Combining theoretical and experimental approaches to understand the circadian clock

This review is intended as a summary of our work carried out as part of the German Research Association (DFG) Center Program on Circadian Rhythms. Over the last six years, our approach to understanding circadian systems combined theoretical and experimental tools, and Gonyaulax and Neurospora have proven ideal for these efforts. Both of these model organisms demonstrate that even simple circadian systems can have multiple light input pathways and more than one rhythm generator. They have both been used to elaborate basic circadian features in conjunction with formal models. The models introduce the “zeitnehmer,” i.e., a clock-regulated input pathway, to the conceptual framework of circadian systems, and proposes networks of individual feedbacks as the basis for circadian rhythmicity.     

Set points,settling points and some alternative models: theoretical options to understand how genes and environments combine to regulate body adiposity

The close correspondence between energy intake and expenditure over prolonged time periods, coupled with an apparent protection of the level of body adiposity in the face of perturbations of energy balance, has led to the idea that body fatness is regulated via mechanisms that control intake and energy expenditure. Two models have dominated the discussion of how this regulation might take place. The set point model is rooted in physiology, genetics and molecular biology, and suggests that there is an active feedback mechanism linking adipose tissue (stored energy) to intake and expenditure via a set point, presumably encoded in the brain. This model is consistent with many of the biological aspects of energy balance, but struggles to explain the many significant environmental and social influences on obesity, food intake and physical activity. More importantly, the set point model does not effectively explain the ‘obesity epidemic’ – the large increase in body weight and adiposity of a large proportion of individuals in many countries since the 1980s. An alternative model, called the settling point model, is based on the idea that there is passive feedback between the size of the body stores and aspects of expenditure. This model accommodates many of the social and environmental characteristics of energy balance, but struggles to explain some of the biological and genetic aspects. The shortcomings of these two models reflect their failure to address the gene-by-environment interactions that dominate the regulation of body weight. We discuss two additional models – the general intake model and the dual intervention point model – that address this issue and might offer better ways to understand how body fatness is controlled.     

An experimental and theoretical approach to determining linkages between geochemical variability and microbial biodiversity in seafloor hydrothermal chimneys

New experimental results of fluid–mineral reactions at hydrothermal conditions relevant to life demonstrate that key redox reactions involving iron, sulfur, and hydrogen remain at disequilibrium at 100 °C, even in a heterogeneous system and thus are energetically favorable for microbial metabolism. Predictions from geochemical models utilizing the experimental results and specific to two contrasting case studies from the East Pacific Rise were statistically characterized and correlated to the energetics of redox reactions available for intra‐chimney microbial populations. In general, predictions of available energy for autotrophic metabolism are largely similar between the mature and the nascent chimneys, although important differences still exist. Metabolic processes predicted by energetics exhibit the same trends observed in the field data for the mature chimney, but overestimate the diversity observed in the nascent chimney. Several combinations of redox reaction pairs are predicted to support mixed consortia, while some combinations appear to favor more versatile microbes capable of utilizing several reactions under rapidly changing environmental conditions within chimney walls. In addition, conditions favorable to elemental sulfur reduction and methanogenesis exhibit a negative control on the diversity of microbial populations within these chimney walls, whereas H₂S oxidation, elemental sulfur oxidation and the knallgas reaction are positively correlated with both abundance and diversity of micro‐organisms. Coupling field observations of both microbial diversity and geochemical heterogeneity with lab‐based experimental and theoretical modeling can facilitate translation of the observed genetic diversity into physiological diversity, thus enhancing understanding of linked phenomena of microbially induced biogeochemical transformations in complex heterogeneous systems.     

Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data

Geneticists have been interested in inbreeding and inbreeding depression since the time of Darwin. Two alternative approaches that can be used to measure how inbred an individual is involve the use of pedigree records to estimate inbreeding coefficients or molecular markers to measure multilocus heterozygosity. However, the relationship between inbreeding coefficient and heterozygosity has only rarely been investigated. In this paper, a framework to predict the relationship between the two variables is presented. In addition, microsatellite genotypes at 138 loci spanning all 26 autosomes of the sheep genome were used to investigate the relationship between inbreeding coefficient and multilocus heterozygosity. Multilocus heterozygosity was only weakly correlated with inbreeding coefficient, and heterozygosity was not positively correlated between markers more often than expected by chance. Inbreeding coefficient, but not multilocus heterozygosity, detected evidence of inbreeding depression for morphological traits. The relevance of these findings to the causes of heterozygosity--fitness correlations is discussed and predictions for other wild and captive populations are presented.     

The long-term adaptation of multicellular model organisms to non-terrestrial and space environments

The main point in this presentation is the following: It is of crucial importance that the Space Agencies define and support the long-term directions for Space Biology Research. The development and upgrading of Facilities and Carriers should be coordinated with the preparatory activities of scientific groups interested in tackling major questions using the future opportunities in the Space Exploration Programs. The current effort in establishing larger Research Networks may lead the way to a successful Space Program in the XXI Century.     

Metabolomics to unveil and understand phenotypic diversity between pathogen populations

Leishmaniasis is a debilitating disease caused by the parasite Leishmania. There is extensive clinical polymorphism, including variable responsiveness to treatment. We study Leishmania donovani parasites isolated from visceral leishmaniasis patients in Nepal that responded differently to antimonial treatment due to differing intrinsic drug sensitivity of the parasites. Here, we present a proof-of-principle study in which we applied a metabolomics pipeline specifically developed for L. donovani to characterize the global metabolic differences between antimonial-sensitive and antimonial-resistant L. donovani isolates. Clones of drug-sensitive and drug-resistant parasite isolates from clinical samples were cultured in vitro and harvested for metabolomics analysis. The relative abundance of 340 metabolites was determined by ZIC-HILIC chromatography coupled to LTQ-Orbitrap mass spectrometry. Our measurements cover approximately 20% of the predicted core metabolome of Leishmania and additionally detected a large number of lipids. Drug-sensitive and drug-resistant parasites showed distinct metabolic profiles, and unsupervised clustering and principal component analysis clearly distinguished the two phenotypes. For 100 metabolites, the detected intensity differed more than three-fold between the 2 phenotypes. Many of these were in specific areas of lipid metabolism, suggesting that the membrane composition of the drug-resistant parasites is extensively modified. Untargeted metabolomics has been applied on clinical Leishmania isolates to uncover major metabolic differences between drug-sensitive and drug-resistant isolates. The identified major differences provide novel insights into the mechanisms involved in resistance to antimonial drugs, and facilitate investigations using targeted approaches to unravel the key changes mediating drug resistance.     

Human evolution and human-influenced evolution of organisms in changing environments

Human evolution and human-influenced evolution of living organisms such as animals,plants,and microorganisms on our planet are among the most active and inspiring topics of scientific research.This is because the evolutionary processes influenced by humans can be detected within a quantifiable period of time,and the consequences of such evolutionary processes vary significantly in terms of their rates and diversification,compared to those under the conditions of no human influences (Hendry et al.,2008).For example,domesticated animals (e.g.,chicken and pig)and plant species (e.g.,rice and maize) have evolved relatively rapidly within the past 10 000 years,which has resulted in tremendous genetic diversity of these domesticates under human influences in different environments (Dorshorst et al.,2011;Huang et al.,2012;Rubin et al.,2012).However,the rapid evolution and changes in these organisms have had significant impacts on the environments that humans and these organisms inhabit.     

Chloroflexus-like organisms from marine and hypersaline environments: Distribution and diversity

We report the presence of a diverse number ofChloroflexus-like organisms in intertidal marine and submerged hypersaline microbial mats using light, infrared fluorescence, and electron microscopy. The intertidal organisms appear morphologically very similar to thermophilicC. aurantiacus while the 2 hypersaline strains are larger and have a more complex ultrastructure composed of chlorosome-bearing internal membranes that appear to arise as invaginations of the cell membrane. By comparing spectroradiometry of microbial mat layers with microscopic observations, we have confirmed that theChloroflexus-like organisms are major constituents of the hypersaline microbial mat communities. In situ studies on mat layers dominated byChloroflexus-like organisms showed that sulfide-dependent photoautotrophic activity sustained by near infrared radiation prevailed. Autoradiographic analyses revealed that autotrophy was sustained in the filaments by 750 nm radiation. Three morphologically distinct strains are now maintained in mixed culture. One of these appears to be growing photoautotrophically.     

The generality of empirical and theoretical explanations of behavior

For theoretical explanations of data, parameter values estimated from a single dependent measure from one procedure are used to predict alternative dependent measures from many procedures. Theoretical explanations were compared to empirical explanations of data in which known functions and principles were used to fit only selected dependent measures. The comparison focused on the ability of theoretical and empirical explanations to generalize across samples of the data, across dependent measures of behavior, and across different procedures. Rat and human data from fixed-interval and peak procedures, in which principles (e.g., scalar timing) are well known, were described and fit by a theory with independent modules for perception, memory, and decision. The theoretical approach consisted of fitting closed-form equations of the theory to response rate gradients calculated from the data, simulating responses using parameter values previously estimated, and comparing theoretical predictions with dependent measures not used to estimate parameters. Although the empirical and theoretical explanations provided similar fits to the response rate gradients that generalized across samples and had the same number of parameters, only the theoretical explanation generalized across procedures and dependent measures.     

Yeast as a model to understand the interaction between genotype and the response to calorie restriction

Calorie restriction is reported to enhance survival and delay the onset of age-related decline in many different species. Several proteins have been proposed to play a role in mediating the response to calorie restriction, including the target of rapamycin kinase, sirtuins, and AMP kinase. An enhanced mechanistic understanding of calorie restriction has popularized the concept of "calorie restriction mimetics", drugs that mimic the beneficial effects of caloire restriction without requiring a reduction in nutrient intake. In theory, such drugs should delay the onset and progression of multiple age-related diseases, similar to calorie restriction in mammals. Despite the potential benefits of such calorie restriction mimetics, however, relatively little is known about the interaction between genetic variation and individual response to calorie restriction. Limited evidence from model systems indicates that genotype plays a large role in determining both the magnitude and direction of effect that calorie restriction has on longevity. Here we present an overview of these data from the perspective of using yeast as a model to study aging and describe an approach we are taking to further characterize the molecular mechanisms underlying genotype-dependent responses to calorie restriction.     

A note on the isolation of psychrotrophic coliform organisms from faecal-polluted environments

The Simmons citrate salicin (SCS) medium was developed for the enrichment and isolation of presumptive psychrotrophic coliforms from polluted environments. The selectivity and resolution of the medium were tested with pure and mixed laboratory cultures. A procedure for the isolation of psychrotrophic coliforms from polluted environments using a lactose-bile broth and SCS medium is presented.     

A note on the isolation of psychrotrophic coliform organisms from faecal-polluted environments

The Simmons citrate salicin (SCS) medium was developed for the enrichment and isolation of presumptive psychrotrophic coliforms from polluted environments. The selectivity and resolution of the medium were tested with pure and mixed laboratory cultures. A procedure for the isolation of psychrotrophic coliforms from polluted environments using a lactose-bile broth and SCS medium is presented.     

Connectivity and resilience of coral reef metapopulations in marine protected areas: matching empirical efforts to predictive needs

Design and decision-making for marine protected areas (MPAs) on coral reefs require prediction of MPA effects with population models. Modeling of MPAs has shown how the persistence of metapopulations in systems of MPAs depends on the size and spacing of MPAs, and levels of fishing outside the MPAs. However, the pattern of demographic connectivity produced by larval dispersal is a key uncertainty in those modeling studies. The information required to assess population persistence is a dispersal matrix containing the fraction of larvae traveling to each location from each location, not just the current number of larvae exchanged among locations. Recent metapopulation modeling research with hypothetical dispersal matrices has shown how the spatial scale of dispersal, degree of advection versus diffusion, total larval output, and temporal and spatial variability in dispersal influence population persistence. Recent empirical studies using population genetics, parentage analysis, and geochemical and artificial marks in calcified structures have improved the understanding of dispersal. However, many such studies report current self-recruitment (locally produced settlement/settlement from elsewhere), which is not as directly useful as local retention (locally produced settlement/total locally released), which is a component of the dispersal matrix. Modeling of biophysical circulation with larval particle tracking can provide the required elements of dispersal matrices and assess their sensitivity to flows and larval behavior, but it requires more assumptions than direct empirical methods. To make rapid progress in understanding the scales and patterns of connectivity, greater communication between empiricists and population modelers will be needed. Empiricists need to focus more on identifying the characteristics of the dispersal matrix, while population modelers need to track and assimilate evolving empirical results.     

From empirical to theoretical models of light response curves - linking photosynthetic and metabolic acclimation

Photosynthesis Research - Light response curves (LRCs) describe how the rate of photosynthesis varies as a function of light. They provide information on the maximum photosynthetic capacity,...     

Adaptive variation in testosterone levels in response to immune activation: empirical and theoretical perspectives

High testosterone levels reflect investment in male reproductive effort through the ability to produce and maintain muscle tissue and thus augment mate attraction and competitive ability. However, high testosterone levels can also compromise survivorship by increasing risk of prostate cancer, production of oxygen radicals, risk of injury due to hormonally-augmented behaviors such as aggression, violence and risk taking, reduced tissue and organ maintenance, negative energy balance from adipose tissue catabolism, and suppression of immune functions. Here, I briefly discuss how inter- and intra-individual variation in human male testosterone levels is likely an adaptive mechanism that facilitates the allocation of metabolic resources, particularly in response to injury, illness or otherwise immune activation. Maintaining low testosterone levels in resource-limited and/or high pathogen-risk environments may avoid some immunosuppression and suspend energetically-expensive anabolic functions. Augmenting testosterone levels in the presence of fertile and receptive mates, areas of high food resource availability, and low disease risk habitats will function to maximize lifetime reproductive success.     

Transitive inference in non-human animals: an empirical and theoretical analysis

Transitive inference has long been considered one of the hallmarks of human deductive reasoning. Recent reports of transitive-like behaviors in non-human animals have prompted a flourishing empirical and theoretical search for the mechanism(s) that may mediate this ability in non-humans. In this paper, I begin by describing the transitive inference tasks customarily used with non-human animals and then review the empirical findings. Transitive inference has been demonstrated in a wide variety of species, and the signature effects that usually accompany transitive inference in humans (the serial position effect and the symbolic distance effect) have also been found in non-humans. I then critically analyze the most prominent models of this ability in non-human animals. Some models are cognitive, proposing for instance that animals use the rules of formal logic or form mental representations of the premises to solve the task, others are based on associative mechanisms such as value transfer and reinforcement and non-reinforcement. Overall, I argue that the reinforcement-based models are in a much better empirical and theoretical position. Hence, transitive inference in non-human animals should be considered a property of reinforcement history rather than of inferential processes. I finalize by shedding some light on some promising lines of research.     

On the theoretical and empirical framework for studying genetic interactions within and among species

We present a quantitative genetic (QG) interpretation of the Bateson-Dobzhansky-Muller (BDM) genetic model of speciation in order to unify the theoretical framework for understanding how the genetic differentiation of populations is associated with the process of speciation. Specifically, we compare the QG theory of joint scaling with the Turelli-Orr mathematical formulation of the BDM model. By formally linking the two models, we show that a wealth of empirical methods from QG can be brought to bear on the study of the genetic architecture of hybrid phenotypes to better understand the connections, if any, between microevolution within populations and macroevolution in the origin of species. By integrating the two theories, we make additional novel predictions that enrich the opportunities for empirically testing speciation genetic theory or facets of it, such as Haldane's rule. We show that the connection between the two theories is simple and straightforward for autosomal genes but not for sex-linked genes. Differences between the two approaches highlight key conceptual issues concerning the relevance of epistasis to evolution within and among lineages and to differences in the process of speciation in hermaphrodites and in organisms with separate sexes.     

Evidence for firm linkages between microtubules and membrane-bounded vesicles

Direct evidence is presented in support of the widely held idea that membrane-bounded vesicles can bind firmly to microtubules. This is shown in P. caudatum which contains ribbons of straight microtubules located in open cytoplasm and uniquely associated with the disk-shaped vesicles. These vesicles frequently lie flat against the face of the ribbons at a constant distance of 30-40 nm. Under certain conditions the ribbons are compressed into zigzag pattern, but the vesicles continue to maintain their 30-40 nm spacing with the tubules and The author's interpretation of this phenomena is that the vesicles and the microtubules are strongly bound together. This interaction appears to be via a filamentous material rather than bridges.