Conditions Under Which Nitrogen Can Limit Steady-State Net Primary Production in a General Class of Ecosystem Models

Human activity is drastically altering global nitrogen (N) availability. The extent to which ecosystems absorb additional N—and with it, additional CO₂—depends on whether net primary production (NPP) is N-limited, so it is important to understand conditions under which N can limit NPP. Here I use a general dynamical model to show that N limitation at steady-state—such as in old-growth forests—depends on the balance of biotically controllable versus uncontrollable N inputs and losses. Steady-state N limitation is only possible when uncontrollable inputs (for example, atmospheric deposition) exceed controllable losses (for example, leaching of plant-available soil N), which is the same as when uncontrollable losses (for example, leaching of plant-unavailable soil N) exceed controllable inputs (biological N fixation). These basic results are robust to many model details, such as the number of plant-unavailable soil N pools and the number and type of N fixers. Empirical data from old-growth tropical (Hawai’i) and temperate (Oregon, Washington, Chile) forests support the model insights. Practically, this means that any N fixer—symbiotic or not—could overcome ecosystem N limitation, so understanding N limitation requires understanding controls on all N fixers. Further, comparing losses of plant-available N to abiotic inputs could offer a rapid diagnosis of whether ecosystems can be N-limited, although the applicability of this result is constrained to ecosystems with a steady-state N cycle such as old-growth forests largely devoid of disturbance.     

The potential of and limitations to marine population prognosis

Following the 19th century recognition and definition of basic ecological entities, functional analysis has been the highlight of this century. The synthesis of these findings enables ecological prognosis. The population as the basic functional unit has been repeatedly treated; in the marine field, fisheries management approaches developed into multi-species population analysis. As in planktology, theoretical ecology, and classic biocoenotic research, the population interactions are of increasing scientific interest. A mathematical model is suggested that combines these extrinsic and intrinsic functional relationships in order to define the fit of the ecological niche to the environment, the decisive measure of the expected population success, and thus of the probable population development needed for prognostic purposes. It is discussed in how far the orientation towards the predictive power or — with respect to the “skill” of meteorological prognoses — the “ecological prognostic skill” improvement may serve as a means to choose the best investigative strategy.     

The Yank of Dobzhansky’s Bequest

Dobzhansky studied mechanisms of balancing selection using systems of inversions in Drosophila and he soon found that changes in inversion frequencies along generations in experimental populations conformed to the expectation for a simple model of heterosis. However, other more complex modes of selection, like rare male advantage, were later found to affect the maintenance of inversion polymorphisms. Here we show that a more realistic (and complex) model than heterosis—integrating all known fitness component estimates obtained in independent experiments for the ST/CH system of inversions in Drosophila pseudoobscura—not only conforms to but actually also predicts the inversion frequencies. This concludes this line of work and points to other selection mechanisms than heterosis that were also considered by Dobzhansky—frequency- and sex-dependent selection—as potential mechanisms of balancing selection responsible for the maintenance of the inversion polymorphisms in Drosophila.     

Artificial neural network model of the relationship between <Emphasis Type="Italic">Betula</Emphasis> pollen and meteorological factors in Szczecin (Poland)

Birch pollen is one of the main causes of allergy during spring and early summer in northern and central Europe. The aim of this study was to create a forecast model that can accurately predict daily average concentrations of Betula sp. pollen grains in the atmosphere of Szczecin, Poland. In order to achieve this, a novel data analysis technique—artificial neural networks (ANN)—was used. Sampling was carried out using a volumetric spore trap of the Hirst design in Szczecin during 2003–2009. Spearman’s rank correlation analysis revealed that humidity had a strong negative correlation with Betula pollen concentrations. Significant positive correlations were observed for maximum temperature, average temperature, minimum temperature and precipitation. The ANN resulted in multilayer perceptrons 366 8: 2928-7-1:1, time series prediction was of quite high accuracy (SD Ratio between 0.3 and 0.5, R > 0.85). Direct comparison of the observed and calculated values confirmed good performance of the model and its ability to recreate most of the variation.     

The prior probabilities of phylogenetic trees

Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different methods of assigning prior probabilities to trees. I argue that priors need to be derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and about macroevolutionary processes more generally.     

Genetic analysis of short term callus culture and morphogenesis in pearl millet,Pennisetum glaucum

Genetic analysis of five in vitro characters was made through a 5 × 5 diallel analysis using callus derived from immature inflorescence segments of pearl millet (Pennisetum glaucum). The characters studied were: — volume of total callus, — frequency of embryogenic calli, — embryogenic callus volume, — growth rate in terms of increase in fresh weight, and — frequency of regeneration. High heritability values and heterosis were noticed for all these characters except for E callus frequency. Additive gene action was predominant for callus growth rate and frequency of regeneration. Of the five inbreds, IP 1346 (= P5) was found to be the best genetic background for embryogenic callus volume, embryogenic growth rate and frequency of regeneration. This revised version was published online in June 2006 with corrections to the Cover Date.     

Scale-up of stirring as foam disruption (SAFD) to industrial scale

Foam disruption by agitation—the stirring as foam disruption (SAFD) technique—was scaled up to pilot and production scale using Rushton turbines and an up-pumping hydrofoil impeller, the Scaba 3SHP1. The dominating mechanism behind SAFD—foam entrainment—was also demonstrated at production scale. The mechanistic model for SAFD defines a fictitious liquid velocity generated by the (upper) impeller near the dispersion surface, which is correlated with complete foam disruption. This model proved to be scalable, thus enabling the model to be used for the design of SAFD applications. Axial upward pumping impellers appeared to be more effective with respect to SAFD than Rushton turbines, as demonstrated by retrofitting a 12,000 l bioreactor, i.e. the triple Rushton configuration was compared with a mixed impeller configuration from Scaba with a 20% lower ungassed power draw. The retrofitted impeller configuration allowed 10% more broth without risking excessive foaming. In this way a substantial increase in the volumetric productivity of the bioreactor was achieved. Design recommendations for the application of SAFD are given in this paper. Using these recommendations for the design of a 30,000 l scale bioreactor, almost foamless Escherichia coli fermentations were realised. Electronic Publication     

Modelling and sensitivity analysis of the reactions involving receptor,G-protein and effector in vertebrate olfactory receptor neurons

A biochemical model of the receptor, G-protein and effector (RGE) interactions during transduction in the cilia of vertebrate olfactory receptor neurons (ORNs) was developed and calibrated to experimental recordings of cAMP levels and the receptor current (RC). The model describes the steps from odorant binding to activation of the effector enzyme which catalyzes the conversion of ATP to cAMP, and shows how odorant stimulation is amplified and delayed by the RGE transduction cascade. A time-dependent sensitivity analysis was performed on the model. The model output—the cAMP production rate—is particularly sensitive to a few, dominant parameters. During odorant stimulation it depends mainly on the initial density of G-proteins and the catalytic constant for cAMP production.     

The Role of Teleological Thinking in Learning the Darwinian Model of Evolution

Human beings are predisposed to think of evolution as teleological—i.e., having a purpose or directive principle—and the ways scientists talk about natural selection can feed this predisposition. This work examines the suggestion that students’ teleological thinking operates as an obstacle when the natural selection evolution model is taught. What we mean by obstacle is an established way of thinking that resists change due to its explanatory power. In light of this approach, the challenges of teaching evolution in biology education have been revised, and improved methodological strategies aimed at a better comprehension of the Darwinian evolution model are suggested.     

New ways of determining structural groups in brown coals and their bioconversion products by FT IR spectroscopy

New methods of determining the structural groups —COOH and —CH₂— have been developed. The investigation of carboxyl groups is possible both after derivatization with p-fluorophenacylbromide and by quantitative interpretation of the Fourier transform infrared (FT IR) spectra. There exists a linear relationship between the results of these two methods that is generally valid for the analysis of all brown coal components. The maximum extinction coefficient of the symmetric stretching vibration band of the CH₂ groups has been determined using model substances. This allows quantification of this structural group directly from the FT IR spectrum. The results agree with the contents of methylene groups as determined by ¹³C-cross polarization–magic angle spinning–nuclear magnetic resonance (¹³C CPMAS NMR) spectroscopy. Using these methods, the COOH and CH₂ groups contained in brown coals of the North Rhine region and in their bioconversion products have been quantified. Received: 21 December 1999 / Received revision: 25 April 2000 / Accepted: 1 May 2000     

Mathematical models of predator/prey/plant interactions in a patch environment

Several tritrophic systems are characterized by local over-exploitation of the food source. Interactions between predatory mites, spider mites and their host plants are an example of such systems: either the spider mites over-exploit local patches of host plants or the spider mites are exterminated by predatory mites. It is often stated that modelling the overall population dynamics of such systems in a realistic way would soon lead to an unmanageable edifice. We advocate, however, the use of physiologically structured population models as a both general and formal mathematical framework. The advantage is that analytically tractable models may be obtained from the complex ‘master’ model by time-scale arguments or special choices of model ingredients. In this way a network of models can be derived, each concentrating on a particular aspect, all inadequate to cover the entire spectrum, but together (we hope) providing a coherent set of insights the relative importance of which can be assessed by computer experiments on the ‘master’ model. In this paper a rather realistic model of predator/prey interactions in an ensemble of host-plant patches is presented and, as an example of our approach, some special cases are derived from that model. Their analysis provided some first, useful insights. It is shown that prolonged duration of the prey-dispersal phase and prey dispersal from predator (-invaded prey) patches may result in a stable steady state, whereas a humped plant-production function may — under certain conditions — result in two stable steady states.     

GLOBIO3: A Framework to Investigate Options for Reducing Global Terrestrial Biodiversity Loss

The GLOBIO3 model has been developed to assess human-induced changes in biodiversity, in the past, present, and future at regional and global scales. The model is built on simple cause–effect relationships between environmental drivers and biodiversity impacts, based on state-of-the-art knowledge. The mean abundance of original species relative to their abundance in undisturbed ecosystems (MSA) is used as the indicator for biodiversity. Changes in drivers are derived from the IMAGE 2.4 model. Drivers considered are land-cover change, land-use intensity, fragmentation, climate change, atmospheric nitrogen deposition, and infrastructure development. GLOBIO3 addresses (i) the impacts of environmental drivers on MSA and their relative importance; (ii) expected trends under various future scenarios; and (iii) the likely effects of various policy response options. GLOBIO3 has been used successfully in several integrated regional and global assessments. Three different global-scale policy options have been evaluated on their potential to reduce MSA loss. These options are: climate-change mitigation through expanded use of bio-energy, an increase in plantation forestry, and an increase in protected areas. We conclude that MSA loss is likely to continue during the coming decades. Plantation forestry may help to reduce the rate of loss, whereas climate-change mitigation through the extensive use of bioenergy crops will, in fact, increase this rate of loss. The protection of 20% of all large ecosystems leads to a small reduction in the rate of loss, provided that protection is effective and that currently degraded protected areas are restored. Author Contributions  RA—Writing, study design, data analyses; MvO—Writing, research; LM— Writing, data analyses; CN—Contribution to method; MB—Research, data analyses; BtB—Contribution to method.     

Some views on the role of noise in “self”-organizing systems

This paper deals with information transfer from the environment and “self”-organization in open, nonlinear systems far from thermodynamic equilibrium — in the presence of either non-stationary phase jitter noise, or amplitude stationary noise. By “self”-organization we mean here the progressive formation within the system of sequential, ordered (coherent) relationships between appropriate dynamical variables-like for example, the phase differences between the oscillating components of the system. We take up (in Section II) the classical Laser as a specific example and examine in detail the influence of phase jitter noise in the mode (phase) locking process. We find—as expected—that phase fluctuations in the cavity cause degradation of the coherent behaviour (i.e. increase the entropy) of the system — which, however, levels off, or saturates with time. Further (in Section III) we examine systems where the number of self-sustained oscillating components may vary with time in such a way that the maximum entropy of the system increases faster than the overall instantaneous entropy. We put forth the hypothesis that in such cases — because of the increase of the redundancy — the system gets organized not just in spite of, but merely because of the presence of Noise. Possible applications in biological systems (especially concerning a model of cerebral organization) are briefly discussed. It is understood here, that the system has to display some preliminary dynamical structure before the organizing procedure takes over. What happens afterwards is the subject of this paper.     

Possible contaminant origins of the red cosmetics decorating ancient burial sites in Japan

Marker elements were estimated from the red cosmetics collected from different ancient burials and mine ruins in three separate districts of Japan. Element levels were displayed in reference to the relative amount to sulfur (RA/S), by which the cosmetics were divided into five types: I—a low Hg/S with a low Fe/S; II—both moderate Hg/S and Fe/S; III—a moderate Hg/S with a high Fe/S; III 2—a high Hg/S with a moderate Fe/S; IV—a high Hg/S with a high Fe/S. The cosmetics can be further characterized by referring to other contaminants such as Zn, Cu, and Mn. These combined analyses with contaminant metals were capable of characterizing the origins of the cosmetics; it is useful to compare them to each other. The cosmetics were identified as being due to several groups of contaminants from ancient mines in Japan, and also with this system analysis of the markers it is possible to identify them from neighboring countries.     

Faunistic similarity and endemism of earthworms in east mediterranean region

The analysis presents earthworm distribution in eight designated tectonic units (C—Cyprus, EP—East Pondites, ET—East Taurus block, Sc—Sakarya continent, Kb—Kırşehir block, L—the Levant, TM—Taurus–Menderes block, WP—West Pondites) in the East Mediterranean region (EM). It represents a full list of earthworm species (N = 81) of the region and reveals significant faunal similarities between Sc + WP, and between Kb + TM. The new Sc + WP unit is characterized by the presence of archaic (Spermophorodrilus) as well as modern earthworm fauna. In contrast, the second newly established Kb + TM unit is characterized by poorly presented earthworm autochthonous fauna and by a lack of endemic species. The analysis done on the species list (N = 73) representing the autochthonous family Lumbricidae showed statistically supported separation of L and EP between themselves and from other designated units. The Levant, part of the Arabian tectonic plate, is characterized by a high level of endemism in ancient (Healyella) and modern (Dendrobaena, Perelia) genera, and by the lack of archaic genera. The EP harbors unique species representing archaic (Eophila), ancient (Healyella), and modern (Allolobophora, Aporrectodea, Dendrobaena and Eisenia) earthworm genera in the EM. The analysis also indicates origin of earthworm fauna in TM and faunistic relationships among the designated units. Clearly, the present-day division of the EM earthworm fauna shows recognizable influences of tectonic history.     

Placozoa: at least two

It was shown that compensatory base changes (CBCs) in internal transcribed spacer 2 (ITS2) sequence-structure alignments can be used for distinguishing species. Using the ITS2 Database in combination with 4SALE — a tool for synchronous RNA sequence and secondary structure alignment and editing — in this study we present an in-depth CBC analysis for placozoan ITS2 sequences and their respective secondary structures. This analysis indicates at least two distinct species in Trichoplax (Placozoa) supporting a recently suggested hypothesis, that Placozoa is “no longer a phylum of one”. The first two authors contributed equally to this work.     

Quantifying the Routes of Transmission for Pandemic Influenza

Motivated by the desire to assess nonpharmaceutical interventions for pandemic influenza, we seek in this study to quantify the routes of transmission for this disease. We construct a mathematical model of aerosol (i.e., droplet-nuclei) and contact transmission of influenza within a household containing one infected. An analysis of this model in conjunction with influenza and rhinovirus data suggests that aerosol transmission is far more dominant than contact transmission for influenza. We also consider a separate model of a close expiratory event, and find that a close cough is unlikely (≈1% probability) to generate traditional droplet transmission (i.e., direct deposition on the mucous membranes), although a close, unprotected and horizontally-directed sneeze is potent enough to cause droplet transmission. There are insufficient data on the frequency of close expiratory events to assess the relative importance of aerosol transmission and droplet transmission, and it is prudent to leave open the possibility that droplet transmission is important until proven otherwise. However, the rarity of close, unprotected and horizontally-directed sneezes—coupled with the evidence of significant aerosol and contact transmission for rhinovirus and our comparison of hazard rates for rhinovirus and influenza—leads us to suspect that aerosol transmission is the dominant mode of transmission for influenza.     

Signs of Anger: Representation of Agonistic Behaviour in Invertebrate Cognition

In this essay I shall examine the representation of aggression and its issues in the model animal, the Fruit Fly, Drosophila melanogaster. The Fruit Fly is the model animal for genetics and more recently neuroscience. On the basis of its behaviour conclusions are being drawn that will help in the development of new treatments for clinical entities like aggression and anxiety disorders—the author questions those findings and asks whether more should be done to focus on the actual biology and behaviour—the Umwelt, instead of trying to bridge the gulf between invertebrate and human behaviours.     

A tissue model for the study of cell proliferation in vitro

Summary A procedure for the cultivation of mesentery is described, in which the culture is fully representative of the tissue of origin. The intact mesenteric membrane—exposed to a minimum of trauma—was spread out over a hole in a filter paper strip in fluid medium and was cultivated free-hanging. Specimens from rats and guinea pigs were used. The organ culture model appears especially apt for cytochemical and proliferation studies. Proliferation variables based on Feulgen DNA analysis in individual, morphologically defined cells and on mitotic counting and radiochemical analysis were estimated. The tissue was fully viable in chemically defined growth medium and showed an almost unaltered light microscopical appearance after up to 52 hr in culture. Supported by the Swedish Cancer Society.