Interactions and trade-offs among physiological determinants of performance and reproductive success

How an animal performs in its natural environment ultimately plays a key role in its reproductive success. While a number of studies have investigated how selection acts on performance-related traits, far fewer studies have examined the mechanisms responsible for variation in performance. Among mechanisms, variable morphology has received the most attention. Although physiological traits have received less attention, they are intrinsically related to performance and ultimately to reproductive success. We present a framework whereby investigators can link some basic physiological functions with organismal performance and ultimately with reproductive success. We propose that performance and ultimately reproductive success are strongly influenced by hormones, immune functions, and energetics. We further argue that no physiological function can be considered in isolation and thus our model emphasizes interactions and trade-offs both within each physiological function as well as among them. Some of the most commonly studied trade-offs are between reproduction and immune functions, with energetics as one of the key common currencies for these trade-offs. From an evolutionary perspective, the largest gaps in our knowledge lie in how these interactions and trade-offs influence reproductive success. We believe that a full understanding of how hormones, immune functions, and energetics influence performance traits related to reproduction and, ultimately, lifetime reproductive success requires recognition of the complex relationships, interactions, and trade-offs among these processes.     

Classical and resource-based competition: a unifying graphical approach

A graphical technique is given for determining the outcome of two species competition for two resources. This method is unifying in the sense that the graphical criterion leading to the various outcomes of competition are consistent across most of the spectrum of resource types (from those that fulfill the same growth needs to those that fulfill different needs) regardless of the classification method used, and the resulting graphs bear a striking resemblance to the well-known phase portraits for two species Lotka–Volterra competition. Our graphical method complements that of Tilman. Both include zero net growth isoclines. However, instead of using the consumption vectors at potential coexistence equilibria to determine input resource concentrations leading to specific competitive outcomes, we introduce curves bounding the feasible set (the set where the resource concentrations of any equilibrium solution must be located). The washout equilibrium (corresponding to the supply point) occurs at an intersection of curves defining the feasible set boundary. The resource concentrations of all other equilibria are found where zero net growth isoclines either intersect each other inside the feasible set or they intersect the feasible set boundary. A species has positive biomass at such an equilibrium only if its zero net growth isocline is involved in such an intersection. The competitive outcomes are then determined from the position of the single species equilibria, just as in the phase portrait analysis for classical competition (rather than from information at potential coexistence equilibria as in Tilman’s method).     

Leptin as a physiological mediator of energetic trade-offs in ecoimmunology: implications for disease

Organisms must distribute sufficient energy among different and often competing physiological systems. This task can become challenging, however, as resources are often limiting, resulting in energetic trade-offs. For example, energetically based trade-offs between the reproductive and immune systems are common across taxa, yet the regulatory mechanisms underlying these trade-offs remain unclear. The adipose tissue hormone leptin is an ideal candidate for the modulation of energetic trade-offs between different physiological systems as this hormone serves as a gage of fat reserves and also modulates a range of physiological activities including the reproductive and immune processes. This article presents a review of the evidence for the role of leptin as a modulator of energetic trade-offs with the immune system and suggests its importance in disease ecology. In addition, we provide a case study of the ornate tree lizard (Urosaurus ornatus), testing whether leptin is involved in mediating a well-documented influence of energy state on the trade-off between reproductive activity and immune function. Overall, the combined results suggest that leptin serves as a proximate endocrine signal of available energy to the immune system, and therefore likely to affect susceptibility to diseases.     

Seasonal changes in vertebrate immune activity: mediation by physiological trade-offs

Animals living in temporally dynamic environments experience variation in resource availability, climate and threat of infection over the course of the year. Thus, to survive and reproduce successfully, these organisms must allocate resources among competing physiological systems in such a way as to maximize fitness in changing environments. Here, we review evidence supporting the hypothesis that physiological trade-offs, particularly those between the reproductive and immune systems, mediate part of the seasonal changes detected in the immune defences of many vertebrates. Abundant recent work has detected significant energetic and nutritional costs of immune defence. Sometimes these physiological costs are sufficiently large to affect fitness (e.g. reproductive output, growth or survival), indicating that selection for appropriate allocation strategies probably occurred in the past. Because hormones often orchestrate allocations among physiological systems, the endocrine mediators of seasonal changes in immune activity are discussed. Many hormones, including melatonin, glucocorticoids and androgens have extensive and consistent effects on the immune system, and they change in systematic fashions over the year. Finally, a modified framework within which to conduct future studies in ecological immunology is proposed, viz. a heightened appreciation of the complex but intelligible nature of the vertebrate immune system. Although other factors besides trade-offs undoubtedly influence seasonal variation in immune defence in animals, a growing literature supports a role for physiological trade-offs and the fitness consequences they sometimes produce.     

Rhodopsin determinants for transducin activation: a gain-of-function approach

Three cytoplasmic loops in the G protein-coupled receptor rhodopsin, C2, C3, and C4, have been implicated as key sites for binding and activation of the visual G protein transducin. Non-helical portions of the C2- and C3-loops and the cytoplasmic helix-8 from the C4 loop were targeted for a "gain-of-function" mutagenesis to identify rhodopsin residues critical for transducin activation. Mutant opsins with residues 140-148 (C2-loop), 229-244 (C3-loop), or 310-320 (C4-loop) substituted by poly-Ala sequences of equivalent lengths served as templates for mutagenesis. The template mutants with poly-Ala substitutions in the C2- and C3-loops formed the 500-nm absorbing pigments but failed to activate transducin. Reverse substitutions of the Ala residues by rhodopsin residues have been generated in each of the templates. Significant ( approximately 50%) restoration of the rhodopsin/transducin coupling was achieved with re-introduction of residues Cys140/Lys141 and Arg147/Phe148 into the C2 template. The reverse substitutions of the C3-loop residues Thr229/Val230 and Ser240/Thr242/Thr243/Gln244 produced a pigment with a full capacity for transducin activation. The C4 template mutant was unable to bind 11-cis-retinal, and the presence of Asn310/Lys311 was required for correct folding of the protein. Subsequent mutagenesis of the C4-loop revealed the role of Phe313 and Met317. On the background of Asn310/Lys311, the inclusion of Phe313 and Met317 produced a mutant pigment with the potency of transducin activation equal to that of the wild-type rhodopsin. Overall, our data support the role of the three cytoplasmic loops of rhodopsin and suggest that residues adjacent to the transmembrane helices are most important for transducin activation.     

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

Background

The etiology of complex diseases is due to the combination of genetic and environmental factors, usually many of them, and each with a small effect. The identification of these small-effect contributing factors is still a demanding task. Clearly, there is a need for more powerful tests of genetic association, and especially for the identification of rare effects

Results

We introduce a new genetic association test based on symbolic dynamics and symbolic entropy. Using a freely available software, we have applied this entropy test, and a conventional test, to simulated and real datasets, to illustrate the method and estimate type I error and power. We have also compared this new entropy test to the Fisher exact test for assessment of association with low-frequency SNPs. The entropy test is generally more powerful than the conventional test, and can be significantly more powerful when the genotypic test is applied to low allele-frequency markers. We have also shown that both the Fisher and Entropy methods are optimal to test for association with low-frequency SNPs (MAF around 1-5%), and both are conservative for very rare SNPs (MAF<1%)

Conclusions

We have developed a new, simple, consistent and powerful test to detect genetic association of biallelic/SNP markers in case-control data, by using symbolic dynamics and symbolic entropy as a measure of gene dependence. We also provide a standard asymptotic distribution of this test statistic. Given that the test is based on entropy measures, it avoids smoothed nonparametric estimation. The entropy test is generally as good or even more powerful than the conventional and Fisher tests. Furthermore, the entropy test is more computationally efficient than the Fisher's Exact test, especially for large number of markers. Therefore, this entropy-based test has the advantage of being optimal for most SNPs, regardless of their allele frequency (Minor Allele Frequency (MAF) between 1-50%). This property is quite beneficial, since many researchers tend to discard low allele-frequency SNPs from their analysis. Now they can apply the same statistical test of association to all SNPs in a single analysis., which can be especially helpful to detect rare effects.     

Permutation-validated principal components analysis of microarray data

Background  

In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting genes are crucial tasks. Multivariate statistical methods have been applied to analyze these large datasets. Less work has been published concerning the assessment of the reliability of gene-selection procedures. Here we describe a method to assess reliability in multivariate microarray data analysis using permutation-validated principal components analysis (PCA). The approach is designed for microarray data with a group structure.     

A principal components analysis of human odontometrics

It has long been recognized that tooth crown diameters in hominoids are all positively intercorrelated one with another. This study reports on sex-specific correlation matrices derived from 2,650 individuals from the Solomon Islands, Melanesia. Mesiodistal and buccolingual diameters of all permanent teeth from one side are used, excluding third molars. Analysis discloses significant sex dimorphism in the strengths of the intercorrelations, with females being better integrated. Principal components analysis (PCA) provides an objective means of data reduction (shown here to be preferable to simple size summation methods) and decorrelation of the resulting linear combinations. Four components are extracted (with results being virtually identical in the two sexes) and arguments are put forth that varimax rotation to "a simpler solution" may be counterproductive. Before rotation, the four components are 1) overall size, 2) buccolingual widths contrasted with mesiodistal lengths, 3) anterior (I,C) contrasted with posterior (P,M) teeth, and 4) premolars contrasted with molars. Most of the explained (shared) variance (63%) extracted by PCA is in overall size of the dentition. There is a strong urge to view the results of these principal components analyses as reflective of biologically and genetically meaningful entities.     

Cross-cultural adaptation of instruments assessing breastfeeding determinants: a multi-step approach

Background

Cross-cultural adaptation is a necessary process to effectively use existing instruments in other cultural and language settings. The process of cross-culturally adapting, including translation, of existing instruments is considered a critical set to establishing a meaningful instrument for use in another setting. Using a multi-step approach is considered best practice in achieving cultural and semantic equivalence of the adapted version. We aimed to ensure the content validity of our instruments in the cultural context of KwaZulu-Natal, South Africa.

Methods

The Iowa Infant Feeding Attitudes Scale, Breastfeeding Self-Efficacy Scale-Short Form and additional items comprise our consolidated instrument, which was cross-culturally adapted utilizing a multi-step approach during August 2012. Cross-cultural adaptation was achieved through steps to maintain content validity and attain semantic equivalence in the target version. Specifically, Lynn’s recommendation to apply an item-level content validity index score was followed. The revised instrument was translated and back-translated. To ensure semantic equivalence, Brislin’s back-translation approach was utilized followed by the committee review to address any discrepancies that emerged from translation.

Results

Our consolidated instrument was adapted to be culturally relevant and translated to yield more reliable and valid results for use in our larger research study to measure infant feeding determinants effectively in our target cultural context.

Conclusions

Undertaking rigorous steps to effectively ensure cross-cultural adaptation increases our confidence that the conclusions we make based on our self-report instrument(s) will be stronger. In this way, our aim to achieve strong cross-cultural adaptation of our consolidated instruments was achieved while also providing a clear framework for other researchers choosing to utilize existing instruments for work in other cultural, geographic and population settings.

     

Stress in plants: physiological approach

The problem of stress in current plant physiology is examined. The review of different points of view on this problem is given.     

Managing water-use trade-offs in a semi-arid river delta to sustain multiple ecosystem services: a modeling approach

Managing trade-offs among water uses in a river basin to sustain multiple ecosystem services is crucial for adaptation to changing river flow regimes. Here we analyze the trade-off between irrigation and fisheries in the Amudarya, a semi-arid river basin in Central Asia, using an optimal control and an agent-based modeling approach. With the optimal control approach (OCA), we identify the economic and ecological conditions for water sharing in a regime where a social manager controls water withdrawals and fish harvesting. With the agent-based model (ABM), we relax some of the assumptions of the OCA to investigate how localized, individual agents with varied water use histories adapt their water use activities to local resource conditions. Variation in the farmers’ initial labor allocations to the two activities results in regimes with only one activity or both. Global returns and income equality are highest in a mixed regime. The mixed regimes also are more robust to water variability because fishing activities can compensate for decreased agricultural performance in the midstream regions. Thus, allowing for multiple uses can improve the coupled social-ecological system’s performance and its resilience. We also observe a lock-in effect similar to the current situation in the Amudarya, where agriculture is the dominant water use and transition to a more balanced allocation has proven to be extremely difficult. As in the ABM, this can to some extent be attributed to the difficulties of achieving sufficient revenues from fishing when agricultural activities upstream are high. Regulations or incentives are needed to overcome those barriers, and to facilitate progress towards integrated water management.     

Sharing the water column: physiological mechanisms underlying species-specific habitat use in tunas

Tuna species support some of the world’s largest commercial and recreational fisheries. Their extensive migratory patterns expose them to multiple national and international fisheries and fishery management regimes. Several prized species have become the focus of global conservation efforts and there is a growing worldwide interest in establishing optimal strategies for sustainable tuna fisheries. Although this task has proven to be very challenging, it has taken on a new sense of urgency in the face of the potential effects of global climate change. A better understanding of the interactions between environmental conditions and tuna physiology and how they affect tuna behavior will offer population and stock assessment modelers and fisheries biologists a more mechanistic understanding of tuna distribution patterns and may help predict changes in both geographic and depth-related movement patterns. Indeed, physiological data comprise a growing component of multi-trait analysis approaches to species conservation. Our review aims to summarize what is known about differences among tuna species in distribution patterns, tolerances to environmental conditions, and physiological characteristics that correlate with the capacity to inhabit cooler (deeper, higher latitude) and even hypoxic waters. To achieve this goal, we discuss how these physiological traits are associated with habitat partitioning within the three-dimensional oceanic environment and with niche expansion into cooler and hypoxic waters. We also point out areas where additional research is needed to predict more accurately how future changes in oceanographic conditions will affect the distributions and movement patterns of tunas and their availability to fisheries.     

Salt stress adaptation of Bacillus subtilis: a physiological proteomics approach

The adaptation to osmotic stress is crucial for growth and survival of Bacillus subtilis in its natural ecosystem. Dual channel imaging and warping of 2-D protein gels were used to visualize global changes in the protein synthesis pattern of cells in response to osmotic stress (6% NaCl). Many vegetative enzymes were repressed in response to salt stress and derepressed after resumption of growth. The enzymes catalyzing the metabolic steps from glucose to 2-oxoglutarate, however, were almost constantly synthesized during salt stress despite the growth arrest. This indicates an enhanced need for the proline precursor glutamate. The synthesis of enzymes involved in sulfate assimilation and in the formation of Fe-S clusters was also induced, suggesting an enhanced need for the formation or repair of Fe-S clusters in response to salt stress. One of the most obvious changes in the protein synthesis profile can be followed by the very strong induction of the SigB regulon. Furthermore, members of the SigW regulon and of the PerR regulon, indicating oxidative stress after salt challenge, were also induced. This proteomic approach provides an overview of cell adaptation to an osmotic upshift in B. subtilis visualizing the most dramatic changes in the protein synthesis pattern.     

On the interpretation of principal components analysis in ecological contexts

Summary Principal components analysis is well suited for many data analysis problems in ecology, particularly for data reduction and hypothesis generation; but the structure of PCA is poorly suited for indirect gradient analysis. Whatever the intended application of PCA, the user must exercise special care in selecting data transformations to prevent the analysis from being overwhelmed by the purely numerical effects in the variance structure of the data.I would like to thank R. H. Whittaker, H. G. Gauch, R. E. Moeller, and S. R. Searle for their guidance and assistance.     

An examination of the thresholds of enrichment: a resource-based growth model

A model of single-species growth in the chemostat on two non-reproducing, growth-limiting, noninhibitory, perfectly substitutable resources is considered. The medium in the growth vessel is enriched by increasing the input concentration of one of the resources. Analytical methods are used to determine the effects of enrichment on the asymptotic behaviour of the model for different dilution rates. It is shown that there exists a threshold value for the dilution rate which depends on the maximal growth rate of the species on each of the resources. Provided the dilution rate is below the threshold, enrichment is beneficial in the sense that the carrying capacity of the environment is increased, regardless of which resource is used to enrich the environment. When the dilution rate is increased beyond the threshold, it becomes important to consider which resource is used for enrichment. For one of the resources it is shown that, while moderate enrichment can be beneficial, sufficient enrichment leads to the extinction of the microbial population. For the other resource, enrichment leads from washout or initial condition dependent outcomes to survival, and is thus beneficial. There are important implications of these results to the management of natural aquatic ecosystems. For example, while enrichment may be beneficial to the microbial species during the summer months, it can lead to their decimation during spring run-off, when the natural dilution rate is higher.Research partially supported by an Ontario Graduate Scholarship. This author's contribution was motivated by results in her Ph.D. thesis at McMaster UniversityResearch supported by the National Sciences and Engineering Research Council of Canada.