What determines the rate of sequence evolution?

High rates of amino-acid sequence evolution have sometimes been considered to be diagnostic for genes undergoing adaptive change. However, two recent studies have shown that rapid evolution of amino-acid sequence can also be congruent with neutrality.     

Does growth rate determine the rate of metabolism in shorebird chicks living in the Arctic?

We measured resting and peak metabolic rates (RMR and PMR, respectively) during development of chicks of seven species of shorebirds: least sandpiper (Calidris minutilla; adult mass 20-22 g), dunlin (Calidris alpina; 56-62 g), lesser yellowlegs (Tringa flavipes; 88-92 g), short-billed dowitcher (Limnodromus griseus; 85-112 g), lesser golden plover (Pluvialis dominicana; 150-156 g), Hudsonian godwit (Limosa haemastica; 205-274 g), and whimbrel (Numenius phaeopus; 380 g). We tested two opposing hypotheses: the growth rate-maturity hypothesis, which posits that growth rate in chicks is inversely related to functional maturity of tissues, and the fast growth rate-high metabolism hypothesis, which suggests that rapid growth is possible only with a concomitant increase in either RMR or PMR. We have found no evidence that chicks of shorebirds with fast growth rates have lower RMRs or lower PMRs, as would be predicted by the growth rate-maturity hypothesis, but our data suggested that faster-growing chest muscles resulted in increased thermogenic capacity, consistent with the fast growth-high metabolism hypothesis. The development of homeothermy in smaller species is a consequence primarily of greater metabolic intensities of heat-generating tissues. The maximum temperature gradient between a chick's body and environment that can be maintained in the absence of a net radiative load increased rapidly with body mass during development and was highest in least sandpipers and lowest among godwits. Chicks of smaller species could maintain a greater temperature gradient at a particular body mass because of their higher mass-specific maximum metabolic rates.     

Evolution of RNA genomes: Does the high mutation rate necessitate high rate of evolution of viral proteins?

Summary RNA genomes have been shown to mutate much more frequently than DNA genomes. It is generally assumed that this results in rapid evolution of RNA viral proteins. Here, an alternative hypothesis is proposed that close cooperation between positive-strand RNA viral proteins and those of the host cells required their coevolution, resulting in similar amino acid substitution rates. Constraints on compatibility with cellular proteins should determine, at any time, the covarion sets in RNA viral proteins. These ideas may be helpful in rationalizing the accumulating data on significant sequence similarities between proteins of positive-strand RNA viruses infecting evolutionarily distant hosts as well as between viral and cellular proteins.     

A mutant β-glucosidase increases the rate of the cellulose enzymatic hydrolysis

The enzymatic hydrolysis of cellulose and lignocellulosic materials is marked by a rate decrease along the reaction time. Cellobiohydrolase slow dissociation from the substrate and its inhibition by the cellobiose produced are relevant factors associated to the rate decrease. In that sense, addition of β-glucosidases to the enzyme cocktails employed in cellulose enzymatic hydrolysis not only produces glucose as final product but also reduces the cellobiohydrolase inhibition by cellobiose. The digestive β-glucosidase GH1 from the fall armyworm Spodoptera frugiperda, hereafter called Sfβgly, containing the mutation L428V showed an increased k_cat for cellobiose hydrolysis. In comparison to assays conducted with the wild-type Sfβgly and cellobiohydrolase TrCel7A, the presence of the mutant L428V increased in 5 fold the initial rate of crystalline cellulose hydrolysis and reduced to one quarter the time needed to TrCel7A produce the maximum glucose yield. As our results show that mutant L428V complement the action of TrCel7A, the introduction of the equivalent replacement in β-glucosidases is a promising strategy to reduce costs in the enzymatic hydrolysis of lignocellulosic materials.     

Evolution: What determines the rate of sequence evolution?

High rates of amino-acid sequence evolution have sometimes been considered to be diagnostic for genes undergoing adaptive change. However, two recent studies have shown that rapid evolution of amino-acid sequence can also be congruent with neutrality.     

Voltage dependence of the effects of (±)-kavain on the rate of inactivation of Na+ channels

The dependence of the efficacy of the influence of a kava-pyrone (±)-kavain (330 µM) on the frequency of activation of Na⁺ channels and voltage dependence of the effects of (±)-kavain on the rate of inactivation of these channels were studied in experiments on isolated neurons from the rat hippocampus. In all series of experiments, the holding potential equalled –100 mV. The efficacy of (±)-kavain-induced blockade of Na⁺ channels was independent of the frequency of stimulation within the range up to 10/sec. In the control experiments, the rate of inactivation increased with the rise of depolarization from –40 mV to +30 mV, and then the saturation effect was observed. At the membrane potential of –40 mV, the rate of (±)-kavain-evoked inactivation increased approximately by a factor of 2.5. At the more positive shifts of the membrane potential, the efficacy of the effects of (±)-kavain on the rate of inactivation became noticeably reduced, and at +30 mV (±)-kavain exerted no distinct influence on this parameter.Neirofiziologiya/Neurophysiology, Vol. 28, No. 6, pp. 312–315, November–December, 1996.     

Could the intrinsic rate of increase represent the fitness in terrestrial ectotherms?

The intrinsic rate of increase (r_m) has been considered as an important indicator of fitness in terrestrial ectotherms since long. It is actually an equivalent to the instantaneous growth rate of the exponential equation for describing the density-independent population growth. In terrestrial ectotherms, r_m has been demonstrated to be temperature-dependent. The temperature at which r_m was maximal, was considered to be the “optimal” temperature for fitness in Amarasekare and Savage (2012), but this definition needs further analysis. Only r_m cannot provide thorough representation of fitness. Because body size can affect the competitive abilities in many terrestrial ectotherms, both population size and body size should be considered in measuring the fitness of ectotherms. The rule of “bigger is better” requires relatively low temperature to increase in body size, whereas relatively high temperature is required for a rapid increase in population size. Thus, there is presumably a trade-off in temperature for adjusting individual body size and population size to achieve maximum fitness. We hypothesized that this temperature could be reflected by the intrinsic optimum temperature for developmental rate in the Sharpe–Schoolfield–Ikemoto model, and it led to a temperature estimate around 20 °C. However, the traditional viewpoint based on the temperature corresponding to the maximal intrinsic rate of increase provides a temperature estimate around 30 °C. This study suggests that a low temperature around 20 °C might authentically represent the optimal ambient temperature for fitness in terrestrial ectotherms. It implies that thermal biologists who are interested in the effect of temperature on the fitness in terrestrial ectotherms should pay more attention to their performance at low temperature rather than high temperature.     

Comparison of the effects of the repetition rate between microsecond and nanosecond pulses: Electropermeabilization-induced electro-desensitization?

Background

Applications of cell electropermeabilization are rapidly growing but basic concepts are still unclear. In particular, the impact of electric pulse repetition rate in the efficiency of permeabilization has not yet been understood.

Methods

The impact of electric pulse repetition rate in the efficiency of permeabilization was analyzed in experiments performed on potato tissue and partially transposed on mice liver. On potato tissue, pulses with durations of 100 μs or 10 ns are applied. The intensity of permeabilization was quantified by means of bioimpedance changes and electric current measurements and a new index was defined.

Results

For the two pulse durations tested, very low repetition rates (below 0.1 Hz) are much more efficient to achieve cell permeabilization in potato tissue. In mice liver, using 100 μs pulses, the influence of the repetition rate is more complex. Indeed, repetition rates of 1 Hz and 10 Hz are more efficient than 100 Hz or 1 kHz, but not the repetition rate of 0.1 Hz for which there is an impact of the living mice organism response.

Conclusions

We propose that the effects reported here might be caused by an electroporation-induced cell membrane ‘electro-desensitization’ which requires seconds to dissipate due to membrane resealing.

General significance

This study not only reinforces previous observations, but moreover it sustains a new concept of ‘electro-desensitization’ which is the first unifying mechanism enabling to explain all the results obtained until now both in vitro and in vivo, with long and short pulses.     

Why use population entropy? It determines the rate of convergence

Summary The population entropy introduced by Demetrius is shown to have a precise dynamical meaning as a measure of convergence rate to the stable age distribution. First the Leslie population model is transformed exactly into a Markov chain on a state space of age-classes. Next the dynamics of convergence from a nonequilibrium state to the stable state are analyzed. The results provide the first clear biological reason why entropy is a broadly useful population statistic.     

Is there an acceleration of the CpG transition rate during the mammalian radiation?

MOTIVATION: In this article we build a model of the CpG dinucleotide substitution rate and use it to challenge the claim that, that rate underwent a sudden mammalian-specific increase approximately 90 million years ago. The evidence supporting this hypothesis comes from the application of a model of neutral substitution rates able to account for elevated CpG dinucleotide substitution rates. With the initial goal of improving that model's accuracy, we introduced a modification enabling us to account for boundary effects arising by the truncation of the Markov field, as well as improving the optimization procedure required for estimating the substitution rates. RESULTS: When using this modified method to reproduce the supporting analysis, the evidence of the rate shift vanished. Our analysis suggests that the CpG-specific rate has been constant over the relevant time period and that the asserted acceleration of the CpG rate is likely an artifact of the original model.     

Universality in neural networks: the importance of the ‘mean firing rate’

We present a general analysis of highly connected recurrent neural networks which are able to learn and retrieve a finite number of static patterns. The arguments are based on spike trains and their interval distribution and require no specific model of a neuron. In particular, they apply to formal two-state neurons as well as to more refined models like the integrate-and-fire neuron or the Hodgkin-Huxley equations. We show that the mean firing rate defined as the inverse of the mean interval length is the only relevant parameter (apart from the synaptic weights) that determines the existence of retrieval solutions with a large overlap with one of the learnt patterns. The statistics of the spiking noise (Gaussian, Poisson or other) and hence the shape of the interval distribution does not matter. Thus our unifying approach explains why, and when, all the different associative networks which treat static patterns yield basically the same results, i.e., belong to the same universality class.     

Effect of oxygen on the rate of β-1,3-glucan microbial exopolysaccharide production

Summary Examination of the relationship between the rate of oxygen transfer and the rate of polymer production revealed an unexpectedly high requirement for oxygen. At a cell density of about 3 g (dry wt)/L, the threshhold value for OTR for optimal synthesis of polymer is about 50 mmoles O₂/L.hr. Whereas Rushton turbines are effecient at transfering oxygen to solution, their use reduces the quality of the recovered polymer. Although better quality polymer can be produced in a reactor employing an agitator which causes less shear stress, the productivity can be compromised due to the inefficiency in OTR. The present study describes operating conditions for the provision of sufficient OTR in a system compatible with the production of high-quality polymer whereby turbine impellers were replaced with a marine-type propeller and mass transfer was assisted by means of a gas dispersion device.     

Seasonal variations in the conception rate of beef cattle in the seasonal—equatorial climate of southern nigeria

Seasonal variations in the frequency of conceptions were analysed from the records of 8,971 beef calves born over a period of ten years (1959–1968) in the Southern Guinea Savannah of Nigeria. Mean annual and monthly conception rates were 72 and 6%, respectively. Highly significant changes in conception rates were observed: the highest number of conceptions occurred in April (7.3%) and the lowest in October (4.4%). The cubic function of the curve depicting the monthly conception rate was highly significant (p < 0.001) and parallelled the change in photoperiod (r = +0.39, p < 0.01). Conception rate was not related to either temperature or precipitation. The evidence suggests a photoperiodic influence on conception rates.

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Zusammenfassung Saisonale Schwankungen in der Konzeptionsrate von Fleischrindern der Guineasavanne Südnigerias wurden anhand von 8.971 Kalbungen aus zehn Jahren (1959–1968) untersucht. Die durchschnittlichen jährlichen und monatlichen Konzeptionsraten betrugen 72 beziehungsweise 6%; jedoch wurden hochsignifikante Abweichungen (p < 0.001) von dem monatlichen Mittelwert festgestellt: die höchste Konzeptionsrate wurde mit 7,3% für April, die niedrigste mit 4,4% für Oktober errechnet. Die mathematische Funktion der Konzeptionsrate folgt einer Sinuskurve, welche der monatlichen Veränderung der Tageslichtlänge parallel läuft (r = +0,39, p < 0.01). Die Konzeptionsrate war nicht mit der Durchschnittstemperatur oder den Niederschlägen korreliert. Diese Ergebnisse lassen vermuten, dass die saisonalen Schwankungen in der Konzeptionsrate zumindest teilweise auf photoperiodische Veränderungen zurückzuführen sind.

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Resume Les variations saisonnières du taux de fécondité de bovins de la savanne du sud de la Guinée (Nigéria) ont été étudiées sur la base de 8971 mises bas ayant eu lieu durant une période de 10 ans. Le taux de fécondité moyen fut de 72% pour l'année et de 6% pour chaque mois. On constate pourtant des différences significatives entre les différents mois: le taux le plus élevé se trouve en avril (7,3%) et le plus bas en octobre (4,4%). La fonction du troisième degré du taux de fécondité est hautement significative (p < 0,001). Elle suit une courbe sinusöidale parallèle à celle de la longueur du jour (r = +0,39, p < 0,01). Il n'y a pas de relation entre le nombre de conceptions et la température ou les précipitations. Par conséquent, seul le photopériodisme semble influencer le nombre des conceptions.

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The permission of the Western Nigeria Development Corporation to analyse and publish their breeding records is gratefully acknowledged.     

Does the rate of ribosomal RNA synthesis vary depending on the number of nucleoli in a nucleus?

Cultured kidney cells of Xenopus laevis were pulse-labeled with [³H]uridine for 10, 20 and 30 min during their logarithmic growth phase and then processed for autoradiography. The labeled cells were assigned into two categories, one- and two-nucleolated cells, and the rate of ribosomal RNA (rRNA) synthesis was measured by counting the number of grains in nucleoli. The results obtained revealed that a two-nucleolated cell incorporated significantly much more radioactivity into its nucleoli than did a one-nucleolated partner for all the periods examined. Cells of these different nucleolar types, however, contained essentially the same amount of rDNA (DNA complementary to rRNA) as estimated by in situ hybridization with [¹²⁵I]rRNA.Although it remains to be proved that the observed increase in incorporation represents the increased rate of rRNA synthesis in two-nucleolated cells, the present findings seem to be very interesting, since they might indicate that the activity of rRNA genes is in some way regulated or affected by their spatial relationship in a cell nucleus.     

Can deleterious mutations explain the time dependency of molecular rate estimates?

It has recently been observed by Ho et al. (Ho SYW, Phillips MJ, Cooper A, Drummond AJ. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 22(7):1561-1568) that apparent rates of molecular evolution increase when measured over short timespans. I investigate whether the data are explainable purely by deleterious mutations. I derive an empirical approximation for the persistence of these mutations in a randomly mating population and, hence, derive lower limits on effective population sizes. These limits are high and get higher if additional reasonable assumptions are made. This casts doubt on whether deleterious mutations are able to explain the apparent rate acceleration.     

Energetics of the smallest: Do bacteria breathe at the same rate as whales?

Power laws describing the dependence of metabolic rate on body mass have been established for many taxa, but not for prokaryotes, despite the ecological dominance of the smallest living beings. Our analysis of 80 prokaryote species with cell volumes ranging more than 1,000,000-fold revealed no significant relationship between mass-specific metabolic rate q and cell mass. By absolute values, mean endogenous mass-specific metabolic rates of non-growing bacteria are similar to basal rates of eukaryote unicells, terrestrial arthropods and mammals. Maximum mass-specific metabolic rates displayed by growing bacteria are close to the record tissue-specific metabolic rates of insects, amphibia, birds and mammals. Minimum mass-specific metabolic rates of prokaryotes coincide with those of larger organisms in various energy-saving regimes: sit-and-wait strategists in arthropods, poikilotherms surviving anoxia, hibernating mammals. These observations suggest a size-independent value around which the mass-specific metabolic rates vary bounded by universal upper and lower limits in all body size intervals.     

Vibrational sensitivity of the wing of the pigeon (Columba livia) — a study using heart rate conditioning

Summary The vibrational sensitivity of awake pigeons was tested with the heart rate conditioning method. This method proved to be a very sensitive instrument for the behavioural measurement of the pigeon's sensitivity to mechanical stimuli.Sine wave vibrational stimuli between 50 and 2000 Hz were applied to the 1st, 7th and 16th primary feathers of the wing. The resulting threshold curves were U- or V-shaped with 3 characteristics: (i) The frequency of best response was either 800 or 900 Hz. (ii) Within the broad frequency range of vibrational sensitivity (50 to 2000 Hz) the sensitivity was extremely high at the best frequency: threshold amplitudes lay between 0.5 and 0.09 m. (iii) The threshold curves showed very sharp tuning at best frequency with bandwidths between 0.3 and 0.7 octaves (measured at best frequency 10fold above threshold). The functional meaning of the characteristic vibrational sensitivity of the wing for flight control is discussed; it is interpreted as an adaptation to special situations occurring during flight.Abbreviations CR conditioned response - CS conditioned stimulus - ECG electrocardiogram - HC(s) Herbst corpuscle(s) - UCS unconditioned stimulus All experiments were carried out at the Ruhr-Universität Bochum, Lehrstuhl für Allgemeine Zoologie     

Estimating the intrinsic rate of increase of Tetranychus urticae: which is the minimum number of immature individuals to consider?

The relationship between the number of immature individuals of Tetranychus urticae used to calculate life table parameters (sex ratio, development time, immature survival and the intrinsic rate of increase) and the accuracy of such determinations has been estimated. Additionally, the approach used in this paper, which considers each female offspring as a separate replicate, has allowed statistical comparison of the parameters obtained. At least the first four eggs from 16 females should be followed up to completion of their development to prevent the occurrence significant differences for the selected parameters. However, our results indicate that optimal sample sizes are different for the different life table parameters considered and should adapt to the preset level of accuracy.