Specific metabolic rate, longevity and "Rubner constant" for birds

An assumption was made that age constituent alpha x(beta) of mortality of individuals in a population in Weibull equation mx = m0 + alpha x(beta) (Ricklefs, 2000) reflects change of specific metabolic rate of one individual with age. Based upon that hypothesis a formula was proposed for relationship of specific metabolic rate of an adult individual after cessation of growth, when mass W is attained, and age t: q(t) = q0(1-omega(beta) + 1t(beta)) where q0 = aW(-b) is value q(t) at the moment of growth cessation and omega = alpha(1/(beta + 1)) is "ageing rate", determined and estimated by R. Ricklefs. Maximum longevity of an individual was determined as [equation: see text], where qcrit is specific metabolic rate at the age tmax. Parameter beta and relationships omega(W) and (qcrit/q0)(W) were approximated for birds from data of Ricklefs. Statistical comparison of results of calculations of tmax was carried out on the basis of the above formula and other known formulas for groups of Passeriformes and non-Passeriformes. Rubner constant [equation: see text] was calculated assuming that body mass of an adult individual (W) is attained in the first year of life (tA = 0). Average values of 602.4 +/- 2.5 kcal g(-1) (n = 83) for non-Passeriformes and 963 +/- 6.3 kcal g(-1) (n = 41) for Passeriformes were obtained.     

Variance of Neutral Genetic Variances within and between Populations for a Quantitative Character

The variances of genetic variances within and between finite populations were systematically studied using a general multiple allele model with mutation in terms of identity by descent measures. We partitioned the genetic variances into components corresponding to genetic variances and covariances within and between loci. We also analyzed the sampling variance. Both transient and equilibrium results were derived exactly and the results can be used in diverse applications. For the genetic variance within populations, sigma 2 omega, the coefficient of variation can be very well approximated as [formula: see text] for a normal distribution of allelic effects, ignoring recurrent mutation in the absence of linkage, where m is the number of loci, N is the effective population size, theta 1(0) is the initial identity by descent measure of two genes within populations and t is the generation number. The first term is due to genic variance, the second due to linkage disequilibrium, and third due to sampling. In the short term, the variation is predominantly due to linkage disequilibrium and sampling; but in the long term it can be largely due to genic variance. At equilibrium with mutation [formula: see text] where u is the mutation rate. The genetic variance between populations is a parameter. Variance arises only among sample estimates due to finite sampling of populations and individuals. The coefficient of variation for sample gentic variance between populations, sigma 2b, can be generally approximated as [formula: see text] when the number of loci is large where S is the number of sampling populations.     

The parasite capacity of the host population

The estimation of parasitic pressure on the host populations is frequently required in parasitological investigations. The empirical values of prevalence of infection are used for this, however the latter one as an estimation of parasitic pressure on the host population is insufficient. For example, the same prevalence of infection can be insignificant for the population with high reproductive potential and excessive for the population with the low reproductive potential. Therefore the development of methods of an estimation of the parasitic pressure on the population, which take into account the features the host population, is necessary. Appropriate parameters are to be independent on view of the researcher, have a clear biological sense and be based on easily available characteristics. The methods of estimation of parasitic pressure on the host at the organism level are based on various individual viability parameters: longevity, resistance to difficult environment etc. The natural development of this approach for population level is the analysis of viability parameters of groups, namely, the changing of extinction probability of host population under the influence of parasites. Obviously, some critical values of prevalence of infection should exist; above theme the host population dies out. Therefore the heaviest prevalence of infection, at which the probability of host population size decreases during the some period is less than probability of that increases or preserves, can serve as an indicator of permissible parasitic pressure on the host population. For its designation the term "parasite capacity of the host population" is proposed. The real parasitic pressure on the host population should be estimated on the comparison with its parasite capacity. Parasite capacity of the host population is the heaviest possible prevalence of infection, at which, with the generation number T approaching infinity, there exists at least one initial population size ni(0) for which the probability of size decrease through T generations is less than the probability of its increase. [formula: see text] The estimation of the probabilities of host population size changes is necessary for the parasite capacity determination. The classical methods for the estimation of extinction probability of population are unsuitable in this case, as these methods require the knowledge of population growth rates and their variances for all possible population sizes. Thus, the development methods of estimate of extinction probability of population, based on the using of available parameters (sex ratio, fecundity, mortality, prevalence of infection PI) is necessary. The population size change can be considered as the Markov process. The probabilities of all changes of population size for a generation in this case are described by a matrix of transition probabilities of Markov process (pi) with dimensions Nmax x Nmax (maximum population size). The probabilities of all possible size changes for T generations can be calculated as pi T. Analyzing the behaviour matrix of transition at various prevalence of infection, it is possible to determine the parasite capacity of the host population. In constructing of the matrix of transition probabilities, should to be taken into account the features the host population and the influence of parasites on its reproductive potential. The set of the possible population size at a generation corresponds to each initial population size. The transition probabilities for the possible population sizes at a generation can be approximated to the binomial distribution. The possible population sizes at a generation nj(t + 1) can be calculated as sums of the number of survived parents N1 and posterities N2; their probabilities--as P(N1) x P(N2). The probabilities of equal sums N1 + N2 and nj(t + 1) > or = Nmax are added. The number of survived parents N1 may range from 0 to (1-PI) x ni(t). The survival probabilities can be estimated for each N1 as [formula: see text] The number of survived posterities N2 may range from 0 to N2max (the maximum number of posterities). N2max is [formula: see text] and the survival probabilities for each N2, is defined as [formula: see text] where [formula: see text], ni(t) is the initial population size (including of males and infected specimens of host), PI is the prevalence of infection, Q1 is the survival probabilities of parents, Pfemales is the frequency of females in the host population, K is the number of posterities per a female, and Q2 is the survival probabilities of posterities. When constructing matrix of transition probabilities of Markov process (pi), the procedure outlined above should be repeated for all possible initial population size. Matrix of transition probabilities for T generations is defined as pi T. This matrix (pi T) embodies all possible transition probabilities from the initial population sizes to the final population sizes and contains a wealth of information by itself. From the practical point of view, however, the plots of the probability of population size decrease are more suitable for analysis. They can be received by summing the probabilities within of lines of matrix from 0 to ni--1 (ni--the population size, which corresponds to the line of the matrix). Offered parameter has the number of advantages. Firstly, it is independent on a view of researcher. Secondly, it has a clear biological sense--this is a limit of prevalence, which is safe for host population. Thirdly, only available parameters are used in the calculation of parasite capacity: population size, sex ratio, fecundity, mortality. Lastly, with the availability of modern computers calculations do not make large labour. Drawbacks of this parameter: 1. The assumption that prevalence of infection, mortality, fecundity and sex ratio are constant in time (the situations are possible when the variability of this parameters can not be neglected); 2. The term "maximum population size" has no clear biological sense; 3. Objective restrictions exist for applications of this mathematical approach for populations with size, which exceeds 1000 specimens (huge quantity of computing operations--order Nmax 3*(T-1), work with very low probabilities). The further evolution of the proposed approach will allow to transfer from the probabilities of size changes of individual populations to be probabilities of size changes of population systems under the influence of parasites. This approach can be used at the epidemiology and in the conservation biology.     

A new parasitological index for the estimation of peculiarities of the relationships between parasite and its host, and biotope of the host

A new parasitological index (hostal-topical index) for the estimation of the degree of ectoparasite's relationship with its host and biotope of the host is proposed: [formula: see text], where [formula: see text]--hostal-topical index; n--amount of ectoparasites of the given species on the given host species in the biotope; N--amount of ectoparasites of all species from the given taxonomic group on the given host species in the biotope; n1--amount of hosts of the given species in the biotope; N1--amount of hosts of all species from the given taxonomic group in the biotope; n2--amount of ectoparasites of the given species in the biotope; N2--amount of ectoparasites of all species from the given taxonomic group in the biotope. Values [formula: see text] < 0.1 indicate that there is a distinct relationship with the biotope in spite of the host; values fallen into the range 0.1 < [formula: see text] < 0.5 indicate a moderate relationship with the biotope through the host; values [formula: see text] > 0.5 indicate a significant relationship with the host. By means of this index we have analyzed peculiarity of several parasitic species of fleas and gamasid mites to their hosts, biotopes, and biotope through the host. As it was found on the materials from different native zones and subzones of the Omsk Region (Western Siberia, Russia), values of the hostal-topical index for polyhostal parasitic species are lesser than those for oligohostal species. Values of this index can be different for the same species in the different native zones and subzones as well as in the different biotopes of the same native zone (subzone).     

Population dynamics of the additive polygenic system under truncation selection]

Common features of the equations describing dynamics of the additive polygenic system under truncation selection are summarized. A combination of parameters playing the role of the effective selective pressure on the ith polygenic locus was revealed. The product of mean relative fitnesses of the individual polygenic loci, [formula: see text], was shown to play the role of relative mean fitness of the polygenic population. This value depends on the measurable parameters of the character distribution in the population: [formula: see text]. It was shown that under the constant population number during truncation selection, the characteristic of the best genotype increases, [formula: see text]; which is also a product of the frequencies of preferable genotypes at individual polygenic loci. This value plays the role of the proportion of the number of the best ("champion") genotype in the population. In fact, this is the champion genotype polygene consensus pattern frequency, which a priori indicates the possibility of the champion pattern fixation. The analogue of Haldane's dilemma for the polygenic system which restrict the number of polygenes simultaneously subjected to adaptive evolution [formula: see text] was obtained for the case of constant effective population number (Ne = const).     

Trans-Theta Logistics: A New Family of Population Growth Sigmoid Functions

Sigmoid functions have been applied in many areas to model self limited population growth. The most popular functions; General Logistic (GL), General von Bertalanffy (GV), and Gompertz (G), comprise a family of functions called Theta Logistic ([Formula: see text] L). Previously, we introduced a simple model of tumor cell population dynamics which provided a unifying foundation for these functions. In the model the total population (N) is divided into reproducing (P) and non-reproducing/quiescent (Q) sub-populations. The modes of the rate of change of ratio P/N was shown to produce GL, GV or G growth. We now generalize the population dynamics model and extend the possible modes of the P/N rate of change. We produce a new family of sigmoid growth functions, Trans-General Logistic (TGL), Trans-General von Bertalanffy (TGV) and Trans-Gompertz (TG)), which as a group we have named Trans-Theta Logistic (T [Formula: see text] L) since they exist when the [Formula: see text] L are translated from a two parameter into a three parameter phase space. Additionally, the model produces a new trigonometric based sigmoid (TS). The [Formula: see text] L sigmoids have an inflection point size fixed by a single parameter and an inflection age fixed by both of the defining parameters. T [Formula: see text] L and TS sigmoids have an inflection point size defined by two parameters in bounding relationships and inflection point age defined by three parameters (two bounded). While the Theta Logistic sigmoids provided flexibility in defining the inflection point size, the Trans-Theta Logistic sigmoids provide flexibility in defining the inflection point size and age. By matching the slopes at the inflection points we compare the range of values of inflection point age for T [Formula: see text] L versus [Formula: see text] L for model growth curves.     

Evaluation of methodology for detection of genetic bottlenecks: inferences from temporally replicated lake trout populations

Statistical methods have been proposed to detect recent bottlenecks on the basis of genetic characterizations of natural populations. In the absence of direct estimates of contemporary or historical population numbers, we tested the indirect M-ratio method based on microsatellite motif size frequency profiles using three historical and three contemporary Great Lakes populations of Salvelinus namaysuch for which severe reductions in population numbers are documented. Simulations employing plausible ranges of empirical population parameter values were used to explore bottleneck likelihood surfaces. We show that single values of the M-ratio are not sufficient to unambiguously infer a bottleneck without knowledge of mutation rates and effective population size (i.e., 4Ne mu or [symbol: see text]). Inferences of the degree of population bottleneck would be best supported if analyses were conducted across plausible ranges of [symbol: see text] and by qualitative comparisons among population samples.     

Limits to the rate of adaptive substitution in sexual populations

In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, [Formula: see text], that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is [Formula: see text], where [Formula: see text] is the population size, [Formula: see text] is the rate of beneficial mutations per genome, and [Formula: see text] is their mean selective advantage. Heritable variance [Formula: see text] in log fitness due to unlinked loci reduces [Formula: see text] by [Formula: see text] under polygamy and [Formula: see text] under monogamy. With a linear genetic map of length [Formula: see text] Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] only through the baseline density: [Formula: see text]. Under the approximation that the interference due to different sweeps adds up, we show that [Formula: see text], implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for [Formula: see text]; for higher [Formula: see text], the rate of adaptation grows above [Formula: see text], but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.     

Structural and bioindicative aspects of fluctuated asymmetry of bilateral organisms

We have proposed and validated a method for quantitative assessment of phenotypic diversity of natural populations. Method is based on the fluctuated asymmetry (FA) indices of bilateral organisms, and it is applicable for biondicative investigations. Convolution of functions was proposed to estimate the mean (population) value of FA complex of features. This function could be written as finit sum [formula: see text] where eta is power of sample invariance (symmetry) for m individuals (i = 1, m). Eta is characterized by n asymmetric characteristics (j = 1, n) for the left (L) and the right (R) sides of the body. We have validated applicability of generalized function of desirability [formula: see text] (where di is partial desirability function [0,1]) for cumulative characterization of environment quality with results of bioindicative investigations. The value of function coincides with the value of symmetry of indicating species in this case.     

X-ray conformational study of hydrazino peptide analogues

We have solved the crystal structures of nine pseudo-peptide analogues deriving from the hydrazino analogue of glycine or valine (N beta H2-N alpha H-C alpha HR-CO2H, R = H or iPr) or proline (N beta H2-N alpha-C alpha H-CO2H) and containing the hydrazide (CO-N beta H-N alpha less than) or N beta-Z-aminoamide [formula; see text] [CO-N alpha(N beta HZ)] peptidomimetic link. This study gives access to the average geometry of these two links, to their inter- and intramolecular interaction modes, and to their influence on the conformational properties of the molecules.     

Seed banks, salmon, and sleeping genes: effective population size in semelparous, age-structured species with fluctuating abundance

Previous studies reached contrasting conclusions regarding how fluctuations in abundance affect Ne in semelparous species with variable age at maturity: that Ne is determined by the arithmetic mean N among the T years within a generation (Ne approximately = T(N)t; monocarpic plants with seed banks) or the harmonic mean (Ne approximately T[symbol: see text]; Pacific salmon). I show that these conclusions arise from different model assumptions rather than inherent differences between the species. Sequentially applying standard, discrete-generation formulas for inbreeding Ne to a series of nominal generations accurately predicts the multigenerational rate of increase in inbreeding. Variability in mean realized reproductive success across years (kt) is the most important factor determining Ne and Ne/N. When abundance is driven by random variation in kt, Ne < or = T[symbol: see text] < T(N)t. With random variation in Nt and constant per capita seed production (C), variation in kt is low and Ne approximately T[symbol: see text]; however, if C varies among years, Ne can be closer to T[symbol: see text]. Because population regulation affects the genetic contribution of entire cohorts of monocarpic perennials, Ne for these species may be more closely approximated by T[symbol: see text] than by T(N)t. With density-dependent compensation, Cov(kt, Nt) < 0, and Ne is further reduced because relatively few breeders make a disproportionate contribution to the next generation.     

Some patterns of age and geographical variation in fish fecundity

Some patterns of age and geographical variation in fecundity indices were analyzed in three freshwater fishes (river perch, bream, and Sevan khramulya). A trend to increase in the ovarian relative weight and mature egg size with age has been revealed. Two species with a wide range (perch and bream) demonstrated a tendency to decrease in the ovarian relative weight and increase in the definitive oocyte weight in females of populations living in the geographical center of the range. The coefficient of correlation between the absolute individual fecundity and body weight of females was proposed as a population marker of the fish reproductive system.     

Neuraminic acid is alpha 2-->3 linked in the lipooligosaccharide of Neisseria meningitidis serogroup B strain 6275.

We have analyzed the sialylated lipooligosaccharide of Neisseria meningitidis 6275. Sialylated oligosaccharide released from strain 6275 lipooligosaccharide by mild hydrolysis was determined to contain N-acetylneuraminic acid linked alpha 2-->3 to terminal galactose as shown below. [formula: see text]     

MamI, a novel class-II restriction endonuclease from Microbacterium ammoniaphilum recognizing 5'-GATNN decreases NNATC-3'

A new site-specific class-II restriction endonuclease, MamI, has been discovered in the nonsporulating Gram+ Microbacterium ammoniaphilum. MamI recognition sequence and cleavage positions were deduced using experimental and computer-assisted mapping and sequencing approaches. MamI cleavage specificity corresponds to: [formula: see text] The novel 43-kD enzyme recognizes a palindromic hexanucleotide interrupted by four ambiguous nucleotides. MamI cleavage positions are located in the center of the recognition sequence resulting in blunt-ended fragments after cleavage in the presence of Mg2+ ions. MamI is inhibited by N6-methyladenine residues. In case of overlapping sequences of MamI and Escherichia coli-coded DNA modification methyltransferase M.EcodamI (5'-[formula: see text]-3'), cleavage of DNA isolated from E. coli wild-type cells will be inhibited. By applying incubation conditions forcing star activity, relaxing of MamI sequence specificity is observed (MamI*).     

Effective Size of Nonrandom Mating Populations

Nonrandom mating whereby parents are related is expected to cause a reduction in effective population size because their gene frequencies are correlated and this will increase the genetic drift. The published equation for the variance effective size, Ne, which includes the possibility of nonrandom mating, does not take into account such a correlation, however. Further, previous equations to predict effective sizes in populations with partial sib mating are shown to be different, but also incorrect. In this paper, a corrected form of these equations is derived and checked by stochastic simulation. For the case of stable census number, N, and equal progeny distributions for each sex, the equation is [formula: see text], where Sk2 is the variance of family size and alpha is the departure from Hardy-Weinberg proportions. For a Poisson distribution of family size (Sk2 = 2), it reduces to Ne = N/(1 + alpha), as when inbreeding is due to selfing. When nonrandom mating occurs because there is a specified system of partial inbreeding every generation, alpha can be substituted by Wright's FIS statistic, to give the effective size as a function of the proportion of inbred mates.     

New tandem-repeating peptide structures in polysialoglycoproteins from the unfertilized eggs of kokanee salmon

New polysialoglycoproteins, designated PSGP(On), were isolated from the fertilized and unfertilized eggs of the kokanee salmon, Oncorhynchus nerka adonis. The polysialylglycan chains consisting of alpha-2,8-linked O-acetylated poly(N-glycolylneuraminyl) chains have recently been characterized. We have now determined the complete amino acid sequence of the tandem-repeating units of PSGP(On) from the unfertilized eggs of kokanee salmon and found that the following two distinct forms are present in PSGP(On) in almost identical amounts: [formula: see text] and [formula: see text] where * denotes the O-glycosylation site and mean value of m, n = about 20. Upon fertilization these high-molecular-weight forms of PSGP(On) were proteolytically cleaved to the corresponding repeating units, low-molecular-weight PSGP(On), by the action of a specific protease (PSGPase) at the position two residues set C-terminally to the Pro residue and N-terminally to the Asp residue, i.e. -Pro-Ser-Xaa-Asp-: [formula: see text] and [formula: see text].     

侧条光唇鱼两邻近地理种群的繁殖生物学特征的差异

2007年7月至2009年6月间,分别于北江中上游及流溪河上游支流采集侧条光唇鱼样本358尾及522尾,对两种群的繁殖生物学特征的差异进行了研究。研究结果显示,两种群雌鱼及雄鱼的最小性成熟年龄均为1 龄,北江种群雌性由1 ~5 龄组成,雄性由1 ~4 组成,性比为雌性：雄性=1:1.73;而流溪河种群雌性由1 ~4 龄组成,雄性由1 ~3 组成,性比为雌性：雄性=1:1.40。北江种群繁殖群体的各年龄组体长及体重均较显著大于流溪河种群。北江种群的繁殖期约为2~10月份,高峰期为3~7月份;而流溪河种群繁殖期为2~8月份,高峰期约为每年的5~7月份;繁殖期内,北江种群雌性及雄性的成熟系数均高于流溪河种群。北江种群各年龄组或体长组的绝对生殖力、体长相对生殖力与体重相对生殖力均极显著地大于流溪河种群。本文结合北江和流溪河在营养状况、捕捞压力及溪流级别上的差异对研究结果进行了分析和讨论。     

Application of DFT methods to the study of the coordination environment of the VO2+ ion in V?proteins

Density functional theory (DFT) methods were used to simulate the environment of vanadium in several V proteins, such as vanadyl-substituted carboxypeptidase (sites A and B), vanadyl-substituted chloroplast F(1)-ATPase (CF(1); site 3), the reduced inactive form of vanadium bromoperoxidase (VBrPO; low- and high-pH sites), and vanadyl-substituted imidazole glycerol phosphate dehydratase (IGPD; sites α, β, and γ). Structural, electron paramagnetic resonance, and electron spin echo envelope modulation parameters were calculated and compared with the experimental values. All the simulations were performed in water within the framework of the polarizable continuum model. The angular dependence of [Formula: see text] and [Formula: see text] on the dihedral angle θ between the V=O and N-C bonds and on the angle φ between the V=O and V-N bonds, where N is the coordinated aromatic nitrogen atom, was also found. From the results it emerges that it is possible to model the active site of a vanadium protein through DFT methods and determine its structure through the comparison between the calculated and experimental spectroscopic parameters. The calculations confirm that the donor sets of sites B and A of vanadyl-substituted carboxypeptidase are [[Formula: see text], H(2)O, H(2)O, H(2)O] and [N(His)(||), N(His)(⊥), [Formula: see text], H(2)O], and that the donor set of site 3 of CF(1)-ATPase is [[Formula: see text], OH(Thr), H(2)O, H(2)O, [Formula: see text]]. For VBrPO, the coordination modes [N(His)(||), N(His)(∠), OH(Ser), H(2)O, H(2)O(ax)] for the low-pH site and [N(His)(||), N(His)(∠), OH(Ser), OH(-), H(2)O(ax)] or [N(His)(||), N(His)(∠), [Formula: see text], H(2)O] for the high-pH site, with an imidazole ring of histidine strongly displaced from the equatorial plane, can be proposed. Finally, for sites α, β, and γ of IGPD, the subsequent deprotonation of one, two, and three imidazole rings of histidine and the participation of a carboxylate group of a glutamate residue ([N(His)(||), [Formula: see text], H(2)O, H(2)O], [N(His)(||), N(His)(||), [Formula: see text], H(2)O], and [N(His)(||), N(His)(||), [Formula: see text], OH(-), [Formula: see text]], respectively) seems to be the most plausible hypothesis.     

Nearest-neighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text].

Thermodynamic parameters derived from optical melting studies are reported for duplex formation by a series of oligoribonucleotides containing G.U mismatches. The results are used to determine nearest-neighbor parameters for helix propagation by G.U mismatches. Surprisingly, the [formula; see text] nearest-neighbor free energy increment in unfavorable in the contexts [formula; see text], and [formula; see text] but favorable in the context [formula; see text]. This is a non-nearest-neighbor effect. In contrast, the [formula; see text] free energy increment is favorable and independent of context. Circular dichroism and imino proton NMR spectra of several sequences do not reveal an obvious structural basis for this dichotomy. For example, all the G.U mismatches have two slowly exchanging imino protons. The imino resonances for the G.U mismatches in GGAGUUCC, GUCGUGAC, and CCUGUAGG, however, broaden at lower temperature than the imino resonances for the interior Watson-Crick base pairs. In contrast, the imino resonances for the G.U mismatches in GGAUGUCC remain sharp at high temperature. The improved parameters for G.U mismatches should improve predictions of RNA structure from sequence.