Time-resolved empirical modelling of seasonal development during phenologically opaque periods

A new approach for the analysis of empirical phenological data is presented which supports oligofactorial seasonality modelling. The temporal resolution of this approach is only limited by the temporal aggregation or sampling frequency (1 day, typically, in the case of weather elements) of the available primary data on the relevant environmental factors. The phenological periods of interest may be phenologically opaque in the sense that they do not contain any phenologically observable events except their onset and end. In traditional approaches, the available primary data are aggregated over the duration of the respective phenological period (weeks or even months, typically, in plant phenology). The new approach is supported by modern mathematical methods, which allow for data analysis under unfavourable conditions of irregular oligofactorial data design, and could thus also upgrade traditional approaches of phenological data analysis.     

Accelerated Biodegradation of High and Low Concentrations of p-Nitrophenol (PNP) by Bacterial Inoculation in Industrial Wastewater: The Role of Inoculum Size on Acclimation Period

The effect of inoculum size on the acclimation period and rate and extent of p-nitrophenol (PNP) degradation at high (1–10 mg/L) and low (26 μg/L) concentrations for two bacteria was determined in defined media as well as industrial wastewater. Increased inoculum size did not affect the acclimation period of either bacterium at high (1–10 mg/L) PNP concentrations. At low PNP concentrations (26 μg/L), the two bacteria behaved differently. The acclimation period was shortened and both the rate and extent of mineralization of PNP were enhanced by increasing the Corynebacterium sp. inoculum size from 3 × 10⁵ to 3 × 10⁶ cells/ml. Addition of phosphate or elimination of predators also reduced the acclimation period. Conversely, increasing the inoculum size from 3 × 10⁵ to 5 × 10⁶ cells/ml of Pseudomonas putida lengthened the acclimation period and reduced both the rate and extent of mineralization. It is suggested that, in a given environment, the success of an introduced species to enhance the degradation of a chemical depends upon (i) concentration of the chemical, (ii) selection of an appropriate microorganism, and (iii) utilization of a suitable inoculum size. Received: 1 April 1996 / Accepted: 6 May 1996     

Aspects of the Life History of the Salema, Sarpa salpa (Pisces, Sparidae), off the Canarian Archipelago (Central-East Atlantic)

Life history of the salema, Sarpa salpa, off the Canarian archipelago was studied from samples collected between January 1998 and December 1999. Fish ranged from 119 to 452 mm in total length and from 24.9 to 1491.7 g in weight. The species was characterized by a protandric hermaphroditism. The overall sex ratio was unbalanced in favour of males (1 : 0.41). The reproductive season extends from September to March, with a peak in spawning activity in December–January. Males reached maturity at a smaller length (226 mm, 2 years old) than females (294 mm, 3 years old). Males, females and all fish showed an isometric growth. The morphometric relationship between length and mass for the whole population was described by the parameters: a = 0.0000134 and b = 3.01. A concentric pattern of opaque and translucent zones was readily distinguishable on the otoliths. Two rings, one opaque and one translucent, were laid down each year on the otoliths; the opaque zone was formed during the summer months, and the translucent zone during the winter months. Individuals aged 0 to 11 years were found. The parameters of the von Bertalanffy growth equation for all individuals were: L = 479 mm, k = 0.212 year^–1, and t₀ = –1.08 year.     

How phenological tracking shapes species and communities in non-stationary environments

Climate change alters the environments of all species. Predicting species responses requires understanding how species track environmental change, and how such tracking shapes communities. Growing empirical evidence suggests that how species track phenologically – how an organism shifts the timing of major biological events in response to the environment – is linked to species performance and community structure. Such research tantalizingly suggests a potential framework to predict the winners and losers of climate change, and the future communities we can expect. But developing this framework requires far greater efforts to ground empirical studies of phenological tracking in relevant ecological theory. Here we review the concept of phenological tracking in empirical studies and through the lens of coexistence theory to show why a community-level perspective is critical to accurate predictions with climate change. While much current theory for tracking ignores the importance of a multi-species context, basic community assembly theory predicts that competition will drive variation in tracking and trade-offs with other traits. We highlight how existing community assembly theory can help understand tracking in stationary and non-stationary systems. But major advances in predicting the species- and community-level consequences of climate change will require advances in theoretical and empirical studies. We outline a path forward built on greater efforts to integrate priority effects into modern coexistence theory, improved empirical estimates of multivariate environmental change, and clearly defined estimates of phenological tracking and its underlying environmental cues.     

Towards interbreed IBD fine mapping of the mh locus: Double-muscling in the Asturiana de los Valles breed involves the same locus as in the Belgian Blue cattle breed

The Spanish ``Asturiana' cattle breed is characterized by the segregation of a genetically determined muscular hypertrophy referred to as double-muscling or ``culones'. We demonstrate by linkage analysis that this muscular hypertrophy involves the mh locus previously shown to cause double-muscling in the Belgian Blue cattle breed, pointing towards locus homogeneity of this trait across both breeds. Moreover, using a twopoint and multipoint maximum likelihood approach, we show that flanking microsatellite markers are in linkage disequilibrium with the mh locus in both breeds albeit with different alleles. Finally, we discuss how allelic homogeneity across breeds might be exploited to achieve efficient genetic fine-mapping of the mh locus. Received: 13 September 1996 / Accepted: 20 January 1997     

Plant-herbivore models, where more grass means fewer grazers

Classical theory has led us to believe that where more grazing is available herbivores will inflict heavier pressure on the grass, thus keeping its height low. This approach is hotly debated, although still widely accepted. Based on field data collected, van der Koppel et al. [van der Koppel, J., Huisman, J., van der Wal, R., Olff, H., 1996. Patterns of herbivory along a productivity gradient: an empirical and theoretical investigation. Ecology 77, 736–745] contest the standard plant-herbivore models, arguing that herbivores do not ‘control’ the plant growth entirely, and propose two differential equation models. In this paper we describe briefly how van der Koppel et al. (1996) derive their uncontrolled plant-herbivore interaction models, and then expand on the specific mathematical results cited in their paper to provide a global overview of the dynamics of such systems, for a broad range of parameter values.     

Krill (Euphausia superba) density, proportional and absolute recruitment and biomass in the Elephant Island region (Antarctic Peninsula) during the period 1977 to 1997

The Elephant Island region (Antarctic Peninsula) was selected as a long-term monitoring site to describe the interannual variability of important krill stock parameters. The analysis reviewed and updated krill density and proportional recruitment indices. Krill absolute recruitment and biomass from net sampling surveys are introduced as additional indices from this time series. New survey results from the past two seasons indicate a very successful 1994/1995 year-class and slightly below average proportional recruitment of the 1995/1996 krill year-class. Absolute recruitment of the 1995/1996 year-class was high compared to preceding years, because total stock size was relatively high in 1996/1997. After a period of low krill density and biomass in the area for almost a decade, krill density and biomass have increased. Caution is expressed as to whether this observed increase represents a long-term recovery of the stock. Received: 15 October 1997 / Accepted: 5 January 1998     

Cell division and the stability of cellular populations

 This paper couples a general d-dimensional (d arbitrary) model for the intracellular biochemistry of a generic cell with a probabilistic division hypothesis and examines the consequence of division for stability of cell function and structure. We show rather surprisingly that cell division is capable of giving rise to a stable population of cells with respect to function and structure even if, in the absence of cell division, the underlying biochemical dynamics are unstable. In the context of a simple example, our stability condition suggests that rapid cell proliferation plays a stabilizing role for cellular populations. Received: 15 January 1996 / Revised version: 31 July 1998     

Satellite-based mapping of the growing season and bioclimatic zones in Fennoscandia

Aim  To test whether satellite-derived NDVI values obtained during the growing season as delimited by the onset of phenological phases can be used to map bioclimatically a large region such as Fennoscandia.
Location  Fennoscandia north of about 58° N and neighbouring parts of NW Russia.
Methods  Phenology data on birch from 15 research stations and the half-monthly GIMMS-NDVI data set with 8 × 8 km² resolution from the period 1982–2002 were used to characterize the growing season. To link surface phenology with NDVI data, new algorithms on a pixel-by-pixel basis that show high correlation with phenophases on birch were developed. Then, time-integrated values (TI NDVI) during the phenologically defined growing season were computed to produce a bioclimatological map of Fennoscandia, which was tested and correlated with growing degree days (GDD) obtained from 20 meteorological stations. The map was also compared vs. traditional bioclimatic maps, and analysed for error factors distorting NDVI values.
Results  The correlation between GDD and TI NDVI data during the phenologically defined growing season was very high. Therefore, the TI NDVI map could be presented as a bioclimatic map reflecting GDD. However, several major areas have interfering factors distorting NDVI values, such as the pixel heterogeneity caused by the altitudinal mosaic in western Norway, the mosaic of lakes in southeastern Finland, and the agriculture-dominated areas in southern Fennoscandia.
Main conclusions  TI NDVI data from the phenologically defined growing season during 1982–2002 in Fennoscandia can be processed as a bioclimatic map reflecting GDD, except for the areas distorting NDVI values by their strong ground-cover heterogeneity.     

Preliminary studies on the molecular basis of hyperphenylalaninemia in Egypt

Mutation analysis at the phenylalanine hydroxylase (PAH) locus was undertaken in 56 Egyptian hyperphenylalaninemic patients. Selected screening for 11 known mutations and denaturing Gradient gel electrophoresis (DGGE) analysis of the entire coding sequence and exon/intron boundaries led to the identification of a new mutation (I224T), four previously described mutations, and several polymorphisms. Overall, 18 mutant alleles could thus be characterized. In contrast to the high mutation detection rate typical of the DGGE-based scanning approach, only 6 of 16 mutant alleles tested were identified. Since BH₄ deficiency could not be excluded in any of these patients, the latter results may be explained by the occurrence of mutations affecting the genes controlling the synthesis and recycling of tetrahydrobiopterin: the cofactor of PAH. An alternative hypothesis is also discussed. Received: 18 October 1995 / Revised: 30 January 1996     

Oogenesis and gonad maturation in the copepodCalanus finmarchicus and the prediction of egg production from preserved samples

 Oogenesis and gonad development of Calanus finmarchicus during the winter spring transition in a fjord in Northern Norway were studied. A combination of observations on whole animals (macroscopic), taking advantage of their transparency, and histological sections was used to establish a system of gonad maturation stages, to describe the spawning cycle and to estimate egg production rates from preserved samples. During their development, oocytes change their shape and size, the morphology of the nucleus, and the appearance of the ooplasm. Four oocyte development stages were identified and related to a macroscopic system of four gonad developmental stages (GS) that can be applied to whole stained animals. During gonad development, the macroscopic morphological modifications of the gonads are mainly manifested in an increase in number and size of the oocytes and their distribution in diverticula and oviducts. The maturation processes during the spawning cycle (the period between egg depositions) were described from histological sections of females preserved at regular intervals after egg deposition. The macroscopic GS did not vary during the spawning cycle. This GS was a highly significant indicator for females, which spawned within 24 h after collection at 5°C. Another histological indicator for the last third of the spawning cycle is the appearance of distinct chromosomes, which, however, are only seen in histological sections. For the prediction of egg production rate of a Calanus population, in addition to the number of females spawning, knowledge of clutch size and the interval of clutch deposition is required. Clutch size was determined by counting the number of the oocyte stages to be released during the next spawning event in serial sections of the gonads. There was no significant difference in clutches laid by the females during 5 days before preservation. From the observations it seems that GS 4 predicts females that are ready to spawn within the minimum spawning interval characterisitic for a given temperature. If this holds true, it should be possible to predict in situ egg production rates solely from preserved samples. Received: 18 August 1995/Accepted: 6 January 1996     

Transition Densities and Sample Frequency Spectra of Diffusion Processes with Selection and Variable Population Size

Advances in empirical population genetics have made apparent the need for models that simultaneously account for selection and demography. To address this need, we here study the Wright–Fisher diffusion under selection and variable effective population size. In the case of genic selection and piecewise-constant effective population sizes, we obtain the transition density by extending a recently developed method for computing an accurate spectral representation for a constant population size. Utilizing this extension, we show how to compute the sample frequency spectrum in the presence of genic selection and an arbitrary number of instantaneous changes in the effective population size. We also develop an alternate, efficient algorithm for computing the sample frequency spectrum using a moment-based approach. We apply these methods to answer the following questions: If neutrality is incorrectly assumed when there is selection, what effects does it have on demographic parameter estimation? Can the impact of negative selection be observed in populations that undergo strong exponential growth?     

Photobiology of the Gonyaulax circadian system. II. Allopurinol inhibits blue-light effects

Light is the main environmental signal (zeitgeber) for practically all circadian systems, but little is known about the transduction mechanisms by which light signals reach the circadian oscillator. To identify components involved in the circadian light transduction pathway in the unicellular alga Gonyaulax polyedra Stein, we assayed inhibitors of pigment synthesis and of flavo-enzymes for their effects on circadian properties such as phase and period. We found that allopurinol, an inhibitor of xanthine oxidoreductase, specifically inhibits the period and phase effects mediated by the blue-light-sensitive input pathway, while the other light input of the Gonyaulax circadian system, that is sensitive to both red and blue light, appears to be unaffected. Received: 27 November 1996 / Accepted: 30 January 1997     

Optimal firing in sparsely-connected low-activity attractor networks

We examine the performance of Hebbian-like attractor neural networks, recalling stored memory patterns from their distorted versions. Searching for an activation (firing-rate) function that maximizes the performance in sparsely connected low-activity networks, we show that the optimal activation function is a threshold-sigmoid of the neuron's input field. This function is shown to be in close correspondence with the dependence of the firing rate of cortical neurons on their integrated input current, as described by neurophysiological recordings and conduction-based models. It also accounts for the decreasing-density shape of firing rates that has been reported in the literature. Received:9 December 1994 / Accepted in revised form: 9 January 1996     

The influence of β-cyclodextrin on the kinetics of 1-en-dehydrogenation of 6α-methylhydrocortisone by Arthrobacter globiformis cells

β-Cyclodextrin changes the kinetic peculiarities of microbial 1-en-dehydrogenation of 6α-methylhydrocortisone: the reaction rate, degree of conversion and respiratory-chain activity are increased. Respiratory-chain activity in the presence of β-cyclodextrin is increased both in the presence and in the absence of 6α-methylhydrocortisone. A mathematical model is proposed to describe the kinetics of the process. This model suggests the formation of different multi-component complexes consisting of inclusion complexes and the functional unit involving the enzyme and the respiratory chain. All the parameters of the model were estimated by data fitting. In the model framework the formation of multi-component complexes leads to an increase of the maximal reaction rate and to a decrease of substrate inhibition. An approach is suggested for optimisation of 6α-methylhydrocortisone 1-en-dehydrogenation in the presence of β-cyclodextrin. The optimal concentrations of 6α-methylhydrocortisone and β-cyclodextrin have been calculated. Received: 26 September 1996 / Received revision: 16 January 1997 / Accepted: 17 January 1997     

Thyroid cancer risk in Belarus after the Chernobyl accident: Comparison with external exposures

Within the time period 1990–1993, childhood thyroid cancer incidence due to the Chernobyl accident increased dramatically in Belarus, especially with regard to the birth cohort January 1, 1971, to May 31, 1986. This rise subsequently slowed down, i.e. during the period 1994–1996. The respective data were analysed and compared with the results of an analysis on the time dependence of thyroid cancer incidence in a pooled cohort of persons who had been exposed during childhood to external radiation with high dose rates. Concerning the period of 5–10 years following exposure, the excess absolute cancer risk per unit thyroid dose in the latter (external) exposure group was found to exceed the one in the Belarus group by a factor of two. This difference, however, is not statistically significant. The age-adjusted average excess absolute risk per unit thyroid dose for the period of 5–50 years following external childhood exposure was found to be 8 female and 14 male cases per 10⁴ person-year · Gy, which is a factor about 2.5 times higher than for the non-adjusted risk in the pooled cohort, as reported by Ron et al. in 1995. Assessments of future excess thyroid cancer cases due to the Chernobyl accident were done on the basis of the time dependence of thyroid cancer risk following external exposure. The thyroid cancer incidence among the birth cohort considered in Belarus and for a period starting from the cessation of the available observation data (1 January 1997) and extending to 50 years after the Chernobyl accident has been estimated to be about 15,000 cases, with an uncertainty range of 5000–45,000 cases. According to our calculations, 80% of these cases exceed the baseline risk under enhanced thyroid surveillance. Received: 8 June 1999 / Accepted in revised form: 20 November 1999     

Estimation of Population Vaccination Effectiveness from HIV Vaccine Trials

Longini , Datta , and Halloran (1996) proposed to design HIV vaccine trials in a way that will permit the simultaneous estimation of the vaccine effects on susceptibility to infection and on infectiousness of vaccine brak-throughs. The main feature of their design is the inclusion of steady partners of trial participants. They estimate four parameters from the vaccine trial: the probability that a susceptible person will become infected from his/her steady partner, the probability of becoming infected from outside the partnership, the vaccine efficacy for susceptibility and the vaccine efficacy for infectiousness. We show how the estimates of these parameters can be used to predict the attack rate in a given population during a specified period following mass-vaccination. This is an iterative method, as the attack rate depends on the HIV prevalence which, in turn, depends on the number of new cases during that period. The same method is also used to estimate the attack rate in that population during the same period in the absence of vaccination. The estimated attack rates allow us to estimate the population vaccination effectiveness, defined as the fraction HIV cases prevented by a vaccination program.     

Is there reproductive diapause in the winterform of pear psylla Cacopsyla bidens?

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Simulation models for European corn borer postdiapause morphogenesis and early infestation of maize in Missouri, USA

 The European corn borer is one of the most damaging insect pests to maize in the United States. Different methods exist for the estimation of time of damage to corn by first generation European corn borer. The most commonly used method is the linear thermal constant concept of phenology which by convention calculates cumulative thermal units from January 1 or another arbitrary date. Linear and nonlinear models based on the thermal units concept developed were to predict and simulate postdiapause development of the European corn borer and subsequent infestation of the maize crop using early spring temperatures (May 1–15) in central Missouri. The developmental rates of European corn borer were obtained from growth chamber investigations that simulated those temperatures, the operational temperatures being selected from a compilation of archival meteorological data from 1948 to 1989. The linear and polynomial regression models were developed to predict phenological stages of the European corn borer using thermal units as developmental rates. The models were compared against each other to determine the better predictor of estimation values: each explained 94 and 98% of the variation in developmental stages, respectively. In addition, the models were tested against independent field data and both models gave good predictions of developmental stages, indicating that either model would be a good predictor. Received: 9 September 1994 / Revised: 28 December 1995 / Accepted: 8 August 1996     

Empirical and virtual investigation of the population dynamics of an alien plant under the constraints of local carrying capacity: Heracleum mantegazzianum in the Czech Republic

During the last decades, invasive alien species have become a global concern because of their ecological and economic impact. Heracleum mantegazzianum (Apiaceae), is a tall monocarpic perennial native to Caucasus and invasive in Europe since the 1950s. Within an interdisciplinary EU project aimed at assessing suitable management strategy, we analysed the demography and ecology of this species in its invasive range. The monitoring of population dynamics in the Czech Republic led to the result that in the observed sites the species showed decreasing populations. To find an explanation for this unexpected result, two types of models were parameterized, based on the empirical data: (1) a stage-based transition matrix model, which projected a continuous negative development, and (2) a spatially explicit individual-based model (IBM), including individual variation. This second model was able to create a population with steady individual numbers. Analyses of the simulation showed that in more than 54% of the simulated years (n=5000) the growth rate was smaller than one. Still, population increase in the remaining years was sufficient to sustain a population. Nevertheless long-term observations document an invasive behaviour of the observed populations. Hence, we could assume temporal changes in the course of an invasion and thus wanted to evaluate the probability of sampling negative growth in dependence of time since first invasion. By using a method from ‘Virtual Ecology’, we approached the question: first we create an invasive population, based on the empirical data of H. mantegazzianum and second empirical sampling techniques were mimicked using the Virtual Ecologist approach. The results demonstrate how the probability of sampling negative growth increases with time since first invasion. Hence, we assume that the studied populations have already reached a maximum of their local invasive potential and thus stagnate in their size.