The Scalpel and the Butterfly: The Conflict between Animal Research and Animal Protection Deborah Rudacille

ABSTRACT

Although there is a substantial body of research on inter-human empathy and inter-animal empathy, there is a dearth of research comparing humans' empathic reactions to humans and animals. To address this issue, three experiments were conducted in which participants read a scenario about a human or animal abuse victim in need of medical attention, and indicated the degree of empathy they had on an emotional response scale. In Experiment 1, women had significantly more empathy for animals than for humans, whereas men tended to express more empathy for humans than for animals. In Experiment 2, adult women expressed the same degree of empathy for a child as for a puppy. Similarly, in Experiment 3, adult men and women expressed the same degree of empathy for a baby as for a puppy. Overall, results indicated that people feel at least as much empathy for animals as for humans. We suggest that an animal target elicits a great deal of empathy partly because it is perceived as not being responsible for having caused the need situation. Future research will show whether empathy for animals translates to prosocial behavior toward them as well.     

A Systems Model Approach to Determining Resilience Surrogates for Case Studies

Resilience theory offers a framework for understanding the dynamics of complex systems. However, operationalizing resilience theory to develop and test empirical hypotheses can be difficult. We present a method in which simple systems models are used as a framework to identify resilience surrogates for case studies. The process of constructing a systems model for a particular case offers a path for identifying important variables related to system resilience, including the slowly-changing variables and thresholds that often are keys to understanding the resilience of a system. We develop a four-step process for identifying resilience surrogates through development of systems models. Because systems model development is often a difficult step, we summarize four basic existing systems models and give examples of how each may be used to identify resilience surrogates. The construction and analysis of simple systems models provides a useful basis for guiding and directing the selection of surrogate variables that will offer appropriate empirical measures of resilience.     

Screening for functional expression and overexpression of a family of diiron-containing interfacial membrane proteins using the univector recombination system

The large number of uncharacterized genes emerging from genome sequencing projects has resulted in a need for quick and reliable screening methods for protein expression parameters. We have utilized the univector plasmid recombination system (as previously reported) to develop a series of vectors for rapid screening for expression in Escherichia coli. A high level of recombinant protein expression is a requirement for purification of protein for structural determination and other purposes. In other applications, successful complementation of a missing enzyme activity in E. coli, as well as directed evolution studies and metabolic engineering, often require a much lower level of protein expression. In this report we describe the construction of a number of new pHOST vectors that can be screened for both low- and high-level expression. We isolated a mutant vector for MBP fusions that exhibited a more optimal level of expression for complementation of aerobic respiration in hemA(-) E. coli, our functional assay for the alternative oxidase. We then demonstrated the use of our system to rapidly screen for both optimal functional expression and optimal overexpression of the alternative oxidase as well as two other members of a family of membrane-bound diiron carboxylate proteins, the plastid terminal oxidase and 5-demethoxyquinone hydroxylase.     

Ecologically Differentiated Rules of Thumb for Habitat Network Design – Lessons from a Formula

The present paper addresses the following typical question of metapopulation management: “What habitat distribution is optimal for metapopulation persistence if a habitat network with a given number and configuration of patches is considered?”. By utilizing a generic metapopulation model and performing a special model analysis, rules of thumb for optimum habitat distribution and a general ‘Principle of Optimality’ are derived. The whole study is based on the application of a formula for the mean lifetime of metapopulations derived in a previous study. Finally, some general conclusions are drawn concerning the potential of using PVA techniques for deriving tools for decision support for conservation management.     

Repetitive mating and female fitness in Dysdercus cardinalis (Hemiptera: Pyrrhocoridae)

Using three mating-treatment groups–pairing with a male for life, pairing with a male from adult emergence to first oviposition, and no pairing (virgin)–of Dysdercus cardinalis females in a laboratory study, the following results were obtained. Most of the virgin females did not lay eggs; those that did oviposited for the first time at a considerably older age than females in the other two groups. In a lifetime, females pairing with a male for life and those pairing with a male up to first oviposition produced essentially the same number of eggs, and this was more than 3.5 times the number of eggs laid by a virgin female. Virgin females produced an average of 1.3 clutches in a lifetime, compared with about 4.5 clutches produced by females in the other two groups. Reproductive span was significantly shorter, and fecundity per day of reproductive span significantly greater, for females pairing with males for life than for those pairing with a male up to first oviposition. Age at death was significantly different amongst females in different mating-treatment groups. Virgin females had the longest life, followed by females pairing with a male up to first oviposition and females pairing with a male for life, in that order. There was a positive correlation between lifetime gross reproduction and age at death for females pairing with a male for life. There was no relationship between these two characters for females pairing with a male up to first oviposition. Both females pairing with a male for life and those pairing with a male to first oviposition exhibited a significant inverse relationship between fecundity per day and age at death. The results obtained indicate that (1) mating is a prerequisite for normal gonadal activity in Dysdercus cardinalis , and (2) repetitive mating increases the rate of reproduction. This would reduce the mean age of parenthood which is inversely related to the intrinsic rate of increase.     

A Major Gene for Resting Metabolic Rate Unassociated with Body Composition: Results from the Québec Family Study

A major gene hypothesis for resting metabolic rate (RMR) was investigated using segregation analysis (POINTER) of data on families participating in Phase 2 of the Québec Family Study. Complete analyses were conducted on RMR adjusted for age, and also on RMR adjusted for age and other covariates, primarily fat mass (FM) and fat-free mass (FFM). Prior to adjustment for covariates, support for a major gene hypothesis was equivocal — i.e., there was evidence for either a major gene or a multifactorial component (i.e., polygenic and/or familial environment). The multifactorial model was preferred over the major gene model, although the latter did segregate according to Mendelian expectations. However, after the effects of FM and FFM were accounted for, a major gene effect was unambiguous and compelling. The putative locus accounted for 57% of the variance, affected 7% of the sample, and led to high values of RMR. The lack of a significant multifactorial effect suggested that the familial etiology of RMR adjusted for FM and FFM was likely to be entirely a function of the major locus. Comparing the RMR results from pre- and post-adjustment for FM and FFM suggests a plausible hypothesis. We know from earlier studies in this sample that there is a putative major gene for FM and a major non-Mendelian effect for FFM. The current study leads us to speculate that: (1) the gene(s) affecting body size and body composition also may have an effect on RMR, and further (2) removal of the effect of the major gene(s) for body size and composition allowed for detection of an additional major gene affecting only the RMR. Thus, RMR appears to be an oligogenic trait.     

Models and estimators linking individual-based and sample-based rarefaction,extrapolation and comparison of assemblages

Aims In ecology and conservation biology, the number of species counted in a biodiversity study is a key metric but is usually a biased underestimate of total species richness because many rare species are not detected. Moreover, comparing species richness among sites or samples is a statistical challenge because the observed number of species is sensitive to the number of individuals counted or the area sampled. For individual-based data, we treat a single, empirical sample of species abundances from an investigator-defined species assemblage or community as a reference point for two estimation objectives under two sampling models: estimating the expected number of species (and its unconditional variance) in a random sample of (i) a smaller number of individuals (multinomial model) or a smaller area sampled (Poisson model) and (ii) a larger number of individuals or a larger area sampled. For sample-based incidence (presence–absence) data, under a Bernoulli product model, we treat a single set of species incidence frequencies as the reference point to estimate richness for smaller and larger numbers of sampling units.Methods The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants.Important findings Surprisingly, for all datasets we examined, the interpolation (rarefaction) curve and the extrapolation curve meet smoothly at the reference sample, yielding a single curve. Moreover, curves representing 95% confidence intervals for interpolated and extrapolated richness estimates also meet smoothly, allowing rigorous statistical comparison of samples not only for rarefaction but also for extrapolated richness values. The confidence intervals widen as the extrapolation moves further beyond the reference sample, but the method gives reasonable results for extrapolations up to about double or triple the original abundance or area of the reference sample. We found that the multinomial and Poisson models produced indistinguishable results, in units of estimated species, for all estimators and datasets. For sample-based abundance data, which allows the comparison of all three models, the Bernoulli product model generally yields lower richness estimates for rarefied data than either the multinomial or the Poisson models because of the ubiquity of non-random spatial distributions in nature.     

Estimation and confidence regions for multi-dimensional effective dose

The problem of finding confidence regions for multiple predictor variables corresponding to given expected values of a response variable has not been adequately resolved. Motivated by an example from a study on hyperbaric exposure using a logistic regression model, we develop a conceptual framework for the estimation of the multi-dimensional effective dose for binary outcomes. The k -dimensional effective dose can be determined by conditioning on k - 1 components and solving for the last component as a conditional univariate effective dose. We consider various approaches for calculating confidence regions for the multi-dimensional effective dose and compare them via a simulation study for a range of possible designs. We analyze data related to decompression sickness to illustrate our procedure. Our results provide a practical approach to finding confidence regions for predictor variables for a given response value.     

A reduced muscle model and planar musculoskeletal model fit for the simulation of whole-body movements

Musculoskeletal models are made to reflect the capacities of the human body in general, and often a specific subject in particular. It remains challenging to both model the musculoskeletal system and then fit the modelled muscles to a specific human subject. We present a reduced muscle model, a planar musculoskeletal model, and a fitting method that can be used to find a feasible set of active and passive muscle parameters for a specific subject. At a minimum, the fitting method requires inverse dynamics data of the subject, a scalar estimate of the peak activation reached during the movement, and a plausible initial estimate for the strength and flexibility of that subject. While additional data can be used to result in a more accurate fit, this data is not required for the method solve for a feasible fit. The minimal input requirements of the proposed fitting method make it well suited for subjects who cannot undergo a maximum voluntary contraction trial, or for whom recording electromyographic data is not possible. To evaluate the model and fitting method we adjust the musculoskeletal model so that it can perform an experimentally recorded stoop-lift of a 15 kg box.     

Mapping quantitative trait Loci underlying fitness-related traits in a free-living sheep population

We searched for quantitative trait loci (QTL) underlying fitness-related traits in a free-living pedigree of 588 Soay sheep in which a genetic map using 251 markers with an average spacing of 15 cM had been established previously. Traits examined included birth date and weight, considered both as maternal and offspring traits, foreleg length, hindleg length, and body weight measured on animals in August and jaw length and metacarpal length measured on cleaned skeletal material. In some cases the data were split to consider different age classes separately, yielding a total of 15 traits studied. Genetic and environmental components of phenotypic variance were estimated for each trait and, for those traits showing nonzero heritability (N= 12), a QTL search was conducted by comparing a polygenic model with a model including a putative QTL. Support for a QTL at genome-wide significance was found on chromosome 11 for jaw length; suggestive QTL were found on chromosomes 2 and 5 (for birth date as a trait of the lamb), 8 (birth weight as a trait of the lamb), and 15 (adult hindleg length). We discuss the prospects for refining estimates of QTL position and effect size in the study population, and for QTL searches in free-living pedigrees in general.     

Quantitative T2 mapping for detection and quantification of thrombophlebitis in a rabbit model

Short peripheral catheter thrombophlebitis (SPCT), a sterile inflammation of the vein wall, is the most common complication associated with short peripheral catheters (SPCs) and affects up to 80% of hospitalized patients receiving IV therapy. Extensive research efforts have been devoted for improvement and optimization of the catheter material, but means for examination of any novel design are limited, inaccurate and require costly comprehensive pre-clinical and clinical trials. Therefore, there is a conclusive need for a reliable quantitative method for evaluation of SPCT, in particular for research purposes examining the thrombophlebitis-related symptoms of any novel catheter design. In this study, we developed for the first time a quantitative MRI based tool for evaluation of SPCT. The extent and severity of SPCT caused by two different commercially available SPCs with known predisposition for thrombophlebitis, were studied in a rabbit model. MRI analysis was consistent with the standardized pathology evaluation and showed remarkable difference in the percent of edema between the experimental groups. These differences were in line with previous studies and provide evidence that this type of analysis may be useful for future assessment of SPCT in vivo. As a non-invasive method, it may constitute a cost effective solution for examination of new catheters and other medical devices, thereby reducing the need for animal sacrifice.     

Cloning Vectors for Rice

We developed various binary vectors that can be used for expressing a foreign gene in rice. Vectors pGA3426, pGA3436, and pGA3626 are intended for overexpression of a gene using the maize Ubiquitin promoter, whereas pGA3780 is for rather mild expression of a gene using the rice Actin1 promoter. Vector pGA3777 is for expressing two genes simultaneously. We also developed binary vectors for expressing a fusion protein with a tag. Four vectors (pGA3427, pGA3428, pGA3429, and pGA3438) are for protein tags with sGFP, HA, His, and Myc, respectively. Vector pGA3383 is for analyzing promoter activity using the GUS reporter. In this vector, multiple cloning sites in front of GUS can be utilized for accepting a promoter fragment. We also generated transient expression vectors for studying the subcellular localization of a protein. Vectors pGA3452, pGA3651, and pGA3652 are for GFP fusion; pGA3574 for RFP fusion; pGA3697 for Myc tag; and pGA3698 for HA tag. In addition, we generated pGA3506, pGA3516, pGA3592, and pGA3593 for facilitating the subcloning of full-length cDNA clones into our binary vectors.     

A disposable and cost efficient microfluidic device for the rapid chip-based electrical detection of DNA

Requirements for a point-of-care device are an easy and robust read-out and – above all – a simple handling. We integrated an established robust electrical read-out for DNA-chips into a microfluidic device, thereby creating an automated analysis system that combines the necessary steps for a chip-based analysis. It is based on the electrical detection of biotin-labeled DNA in a gap between two microstructured electrodes on the surface of a DNA-chip. The biotin serves as binding molecule for streptavidin-conjugated horseradish peroxidase. A following enzyme-induced silver deposition bridges the gap by a conductive layer. The miniaturized chip gives the possibility to realize a durable system suitable for point-of-care applications.To enable an initial automation, all corresponding process steps were executed in a miniaturized silicone flow cell. The required defined temperatures for the hybridization and the washing steps can be adjusted by a heating foil.This paper characterizes the performance of the flow cell based system in terms of reaction speed and analysis time, sensitivity as well as specificity, and the comparison to a conventional system, without flow cell. These first steps of automation and integration will help to realize a laboratory-independent bioanalytical tool, for the use outside of specialized laboratories for fast analysis of different chemical and biological applications.     

Preservation of immobilized bacterial cell-matrix by drying for direct use in microbial sensors

A simple and effective method for the drying of immobilized bacterial cells to be used directly in a microbial biosensor for measurement of activity is reported. As a case example, plasmid-bearing cells of Alcaligenes eutrophus JMP 134, DSM 4058 were immobilized on various carriers and liquid-dried. The dried cell-matrix was used directly after rehydration/reactivation as the biological component of a biosensor for determining the concentration of xenobiotic compounds in the environment. Good viability results were obtained after long-term storage and cells exhibited no loss of plasmids responsible for the 2,4-dichlorophenoxyacetic acid (2,4-D) degradation. The activity of the cells for 2,4-D was proved using a respiration electrode. No time-consuming, repeated cell cultivation and harvesting was required, as the cells preserved from a single batch served as a continuous source for activity measurements. Many other microbial cultures can be preserved by this method and the cells preserved in the form of immobilized dried cell-matrix can be used directly to perform enzymatic tests, complex biochemical conversions and for production in the reactors. The dried cell-matrix can serve as a stable interchangeable component for a multipurpose biosensor.     

Loss of gametophytic self-incompatibility with evolution of inbreeding depression

Gametophytic self-incompatibility (SI) in plants is a widespread mechanism preventing self-fertilization and the ensuing inbreeding depression, but it often evolves to self-compatibility. We analyze genetic mechanisms for the breakdown of gametophytic SI, incorporating a dynamic model for the evolution of inbreeding depression allowing for partial purging of nearly recessive lethal mutations by selfing, and accounting for pollen limitation and sheltered load linked to the S-locus. We consider two mechanisms for the breakdown of gametophytic SI: a nonfunctional S-allele and an unlinked modifier locus that inactivates the S-locus. We show that, under a wide range of conditions, self-compatible alleles can invade a self-incompatible population. Conditions for invasion are always less stringent for a nonfunctional S-allele than for a modifier locus. The spread of self-compatible genotypes is favored by extremely high or low selfing rates, a small number of S-alleles, and pollen limitation. Observed parameter values suggest that the maintenance of gametophytic SI is caused by a combination of high inbreeding depression in self-incompatible populations coupled with intermediate selfing rates of the self-compatible genotypes and sheltered load linked to the S-locus.     

Optimization of batch processes involving simultaneous enzymatic and microbial reactions

Two general models for batch simultaneous enzymatic and microbial reaction (SEMR) processes are presented, the second derived from and simpler than the first and accounting for enzyme denaturation. Using the second model and parameter values from the literature, simulation was used to examine a range of enzyme addition rate strategies (in which the rate was a linear function of time) for a relatively fast ethanol fermentation and for a longer duration citric acid fermentation, both using cellulose as the substrate. For the ethanol process it is optimal (for a specific objective function which accounts for product value and enzyme cost) to add all the enzyme at the beginning of the process. But for the citric acid process a linearly decreasing enzyme addition rate, coupled with the addition of a small fraction of the enzyme at time zero, is better than pure batch operation or operation with the best constant enzyme feed rate.     

An optimal shape problem related to the realistic design of river fishways

A river fishway is a hydraulic structure that facilitates fish in overcoming obstacles (dams, waterfalls, etc.) to their spawning and other migrations in rivers. In this work we present a mathematical formulation of an optimal design problem for a vertical slot fishway, where the state system is given by the 2D shallow water equations fixing the height and velocity of water, the design variables are the geometry of the slots, and the objective function is determined by the existence of rest areas for fish and of a water velocity suitable for fish swimming capability. We also derive an expression for the gradient of the objective function via the adjoint system. From the numerical point of view, we present a characteristic-Galerkin method for solving the shallow water equations, and a direct search algorithm for the computation of the optimal design variables. Finally, we give numerical results obtained for a standard ten pools channel.     

A generalized heterozygote deficiency assessed with microsatellites in French common ash populations

Common ash is a temperate forest tree with a colonizing behaviour, a discontinuous spatial distribution and a peculiar and poorly known mating system. Microsatellite markers were used to study the genetic structure in natural populations of common ash. Twelve populations located in northeastern France were analysed at five loci. Levels of genetic variability within and among stands were estimated for the seedling and adult stages. As expected for a forest tree, our results reveal high levels of intrapopulation diversity and a low genetic differentiation between stands. However, a general and significant heterozygote deficiency was found, with a mean F(IS) of 0.163 for the seedlings and of 0.292 for the adult trees. The different explanations for such an excess homozygosity are discussed: a nonMendelian inheritance of alleles, the presence of null alleles, a Wahlund effect and assortative mating.     

A Bayesian Semiparametric Survival Model with Longitudinal Markers

Summary We consider inference for data from a clinical trial of treatments for metastatic prostate cancer. Patients joined the trial with diverse prior treatment histories. The resulting heterogeneous patient population gives rise to challenging statistical inference problems when trying to predict time to progression on different treatment arms. Inference is further complicated by the need to include a longitudinal marker as a covariate. To address these challenges, we develop a semiparametric model for joint inference of longitudinal data and an event time. The proposed approach includes the possibility of cure for some patients. The event time distribution is based on a nonparametric Pólya tree prior. For the longitudinal data we assume a mixed effects model. Incorporating a regression on covariates in a nonparametric event time model in general, and for a Pólya tree model in particular, is a challenging problem. We exploit the fact that the covariate itself is a random variable. We achieve an implementation of the desired regression by factoring the joint model for the event time and the longitudinal outcome into a marginal model for the event time and a regression of the longitudinal outcomes on the event time, i.e., we implicitly model the desired regression by modeling the reverse conditional distribution.     

Site-dependent Life-Cycle Impact Assessment in Sweden (5 pp)

Goal, Scope and Background Although LCA is traditionally a site-independent tool, there is currently a trend towards making LCA more site-dependent if not site-specific. For Europe, site-dependent impact factors have been calculated on a country basis for acidification, terrestrial eutrophication and toxicological impacts. It is, however, an open question whether this is the optimum level for site-dependent factors. The aim of this paper is to develop site-dependent characterisation factors for different parts of Sweden for air emissions of NOx, SOx and particulates regarding ecosystem and human health impacts. Based on experiences from a case-study, the usability of the site-dependent factors for LCA are discussed, as well as the appropriate level of site-dependency for ecosystem and human health impacts. Method logy. The Ecosense model is used for calculating site-dependent factors for some atmospheric pollutants. Characterisation factors are calculated for four different places in Sweden with two different stack heights. Results and Conclusions The characterisation factors for ecosystem impacts show fairly small differences between different parts of Sweden (within a factor of two). For health impacts, the differences between different parts of the country were larger and more significant (up to one order of magnitude). Also the difference between low and high stack heights may be relevant, especially in densely populated areas. These results suggest that for ecosystems, site-dependent characterisation factors for the considered atmospheric pollutants on a country level may be sufficient for most applications. However, for health impacts, site-dependent factors on a country level may be inappropriate. Beside LCA, the calculated factors and the methodology used should also be useful for other environmental system analysis tools, such as Strategic Environmental Assessment, Cost-Benefit Analysis and Environmental Management Systems.