Emergent and effective properties in ecology and evolution

Emergent properties are often discussed in arguments concerning relationships among different levels. However, the different definitions of emergent properties sometimes confuse the arguments about macro-level phenomena, since some authors regard emergent properties not only as observable global patterns but as properties that affect and cause change in ecological and evolutionary processes. Thus it is important to distinguish higher-level or larger-scale properties that can influence particular ecological and evolutionary processes from those that cannot. I call the former properties effective properties. I gave examples that show why the distinctions between effective and non-effective properties are important.

     

Statistical analysis of the physical properties of the 20 naturally occurring amino acids

In order to describe the conformational and other physical properties of the 20 naturally occurring amino acid residues with a minimum number of parameters, several multivariate statistical analyses were applied to 188 of their physical properties and ten orthogonal properties (factors) were obtained for the 20 amino acids without losing the information contained in the original physical properties. The analysis consisted of three main steps. First, 72 of the physical properties were eliminated from further consideration because they did not pass statistical tests that they follow a normal distribution. Second, the remaining 116 physical properties of the amino acids were classified by a cluster analysis to eliminate duplications of highly correlated physical properties. This led to nine clusters, each of which was characterized by an average characteristic property, namely bulk, two hydrophobicity indices for free amino acids, one hydrophobicity index for amino acid residues in a protein, two types of -structure preference, -helix preference, and two types of bend-structure preference. The physical properties within a given cluster were highly correlated with each other, but the correlation between clusters was low. Third, a factor analysis was applied to the nine average classified properties and 16 additional physical properties to obtain a small number of orthogonal properties (ten factors). Four of these factors arise from the nine characteristic properties, and the remaining six factors were obtained from the 16 physical properties not included in the nine characteristic properties. Finally, most of the 188 physical properties could be expressed as a sum of these ten orthogonal factors, with appropriate weighting factors. Since these factors contain information relating almost all properties of all 20 amino acids, it is possible to estimate the numerical values of a property for one or two amino acids for which experimental data for this property are not available. For example, the estimated values for the Zimm-Bragg parameters at 20°C are 0.66 and 0.92 for proline and cysteine, respectively, computed from the first four factors.     

Functional finishing of health care cotton for enhanced efficiency of antibacterial activity by chitosan and herbal nanocomposites

To enhance the efficiency of biological, chemical and physical properties like antibacterial activity, wash durability, air-permeability and biocompatibility of cotton fabric finished with chitosan and herbal nanocomposites. Extracts of Cassia angustifolia and Tamarindus indica with chitosan solution was bulk finished on 40s cotton fabrics. To increase the functional properties, chitosan and herbal extract nanocomposites were finished on to another set of fabrics (nanocomposite finishing). Different functional properties were carried out for both the sets of fabrics and comparatively analyzed. Antibacterial activity, physical properties and biocompatible properties of the finished fabric were determined. Antibacterial activity of nanocomposite finished fabrics showed inhibitory zones of 33 mm for E. coli and 31.6 mm for S. aureus. Nanocomposite finished fabrics showed good durable properties and physical properties than bulk finished fabrics. The study concludes that, nanocomposites could provide better functional properties than the bulk finished fabrics. The nano sized particles in the composites was considered significant for its functional applications in hospital based fabrics to prevent the transmission of nosocomial infections.     

Enzymology in vivo using NMR and molecular genetics

Models of metabolic flux regulation are frequently based on an extrapolation of the kinetic properties of enzymes measured in vitro to the intact cell. Such an extrapolation assumes a detailed knowledge of the intracellular environment of these enzymes in terms of their free substates and effectors concentrations and possible interaction with other cellular macromolecules, which may modify their kinetic properties. These is a considerable incentive, therefore, to study the properties of enzymes directly in vivo. We have been using non-invasive NMR techniques, in conjunction with molecular genetic manipulation of enzyme levels, to study the kinetic properties of individual enzymes in vivo. We have also developed a novel strategy which has allowed us to monitor, by NMR, the ligand binding properties and mobilities of enzymes in the intact cell. This technique may also allow us to measured the diffusion coefficients of these proteins in the cell. These studies should give new insight into the properties of enzymes in vivo     

Evolutionary rate heterogeneity between multi- and single-interface hubs across human housekeeping and tissue-specific protein interaction network: Insights from proteins' and its partners' properties

Integrating gene expression into protein-protein interaction network (PPIN) leads to the construction of tissue-specific (TS) and housekeeping (HK) sub-networks, with distinctive TS- and HK-hubs. All such hub proteins are divided into multi-interface (MI) hubs and single-interface (SI) hubs, where MI hubs evolve slower than SI hubs. Here we explored the evolutionary rate difference between MI and SI proteins within TS- and HK-PPIN and observed that this difference is present only in TS, but not in HK-class. Next, we explored whether proteins' own properties or its partners' properties are more influential in such evolutionary discrepancy. Statistical analyses revealed that this evolutionary rate correlates negatively with protein's own properties like expression level, miRNA count, conformational diversity and functional properties and with its partners' properties like protein disorder and tissue expression similarity. Moreover, partial correlation and regression analysis revealed that both proteins' and its partners' properties have independent effects on protein evolutionary rate.     

A correlation between concanavalin A resistance and specific alterations in growth and surface membrane-associated properties.

Mammalian cells selected for resistance to concanavalin A (ConA) cytotoxicity exhibit modifications in some fundamental cellular properties. Three independently isolated ConA-resistant hamster cell lines exhibit a complex phenotype which includes: obvious temperature-sensitive growth properties; altered cellular morphology on solid surfaces; enhanced sensitivity to membrane-active agents such as phenethyl alcohol and sodium butyrate; altered lectin agglutination properties; modified adhesiveness to substratum properties; and defective lectin-receptor mobility characteristics. Selection of a reverant cell line which showed a near wild-type sensitivity to the cytotoxic effects of ConA also showed growth and membrane-associated properties that were very similar to parental wild-type cells. Somatic cell hybrids formed through the fusion of wild-type and lectin-resistant cells exhibited the ConA-sensitive phenotype, and possessed growth and membrane-associated properties that were very similar to pseudodiploid wild-type cells and control cultures of pseudotetraploid hybrid cells. The results presented in this communication support the view that ConA is an excellent selective agent for obtaining mammalian cells with altered growth and surface membrane properties and provides convincing evidence that the altered cellular properties exhibited by the lectin-resistant cell lines are directly related to ConA resistance.     

Child-Report Measures of Occupational Performance: A Systematic Review

Introduction

Improving occupational performance is a key service of occupational therapists and client-centred approach to care is central to clinical practice. As such it is important to comprehensively evaluate the quality of psychometric properties reported across measures of occupational performance; in order to guide assessment and treatment planning.

Objective

To systematically review the literature on the psychometric properties of child-report measures of occupational performance for children ages 2–18 years.

Methods

A systematic search of the following six electronic databases was conducted: CINAHL; PsycINFO; EMBASE; PubMed; the Health and Psychosocial Instruments (HAPI) database; and Google Scholar. The quality of the studies was evaluated against the COSMIN taxonomy of measurement properties and the overall quality of psychometric properties was evaluated using pre-set psychometric criteria.

Results

Fifteen articles and one manual were reviewed to assess the psychometric properties of the six measures–the PEGS, MMD, CAPE, PAC, COSA, and OSA- which met the inclusion criteria. Most of the measures had conducted good quality studies to evaluate the psychometric properties of measures (PEGS, CAPE, PAC, OSA); however, the quality of the studies for two of these measures was relatively weak (MMD, COSA). When integrating the quality of the psychometric properties of the measures with the quality of the studies, the PAC stood out as having superior psychometric qualities.

Conclusions

The overall quality of the psychometric properties of most measures was limited. There is a need for continuing research into the psychometric properties of child-report measures of occupational performance, and to revise and improve the psychometric properties of existing measures.     

Dilemma of Dilemmas: How Collective and Individual Perspectives Can Clarify the Size Dilemma in Voluntary Linear Public Goods Dilemmas

Empirical findings on public goods dilemmas indicate an unresolved dilemma: that increasing size—the number of people in the dilemma—sometimes increases, decreases, or does not influence cooperation. We clarify this dilemma by first classifying public goods dilemma properties that specify individual outcomes as individual properties (e.g., Marginal Per Capita Return) and group outcomes as group properties (e.g., public good multiplier), mathematically showing how only one set of properties can remain constant as the dilemma size increases. Underpinning decision-making regarding individual and group properties, we propose that individuals are motivated by both individual and group preferences based on a theory of collective rationality. We use Van Lange''s integrated model of social value orientations to operationalize these preferences as an amalgamation of outcomes for self, outcomes for others, and equality of outcomes. Based on this model, we then predict how the public good''s benefit and size, combined with controlling individual versus group properties, produce different levels of cooperation in public goods dilemmas. A two (low vs. high benefit) by three (2-person baseline vs. 5-person holding constant individual properties vs. 5-person holding constant group properties) factorial experiment (group n = 99; participant n = 390) confirms our hypotheses. The results indicate that when holding constant group properties, size decreases cooperation. Yet when holding constant individual properties, size increases cooperation when benefit is low and does not affect cooperation when benefit is high. Using agent-based simulations of individual and group preferences vis-à-vis the integrative model, we fit a weighted simulation model to the empirical data. This fitted model is sufficient to reproduce the empirical results, but only when both individual (self-interest) and group (other-interest and equality) preference are included. Our research contributes to understanding how people''s motivations and behaviors within public goods dilemmas interact with the properties of the dilemma to lead to collective outcomes.     

Volatile anesthetics inhibit sodium channels without altering bulk lipid bilayer properties

Although general anesthetics are clinically important and widely used, their molecular mechanisms of action remain poorly understood. Volatile anesthetics such as isoflurane (ISO) are thought to alter neuronal function by depressing excitatory and facilitating inhibitory neurotransmission through direct interactions with specific protein targets, including voltage-gated sodium channels (Na_v). Many anesthetics alter lipid bilayer properties, suggesting that ion channel function might also be altered indirectly through effects on the lipid bilayer. We compared the effects of ISO and of a series of fluorobenzene (FB) model volatile anesthetics on Na_v function and lipid bilayer properties. We examined the effects of these agents on Na_v in neuronal cells using whole-cell electrophysiology, and on lipid bilayer properties using a gramicidin-based fluorescence assay, which is a functional assay for detecting changes in lipid bilayer properties sensed by a bilayer-spanning ion channel. At clinically relevant concentrations (defined by the minimum alveolar concentration), both the FBs and ISO produced prepulse-dependent inhibition of Na_v and shifted the voltage dependence of inactivation toward more hyperpolarized potentials without affecting lipid bilayer properties, as sensed by gramicidin channels. Only at supra-anesthetic (toxic) concentrations did ISO alter lipid bilayer properties. These results suggest that clinically relevant concentrations of volatile anesthetics alter Na_v function through direct interactions with the channel protein with little, if any, contribution from changes in bulk lipid bilayer properties. Our findings further suggest that changes in lipid bilayer properties are not involved in clinical anesthesia.     

Six months of disuse during hibernation does not increase intracortical porosity or decrease cortical bone geometry,strength, or mineralization in black bear (Ursus americanus) femurs

Disuse typically uncouples bone formation from resorption, leading to bone loss which compromises bone mechanical properties and increases the risk of bone fracture. Previous studies suggest that bears can prevent bone loss during long periods of disuse (hibernation), but small sample sizes have limited the conclusions that can be drawn regarding the effects of hibernation on bone structure and strength in bears. Here we quantified the effects of hibernation on structural, mineral, and mechanical properties of black bear (Ursus americanus) cortical bone by studying femurs from large groups of male and female bears (with wide age ranges) killed during pre-hibernation (fall) and post-hibernation (spring) periods. Bone properties that are affected by body mass (e.g. bone geometrical properties) tended to be larger in male compared to female bears. There were no differences (p>0.226) in bone structure, mineral content, or mechanical properties between fall and spring bears. Bone geometrical properties differed by less than 5% and bone mechanical properties differed by less than 10% between fall and spring bears. Porosity (fall: 5.5±2.2%; spring: 4.8±1.6%) and ash fraction (fall: 0.694±0.011; spring: 0.696±0.010) also showed no change (p>0.304) between seasons. Statistical power was high (>72%) for these analyses. Furthermore, bone geometrical properties and ash fraction (a measure of mineral content) increased with age and porosity decreased with age. These results support the idea that bears possess a biological mechanism to prevent disuse and age-related osteoporoses.     

Mechanical properties of spider dragline silk: humidity, hysteresis, and relaxation

Spider silk is well-known for its outstanding mechanical properties. However, there is a significant variation of these properties in literature and studies analyzing large numbers of silk samples to explain these variations are still lacking. To fill this gap, the following work examines the mechanical properties of major ampullate silk based on a large ensemble of threads from Nephila clavipes and Nephila senegalensis. In addition, the effect of relative humidity (RH) on the mechanical properties was quantified. The large effect of RH on the mechanical properties makes it plausible that the variation in the literature values can to a large extent be attributed to changes in RH. Spider silk’s most remarkable property—its high tenacity—remains unchanged. In addition, this work also includes hysteresis as well as relaxation measurements. It is found that the relaxation process is well described by a stretched exponential decay.     

Non-destructive assessment of human ribs mechanical properties using quantitative ultrasound

Advanced finite element models of the thorax have been developed to study, for example, the effects of car crashes. While there is a need for material properties to parameterize such models, specific properties are largely missing. Non-destructive techniques applicable in vivo would, therefore, be of interest to support further development of thorax models. The only non-destructive technique available today to derive rib bone properties would be based on quantitative computed tomography that measures bone mineral density. However, this approach is limited by the radiation dose. Bidirectional ultrasound axial transmission was developed on long bones ex vivo and used to assess in vivo health status of the radius. However, it is currently unknown if the ribs are good candidates for such a measurement. Therefore, the goal of this study is to evaluate the relationship between ex vivo ultrasonic measurements (axial transmission) and the mechanical properties of human ribs to determine if the mechanical properties of the ribs can be quantified non-destructively. The results show statistically significant relationships between the ultrasonic measurements and mechanical properties of the ribs. These results are promising with respect to a non-destructive and non-ionizing assessment of rib mechanical properties.     

Relationships between Perceptual Attributes and Rheology in Over-the-Counter Vaginal Products: A Potential Tool for Microbicide Development

Vaginal microbicides are believed to have substantial potential to empower women to protect themselves from HIV, although clinical trials to date have had mixed results at best. Issues with patient adherence in these trials suggest additional emphasis should be placed on optimizing acceptability. Acceptability is driven, in part, by the sensory properties of the microbicide, so better understanding of the relationships between sensory properties and the physical and rheological properties of microbicides should facilitate the simultaneous optimization of sensory properties in parallel with the biophysical properties required for drug deployment. Recently, we have applied standard methods to assess the potential acceptability of microbicide prototypes ex vivo and to quantify the sensory properties of microbicide surrogates. Here, we link quantitative perceptual data to the rheological properties of 6 over-the counter (OTC) vaginal products used as ex vivo microbicide surrogates. Shear-thinning behavior (n) and tan δ (10 rad/s) showed no relationship with any perceptual attributes while shear storage modulus, G’ (10 rad/s) was correlated with some attributes, but did not appear to be a strong predictor of sensory properties. Conversely, the storage loss modulus, G” (10 rad/s) and the consistency coefficient, K, were correlated with several sensory attributes: stickiness, rubberiness, and uniform thickness for G’’ and stickiness, rubberiness, and peaking for K. Although these relationships merit confirmation in later studies, this pilot study suggests rheological principles can be used to understand the sensory properties evoked by microbicide surrogates assessed ex vivo. Additional work is needed to determine if these findings would apply for microbicides in vivo.     

Classification of drugs based on properties of sodium channel inhibition: a comparative automated patch-clamp study

Background

There is only one established drug binding site on sodium channels. However, drug binding of sodium channels shows extreme promiscuity: ∼25% of investigated drugs have been found to potently inhibit sodium channels. The structural diversity of these molecules suggests that they may not share the binding site, and/or the mode of action. Our goal was to attempt classification of sodium channel inhibitors by measuring multiple properties of inhibition in electrophysiology experiments. We also aimed to investigate if different properties of inhibition correlate with specific chemical properties of the compounds.

Methodology/Principal Findings

A comparative electrophysiological study of 35 compounds, including classic sodium channel inhibitors (anticonvulsants, antiarrhythmics and local anesthetics), as well as antidepressants, antipsychotics and neuroprotective agents, was carried out using rNav1.2 expressing HEK-293 cells and the QPatch automatic patch-clamp instrument. In the multi-dimensional space defined by the eight properties of inhibition (resting and inactivated affinity, potency, reversibility, time constants of onset and offset, use-dependence and state-dependence), at least three distinct types of inhibition could be identified; these probably reflect distinct modes of action. The compounds were clustered similarly in the multi-dimensional space defined by relevant chemical properties, including measures of lipophilicity, aromaticity, molecular size, polarity and electric charge. Drugs of the same therapeutic indication typically belonged to the same type. We identified chemical properties, which were important in determining specific properties of inhibition. State-dependence correlated with lipophilicity, the ratio of the neutral form of molecules, and aromaticity: We noticed that the highly state dependent inhibitors had at least two aromatic rings, logP>4.0, and pKa<8.0.

Conclusions/Significance

The correlations of inhibition properties both with chemical properties and therapeutic profiles would not have been evident through the sole determination of IC₅₀; therefore, recording multiple properties of inhibition may allow improved prediction of therapeutic usefulness.     

The impact of seaweed life phase and postharvest storage duration on the chemical and rheological properties of hybrid carrageenans isolated from Portuguese Mastocarpus stellatus

Variations in chemical and gelling characteristics of hybrid carrageenan extracted from Mastocarpus stellatus seaweeds are studied in order to explore potential links between the seaweeds life phase, the seaweeds postharvest storage duration and the phycocolloids properties. Chemical structures of phycocolloids were assessed by Fourier Transform Infrared spectroscopy (FTIR) and ¹H NMR spectroscopy. Rheological properties of hybrid carrageenans, such as intrinsic viscosity ([η]), gel elasticity (G₀), gel setting temperature (T_g) and gel melting temperature (T_m), were measured with a stress rheometer. Seasonal variation in the degree of sulphates of native extracts and in their corresponding gelling properties is found. The minimum in gelling properties coincides with a minimum of fructified gametophytes in populations harvested during the cold season. Alkali treated extracts also show minimum gelling properties during the cold season but no correlation with variations in the chemical characteristics could be identified. The gel setting temperature is the only significant change in the properties of hybrid carrageenans extracted from dried seaweeds stored over 39 months in opaque and sealed plastic bags. These results point to non trivial relationships between the life stages of M. stellatus seaweeds, the chemical structure and gel properties of the alkali-extracted phycocolloids, and suggest a route towards the sustainable exploitation of the natural resource.     

Boron- and nitrogen-doped carbon nanotubes and graphene

Multi-walled, single-walled and double-walled carbon nanotubes as well as graphene can be doped with boron and nitrogen. B₂H₆ has been generally used as the boron source while NH₃ or pyridine is employed as the nitrogen source. Doping carbon nanotubes and graphene with boron and nitrogen brings about significant changes in the electronic structure and properties. Such doping not only results in desirable properties but also allows manipulation of properties for specific purposes. Doping with boron- and nitrogen-causes marked changes in the Raman spectra of the carbon nanostructures. In this article, we present the synthesis, characterization and properties of boron- and nitrogen-doped carbon nanotubes and graphene.     

Mechanical properties of porcine brain tissue in vivo and ex vivo estimated by MR elastography

The mechanical properties of brain tissue in vivo determine the response of the brain to rapid skull acceleration. These properties are thus of great interest to the developers of mathematical models of traumatic brain injury (TBI) or neurosurgical simulations. Animal models provide valuable insight that can improve TBI modeling. In this study we compare estimates of mechanical properties of the Yucatan mini-pig brain in vivo and ex vivo using magnetic resonance elastography (MRE) at multiple frequencies. MRE allows estimations of properties in soft tissue, either in vivo or ex vivo, by imaging harmonic shear wave propagation. Most direct measurements of brain mechanical properties have been performed using samples of brain tissue ex vivo. It has been observed that direct estimates of brain mechanical properties depend on the frequency and amplitude of loading, as well as the time post-mortem and condition of the sample. Using MRE in the same animals at overlapping frequencies, we observe that porcine brain tissue in vivo appears stiffer than porcine brain tissue samples ex vivo at frequencies of 100 Hz and 125 Hz, but measurements show closer agreement at lower frequencies.     

New Potentially Probiotic Strains Isolated from Humans – Comparison of Properties with Strains from Probiotic Products and ATCC Collection

Lactic acid bacteria are used in various types of probiotic products. Due to the constantly growing probiotics market, new strains with pro-health properties are sought. The present study compared 39 strains of Lactobacillus, Lacticaseibacillus, and Lactiplantibacillus, isolated from probiotic products and healthy people. The current research aimed to search for new, potentially probiotic strains. For this purpose the relationship between Lactobacillaceae strains was carried out; moreover, the basic properties of probiotic microorganisms, such as survival at low pH and bile salt environment, antibiotic susceptibility, aggregation and antagonism were estimated. The properties of these isolates were also compared with the properties of probiotic strains from the ATCC collection. In comparing the genetic relationship (PFGE method) between the tested isolates, it was observed that some of them show a high degree of similarity. All tested strains tolerated an environment with a pH value of 3.0, and the addition of 0.3% bile salt; showed auto-aggregation properties and displayed antagonism against pathogenic microorganisms. In the present study, the bacteria were susceptible to tetracycline, chloramphenicol and ampicillin; the resistance to vancomycindepended on the bacteria type. All the properties were strain-depended. Most of the tested strains had properties comparable to the reference strains. Three L. acidophilus strains isolated from cervical swabs seem to be promising candidates for probiotic strains. Key words: lactobacilli, PFGE, antimicrobial susceptibility, antagonism     

Electric field distribution in biological systems

Electric field distribution in biological systems was investigated. In the analysis both the conductive and the dielectric properties of biological systems were considered. Making use of the complex dielectric coefficient, equations which describe the electric field behavior in such media, were formulated. These equations were solved numerically for a few biological systems. The solutions show that the macroscopic field distribution, for example, the refraction of the ECG wave upon passing from one tissue into another, is mainly determined by the tissue's conductive properties (in the frequency range of 0–10⁸ Hz). However, the microscopic field distribution around the individual cells is determined by the conductive, the dielectric or both properties, depending on the frequency. At frequencies below 10⁴ Hz the field configuration is determined largely by the system's conductive properties. At frequencies above 10⁷ – 10⁸ Hz, by the dielectric properties and in the range of 10⁴ – 10⁶ Hz both properties affect the field distribution. In this range the field direction may be shifted by as much as 90° by relatively small frequency changes.     

Sequence-specific dynamic information in proteins

We examine the local and global properties of the average B-factor, 〈B〉, as a residue-specific indicator of protein dynamic characteristics. It has been shown that values of 〈B〉 for the 20 amino acids differ in a statistically significant manner, and that, while strongly determined by the static physical properties of amino acids, they also encode averaged information about the influence of global fold on single-residue dynamics. Therefore, complete sequences of amino acids also encode fold-related global dynamic information, in addition to the local information that arises from static physical properties. We show that the relative magnitudes of these two contributions can be determined using Fourier methods, which represent the global properties of the sequences. It has also been shown that the behavior of Fourier components of 〈B〉 differs, with very high statistical significance, between structural groups, and that this information is not available from a comparable analysis of static amino acid properties.