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.     

An S-Curve-Based Approach of Identifying Biological Sequences

The main idea of S-curve diagram is to assign different angle values (from 0° to 180°) to different nucleotide acid residues or to different protein amino acids, and then according to cos α _j and sin α _j , the values are accumulated to construct an S-curve diagram, which is in strict one-to-one correspondence with the biological sequence. In addition, the S-curve diagram proves to be without the degeneracy phenomenon, so that both the degeneracy problem represented by diagrams and the problem of visualization for biological sequence data are solved. Meanwhile, a new approach to differentiate the similarity of biological sequences—the degree of similarity—is put forward on the basis of the S-curve diagram. To put it in detail, the least square approach is first adopted to obtain a straight line equation according to the S-curve diagram, then according to the distance formula of the point to the straight line, the average ratio of square sum for the distance between the S-curve and the straight line is calculated, and finally, the similarity of the biological sequences is presented by the new standard—the degree of similarity. As is shown by the experimental results, the S-curve diagram can better represent biological sequences (such as protein’s) within Cartesian coordinate system, and the mutation point of biological sequence. Thus, it turns out that the new standard—the degree of similarity is of obviously great advantage.     

Differential gene expression in anticancer drug- and TRAIL-mediated apoptosis in renal cell carcinomas

Renal cell carcinomas (RCC) exhibit marked differences in susceptibility towards anticancer drug- and TRAIL-induced apoptosis. However, the underlying mechanisms determining apoptosis-sensitivity or -resistance are not well understood. The purpose of this study was to compare gene expression patterns induced by DNA-damage- and death receptor-induced apoptosis and to detect differentially expressed genes responsible for differences in apoptosis-susceptibility. Therefore, we performed a comparative cDNA-array analysis in an apoptosis-resistant and an apoptosis-sensitive RCC cell line. In the sensitive cell line an upregulation of multiple E2F1- and p53-inducible proapaptotic and cell-cycle regulating target genes by Topotecan as well as TRAIL was observed. Interestingly, several antiapoptotic NFκB-dependent target genes were also induced. In the resistant cell line, however, only a small number of E2F1-, p53- and NFκB-dependent target genes were differentially regulated. Conclusively, anticancer drug- as well as TRAIL-sensitivity go along with an upregulation of multiple proapoptotic genes. In contrast, the mechanisms of apoptosis-resistance are—at least in part—located upstream of gene induction and seem not to depend upon upregulation of de-novo-synthesized antiapoptotic genes. Conclusively, the proapoptotic stimuli are confronted with a cellular context which allows apoptosis to be conducted—in the sensitive cell line—or not—in the resistant cell line. Electronic Supplementary Material The online version of this article (doi: ) contains supplementary material, which is available to authorized users. Sebastian Heikaus and Ercan Casliskan contributed equally to this work. This work was supported by the ’Deutsche Forschungsgemeinschaft (DFG).     

Marker-assisted selection and evaluation of the QTL for stigma exsertion under japonica rice genetic background

Stigma exsertion is one of the important traits which contribute to the efficient improvement of commercial seed production in hybrid rice. In order to understand the genetic factors involved in the stigma exsertion of an indica variety—IR24—a QTL analysis was conducted using the F₂ population between a japonica variety—Koshihikari—and a breeding line showing exserted stigma selected from the backcross population between IR24 as a donor and japonica varieties. As a result, a highly significant QTL (qES3), which had been predicted in the recombinant inbred population of IR24, was confirmed at the centromeric region on chromosome 3. qES3 increases about 20% of the frequency of the exserted stigmas at the IR24 allele and explains about 32% of the total phenotypic variance. A QTL near-isogenic line for qES3 increased the frequency of the exserted stigma by 36% compared to that of Koshihikari in a field evaluation, which suggests that qES3 is a promising QTL for the development of a maternal line for hybrid rice. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. Maiko Miyata and Toshio Yamamoto contributed equally to this study.     

On the iterated prisoner's dilemma in a finite population

Two standard assumptions in analytical work on the iterated prisoner's dilemma are that the population is infinite, and that opponents—though randomly selected—are fixed for the duration of the game. This paper explores the consequences of relaxing both assumptions. It is shown in particular that if opponents are drawn at random throughout the game, then stable cooperation via reciprocity requires both that the probability of a further interaction be sufficiently high—higher than when opponents are fixed—and that the population not exceed a certain critical size, which depends on the probability of further interaction.     

Post-Fire Resource Redistribution in Desert Grasslands: A Possible Negative Feedback on Land Degradation

Desert grasslands, which are very sensitive to external drivers like climate change, are areas affected by rapid land degradation processes. In many regions of the world the common form of land degradation involves the rapid encroachment of woody plants into desert grasslands. This process, thought to be irreversible and sustained by biophysical feedbacks of global desertification, results in the heterogeneous distribution of vegetation and soil resources. Most of these shrub-grass transition systems at the desert margins are prone to disturbances such as fires, which affect the interactions between ecological, hydrological, and land surface processes. Here we investigate the effect of prescribed fires on the landscape heterogeneity associated with shrub encroachment. Replicated field manipulation experiments were conducted at a shrub-grass transition zone in the northern Chihuahuan desert (New Mexico, USA) using a combination of erosion monitoring techniques, microtopography measurements, infiltration experiments, and isotopic studies. The results indicate that soil erosion is more intense in burned shrub patches compared to burned grass patches and bare interspaces. This enhancement of erosion processes, mainly aeolian, is attributed to the soil–water repellency induced by the burning shrubs, which alters the physical and chemical properties of the soil surface. Further, we show that by enhancing soil erodibility fires allow erosion processes to redistribute resources accumulated by the shrub clumps, thereby leading to a more homogeneous distribution of soil resources. Thus fires counteract or diminish the heterogeneity-forming dynamics of land degradation associated with shrub encroachment by enhancing local-scale soil erodibility. Author Contributions  SR—Conceived of or designed study, performed research, analyzed data, wrote the paper; PD—Conceived of or designed study, performed research, wrote the paper; LW—Performed research, analyzed data; GO—Contributed new methods, analyzed data; SC—Conceived of or designed study; CW—Performed research, contributed new methods or models; and SM—Contributed new methods or models.     

Modeling immunotherapy for allergy

Type I hypersensitivity, which functions to protect the organism from parasites, is caused by binding of antigen to IgE antibodies pre-attached to the cell surface of tissue mast cells and their circulating counterparts, the basophils. In “allergy,” type I hypersensitivity is inappropriately induced by protein-based foreign substances (such as pollen) or protein components of insect stings, which in the normal course of events would be cleared from the organism without causing any damage. Paradoxically, a successful clinical treatment of allergy involves repeated immunization of allergic persons with low doses of the allergen—immunotherapy. Investigation of the available experimental evidence leads to the conclusion that the phenomena of immunotherapy are best addressed in terms of the interplay among the mechanism(s) of immune memory—Th1/Th2 cross-regulation—and the physical compart-mentalization of the immune system. These conclusions are illustrated with a numerical simulation.     

Two Approaches to the Study of the Origin of Life

This paper compares two approaches that attempt to explain the origin of life, or biogenesis. The more established approach is one based on chemical principles, whereas a new, yet not widely known approach begins from a physical perspective. According to the first approach, life would have begun with—often organic—compounds. After having developed to a certain level of complexity and mutual dependence within a non-compartmentalised organic soup, they would have assembled into a functioning cell. In contrast, the second, physical type of approach has life developing within tiny compartments from the beginning. It emphasises the importance of redox reactions between inorganic elements and compounds found on two sides of a compartmental boundary. Without this boundary, “life” would not have begun, nor have been maintained; this boundary—and the complex cell membrane that evolved from it—forms the essence of life.     

Assessment of higher insect taxa as bioindicators for different logging-disturbance regimes in lowland tropical rain forest in Sabah, Malaysia

One of the serious environmental problems since the 1980s has been the conflict between the high rate of deforestation and maintenance of healthy ecosystem services and biological values in tropical forests. There is an urgent demand for setting up an appropriate environmental assessment to keep healthy ecosystem functions and biodiversity along with sustainable forest use based on ecology. In this study, we tried to assess logging-disturbance effects on the abundances of several flying insect groups (higher-taxon approach) in lowland tropical rain forest (Deramakot Forest Reserve, Sabah, Malaysia), while considering seasonal changes and vertical forest stratification. The season was the most important factor affecting the abundances of all the insect groups. Effects of logging disturbance were prominent in the understorey but obscure in the canopy. Changes in physical conditions caused by logging—possibly an increased evaporation due to solar radiation—may have decreased the abundance of desiccation-sensitive insects, especially in the understorey. There are also two probable reasons for the difference between events in the understorey and those in the canopy: (1) noise effects of various physical, environmental factors may have obscured insect responses to logging disturbance in the canopy; (2) higher spatio-temporal variation in quality and quantity of living food resources—such as leaves, flowers and fruits—provided in the canopy may have affected the abundance of their consumer insects independently of logging disturbance. Thus, this study suggests that the abundance of some insect groups at higher-taxon level, especially in the understorey, can be used as bioindicators for assessing effects of logging disturbance on the forest ecosystem.     

Soil penetrability as a key factor affecting the nesting of burrowing birds

Soil penetrability resistance was found to be crucial for nest site selection of all three Central European burrowing bird species—Sand Martins (Riparia riparia), European Bee-eaters (Merops apiaster), and Eurasian Kingfishers (Alcedo atthis). Soil penetrability resistance measurements were used to find out whether increased hardness of unexcavated banks is the key factor affecting the presence of burrowing birds. All three species avoided banks composed of too compact or too loose soils. Birds discriminated not only between high- and low-quality breeding banks, but also between different soil strata within banks. In banks with generally low penetrability resistance, Sand Martins preferred soil strata with the highest available penetrability resistance and compactness to avoid hole collapses. There was a preference for hard soil below holes to serve as a resistant platform when birds begin to dig their holes. In Sand Martins, the penetrability resistance level affected physical characteristics of holes such as tunnel length and dimensions of the orifices. Excessive compactness—and probably not high talus presence—was a major cause of abandonment of Sand Martin localities. A high penetrability resistance is the crucial factor for site selection in Sand Martins.     

A note on a paper by Erik Volz: SIR dynamics in random networks

Recent work by Volz (J Math Biol 56:293–310, 2008) has shown how to calculate the growth and eventual decay of an SIR epidemic on a static random network, assuming infection and recovery each happen at constant rates. This calculation allows us to account for effects due to heterogeneity and finiteness of degree that are neglected in the standard mass-action SIR equations. In this note we offer an alternate derivation which arrives at a simpler—though equivalent—system of governing equations to that of Volz. This new derivation is more closely connected to the underlying physical processes, and the resulting equations are of comparable complexity to the mass-action SIR equations. We further show that earlier derivations of the final size of epidemics on networks can be reproduced using the same approach, thereby providing a common framework for calculating both the dynamics and the final size of an epidemic spreading on a random network. Under appropriate assumptions these equations reduce to the standard SIR equations, and we are able to estimate the magnitude of the error introduced by assuming the SIR equations.     

Two exceptional sets of physiological clearance curves and their mathematical form: Test cases?

Amiodarone concentrationsy(t) have been measured from 1 min to more than 50 days following 10 min of infusion, with about 40 observations on each of six normal subjects (Tuckeret al., 1984,Eur. J. clin. Pharmacol. 26, 655–656). The form of the log-log plots—ln(y) vs ln(t)—is investigated. These appear to show three phases. First there is a rapid decrease ofy(t). then a straight line corresponding to a small negative power oft, ca −0.3, and this line changes continuously but quickly at about 0.5 day into a steeper line that is almost straight. For the curve fitting a simple “spline-type” device was successful. Two continuity conditions were imposed at the time of changeover, which was one of the unknown parameters. The results are compared in detail with those from a set of 15 radiocalcium curves obtained during 2 weeks or more from a single injection of⁴⁷Ca (Neeret al., 1967,J. clin. Invest. 46, 1364–1379). Again two power functions of time can be seen. The changeover is much more gradual than with amiodarone, and the fits are still better. Both sets of curves are fitted with fewer adjustable parameters than with the usual multiexponentials that are interpreted in terms of homogeneous compartments. Theoretical and practical implications are mentioned. There is much indirect evidence that hundreds of other clearance curves may consist largely of one or two of such power functions of time.     

Question 3: The Problem of Macromolecular Sequences: The Forgotten Stumbling Block

The Author agrees in principle with the question/statement, but states also that an important qualification is needed within this question. In fact, it is not possible by the bottom up approach to find the conditions for the synthesis of our actual proteins—lysozyme, chymotrypsin or the like—however it is possible to show experimentally that co-oligopeptides chains of that length can be produced by prebiotic reactions. Considering such a synthesis, it is important to recall that proteins—and nucleic acids—are not simply polymers, but are co-polymers, and the kinetics and thermodynamics attending the synthesis of copolymers poses stringent constraints for the biogenesis and growth of specific sequences. Such constraints are examined and discussed. Presented at: International School of Complexity–4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

Morphology of two eastern Pacific eelpouts (Pisces,Zoarcidae, Lycodes) in connection with features of distribution of species with a double lateral line

Morphology of two endemic eastern Pacific species of eelpouts—blackbelly Lycodes pacificus Collett, 1879 and bigfin L. cortezianus Gilbert, 1891—were studied. It was shown that these two species are characterized by unreduced seismosensory system of the head and belong to a species group with a double lateral line. It was suggested that the ancestral form of this species group could have possibly dispersed in the Atlantic Ocean through the Panama Canal in the pre-Pleistocene time. It is likely that the antitropical distribution of the Newfoundland eelpout L. terranovae is related this event.     

An extraordinarily high level of IL-15 expression by a cell line transduced with a modified BMGneo vector displays hypoxic upregulation

Interleukin (IL)-15 expression level is tightly controlled in mammalian cells by various mechanisms. In order to achieve higher expression levels of IL-15, many attempts have been made, but the highest expression rate among those reported is still only 13.3 ng/10⁶ cells/24 h. Here we report that a selected human embryonic kidney 293 (HEK293) cell line, denoted 293HAN cells, which can survive and proliferate under conditions of hypoxia, acidity, and nutritional depletion (HAN), after transduction—with a modified BMGneo vector—can produce functional human IL-15 at the extremely high rate of 890 ng/10⁶ cells/24 h under normoxic conditions—a 67-fold increase. This is as a result of multiple episomally based vector copy numbers per cell. An extra benefit was that the BMGneo vector was found to be inducible in hypoxia and allowed a further approximately threefold upregulation of the human IL-15 level which made these 293HAN cells, transduced with the modified BMGneo vector, a very promising tool for high IL-15 production (∼200-fold increase above that of baseline normoxia). The mechanism of hypoxic upregulation was found to be related to the mouse MT-1 promoter present in the vector. These authors contributed equally to this paper.     

Tablet formulation studies on nimesulide and meloxicam-cyclodextrin binary systems

The objective of this work was to develop tablet formulations of nimesulide-β-cyclodextrin (NI-β-CD) and meloxicam-γ-cyclodextrin (ME-γ-CD) binary systems. In the case of nimesulide, 3 types of binary systems—physical mixtures, kneaded systems, and coevaporated systems—were studied. In the case of meloxicam, 2 types of binary systems—physical mixtures and kneaded systems—were investigated. Both drug-CD binary systems were prepared at 1∶1 and 1∶2 molar ratio (1∶1M and 1∶2M) and used in formulation studies. The tablet formulations containing drug-CD binary systems prepared by the wet granulation and direct compression methods showed superior dissolution properties when compared with the formulations of the corresponding pure drug formulations. Overall, the dissolution properties of tablet formulations prepared by the direct compression method were superior to those of tablets prepared by the wet granulation method. Selected tablet formulations showed good stability with regard to drug content, disintegration time, hardness, and in vitro dissolution properties over 6 months at 40°C±2°C and 75% relative humidity. Published: May 11, 2007     

Left-hand Preference for a Complex Manual Task in a Population of Wild Siamangs (<Emphasis Type="BoldItalic">Symphalangus syndactylus</Emphasis>)

Many hypotheses have been proposed linking the emergence of lateralized activities—such as handedness—in primates, with hemispheric specialization and the evolution of complex communication such as human language. Although data to test these ideas are rapidly accumulating for many primate taxa, some species are still largely unexplored, especially under natural conditions. I present the first data on a population of wild siamangs (Symphalangus syndactylus), highly arboreal small apes. Preference for the left hand is shown both at the individual and population levels for a complex manual task: collecting and drinking water from tree holes. There was no difference in hand preference between males and females, and immature individuals showed more variable patterns than adults. These results are consistent with the postural origins theory, allow a new interpretation of the findings of comparable studies, and indicate a useful behavior for future investigations of laterality in wild primates.     

Theory predicts a rapid transition from niche-structured to neutral biodiversity patterns across a speciation-rate gradient

A central challenge in community ecology is to predict patterns of biodiversity with mechanistic models. The neutral model of biodiversity is a simple model that appears to provide parsimonious and accurate predictions of biodiversity patterns in some ecosystems, even though it ignores processes such as species interactions and niche structure. In a recent paper, we used analytical techniques to reveal why the mean predictions of the neutral model are robust to niche structure in high diversity but not low-diversity ecosystems. In the present paper, we explore this phenomenon further by generating stochastic simulated data from a spatially implicit hybrid niche-neutral model across different speciation rates. We compare the resulting patterns of species richness and abundance with the patterns expected from a pure neutral and a pure niche model. As the speciation rate in the hybrid model increases, we observe a surprisingly rapid transition from an ecosystem in which diversity is almost entirely governed by niche structure to one in which diversity is statistically indistinguishable from that of the neutral model. Because the transition is rapid, one prediction of our abstract model is that high-diversity ecosystems such as tropical forests can be approximated by one simple model—the neutral model—whereas low-diversity ecosystems such as temperate forests can be approximated by another simple model—the niche model. Ecosystems that require the hybrid model are predicted to be rare, occurring only over a narrow range of speciation rates.     

Structural Features of Transiently Modified Beta-Lactoglobulin Relevant to the Stable Binding of Large Hydrophobic Molecules

Binding sites for hydrophobic molecules on bovine β-lactoglobulin, and their susceptibility to temperature, were studied by using various spectroscopic probes. Binding of probes carrying a single fluorophore moiety, a single nitroxide moiety, or both moieties on the same molecule, was followed by EPR and fluorescence. The presence of a fatty acid side chain in the dual probes was found to be required for binding to β-lactoglobulin. Binding occurred only after the protein was heated at temperatures below the threshold for its irreversible denaturation. Binding became extremely tight and stable upon cooling of the protein–probe mixture. Comparison among the various probes suggests that multiple binding sites for hydrophobes are present in the native protein, and in the partially—and reversibly—modified form of β-lactoglobulin present in solution at neutral pH and subdenaturing temperatures. Thus, the specificity of hydrophobes binding to β-lactoglobulin may be modulated by simple physical treatment of the protein.     

Phosphorus Flow in a Watershed-Lake Ecosystem

Cultural eutrophication of lakes caused by excess phosphorus (P) loading from agricultural areas is a persistent and serious environmental problem. We quantified P flows in a watershed-lake ecosystem using a simple mathematical model that coupled in-lake and upland processes to assess and compare the long-term impacts of various management strategies. Our model compares abatement by in-lake strategies (such as increasing the flux of P from algae to consumers and alum application) with riparian management to decrease P flow and with balancing P budgets at the watershed scale. All of these strategies are effective to some extent. However, only reducing the amount of fertilizer P imported to the watershed will decrease the total P in the system at steady state. Soil P—a large reservoir with slow turnover rate—governs long-term flux to the lake and must be decreased in size to maintain long-term control of eutrophication. Received 2 August 1999; accepted 12 April 2000.