Do small-scale exclosure/enclosure experiments predict the effects of large-scale extirpation of freshwater migratory fauna?

A variety of theoretical and empirical studies indicate that the abilities of small-scale experiments to predict responses to large-scale perturbations vary. Small-scale experiments often do not predict the directions of large-scale responses, and relatively few empirical studies have examined whether small-scale experiments predict the magnitudes of large-scale responses. Here we present an empirical example of small-scale manipulations predicting not only the directions but also the magnitudes of the effects of whole-catchment, decades-long decimation of migratory freshwater shrimp populations. In streams of Puerto Rico (USA), we used arena sizes of < 2 m² in 1- to 4-week exclosure/enclosure experiments. Effects of small-scale experiments largely matched those of large-scale shrimp loss above dams for a variety of response variables (abiotic and biotic factors including epilithic fine sediments, algae and organic matter, and invertebrate grazers, detritivores, and predators). The results of our extrapolation contrast with studies of small- versus large-scale perturbations in the temperate zone. Our findings are likely explained by: a set of response variables that are more dominated by within-patch processes than exchange processes, an experimental manipulation that encompassed the characteristic scales of response variables, our use of open arenas lacking cage artifacts, and/or our combination of two distinct experimental approaches (exclosures and enclosures). Based on our study design, we suggest that extrapolation across experimental scales can be greatly enhanced by embedding open arenas within large-scale conditions that represent all treatment levels. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

FURTHER OBSERVATIONS ON THE INFLUENCE OF SALTS WHEN INJECTED INTO THE ANIMAL BODY

A satisfactory correlation of our observations dealing with the influence of salts and those dealing with the influence of x-rays is not possible at present. Any far reaching conclusion is not permitted because the information we have at this time regarding the physical chemical conditions concerned in the process of injury, as well as that pertaining to the nature of radio-chemical reactions, is too meager. As far as the experiments with salts are concerned, it may be said that we are dealing with ion effects, and their importance in physiological processes is made clear by the investigations of Loeb (3) and those of Osterhout (4). The results that we have obtained in our experiments present an interesting analogy between the effect of x-rays and certain salts on the lymphoid elements of the animal body. We regard this analogy as significant in that it presents suggestions regarding the chemical nature of x-ray effects in the animal body.     

Self-protection promotes altruism

Self-protection tendencies allowed our human ancestors to survive and thrive. In three experiments, we find that individuals who have a salient self-protection motive are more altruistic to others, such as by helping them out or offering them more money in the dictator game paradigm. Self-protecting individuals desire to “bind together” as there is “safety in numbers”, and being altruistic to others should be one (but not the only) way to achieve this goal. Consistent with this reasoning, we find across three behavioral experiments using both non-monetary (Experiment 1) and monetary altruistic contexts (Experiments 2–3) that self-protecting individuals are more altruistic when the altruism is not anonymous (Experiment 1) and when they have the reasonable expectation of future interaction with the recipient (Experiment 2), both of which are situations that should increase affiliation. The effect attenuates when altruism does not help self-protecting individuals, such as when money is donated to impersonal organizations rather than individuals (Experiment 3). We finally discuss the theoretical contributions as well as limitations of our work.     

On the Social Behaviour of Cells

Polystyrene Petri dishes are in use in hundreds of thousands of laboratories world wide. Cell culture experiments performed in them provide fundamental information in a wide range of applications, including but not limited to testing novel biomaterials and pharmaceuticals, and stem cell research. These experiments cost billions of dollars per year. In this study we report on a potential deficiency of polystyrene Petri dishes, possibly caused by an increase in interracial pH under relevant culture condi-tions and affecting cell performance. We conclude that cell performance on Petri dishes could be improved by improving the Petri dishes. As a spin-off of our study we postulate the concept that cancer cells and stem cells are social. It is impossible to validate this concept on the basis of the model established in this paper. However. the coherence of our insights may encourage further study and lead to the development of a qualitative improvement of cell culture devices, including Petri dishes and culture flasks, to the identification of potential strategies for chemotherapy and chemoprevention that could suppress progression of metastasis, and to the establishment of improved settings for tissue engineering and stem cell research. An immediate recom-mendation of our study is to use chemically and biologically inert substrates for important cell culture experiments, for example, nanocrystalline diamond.     

Intrinsic signals regulate the initial steps of myogenesis in vertebrates

In vertebrates, despite the evidence that extrinsic factors induce myogenesis in naive mesoderm, other experiments argue that the initiation of the myogenic program may take place independent of these factors. To resolve this discrepancy, we have re-addressed this issue, using short-term in vivo microsurgery and culture experiments in chick. Our results show that the initial expression of the muscle-specific markers Myf5 and MyoD is regulated in a mesoderm-autonomous fashion. The reception of a Wnt signal is required for MyoD, but not Myf5 expression; however, we show that the source of the Wnt signal is intrinsic to the mesoderm. Gain- and loss-of-function experiments indicate that Wnt5b, which is expressed in the presomitic mesoderm, represents the MyoD-activating cue. Despite Wnt5b expression in the presomitic mesoderm, MyoD is not expressed in this tissue: our experiments demonstrate that this is due to a Bmp inhibitory signal that prevents the premature expression of MyoD before somites form. Our results indicate that myogenesis is a multistep process which is initiated prior to somite formation in a mesoderm-autonomous fashion; as somites form, influences from adjacent tissues are likely to be required for maintenance and patterning of early muscles.     

FACTORS ASSOCIATED WITH HOST SPECIFICITY IN SPOROCLADOPSIS NOVAE-ZELANDIAE (CHLOROPHYTA)1

This study tests the hypotheses that substrate stability and rugose microtopography are the main factors that determine the tissue-specific epiphytism in the chlorophyte Sporocladopsis novae-zelandiae Chapman. Both in vitro and field experiments showed that the epiphyte did not develop on stable algal surfaces nor on artificial (smooth or rugose) substrata. In field experiments, however, other macroalgae settled more abundantly on rugose substrata. Similarly, our field experiments did not support the hypothesis that the physical environment provided by the spatial location of the host in the intertidal or subtidal was a relevant factor associated with specificity. In contrast, our laboratory experiments suggested that some component of the host cell wall might trigger the formation of penetrating rhizoids. These did not develop in isolated cultures of the epiphyte but were detected when the epiphyte contacted its natural host. Also, preliminary results showed that rhizoid-like structures developed, although at very low frequency, only in plants grown in culture medium containing a crude extract of sorus cortical tissue.     

Biogeography of sponge chemical ecology: comparisons of tropical and temperate defenses

Examples from both marine and terrestrial systems have supported the hypothesis that predation is higher in tropical than in temperate habitats and that, as a consequence, tropical species have evolved more effective defenses to deter predators. Although this hypothesis was first proposed for marine sponges over 25 years ago, our study provides the first experimental test of latitudinal differences in the effectiveness of sponge chemical defenses. We collected 20 common sponge species belonging to 14 genera from tropical Guam and temperate Northeast Spanish coasts (Indo-Pacific and Mediterranean biogeographic areas) and conducted field-based feeding experiments with large and small fish predators in both geographic areas. We use the term global deterrence to describe the deterrent activity of a sponge extract against all of the predators used in our experiments and to test the hypothesis that sponges from Guam are chemically better defended than their Mediterranean counterparts. Sympatric and allopatric deterrence refer to the average deterrent activity of a sponge against sympatric or allopatric predators. All of the sponges investigated in this study showed deterrent properties against some predators. However, 35% of the sponge species were deterrent in at least one but not in all the experiments, supporting the idea that predators can respond to chemical defenses in a species-specific manner. Tropical and temperate sponges have comparable global, sympatric, and allopatric deterrence, suggesting not only that chemical defenses from tropical and temperate sponges are equally strong but also that they are equally effective against sympatric and allopatric predators. Rather than supporting geographic trends in the production of chemical defenses, our data suggest a recurrent selection for chemical defenses in sponges as a general life-history strategy.     

Modeling and Estimation of Kinetic Parameters and Replicative Fitness of HIV-1 from Flow-Cytometry-Based Growth Competition Experiments

Growth competition assays have been developed to quantify the relative fitness of HIV-1 mutants. In this article, we develop mathematical models to describe viral/cellular dynamic interactions in the assay system from which the competitive fitness indices or parameters are defined. In our previous HIV-viral fitness experiments, the concentration of uninfected target cells was assumed to be constant (Wu et al. 2006). But this may not be true in some experiments. In addition, dual infection may frequently occur in viral fitness experiments and may not be ignorable. Here, we relax these two assumptions and extend our earlier viral fitness model (Wu et al. 2006). The resulting models then become nonlinear ODE systems for which closed-form solutions are not achievable. In the new model, the viral relative fitness is a function of time since it depends on the target cell concentration. First, we studied the structure identifiability of the nonlinear ODE models. The identifiability analysis showed that all parameters in the proposed models are identifiable from the flow-cytometry-based experimental data that we collected. We then employed a global optimization approach (the differential evolution algorithm) to directly estimate the kinetic parameters as well as the relative fitness index in the nonlinear ODE models using nonlinear least square regression based on the experimental data. Practical identifiability was investigated via Monte Carlo simulations.     

Can the Results of Biodiversity-Ecosystem Productivity Studies Be Translated to Bioenergy Production?

Biodiversity experiments show that increases in plant diversity can lead to greater biomass production, and some researchers suggest that high diversity plantings should be used for bioenergy production. However, many methods used in past biodiversity experiments are impractical for bioenergy plantings. For example, biodiversity experiments often use intensive management such as hand weeding to maintain low diversity plantings and exclude unplanted species, but this would not be done for bioenergy plantings. Also, biodiversity experiments generally use high seeding densities that would be too expensive for bioenergy plantings. Here we report the effects of biodiversity on biomass production from two studies of more realistic bioenergy crop plantings in southern Michigan, USA. One study involved comparing production between switchgrass (Panicum virgatum) monocultures and species-rich prairie plantings on private farm fields that were managed similarly to bioenergy plantings. The other study was an experiment where switchgrass was planted in monoculture and in combination with increasingly species-rich native prairie mixtures. Overall, we found that bioenergy plantings with higher species richness did not produce more biomass than switchgrass monocultures. The lack of a positive relationship between planted species richness and production in our studies may be due to several factors. Non-planted species (weeds) were not removed from our studies and these non-planted species may have competed with planted species and also prevented realized species richness from equaling planted species richness. Also, we found that low seeding density of individual species limited the biomass production of these individual species. Production in future bioenergy plantings with high species richness may be increased by using a high density of inexpensive seed from switchgrass and other highly productive species, and future efforts to translate the results of biodiversity experiments to bioenergy plantings should consider the role of seeding density.     

Coinfection and superinfection in RNA virus populations: a selection-mutation model

In this paper, we present a general selection-mutation model of evolution on a one-dimensional continuous fitness space. The formulation of our model includes both the classical diffusion approach to mutation process as well as an alternative approach based on an integral operator with a mutation kernel. We show that both approaches produce fundamentally equivalent results. To illustrate the suitability of our model, we focus its analytical study into its application to recent experimental studies of in vitro viral evolution. More specifically, these experiments were designed to test previous theoretical predictions regarding the effects of multiple infection dynamics (i.e., coinfection and superinfection) on the virulence of evolving viral populations. The results of these experiments, however, did not match with previous theory. By contrast, the model we present here helps to understand the underlying viral dynamics on these experiments and makes new testable predictions about the role of parameters such the time between successive infections and the growth rates of resident and invading populations.     

Creation of an experimental rearing environment for microbiome animal research using an individually ventilated cage system and bioBUBBLE enclosure

To avoid microbial contamination risk, vinyl film isolators are generally used in animal microbiome experiments involving germ-free (GF) mice and/or gnotobiotic (GB) mice. However, it can take several months to gain expertise in operating the isolator competently. Furthermore, sterilization and sterility testing, which are essential for isolator preparation, can take more than 20 days. Hence, we built an experimental rearing environment that combines an individual ventilation cage system and a bioBUBBLE clean room enclosure to easily set up an experimental animal microbiome environment for animal facilities. In this work, a three-step evaluation was conducted. First, we examined whether GF mice can be maintained in this rearing environment without bacterial contamination. Next, we examined whether GF and GB mice can be maintained without cross-contamination in one individual ventilation cage rack. Finally, we tested whether GF mice can be maintained in a biological safety cabinet controlled by negative pressure. In our series of experiments, no microbial contamination occurred over more than 3 months. These results indicated that our rearing system that combines the individual ventilation cage and bioBUBBLE systems can be used not only for experiments with GF mice but also for Biosafety Level 2 experiments that handle bacteria. Our system can mitigate various disadvantages of using vinyl film isolators. In conclusion, we established an experimental method with improved working time and efficiency compared with those of the previous vinyl isolator method.     

Induced Resistance in Wild Tobacco with Clipped Sagebrush Neighbors: The Role of Herbivore Behavior

Previous experiments showed that wild tobacco plants with experimentally clipped sagebrush neighbors experienced less damage by grasshoppers than tobacco plants with unclipped sagebrush neighbors. This result could have been caused by grasshoppers preferring not to feed near clipped sagebrush. This hypothesis was tested in field choice experiments using six grasshopper species feeding on an unresponsive and uniformly palatable food. When offered food that was either close to clipped sagebrush or close to unclipped sagebrush, grasshoppers showed no preference. When offered food that was either close to sagebrush (3 cm) or far from sagebrush (30 cm), grasshoppers preferred to feed far from sagebrush. However, this preference was similar whether or not the sagebrush had been clipped. Avoidance of feeding near clipped sagebrush, independent of changes in tobacco, was not found to contribute to our earlier result that tobacco near clipped sagebrush suffered less herbivory than tobacco near unclipped sagebrush.     

Close Interactions between Mesenchymal Stem Cells and Neuroblastoma Cell Lines Lead to Tumor Growth Inhibition

Mesenchymal stem cells (MSCs) have attracted much interest in oncology since they exhibit marked tropism for the tumor microenvironment and support or suppress malignant cell growth depending on the tumor model tested. The aim of this study was to investigate the role of MSCs in the control of the growth of neuroblastoma (NB), which is the second most common solid tumor in children. In vivo experiments showed that systemically administered MSCs, under our experimental conditions, did not home to tumor sites and did not affect tumor growth or survival. However, MSCs injected intratumorally in an established subcutaneous NB model reduced tumor growth through inhibition of proliferation and induction of apoptosis of NB cells and prolonged the survival of hMSC-treated mice. The need for contact between MSCs and NB cells was further supported by in vitro experiments. In particular, MSCs were found to be attracted by NB cells, and to affect NB cell proliferation with different results depending on the cell line tested. Moreover, NB cells, after pre-incubation with hMSCs, acquired a more invasive behavior towards CXCL12 and the bone marrow, i.e., the primary site of NB metastases. In conclusion, this study demonstrates that functional cross-talk between MSCs and NB cell lines used in our experiments can occur only within short range interaction. Thus, this report does not support the clinical use of MSCs as vehicles for selective delivery of antitumor drugs at the NB site unless chemotherapy and/or radiotherapy create suitable local conditions for MSCs recruitment.     

Setting the Record Straight on Data Supporting Postnatal Oogenesis in Female Mammals

Of all the ‘certainties’ in mammalian female reproductive biology, the concept that a non-renewing oocyte reserve is set forth in the ovaries at birth may be the most longstanding and widely held. However, when data from our studies of oocyte apoptosis unintentionally began to contradict this theory in the latter part of 2002, we embarked on an investigation, unbiased by any pre-conceived dogmas, to determine if oocyte production persists in adult female mice. In 2004, we presented our first experimental findings in the journal Nature, which indicated that oogenesis indeed continues in adulthood. Amidst widespread skepticism, we moved forward with our studies and this year published our follow-up experiments in the journal Cell. Results from this latter body of work not only reinforced our earlier conclusions but also identified bone marrow as a surprising source of oocyte-producing germ cells in adults. Although this study has also been met with skepticism, doubts raised in commentaries on our work are largely based on inaccurate or incomplete assessments of our experimental models and results. Here we have attempted to clarify published misperceptions and misinterpretations of our data, and offer additional insights that challenge the idea of fixed endowment of oocytes at birth.     

Binding of myosin subfragment-1 to F-actin.

During a part of the hydrolytic cycle, myosin head (S1) carries no nucleotide and binds strongly to an actin filament forming a rigor bond. At saturating concentration of S1 in rigor, S1 is well known to form 1:1 complex with actin. However, we have provided evidence that under certain conditions S1 could also form a complex with 2 actin monomers in a filament (Andreev, O.A. & Borejdo, J. (1991) Biochem. Biophys. Res. Comm. 177, 350-356). This view was recently challenged by Carlier & Didry (Carlier, M-F. & Didry, D. (1992) Biochem. Biophys. Res. Comm. 183, 970-974) who interpreted our data by suggesting that F-actin underwent a simple depolymerization and implied that, when only actin in the F-form was scored, the real stoichiometry in our experiments was 1:1. We show here that under conditions of our experiments less than 8% of actin was depolymerized. Moreover, we have repeated the experiments in the presence of phalloidin and show that under these conditions too, when S1 was added slowly to a fixed concentration of F-actin, it formed a different complex with F-actin than when it was added quickly. This confirms our original conclusion that S1 can bind actin in two different ways and shows that depolymerization of F-actin is not responsible for this finding.     

Effect of Diet and Strain Difference on the Virulence of Staphylococcus aureus for Mice

Years of intensive investigations in our laboratories on staphylococcal infections in mice have indicated a gradual decrease in the virulence of Staphylococcus aureus for this animal, particularly the strain we were using, the random-bred BT mouse. The present investigations, based on changes in diet and strain differences in mice, were undertaken in an attempt to improve susceptibility of our stock strain, on the one hand, and to determine whether susceptibility was influenced by genetic strain differences, on the other. In the first series of experiments, littermate mice of the BT strain were placed on different diets: one group received a commercial diet; the other, a basic diet previously established in our laboratories as adequate for growth requirements of the animals. An increase in the susceptibility of the animals to staphylococcal infection was noted in the mice receiving the basic diet. In the second series of investigations, three other strains of mice (the Swiss albino, the C3H/HeJ, and the C57B1) previously not used by our laboratories in staphylococcal experiments were studied for staphylococcal susceptibility. These experiments revealed that all of these strains of mice were highly susceptible to the infection, even though they were maintained on a commercial diet.     

The nature and context of exploratory experimentation: an introduction to three case studies of exploratory research

My aim in this article is to introduce readers to the topic of exploratory experimentation and briefly explain how the three articles that follow, by Richard Burian, Kevin Elliott, and Maureen O'Malley, advance our understanding of the nature and significance of exploratory research. I suggest that the distinction between exploratory and theory-driven experimentation is multidimensional and that some of the dimensions are continuums. I point out that exploratory experiments are typically theory-informed even if they are not theory-driven. I also distinguish between research programs and experiments. Research programs that are largely exploratory, such as the ones discussed in these case studies, can involve both exploratory and theory-driven experimentation.     

The human embryo: a scientist's point of view

...Thus, my judgement is that a human embryo is not a human person, and so we may do experiments on it which involve killing it. But my judgement is also that a human embryo has the potential to become a human being. The consequence of this attribute is that it imposes limits on the kinds of experiments which may be performed on human embryos. It is this which sets the boundaries. Experiments which may harm the embryo while still allowing it subsequently to realise its potential, and become a person, should not be permitted. It is the potentiality of the human embryo which governs our behaviour towards it. Its potential makes it special, and radically different from any other human tissue. This potential which the early embryo has means that great respect must always be accorded it, and great thought and care must surround any dealings with it....     

Lab and field experiments: Are they the same animal?

To advance our understanding of biological processes we often plan our experiments based on published data. This can be confusing though, as data from experiments performed in a laboratory environment are sometimes different from, or completely opposite to, findings from similar experiments performed in the “real world”. In this mini-review, we discuss instances where results from laboratory experiments differ as a result of laboratory housing conditions, and where they differ from results gathered in the field environment. Experiments involving endocrinology and behavior appear to be particularly susceptible to influence from the environment in which they are performed.As such, we have attempted to promote discussion of the influence of housing environment on the reproductive axis, circadian biology and behavior, immune function, stress biology, neuroplasticity and photoperiodism. For example, why should a rodent species be diurnal in one housing environment yet nocturnal in another? Are data that are gathered from experiments in the laboratory applicable to the field environment, and vice-versa? We hope not only to highlight the need for experiments in both lab and field when looking at complex biological systems, but also to promote frank discussion of discordant data. Perhaps, just as study of individual variation has been gaining momentum in recent years, data from variation between experimental arenas can provide us with novel lines of research.     

Estimation of the rate and effect of new beneficial mutations in asexual populations

The rate and effect of available beneficial mutations are key parameters in determining how a population adapts to a new environment. However, these parameters are poorly known, in large part because of the difficulty of designing and interpreting experiments to examine the rare and intrinsically stochastic process of mutation occurrence. We present a new approach to estimate the rate and selective advantage of beneficial mutations that underlie the adaptation of asexual populations. We base our approach on the analysis of experiments that track the effect of newly arising beneficial mutations on the dynamics of a neutral marker in evolving bacterial populations and develop efficient estimators of mutation rate and selective advantage. Using extensive simulations, we evaluate the accuracy of our estimators and conclude that they are quite robust to the use of relatively low experimental replication. To validate the predictions of our model, we compare theoretical and experimentally determined estimates of the selective advantage of the first beneficial mutation to fix in a series of ten replicate populations. We find that our theoretical predictions are not significantly different from experimentally determined selection coefficients. Application of our method to suitably designed experiments will allow estimation of how population evolvability depends on demographic and initial fitness parameters.