bluuebunny/crossref_metadata_2025 huggingface dataset:
Community food web, decomposition and nitrogen mineralisation in a stratified Scots pine forest soil
Authors: Berg Matty , De Ruiter Peter , Didden Wim , Janssen Martien , Schouten Ton , Verhoef Herman
Published: August 2004

A soil community food web model was used to improve the understanding of what factors govern the mineralisation of nutrients and carbon and the decay of dead organic matter. The model derives the rates of C and N mineralisation by organisms by splitting their uptake rate of food resources into a rate at which faeces or prey remains are added to detritus, a rate at which elements are incorporated into biomass, and a rate at which elements are released by organisms as inorganic compounds. The functioning of soil organisms in the mineralisation of C and N was modelled in the soil horizon of a Scots pine forest. The organic horizon was divided into three distinct layers, representing successive stages of decay, i.e. litter, fragmented litter, and humus. Each of the layers had a different, quantitative, biota composition. For each layer the annual C and N mineralisation rates were simulated and compared to observed C and N mineralisation rates from organic matter in stratified litterbags. Simulated C and N mineralisation was relatively close to measured losses of C and N, but the fit was not perfect. Discrepancies between the observed and predicted mineralisation rates are discussed in terms of variation in model parameter values of those organisms that showed the highest contribution to mineralisation rates. The measured, and by the model predicted, significant decrease in mineralisation rates down the profile was not explained by the biomass of the primary decomposers and only partly by the total food web biomass. Modelling results indicated that indirect effects of soil fauna, due to trophic interactions with their resources, are an important explanatory factor. In addition, the analyses suggest that community food web structure is an important factor in the regulation of nutrient mineralisation. The model provided the means to evaluate the contribution of functionally defined groups of organisms, structured in a detrital food web, to losses of C and N from successive decay stages.
Invasion and persistence of plant parasites in a spatially structured host population
Authors: Park Andrew W. , Gubbins Simon , Gilligan Christopher A.
Published: August 2004

Spatial structure is of central importance in the dynamics of plant‐parasite interactions and is imposed by the growth habit and distribution of host plants and by parasite dispersal which is frequently restricted. To investigate the effects of spatial heterogeneity on the dynamics of plant parasites we introduce a simple model for epidemic development within a spatially structured host population. Here the host population is subdivided into a number of patches which are linked to allow for transmission from one patch to another with the connections defining the spatial structure of the host population. Three key parameters are identified that play a critical role in the ability of the parasite to invade and persist within the host population: the within‐patch parasite basic reproductive number which characterises the infection dynamics at the local spatial scale; and the neighbourhood of interaction which describes which patches interact with which and the strength of coupling between patches within the neighbourhood which together characterise the spread of the parasite over larger spatial scales. Using both deterministic and stochastic formulations of the model, we investigate how the thresholds and probabilities of invasion and persistence are affected by these parameters, by demographic stochasticity and by differences in the initial level of infection.
Comparing the genetic population structure of two species of arctic lemmings: more local differentiation in Lemmus trimucronatus than in Dicrostonyx groenlandicus
Authors: Ehrich Dorothee , Krebs Charles J. , Kenney Alice J. , Stenseth Nils Chr.
Published: August 2004

Collared and brown lemmings (Dicrostonyx groenlandicus and Lemmus trimucronatus) are two largely sympatric and ecologically comparable species of arctic microtine rodents, differing however in some respects which allow us to hypothesise differences in the genetic structure of their populations. Collared lemmings are particularly well adapted to life at high latitude, they occasionally emerge to the surface of the snow and may disperse over larger distances than brown lemmings – possibly even over snow and ice. This should result in more local differentiation among populations of brown lemmings than among populations of collared lemmings. We compared the genetic population structure between the two lemming species in a fragmented landscape with small islands in the central Canadian Arctic using four microsatellite loci and partial mitochondrial control region sequences. Both types of genetic markers showed higher differentiation (FST values) among local populations for brown lemmings than for collared lemmings. We discuss to what extent the observed genetic differences may be explained by differences in dispersal rates in addition to differences in average effective population size.
Aerial dispersal of phytoseiid mites (Acari: Phytoseiidae): estimating falling speed and dispersal distance of adult females
Authors: Jung Chuleui , Croft Brian A.
Published: August 2004

Aerial dispersal is important to immigration and redistribution of phytoseiid mites that often can provide biological control of spider mite pests. Falling speed of a mite and wind largely determine dispersal distance of such a passively blown organism. A diffusion model of wind‐blown phytoseiids could provide insight into their dispersal. To this end, we measured body weights and falling speeds of adult females of 13 phytoseiid and one tetranychid mite species. These data were then incorporated into seed dispersal models (Greene and Johnson, Okubo and Levin) and results were compared to mite dispersal distances in wind tunnel, greenhouse and field.  Weights of phytoseiid species ranged from 5.25 to 2l.7 μg; starved mites weighed less than fed mites. Geometric diameters (dg) of idiosomas were correlated to weights. Falling speeds for phytoseiids were 0.39–0.73 m/s, and less than for T. urticae (0.79 m/s) in still air. In some species, active mites had slower falling speeds than inactive (anesthetized) mites indicating that behavior may influence falling. Starved mites had significantly slower falling speeds than fed mites and dispersed farther. Equation‐based estimates of falling speed were close to measured ones (2–8% deviation) for some species. There were significant relationships between falling speed and body weight and morphological traits. Greene and Johnson's seed dispersal model provided better fits to dispersal of mites in the wind tunnel, greenhouse and field studies than Okubo and Levin's model. Limits of models in describing mite dispersal distance and applications to IPM are discussed.
The functional response of a predatory plant preying on swarming zooplankton
Authors: Englund Göran , Harms Sabine
Published: August 2004

In a laboratory study, we determined the functional response of the carnivorous aquatic plant Utricularia vulgaris feeding on Polyphemus pediculus, a cladoceran zooplankton that forms swarms. The number of prey eaten increased linearly with prey density up to a density of 35 prey per 125 ml and decreased slightly above this density. Independent estimates of handling time showed that the number eaten was not limited by handling. Thus, we hypothesized that the functional response levelled off because attack rate decreased with increasing density. Direct observations of the predation act at high and low prey densities showed that prey per capita mortality rate was markedly lower at high densities. An analysis of the components of the predation cycle showed that encounter rate and attack probability but not capture success decreased with increasing prey density. We, then, studied the degree of aggregation and the movement behaviour of Polyphemus. The tendency to form swarms increased with density and this was associated with reduced swimming speed and swimming along a more tortuous path. Presence of Utricularia leaves did not influence the spatial distribution and swimming behaviour of Polyphemus. We concluded that the unusual shape of the functional response was due to density dependent prey mortality rates that resulted from a density dependent tendency to form swarms. We, therefore, suggested a modification of Holling's type II functional response model that included density dependent attack rate and this model fitted data significantly better than the original model.
Does population ecology have general laws?
Authors: Turchin Peter
Published: August 2004

There is a widespread opinion among ecologists that ecology lacks general laws. In this paper I argue that this opinion is mistaken. Taking the case of population dynamics, I point out that there are several very general law‐like propositions that provide the theoretical basis for most population dynamics models that were developed to address specific issues. Some of these foundational principles, like the law of exponential growth, are logically very similar to certain laws of physics (Newton's law of inertia, for example, is almost a direct analogue of exponential growth). I discuss two other principles (population self‐limitation and resource‐consumer oscillations), as well as the more elementary postulates that underlie them. None of the “laws” that I propose for population ecology are new. Collectively ecologists have been using these general principles in guiding development of their models and experiments since the days of Lotka, Volterra, and Gause.
Logic of experiments in ecology: is pseudoreplication a pseudoissue?
Authors: Oksanen Lauri
Published: August 2004

Hurlbert divides experimental ecologist into ‘those who do not see any need for dispersion (of replicated treatments and controls), and those who do recognize its importance and take whatever measures are necessary to achieve a good dose of it’. Experimental ecologists could also be divided into those who do not see any problems with sacrificing spatial and temporal scales in order to obtain replication, and those who understand that appropriate scale must always have priority over replication. If an experiment is conducted in a spatial or temporal scale, where the predictions of contesting hypotheses are convergent or ambiguous, no amount of technical impeccability can make the work instructive. Conversely, replication can always be obtained afterwards, by conducting more experiments with basically similar design in different areas and by using meta‐analysis. This approach even reduces the sampling bias obtained if resources are allocated to a small number of well‐replicated experiments. For a strict advocate of the hypothetico‐deductive method, replication is unnecessary even as a matter of principle, unless the predicted response is so weak that random background noise is a plausible excuse for a discrepancy between predictions and results. By definition, a prediction is an ‘all‐statement’, referring to all systems within a well‐defined category. What applies to all must apply to any. Hence, choosing two systems and assigning them randomly to a treatment and a control is normally an adequate design for a deductive experiment. The strength of such experiments depends on the firmness of the predictions and their a priori probability of corroboration. Replication is but one of many ways of reducing this probability. Whether the experiment is replicated or not, inferential statistics should always be used, to enable the reader to judge how well the apparent patterns in samples reflect real patterns in statistical populations. The concept ‘pseudoreplication’ amounts to entirely unwarranted stigmatization of a reasonable way to test predictions referring to large‐scale systems.
Predator‐prey interactions in a nonequilibrium context: the metapopulation approach to modeling “hide‐and‐seek” dynamics in a spatially explicit tri‐trophic system
Authors: Nachman Gösta
Published: August 2004

Predators and prey are usually heterogeneously distributed in space so that the ability of the predators to respond to the distribution of their prey may have a profound influence on the stability and persistence of a predator‐prey system. A special type of dynamics is “hide‐and‐seek” characterized by a high turnover rate of local populations of prey and predators, because once the predators have found a patch of prey they quickly overexploit it, whereupon the starving predators either should move to better places or die. Continued persistence of prey and predators thus hinges on a long‐term balance between local extinctions and founding of new subpopulations. The colonization rate depends on the rate of emigration from occupied patches and the likelihood of successfully arriving at a suitable new patch, while extinction rate depends on the local population dynamics. Since extinctions and colonizations are both discrete probabilistic events, these phenomena are most adequately modeled by means of a stochastic model. In order to demonstrate the qualitative differences between a deterministic and stochastic approach to population dynamics, a spatially explicit tritrophic predator‐prey model is developed in a deterministic and a stochastic version. The model is parameterized using data for the two‐spotted spider mite (Tetranychus urticae) and the phytoseiid mite predator Phytoseiulus persimilis inhabiting greenhouse cucumbers.  Simulations show that the deterministic and stochastic approaches yield different results. The deterministic version predicts that the populations will exhibit violent fluctuations, implying that the system is fundamentally unstable. In contrast, the stochastic version predicts that the two species will be able to coexist in spite of frequent local extinctions of both species, provided the system consists of a sufficiently large number of local populations. This finding is in agreement with experimental results. It is therefore concluded that demographic stochasticity in combination with dispersal is capable of producing and maintaining sufficient asynchrony between local populations to ensure long‐term regional (metapopulation) persistence.
Regulation, cycles and stability in northern carnivore‐herbivore systems: back to first principles
Authors: Oksanen Tarja , Oksanen Lauri , Schneider Michael , Aunapuu Maano
Published: August 2004

In studies on dynamics of northern predator‐prey systems, two assumptions are often made. First, the bifurcation from stable to cyclic dynamics is seen as a consequence of changing generalist‐specialist ratio, ultimately due to reduced prey diversity at high latitudes and the negative impact of snow on the efficiency of generalists as predators of small, folivorous mammals. Supposedly, the primary mechanism is the qualitative difference between the functional response of specialist and generalist predators. Second, the interaction between large predators and ungulates is supposed to be prone to lead to two alternative equilibria, one where predation regulates ungulates at a relatively low equilibrium and another, where ungulate densities are close to carrying capacity. In the first‐mentioned issue, our analysis corroborates the general idea of snow favoring specialists and leading to cycles. However, differences in functional response appear to be of secondary importance only, and rather special conditions are required for generalists to have a stabilizing type III functional response. A destabilizing type II functional response or a slight modification of it should be common in generalists, too, as also indicated by the classical experiments. Stability of generalist dominated systems seems primarily to derive from their relative inefficiency, allowing prey's density‐dependent mechanisms to play a bigger role in the neighborhood of the equilibrium. Moreover, the main destabilizing impact of deep, long‐lasting snow cover appears to lie in the protection it offers to the efficient but vulnerable specialists, which are eliminated or marginalized by intraguild predation in areas with snow‐free winters, unless the habitat offers some other form of efficient protection. As for the conjecture of multiple equilibria in northern wolf‐ungulate systems, it seems to be derived from an erroneous operational definition of numerical response and has little if any empirical support. Available data suggest that predation limitation of folivorous mammals prevails along the entire gradient from relatively productive low arctic habitats to the humid parts of the temperate zone, provided that the numbers of predators are not controlled by man.
The applicability of metapopulation theory to large mammals
Authors: Elmhagen Bodil , Angerbjörn Anders
Published: August 2004

Metapopulation theory has become a common framework in conservation biology and it is sometimes suggested that a metapopulation approach should be used for management of large mammals. However, it has also been suggested that metapopulation theory would not be applicable to species with long generations compared to those with short ones. In this paper, we review how and on what empirical ground metapopulation terminology has been applied to insects, small mammals and large mammals. The review showed that the metapopulation term sometimes was used for population networks which only fulfilled the broadest possible definition of a metapopulation, i.e. they were subpopulations connected by migrating individuals. We argue that the metapopulation concept should be reserved for networks that also show some kind of metapopulation dynamics. Otherwise it applies to almost all populations and loses its substance. We found much empirical support for metapopulation dynamics in both insects and small mammals, but not in large mammals. A possible reason is the methods used to confirm the existence of metapopulation dynamics. For insects and small mammals, the common approach is to study population turnover through patch occupancy data. Such data is difficult to obtain for large mammals, since longer temporal scales need to be covered to record extinctions and colonizations. Still, many populations of large mammals are exposed to habitat fragmentation and the resulting subpopulations sometimes have high risks of extinction. If there is migration between the subpopulations, the metapopulation framework could provide valuable information on their population dynamics. We suggest that a metapopulation approach can be interesting for populations of large mammals, when there are discrete breeding subpopulations and when these subpopulations have different growth rates and demographic fates. Thus, a comparison of the subpopulations’ demographic fates, rather than subpopulation turnover, can be a feasible alternative for studies of metapopulation dynamics in large mammals.
Field biology, food web models, and management: challenges of context and scale
Authors: Power Mary E.
Published: August 2004

Managers are increasingly aware of the need for science to inform the stewardship of natural lands and resources. If ecologists are to address this need, we must increase the scope of our inferences, while maintaining sufficient resolution and realism to predict trajectories of specific populations or ecosystem variables. Food chain and simple food web models, used either as core or component hypotheses, can help us to meet this challenge. The simple mass balance logic of dynamic food chain or food web models can organize our thinking about a range of applied problems, such as evaluating controls over populations of concern, or of biotic assemblages that affect important ecosystem properties. In other applications, a food chain or web may be incorporated as one element in models of regional mass balances affecting resources or environments. Specific predictions of food web models will often fail because of inadequate resolution (e.g., of functionally significant differences among taxa within “trophic levels”) or insufficient scope (e.g., of spatio‐temporal variation over scales relevant to management). Increasing use of tracers to delimit spatial scales of food web interactions will reduce, but not eliminate, this limitation. If used with skepticism and vigilance to local natural history, however, food chain or simple food web models can promote the iterative feedback between prediction, falsification by observation, and new prediction central to hypothetico‐deductive science and adaptive management. Experience argues that this stepwise path is the fastest towards better understanding and control of our impacts on nature.
Venue and outcome in ecological experiments: manipulations of larval anurans
Authors: Skelly David K. , Kiesecker Joseph M.
Published: August 2004

The choice of venue is believed to be a critical decision for ecologists conducting experiments, yet the existence of tradeoffs in design and the impact of venue on outcome have not been quantitatively evaluated. To these ends we reviewed a set of 227 comparisons from 52 studies designed to quantify the effect of density on the growth performance of larval anurans. We predicted that both design and outcome would be related to experimental venue (laboratory, mesocosm, and field). We found that, in contrast to our predictions, laboratory experiments did not include more factors or yield more precise estimates of responses compared with mesocosm and field manipulations. In partial support of our prediction, we found that laboratory experiments did utilize somewhat larger numbers of replicates and included more levels per factor compared to the alternative venues. In addition we found that, as predicted, raising tadpoles at higher densities of conspecifics, or in the presence of heterospecifics tended to decrease growth. This effect, consistent with competition, was strongly dependent on experimental venue. In particular, we found that interspecific effects were much stronger in mesocosm versus field manipulations. This result is particularly relevant because conceptions of amphibian assemblages have included interspecific competition as integral to natural patterns of amphibian distribution. We conclude that hypothesized tradeoffs among experimental venues have not acted in a particularly strong way in shaping the design of tadpole density manipulations. However, venue may mediate strong effects on the outcome of such experiments. Quantification of such methodology based biases will help ecologists more effectively match the goals of their experiments with decisions regarding venue.
Reconstruing the Digital Divide from the Perspective of a Large, Poor, Developing Country
Authors: James Jeffrey
Published: August 2004

The global digital divide is usually measured in terms of differences between rich and poor countries in the extent to which they use ICTs in general and the Internet in particular. Such a view of the problem, however, ignores the fact that there are all kinds of ways in which poor, illiterate persons in developing countries benefit from the Internet without any use of computers and Internet connectivity. Most of these benefits occur as a result of intermediaries who, in one way or another, transfer relevant parts of the knowledge available from the technology to recipients in a form that is relevant to their specific needs. Using India as an illustration of this argument, we find that usage understates actual beneficiaries by at least 30 percent. On the basis of this finding, we suggest that a reconstrued notion of the digital divide be based on usage as well as other more indirect forms of benefit from the Internet in developing countries. To this end, much more needs to be known about these other forms of benefit in a large sample of countries in addition to India.
Effects of UV irradiation on barley and tomato leaves: thermoluminescence as a method to screen the impact of UV radiation on crop plants
Authors: Gilbert Matthias , Skotnica Jiri , Weingart Ilka , Wilhelm Christian
Published: August 2004

The effect of different UV intensities and irradiation times on barley and tomato leaves was investigated by analysis of thermoluminescence (TL) and chlorophyll (chl) fluorescence measurements. Epifluorescence microscopy was used to estimate the epidermal UV transmittance of leaves. In barley a strong supression of TL emission from the S2QB– (B-band) and the S2QA– (Q-band) charge recombination was observed increasing with prolonged UV exposure. Primary barley leaves were more sensitive to UV than secondary leaves. In tomato plants a decrease in the B-band only takes place at very high UV intensities and after prolonged exposure times (4 h). The impact of UV in cotyledons was more pronounced than in pinnate leaves of tomato plants. The strong differences in sensitivity to UV in the investigated barley and tomato variety may be due to different concentrations of UV screening pigments in the epidermal layer as demonstrated by epifluorescence measurements. The results show that TL has the same potential to analyse the sensitivity or tolerance of crop plants to UV irradiation as routine fluorescence techniques. Furthermore, TL is directly monitoring the radical pair states of PSII and can distinguish between UV-induced donor and acceptor site-related damage.
Changes in photosynthetic pigment composition and absorbed energy allocation during salt stress and CAM induction in Mesembryanthemum crystallinum
Authors: Barker David H. , Marszalek Jeff , Zimpfer Jeff F. , Adams III William W.
Published: August 2004

Mesembryanthemum crystallinum L. undergoes a transition from the C3 photosynthetic pathway to crassulacean acid metabolism (CAM) in response to increasing salinity. As a consequence, growth is greatly reduced and less light energy is utilised in carbon fixation, leading to an increase in dissipation of thermal energy to remove potentially dangerous excess excitation energy. The pigment composition of plants grown for 4 weeks at 20 mm (low) and 400 mm (high) NaCl was sampled, and photochemical performance, tissue acidity and growth were sampled at 2 and 4 weeks. High-salt-grown plants, which switched to CAM, accumulated only 25% of the fresh weight of low-salt-grown plants, which maintained C3 photosynthesis. Predawn Fv / Fm and de-epoxidation of violaxanthin [(A + Z) / (V + A + Z)] was similar between plants after 2 and 4 weeks, revealing no sustained depression in PSII efficiency under the high-salt treatment. However, at midday under high photosynthetic photon flux densities (PPFD) high-salt plants displayed lower PSII efficiency, higher (A + Z) / (V + A + Z) and greater allocation of energy to thermal dissipation over photochemistry than low-salt plants. Pigment contents were similar between treatments for the first 3 weeks, but after 4 weeks high-salt plants had accumulated significantly less chlorophyll and lutein than low-salt plants. However, V + A + Z content did not differ. High-salt treatment, leading to CAM photosynthesis and substantial reduction in growth, was associated with increased allocation of energy to xanthophyll cycle-dependent energy dissipation at high light and adjustment of thylakoid pigment composition.
Effects of lincomycin on PSII efficiency, non-photochemical quenching, D1 protein and xanthophyll cycle during photoinhibition and recovery
Authors: Bachmann Kristine Mueh , Ebbert Volker , Adams III William W. , Verhoeven Amy S. , Logan Barry A. , Demmig-Adams Barbara
Published: August 2004

Leaves of Parthenocissus quinquefolia (L.) Planch. (Virginia creeper) were treated with lincomycin (an inhibitor of chloroplast-encoded protein synthesis), subjected to a high-light treatment and allowed to recover in low light. While lincomycin-treated leaves had similar characteristics as controls after a 1 h exposure to high light, total D1 levels in lincomycin-treated leaves were half those in controls at the end of the recovery period. In addition, lincomycin delayed recovery of maximal PSII efficiency of open centers (ratio of variable to maximal chlorophyll fluorescence, F v / F m) and of estimated PSII photochemistry rate upon return to low light subsequent to the high-light treatment. Furthermore, lincomycin treatment slowed the removal of zeaxanthin (Z) and antheraxanthin (A) during recovery in low light, and the level of thermal energy dissipation (non-photochemical fluorescence quenching, NPQ) remained elevated. In lincomycin-treated leaves infiltrated with the uncoupler nigericin immediately after high-light exposure, thermal energy dissipation, sustained with lincomycin alone, declined quickly to control levels. In summary, lincomycin treatment affected not only D1 protein turnover but also xanthophyll-cycle operation and thermal-energy dissipation. The latter effect was apparently a result of the maintenance of a high trans-thylakoid proton gradient. Similar effects were also seen subsequent to short-term exposures to high light in lincomycin-treated Spinacia oleracea L. (spinach) leaves. In contrast, lincomycin treatments under low-light levels did not induce Z formation or NPQ. These results suggest that lincomycin has the potential to lower PSII efficiency (F v / F m) through inhibition of NPQ relaxation and Z + A removal subsequent to high-light exposures.
Low temperature effects on grapevine photosynthesis: the role of inorganic phosphate
Authors: Hendrickson Luke , Chow Wah Soon , Furbank Robert T.
Published: August 2004

The photosynthetic response of grapevine leaves (Vitis vinifera L. cv. Riesling) to low temperature was studied to determine the role of end-product limitation and orthophosphate (Pi) recycling to the chloroplast under these conditions. As reported previously, the response of photosynthesis in air to stomatal conductance declined at temperatures below 15°C, suggesting that at low temperatures inhibition of photosynthesis in grapevine has a strong non-stomatal component. Stimulation of carbon assimilation at ambient CO2 by reducing O2 from 21 to 2 kPa, O2 declined to zero below 15°C, a phenomenon often associated with a restriction in photosynthesis due to end-product-synthesis limitation. This stimulation could be restored by feeding Pi. Photosynthesis in leaf disks at both high and low irradiances in non-photorespiratory conditions (1% CO2) was highly sensitive to reductions in temperature. Below 15°C, feeding Pi caused a large stimulation of photosynthetic O2 evolution. Metabolite measurements indicated that despite a decline in Rubisco carbamylation state, ribulose 1,5-bisphosphate (RuBP) levels dropped at low temperature and the ratio of 3-phosphoglycerate (3-PGA) to triose phosphate (TP) remained largely unchanged. These results suggest that grapevine-leaf photosynthesis is severely restricted at low temperature by non-stomatal mechanisms. The return of Pi to the chloroplast plays an important role in this limitation but a coordinated set of regulatory processes maintain a homeostasis of phosphorylated sugar levels.
The lutein epoxide cycle in vegetative buds of woody plants
Authors: García-Plazaola José I. , Hormaetxe Koldobika , Hernández Antonio , Olano José M. , Becerril José M.
Published: August 2004

Recent works have shown that two xanthophyll cycles operate simultaneously in several plant species: the ubiquitous violaxanthin + anteraxanthin + zeaxanthin (VAZ) cycle and the lutein epoxide (Lx) cycle. In the present work we tested for the presence of the Lx cycle in vegetative buds of woody plants. After an extensive screening of 130 species, we have shown that Lx is present in buds of many different plant species and leaf primordia are enriched in Lx compared with leaves. As a result, the Lx pool was higher than the violaxanthin (V) pool in several species. Although Lx can be potentially de-epoxidised in buds, light attenuation by scales inhibited the daily operation of the Lx cycle. This finding would imply that the Lx cycle is not involved in short-term reversible photoprotection in buds. However, a light-induced decrease in Lx was observed through the winter. An extensive screening of 130 species in 49 families conducted to elucidate the taxonomic extension of this cycle showed a widespread presence of the Lx cycle. The presence of Lx has a high fidelity at the family level, but its presence in unrelated taxa suggests that this character has appeared independently in several different groups of plants.
De novo protein synthesis in relation to ammonia and proline accumulation in water stressed white clover
Authors: Kim Tae-Hwan , Lee Bok-Rye , Jung Woo-Jin , Kim Kil-Yong , Avice Jean-Christophe , Ourry Alain
Published: August 2004

The kinetics of protein incorporation from newly-absorbed nitrogen (N, de novo protein synthesis) was estimated by 15N tracing in 18-week-old white clover plants (Trifolium repens L. cv. Regal) during 7 d of water-deficit treatment. The physiological relationship between kinetics and accumulation of proline and ammonia in response to the change in leaf-water parameters was also assessed. All leaf-water parameters measured decreased gradually under water deficit. Leaf and root dry mass was not significantly affected during the first 3 d when decreases in leaf-water parameters were substantial. However, metabolic parameters such as total N, proline and ammonia were significantly affected within 1 d of commencement of water-deficit treatment. Water-deficit treatment significantly increased the proline and NH3–NH4+ concentrations in both leaves and roots. There was a marked reduction in the amount of N incorporated into the protein fraction from the newly absorbed N (NANP) in water-deficit stressed plants, particularly in leaf tissue. This reduction in NANP was strongly associated with an increased concentration of NH3–NH4+ in roots (P≤0.05) and proline (P≤0.01) in leaves and roots. These results suggest that proline accumulation may be a sensitive biochemical indicator of plant water status and of the dynamics of de novo protein synthesis in response to stress severity.
Hydraulics of plant growth
Authors: Boyer John S. , Silk Wendy K.
Published: August 2004

Multicellular plants rely on growth in localised regions that contain small, undifferentiated cells and may be many millimetres from the nearest differentiated xylem and phloem. Water and solutes must move to these small cells for their growth. Increasing evidence indicates that after exiting the xylem and phloem, water and solutes are driven to the growing cells by gradients in water potential and solute potential or concentration. The gradients are much steeper than in the vascular transport system and can change in magnitude or suffer local disruption with immediate consequences for growth. Their dynamics often obscure how turgor drives wall extension for growth, and different flow paths for roots and shoots have different dynamics. In this review, the origins of the gradients, their mode of action and their consequences are discussed, with emphasis on how their dynamics affect growth processes.
The time course of visual information accrual guiding eye movement decisions
Authors: Caspi Avi , Beutter Brent R. , Eckstein Miguel P.
Published: August 2004

Saccadic eye movements are the result of neural decisions about where to move the eyes. These decisions are based on visual information accumulated before the saccade; however, during an ≈100-ms interval immediately before the initiation of an eye movement, new visual information cannot influence the decision. Does the brain simply ignore information presented during this brief interval or is the information used for the subsequent saccade? Our study examines how and when the brain integrates visual information through time to drive saccades during visual search. We introduce a new technique, saccade-contingent reverse correlation, that measures the time course of visual information accrual driving the first and second saccades. Observers searched for a contrast-defined target among distractors. Independent contrast noise was added to the target and distractors every 25 ms. Only noise presented in the time interval in which the brain accumulates information will influence the saccadic decisions. Therefore, we can retrieve the time course of saccadic information accrual by averaging the time course of the noise, aligned to saccade initiation, across all trials with saccades to distractors. Results show that before the first saccade, visual information is being accumulated simultaneously for the first and second saccades. Furthermore, information presented immediately before the first saccade is not used in making the first saccadic decision but instead is stored and used by the neural processes driving the second saccade.
Repriming the actomyosin crossbridge cycle
Authors: Steffen Walter , Sleep John
Published: August 2004

The central features of the mechanical cycle that drives the contraction of muscle are two translational steps: the working stroke, whereby an attached myosin crossbridge moves relative to the actin filament, and the repriming step, in which the crossbridge returns to its original orientation. Although the mechanism of the first of these is understood in some detail, that of the second has received less attention. Here, we show that repriming occurs after detachment of the crossbridge from the actin, rather than intervening between two actomyosin states with ATP bound [Eisenberg, E. & Greene, L. E. (1980)
Annu. Rev. Physiol.
42, 293–309]. To discriminate between these two models we investigated the single-molecule mechanics of the myosin–actin interaction in the presence of ATP analogues such as GTP, for which the hydrolytic step itself limits the actomyosin GTPase rate to a much lower rate than for ATP. The lifetimes of bound states was proportional to 1/[GTP], indicating that during the bound period myosin was in the actomyosin rigor configuration. Moreover, despite the very low actomyosin GTPase, the rate of actin binding and formation of the rigor state was higher than with ATP; it follows that most interactions with actin result in the release of GTP and not of the products, GDP and phosphate. There was no significant movement of the actin during this interaction, so repriming must occur while myosin is dissociated, as in the original Lymn–Taylor scheme [Lymn, R. W. & Taylor, E. W. (1971)
Biochemistry
10, 4617–4624].
Modeling the site-specific variation of selection patterns along lineages
Authors: Guindon Stéphane , Rodrigo Allen G. , Dyer Kelly A. , Huelsenbeck John P.
Published: August 2004

The unambiguous footprint of positive Darwinian selection in protein-coding DNA sequences is revealed by an excess of nonsynonymous substitutions over synonymous substitutions compared with the neutral expectation. Methods for analyzing the patterns of nonsynonymous and synonymous substitutions usually rely on stochastic models in which the selection regime may vary across the sequence but remains constant across lineages for any amino acid position. Despite some work that has relaxed the constraint that selection patterns remain constant over time, no model provides a strong statistical framework to deal with switches between selection processes at individual sites during the course of evolution. This paper describes an approach that allows the site-specific selection process to vary along lineages of a phylogenetic tree. The parameters of the switching model of codon substitution are estimated by using maximum likelihood. The analysis of eight HIV-1
env
homologous sequence data sets shows that this model provides a significantly better fit to the data than one that does not take into account switches between selection patterns in the phylogeny at individual sites. We also provide strong evidence that the strength and the frequency of occurrence of selection might not be estimated accurately when the site-specific variation of selection regimes is ignored.
Kinetic control of dimer structure formation in amyloid fibrillogenesis
Authors: Hwang Wonmuk , Zhang Shuguang , Kamm Roger D. , Karplus Martin
Published: August 2004

Amyloid fibril formation involves nonfibrillar oligomeric intermediates, which are important as possible cytotoxic species in neurodegenerative diseases. However, their transient nature and polydispersity have made it difficult to identify their formation mechanism or structure. We have investigated the dimerization process, the first step in aggregate formation, by multiple molecular dynamics simulations of five β-sheet-forming peptides. Contrary to the regular β-sheet structure of the amyloid fibril, the dimers exhibit all possible combinations of β-sheets, with an overall preference for antiparallel arrangements. Through statistical analysis of 1,000 dimerization trajectories, each 1 ns in length, we have demonstrated that the observed distribution of dimer configurations is kinetically determined; hydrophobic interactions orient the peptides so as to minimize the solvent accessible surface area, and the dimer structures become trapped in energetically unfavorable conformations. Once the hydrophobic contacts are present, the backbone hydrogen bonds form rapidly by a zipper-like mechanism. The initial nonequilibrium structures formed are stable during the 1-ns simulation time for all five peptides at room temperature. In contrast, at higher temperatures, where rapid equilibration among different configurations occurs, the distribution follows the global energies. The relaxation time of dimers at room temperature was estimated to be longer than the time for diffusional encounters with other oligomers at typical concentrations. These results suggest that kinetic trapping could play a role in the structural evolution of early aggregates in amyloid fibrillogenesis.
Most of ADP·glucose linked to starch biosynthesis occurs outside the chloroplast in source leaves
Authors: Baroja-Fernández Edurne , Muñoz Francisco José , Zandueta-Criado Aitor , Morán-Zorzano María Teresa , Viale Alejandro Miguel , Alonso-Casajús Nora , Pozueta-Romero Javier
Published: August 2004

Sucrose and starch are end products of two segregated gluconeogenic pathways, and their production takes place in the cytosol and chloroplast of green leaves, respectively. According to this view, the plastidial ADP·glucose (ADPG) pyrophosphorylase (AGP) is the sole enzyme catalyzing the synthesis of the starch precursor molecule ADPG. However, a growing body of evidences indicates that starch formation involves the import of cytosolic ADPG to the chloroplast. This evidence is consistent with the idea that synthesis of the ADPG linked to starch biosynthesis takes place in the cytosol by means of sucrose synthase, whereas AGP channels the glucose units derived from the starch breakdown. To test this hypothesis, we first investigated the subcellular localization of ADPG. Toward this end, we constructed transgenic potato plants that expressed the ADPG-cleaving adenosine diphosphate sugar pyrophosphatase (ASPP) from
Escherichia coli
either in the chloroplast or in the cytosol. Source leaves from plants expressing ASPP in the chloroplast exhibited reduced starch and normal ADPG content as compared with control plants. Most importantly however, leaves from plants expressing ASPP in the cytosol showed a large reduction of the levels of both ADPG and starch, whereas hexose phosphates increased as compared with control plants. No pleiotropic changes in photosynthetic parameters and maximum catalytic activities of enzymes closely linked to starch and sucrose metabolism could be detected in the leaves expressing ASPP in the cytosol. The overall results show that, essentially similar to cereal endosperms, most of the ADPG linked to starch biosynthesis in source leaves occurs in the cytosol.
Identification of a quinone-sensitive redox switch in the ArcB sensor kinase
Authors: Malpica Roxana , Franco Bernardo , Rodriguez Claudia , Kwon Ohsuk , Georgellis Dimitris
Published: August 2004

Escherichia coli
senses and signals anoxic or low redox conditions in its growth environment by the Arc two-component system. Under anaerobic conditions, the ArcB sensor kinase autophosphorylates and transphosphorylates ArcA, a global transcriptional regulator that controls the expression of numerous operons involved in respiratory or fermentative metabolism. Under aerobic conditions, the kinase activity of ArcB is inhibited by the quinone electron carriers that act as direct negative signals. Here, we show that the molecular mechanism of kinase silencing involves the oxidation of two cytosol-located redox-active cysteine residues that participate in intermolecular disulfide bond formation, a reaction in which the quinones provide the source of oxidative power. Thus, a pivotal link in the Arc signal transduction pathway connecting the redox state of the quinone pool to the transcriptional apparatus is elucidated.
Gene interactions in the DNA damage-response pathway identified by genome-wide RNA-interference analysis of synthetic lethality
Authors: van Haaften Gijs , Vastenhouw Nadine L. , Nollen Ellen A. A. , Plasterk Ronald H. A. , Tijsterman Marcel
Published: August 2004

Here, we describe a systematic search for synthetic gene interactions in a multicellular organism, the nematode
Caenorhabditis elegans
. We established a high-throughput method to determine synthetic gene interactions by genome-wide RNA interference and identified genes that are required to protect the germ line against DNA double-strand breaks. Besides known DNA-repair proteins such as the
C. elegans
orthologs of TopBP1, RPA2, and RAD51, eight genes previously unassociated with a double-strand-break response were identified. Knockdown of these genes increased sensitivity to ionizing radiation and camptothecin and resulted in increased chromosomal nondisjunction. All genes have human orthologs that may play a role in human carcinogenesis.
Multiple ATP-hydrolyzing sites that potentially function in cytoplasmic dynein
Authors: Takahashi Yoshinori , Edamatsu Masaki , Toyoshima Yoko Y.
Published: August 2004

Cytoplasmic dynein is a minus-end-directed microtubule motor involved in numerous essential processes within eukaryotic cells, such as nuclear segregation and trafficking of intracellular particles. The motor domain of the dynein heavy chain comprises six tandemly linked AAA (ATPase associated with diverse cellular activities) modules (AAA1–AAA6). The first four modules include nucleotide-binding sites (Walker A or P-loop motifs), and each of the four sites appears to bind ATP. However, the role and the function of each binding site are unknown. Especially, the question of which P-loops are ATP-hydrolyzing sites has not been answered, because it is difficult to measure the ATPase activity of each P-loop. Here, we purified several truncated
Saccharomyces cerevisiae
cytoplasmic dynein fragments and their mutants expressed in
Escherichia coli
and then measured their ATPase activities. Our results suggest that there are multiple ATP-binding sites that have abilities to hydrolyze ATP in cytoplasmic dynein. Furthermore, a single AAA module is insufficient for ATP hydrolysis, and the adjacent module facing the ATP-binding site is necessary for ATP-hydrolyzing activity.