Multiple mechanisms shape selectivity for FM sweep rate and direction in the pallid bat inferior colliculus and auditory cortex

The inferior colliculus and auditory cortex of the pallid bat contain a large percentage of neurons that are highly selective for the direction and rate of the downward frequency modulated (FM) sweep of the bat’s echolocation pulse. Approximately 25% of neurons tuned to the echolocation pulse respond exclusively to downward FM sweeps. This review focuses on the finding that this selectivity is generated by multiple mechanisms that may act alone or in concert. In the inferior colliculus, selectivity for sweep rate is shaped by at least three mechanisms: shortpass or bandpass tuning for signal duration, delayed high-frequency inhibition that prevents responses to slow sweep rates, and asymmetrical facilitation that occurs only when two tones are presented at appropriate delays. When acting alone, the three mechanisms can produce essentially identical rate selectivity. Direction selectivity can be produced by two mechanisms: an early low-frequency inhibition that prevents responses to upward sweeps, and the same asymmetrical two-tone inhibition that shapes rate tuning. All mechanisms except duration tuning are also present in the auditory cortex. Discussion centers on whether these mechanisms are redundant or complementary.     

Network Models of Frequency Modulated Sweep Detection

Frequency modulated (FM) sweeps are common in species-specific vocalizations, including human speech. Auditory neurons selective for the direction and rate of frequency change in FM sweeps are present across species, but the synaptic mechanisms underlying such selectivity are only beginning to be understood. Even less is known about mechanisms of experience-dependent changes in FM sweep selectivity. We present three network models of synaptic mechanisms of FM sweep direction and rate selectivity that explains experimental data: (1) The ‘facilitation’ model contains frequency selective cells operating as coincidence detectors, summing up multiple excitatory inputs with different time delays. (2) The ‘duration tuned’ model depends on interactions between delayed excitation and early inhibition. The strength of delayed excitation determines the preferred duration. Inhibitory rebound can reinforce the delayed excitation. (3) The ‘inhibitory sideband’ model uses frequency selective inputs to a network of excitatory and inhibitory cells. The strength and asymmetry of these connections results in neurons responsive to sweeps in a single direction of sufficient sweep rate. Variations of these properties, can explain the diversity of rate-dependent direction selectivity seen across species. We show that the inhibitory sideband model can be trained using spike timing dependent plasticity (STDP) to develop direction selectivity from a non-selective network. These models provide a means to compare the proposed synaptic and spectrotemporal mechanisms of FM sweep processing and can be utilized to explore cellular mechanisms underlying experience- or training-dependent changes in spectrotemporal processing across animal models. Given the analogy between FM sweeps and visual motion, these models can serve a broader function in studying stimulus movement across sensory epithelia.     

Molecular origin of mitotic aneuploidies in preimplantation embryos

Mitotic errors are common in human preimplantation embryos. The occurrence of mitotic errors is highest during the first three cleavages after fertilization and as a result about three quarters of human preimplantation embryos show aneuploidies and are chromosomally mosaic at day three of development. The origin of these preimplantation mitotic aneuploidies and the molecular mechanisms involved are being discussed in this review.At later developmental stages the mitotic aneuploidy rate is lower. Mechanisms such as cell arrest, apoptosis, active correction of the aneuploidies and preferential allocation of the aneuploid cells to the extra-embryonic tissues could underlie this lower rate.Understanding the mechanisms that cause mitotic aneuploidies in human preimplantation embryos and the way human preimplantation embryos deal with these aneuploidies might lead to ways to limit the occurrence of aneuploidies, in order to ultimately increase the quality of embryos and with that the likelihood of a successful pregnancy in IVF/ICSI. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.     

Prediction and Dissection of Widely-Varying Association Rate Constants of Actin-Binding Proteins

Actin is an abundant protein that constitutes a main component of the eukaryotic cytoskeleton. Its polymerization and depolymerization are regulated by a variety of actin-binding proteins. Their functions range from nucleation of actin polymerization to sequestering G-actin in 1∶1 complexes. The kinetics of forming these complexes, with rate constants varying at least three orders of magnitude, is critical to the distinct regulatory functions. Previously we have developed a transient-complex theory for computing protein association mechanisms and association rate constants. The transient complex refers to an intermediate in which the two associating proteins have near-native separation and relative orientation but have yet to form short-range specific interactions of the native complex. The association rate constant is predicted as k _a = k _a0 , where k _a0 is the basal rate constant for reaching the transient complex by free diffusion, and the Boltzmann factor captures the bias of long-range electrostatic interactions. Here we applied the transient-complex theory to study the association kinetics of seven actin-binding proteins with G-actin. These proteins exhibit three classes of association mechanisms, due to their different molecular shapes and flexibility. The 1000-fold k _a variations among them can mostly be attributed to disparate electrostatic contributions. The basal rate constants also showed variations, resulting from the different shapes and sizes of the interfaces formed by the seven actin-binding proteins with G-actin. This study demonstrates the various ways that actin-binding proteins use physical properties to tune their association mechanisms and rate constants to suit distinct regulatory functions.     

Multiple mechanisms of spike-frequency adaptation in motoneurones.

Spike-frequency adaptation is the continuous decline in discharge rate in response to a constant stimulus. We have described three distinct phases of adaptation in rat hypoglossal motoneurones: initial, early and late. The initial phase of adaptation is over in one or two intervals, and is primarily due to summation of the calcium-activated potassium conductance underlying the medium duration afterhyperpolarization (mAHP). The biophysical mechanisms underlying the later phases of adaptation are not well understood. Two of the previously-proposed mechanisms for adaptation are an increase in outward current flowing through calcium-activated potassium channels and increasing outward current produced by the electrogenic sodium-potassium pump. We found that neither of these mechanisms are necessary for the expression of the early and late phases of adaptation. The magnitude of the initial phase of adaptation was reduced when the calcium in the external solution was replaced with manganese, but the magnitudes of the early and late phases were consistently increased under these conditions. Partial blockade of the sodium-potassium pump with ouabain had no significant effect on any of the three phases of adaptation. Our current working hypothesis is that the magnitude of late adaptation depends upon the interplay between slow inactivation of sodium currents, that tends to decrease discharge rate, and the slow activation or facilitation of a calcium current that tends to increase discharge rate. Adaptation is often associated with a progressive decrease in the peak amplitude and rate of rise of action potentials, and a computer model that incorporated slow inactivation of sodium channels reproduced this phenomenon. However, the time course of adaptation does not always parallel changes in spike shape, indicating that the progressive activation of another inward current might oppose the decline in frequency caused by slow sodium inactivation.     

THE MAINTENANCE OF GENETIC VARIATION FOR OVIPOSITION RATE IN TWO‐SPOTTED SPIDER MITES: INFERENCES FROM ARTIFICIAL SELECTION

Despite the directional selection acting on life‐history traits, substantial amounts of standing variation for these traits have frequently been found. This variation may result from balancing selection (e.g., through genetic trade‐offs) or from mutation‐selection balance. These mechanisms affect allele frequencies in different ways: Under balancing selection alleles are maintained at intermediate frequencies, whereas under mutation‐selection balance variation is generated by deleterious mutations and removed by directional selection, which leads to asymmetry in the distribution of allele frequencies. To investigate the importance of these two mechanisms in maintaining heritable variation in oviposition rate of the two‐spotted spider mite, we analyzed the response to artificial selection. In three replicate experiments, we selected for higher and lower oviposition rate, compared to control lines. A response to selection only occurred in the downward direction. Selection for lower oviposition rate did not lead to an increase in any other component of fitness, but led to a decline in female juvenile survival. The results suggest standing variation for oviposition rate in this population consists largely of deleterious alleles, as in a mutation‐selection balance. Consequently, the standing variation for this trait does not appear to be indicative of its adaptive potential.     

Growth rate plasticity to temperature in two damselfly species differing in latitude: contributions of behaviour and physiology

Plasticity in growth rate may be driven by behavioural and physiological mechanisms. Although these underlying mechanisms have direct implications for the importance of ecological and physiological costs associated with rapid growth, the contribution of behaviour and physiology to temperature-mediated plasticity in growth rate has largely been neglected. We studied the temperature-dependence of growth rate and its underlying behavioural and physiological mechanisms in two congeneric damselfly species that differ in latitudinal distribution. Larvae were reared from the egg stage at three temperatures (17°C, 22°C and 27°C). Within each species, growth rates showed a quadratic response curve with an optimum at 22°C. Behaviour, as measured by food intake, and physiology, as measured by growth efficiency and heartbeat as proxy for metabolic rate, jointly contributed to this temperature-induced plasticity in growth rate. At each temperature, growth rates were higher in the northern species. In line with the few other studies that compared northern and southern populations, both an increased food uptake and growth efficiency caused this pattern. Together with previous studies that focused on the population level, our results tentatively suggest that not only the latitudinal patterns in growth rate but also the mechanistic basis are similar at the species and at the population level.     

The mechanism of the phosphoglucomutase reaction. Studies on rabbit muscle phosphoglucomutase with flux techniques

1. The kinetics of phosphoglucomutases from different sources are discussed and it is concluded that on the available evidence there are in all cases three possible mechanisms for the reaction. These are an indirect transfer of phosphate involving the phosphoenzyme (mechanism 1), a direct transfer of phosphate (mechanism 2), and an intermolecular transfer of phosphate from glucose 1,6-diphosphate to the substrate (mechanism 3). Conventional net flux measurements are shown not to differentiate between these mechanisms. 2. Flux equations are developed and it is shown that there are three flux ratios that characterize and distinguish between the mechanisms. 3. To examine these flux ratios induced-transport tests are described with ¹⁴C- and ³²P-labelled substrates. The fluxes determined with ¹⁴C- and ³²P-labelled substrates are also compared at chemical equilibrium. 4. With rabbit muscle phosphoglucomutase the results of these tests were completely consistent with mechanism 1 and unequivocally excluded any substantial part of the reaction proceeding by mechanism 2 or mechanism 3. Evidence was also obtained for an isomerization of the phosphoenzyme with an apparent rate constant about 4·5×10⁷sec.⁻¹. Taking into account the activity coefficients of the substrates the true rate constant appears to be about one-sixth of this value. 5. Isotope effects and non-ideal behaviour of the solutions are discussed and the activity coefficients of the substrates are shown to be equal by measurement of the depression of freezing point. It is concluded that these factors do not influence the tests significantly. 6. Alternative mechanisms are considered and it is concluded that the tests show that the glucose residue is transferred directly, that the phosphate is transferred indirectly with one intermediate phosphate, and that there is an isomerization of the free phosphoenzyme without reference to any other details of the reaction. Further, no assumptions are required about the constancy of rate constants. 7. The relative merits of induced transport and product inhibition for detecting isomerization of the enzyme are discussed. It is concluded that the induced-transport test is more sensitive and that its interpretation is less equivocal. 8. The application of the tests to other enzyme systems is briefly considered.     

Dynamic characteristics of transient responses

Transient responses of signaling molecules are seen in a wide variety of cellular processes that are mediated by distinct molecular mechanisms. Although transient responses might intuitively be thought to depend on the absolute concentration of growth factors or the intensity of stimulation, we here introduce that some transient responses are prompted by temporal rate of increase of stimulation, rather than intensity of stimulation, by three independent mechanisms. These include the Ras system with fast activation and slow inactivation, the ERK-dependent negative feedback loop system, and the receptor degradation system, all of which can be commonly seen in various signaling networks. In addition, we show the distinct transient and steady state characteristics of these systems.     

A rapid direct assay for the determination of the separate activities of the three arylsulphatases of Aspergillus oryzae.

1. The three arylsulphatases of Aspergillus oryzae exhibit pronounced kinetic differences and substrate specificities. Arylsulphatase I hydrolyses all substrates tested, whereas arylsulphatase III will not hydrolyse tyrosine O-sulphate or phenolphthalein disulphate. Arylsulphatase II does not hydrolyse p-nitrophenyl sulphate or phenolphthalein disulphate at appreciable rates in the absence of added phenolic compounds. Phenols such as tyramine increase the rate of hydrolysis of these substances by this enzyme 1000-fold. At pH 6.9 arylsulphatase I exhibits an apparent Km of 0.1 mM for p-nitrophenyl sulphate, whereas the Km of arylsulphatase III for this substrate is 1 mM. 2. These differences were utilized to develop an assay procedure which can be used to determine the separate activities of the three enzymes present in mixtures. This assay has potential use as a means of examining the relative activities of the three enzymes in investigations of the differences in the mechanisms regulating their synthesis.     

The interpretation of kinetic data for enzyme-catalysed reactions involving three substrates

The analysis and interpretation of initial-rate data for reactions involving three substrates, obtained in suitably designed experiments, are discussed. Possible mechanisms for such reactions are classified, the rate equations are compared and the extent to which they can be distinguished experimentally is considered.     

Translational control of growth factor and proto-oncogene expression

Control of translation is now understood to be one of the major regulatory events in eukaryotic gene expression. Moreover there is evidence which suggests that aberrant expression of growth-related genes by translational mechanisms makes a significant contribution to cell transformation. However, the mechanisms which regulate translation of specific growth-related mRNAs have yet to be fully elucidated. The majority of these mRNAs have long 5' untranslated regions (UTRs) and three features which are important in translational control have been identified, namely (i) structured regions which inhibit the scanning mechanisms of translation, (ii) regulatory upstream open reading frames and (iii) internal ribosome entry segments which are capable of initiating cap-independent translation. In this review the translational regulation of specific mRNAs encoding growth factors and proto-oncogenes by these three mechanisms will be discussed, together with examples of altered translational regulation in neoplasia.     

Analysis of Ter-Ter enzyme kinetic mechanisms by computer simulation of isotope exchange at chemical equilibrium: development and application of ISOTER, a personal-computer-based program

A convenient, personal-computer-based program has been developed that allows simulation of isotopic exchange kinetics at chemical equilibrium catalyzed by a three reactant-three product (TerTer) enzyme system: A + B + C integral of P + Q + R. This program, ISOTER, utilizes a rapid algebraic method to calculate the exchange rate between any reactant-product pair as a function of the substrate concentration and avoids altogether the necessity of deriving an explicit (but cumbersome and impractical) equation for exchange rate. ISOTER was used to generate model saturation patterns for 16 different TerTer kinetic mechanisms, varying different combinations of reactant-product pairs in constant ratio at equilibrium: [all substrates], [A, P], [B, Q], and [C, R], while holding the nonvaried components constant. These model studies indicate that virtually every one of these mechanisms can be distinguished from the others. In addition, ISOTER has been used to fit multiple sets of experimental data for Escherichia coli glutamine synthetase, which produced a set of rate constants consistent with the previously proposed "preferred order random" kinetic mechanism.     

General theory of competitive coexistence in spatially-varying environments

A general model of competitive and apparent competitive interactions in a spatially-variable environment is developed and analyzed to extend findings on coexistence in a temporally-variable environment to the spatial case and to elucidate new principles. In particular, coexistence mechanisms are divided into variation-dependent and variation-independent mechanisms with variation-dependent mechanisms including spatial generalizations of relative nonlinearity and the storage effect. Although directly analogous to the corresponding temporal mechanisms, these spatial mechanisms involve different life history traits which suggest that the spatial storage effect should arise more commonly than the temporal storage effect and spatial relative nonlinearity should arise less commonly than temporal relative nonlinearity. Additional mechanisms occur in the spatial case due to spatial covariance between the finite rate of increase of a local population and its local abundance, which has no clear temporal analogue. A limited analysis of these additional mechanisms shows that they have similar properties to the storage effect and relative nonlinearity and potentially may be considered as enlargements of the earlier mechanisms. The rate of increase of a species perturbed to low density is used to quantify coexistence. A general quadratic approximation, which is exact in some important cases, divides this rate of increase into contributions from the various mechanisms above and admits no other mechanisms, suggesting that opportunities for coexistence in a spatially-variable environment are fully characterized by these mechanisms within this general model. Three spatially-implicit models are analyzed as illustrations of the general findings and of techniques using small variance approximations. The contributions to coexistence of the various mechanisms are expressed in terms of simple interpretable formulae. These spatially-implicit models include a model of an annual plant community, a spatial multispecies version of the lottery model, and a multispecies model of an insect community competing for spatially-patchy and ephemeral food.     

Dynamic Mechanisms of Neocortical Focal Seizure Onset

Recent experimental and clinical studies have provided diverse insight into the mechanisms of human focal seizure initiation and propagation. Often these findings exist at different scales of observation, and are not reconciled into a common understanding. Here we develop a new, multiscale mathematical model of cortical electric activity with realistic mesoscopic connectivity. Relating the model dynamics to experimental and clinical findings leads us to propose three classes of dynamical mechanisms for the onset of focal seizures in a unified framework. These three classes are: (i) globally induced focal seizures; (ii) globally supported focal seizures; (iii) locally induced focal seizures. Using model simulations we illustrate these onset mechanisms and show how the three classes can be distinguished. Specifically, we find that although all focal seizures typically appear to arise from localised tissue, the mechanisms of onset could be due to either localised processes or processes on a larger spatial scale. We conclude that although focal seizures might have different patient-specific aetiologies and electrographic signatures, our model suggests that dynamically they can still be classified in a clinically useful way. Additionally, this novel classification according to the dynamical mechanisms is able to resolve some of the previously conflicting experimental and clinical findings.     

Mechanisms and rate equations for dissociating systems.

The results presented in the previous paper (Boeker, E.A. (1978), Biochemistry 17 (preceding paper in this issue) indicate that the dissociation of the decamer of arginine decarboxylase of Escherichia coli B is enhanced by Na+ and retarded by H+. In this system, substances which increase the rate of dissociation can be treated kinetically either as substrates or activators, and substances which retard dissociation can be treated as products or inhibitors. In addition, the events needed for dissociation can occur in an ordered or a random sequence, and the dissociation itself, from a decamer to five dimers, can be a sequential or a concerted process. In order to provide a framework for the experimental results, mechanisms for the dissociation of arginine decarboxylase that take all of these factors into account are described. In addition, it is shown that the usual methods of steady-state kinetics can be applied to these systems when true initial rates are measured; rate equations are presented for each mechanism. The results can be used for any dissociating of three or more subunits and will describe the dissociation of a dimer under certain conditions.     

Rates of recombination in the ribosomal DNA of apomictically propagated Daphnia obtusa lines

Ribosomal (r)DNA undergoes concerted evolution, the mechanisms of which are unequal crossing over and gene conversion. Despite the fundamental importance of these mechanisms to the evolution of rDNA, their rates have been estimated only in a few model species. We estimated recombination rate in rDNA by quantifying the relative frequency of intraindividual length variants in an expansion segment of the 18S rRNA gene of the cladoceran crustacean, Daphnia obtusa, in four apomictically propagated lines. We also used quantitative PCR to estimate rDNA copy number. The apomictic lines were sampled every 5 generations for 90 generations, and we considered each significant change in the frequency distribution of length variants between time intervals to be the result of a recombination event. Using this method, we calculated the recombination rate for this region to be 0.02-0.06 events/generation on the basis of three different estimates of rDNA copy number. In addition, we observed substantial changes in rDNA copy number within and between lines. Estimates of haploid copy number varied from 53 to 233, with a mean of 150. We also measured the relative frequency of length variants in 30 lines at generations 5, 50, and 90. Although length variant frequencies changed significantly within and between lines, the overall average frequency of each length variant did not change significantly between the three generations sampled, suggesting that there is little or no bias in the direction of change due to recombination.     

Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes

Allosteric mechanisms are widely used in nature to control the rates of enzymatic reactions, but little is known about RNA catalysts controlled by these principles. The only natural allosteric ribozyme reported to date catalyzes an RNA cleavage reaction, and so do almost all artificial systems. RNA has, however, been shown to accelerate a much wider range of chemical reactions. Here we report that RNA catalysts for organic reactions can be put under the stringent control of effector molecules by straight-forward rational design. This approach uses known RNA sequences with catalytic and ligand-binding properties, and exploits weakly conserved sequence elements and available structural information to induce the formation of alternative, catalytically inactive structures. The potential and general applicability is demonstrated by the design of three different systems in which the rate of a catalytic carbon–carbon bond forming reaction is positively regulated up to 2100-fold by theophylline, tobramycin and a specific mRNA sequence, respectively. Although smaller in size than a tRNA, all three ribozymes show typical features of allosteric metabolic enzymes, namely high rate acceleration and tight allosteric regulation. Not only do these findings demonstrate RNA's power as a catalyst, but also highlight on RNA's capabilities as signaling components in regulatory networks.