Nonlinear Enzyme Kinetics Can Lead to High Metabolic Flux Control Coefficients: Implications for the Evolution of Dominance

In a classic study, Kacser & Burns (1981, Genetics 97, 639-666) demonstrated that given certain plausible assumptions, the flux in a metabolic pathway was more or less indifferent to the activity of any of the enzymes in the pathway taken singly. It was inferred from this that the observed dominance of most wild-type alleles with respect to loss-of-function mutations did not require an adaptive, meaning selectionist, explanation. Cornish-Bowden (1987, J. theor. Biol. 125, 333-338) showed that the Kacser-Burns inference was not valid when substrate concentrations were large relative to the relevant Michaelis constants. We find that in a randomly constructed functional pathway, even when substrate levels are small, one can expect high values of control coefficients for metabolic flux in the presence of significant nonlinearities as exemplified by enzymes with Hill coefficients ranging from two to six, or by the existence of oscillatory loops. Under these conditions the flux can be quite sensitive to changes in enzyme activity as might be caused by inactivating one of the two alleles in a diploid. Therefore, the phenomenon of dominance cannot be a trivial ''default'' consequence of physiology but must be intimately linked to the manner in which metabolic networks have been moulded by natural selection.

Paramagnetic probes in membrane biophysics

The use of paramagnetic probes in membrane research is reviewed. Electron paramagnetic resonance studies on model and biological membranes doped with covalent and non-covalent spin-labels have been discussed with special emphasis on the methodology and the type of information obtainable on several important phenomena like membrane fluidity, lipid flip-flop, lateral diffusion of lipids, lipid phase separation, lipid bilayer phase transitions, lipid-protein interactions and membrane permeability. Nuclear magnetic resonance spectroscopy has also been effectively used to study the conformations of cation mediators across membranes and to analyse in detail the transmembrane ionic motions at the mechanistic level.

Effect of antiserum to luteinizing hormone (LHAS) on the physiology of the epididymis and accessory glands in the albino rat

Rabbit antiserum specific to ovine luteinizing hormone free of contaminating antibodies to nonspecific proteins and FSH was administered to adult, intact rats at a dose of 0.1 and 0.2 ml/day for five days. LHAS had no effect on the weights of the epididymis but decreased their secretory activity to castrate level. Administration of 0.2 ml of LHAS or castration resulted in a marked and comparable reduction in the weights and secretory activity of the accessory glands. LHAS, even at a lower dose (0.1 ml/day), caused a significant reduction in the content of sialic acid in the vas deferons and Cowper's glands. These results are discussed in relation to the factors that regulate the functions of the epididymis and accessory glands.

Hierarchical modelling of acclimatory processesstar, open

The term acclimation has been used with several connotations in the field of acclimatory physiology. An attempt has been made, in this paper, to define precisely the term “acclimation” for effective modelling of acclimatory processes. Acclimation is defined with respect to a specific variable, as cumulative experience gained by the organism when subjected to a step change in the environment. Experimental observations on a large number of variables in animals exposed to sustained stress, show that after initial deviation from the basal value (defined as “growth”), the variables tend to return to basal levels (defined as “decay”). This forms the basis for modelling biological responses in terms of their growth and decay. Hierarchical systems theory as presented by Mesarovic, Macko & Takahara (1970) facilitates modelling of complex and partially characterized systems. This theory, in conjunction with “growth-decay” analysis of biological variables, is used to model temperature regulating system in animals exposed to cold. This approach appears to be applicable at all levels of biological organization. Regulation of hormonal activity which forms a part of the temperature regulating system, and the relationship of the latter with the “energy” system of the animal of which it forms a part, are also effectively modelled by this approach. It is believed that this systematic approach would eliminate much of the current circular thinking in the area of acclimatory physiology.

Analysis of the amino acid sequences of plant Bowman-Birk inhibitors

Plant seeds contain a large number of protease inhibitors of animal, fungal, and bacterial origin. One of the well-studied families of these inhibitors is the Bowman-Birk family(BBI). The BBIs from dicotyledonous seeds are 8K, double-headed proteins. In contrast, the 8K inhibitors from monocotyledonous seeds are single headed. Monocots also have a 16K, double-headed inhibitor. We have determined the primary structure of a Bowman-Birk inhibitor from a dicot, horsegram, by sequential edman analysis of the intact protein and peptides derived from enzymatic and chemical cleavage. The 76-residue-long inhibitor is very similar to that ofMacrotyloma axillare. An analysis of this inhibitor along with 26 other Bowman-Birk inhibitor domains (MW 8K) available in the SWISSPROT databank revealed that the proteins from monocots and dicots belong to related but distinct families. Inhibitors from monocots show larger variation in sequence. Sequence comparison shows that a crucial disulphide which connects the amino and carboxy termini of the active site loop is lost in monocots. The loss of a reactive site in monocots seems to be correlated to this. However, it appears that this disulphide is not absolutely essential for retention of inhibitory function. Our analysis suggests that gene duplication leading to a 16K inhibitor in monocots has occurred, probably after the divergence of monocots and dicots, and also after the loss of second reactive site in monocots.

Solution NMR studies of acetohydroxy acid synthase I: Identification of the sites of inter-subunit interactions using multidimensional NMR methods

The novel multidomain organization in the multimeric Escherichia coli AHAS I (ilvBN) enzyme has been dissected to generate polypeptide fragments. These fragments when cloned, expressed and purified reassemble in the presence of cofactors to yield a catalytically competent enzyme. Structural characterization of AHAS has been impeded due to the fact that the holoenzyme is prone to dissociation leading to heterogeneity in samples. Our approach has enabled the structural characterization using high-resolution nuclear magnetic resonance methods. Near complete sequence specific NMR assignments for backbone H-N, N-15, C-13 alpha and C-13(beta) atoms of the FAD binding domain of ilvB have been obtained on samples isotopically enriched in H-2, C-13 and N-15. The secondary structure determined on the basis of observed C-13(alpha) secondary chemical shifts and sequential NOEs indicates that the secondary structure of the FAD binding domain of E. coli AHAS large Subunit (ilvB) is similar to the structure of this domain in the catalytic subunit of yeast AHAS. Protein-protein interactions involving the regulatory subunit (ilvN) and the domains of the catalytic subunit (ilvB) were studied using circular dichroic and isotope edited solution nuclear magnetic resonance spectroscopic methods. Observed changes in circular dichroic spectra indicate that the regulatory subunit (ilvN) interacts with ilvB alpha and ilvB beta domains of the catalytic subunit and not with the ilvB gamma domain. NMR chemical shift mapping methods show that ilvN binds close to the FAD binding site in ilvB beta and proximal to the intrasubunit ilvB alpha/ilvB beta domain interface. The implication of this interaction on the role of the regulatory subunit oil the activity of the holoenzyme is discussed. NMR studies of the regulatory domains show that these domains are structured in solution. Preliminary evidence for the interaction of ilvN with the metabolic end product of the pathway, viz., valine is also presented.

Kinetic characterization of rat brain type IIA sodium channel alpha-subunit stably expressed in a somatic cell line

1. The rat brain type IIA Na+ channel alpha-subunit was stably expressed in Chinese hamster ovary (CHO) cells. Current through the expressed Na+ channels was studied using the whole-cell configuration of the patch clamp technique. The transient Na+ current was sensitive to TTX and showed a bell-shaped peak current vs. membrane potential relation. 2. Na+ current inactivation was better described by the sum of two exponentials in the potential range -30 to +40 mV, with. a dominating fast component and a small slower component. 3. The steady-state inactivation, h(infinity), was related to potential by a Boltzmann distribution, underlying thr ee states of the inactivation gate. 4. Recovery of the channels from inactivation at different potentials in the range -70 to -120 mV were characterized by al? initial delay which decreased with hyperpolarization. The time course was well fitted by the sum of two exponentials. In this case the slower exponential was the major component, and both time constants decreased with hyperpolarization. 5. For a working description of the Na+ channel inactivation in this preparation, with a minimal deviation from the Hodgkin-Huxley model, a three-state scheme of the form O reversible arrow I-1 reversible arrow I-2 was proposed, replacing the original two-state scheme of the Hodgkin-Huxley model, and the rate constants are reported. 6. The instantaneous current-voltage relationship showed marked deviation from linearity and was satisfactorily fitted by the constant-field equation. 7. The time course of activation was described by an m(x) model. However, the best-fitted value of x varied with the membrane potential and had a mean value of 2. 8. Effective gating charge was determined to be 4.7e from the slope of the activation plot, plotted on a logarithmic scale. 9. The rate constants of activation, alpha(m) and beta(m), were determined. Their functional dependence on the membrane potential was investigated.

Mycobacterial Stress Regulation: The Dps ``Twin Sister'' Defense Mechanism and Structure-Function Relationship

In this work, we have tried to emphasize the connection between mycobacterial growth and regulation of gene expression. Utilization of multiple carbon sources and diauxic growth helps bacteria to regulate gene expression at an optimum level so that the inhospitable conditions encountered during nutrient depletion can be circumvented. These aspects will be discussed with respect to mycobacterial growth in subsequent sections. Identification and characterization of genes induced under such conditions is helpful to understand the physiology of the bacterium. Although it is necessary to compare the total expression profile of proteins as they transit from vegetative growth to stationary phase, at times a lot of insights can be deciphered from the expression pattern of one or two proteins. We have compared the protein expression and sigma factor selectivity of two such proteins in M. smegmatis to understand the differential regulation of genes playing diverse function in the same species. Some newer insights on the structure and function of one of the Dps proteins are also explained.

Selective attention in a synchronising bushcricket: physiology

Synchronising bushcricket males achieve synchrony by delaying their chirps in response to calling neighbours. In multi-male choruses, males that delay chirps in response to all their neighbours would remain silent most of the time and be unable to attract mates. This problem could be overcome if the afferent auditory system exhibited selective attention, and thus a male interacted only with a subset of neighbours. We investigated whether individuals of the bushcricket genus Mecopoda restricted their attention to louder chirps neurophysiologically, behaviourally and through spacing. We found that louder leading chirps were preferentially represented in the omega neuron but the representation of softer following chirps was not completely abolished. Following chirps that were 20 dB louder than leading chirps were better represented than leading chirps. During acoustic interactions, males synchronised with leading chirps even when the following chirps were 20 dB louder. Males did not restrict their attention to louder chirps during interactions but were affected by all chirps above a particular threshold. In the field, we found that males on average had only one or two neighbours whose calls were above this threshold. Selective attention is thus achieved in this bushcricket through spacing rather than neurophysiological filtering of softer signals.

Selective attention in a synchronising bushcricket: physiology, behaviour and ecology

Synchronising bushcricket males achieve synchrony by delaying their chirps in response to calling neighbours. In multi-male choruses, males that delay chirps in response to all their neighbours would remain silent most of the time and be unable to attract mates. This problem could be overcome if the afferent auditory system exhibited selective attention, and thus a male interacted only with a subset of neighbours. We investigated whether individuals of the bushcricket genus Mecopoda restricted their attention to louder chirps neurophysiologically, behaviourally and through spacing. We found that louder leading chirps were preferentially represented in the omega neuron but the representation of softer following chirps was not completely abolished. Following chirps that were 20 dB louder than leading chirps were better represented than leading chirps. During acoustic interactions, males synchronised with leading chirps even when the following chirps were 20 dB louder. Males did not restrict their attention to louder chirps during interactions but were affected by all chirps above a particular threshold. In the field, we found that males on average had only one or two neighbours whose calls were above this threshold. Selective attention is thus achieved in this bushcricket through spacing rather than neurophysiological filtering of softer signals.

Selective attention in a synchronising bushcricket: physiology, behaviour and ecology

Synchronising bushcricket males achieve synchrony by delaying their chirps in response to calling neighbours. In multi-male choruses, males that delay chirps in response to all their neighbours would remain silent most of the time and be unable to attract mates. This problem could be overcome if the afferent auditory system exhibited selective attention, and thus a male interacted only with a subset of neighbours. We investigated whether individuals of the bushcricket genus Mecopoda restricted their attention to louder chirps neurophysiologically, behaviourally and through spacing. We found that louder leading chirps were preferentially represented in the omega neuron but the representation of softer following chirps was not completely abolished. Following chirps that were 20 dB louder than leading chirps were better represented than leading chirps. During acoustic interactions, males synchronised with leading chirps even when the following chirps were 20 dB louder. Males did not restrict their attention to louder chirps during interactions but were affected by all chirps above a particular threshold. In the field, we found that males on average had only one or two neighbours whose calls were above this threshold. Selective attention is thus achieved in this bushcricket through spacing rather than neurophysiological filtering of softer signals.

Stress responses in mycobacteria

Mycobacterium tuberculosis is a successful pathogen that overcomes numerous challenges presented by the immune system of the host. This bacterium usually establishes a chronic infection in the host where it may silently persist inside a granuloma until, a failure in host defenses, leads to manifestation of the disease. None of the conventional anti-tuberculosis drugs are able to target these persisting bacilli. Development of drugs against such persisting bacilli is a constant challenge since the physiology of these dormant bacteria is still not understood at the molecular level. Some evidence suggests that the in vivo environment encountered by the persisting bacteria is anoxic and nutritionally starved. Based on these assumptions, anaerobic and starved cultures are used as models to study the molecular basis of dormancy. This review outlines the problem of persistence of M. tuberculosis and the various in vitro models used to study mycobacterial latency. The basis of selecting the nutritional starvation model has been outlined here. Also, the choice of M. smegmatis as a model suitable for studying mycobacterial latency is discussed. Lastly, general issues related to oxidative stress and bacterial responses to it have been elaborated. We have also discussed general control of OxyR-mediated regulation and emphasized the processes which manifest in the absence of functional OxyR in the bacteria. Lastly, a new class of protein called Dps has been reviewed for its important role in protecting DNA under stress.

High cholesterol diet and esterification of cholesterol by the intestinal mucosa of rats

Young male rats maintained on a diet containing 1% cholesterol were sacrificed at the end of 1st, 2nd, 3rd, 5th, and 7th week. Acetone powders prepared from their intestinal mucosa and pancreas were tested for the synthetic and hydrolytic activities for Vitamin A and cholesterol esters. The esterifying activity of the mucosal enzymes for both Vitamin A and cholesterol increased progressively up to the end of the 5th week; the increase in esterification of cholesterol was more marked with respect to saturated fatty acids, as compared to the unsaturated ones. The pancreatic enzymes remained unaffected. It is suggested that one of the reasons for the accumulation of cholesterol esters in animal tissues may be the increased esterification of the sterol in the mucosa induced by dietary cholesterol.

Choosing an appropriate index to construct dominance hierarchies in animal societies: a comparison of three indices

A plethora of indices have been proposed and used to construct dominance hierarchies in a variety of vertebrate and invertebrate societies, although the rationale for choosing a particular index for a particular species is seldom explained. In this study, we analysed and compared three such indices, viz Clutton-Brock et al.'s index (CBI), originally developed for red deer, Cervus elaphus, David's score (DS) originally proposed by the statistician H. A. David and the frequency-based index of dominance (FDI) developed and routinely used by our group for the primitively eusocial wasps Ropalidia marginata and Ropalidia cyathiformis. Dominance ranks attributed by all three indices were strongly and positively correlated for both natural data sets from the wasp colonies and for artificial data sets generated for the purpose. However, the indices differed in their ability to yield unique (untied) ranks in the natural data sets. This appears to be caused by the presence of noninteracting individuals and reversals in the direction of dominance in some of the pairs in the natural data sets. This was confirmed by creating additional artificial data sets with noninteracting individuals and with reversals. Based on the criterion of yielding the largest proportion of unique ranks, we found that FDI is best suited for societies such as the wasps belonging to Ropalidia, DS is best suited for societies with reversals and CBI remains a suitable index for societies such as red deer in which multiple interactions are uncommon. (C) 2009 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Crystal structure of hexanediamine-glutamic acid complex

Polyamines are some of the most important and ubiquitous small molecules that modulate several functions of plant, animal and bacterial cells. Despite the simplicity of their chemical structure, their specific interactions with other biomolecules cannot be explained solely on the basis of their electrostatic properties. To evolve a structural understanding on the specificity of these interactions it is necessary to determine the structure of complexes of polyamines with other, representative biomolecules. This paper reports the structure of the 1:2 complex of hexanediamine and L-glutamic acid. The complex crystallizes in the monoclonic space group P2(1) with a = 5.171(1) angstrom, b = 22.044(2) angstrom, c = 10.181(2) angstrom and beta = 104.51(1)-degrees. The structure was refined to an R factor of 6.6%. The structures of these complexes not only suggest the importance of hydrogen-bonding interactions of polyamines but also provide some insight into other complementary interactions probably important for the specificity of biomolecular interactions.