Maternal effects in Daphnia: what mothers are telling their offspring and do they listen?

Maternal effects can significantly impact offspring performance. Provisioning of offspring with energy stores can quantitatively alter their growth rates, survivorship, and future fecundity, and influence population regulatory mechanisms. In this paper, we show that maternal effects can also qualitatively affect offspring reproduction (i.e. their mode of reproduction). The freshwater herbivore Daphnia pulex can change the amount of energy allocated between asexual and ephippial egg production. Our experiments on individuals, experiencing “step‐up” or “step‐down” food manipulations, reveal that offspring qualitatively shift their energy allocation away from asexual reproduction to ephippial egg production when there is a simple mismatch between maternal and offspring food environments. We show that the response is asymmetric with respect to changes in food level, ephippial egg production is higher with a greater mismatch between environments, and that the effect can be observed in dynamic experimental populations. These results point to a “generational memory” that could challenge our interpretation of field patterns and mechanisms influencing population dynamics in Daphnia–algal systems.     

Non-linear arrhenius plots and the analysis of reaction and motional rates in biological membranes

We have systematically derived the rate-temperature relationships for a variety of models of membrane rate processes (particularly enzymic reactions) in order to predict the Arrhenius plot shape(s) appropriate to each model. We have explicitly considered the fact that most thermotropic changes in biological systems extend over finite and sometimes very broad temperature ranges. The rate-temperature relationships for most of the models considered can be expressed in a common, rather simple mathematical form suitable for application in computer data analysis. Only a few models predict Arrhenius plots with the “biphasic linear” form commonly reported in studies of membrane enzymes. However, many of the models yield plots which can be fitted to two intersecting lines within a quite modest experimental error, especially if the change in the slope of the plot around its “break” corresponds to a change in activation enthalpy of less than 15–20 kcal mol^?1. In general, Arrhenius-type plots of motional and reaction rates in membranes are found to be capable of indicating the midpoint but not the endpoints or the overall width of thermotropic transitions in the state of membrane components. Our findings clearly indicate a need for a more rigorous analysis of Arrhenius plot data in terms of graph shapes other than sets of intersecting lines and for more cautious interpretation of Arrhenius plot “breaks” with regard to their physical basis.     

Vertebral evolution and ontogenetic allometry: The developmental basis of extreme body shape divergence in microcephalic sea snakes

Snakes exhibit a diverse array of body shapes despite their characteristically simplified morphology. The most extreme shape changes along the precloacal axis are seen in fully aquatic sea snakes (Hydrophiinae): “microcephalic” sea snakes have tiny heads and dramatically reduced forebody girths that can be less than a third of the hindbody girth. This morphology has evolved repeatedly in sea snakes that specialize in hunting eels in burrows, but its developmental basis has not previously been examined. Here, we infer the developmental mechanisms underlying body shape changes in sea snakes by examining evolutionary patterns of changes in vertebral number and postnatal ontogenetic growth. Our results show that microcephalic species develop their characteristic shape via changes in both the embryonic and postnatal stages. Ontogenetic changes cause the hindbodies of microcephalic species to reach greater sizes relative to their forebodies in adulthood, suggesting heterochronic shifts that may be linked to homeotic effects (axial regionalization). However, microcephalic species also have greater numbers of vertebrae, especially in their forebodies, indicating that somitogenetic effects also contribute to evolutionary changes in body shape. Our findings highlight sea snakes as an excellent system for studying the development of segment number and regional identity in the snake precloacal axial skeleton.     

Intuitive,but not simple: Including explicit water molecules in protein–protein docking simulations improves model quality

Characterizing the nature of interaction between proteins that have not been experimentally cocrystallized requires a computational docking approach that can successfully predict the spatial conformation adopted in the complex. In this work, the Hydropathic INTeractions (HINT) force field model was used for scoring docked models in a data set of 30 high‐resolution crystallographically characterized “dry” protein–protein complexes and was shown to reliably identify native‐like models. However, most current protein–protein docking algorithms fail to explicitly account for water molecules involved in bridging interactions that mediate and stabilize the association of the protein partners, so we used HINT to illuminate the physical and chemical properties of bridging waters and account for their energetic stabilizing contributions. The HINT water Relevance metric identified the “truly” bridging waters at the 30 protein–protein interfaces and we utilized them in “solvated” docking by manually inserting them into the input files for the rigid body ZDOCK program. By accounting for these interfacial waters, a statistically significant improvement of ～24% in the average hit‐count within the top‐10 predictions the protein–protein dataset was seen, compared to standard “dry” docking. The results also show scoring improvement, with medium and high accuracy models ranking much better than incorrect ones. These improvements can be attributed to the physical presence of water molecules that alter surface properties and better represent native shape and hydropathic complementarity between interacting partners, with concomitantly more accurate native‐like structure predictions. Proteins 2014; 82:916–932. © 2013 Wiley Periodicals, Inc.     

Rapid,gregarious settlement of the larvae of the marine echiuran Urechis caupo Fisher & MacGinitie 1928

Larvae of Urechis caupo Fisher & MacGinitie, reared in the laboratory, were exposed to potential settlement stimuli, including natural sediment from adult burrows, and “scent” obtained from the skin of adult animals. Competent larvae settled rapidly and specifically in response to adult burrow sediment when compared with their responses to other natural and abiotic sediments. Larvae also responded specifically to chemical “scent” from adult animals when the “scent” of another echiuran worm, Listriolobus pelodes Fisher served as a control. Larval responses to chemical “scent” were as great as their responses to natural burrow sediment. Hence, it is likely that larvae settle gregariously in nature in response to “scent” on sediment grains of adult burrows. The chemical “scent” had a molecular weight between ≈3500 and 14000 daltons, as determined by dialysis. It quickly lost its effectiveness in promoting settlement after it was heated to 80 °C, but was relatively stable at ambient ocean temperatures, retaining its effectiveness for several days. It was soluble in sea water. However, larvae did not respond to the chemical “scent”, unless it was adsorbed onto a surface. Purely tactile stimuli, such as the shape, texture, and size-distribution of particles, were not important settlement cues during these experiments.     

Modeling and simulation of biological systems from image data

This essay provides an introduction to the terminology, concepts, methods, and challenges of image‐based modeling in biology. Image‐based modeling and simulation aims at using systematic, quantitative image data to build predictive models of biological systems that can be simulated with a computer. This allows one to disentangle molecular mechanisms from effects of shape and geometry. Questions like “what is the functional role of shape” or “how are biological shapes generated and regulated” can be addressed in the framework of image‐based systems biology. The combination of image quantification, model building, and computer simulation is illustrated here using the example of diffusion in the endoplasmic reticulum.     

Finite element modeling of shell shape in the freshwater turtle Pseudemys concinna reveals a trade‐off between mechanical strength and hydrodynamic efficiency

Aquatic species can experience different selective pressures on morphology in different flow regimes. Species inhabiting lotic regimes often adapt to these conditions by evolving low‐drag (i.e., streamlined) morphologies that reduce the likelihood of dislodgment or displacement. However, hydrodynamic factors are not the only selective pressures influencing organismal morphology and shapes well suited to flow conditions may compromise performance in other roles. We investigated the possibility of morphological trade‐offs in the turtle Pseudemys concinna. Individuals living in lotic environments have flatter, more streamlined shells than those living in lentic environments; however, this flatter shape may also make the shells less capable of resisting predator‐induced loads. We tested the idea that “lotic” shell shapes are weaker than “lentic” shell shapes, concomitantly examining effects of sex. Geometric morphometric data were used to transform an existing finite element shell model into a series of models corresponding to the shapes of individual turtles. Models were assigned identical material properties and loaded under identical conditions, and the stresses produced by a series of eight loads were extracted to describe the strength of the shells. “Lotic” shell shapes produced significantly higher stresses than “lentic” shell shapes, indicating that the former is weaker than the latter. Females had significantly stronger shell shapes than males, although these differences were less consistent than differences between flow regimes. We conclude that, despite the potential for many‐to‐one mapping of shell shape onto strength, P. concinna experiences a trade‐off in shell shape between hydrodynamic and mechanical performance. This trade‐off may be evident in many other turtle species or any other aquatic species that also depend on a shell for defense. However, evolution of body size may provide an avenue of escape from this trade‐off in some cases, as changes in size can drastically affect mechanical performance while having little effect on hydrodynamic performance. J. Morphol. 2011. © 2011 Wiley‐Liss, Inc.     

Testing of geroprotectors in experiments on cell cultures: Choosing the correct model system

We believe that cytogerontological models, such as the Hayflick model, though very useful for experimental gerontology, are based only on certain correlations and do not directly apply to the gist of the aging process. Thus, the Hayflick limit concept cannot explain why we age, whereas our “stationary phase aging” model appears to be a “gist model,” since it is based on the hypothesis that the main cause of both various “age-related” changes in stationary cell cultures and similar changes in the cells of aging multicellular organism is the restriction of cell proliferation. The model is applicable to experiments on a wide variety of cultured cells, including normal and transformed animal and human cells, plant cells, bacteria, yeasts, mycoplasmas, etc. The results of relevant studies show that cells in this model die out in accordance with the Gompertz law, which describes exponential increase of the death probability with time. Therefore, the “stationary phase aging” model may prove effective in testing of various geroprotectors (anti-aging factors) and geropromoters (pro-aging factors) in cytogerontological experiments. It should be emphasized, however, that even the results of such experiments do not always agree with the data obtained in vivo and therefore cannot be regarded as final but should be verified in studies on laboratory animals and in clinical trials (provided this complies with ethical principles of human subject research).     

The Total Least Squares Method in Individual Bioequivalence Evaluation

We propose a simple method for comparison of series of matched observations. While in all our examples we address “individual bioequivalence” (IBE), which is the subject of much discussion in pharmaceutical statistics, the methodology can be applied to a wide class of cross‐over experiments, including cross‐over imaging. From the statistical point of view the considered models belong to the class of the “error‐in‐variables” models. In computational statistics the corresponding optimization method is referred to as the “least squares distance” and the “total least squares” method. The derived confidence regions for both intercept and slope provide the basis for formulation of the IBE criteria and methods for its assessing. Simple simulations show that the proposed approach is very intuitive and transparent, and, at the same time, has a solid statistical and computational background.     

How well do reduced models capture the dynamics in models of interacting neurons?

This paper introduces a class of stochastic models of interacting neurons with emergent dynamics similar to those seen in local cortical populations. Rigorous results on existence and uniqueness of nonequilibrium steady states are proved. These network models are then compared to very simple reduced models driven by the same mean excitatory and inhibitory currents. Discrepancies in firing rates between network and reduced models are investigated and explained by correlations in spiking, or partial synchronization, working in concert with “nonlinearities” in the time evolution of membrane potentials. The use of simple random walks and their first passage times to simulate fluctuations in neuronal membrane potentials and interspike times is also considered.

     

Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean

Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA‐defined Operational Taxonomic Units, OTUs) across 108 globally‐distributed surface ocean stations. We grouped taxa based on their SpAD shape (“normal‐like”‐ abundant and ubiquitous; “logistic”‐ globally rare, present in few sites; and “bimodal”‐ abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan “normal‐like” OTUs, yet there was a gradual shift towards assemblages dominated by “logistic” taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer “normal‐like” shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members.     

Current flow and potential in a three-dimensional syncytium

Analytical solutions are obtained describing the spread of potential in a continuous syncytium which is the three-dimensional analogue of the “cable” and “thin sheet” models. Two discrete (finite-element) models are also developed and their behaviour shown to agree with that of the continuous model. All three models are able to account for the peculiarities of passive responses to intracellular current injection in tissues such as cardiac and smooth muscle. The time course and spread of junction potentials in electrically coupled tissues is discussed.     

Prezygapophyseal articular facet shape in the catarrhine thoracolumbar vertebral column

Two contrasting patterns of lumbar vertebral morphology generally characterize anthropoids. “Long‐backed” monkeys are distinguished from “short‐backed” apes [Benton: The baboon in medical research, Vol. 2 (1967:201)] with respect to several vertebral features thought to afford greater spinal flexibility in the former and spinal rigidity in the latter. Yet, discussions of spinal mobility are lacking important functional insight that can be gained by analysis of the zygapophyses, the spine's synovial joints responsible for allowing and resisting intervertebral movements. Here, prezygapophyseal articular facet (PAF) shape in the thoracolumbar spine of Papio, Hylobates, Pongo, Gorilla, and Pan is evaluated in the context of the “long‐backed” versus “short‐backed” model. A three‐dimensional geometric morphometric approach is used to examine how PAF shape changes along the thoracolumbar vertebral column of each taxon and how PAF shape varies across taxa at corresponding vertebral levels. The thoracolumbar transition in PAF shape differs between Papio and the hominoids, between Hylobates and the great apes, and to a lesser extent, among great apes. At the level of the first lumbar vertebra, the PAF shape of Papio is distinguished from that of hominoids. At the level of the second lumbar vertebra, there is variation to some extent among all taxa. These findings suggest that morphological and functional distinctions in primate vertebral anatomy may be more complex than suggested by a “long‐backed” versus “short‐backed” dichotomy. Am J Phys Anthropol 142:600–612, 2010. © 2010 Wiley‐Liss, Inc.     

Field- and Lab-Based Potentiometric Titrations of Microbial Mats from the Fairmont Hot Spring,Canada

Potentiometric titrations are an effective tool to constrain the protonation constants and site concentrations for microbial surface ligands. Protonation models developed from these experiments are often coupled with data from metal adsorption experiments to calculate microbial ligand-metal binding constants. Ultimately, the resulting surface complexation models can be used to predict metal immobilization behavior across diverse chemical conditions. However, most protonation and metal-ligand thermodynamic constants have been generated in laboratory experiments that use cultured microbes which may differ in their chemical reactivity from environmental samples. In this study, we investigate the use of in situ field potentiometric titrations of microbial mats at a carbonate hot spring located at Fairmont Hot Springs, British Columbia, with the aim to study microbial reactivities in a natural field system. We found that authigenic carbonate minerals complicated the potentiometric titration process due to a “carbonate spike” introduced by the contribution of inorganic carbonate mineral dissolution and subsequent carbonate speciation changes during the transition from low to high pH. This inhibits the determination of microbial surface ligand variety and concentrations. Our preliminary study also highlights the need for developing novel probes to quantify in situ microbial mat reactivity in future field investigations.     

Question of “head preference” in response to worm-like dummies during prey-capture of toads,Bufo bufo

If a black worm-like dummy is moving against a white background, toads fixate and snap at the leading end of the stimulus. This “head preference” phenomenon is — within limits — independent of (i) background structure, and (ii) stripe length. “Head preference” can be disturbed by reducing the amount of the stimulus background contrast as well as by point structures incorporated in the worm-like shape of the stimulus. If the stimulus-background contrast of the worm dummy is reversed, toads exhibit a clear preference in fixating and snapping for the trailing end of the stimulus. This “tail preference” is independent of changes in (i) and (ii). The neural basis of “head preference” or “tail preference” respectively, is discussed.     

REVISING A CLASSIC BUTTERFLY MIMICRY SCENARIO: DEMONSTRATION OF MÜLLERIAN MIMICRY BETWEEN FLORIDA VICEROYS (LIMENITIS ARCHIPPUS FLORIDENSIS) AND QUEENS (DANAUS GILIPPUS BERENICE)

Batesian and Müllerian mimicry relationships differ greatly in terms of selective pressures affecting the participants; hence, accurately characterizing a mimetic interaction is a crucial prerequisite to understanding the selective milieux of model, mimic, and predator. Florida viceroy butterflies (Limenitis archippus floridensis) are conventionally characterized as palatable Batesian mimics of distasteful Florida queens (Danaus gilippus berenice). However, recent experiments indicate that both butterflies are moderately distasteful, suggesting they may be Müllerian comimics. To directly test whether the butterflies exemplify Müllerian mimicry, I performed two reciprocal experiments using red-winged blackbird predators. In Experiment 1, each of eight birds was exposed to a series of eight queens as “models,” then offered four choice trials involving a viceroy (the putative “mimic”) versus a novel alternative butterfly. If mimicry was effective, viceroys should be attacked less than alternatives. I also compared the birds' reactions to solo viceroy “mimics” offered before and after queen models, hypothesizing that attack rate on the viceroy would decrease after birds had been exposed to queen models. In Experiment 2, 12 birds were tested with viceroys as models and queens as putative mimics. The experiments revealed that (1) viceroys and queens offered as models were both moderately unpalatable (only 16% entirely eaten), (2) some birds apparently developed conditioned aversions to viceroy or queen models after only eight exposures, (3) in the subsequent choice trials, viceroy and queen “mimics” were attacked significantly less than alternatives, and (4) solo postmodel mimics were attacked significantly less than solo premodel mimics. Therefore, under these experimental conditions, sampled Florida viceroys and queens are comimics and exemplify Müllerian, not Batesian, mimicry. This compels a reassessment of selective forces affecting the butterflies and their predators, and sets the stage for a broader empirical investigation of the ecological and evolutionary dynamics of mimicry.     

Insider Censoring: Distortion of Data with Nondetects

Environmental data often include low-level concentrations below reporting limits. These data may be reported as “< RL,” where RL is one of several types of reporting limits. Some values also may be reported as a single number, but flagged with a qualifier (J-values) to indicate a difference in precision as compared to values above the RL. A currently used method for reporting censored environmental data called “insider censoring” produces a strong upward bias, while also distorting the shape of the data distribution. This results in inaccurate estimates of summary statistics and regression coefficients, distorts evaluations of whether data follow a normal distribution, and introduces inaccuracies into risk assessments and models. Insider censoring occurs when data measured as below the detection limit (< DL) are reported as less than the higher quantitation limit (< QL), whereas values between the DL and QL are reported as individual numbers. Three unbiased alternatives to insider censoring are presented so that laboratories and their data users can recognize, and remedy, this problem.     

The cycle of mussels: long-term dynamics of mussel beds on intertidal soft bottoms at the White Sea

Dense blue mussel assemblages are unstable, their structure changing from year to year. Three types of models can be used to describe this instability: (1) “exogenous” model based on regional temperature fluctuations, (2) “endogenous” deterministic model associated with negative impact of adult mussels on juveniles and (3) “density-linked stochasticity” model based on positive feedbacks resulting in overcrowding and destabilizing the settlement. We compared predictions deduced from these models with a time series based on the results of long-term (18 years) monitoring of abundance and demographic structure of three mussel beds at the White Sea. Most of our findings agreed well with the predictions deduced from the endogenous model. In particular, (1) long-term changes in mussel abundance and demographic structure were strictly cyclic, with non-matching periods (5–9 years) at different sites; (2) stages with the dominance of old mussels alternated with those where juveniles dominated and (3) some signals of delayed density dependence were revealed. However, the time series also contained elements of long-term trends, which may testify to the involvement of some exogenous factors (probably long-term climate changes).     

On the Additive and Multiplicative Models of Relative Risk

Two popular models of absence of synergism in epidemiologic cohort studies are analyzed and compared. It is shown that the statistical concept of the union of independent events that traditionally has given rise to the “additive” model of relative risk can also generate the “multiplicative” model of relative risk. In fact, the same set of approximating conditions can be used to generate both models, which suggests a lack of identifiability under the traditional approach. An alternate approach is proposed in this paper. The new approach does not require the assumption that background risk factors are independent from causal agents of interest. The concept of “dose additivity” is discussed.