Predicting and avoiding subcellular compartmentalization artifacts arising from acetoxymethyl ester calcium imaging probes. The case of fluo-3 AM and a general account of the phenomenon including a problem avoidance chart

Abstract

Stimulated by difficulties experienced when using fluo-3 AM, we developed a general mechanistic model to aid understanding and practical application of calcium probes applied as acetoxymethyl (AM) esters. Several practical issues previously overlooked or under-emphasized are considered by this model. First, some AM ester probes are “super” lipophilic, e.g., calcium orange, fluo-3, fura red, and these are trapped in the plasma membrane. Entry of such compounds into cells requires the presence of serum albumin in the incubation medium or esterase in the plasma membrane or both. Second, visible cytosolic calcium signals require significant cytosolic esterase, which varies considerably among cell lines and within cell populations of a single cell line. Finally, compartmentalization artefacts are most likely when incompletely hydrolyzed esters are present in the cytosol. This can occur because of low cytosolic esterase concentration or activity, and especially when long incubation times or high extracellular probe concentrations are used. An additional factor favoring compartmentalization is the presence of the “salt” form of the probe in the cytosol in the absence of significant concentrations of calcium ions. We provide an algorithmic chart to aid assessment of possible compartmentalization, guides to relevant QSAR models, and notes on estimation of the structural parameters required when using these models.     

Models for alarm call behaviour

The evolution of alarm call behaviour under individual selection is studied. Four mathematical models of increasing complexity are proposed and analysed. Theoretical conditions for the evolution of “selfish”, “mutualistic”, “altruistic” or “spiteful” alarm calls are established. The models indicate that the hypotheses of benefits of retaining group members or avoiding group detection are not sufficient to explain the evolution of alarm call behaviour, but serve as a complementary factor to facilitate its evolution in most cases. It is hypothesized that the evolution of alarm calls between non-kin should evolve probably when calls are mutualistic, mildly altruistic and there are beneficial group size effects against predation.     

Two-enzyme active transport in vitro with ph induced asymmetrical functional structures.: III. Discussions based on numerical treatments of the time-dependent evolutions

Three complementary models have been considered in which pH gradients (step function. linear pH or linear H^?) impose asymmetry on a two-enzyme mixture. If the “combined pH dependences” of enzymes is pro-asymmetrical, the pH gradient induces an asymmetrical distribution of potential activities (“latent” asymmetry of functional structure). When substrate is added, “developed” asymmetry of effective activities appears which results in “substrate space wave” and pumping when the catalysed reaction couple is “inversible”. It is shown that only one steady state exists for a given boundary condition and is attained when the “combined effective activity” of enzymes is nil: the stationary flux with symmetrical boundaries or the stationary load with moving boundaries is proportional to “effective global activities” of enzymes. “Equivalent square models” could be proposed that would be able to describe “functional” or “permanent” structure pumps as well. These models belong to the thermodynamic branch and the asymmetrical “space wave” substrate concentration profiles obtained must be distinguished from dissipative structures. It appears that such primary active transport pumps are chemical equivalents of heat pumps.     

10,000 Years “High on the Hog”: Some Remarks on the Human-Animal Relationship

Abstract

The pig has a contradictory image. It is the symbol of luck, thrift, prosperity, or fertility. At the same time, it is identified with negative characteristics such as impurity (in a literal as well as a figurative sense), lechery, falseness, and craving for power. Although the pig is honored as a deity in many cultures, the epithet “swine” has been used as an insult in the Occident, at least since Pindar. Wieland described the pig as the “true antithesis of grace” (Mangold 1973). And Gottfried Benn made the bitter equation “the crown of creation, that swine, man” (1968). How, where, and when did these varying judgments come about in the course of history? What experiences and events, what special characteristics of the species, induced them? The first part of this article will trace the foundation of these references in the most important phases of the natural history of the domestic swine. The second part will summarize the relationships between the species Homo and Sus.     

When will evolution lead to deceptive signaling in the Sir Philip Sidney game?

Sir Philip Sidney games are a widely used model of simple signaling. Johnstone and Grafen [Johnstone, R.A., Grafen, A., 1993. Dishonesty and the handicap principle. Animal Behaviour 46, 759–764] present a version in which the Evolutionarily Stable Strategy (ESS) is for most signalers to “honestly” signal, with a small minority of signalers who “cheat”. This model is among the most frequently cited papers on the topic of “dishonest” signaling and supports the view that signals may be “dishonest” as long as they are “honest on average”. Using genetic algorithms, we demonstrate that another solution exists to the game, an evolutionarily stable set of Nash equilibria in which members of the set never signal and all donors give their resource. Payoffs to players using this set of strategies is greater those when playing the “dishonest” signaling ESS. We demonstrate that a random population is far more likely to evolve to this non-communicating strategy set than the “dishonest” signaling ESS. We also discuss the dynamics of biological game theory models and the advances of genetic algorithms as a heuristic solution method for these models.     

The SER Standards,cultural ecosystems,and the nature‐culture nexus—a reply to Evans and Davis

Evans and Davis claim the SER Standards use a “pure naturalness” model for restoration baselines and exclude most cultural ecosystems from the ecological restoration paradigm. The SER Standards do neither. The SER Standards consider both “natural” ecosystems (that are unequivocally not cultural) and “similar” cultural ecosystems as suitable reference models. Furthermore, Evans and Davis propose assessing whether a cultural ecosystem exhibits “good, bad, or neutral impacts from humans on ecosystems” as the basis for reference models. We argue that such an approach would overlook the indispensability of native ecosystem benchmarks to measure human impacts and provide a springboard for social‐ecological restoration.     

Behaviors of impurity in ITER plasma with standard type I ELMy H-mode and steady-state scenarios

Self-consistent simulations of impurity behaviors in ITER plasmas in standard Type I ELMy H-mode and steady-state scenarios are investigated using 1.5D BALDUR integrated predictive modeling code. In these simulations, the plasma core transports, including electron and ion thermal, hydrogenic and impurity transports, are predicted using a linear combination of anomalous and neoclassical transports. An anomalous transport is calculated using a theory-based Multimode (MMM95) model; while the neoclassical transport is calculated using NCLASS model. The temperature and density boundary conditions are described at the top of the pedestal. Two different models for hydrogenic and impurity boundary density conditions are considered. The first model is called a “static boundary density model,” in which the hydrogenic and impurity densities at the boundary are fixed. For the second model, called a “dynamic boundary density model,” the hydrogenic and impurity densities at the boundary are assumed to be a large fraction of its line-averaged density. For simplicity, the pedestal temperature is assumed to be a constant in all simulations. The combination of a core transport model together with the boundary density models is used to simulate the time evolution of plasma current, temperature, and density profiles for ITER plasmas in standard type I ELMy H-mode and steady-state scenarios. As a result, the behaviors of impurity in ITER plasmas can be investigated. It is found in both ITER scenarios that the total amount of impurity, including beryllium and helium, in plasma core increases rapidly in early state and reaches a steady-state value. The level of impurity content in the steady state depends sensitively on the impurity boundary conditions. The effective charge at the edge is found to be about 1.4 and 1.1 using a static boundary density model and a dynamic boundary density model, respectively. It is also found that the hydrogenic and impurity transports in ITER plasmas for both scenarios is dominated by the kinetic ballooning modes, while the ITG and TEM modes provide the largest contributions for both thermal transports in most of region. In addition, a sensitivity study is carried out to investigate the impacts of pedestal temperature, pedestal density and line-averaged density on the impurity behaviors. It is found that increasing the pedestal temperature results in a reduction of the impurity content. On the other hand, increasing the pedestal density, line-averaged density or impurity influx result in an increase of the impurity content.     

Cross-Sectional Study of Characteristics of Owners and Nonowners Surrendering Cats to Four Australian Animal Shelters

Unwanted cats surrendered to nonhuman animal shelters are generally categorized as either “owned” or “stray.” This classification is misleading because “stray” cats may include many “semiowned” cats, for which people provide care but who are not perceived as being owned. This differentiation is important because effective strategies designed to reduce cat admissions to, and euthanasia rates in, shelters rely on accurate information about cat populations contributing to shelter intake; cat semiowners will likely respond to different strategies than people with no relationship with the cats they surrender. People surrendering cats to four Australian animal shelters were surveyed to identify factors associated with perception of ownership. Many self-classified nonowners had fed the cats they surrendered, often for a considerable period of time. The factor most strongly associated with ownership perception was an increasing association time with the cat. These findings confirm that enduring relationships between surrenderers and cats, consistent with cat semiownership, are common for cats surrendered to Australian animal shelters. This finding should be taken into account when planning education messages and cat population management strategies aimed at reducing cat admissions.     

The limited depletion of cholesterol from erythrocyte membranes on treatment with incubated plasma

About 35% of the cholesterol of human erythrocyte membranes can be removed by the “preincubated plasma” technique (Murphy, J.R. (1962) J. Lab. Clin. Med. 60, 86–109), in which erythrocytes are extracted with plasma that has been preincubated to esterify a portion of its lipoprotein cholesterol. The limitation on the cholesterol depletion is shown not to be a result of insufficient plasma capacity to take up additional cholesterol or of changes in the plasma during the extraction.The maximum cholesterol depletion from “ghosts” was the same as that from whole cells. “Inside-out” membrane vesicles (Steck, T.L. (1974) in Methods in Membrane Biology (Korn, E., ed.), Vol. 2, pp. 245–281) were utilized to determine if the limitation to cholesterol depletion is a result of the remaining cholesterol being 1located at the membrane inner surface and therefore not accessible to the plasma. No further cholesterol depletion occurred when “inside-out” vesicles, prepared from erythrocytes which were depleted of cholesterol by the usual method, were extracted. Also, “inside-out” vesicles prepared from untreated erythrocytes gave the same cholesterol depletion as is usually attained.The maximal cholesterol depletion was unaffected by a number of modifications of the extracting preincubated plasma: addition of lysolecithin or albumin, dialysis against isotonic buffer, and variation in pH of the preincubated plasma from 6.0 to 9.0.It is concluded that the limitation on the cholesterol depletion is a result of a firm binding of the remaining cholesterol.     

Coexistence and displacement in consumer-resource systems with local and shared resources

Competition for local and shared resources is widespread. For example, colonial waterbirds consume local prey in the immediate vicinity of their colony, as well as shared prey across multiple colonies. However, there is little understanding of conditions facilitating coexistence vs. displacement in such systems. Extending traditional models based on type I and type II functional responses, we simulate consumer-resource systems in which resources are “substitutable,” “essential,” or “complementary.” It is shown that when resources are complementary or essential, a small increase in carrying capacity or decrease in handling time of a local resource may displace a spatially separate consumer species, even when the effect on shared resources is small. This work underscores the importance of determining both the nature of resource competition (substitutable, essential, or complementary) and appropriate scale-dependencies when studying metacommunities. We discuss model applicability to complex systems, e.g., urban wildlife that consume natural and anthropogenic resources which may displace rural competitors by depleting shared prey.     

So what is a species anyway? A primatological perspective

Since Darwin's time, the question “what a species” has provoked fierce disputes and a tremendous number of publications, from short opinion papers to thick volumes. 1 The debates covered fundamental philosophical questions, such as: Do species exist at all independently of a human observer or are they just a construct of the human mind to categorize nature's organismic diversity and serve as a semantic tool in human communication about biodiversity? 2 - 4 or: Are species natural kinds (classes) or individuals that are “born” by speciation, change in course of time, and finally “die” when they go extinct or diverge into new species? 5 - 8 Also included was the problem of species as taxa (taxonomic) versus species as products of the speciation process (evolutionary). 9 More pragmatic issues arose, such as: How can we reliably delineate and delimitate species? 10 , 11 The great interest in what a species is reflects the importance of “species” as fundamental units in most fields of biology, especially evolutionary biology, ecology, and conservation. 2 , 12 - 14     

Genetic-gonadal-genitals sex (3G-sex) and the misconception of brain and gender,or, why 3G-males and 3G-females have intersex brain and intersex gender

The categorization of individuals as “male” or “female” is based on chromosome complement and gonadal and genital phenotype. This combined genetic-gonadal-genitals sex, here referred to as 3G-sex, is internally consistent in ~99% of humans (i.e., one has either the “female” form at all levels, or the “male” form at all levels). About 1% of the human population is identified as “intersex” because of either having an intermediate form at one or more levels, or having the “male” form at some levels and the “female” form at other levels. These two types of “intersex” reflect the facts, respectively, that the different levels of 3G-sex are not completely dimorphic nor perfectly consistent. Using 3G-sex as a model to understand sex differences in other domains (e.g., brain, behavior) leads to the erroneous assumption that sex differences in these other domains are also highly dimorphic and highly consistent. But parallel lines of research have led to the conclusion that sex differences in the brain and in behavior, cognition, personality, and other gender characteristics are for the most part not dimorphic and not internally consistent (i.e., having one brain/gender characteristic with the “male” form is not a reliable predictor for the form of other brain/gender characteristics). Therefore although only ~1% percent of humans are 3G-“intersex”, when it comes to brain and gender, we all have an intersex gender (i.e., an array of masculine and feminine traits) and an intersex brain (a mosaic of “male” and “female” brain characteristics).     

Assessing multitemporal calibration for species distribution models

Species distribution models (SDMs), the most prominent tool in modern biogeography, rely on the assumptions that (i) species distribution is in equilibrium with the environment and (ii) that climatic niche has been conserved throughout recent geological time. These issues affect the spatial and temporal transferability of SDMs, limiting their reliability for applications such as when studying effects of past climate change on species distribution and extinctions. The integration of paleontological and neontological data for a multitemporal calibration and validation of SDMs has been suggested for improving SDMs flexibility. Here, we provide an empirical test for a multitemporal calibration, employing virtual species (i.e., with perfectly-known distributions) and comparing them directly with monotemporal SDMs (i.e., SDM calibrated in a single time layer). We used 1kyr-interval scenarios throughout the last 22 kyr BP for two ecologically different species in South America (a “hot and wet” species and a “cold and dry” species). Models with multitemporal calibration performed similarly to models with monotemporal calibration, regardless of species, sample sizes, and time frame. However, multitemporal calibration performed better when dealing with non-analogous climates among time layers. By improving the temporal SDMs transferability, multitemporal calibration opens new avenues for integrating fossil and recent occurrence data, which may substantially benefit biogeography and paleoecology.     

Transgressive Hybrids as Hopeful Monsters

The origin of novelty is a critical subject for evolutionary biologists. Early geneticists speculated about the sudden appearance of new species via special macromutations, epitomized by Goldschmidt’s infamous “hopeful monster”. Although these ideas were easily dismissed by the insights of the Modern Synthesis, a lingering fascination with the possibility of sudden, dramatic change has persisted. Recent work on hybridization and gene exchange suggests an underappreciated mechanism for the sudden appearance of evolutionary novelty that is entirely consistent with the principles of modern population genetics. Genetic recombination in hybrids can produce transgressive phenotypes, “monstrous” phenotypes beyond the range of parental populations. Transgressive phenotypes can be products of epistatic interactions or additive effects of multiple recombined loci. We compare several epistatic and additive models of transgressive segregation in hybrids and find that they are special cases of a general, classic quantitative genetic model. The Dobzhansky-Muller model predicts “hopeless” monsters, sterile and inviable transgressive phenotypes. The Bateson model predicts “hopeful” monsters with fitness greater than either parental population. The complementation model predicts both. Transgressive segregation after hybridization can rapidly produce novel phenotypes by recombining multiple loci simultaneously. Admixed populations will also produce many similar recombinant phenotypes at the same time, increasing the probability that recombinant “hopeful monsters” will establish true-breeding evolutionary lineages. Recombination is not the only (or even most common) process generating evolutionary novelty, but might be the most credible mechanism for sudden appearance of new forms.     

Communication and collective action: language and the evolution of human cooperation

All social species face various “collective action problems” (CAPs) or “social dilemmas,” meaning problems in achieving cooperating when the best move from a selfish point of view yields an inferior collective outcome. Compared to most other species, humans are very good at solving these challenges, suggesting that something rather peculiar about human sociality facilitates collective action. This article proposes that language — the uniquely human faculty of symbolic communication — fundamentally alters the possibilities for collective action. I explore these issues using simple game-theoretic models and empirical evidence (both ethnographic and experimental). I review several standard mechanisms for the evolution of cooperation — mutualism, reciprocal altruism, indirect reciprocity and signaling — highlighting their limitations when it comes to explaining large-group cooperation, as well as the ways in which language helps overcome those limitations. Language facilitates complex coordination and is essential for establishing norms governing production efforts and distribution of collective goods that motivate people to cooperate voluntarily in large groups. Language also significantly lowers the cost of detecting and punishing “free riders,” thus greatly enhancing the scope and power of standard conditional reciprocity. In addition, symbolic communication encourages new forms of collectively beneficial displays and reputation management — what evolutionists often term “signaling” and “indirect reciprocity.” Thus, language reinforces existing forces that favor the evolution of cooperation, as well as creating new opportunities for collective action not available even to our closest primate relatives.     

The influence of the extraction procedure on yield of indole-3-acetic acid in plant extracts

Different types of plant material, including both dry and swollen maize kernels, swollen bean seeds, bean seedlings and dry rose seeds, were extracted by different methods and the yield of IAA was determined with the indolo-α-pyrone method. Extraction of dry maize kernels during short time experiments, varying from 3 to 24 h, gave the highest IAA yield when methanol was the extractant and a significant lower yield when diethyl ether or dichloromethane were used. The duration of the extraction period increased the yield with all the extractants. Progressive extractions for several days or weeks had little effect on the yield when 100% acetone was used in contrast to methanol and ether as extractants, which increased the yield during prolonged extraction. Extractions of tissue treated to 100°C for 1 h contradicted the hypothesis that IAA is enzymatically liberated during ether extraction. Water in the extractant solvents increased the yields. This was most pronounced when aqueous acetone was used instead of 100% acetone. Increased extraction temperature augmented the IAA yields. The yield of IAA from other types of tissue extracted with methanol for periods of 3 or 24 h was, however, independent of the duration of the extraction time. This indicates that some tissues contain less not easily extractable IAA than dry maize kernels. The terms “free” and “bound” IAA are discussed; they should be replaced by “easily extractable” and “not easily extractable” IAA. The results also show that IPyA in vitro can partly be converted to IAA during extraction and fractionation.     

Optimal Mating Strategies for Preferentially Outcrossing Simultaneous Hermaphrodites in the Presence of Predators

The optimal timing for initiating reproduction (i.e., the age at first reproduction) is a critical life history trait describing aspects of an individual’s resource-allocation strategy. Recent theoretical and empirical work has demonstrated that this trait is also tied to mating system expression when individuals have the opportunity to reproduce via both self-fertilization and cross-fertilization. A strategy of “delayed selfing” has emerged as a “best of both worlds” arrangement where, in the absence of a mate, an individual will delay reproduction (selfing) to “wait” for a mate. Herein, we extend previously developed predictive optimization models for the timing of reproduction to a situation where organisms can allocate their resources to size-dependent and size-independent defensive strategies to counter the threat of predation. By incorporating inducible defenses into a predictive framework for analyzing life history expression and evolution, we can more accurately evaluate the role that allocation strategy plays in altering the optimal waiting time. We compare our model to previous models and empirical results highlighting that incorporation of inducible defenses into the model broadens the parameter space in which a waiting time is expected and often leads to a predicted waiting time that is longer than in the situation without inducible defenses. In particular, a waiting time is predicted to exist regardless of the strength of inbreeding depression in the population.     

Complete parameter bounds and quasiidentifiability conditions for a class of unidentifiable linear systems

Lack of unique structural identifiability for parameters of dynamic system models is a very common situation with practical experimental schemes, particularly when studying biological systems. However, for well-structured (e.g., multicompartmental) models, it is often possible to localize unidentifiable parameters between finite limits (“interval identifiability”), using the same data base, and under certain conditions these limits nearly coincide. Two new results in this area are presented: (1) The smallest ranges on all unidentifiable rate constants and pool sizes of the most general n-compartment mammillary system are derived, in an easy-to-program algorithmic form, for the common case of input forcing and output measurements in the central pool only. From these results we see why elimination rate constants (“leaks”) are difficult to distinguish from zero, whereas exchange rate constants between pools, and pool sizes, may be bounded very tightly in certain circumstances. (2) The notion of quasiidentifiability, or sufficient identifiability for practical purposes, is introduced to quantify these circumstances. Each of the rate constants between central and peripheral pools, and all pool sizes, are quasiidentifiable if the magnitude of the ratio of the coefficient to the eigenvalue of the slowest mode is very much greater than the largest coefficient in the sum-of-exponentials response function. Also quasiidentifiability is a necessary condition for applicability of noncompartmental analysis to estimate pool sizes and residence times of mammillary systems with “leaky” noncentral pools.