On the sampling variance of intraclass correlations and genetic correlations.

Widely used standard expressions for the sampling variance of intraclass correlations and genetic correlation coefficients were reviewed for small and large sample sizes. For the sampling variance of the intraclass correlation, it was shown by simulation that the commonly used expression, derived using a first-order Taylor series performs better than alternative expressions found in the literature, when the between-sire degrees of freedom were small. The expressions for the sampling variance of the genetic correlation are significantly biased for small sample sizes, in particular when the population values, or their estimates, are close to zero. It was shown, both analytically and by simulation, that this is because the estimate of the sampling variance becomes very large in these cases due to very small values of the denominator of the expressions. It was concluded, therefore, that for small samples, estimates of the heritabilities and genetic correlations should not be used in the expressions for the sampling variance of the genetic correlation. It was shown analytically that in cases where the population values of the heritabilities are known, using the estimated heritabilities rather than their true values to estimate the genetic correlation results in a lower sampling variance for the genetic correlation. Therefore, for large samples, estimates of heritabilities, and not their true values, should be used.     

Additive genetic variance and covariance between relatives in synthetic wheat crosses with variable parental ploidy levels

Cultivated bread wheat (Triticum aestivum L.) is an allohexaploid species resulting from the natural hybridization and chromosome doubling of allotetraploid durum wheat (T. turgidum) and a diploid goatgrass Aegilops tauschii Coss (Ae. tauschii). Synthetic hexaploid wheat (SHW) was developed through the interspecific hybridization of Ae. tauschii and T. turgidum, and then crossed to T. aestivum to produce synthetic hexaploid wheat derivatives (SHWDs). Owing to this founding variability, one may infer that the genetic variances of native wild populations vs improved wheat may vary due to their differential origin and evolutionary history. In this study, we partitioned the additive variance of SHW and SHWD with respect to their breed origin by fitting a hierarchical Bayesian model with heterogeneous covariance structure for breeding values to estimate variance components for each breed category, and segregation variance. Two data sets were used to test the proposed hierarchical Bayesian model, one from a multi-year multi-location field trial of SHWD and the other comprising the two species of SHW. For the SHWD, the Bayesian estimates of additive variances of grain yield from each breed category were similar for T. turgidum and Ae. tauschii, but smaller for T. aestivum. Segregation variances between Ae. tauschii—T. aestivum and T. turgidum—T. aestivum populations explained a sizable proportion of the phenotypic variance. Bayesian additive variance components and the Best Linear Unbiased Predictors (BLUPs) estimated by two well-known software programs were similar for multi-breed origin and for the sum of the breeding values by origin for both data sets. Our results support the suitability of models with heterogeneous additive genetic variances to predict breeding values in wheat crosses with variable ploidy levels.     

Standard deviations and correlations of GC levels in DNA sequences

In a DNA sequence that exhibits long-range correlations, standard deviations among the GC levels of its segments can be up to an order of magnitude higher than in a sequence consisting of independent, identically distributed nucleotides. Conversely, plots of inter-segment standard deviations vs. segment length reveal quantitative information about the correlations present in a sequence. We present and discuss formulae that relate long-range (power-law) correlations between the nucleotides of a sequence to the expected standard deviations of the GC levels of its segments, and to the correlations between them.     

The limits to cost-free signalling of need between relatives

Theoretical models have demonstrated the possibility of stable cost-free signalling of need between relatives. The stability of these cost-free equilibria depends on the indirect fitness cost of cheating and deceiving a donor into giving away resources. We show that this stability is highly sensitive to the distribution of need among signallers and receivers. In particular, cost-free signalling is likely to prove stable only if there is very large variation in need (such that the least-needy individuals stand to gain much less than the most-needy individuals from additional resources). We discuss whether these conditions are likely to be found in altricial avian breeding systems--the most intensively studied instance of signalling of need between relatives. We suggest that cost-free signalling is more likely to prove stable and will provide parents with more information during the earlier phases of chick growth, when parents can more easily meet the demands of a brood (and chicks are more likely to reach satiation). Later, informative yet cost-free signalling is unlikely to persist.     

The donation game with roles played between relatives

We consider a social game with two choices, played between two relatives, where roles are assigned to individuals so that the interaction is asymmetric. Behaviour in each of the two roles is determined by a separate genetic locus. Such asymmetric interactions between relatives, in which individuals occupy different behavioural contexts, may occur in nature, for example between adult parents and juvenile offspring. The social game considered is known to be equivalent to a donation game with non-additive payoffs, and has previously been analysed for the single locus case, both for discrete and continuous strategy traits. We present an inclusive fitness analysis of the discrete trait game with roles and recover equilibrium conditions including fixation of selfish or altruistic behaviour under both behavioural contexts, or fixation of selfish behaviour under one context and altruistic behaviour under the other context. These equilibrium solutions assume that the payoff matrices under each behavioural context are identical. The equilibria possible do depend crucially, however, on the deviation from payoff additivity that occurs when both interacting individuals act altruistically.     

Homology and structure-function correlations between alpha 1-acid glycoprotein and serum retinol-binding protein and its relatives

Although the serum protein alpha 1-acid glycoprotein (AGP) or orosomucoid has been extensively studied, its relationships with other proteins have been controversial and its precise physiological function has remained unclear. It is shown here that AGP is significantly similar in amino acid sequence and in the locations of introns in its structural gene to members of a protein superfamily that includes serum retinol-binding protein (RBP), beta-lactoglobulin (LG), alpha 2u-globulin, and protein HC (alpha 1-microglobulin). The view that the three-dimensional structure of AGP is closely similar to the published structures of RBP and LG is supported by its homology with these proteins, similarities in disulfide bond arrangements, and its secondary structure profile, predicted from the amino acid sequence. The relationship of AGP with this particular protein family indicates that its well-characterized ability to bind lipophilic drugs and certain steroids is a reflection of its true biological role. It is proposed that AGP and the other members of this extensive group of proteins should be designated lipocalins to reflect a common ability to bind lipophiles by enclosure within their structures in a manner that minimizes solvent contact.     

New approach to analysis of deviations from hyperbolic law in enzyme kinetics

An empirical equation that describes deviations from Michaelian kinetics is proposed. The equation allows the limiting values of the Michaelis constant at v/Vmax --> 0 and v/Vmax --> 1 to be estimated (v is the rate of the enzymatic reaction and Vmax is the limiting value of v at saturating concentrations of substrate). The applicability of the equation is demonstrated for kinetic data obtained for glutamate dehydrogenases from various sources (negative kinetic cooperativity for coenzyme) and for biosynthetic threonine deaminase from pea seedlings (sharper approaching the limiting value of the enzymatic reaction rate with increasing substrate concentration in comparison with the hyperbolic law). The negative cooperativity for the function of saturation of protein by ligand is also analyzed (data on binding of spin-labeled NAD, NADH, and NADPH by beef liver glutamate dehydrogenase and binding of cupric ions by BSA are used as examples).     

Developments from analysis of variance through to generalized linear models and beyond

The collaborations between statisticians and biologists during the 100 years since AAB was founded have led to a very impressive list of statistical techniques, whose use now goes well beyond agriculture and biology. One example is the maximum likelihood methodology for probit analysis, arising from the collaboration between Sir Ronald Fisher and Chester Bliss. Others include analysis of variance, design of experiments, generalized linear models and the residual, or restricted, maximum likelihood (REML) algorithm for fitting unbalanced linear mixed models.     

Complementation between mutants of Phycomyces deficient with respect to carotenogenesis

Summary White and red mutants of Phycomyces, derived from two independent wild types (yellow) by mutagenesis using nitrosoguanidine, either in a single step (26 white, 5 red mutants), or in two steps (10 white mutants, from one of the red mutants) were studied with respect to complementation in heterokaryons. The tests clearly establish the involvement of three and only three genes, here named carA, carB, and carB. The carA and the carR mutants are white, the carA mutants do not accumulate phytoene, the carB mutants do. The carR mutants are red and accumulate lycopene. The two step mutants are either carA and carR, or carB and carR double mutants. A few of the white mutants obtained in a single mutagenization step are affected in carA and carR. They may be polar mutants in an operon or accidental double mutants.     

Study of the interactions between cereals with respect to the soil nitrate nitrogen

The interactions between cereals—wheat, barley, rye and oats—in combined cultivation in mixtures of always two species in relation 1:1 in the initial phase of growth were studied. During thirty days’ cultivation in pots the growth of the experimental plants in pure cultures and in mixtures and the changes of the nitrate nitrogen content of the soil in the experimental vessels were followed. The experiments showed that all tested species of cereals interacted with each other during the growth in mixture. The growth changes began soon after sowing, were of a stimulating and inhibiting character and increased during the growth. An exception was the small reaction of oats to rye. Decrease of the nitrate nitrogen content was determined in the soil of the experimental vessels during the cultivation of the plants. The changes of the nitrate nitrogen in the soil corresponded on the whole with the exception of the last phases of the experiments to the growth intensity of the experimental plants. No essential differences, either in the content or in the rate of the decrease of nitrate nitrogen, were found in the soil of control plants and in the soil of plant mixtures. Small differences which were manifested cannot be considered the primary cause of the mutual relations of cereals. The cause of the mutual relations may be attributed to allelopathic factors.     

Cross-tolerance between ethanol and levorphanol with respect to stimulation of plasma corticosterone

Male rats chronically intoxicated with ethanol for at least two days were tolerant to the ethanol-induced stimulation of hypothalamic-pituitary-adrenal axis. Chronically intoxicated rats also were tolerant to stimulation of this axis by levorphanol but not by amphetamine or ether. In a similar manner, animals treated with levorphanol for two days were tolerant to stimulation of the hypothalamic-pituitary-adrenal axis by either levorphanol or ethanol. These observations provide further support for the hypothesis that endogenous opioids may be involved in the development of tolerance to ethanol.     

Polymorphism analysis of Haemophilus influenzae strains isolated from healthy children with respect to amplification reaction

The random-amplified polymorphic DNA (RAPD) assay was used to generate DNA fingerprints for 44 isolates H. influenzae obtained from healthy children. Problems with reproducibility and discriminatory power, frequently cited in the literature, were overcome by optimization procedure allowing to achieve reliable conditions for H. influenzae analysed. Particular parameters of RAPD fingerprinting were evaluated with respect to selection of best working primer, DNA polymerase and DNA concentration for amplification pattern. This study proved high sensitivity and efficiency of optimized RAPD profiling applicable for searching the epidemiology traces.     

Deriving ecological relationships from geographical correlations between host and parasitic species: an example with orchid bees

Aim  To investigate biogeographical patterns of cleptoparasitic Exaerete bee species and their orchid bee hosts.
Location  Neotropical region, from Central America to southern Brazil.
Methods  Correlations between relative frequencies of cleptoparasitic Exaerete species and their host Eulaema species were employed to investigate the geographical association between such species pairs.
Results  Our data support the current proposition that the Eulaema meriana / Eulaema flavescens complex is the main host for Exaerete frontalis . Contrary to current belief, however, Eulaema nigrita apparently is not the only and, in some regions, not the most important host for Exaerete smaragdina .
Main conclusions  Current knowledge on cleptoparasite host associations among orchid bees is based on fortuitous observations, and in some instances generalizations from such observations are not corroborated by the frequencies and distributions of the bees involved. Our data suggest that cleptoparasitic pressure, rather than other features of the forest environment, may be responsible for the low abundance of E. nigrita in the Amazonian forests.     

Prokaryotes: an overview with respect to biodiversity and environmental importance

A short overview of the biodiversity of prokaryotes (the domains bacteria and archaea) is given, with respect to morpholoy, physiology, and biochemistry. The importance of prokaryotes in food chains, nutrient and biogeochemical cycles, and for the maintenance of a balanced atmosphere is explained and stressed. The involvement of prokaryotes in symbiotic mutualisms and in pathogenicity is discussed.     

Scale-dependent spatial variance patterns and correlations of seabirds and prey in the southeastern Bering Sea as revealed by spectral analysis

Uni- and bivariate spectral analyses of the spatial distribution of thick-billed murres Uria lomvia and acoustic estimates of prey biomass in the southeastern Bering Sea were used to examine the spatial variance patterns of a predator and its prey at multiple spatial scales. Power, phase and coherency spectra from individual transects, as well as those averaged over all transects, were examined. The average spectra, representing a temporal scale of months, showed that murres and prey had similar spatial variance patterns and were positively correlated over the range of spatial scales studied. The individual spectra, representing a temporal scale of hours, showed several patterns that were not evident in the average spectra. In particular, the transect-level analyses showed that the correlation between murres and prey was poor at spatial scales where prey variance was relatively low. This result suggests a new hypothesis to explain poor small-scale correlations between consumers and resources: resource distribution is relatively uniform at small scales resulting in only a slight increase in foraging return for consumers showing an aggregative response at these scales. The differences among spatial scales and between the average and individual spectra illustrate how ecological patterns can vary with temporal and spatial scale.