Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE)

Automated assignment of NOESY spectra is a prerequisite for automated structure determination of biological macromolecules. With the program KNOWNOE we present a novel, knowledge based approach to this problem. KNOWNOE is devised to work directly with the experimental spectra without interference of an expert. Besides making use of routines already implemented in AUREMOL, it contains as a central part a knowledge driven Bayesian algorithm for solving ambiguities in the NOE assignments. These ambiguities mainly arise from chemical shift degeneration which allows multiple assignments of cross peaks. Using a set of 326 protein NMR structures, statistical tables in the form of atom-pairwise volume probability distributions (VPDs) were derived. VPDs for all assignment possibilities relevant to the assignments of interproton NOEs were calculated. With these data for a given cross peak with N possible assignments A _i(i = 1,...,N) the conditional probabilities P(A _i, a|V ₀) can be calculated that the assignment A _idetermines essentially all (a-times) of the cross peak volume V ₀. An assignment A _kwith a probability P(A _k, a|V ₀) higher than 0.8 is transiently considered as unambiguously assigned. With a list of unambiguously assigned peaks a set of structures is calculated. These structures are used as input for a next cycle of iteration where a distance threshold D _maxis dynamically reduced. The program KNOWNOE was tested on NOESY spectra of a medium size protein, the cold shock protein (TmCsp) from Thermotoga maritima. The results show that a high quality structure of this protein can be obtained by automated assignment of NOESY spectra which is at least as good as the structure obtained from manual data evaluation.     

On the need to incorporate sensitivity to CO2 transfer conductance into the Farquhar–von Caemmerer–Berry leaf photosynthesis model

Virtually all current estimates of the maximum carboxylation rate (V_cmax) of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) and the maximum electron transport rate (J_max) for C₃ species implicitly assume an infinite CO₂ transfer conductance (g_i). And yet, most measurements in perennial plant species or in ageing or stressed leaves show that g_i imposes a significant limitation on photosynthesis. Herein, we demonstrate that many current parameterizations of the photosynthesis model of Farquhar, von Caemmerer & Berry (Planta 149, 78–90, 1980 ) based on the leaf intercellular CO₂ concentration (C_i) are incorrect for leaves where g_i limits photosynthesis. We show how conventional A–C_i curve (net CO₂ assimilation rate of a leaf –A_n– as a function of C_i) fitting methods which rely on a rectangular hyperbola model under the assumption of infinite g_i can significantly underestimate V_cmax for such leaves. Alternative parameterizations of the conventional method based on a single, apparent Michaelis–Menten constant for CO₂ evaluated at C_i[K_m(CO₂)_i] used for all C₃ plants are also not acceptable since the relationship between V_cmax and g_i is not conserved among species. We present an alternative A–C_i curve fitting method that accounts for g_i through a non‐rectangular hyperbola version of the model of Farquhar et al. (1980 ). Simulated and real examples are used to demonstrate how this new approach eliminates the errors of the conventional A–C_i curve fitting method and provides V_cmax estimates that are virtually insensitive to g_i. Finally, we show how the new A–C_i curve fitting method can be used to estimate the value of the kinetic constants of Rubisco in vivo is presented     

Comparison of parameters estimated from A/Ci and A/Cc curve analysis

The parameters estimated from traditional A/C _i curve analysis are dependent upon some underlying assumptions that substomatal CO₂ concentration (C _i) equals the chloroplast CO₂ concentration (C _c) and the C _i value at which the A/C _i curve switches between Rubisco- and electron transport-limited portions of the curve (C _i-t) is set to a constant. However, the assumptions reduced the accuracy of parameter estimation significantly without taking the influence of C _i-t value and mesophyll conductance (g _m) on parameters into account. Based on the analysis of Larix gmelinii’s A/C _i curves, it showed the C _i-t value varied significantly, ranging from 24 Pa to 72 Pa and averaging 38 Pa. t-test demonstrated there were significant differences in parameters respectively estimated from A/C _i and A/C _c curve analysis (p<0.01). Compared with the maximum ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) carboxylation rate (V_cmax), the maximum electron transport rate (J_max) and J_max/V_cmax estimated from A/C _c curve analysis which considers the effects of g _m limit and simultaneously fits parameters with the whole A/C _c curve, mean V_cmax estimated from A/C _i curve analysis (V_cmax-C _i) was underestimated by 37.49%; mean Jmax estimated from A/C _i curve analysis (J_max-C _i) was overestimated by 17.8% and (J_max-C _i)/(V_cmax-C _i) was overestimated by 24.2%. However, there was a significant linear relationship between V_cmax estimated from A/C _i curve analysis and V_cmax estimated from A/C _c curve analysis, so was it J_max (p<0.05).     

The influence of maximal aerobic power on recovery of skeletal muscle following anaerobic exercise

Phosphorus magnetic resonance spectroscopy (³¹P-MRS) was used to investigate the influence of maximal aerobic power (˙VO _2max) on the recovery of human calf muscle from high-intensity exercise. The (˙VOO_2max) of 21 males was measured during treadmill exercise and subjects were assigned to either a low-aerobic-power (LAP) group (n = 10) or a high-aerobic-power (HAP) group (n = 11). Mean (SE) ˙VO _2max of the groups were 46.6 (1.1) and 64.4 (1.4) ml · kg⁻¹ · min⁻¹, respectively. A calf ergometry work capacity test was used to assign the same relative exercise intensity to each subject for the MRS protocol. At least 48 h later, subjects performed the rest (4 min), exercise (2 min) and recovery (10 min) protocol in a 1.5 T MRS scanner. The relative concentration of phosphocreatine (PCr) was measured throughout the protocol and intracellular pH (pH_i) was determined from the chemical shift between inorganic phospate (P_i) and PCr. End-exercise PCr levels were 27 (3.4) and 25 (3.5)% of resting levels for LAP and HAP respectively. Mean resting pH_i was 7.07 for both groups, and following exercise it fell to 6.45 (0.04) for HAP and 6.38 (0.04) for LAP. Analysis of data using non-linear regression models showed no differences in the rate of either PCr or pH_i recovery. The results suggest that ˙VO_2max is a poor predictor of metabolic recovery rate from high-intensity exercise. Differences in recovery rate observed between individuals with similar ˙VO_2max imply that other factors influence recovery. Accepted: 17 December 1996     

In silico optimization of pharmacokinetic properties and receptor binding affinity simultaneously: a ‘parallel progression approach to drug design’ applied to β-blockers

The present work exploits the potential of in silico approaches for minimizing attrition of leads in the later stages of drug development. We propose a theoretical approach, wherein ‘parallel’ information is generated to simultaneously optimize the pharmacokinetics (PK) and pharmacodynamics (PD) of lead candidates. β-blockers, though in use for many years, have suboptimal PKs; hence are an ideal test series for the ‘parallel progression approach’. This approach utilizes molecular modeling tools viz. hologram quantitative structure activity relationships, homology modeling, docking, predictive metabolism, and toxicity models. Validated models have been developed for PK parameters such as volume of distribution (log V_d) and clearance (log Cl), which together influence the half-life (t_1/2) of a drug. Simultaneously, models for PD in terms of inhibition constant pK_i have been developed. Thus, PK and PD properties of β-blockers were concurrently analyzed and after iterative cycling, modifications were proposed that lead to compounds with optimized PK and PD. We report some of the resultant re-engineered β-blockers with improved half-lives and pK_i values comparable with marketed β-blockers. These were further analyzed by the docking studies to evaluate their binding poses. Finally, metabolic and toxicological assessment of these molecules was done through in silico methods. The strategy proposed herein has potential universal applicability, and can be used in any drug discovery scenario; provided that the data used is consistent in terms of experimental conditions, endpoints, and methods employed. Thus the ‘parallel progression approach’ helps to simultaneously fine-tune various properties of the drug and would be an invaluable tool during the drug development process.     

Activation and inhibition of mitochondrial adenosine triphosphatase by various anions and other agents

The activating or inhibiting actions of a variety of anion species and of oligomycin, aurovertin and Dio-9 on the ATPase of a sonic particle preparation of rat liver mitochondria have been characterized by measurements of the relevantV _max,K _i andK _m values.The normalV _max was increased by a factor near 7 by the anions: dichromate, chromate, pyrophosphate, orthophosphate, orthoarsenate and sulphate. The fully activating concentration varied from about 2 mM for dichromate to 150 mM for sulphate. The increase inV _max was accompanied by a time-dependent decrease in (K _i)ADP, but there was no change in (K _m)ATP. The increase inV _max by the activating anions was abolished by aurovertin; but in presence of oligomycin, the lowV _max was increased by the activating anions by the same factor as theV _max in absence of oligomycin.Certain anions, notably azide, decreasedV _max, but did not affect (K _i)ADP or (K _m)ATP. The decrease inV _max by azide and oligomycin were approximately additive. Even at high concentration, Dio-9 was without detectable effect on the ATPase, but it had a gramicidinlike effect on the intact mitochondria.The specificity of the ATPase for ATP relative to GTP was found to be attributable to the high value of (V _max)ATP compared with (V _max)GTP. The values of (K _m)ATP and (K _m)GTP were virtually the same.Some rationalization of these and other supporting observations is attempted in terms of present knowledge of the constitution of the ATPase complex.     

Qualitative effects of patchy stomatal conductance distribution features on gas-exchange calculations

The qualitative influence of patchy stomatal conductance distributions on the values of photosynthesis (A) and intercellular CO₂ concentration (c_i) as determined by gas-exchange measurements were investigated using computer modelling. Gas-exchange measurements were simulated for different conductance distributions by modelling photosynthesis explicitly for each patch, summing these rates, and inferring c_i from a diffusion equation. Qualitative relationships are presented between conductance distribution features and the difference between assimilation rates measured for patchy and homogeneous leaves at the same c_i (A_p and A_h, respectively). These data show that, although most conductance distributions have little effect on the value of A measured for a given c_i, some distribution features (which we have termed ‘bimodality’, ‘position’, ‘skewness’ and ‘range’) play a key role in controlling the magnitude of these effects. Distributions that are more nearly bimodal, span regions of lower conductance, are right-skewed, or have broader conductance ranges are associated with larger effects on the A(c_i) relationship. To clarify our mathematical analysis and illustrate some of the trends it predicts, we present conductance distributions and gas-exchange data from leaves of Malus dolgo var. Spring Snow Dial were treated with ABA. The results are discussed in the light of recent controversy over the effect of patchy stomatal conductance on gas-exchange data.     

Evidence for the Sequential Formation of Two Complexes Between an Uptake Inhibitor, GBR 12783 [1-[2-(Diphenylmethoxy)ethyl]-4-(3-Phenyl-2-Propenyl)piperazine], and the Neuronal Transporter of Dopamine

Abstract : Incubation of a crude synaptosomal fraction from rat striatum with GBR 12783 at 37°C produced an inhibition of the specific uptake of [³H]dopamine that increased with time. The inhibition increased when GBR 12783 was present during preincubation and incubation (IC₅₀ = 1.85 ± 0.1 nM) instead of incubation alone (IC₅₀ = 25 ± 3.5 nM). Time-course studies of uptake inhibition demonstrated that a first collision transporter-inhibitor complex (TI) was formed immediately after addition of GBR 12783 so that the initial uptake velocity (V_o) decreased for increasing concentrations of inhibitor (K_i≥ 20 nM). TI slowly isomerized to a more stable complex TI^* (K^*_i≤ 5 nM) with a value of t_1/2 = 20-270 s. Fits of data to model 2 in which the steady-state uptake (V_S) is set to zero were generally preferred, suggesting that formation of TI^* could tend to irreversibility, as a consequence of a very low reverse isomerization. As expected, k, V_o, and V_S tended to steady-state values in an asymptotic manner for high concentrations of GBR 12783. GBR 12783 at 2.5 nM produced a mixed inhibition of the uptake, with an increase in K_M and a decrease in V_max ; these effects were improved for 10 nM GBR 12783 and at 20°C. These results are discussed in relation to previous data concerning [³H]GBR 12783 binding. The present work gives the first experimental demonstration that dopamine uptake blockers can act according to a two-step mechanism of inhibition ; this is of great interest, because these inhibitors can oppose the effects of cocaine or amphetamine on the transporter according to a reaction that is partly nondependent on the concentration of the abused agent.     

Additive and testcross genetic variances in crosses among recombinant inbreds

 Breeders desire populations with a high mean performance and a large genetic variance. Theory and methods are lacking for predicting additive variance (V _A ) and testcross variance (V _T ) in biparental populations. Breeders have unsuccessfully attempted to predict V _A based on the coefficient of coancestry ( f ) or molecular-marker similarity between parents. In this paper, we derive the expected values of V _A and V _T in biparental populations, examine the variability of V _A among biparental crosses, and discuss how V _A and V _T may be predicted in applied breeding programs. Suppose i is a recombinant inbred derived from the cross between inbreds P ₁ and P ₂, and inbred j is not a direct descendant of i. Let V _A(i,j) be the additive variance in the F₂ of the (i×j) biparental cross. Let V _T(i, j) be the variance among testcrosses of F₂ individuals with a specific unrelated inbred or population. Assuming linkage equilibrium and the absence of epistasis, V _A(i, j) =λV _A(P1, j) +(1−λ) V _A(P2, j) , where λ= parental contribution of P ₁ to i. Similarly, V _T(i, j) = λV _T(P1, j) +(1−λ) V _T(P2, j) . Additive variance in crosses between recombinant inbreds cannot be modelled as a function of  f if, as indicated in the literature, V _A differs among crosses of founder inbreds. If molecular-marker similarity between parents is used as an estimate of f, then a strong linear relationship is likewise not expected between V _A and marker similarity. Differences between the actual and expected λ led to variation in V _A . In applied breeding programs, modelling V _A or V _T in biparental crosses may be feasible with estimates of V _A or V _T in prior crosses and information on λ obtained from molecular-marker data. Received: 23 September 1997 / Accepted: 30 December 1997     

Retrospective analysis of biochemical limitations to photosynthesis in 49 species: C4 crops appear still adapted to pre-industrial atmospheric [CO2]

Leaf CO₂ uptake (A) in C₄ photosynthesis is limited by the maximum apparent rate of PEPc carboxylation (V_pmax) at low intercellular [CO₂] (c_i) with a sharp transition to a c_i-saturated rate (V_max) due to co-limitation by ribulose-1:5-bisphosphate carboxylase/oxygenase (Rubisco) and regeneration of PEP. The response of A to c_i has been widely used to determine these two parameters. V_max and V_pmax depend on different enzymes but draw on a shared pool of leaf resources, such that resource distribution is optimized, and A maximized, when V_max and V_pmax are co-limiting. We collected published A/c_i curves in 49 C₄ species and assessed variation in photosynthetic traits between phylogenetic groups, and as a function of atmospheric [CO₂]. The balance of V_max-V_pmax varied among evolutionary lineages and C₄ subtypes. Operating A was strongly V_max-limited, such that re-allocation of resources from V_pmax towards V_max was predicted to improve A by 12% in C₄ crops. This would not require additional inputs but rather altered partitioning of existing leaf nutrients, resulting in increased water and nutrient-use efficiency. Optimal partitioning was achieved only in plants grown at pre-industrial atmospheric [CO₂], suggesting C₄ crops have not adjusted to the rapid increase in atmospheric [CO₂] of the past few decades.     

Intracellular K+ activities and cell membrane potentials in a K+-transporting epithelium,the midgut of tobacco hornoworm (Manduca sexta)

Summary Transbasal electrical potential (V _b) and intraepithelial potassium chemical activity ((K⁺) _i ) were measured in isolated midgut epithelium of tobacco hornworm (Manduca sexta) using double-barrelled glass microelectrodes. Values ofV _b ranging from +8 to –48 mV (relative to blood side) were recorded. For all sites, (K⁺) _i is within a few millivolts of electrochemical equilibrium with the blood side bathing solution. Sites more negative than –20 mV show relatively high sensitivity ofV _b to changes in blood side K⁺ concentration: 43% of these sites can be marked successfully with iontophoresed Lucifer yellow CH dye and shown to represent epithelial cells of all three types present in the midgut. In about half of successful marks, dye-coupling of several adjacent cells is seen. Low potential sites — those withV _b less negative than –20 mV —typically do not show high sensitivity ofVb to changes of external K⁺, but rather (K⁺) _i rapidly approaches the K⁺ activity of blood side bathing solution. These sites can seldom be marked with Lucifer yellow (4% success). The mean (K⁺) _i of the high potential sites is 95±29 (sd)mm under standard conditions, a value which is in accord with published values for the whole tissue.     

Effect of adherence,cell morphology,and lipopolysaccharide on potassium conductance and passive membrane properties of murine macrophage J774.1 cells

Summary The effects of adherence, cell morphology, and lipopolysaccharide on electrical membrane properties and on the expression of the inwardly rectifying K conductance in J774.1 cells were investigated. Whole-cell inwardly rectifying K currents (K _i), membrane capacitance (C _m), and membrane potential (V _m) were measured using the patch-clamp technique. SpecificK _i conductance (G _K i, whole-cell Ki conductance corrected for leak and normalized to membrane capacitance) was measured as a function of time after adherence, and was found to increase almost twofold one day after plating. Membrane potential (V _m) also increased from –42±4 mV (n=32) to –58±2 mV (n=47) over the same time period.G _K i andV _m were correlated with each other;G _L (leak conductance normalized to membrane capacitance) andV _m were not. The magnitudes ofG _K i andV _m 15 min to 2 hr after adherence were unaffected by the presence of 100 m cycloheximide, but the increase inG _K iandV _m that normally occurred between 2 and 8 hr after adherence was abolished by cycloheximide treatment. Membrane properties were analyzed as a function of cell morphology, by dividing cells into three categories ranging from small round cells to large, extremely spread cells. The capacitance of spread cells increased more than twofold within one day after adherence, which indicates that spread cells inserted new membrane. Spread cells had more negative resting membrane potentials than round cells, butG _K i andG _L were not significantly different. Lipopolysaccharide-(LPS; 1 or 10 g/ml) treated cells showed increasedC _m compared to control cells plated for comparable times. In contrast to the effect of adherence, LPS-treated cells exhibited a significantly lowerG _K i than control cells, indicating that the additional membrane did not have as high a density of functionalG _K i channels. We conclude that both adherence and LPS treatment increase the total surface membrane area of J774 cells and change the density of Ki channels. In addition, this study demonstrates that membrane area and density of Ki channels can vary independently of one another.     

A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011

The initial genome‐scale reconstruction of the metabolic network of Escherichia coli K‐12 MG1655 was assembled in 2000. It has been updated and periodically released since then based on new and curated genomic and biochemical knowledge. An update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. iJO1366 was (1) updated in part using a new experimental screen of 1075 gene knockout strains, illuminating cases where alternative pathways and isozymes are yet to be discovered, (2) compared with its predecessor and to experimental data sets to confirm that it continues to make accurate phenotypic predictions of growth on different substrates and for gene knockout strains, and (3) mapped to the genomes of all available sequenced E. coli strains, including pathogens, leading to the identification of hundreds of unannotated genes in these organisms. Like its predecessors, the iJO1366 reconstruction is expected to be widely deployed for studying the systems biology of E. coli and for metabolic engineering applications.     

Uptake kinetics and assimilation of phosphorus byCatenella nipaeandUlva lactucacan be used to indicate ambient phosphate availability

Uptake, assimilation and compartmentation of phosphate were studied in the opportunist green macroalgaUlva lactucaand the estuarine red algal epiphyteCatenella nipae. The Michaelis–Menten model was used to describe uptake rates of inorganic phosphate (P_i) at different concentrations. Maximum uptake rates (V _max) of P-starved material exceededV _maxof P-enriched material; this difference was greater forC. nipae. Uptake and allocation of phosphorus (P) to internal pools was measured using trichloroacetic acid (TCA) extracts and³²P. Both species demonstrated similar assimilation paths: when P-enriched, most³²P accumulated as free phosphate. When unenriched,³²P was rapidly assimilated into the TCA-insoluble pool.C. nipaeconsistently assimilated more³²P into this pool thanU. lactuca, indicatingC. nipaehas a greater P-storage capacity. In both species,³²P release data showed two internal compartments with very different biological half-lives. The rapidly exchanging compartment had a short half-life of 2 to 12 min, while the slowly exchanging compartment had a much longer half-life of 12 days in P-starvedC. nipaeor 4 days in P-starvedU. lactuca. In both species, the slowly exchanging compartment accounted for more than 90% of total tissue.U. lactucaandC. nipaeresponded differently to high external P_i.U. lactucarapidly took up P_i, transferring this P_iinto tissue phosphate and TCA-soluble P in a few hours (90% of total P).C. nipaetook up P_iat lower rates and stored much of this P in less mobile TCA-insoluble forms. Long-term storage of refractory forms of P makesC. nipaea useful bioindicator of the prevailing conditions of P_iavailability over at least the previous 7 days, whereas the P-status ofU.lactucamay reflect conditions over no more than the previous few hours or days.C. nipaeis a more useful bioindicator for P status of estuarine and marine waters thanU. lactuca.     

Using the rapid A‐Ci response (RACiR) in the Li‐Cor 6400 to measure developmental gradients of photosynthetic capacity in poplar

The rapid A‐C_i response (RACiR) technique alleviates limitations of measuring photosynthetic capacity by reducing the time needed to determine the maximum carboxylation rate (V_cmax) and electron transport rate (J_max) in leaves. Photosynthetic capacity and its relationships with leaf development are important for understanding ecological and agricultural productivity; however, our current understanding is incomplete. Here, we show that RACiR can be used in previous generation gas exchange systems (i.e., the LI‐6400) and apply this method to rapidly investigate developmental gradients of photosynthetic capacity in poplar. We compared RACiR‐determined V_cmax and J_max as well as respiration and stomatal conductance (g_s) across four stages of leaf expansion in Populus deltoides and the poplar hybrid 717‐1B4 (Populus tremula × Populus alba). These physiological data were paired with leaf traits including nitrogen concentration, chlorophyll concentrations, and specific leaf area. Several traits displayed developmental trends that differed between the poplar species, demonstrating the utility of RACiR approaches to rapidly generate accurate measures of photosynthetic capacity. By using both new and old machines, we have shown how more investigators will be able to incorporate measurements of important photosynthetic traits in future studies and further our understanding of relationships between development and leaf‐level physiology.     

Separate and combined effects of temperature and hypoxia on breathing pattern in the domestic fowl

Summary Minute ventilation (V _E), tidal volume (V _T), respiratory frequency (f) and clavicular air sac gas composition were measured in conscious domestic fowl breathing air and hypoxic gas mixtures at neutral (18±1°C) and raised (33±1°C) air temperatures. Increases inV _E caused by inhalation of 10%, 8% or 6.5% O₂ in N₂, respectively, were independent of temperature although at each level the absoluteV _E was ca. 21·min⁻¹ greater in the panting birds. Changes in respiratory pattern during hypoxia were markedly dependent on temperature. At 18°C almost all of the increasedV _E resulted from increasedf. At 33°C hypoxia led to a strong suppression off and increase inV _T. It is concluded that hyperthermia and hypoxia are additive and non-interactive in their effects on ventilatory drive, in agreement with previously reported effects of hypercapnia and physical exercise on breathing in panting fowl.     

Hepatocyte water volume and potassium activity during hypotonic stress

Hepatocytes exhibit a regulatory volume decrease (RVD) during hypotonic shock, which comprises loss of intracellular K⁺ and Cl^– accompanied by hyperpolarization of transmembrane potential (V _m ) due to an increase in membrane K⁺ conductance, (G _K). To examine hepatocyte K⁺ homeostasis during RVD, double-barrel, K⁺-selective microelectrodes were used to measure changes in steady-state intracellular K⁺ activity (a _K ⁱ ) and V _m during hyposmotic stress. Cell water volume change was evaluated by measuring changes in intracellular tetramethylammonium (TMA⁺). Liver slices were superfused with modified Krebs physiological salt solution. Hyposmolality (0.8×300 mosm) was created by a 50 mm step-decrease of external sucrose concentration. Hepatocyte V _m hyperpolarized by 19 mV from –27 ± 1 to –46 ± 1 mV and a _K ⁱ decreased by 14% from 91 ± 4 to 78 ± 4 mm when slices were exposed to hyposmotic stress for 4–5 min. Both V _m and a _K ⁱ returned to control level after restoring isosmotic solution. In paired measurements, hypotonic stress induced similar changes in V _m and a _K ⁱ both control and added ouabain (1 mm) conditions, and these values returned to their control level after the osmotic stress. In another paired measurement, hypotonic shock first induced an 18-mV increase in V _m and a 15% decrease in a _K ⁱ in control condition. After loading hepatocytes with TMA⁺, the same hypotonic shock induced a 14-mV increase in V _m and a 14% decrease in a _TMA ⁱ . This accounted for a 17% increase of intracellular water volume, which was identical to the cell water volume change obtained when a _K ⁱ was used as the marker. Nonetheless, hyposmotic stress-induced changes in V _m and a _K ⁱ were blocked partly by Ba²⁺ (2 mm). We conclude that (i) hepatocyte V _m increases and a _K ⁱ decreases during hypotonic shock; (ii) the changes in hepatocyte V _m and a _K ⁱ during and after hypotonic shock are independent of the Na⁺-K⁺ pump; (iii) the decrease in a _K ⁱ during hypotonic stress results principally from hepatocyte swelling.This work was supported by grant AA-08867 from the Alcohol, Drug Abuse, and Mental Health Association.     

Multilocus epistasis,linkage, and genetic variance in breeding populations with few parents

In a previous study of maize (Zea mays L.) populations formed from few parents, we found that estimates of genetic variances were inconsistent with a simple additive genetic model. Our objective in the current study was to determine how multilocus epistasis and linkage affect the loss of genetic variance in populations created from a small number of parents (N). In simulation experiments, F₂ individuals from the same single cross were intermated to form progeny populations from N = 1, 2, 4, and 8 parents. Additive gene effects and metabolic flux epistasis due to L = 10, 50, and 100 loci were modeled. For additive, additive-with-linkage, epistatic, and epistasis-with-linkage models, we estimated the ratio between total genetic variance in the progeny population (V _N ) and base population (V _B ) as well as the 95th (Δ_95%) and 75th (Δ_75%) percentile differences between the estimated V _N /V _B and the V _N /V _B expected for the additive model. The mean V _N /V _B ratio was lower under epistasis than under additivity, indicating that metabolic flux epistasis hastens the decline in genetic variance due to small N. In contrast, Δ_95% was higher with epistasis than with additivity across the different levels of N and L. Linkage had little effect on the mean V _N /V _B , whereas it increased Δ_95% and Δ_75% under both additivity and epistasis. Smaller N and L led to higher V _N /V _B particularly when epistasis was present. Overall, the results indicated that while metabolic flux epistasis led to a faster average decline in genetic variance, it also led to greater variability in this decline to the point that V _N /V _B was larger than expected in many populations.     

Intracellular Ca(2+) oscillations induced by over-expressed Ca(V)3.1 T-type Ca(2+) channels in NG108-15 cells

T-type Ca²⁺ channel family includes three subunits Ca_V3.1, Ca_V3.2 and Ca_V3.3 and have been shown to control burst firing and intracellular Ca²⁺ concentration ([Ca²⁺]_i) in neurons. Here, we investigated whether Ca_V3.1 channels could generate a pacemaker current and contribute to cell excitability. Ca_V3.1 clones were over-expressed in the neuronal cell line NG108-15. Ca_V3.1 channel expression induced repetitive action potentials, generating spontaneous membrane potential oscillations (MPOs) and concomitant [Ca²⁺]_i oscillations. These oscillations were inhibited by T-type channels antagonists and were present only if the membrane potential was around −61 mV. [Ca²⁺]_i oscillations were critically dependent on Ca²⁺ influx through Ca_V3.1 channels and did not involve Ca²⁺ release from the endoplasmic reticulum. The waveform and frequency of the MPOs are constrained by electrophysiological properties of the Ca_V3.1 channels. The trigger of the oscillations was the Ca_V3.1 window current. This current induced continuous [Ca²⁺]_i increase at −60 mV that depolarized the cells and triggered MPOs. Shifting the Ca_V3.1 window current potential range by increasing the external Ca²⁺ concentration resulted in a corresponding shift of the MPOs threshold. The hyperpolarization-activated cation current (I_h) was not required to induce MPOs, but when expressed together with Ca_V3.1 channels, it broadened the membrane potential range over which MPOs were observed. Overall, the data demonstrate that the Ca_V3.1 window current is critical in triggering intrinsic electrical and [Ca²⁺]_i oscillations.     

Role of ionization of the phosphate cosubstrate on phosphorolysis by purine nucleoside phosphorylase (PNP) of bacterial (<Emphasis Type="Italic">E. coli</Emphasis>) and mammalian (human) origin

Kinetics of the reactions of purine nucleoside phosphorylases (PNP) from E. coli (PNP-I, the product of the deoD gene) and human erythrocytes with their natural substrates guanosine (Guo), inosine (Ino), a substrate analogue N(7)-methylguanosine (m⁷Guo), and orthophosphate (P_i, natural cosubstrate) and its thiophosphate analogue (SP_i), found to be a weak cosubstrate, have been studied in the pH range 5–8. In this pH range Guo and Ino exist predominantly in the neutral forms (pK_a 9.2 and 8.8); m⁷Guo consists of an equilibrium mixture of the cationic and zwitterionic forms (pK_a 7.0); and P_i and SP_i exhibit equilibria between monoanionic and dianionic forms (pK_a 6.7 and 5.4, respectively). The phosphorolysis of m⁷Guo (at saturated concentration) with both enzymes exhibits Michaelis kinetics with SP_i, independently of pH. With P_i, the human enzyme shows Michaelis kinetics only at pH ∼5. However, in the pH range 5–8 for the bacterial enzyme, and 6–8 for the human enzyme, enzyme kinetics with P_i are best described by a model with high- and low-affinity states of the enzymes, denoted as enzyme-substrate complexes with one or two active sites occupied by P_i, characterized by two sets of enzyme-substrate dissociation constants (apparent Michaelis constants, K _m1 and K _m2) and apparent maximal velocities (V _max1 and V _max2). Their values, obtained from non-linear least-squares fittings of the Adair equation, were typical for negative cooperativity of both substrate binding (K _m1 < K _m2) and enzyme kinetics (V _max1/K _m1 > V _max2/K _m2). Comparison of the pH-dependence of the substrate properties of P_i versus SP_i points to both monoanionic and dianionic forms of P_i as substrates, with a marked preference for the dianionic species in the pH range 5–8, where the population of the P_i dianion varies from 2 to 95%, reflected by enzyme efficiency three orders of magnitude higher at pH 8 than that at pH 5. This is accompanied by an increase in negative cooperativity, characterized by a decrease in the Hill coefficient from n _H ∼1 to n _H ∼0.7 for Guo with the human enzyme, and to n _H ∼0.7 and 0.5 for m⁷Guo with the E. coli and human enzymes, respectively. Possible mechanisms of cooperativity are proposed. Attention is drawn to the substrate properties of SP_i in relation to its structure.