Modeling the effects of enclosure size on geometry learning

Several recent studies have shown that chickens, fish, and humans trained to find a reward in a corner of a rectangular enclosure with distinctive features rely more on the geometry of the enclosure in small enclosures and rely more on the features in large enclosures. Here, these results are modeled using a recent associative model of geometry learning [Miller, N.Y., Shettleworth, S.J., 2007. Learning about environmental geometry: an associative model. J. Exp. Psychol. Anim. B 33, 191–212]. By adjusting the salience of either geometric or featural information or both the model is capable of reproducing much of the data on the effects of enclosure size on geometry learning.     

Modeling the effects of musculoskeletal geometry on scapulohumeral muscle moment arms and lines of action

Abstract

Biomechanical investigations examining shoulder function commonly observe a high degree of inter-individual variability in muscle activity and kinematic patterns during static and dynamic upper extremity exertions. Substantial differences in musculoskeletal geometry between individuals can alter muscle moment arms and lines of action that, theoretically, alter muscle activity and shoulder kinematics. The purposes of this research were to: (i) quantify model-predicted functional roles (moment arms, lines of action) of the scapulohumeral muscles, (ii) compare model predictions to experimental data in the literature, and (iii) evaluate sensitivity of muscle functional roles due to changes in muscle attachment locations using probabilistic modeling. Monte Carlo simulations were performed to iteratively adjust muscle attachment locations at the clavicle, scapula, and humerus of the Delft Shoulder and Elbow Model in OpenSim. Muscle moment arms and lines of action were quantified throughout arm elevation in the scapular plane. In general, model-predicted moment arms agreed well with the reviewed literature; however, notable inconsistencies were observed when comparing lines of action. Variability in moment arms and lines of action were muscle-specific, with 2 standard deviations in moment arm and line of actions as high as 25.8?mm and 18.8° for some muscles, respectively. Moment arms were particularly sensitive to changes in attachment site closest to the joint centre. Variations in muscle functional roles due to differences in musculoskeletal geometry are expected to require different muscle activity and movement patterns for upper extremity exertions.     

Indentation testing of human articular cartilage: effects of probe tip geometry and indentation depth on intra-tissue strain

Experimental determination of intra-tissue deformation during clinically applicable rapid indentation testing would be useful for understanding indentation biomechanics and for designing safe indentation probes and protocols. The objectives of this study were to perform two-dimensional (2-D) indentation tests, using indenters and protocols that are analogous to those in clinically oriented probes, of normal adult-human articular cartilage in order to determine: (1) intra-tissue strain maps and regions of high strain magnitude, and (2) the effects on strain of indenter geometry (rectangular prismatic and cylindrical) and indentation depth (40-190 microm). Epifluorescence microscopy of samples undergoing indentation and subsequent video image correlation analysis allowed determination of strain maps. Regions of peak strain were near the "edges" of indenter contact with the cartilage surface, and the strain magnitude in these regions ranged from approximately 0.05 to approximately 0.30 in compression and shear, a range with known biological consequences. With increasing indentation displacement, strain magnitudes generally increased in all regions of the tissue. Compared to indentation using a rectangular prismatic tip, indentation with a cylindrical tip resulted in slightly higher peak strain magnitudes while influencing a smaller region of cartilage. These results may be used to refine clinical indenters and indentation protocols.     

Temperature and water content effects on the viscoelastic behavior of<Emphasis Type="Italic"> Tilia americana</Emphasis> (Tiliaceae) sapwood

The effects of temperature and water content on the viscoelasticity of living and dehydrated Tilia americana sapwood were examined using transient creep (time- and load-dependent deformation) tests under sustained bending loads. Creep tests were performed at 21.1°C and –20.5°C to determine the magnitudes and types of strains in living and dehydrated samples. Temperature had no effect on the creep rate of living sapwood. However, the creep rate of dehydrated samples at –20.5°C was significantly faster than that at 21.1°C. Regardless of temperature, sapwood had a faster creep rate than dehydrated samples. With small bending loads, the residual strains in sapwood were larger at 21.1°C compared to –20.5°C. Temperature did not significantly affect the residual strains in dehydrated samples. For small bending loads, frozen sapwood recovered all residual creep strains when thawed. With larger loads, residual and plastic (permanent) strains increased. We speculate that ice formation in cell lumens partially dehydrates (and thus stiffens and strengthens) cell wall materials and prevents cell wall buckling and elastic restoration after unloading. However, when thawed, sapwood can elastically restore its original configuration, provided it is not excessively bent (by ice or snow accumulations) when frozen.     

The combined effects of temporal autocorrelation and the costs of plasticity on the evolution of plasticity

Adaptive phenotypic plasticity is an important source of intraspecific variation, and for many plastic traits, the costs or factors limiting plasticity seem cryptic. However, there are several different factors that may constrain the evolution of plasticity, but few models have considered costs and limiting factors simultaneously. Here we use a simulation model to investigate how the optimal level of plasticity in a population depends on a fixed maintenance fitness cost for plasticity or an incremental fitness cost for producing a plastic response in combination with environmental unpredictability (environmental fluctuation speed) limiting plasticity. Our model identifies two mechanisms that act, almost separately, to constrain the evolution of plasticity: (i) the fitness cost of plasticity scaled by the nonplastic environmental tolerance, and (ii) the environmental fluctuation speed scaled by the rate of phenotypic change. That is, the evolution of plasticity is constrained by the high cost of plasticity in combination with high tolerance for environmental variation, or fast environmental changes in combination with slow plastic response. Qualitatively similar results are found when maintenance and incremental fitness costs of plasticity are incorporated, although a larger degree of plasticity is selected for with an incremental cost. Our model highlights that it is important to consider direct fitness costs and phenotypic limitations in relation to nonplastic environmental tolerance and environmental fluctuations, respectively, to understand what constrains the evolution of phenotypic plasticity.     

The role of particles on the biogeochemical cycling of domoic acid and its isomers in natural water matrices

The adsorption of dissolved domoic acid (DA) and its geometrical isomers was assessed in aqueous solutions containing various types of particles. In one series of experiments carried out in coastal seawater, detectable net adsorption of 100 nM DA occurred only onto natural seawater particles (unfiltered seawater) and 0.5 g L⁻¹ chromatographic silica (18%) in 0.2 μm-filtered seawater. Some net adsorption (<5%) also occurred in the 0.5 g L⁻¹ suspension of estuarine sediment and 0.5 g L⁻¹ solution of humic acid in filtered seawater. No losses were seen in 0.5 g L⁻¹ suspensions of illite, kaolinite, montmorillonite, and silica sand. Biological degradation accounted for small losses (8–10%) in filtered seawater without particles. A second series of experiments using organic-free, <5 μm fractions of kaolinite and montmorillonite in deionized water (DIW) demonstrated that 70% of DA adsorbed onto kaolinite, but only 5% onto montmorillonite. Geometrical isomers of DA (iso-DA D, E, and F) showed negligible adsorption (0–8%) onto a variety of particles in filtered seawater, suggesting that major ions in seawater neutralize electrostatic attractions between particles and DA isomers. These results suggest that DA and its isomers are relatively hydrophilic and not particle reactive. Our data suggest that photochemical and biological degradation of dissolved DA and its isomers appears to occur in bulk surface seawater and its transport to bottom sediments must be mainly biologically driven.     

Derivation of the Stress-Strain Behavior of the constituents of Bio-Inspired Layered TiO₂/PE-Nanocomposites by Inverse Modeling Based on FE-Simulations of Nanoindentation Test

Owing to the apparent simple morphology and peculiar properties, nacre, an iridescent layer, coating of the inner part of mollusk shells, has attracted considerable attention of biologists, material scientists and engineers. The basic structural motif in nacre is the assembly of oriented plate-like aragonite crystals with a ’brick’ (CaCO₃ crystals) and ’mortar’ (macromolecular components like proteins) organization. Many scientific researchers recognize that such structures are associated with the excellent mechanical properties of nacre and biomimetic strategies have been proposed to produce new layered nanocomposites. During the past years, increasing efforts have been devoted towards exploiting nacre’s structural design principle in the synthesis of novel nanocomposites. However, the direct transfer of nacre’s architecture to an artificial inorganic material has not been achieved yet. In the present contribution we report on laminated architecture, composed of the inorganic oxide (TiO₂) and organic polyelectrolyte (PE) layers which fulfill this task.
To get a better insight and understanding concerning the mechanical behaviour of bio-inspired layered materials consisting of oxide ceramics and organic layers, the elastic-plastic properties of titanium dioxide and organic polyelectrolyte phase are determined via FE-modelling of the nanoindentation process. With the use of inverse modeling and based on numerical models which are applied on the microscopic scale, the material properties of the constituents are derived.     

Comparing the effects of rapid evolution and phenotypic plasticity on predator-prey dynamics

Ecologists have increasingly focused on how rapid adaptive trait changes can affect population dynamics. Rapid adaptation can result from either rapid evolution or phenotypic plasticity, but their effects on population dynamics are seldom compared directly. Here we examine theoretically the effects of rapid evolution and phenotypic plasticity of antipredatory defense on predator-prey dynamics. Our analyses reveal that phenotypic plasticity tends to stabilize population dynamics more strongly than rapid evolution. It is therefore important to know the mechanism by which phenotypic variation is generated for predicting the dynamics of rapidly adapting populations. We next examine an advantage of a phenotypically plastic prey genotype over the polymorphism of specialist prey genotypes. Numerical analyses reveal that the plastic genotype, if there is a small cost for maintaining it, cannot coexist with the pairs of specialist counterparts unless the system has a limit cycle. Furthermore, for the plastic genotype to replace specialist genotypes, a forced environmental fluctuation is critical in a broad parameter range. When these results are combined, the plastic genotype enjoys an advantage with population oscillations, but plasticity tends to lose its advantage by stabilizing the oscillations. This dilemma leads to an interesting intermittent limit cycle with the changing frequency of phenotypic plasticity.     

Developmental plasticity and maternal effects of reproductive characteristics in the frog,Bombina orientalis

Summary Life history theory suggests that reproductive characteristics such as ovum size and clutch size should be well buffered against vararies of the environment. However, studies which demonstrate environmental sensitivity of reproductive characteristics are increasing in number, as are studies which find that maternal effects are responsible for much of the variation in developmental and growth rates in embryonic and larval fish and amphibians. The data reported here demonstrate that the environment, in terms of temperature and food availability that a specific individual encounters during vitellogenesis, exerts a strong influence on both egg size and number. Warmer temperatures and less food decrease ovum size, while colder temperatures and less food decrease clutch size. The variation in ovum size that is induced by the environment can exert a strong influence on variation in offspring development and growth and serve as an excellent model for studies on the evolution of developmental plasticity.     

Genetic Allee effects on performance, plasticity and developmental stability in a clonal plant

Negative effects of small population size on fitness, so-called Allee effects, may threaten population persistence even in intact habitat remnants. We studied genotypes of 14 isolated populations of the clonal plant Ranunculus reptans, for which molecular genetic (RAPD-) variability is higher for large than for small populations. In a competition-free greenhouse environment vegetative offspring of genotypes from large populations produced more rosettes and flowers, indicating higher fitness. Within-genotype coefficients of variation in performance traits, indicating developmental instability, were lower for genotypes from populations with higher RAPD-variability. In competition with a taller grass, we found relative reduction in leaf length less pronounced for plants from large populations, suggesting higher adaptive plasticity. Our experimental study of a plant with predominantly vegetative reproduction suggests, that negative genetic effects of recent habitat fragmentation, which so far rather were expected in plants with frequent sexual reproduction, are more severe and more common than previously acknowledged.     

Modifying effects of phenotypic plasticity on interactions among natural selection, adaptation and gene flow

Divergent natural selection, adaptive divergence and gene flow may interact in a number of ways. Recent studies have focused on the balance between selection and gene flow in natural populations, and empirical work has shown that gene flow can constrain adaptive divergence, and that divergent selection can constrain gene flow. A caveat is that phenotypic diversification may be under the direct influence of environmental factors (i.e. it may be due to phenotypic plasticity), in addition to partial genetic influence. In this case, phenotypic divergence may occur between populations despite high gene flow that imposes a constraint on genetic divergence. Plasticity may dampen the effects of natural selection by allowing individuals to rapidly adapt phenotypically to new conditions, thus slowing adaptive genetic divergence. On the other hand, plasticity may promote future adaptive divergence by allowing populations to persist in novel environments. Plasticity may promote gene flow between selective regimes by allowing dispersers to adapt to alternate conditions, or high gene flow may result in the selection for increased plasticity. Here I expand frameworks for understanding relationships among selection, adaptation and gene flow to include the effects of phenotypic plasticity in natural populations, and highlight its importance in evolutionary diversification.     

Age-dependent effects of chronic stress on brain plasticity and depressive behavior

Exposure to chronic mild stress (CMS) is known to induce anhedonia in adult animals, and is associated with induction of depression in humans. However, the behavioral effects of CMS in young animals have not yet been characterized, and little is known about the long-term neurochemical effects of CMS in either young or adult animals. Here, we found that CMS induces anhedonia in adult but not in young animals, as measured by a set of behavioral paradigms. Furthermore, while CMS decreased neurogenesis and levels of brain-derived neurotrophic factor (BDNF) in the hippocampus of adult animals, it increased these parameters in young animals. We also found that CMS altered alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA) receptor GluR1 subunit levels in the hippocampus and the nucleus accumbens of adult, but not young animals. Finally, no significant differences were observed between the effects of CMS on circadian corticosterone levels in the different age groups. The substantially different neurochemical effects chronic stress exerts in young and adult animals may explain the behavioral resilience to such stress young animals possess.     

Inhibitory effects of caffeine on gustatory plasticity in the nematode Caenorhabditis elegans

The effects of caffeine on salt chemotaxis learning were investigated using the nematode Caenorhabditis elegans. To estimate the degree of salt chemotaxis learning, nematodes were placed in a mixed solution of NaCl and caffeine, and then the chemotaxis index of NaCl was obtained from the nematodes placed on agar medium after pre-exposure to caffeine concentrations of 0.01, 0.1, 0.3, and 1.0%. Locomotor activity and preference behavior for caffeine were also estimated under these caffeine conditions. Nematodes pre-exposed to 0.3% caffeine showed inhibition of salt chemotaxis learning. Additional experiments indicated that nematodes showed a preference response to the middle concentration of caffeine (0.1%), with preference behavior declining in the 0.3% caffeine condition. Stable locomotor activity was observed under 0.01–0.3% caffeine conditions. These results suggest that salt chemotaxis learning with 0.3% caffeine is useful for investigating the effects of caffeine on learning in nematodes.     

Anion- and pH-linked effects on the heme-iron geometry in ferrous nitrosylated monomeric myoglobins

 The cooperative effect of anions and proton concentration on the EPR spectroscopic properties of the ferrous nitrosylated derivative of monomeric Mb from loggerhead sea turtle (Caretta caretta), sperm whale (Physeter catodon), and horse (Caballus caballus) has been investigated between pH 4.5 and 9.0, at 100 K. In the absence of anions, an EPR spectrum characteristic of the hexa-coordinated species of ferrous nitrosylated Mb with an axial geometry is observed, which is unaffected by pH. On the other hand, a transition toward a species characterized by an EPR spectrum corresponding to a hexa-coordinated rhombic geometry takes place in the presence of phosphate, acetate, citrate, sulfate, and chloride. Only the hexa-coordinated form characterized by the rhombic EPR spectrum appears then to undergo a pH-dependent transition toward the penta-coordinated species. Present results show clear-cut evidence for the spectroscopic coupling of proton and anion binding sites with the Mb reactive center, indicating that an allosteric mechanism might modulate the proximal HisF8-heme-NO geometry in monomeric hemoproteins. Received: 15 December 1997 / Accepted: 15 June 1998     

Collagen fiber orientation and geometry effects on the mechanical properties of secondary osteons.

The effects of collagen fiber orientation and osteon geometry on the mechanical properties of secondary osteons under axial compression/tension and combined loadings (compression, bending and torsion) were investigated using a composite-beam finite-element model. Three cross-sectional shapes of secondary osteons were studied to show the effect of geometry. The results of stiffness are presented using the tension and compression properties for each lamella. The model shows that the mechanical properties of osteons are enhanced in bending and torsion when collagen fibers are oriented within 30 degrees of the loading axis. Osteons with alternating lamellar orientation are not well adapted to resist torsional moments, but alternate collagen fiber orientation has virtually no effect on the bending stiffness of osteons. Fiber orientation affects the mechanical properties less significantly when osteons are non-circular. Collagen fiber orientation and osteon geometry interact to determine the mechanical behavior of the osteon, and may act in a compensatory manner in the adaptive process.     

The effects of various soils,different provenances and air pollution on root tip chromosomes in Norway spruce

The classification of chromosomal aberrations was used to characterize different factors affecting chromosomes in the root meristem of Norway spruce [Picea abies (L.) Karst.] trees. It is important to know the most significant factor affecting the chromosomes in the root meristem of plants at natural sites. The results suggest that an intensive site effect is more significant than the soil or the provenance of the individual. This cytogenetic plant test system was also used to investigate 5-year-old spruce trees exposed in environmental chambers to elevated concentrations of carbon dioxide (750 cm³m^–3) and ozone (0.08 cm³m^–3) as single variables or in combination, and then transferred to a field for observation of a memory effect. The fumigated variants showed an increased number of chromosomal aberrations compared to the controls, which carried on as a memory effect in the root meristems far beyond the fumigation period.     

Soil-derived organic particles and their effects on the community of culturable microorganisms

Soil microbial community interacts with a range of particulate material in the soil, consisting of both inorganic and organic compounds with different levels of water solubility. Though sparingly water-soluble and insoluble organic compounds in the soil may affect living organisms, they are difficult to introduce into microbiological media. Their biological activity (i.e., their effect on soil microorganisms) thus has been almost neglected in most of the cultivation assays. To fill this gap, we propose the use of fine organic particles prepared from soil organic matter that are introduced into a laboratory medium where microbial community is cultivated. To this purpose, submicrometer particles consisting of sparingly water-soluble or insoluble soil organic matter were obtained from humic horizons of two soils by precipitation of organics dissolved in tetrahydrofuran by addition of water. The particles could then be size fractionated by centrifugation, and coarse fraction obtained from humic horizon formed under spruce forest was tested for effects on complex microbial community developing under laboratory conditions. The results indicate that low concentration (20 mg/L) of the particles is efficient to affect the composition of the bacterial community revealed by terminal restriction fragment length polymorphism. The work contributes to understanding the factors that determine the composition of soil microbial community.