally characterized Nudix proteins, whose functions were unknown. These proteins were screened for hydrolase activity against a 74‐compound library of known Nudix enzyme substrates. We found substrates for four enzymes with k_cat/K_m values >10,000 M^?1 s^?1: Q92EH0_LISIN of Listeria innocua serovar 6a against ADP‐ribose, Q5LBB1_BACFN of Bacillus fragilis against 5‐Me‐CTP, and Q0TTC5_CLOP1 and Q0TS82_CLOP1 of Clostridium perfringens against 8‐oxo‐dATP and 3'‐dGTP, respectively. To ascertain whether these identified substrates were physiologically relevant, we surveyed all reported Nudix hydrolytic activities against NTPs. Twenty‐two Nudix enzymes are reported to have activity against canonical NTPs. With a single exception, we find that the reported k_cat/K_m values exhibited against these canonical substrates are well under 10⁵ M^?1 s^?1. By contrast, several Nudix enzymes show much larger k_cat/K_m values (in the range of 10⁵ to >10⁷ M^?1 s^?1) against noncanonical NTPs. We therefore conclude that hydrolytic activities exhibited by these enzymes against canonical NTPs are not likely their physiological function, but rather the result of unavoidable collateral damage occasioned by the enzymes' inability to distinguish completely between similar substrate structures. Proteins 2016; 84:1810–1822. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

Effect of temperature on DNA secondary structure in the absence and presence of 0.5 M tetramethylammonium chloride

Changes in the average secondary structures of three different linear DNAs over the premelting region from 5 to 60°C were investigated by measuring their CD spectra and also their torsion elastic constants (〈α〉) by time-resolved fluorescence polarization anisotropy. For one of these DNAs, the HaeII fragment of pBR322, the apparent diffusion coefficients [D_app (k)] at small and large scattering vectors (k) were also measured by dynamic light scattering. With increasing temperature, all three DNAs exhibited typical premelting changes in their CD spectra, and these were accompanied by 1.4- to 1.7-fold decreases in 〈α〉. Also for the 1876 base pair fragment, D_app(k) at large scattering vectors, which is sensitive to the dynamic bending rigidity, decreased by 17%, even though there was no change at small scattering vectors, where D_app(k) = D₀ is the translational diffusion coefficient of the center-of-mass. These observations demonstrate conclusively that the premelting CD changes of these DNAs are associated with a significant change in average secondary structure and mechanical properties, though not in persistence length. In the presence of 0.5 M tetramethylammonium chloride (TMA-Cl) the premelting change in CD is largely suppressed, and the corresponding changes in 〈α〉 and D_app(k) at large scattering vectors are substantially diminished. These observations suggest that TMA-Cl, which binds preferentially to A · T-rich regions and stabilizes those regions (relative to G · C-rich regions) against melting, effectively stabilizes the prevailing low-temperature secondary structure sufficiently that the DNA is effectively trapped in that state over the temperature range observed. © 1998 John Wiley & Sons, Inc. Biopoly 45: 503–515, 1998     

Mechanobiology of soft skeletal tissue differentiation—a computational approach of a fiber-reinforced poroelastic model based on homogeneous and isotropic simplifications

The material properties of multipotent mesenchymal tissue change dramatically during the differentiation process associated with skeletal regeneration. Using a mechanobiological tissue differentiation concept, and homogeneous and isotropic simplifications of a fiber-reinforced poroelastic model of soft skeletal tissues, we have developed a mathematical approach for describing time-dependent material property changes during the formation of cartilage, fibrocartilage, and fibrous tissue under various loading histories. In this approach, intermittently imposed fluid pressure and tensile strain regulate proteoglycan synthesis and collagen fibrillogenesis, assembly, cross-linking, and alignment to cause changes in tissue permeability (k), compressive aggregate modulus (H_A), and tensile elastic modulus (E). In our isotropic model, k represents the permeability in the least permeable direction (perpendicular to the fibers) and E represents the tensile elastic modulus in the stiffest direction (parallel to the fibers). Cyclic fluid pressure causes an increase in proteoglycan synthesis, resulting in a decrease in k and increase in H_A caused by the hydrophilic nature and large size of the aggregating proteoglycans. It further causes a slight increase in E owing to the stiffness added by newly synthesized type II collagen. Tensile strain increases the density, size, alignment, and cross-linking of collagen fibers thereby increasing E while also decreasing k as a result of an increased flow path length. The Poisson's ratio of the solid matrix, _s, is assumed to remain constant (near zero) for all soft tissues. Implementing a computer algorithm based on these concepts, we simulate progressive changes in material properties for differentiating tissues. Beginning with initial values of E=0.05 MPa, H_A=0 MPa, and k=1×10^–13 m⁴/Ns for multipotent mesenchymal tissue, we predict final values of E=11 MPa, H_A=1 MPa, and k=4.8×10^–15 m⁴/Ns for articular cartilage, E=339 MPa, H_A=1 MPa, and k=9.5×10^–16 m⁴/Ns for fibrocartilage, and E=1,000 MPa, H_A=0 MPa, and k=7.5×10^–16 m⁴/Ns for fibrous tissue. These final values are consistent with the values reported by other investigators and the time-dependent acquisition of these values is consistent with current knowledge of the differentiation process.