Food Selectivity and Diet Switch Can Explain the Slow Feeding of Herbivorous Coral-Reef Fishes during the Morning

Most herbivorous coral-reef fishes feed slower in the morning than in the afternoon. Given the typical scarcity of algae in coral reefs, this behavior seems maladaptive. Here we suggest that the fishes'' slow feeding during the morning is an outcome of highly selective feeding on scarcely found green algae. The rarity of the food requires longer search time and extended swimming tracks, resulting in lower bite rates. According to our findings by noon the fish seem to stop their search and switch to indiscriminative consumption of benthic algae, resulting in apparent higher feeding rates. The abundance of the rare preferable algae gradually declines from morning to noon and seems to reach its lowest levels around the switch time. Using in situ experiments we found that the feeding pattern is flexible, with the fish exhibiting fast feeding rates when presented with ample supply of preferable algae, regardless of the time of day. Analyses of the fish''s esophagus content corroborated our conclusion that their feeding was highly selective in the morning and non-selective in the afternoon. Modeling of the fishes'' behavior predicted that the fish should perform a diel diet shift when the preferred food is relatively rare, a situation common in most coral reefs found in a warm, oligotrophic ocean.     

Type-IV Pilus Deformation Can Explain Retraction Behavior

Polymeric filament like type IV Pilus (TFP) can transfer forces in excess of 100 pN during their retraction before stalling, powering surface translocation(twitching). Single TFP level experiments have shown remarkable nonlinearity in the retraction behavior influenced by the external load as well as levels of PilT molecular motor protein. This includes reversal of motion near stall forces when the concentration of the PilT protein is loweblack significantly. In order to explain this behavior, we analyze the coupling of TFP elasticity and interfacial behavior with PilT kinetics. We model retraction as reaction controlled and elongation as transport controlled process. The reaction rates vary with TFP deformation which is modeled as a compound elastic body consisting of multiple helical strands under axial load. Elongation is controlled by monomer transport which suffer entrapment due to excess PilT in the cell periplasm. Our analysis shows excellent agreement with a host of experimental observations and we present a possible biophysical relevance of model parameters through a mechano-chemical stall force map.     

Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans

Considering the recent experimental discovery of Green et al that present-day non-Africans have 1 to of their nuclear DNA of Neanderthal origin, we propose here a model which is able to quantify the genetic interbreeding between two subpopulations with equal fitness, living in the same geographic region. The model consists of a solvable system of deterministic ordinary differential equations containing as a stochastic ingredient a realization of the neutral Wright-Fisher process. By simulating the stochastic part of the model we are able to apply it to the interbreeding ofthe African ancestors of Eurasians and Middle Eastern Neanderthal subpopulations and estimate the only parameter of the model, which is the number of individuals per generation exchanged between subpopulations. Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability. The results are compatible with a long coexistence time of 130,000 years, a total interbreeding population of order individuals, and with all living humans being descendants of Africans both for mitochondrial DNA and Y chromosome.     

Monitoring Escape and Feeding Behaviours of Cruiser Fish by Inertial and Magnetic Sensors

A method was developed and applied for monitoring two types of fast-start locomotion (feeding and escape) of a cruiser fish, Japanese amberjacks Seriola quinqueradiata. A data logger, which incorporated a 3-axis gyroscope, a 3-axis accelerometer and a 3-axis magnetometer, was attached to the five fish. The escape, feeding and routine movements of the fish, which were triggered in tank experiments, were then recorded by the data logger and video cameras. The locomotor variables, calculated based on the high resolution measurements by the data logger (500 Hz), were investigated to accurately detect and classify the types of fast-track behaviour. The results show that fast-start locomotion can be detected with a high precision (0.97) and recall rate (0.96) from the routine movements. Two types of fast-start movements were classified with high accuracy (0.84). Accuracy was greater if the data were obtained from the data logger, which combined an accelerometer, a gyroscope and a magnetometer, than if only an accelerometer (0.80) or a gyroscope (0.66) was used.     

The Winch Model Can Explain both Coordinated and Uncoordinated Stepping of Cytoplasmic Dynein

Cytoplasmic dynein moves processively along microtubules, but the mechanism of how its heads use the energy from ATP hydrolysis, coupled to a linker swing, to achieve directed motion, is still unclear. In this article, we present a theoretical model based on the winch mechanism in which the principal direction of the linker stroke is toward the microtubule-binding domain. When mechanically coupling two identical heads (each with postulated elastic properties and a minimal ATPase cycle), the model reproduces stepping with 8-nm steps (even though the motor itself is much larger), interhead coordination, and processivity, as reported for mammalian dyneins. Furthermore, when we loosen the elastic connection between the heads, the model still shows processive directional stepping, but it becomes uncoordinated and the stepping pattern shows a greater variability, which reproduces the properties of yeast dyneins. Their slower chemical kinetics allows processive motility and a high stall force without the need for coordination.     

The Winch Model Can Explain both Coordinated and Uncoordinated Stepping of Cytoplasmic Dynein

Cytoplasmic dynein moves processively along microtubules, but the mechanism of how its heads use the energy from ATP hydrolysis, coupled to a linker swing, to achieve directed motion, is still unclear. In this article, we present a theoretical model based on the winch mechanism in which the principal direction of the linker stroke is toward the microtubule-binding domain. When mechanically coupling two identical heads (each with postulated elastic properties and a minimal ATPase cycle), the model reproduces stepping with 8-nm steps (even though the motor itself is much larger), interhead coordination, and processivity, as reported for mammalian dyneins. Furthermore, when we loosen the elastic connection between the heads, the model still shows processive directional stepping, but it becomes uncoordinated and the stepping pattern shows a greater variability, which reproduces the properties of yeast dyneins. Their slower chemical kinetics allows processive motility and a high stall force without the need for coordination.     

The SH2 Domain Interaction Landscape

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Highlights? The recognition specificity of 70 SH2 domains is probed ? Recognition specificity diverges faster than sequence ? PepspotDB is a database of protein interactions mediated by SH2 domains     

Can Individual Differences in History of Dominance Explain the Development of Linear Dominance Hierarchies?

Observed dominance hierarchies are often more linear than expected from randomly-formed dominance relationships, and in triads of animals attacks are distributed non-randomly. I hypothesize that an individual's history of dominance affects its probability of initiating aggressive interactions in the future and that individuals with winning records are more likely to initiate (winning begets initiating). Consistent with this hypothesis, evidence is presented that dominant individuals are more likely to attack than subordinate individuals. The winning begets initiating hypothesis may also explain why correlations between predicted dominance ranks (based on size, age etc.) and observed dominance ranks can be low: If the cost of engaging in and losing an interaction is high relative to the potential benefits of winning, then a large individual conditioned to be subordinate may refrain from contesting smaller, dominant individuals despite its actual competitive superiority.     

Curvature-Sensitive Kinesin Binding Can Explain Microtubule Ring Formation and Reveals Chaotic Dynamics in a Mathematical Model

Microtubules are filamentous tubular protein polymers which are essential for a range of cellular behaviour, and are generally straight over micron length scales. However, in some gliding assays, where microtubules move over a carpet of molecular motors, individual microtubules can also form tight arcs or rings, even in the absence of crosslinking proteins. Understanding this phenomenon may provide important explanations for similar highly curved microtubules which can be found in nerve cells undergoing neurodegeneration. We propose a model for gliding assays where the kinesins moving the microtubules over the surface induce ring formation through differential binding, substantiated by recent findings that a mutant version of the motor protein kinesin applied in solution is able to lock-in microtubule curvature. For certain parameter regimes, our model predicts that both straight and curved microtubules can exist simultaneously as stable steady states, as has been seen experimentally. Additionally, unsteady solutions are found, where a wave of differential binding propagates down the microtubule as it glides across the surface, which can lead to chaotic motion. Whilst this model explains two-dimensional microtubule behaviour in an experimental gliding assay, it has the potential to be adapted to explain pathological curling in nerve cells.     

Heat Loss May Explain Bill Size Differences between Birds Occupying Different Habitats

Background

Research on variation in bill morphology has focused on the role of diet. Bills have other functions, however, including a role in heat and water balance. The role of the bill in heat loss may be particularly important in birds where water is limiting. Song sparrows localized in coastal dunes and salt marsh edge (Melospiza melodia atlantica) are similar in size to, but have bills with a 17% greater surface area than, those that live in mesic habitats (M. m. melodia), a pattern shared with other coastal sparrows. We tested the hypotheses that sparrows can use their bills to dissipate “dry” heat, and that heat loss from the bill is higher in M. m. atlantica than M. m. melodia, which would indicate a role of heat loss and water conservation in selection for bill size.

Methodology/Principal Findings

Bill, tarsus, and body surface temperatures were measured using thermal imaging of sparrows exposed to temperatures from 15–37°C and combined with surface area and physical modeling to estimate the contribution of each body part to total heat loss. Song sparrow bills averaged 5–10°C hotter than ambient. The bill of M. m atlantica dissipated up to 33% more heat and 38% greater proportion of total heat than that of M. m. melodia. This could potentially reduce water loss requirements by approximately 7.7%.

Conclusions/Significance

This >30% higher heat loss in the bill of M. m. atlantica is independent of evaporative water loss and thus could play an important role in the water balance of sparrows occupying the hot and exposed dune/salt marsh environments during the summer. Heat loss capacity and water conservation could play an important role in the selection for bill size differences between bird populations and should be considered along with trophic adaptations when studying variation in bill size.     

赤腹松鼠采食选择的季节性变化

2008年9月至2010年8月,对广西宜州龙江河畔赤腹松鼠采食选择的季节性变化进行分析.赤腹松鼠对榕树的采食量最大,约占总采食量的36.53%,食物采食选择的种类存在显著差异(P<0.05),各季节采食的种类无显著变化(P>0.05);取食偏好分析、食物生态位宽度和重叠度结果表明,夏季的生态位宽度最大,为4.1545,秋季的生态位宽度最小,为3.5001,夏季和秋季的生态位重叠度最大,为0.9882,夏季和冬季的生态位重叠度最小,为0.9343.     

A General Model for Toxin-Antitoxin Module Dynamics Can Explain Persister Cell Formation in E. coli

Toxin-Antitoxin modules are small operons involved in stress response and persister cell formation that encode a “toxin” and its corresponding neutralizing “antitoxin”. Regulation of these modules involves a complex mechanism known as conditional cooperativity, which is supposed to prevent unwanted toxin activation. Here we develop mathematical models for their regulation, based on published molecular and structural data, and parameterized using experimental data for F-plasmid ccdAB, bacteriophage P1 phd/doc and E. coli relBE. We show that the level of free toxin in the cell is mainly controlled through toxin sequestration in toxin-antitoxin complexes of various stoichiometry rather than by gene regulation. If the toxin translation rate exceeds twice the antitoxin translation rate, toxins accumulate in all cells. Conditional cooperativity and increasing the number of binding sites on the operator serves to reduce the metabolic burden of the cell by reducing the total amounts of proteins produced. Combining conditional cooperativity and bridging of antitoxins by toxins when bound to their operator sites allows creation of persister cells through rare, extreme stochastic spikes in the free toxin level. The amplitude of these spikes determines the duration of the persister state. Finally, increases in the antitoxin degradation rate and decreases in the bacterial growth rate cause a rise in the amount of persisters during nutritional stress.     

The Protein Interaction Landscape of the Human CMGC Kinase Group

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Emergence of Collective Territorial Defense in Bacterial Communities: Horizontal Gene Transfer Can Stabilize Microbiomes

Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving a varied metabolic repertoire of the constituent species. In other words horizontal transfer of resistance genes makes a community compatible in terms of exoproducts and capable to maintain a varied and mature metagenome. The same property may allow microbiota to protect a host organism, or if used as a microbial therapy, to purge pathogens and restore a protective environment.     

Bacterial Strains Isolated from Different Niches Can Exhibit Different Patterns of Adhesion to Substrata

Various mechanisms have been demonstrated to be operative in bacterial adhesion to surfaces, but whether bacterial adhesion to surfaces can ever be captured in one generally valid mechanism is open to question. Although many papers in the literature make an attempt to generalize their conclusions, the majority of studies of bacterial adhesion comprise only two or fewer strains. Here we demonstrate that three strains isolated from a medical environment have a decreasing affinity for substrata with increasing surface free energy, whereas three strains from a marine environment have an increasing affinity for substrata with increasing surface free energy. Furthermore, adhesion of the marine strains related positively with substratum elasticity, but such a relation was absent in the strains from the medical environment. This study makes it clear that strains isolated from a given niche, whether medical or marine, utilize different mechanisms in adherence, which hampers the development of a generalized theory for bacterial adhesion to surfaces.     

Organic Farming: Biodiversity Impacts Can Depend on Dispersal Characteristics and Landscape Context

Organic farming, a low intensity system, may offer benefits for a range of taxa, but what affects the extent of those benefits is imperfectly understood. We explored the effects of organic farming and landscape on the activity density and species density of spiders and carabid beetles, using a large sample of paired organic and conventional farms in the UK. Spider activity density and species density were influenced by both farming system and surrounding landscape. Hunting spiders, which tend to have lower dispersal capabilities, had higher activity density, and more species were captured, on organic compared to conventional farms. There was also evidence for an interaction, as the farming system effect was particularly marked in the cropped area before harvest and was more pronounced in complex landscapes (those with little arable land). There was no evidence for any effect of farming system or landscape on web-building spiders (which include the linyphiids, many of which have high dispersal capabilities). For carabid beetles, the farming system effects were inconsistent. Before harvest, higher activity densities were observed in the crops on organic farms compared with conventional farms. After harvest, no difference was detected in the cropped area, but more carabids were captured on conventional compared to organic boundaries. Carabids were more species-dense in complex landscapes, and farming system did not affect this. There was little evidence that non-cropped habitat differences explained the farming system effects for either spiders or carabid beetles. For spiders, the farming system effects in the cropped area were probably largely attributable to differences in crop management; reduced inputs of pesticides (herbicides and insecticides) and fertilisers are possible influences, and there was some evidence for an effect of non-crop plant species richness on hunting spider activity density. The benefits of organic farming may be greatest for taxa with lower dispersal abilities generally. The evidence for interactions among landscape and farming system in their effects on spiders highlights the importance of developing strategies for managing farmland at the landscape-scale for most effective conservation of biodiversity.     

Feeding of Burbot, Lota lota, at Different Temperatures

Daily food intake of adult burbot, Lota lota, fed on vendace, Coregonus albula, were estimated experimentally at four different water temperatures (2.4, 5.1, 10.8 and 23.4°C). Mean daily food intake (MDI; g d^–1) and relative daily food intake (RDI; g g^–1 d^–1) increased with temperature from 2.4 to 10.8°C and decreased at 23.4°C. Temperatures of maximum daily food intake values were 13.6°C for MDI and 14.4°C for RDI. No correlation between food intake values and burbot weight was observed. RDI values were used to estimate annual food consumption of burbot population. Annual food consumption estimates were 9.7kg ha^–1 and 24.3kg ha^–1 when burbot biomass was 2.0 or 5.0kg ha^–1, respectively.