An experimental removal of a territorial pomacentrid: effects on the occurrence and behavior of competitors

Synopsis Stegastes fasciolatus is the most common territorial damselfish in the shallow waters of Hawaii. Territorial defense was observed against other herbivorous fishes, especially acanthorids, scarids and one omnivorous chaetodontid. One acanthurid,Acanthurus nigrofuscus was found to differ in abundance and social behavior in areas whereS. fasciolatus was present, compared to areas where it was absent. The chaetodontid,Chaetodon quadrimaculatus was sheltered during the day in areas where the pomacentrid was abundant, apparently feeding at night. In other areas it fed during the day and at night, depending on the phase of the moon.S. fasciolatus were then experimentally removed from one study site, to test whether the differences in abundance and behavior of the other species were due to the presence of the damselfish. There was a significant increase in numbers of the surgeonfishAcanthurus nigrofuscus in the removal area, as well as changes in social behavior from schooling to defense of small territories. The butterflyfish,C. quadrimaculatus, was observed to forage during the day in the removal area. There were no significant changes in the control sites. The presence of the interspecifically territorial damselfish,S. fasciolatus, thus appears to be an important determinant of the behavior of these potential food competitors.     

A model for unequal ventilation of the lungs assuming a common dead space and two separate dead spaces

This is a model for the time-variation of helium concentrations in lung wash-out curves. The helium (or other inert gas) is in a spirometer, which is connected by a common dead space to two separate dead spaces, each of which leads into a chamber. The chambers expand and contract, thus taking in some helium at each “breath.” Equations for the changes in helium concentration in each part of the system are set up; in this way difference equations are derived for the amount of helium in the spirometer after each breath, in and out, and complete solutions when the initial concentration is zero in all parts of the system except the spirometer. A simple solution when the chambers do not essentially differ (“equal ventilation”) is compared with the general case. The concept of “unequal lung ventilation” is discussed critically in relation to the model; some physiological interpretations are also mentioned. Numerical examples are given to show the effect of changes in various constants, in particular tidal volumes, end volumes, and the common dead space.     

Tracing genomic variations in two highly virulent Yersinia enterocolitica strains with unequal ability to compete for host colonization

ABSTRACT: BACKGROUND: Yersinia enterocolitica is a gastrointestinal foodborne pathogen found worldwide and which especially affects infants and young children. While different bioserotypes have been associated with varying pathogenicity, research on Y. enterocolitica is mainly conducted on the highly virulent mouse-lethal strains of biotype 1B and serotype O:8. We demonstrate here that two Y. enterocolitica bioserotype 1B/O:8 strains, 8081 and WA-314, display different virulence and fitness properties in a mouse model. In vivo co-infection experiments revealed that strain WA-314 overcomes strain 8081 in the colonization of spleen and liver. To trace the reasons of this incongruity, we present here the first high-quality sequence of the whole genome of strain WA-314 and compare it to the published genome of strain 8081. RESULTS: Regions previously accepted as unique to strain 8081, like the YAPI and YGI-3 genomic islands, are absent from strain WA-314, confirming their strain-specificity. On the other hand, some fitness- and bacterial competition-associated features, such as a putative colicin cluster and a xenobiotic-acyltransferase-encoding gene, are unique to strain WA-314. Additional acquisitions of strain WA-314 are seven prophage-like regions. One of these prophages, the 28-kb P4-like prophage YWA-4, encodes a PilV-like protein that may be used for adhesion to and invasion of the intestinal cells. Furthermore, a putative autotransporter and two type 1 fimbrial proteins of strain WA-314 show a sequence similarity <50% with the orthologous proteins in strain 8081. The dissimilar sequences of these proteins indicate possible different functions or interaction modes, reflecting the specific adhesion properties of Y. enterocolitica strains 8081 and WA-314 and thus the different efficiency of host colonization. Further important differences were found in two pYV plasmid-encoded virulence factors, YopM and YscP. The impact of these differences on virulence is discussed. CONCLUSIONS: Our study emphasizes that the virulence of pathogens can be increased, by acquiring new genes and/or improving the function of essential virulence proteins, resulting in permanently hyper-virulent strains. This work also highlights the importance of addressing genetic and phenotypic variations among closely related bacterial strains, even those belonging to the same bioserotype.     

Evolution of biochemical systems with specific chiralities: a model involving territorial behaviour

In a racemic assembly of stereospecifically reproducing organisms, enantiomeric forms would separate territorially if each organism consisted of two parts, one mobile and the other sessile. Partial destruction could then readily lead to the eventual dominance of organisms of one chirality.     

A model for the interaction of muscle cross-bridges with ligands which compete with ATP

A model is presented to describe the inhibition of muscle fiber contraction by ligands that compete with MgATP. Two ligands, adenosine 5' (beta, gamma-imido) triphosphate (AMPPNP) and pyrophosphate (PPi), decrease the force developed in isometric contractions and act as weak competitive inhibitors of the maximum velocity of contraction (Pate & Cooke, 1985). These observations provide information on the energetics of actomyosin ligand states at the end of the power-stroke where MgATP dissociates the myosin cross-bridge from actin, and they are analysed in terms of a seven state model of cross-bridge kinetics. The model can reconcile the observations that these ligands bind tightly to fibers, Kd = 10(-4) M, while they are only weak inhibitors of fiber velocity, Ki = 2 X 10(-3) M. It provides a reasonable fit to the data and leads to several conclusions concerning the properties of the cross-bridge states. The states with bound ligand are shifted axially so that they occur earlier in the power-stroke than the nucleotide-free rigor state. This shift also explains the axial lengthening seen upon addition of ligands to rigor fibers. We can conclude that these ligands cause small perturbations in the cross-bridge configuration rather than large shifts. A second conclusion is that cross-bridges do not detach from actin during their power-strokes. Instead they traverse the entire length of the power stroke and are detached only at the end, leading to the suggestion that the cycling of bridges in isometric fibers is due to fluctuations in the relative positions of thick and thin filaments. With some further assumptions, the model also explains many of the rate constants and equilibrium constants of the actin-myosin-ligand interaction that have been measured in solution.     

A new model for growth factor activation: type II receptors compete with the prodomain for BMP-7

Bone morphogenetic proteins (BMPs) are morphogens with long-range signaling activities. BMP-7 is secreted as a stable complex consisting of a growth factor noncovalently associated with two propeptides. In other transforming growth factor-β-like growth factor complexes, the prodomain (pd) confers latency to the complex. However, we detected no difference in signaling capabilities between the growth factor and the BMP-7 complex in multiple in vitro bioactivity assays. Biochemical and biophysical methods elucidated the interaction between the BMP-7 complex and the extracellular domains of its type I and type II receptors. Results showed that type II receptors, such as BMP receptor II, activin receptor IIA, and activin receptor IIB, competed with the pd for binding to the growth factor and displaced the pd from the complex. In contrast, type I receptors interacted with the complex without displacing the pd. These studies suggest a new model for growth factor activation in which proteases or other extracellular molecules are not required and provide a molecular mechanism consistent with a role for BMP receptors in the establishment of early morphogen gradients.     

The bulky and the sweet: How neutralizing antibodies and glycan receptors compete for virus binding

Numerous viruses rely on glycan receptor binding as the initial step in host cell infection. Engagement of specific glycan receptors such as sialylated carbohydrates, glycosaminoglycans, or histo‐blood group antigens can determine host range, tissue tropism, and pathogenicity. Glycan receptor‐binding sites are typically located in exposed regions on viral surfaces—sites that are also generally prone to binding of neutralizing antibodies that directly interfere with virus‐glycan receptor interactions. In this review, we examine the locations and architecture of the glycan‐ and antibody‐binding sites in four different viruses with stalk‐like attachment proteins (reovirus, influenza virus, norovirus, and coronavirus) and investigate the mechanisms by which antibodies block glycan recognition. Those viruses exemplify that direct molecular mimicking of glycan receptors by antibodies is rare and further demonstrate that antibodies often partly overlap or bind sufficiently close to the receptor‐binding region to hinder access to this site, achieving neutralization partially because of the epitope location and partly due to their sheer size.     

The osmotic magnetometer: a new model for magnetite-based magnetoreceptors in animals

Homing pigeons and migratory birds are well known examples for animals that use the geomagnetic field for their orientation. Yet, neither the underlying receptor mechanism nor the magnetoreceptor itself is known. Recently, an innervated structure containing clusters of magnetite nanocrystals was identified in the upper beak skin of the homing pigeon. Here we show theoretically that such a cluster has a magnetic-field-dependent shape, even in fields as weak as the Earth's magnetic field; by converting magnetic stimuli into mechanical strain, the clusters can be assumed as primary units of magnetoperception in homing pigeons. Since the orientation of the strain ellipsoid indicates the direction of the external magnetic field, a cluster of magnetite nanocrystals also has the potential to serve as the basis of the so-called inclination compass of migratory birds. It is quantitatively demonstrated that the magnetic-field-induced shape change of a cluster can be amplified as well as counterbalanced by means of osmotic pressure regulation, which offers an elegant possibility to determine the magnetic field strength just by measuring changes in concentration. Received: 18 May 1998 / Revised version: 11 February 1999 / Accepted: 11 February 1999     

Probing protein fold space with a simplified model

We probe the stability and near-native energy landscape of protein fold space using powerful conformational sampling methods together with simple reduced models and statistical potentials. Fold space is represented by a set of 280 protein domains spanning all topological classes and having a wide range of lengths (33-300 residues) amino acid composition and number of secondary structural elements. The degrees of freedom are taken as the loop torsion angles. This choice preserves the native secondary structure but allows the tertiary structure to change. The proteins are represented by three-point per residue, three-dimensional models with statistical potentials derived from a knowledge-based study of known protein structures. When this space is sampled by a combination of parallel tempering and equi-energy Monte Carlo, we find that the three-point model captures the known stability of protein native structures with stable energy basins that are near-native (all α: 4.77 Å, all β: 2.93 Å, α/β: 3.09 Å, α+β: 4.89 Å on average and within 6 Å for 71.41%, 92.85%, 94.29% and 64.28% for all-α, all-β, α/β and α+β, classes, respectively). Denatured structures also occur and these have interesting structural properties that shed light on the different landscape characteristics of α and β folds. We find that α/β proteins with alternating α and β segments (such as the β-barrel) are more stable than proteins in other fold classes.     

Pollen layering and male–male competition: Quantum dots demonstrate that pollen grains compete for space on pollinators

Premise

Almost nothing is known about what happens to pollen grains once they attach to pollinators, although some have postulated that pollen from different donors may form complex, two- or three-dimensional landscapes (e.g., layers or mosaics) that can facilitate male–male competition. For example, pollen that is already on pollinators may preclude the deposition of subsequent pollen grains.

Methods

Using quantum dots to mark the pollen of individual flowers, we explored the possibilities of layering and preclusion in a fly-pollinated iris, Moraea lurida.

Results and Conclusions

The proportion of labeled pollen from the last flower visited diminished in sequential pollen samples taken from the top to the bottom of the pollen load, representing the first empirical evidence for pollen layering. However, the consequences in terms of pollen preclusion were equivocal: Although the pre-existing pollen load size was not a good predictor of new pollen receipt, labeled pollen loads from the last flower visited were significantly smaller than pollen loads from the previous flower visited. Thus, pollen from the previous flower may preclude pollen placement from a subsequently visited flower, and pollen from different flowers may compete for space on pollinators.

     

HLMethy: a machine learning-based model to identify the hidden labels of m6A candidates

Plant Molecular Biology - PpCBF2 directly binds to the promoters of PpCBF3 and PpCBF4 to activate their expressions and selectively regulates PpDAMs during the leaf bud endodormancy process of...     

Discussion for animal experiments in space: ethical standard and responsibility of researchers for space experiments using laboratory animals.

International efforts to standardize regulations and study designs and to promote the principles of Reduction, Replacement, and Refinement (the 3 Rs) have reduced and refined animal use. In NASA ARC and KSC, researchers are responsible only for activities related directly to the conduct of their animal experiments. The IACUC plays an important role in conformity with NIH policies. Even if researchers design protocols of the space life science in Japan, the animal experiments should be carried out under the global harmonized conditions in accordance with NIH/NASA policies, guides and rules. It is important that researchers himself must look forward the ethical animal experiment.     

Spatial-pattern analysis in a territorial spider: evidence for multi-scale effects

Territorial animals maintain a certain distance to neighbouring conspecifics, presumably leading to a regular spatial pattern through social spacing. Nevertheless, most animal populations are assumed to show aggregation at certain distance ranges, reflecting the scale dependency of spatial patterns. Leucorchestris arenicola (Araneae: Sparassidae) is a burrow-living spider species that shows territorial behaviour against conspecifics. A multi-scale approach in spatial analysis revealed that territory owners had fewer neighbours than expected under spatial randomness at distances up to 6 m. Behavioural field experiments showed that territory owners were able to perceive and react to burrow constructing neighbours up to at least 4 m distance from their own burrow. At larger distances individuals were often more aggregated than expected under spatial randomness. Analysing adult and immature relationships showed attraction between different development stages at small distances and avoidance at larger distances. The analysis reveals diverse spatial patterns in a territorial and cannibalistic species, showing that both behaviour and environment affect pattern development at different distances. The study outlines the importance of multi-scale approaches for spatial analysis and the need for accompanying experiments to facilitate the interpretation of results.     

Stage-dependent predation on competitors: consequences for the outcome of a mosquito invasion

1. Predator-mediated coexistence occurs when predation allows competitors to coexist, due to preferential consumption of a superior competitor relative to an inferior competitor. Differences between the native treehole mosquito ( Aedes triseriatus ) and the co-occurring Asian tiger mosquito ( Aedes albopictus ) in anti-predatory larval behaviours account, in part, for the greater vulnerability of this invasive species to native predatory midge ( Corethrella appendiculata ). We test the hypothesis that stage-dependent differences in the sizes of A. albopictus and A. triseriatus larvae, relative to the size-limited C. appendiculata , contribute to differential consumption and the likelihood of predator-mediated coexistence of these competitors.
2. In all instars, larvae of A. triseriatus were larger than A. albopictus of the same stage. Third and fourth instar C. appendiculata selectively consumed late-stage A. albopictus in preference to same-stage A. triseriatus . Small, early-stage prey larvae did not differ in vulnerability to predation, but large, late-stage larvae differed significantly in vulnerability to predation, probably owing to size-limited predation by fourth instar C. appendiculata. This effect was less pronounced for third instar C. appendiculata .
3. Prey size, in conjunction with anti-predatory behavioural responses, alters the probability of predator-mediated coexistence. A stage-structured predation model showed that equally vulnerable early stages reduce the range of environmental conditions (productivities) in which predator-mediated coexistence is possible, increasing the likelihood of both competitive exclusion of the resident species or failure of the invasive to establish. These results underscore the importance of stage-dependent interspecific differences in predator–prey interactions for determining how predators may affect community composition.     

食果动物传播种子的跟踪技术

研究食果动物传播种子的主要问题之一是难以跟踪种子命运和估计种子域。到目前为止,已有不少方法用于研究食果动物与种子扩散和种子命运的关系,如直接观察法、同位素标记法、金属标记法、磁铁标记法、荧光染料法、微粒体标记法、线标法和遗传技术等。近年来,一些研究将数字编号用于种子标记,并已成为发展的主流。本文综述了以往跟踪种子命运和估计种子域的一些重要方法,并讨论了它们各自的优缺点及其应用。     

Roots in space: a spatially explicit model for below-ground competition in plants

Game theory provides an untapped framework for predicting how below-ground competition will influence root proliferation in a spatially explicit environment. We model root competition for space as an evolutionary game. In response to nutrient competition between plants, an individual's optimal strategy (the spatial distribution of root proliferation) depends on the rooting strategies of neighbouring plants. The model defines and predicts the fundamental (in the absence of competition) and realized (in the presence of competition) root space of an individual plant. Overlapping fundamental root spaces guarantee smaller, yet still overlapping, realized root spaces as individuals concede some but not all space to a neighbour's roots. Root overlap becomes an intentional consequence of the neighbouring plants playing a nutrient foraging game. Root proliferation and regions of root overlap should increase with soil fertility, decline with the distance cost of root production (e.g. soil compactness) and shift with competitive asymmetries. Seemingly erratic patterns of root proliferation and root overlap become the expected outcome of nutrient foraging games played in soils with small-scale heterogeneities in nutrient availability.