Universal DNA methylation age across mammalian tissues

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

Testing hypotheses for maternal effects in Daphnia magna

Maternal effects are widely observed, but their adaptive nature remains difficult to describe and interpret. We investigated adaptive maternal effects in a clone of the crustacean Daphnia magna, experimentally varying both maternal age and maternal food and subsequently varying food available to offspring. We had two main predictions: that offspring in a food environment matched to their mothers should fare better than offspring in unmatched environments, and that offspring of older mothers would fare better in low food environments. We detected numerous maternal effects, for example offspring of poorly fed mothers were large, whereas offspring of older mothers were both large and showed an earlier age at first reproduction. However, these maternal effects did not clearly translate into the predicted differences in reproduction. Thus, our predictions about adaptive maternal effects in response to food variation were not met in this genotype of Daphnia magna.

Fecundity compensation and tolerance to a sterilizing pathogen in Daphnia

Hosts are armed with several lines of defence in the battle against parasites: they may prevent the establishment of infection, reduce parasite growth once infected or persevere through mechanisms that reduce the damage caused by infection, called tolerance. Studies on tolerance in animals have focused on mortality, and sterility tolerance has not been investigated experimentally. Here, we tested for genetic variation in the multiple steps of defence when the invertebrate Daphnia magna is infected with the sterilizing bacterial pathogen Pasteuria ramosa: anti-infection resistance, anti-growth resistance and the ability to tolerate sterilization once infected. When exposed to nine doses of a genetically diverse pathogen inoculum, six host genotypes varied in their average susceptibility to infection and in their parasite loads once infected. How host fecundity changed with increasing parasite loads did not vary between genotypes, indicating that there was no genetic variation for this measure of fecundity tolerance. However, genotypes differed in their level of fecundity compensation under infection, and we discuss how, by increasing host fitness without targeting parasite densities, fecundity compensation is consistent with the functional definition of tolerance. Such infection-induced life-history shifts are not traditionally considered to be part of the immune response, but may crucially reduce harm (in terms of fitness loss) caused by disease, and are a distinct source of selection on pathogens.

Genetic variation for maternal effects on parasite susceptibility

The expression of infectious disease is increasingly recognized to be impacted by maternal effects, where the environmental conditions experienced by mothers alter resistance to infection in offspring, independent of heritability. Here, we studied how maternal effects (high or low food availability to mothers) mediated the resistance of the crustacean Daphnia magna to its bacterial parasite Pasteuria ramosa. We sought to disentangle maternal effects from the effects of host genetic background by studying how maternal effects varied across 24 host genotypes sampled from a natural population. Under low-food conditions, females produced offspring that were relatively resistant, but this maternal effect varied strikingly between host genotypes, i.e. there were genotype by maternal environment interactions. As infection with P. ramosa causes a substantial reduction in host fecundity, this maternal effect had a large effect on host fitness. Maternal effects were also shown to impact parasite fitness, both because they prevented the establishment of the parasites and because even when parasites did establish in the offspring of poorly fed mothers, and they tended to grow more slowly. These effects indicate that food stress in the maternal generation can greatly influence parasite susceptibility and thus perhaps the evolution and coevolution of host-parasite interactions.

Identifying energy constraints to parasite resistance

Life-history theory suggests that energetically expensive traits may trade off against each other, resulting in costs associated with the development or maintenance of a particular phenotype. The deployment of resistance mechanisms during parasite exposure is one such trait, and thus their potential benefit in fighting off parasites may be offset by costs to other fitness-related traits. In this study, we used trade-off theory as a basis to test whether stimulating an increased development rate in juvenile Daphnia would reveal energetic constraints to its ability to resist infection upon subsequent exposure to the castrating parasite, Pasteuria ramosa. We show that the presumably energetically expensive process of increased development rate does result in more infected hosts, suggesting that parasite resistance requires the allocation of resources from a limited source, and thus has the potential to be costly.

Gastric emptying of hexose sugars: role of osmolality, molecular structure and the CCK₁ receptor

BACKGROUND

It is widely reported that hexose sugars slow gastric emptying (GE) via osmoreceptor stimulation but this remains uncertain. We evaluated the effects of a panel of hexoses of differing molecular structure, assessing the effects of osmolality, intra-individual reproducibility and the role of the CCK(1) receptor, in the regulation of GE by hexoses.

METHODS

Thirty one healthy non-obese male and female subjects were studied in a series of protocols, using a (13) C-acetate breath test to evaluate GE of varying concentrations of glucose, galactose, fructose and tagatose, with water, NaCl and lactulose as controls. GE was further evaluated following the administration of a CCK(1) receptor antagonist. Three subjects underwent repeated studies to evaluate intra-individual reproducibility.

KEY RESULTS

At 250 mOsmol, a hexose-specific effect was apparent: tagatose slowed GE more potently than water, glucose and fructose (P < 0.05). Fructose (P < 0.05) also slowed GE, but with substantial inter-, but not intra-, individual differences. As osmolality increased further the hexose-specific differences were lost. At 500 mOsmol, all hexoses slowed GE compared with water (P < 0.05), whereas lactulose and saline did not. The slowing of GE by hexose sugars appeared to be CCK(1) receptor-dependent.

CONCLUSIONS & INFERENCES

The effects of hexose sugars on GE appear related to their molecular structure rather than osmolality per se, and are, at least in part, CCK(1) receptor-dependent.

Exploring the molecular landscape of host-parasite coevolution

Host-parasite coevolution is a dynamic process that can be studied at the phenotypic, genetic, and molecular levels. Although much of what we currently know about coevolution has been learned through phenotypic measures, recent advances in molecular techniques have provided tools to greatly deepen this research. Both the availability of full-genome sequences and the increasing feasibility of high-throughput gene expression profiling are leading to the discovery of genes that have a key role in antagonistic interactions between naturally coevolving species. Identification of such genes can enable direct observation, rather than inference, of the host-parasite coevolutionary dynamic. The Daphnia magna-Pasteuria ramosa host-parasite model is a prime example of an interaction that has been well studied at the population and whole-organism levels, and much is known about genotype- and environment-specific interactions from a phenotypic perspective. Now, with the recent completion of genome sequences for two Daphnia species, and a transcriptomics project under way, coevolution between these two enemies is being investigated directly at the level of interacting genes.

Temperature-dependent costs of parasitism and maintenance of polymorphism under genotype-by-environment interactions

The maintenance of genetic variation for infection-related traits is often attributed to coevolution between hosts and parasites, but it can also be maintained by environmental variation if the relative fitness of different genotypes changes with environmental variation. To gain insight into how infection-related traits are sensitive to environmental variation, we exposed a single host genotype of the freshwater crustacean Daphnia magna to four parasite isolates (which we assume to represent different genotypes) of its naturally co-occurring parasite Pasteuria ramosa at 15, 20 and 25 degrees C. We found that the cost to the host of becoming infected varied with temperature, but the magnitude of this cost did not depend on the parasite isolate. Temperature influenced parasite fitness traits; we found parasite genotype-by-environment (G x E) interactions for parasite transmission stage production, suggesting the potential for temperature variation to maintain genetic variation in this trait. Finally, we tested for temperature-dependent relationships between host and parasite fitness traits that form a key component of models of virulence evolution, and we found them to be stable across temperatures.

Population genetics of Plasmodium resistance genes in Anopheles gambiae: no evidence for strong selection

Anopheles mosquitoes are the primary vectors for malaria in Africa, transmitting the disease to more than 100 million people annually. Recent functional studies have revealed mosquito genes that are crucial for Plasmodium development, but there is presently little understanding of which genes mediate vector competence in the wild, or evolve in response to parasite-mediated selection. Here, we use population genetic approaches to study the strength and mode of natural selection on a suite of mosquito immune system genes, CTL4, CTLMA2, LRIM1, and APL2 (LRRD7), which have been shown to affect Plasmodium development in functional studies. We sampled these genes from two African populations of An. gambiae s.s., along with several closely related species, and conclude that there is no evidence for either strong directional or balancing selection on these genes. We highlight a number of challenges that need to be met in order to apply population genetic tests for selection in Anopheles mosquitoes; in particular the dearth of suitable outgroup species and the potential difficulties that arise when working within a closely-related species complex.

The causes and consequences of variation in offspring size: a case study using Daphnia

Offspring size can have large and direct fitness implications, but we still do not have a complete understanding of what causes offspring size to vary. Daphnia (water fleas) generally produce fewer and larger offspring when food is limited. Here, we use a mathematical model to show that this could be explained by either: (1) an advantage of producing larger eggs when food is limited; or (2) a lower boundary on egg volume (below which eggs do not have sufficient resources to be viable), that is similar in volume to the evolutionarily stable egg volume predicted by standard clutch size models. We tested the first possibilities experimentally by placing offspring from mothers kept at two food treatments (high and low - leading to relatively small and large eggs respectively) into two food treatments (same as maternal treatments, in a fully factorial design) and measuring their fitness (reproduction, age at maturity, and size at maturity). We also tested survival under starvation conditions of offspring produced from mothers at low and high food treatments. We found that (larger) offspring produced by low-food mothers actually had lower fitness as they took longer to reproduce, regardless of their current food treatment. Additionally, we found no survival advantage to being born of a food-stressed mother. Consequently, our results do not support the hypothesis that there is an advantage to producing larger eggs when food is limited. In contrast, data from the literature support the importance of a lower boundary on egg size.

Testing the pluralist approach to sex: the influence of environment on synergistic interactions between mutation load and parasitism in Daphnia magna

Both deleterious mutations and parasites have been acknowledged as potential selective forces responsible for the evolutionary maintenance of sexual reproduction. The pluralist approach to sex proposes that these two factors may have to interact synergistically in order to stabilize sex, and one of the simplest ways this could occur is if parasites are capable of causing synergistic epistasis between mutations in their hosts. However, the effects of both deleterious mutations and parasitism are known to be influenced by a range of environmental factors, so the nature of the interaction may depend upon the organisms' environment. Using chemically mutated Daphnia magna lines, we examined the effects of mutation and parasitism under a range of temperature and food regimes. We found that although parasites were capable of causing synergistic epistasis between mutations in their hosts, these effects were dependent upon an interaction between parasite genotype and temperature.

Parasite-mediated selection and the role of sex and diapause in Daphnia

To gain insight into parasite-mediated natural selection, we studied a natural population of the crustacean Daphnia magna during a severe epidemic of the bacterial parasite Pasteuria ramosa. We also investigated the relationship between susceptibility and the production of resting eggs, which are only produced during the sexual phase of reproduction. Live host samples were taken before and after this epidemic and resistance to P. ramosa was examined in the laboratory. Host clones collected after the epidemic were more resistant to P. ramosa than were those collected pre-epidemic, which is consistent with parasite-mediated selection. In our study population, asexually reproducing females were observed across the entire study period, but females carrying resting eggs were observed only prior to the epidemic. For hosts isolated in this pre-epidemic period, we found evidence that those carrying resting eggs (at the time of collection) were more susceptible than those that were reproducing asexually. This was especially apparent for measures of parasite growth, although not all measures of infection success conclusively supported this pattern. Nevertheless, the data suggest that some genotypes invest heavily in diapause at the expense of immunocompetence. Sex could therefore inhibit the evolution of resistance because each spring new genotypes will hatch from resting eggs that are relatively susceptible as they were not exposed to the previous years bout of parasite-mediated selection.

The evolution of immune-related genes from disease carrying mosquitoes: diversity in a peptidoglycan- and a thioester-recognizing protein

Adaptive polymorphism may be common in immune system genes as co-evolutionary interactions foster diversity; either through ongoing positive selection (arms races), or balancing selection. DNA sequence diversity in two putative immune system genes was examined in species of the genus Anopheles and from Aedes aegypti. For one gene, encoding the peptidoglycan recognizing protein PGRPLB, there was evidence of purifying selection, suggesting that selection acts to eliminate sequence variation. For another gene, encoding the thioester-containing protein TEP3, higher levels of amino acid replacement were found than would be expected under neutral models of evolution - an indication that this gene has been subject to repeated bouts of positive selection.

Role of cholecystokinin in appetite control and body weight regulation

Summary Cholecystokinin (CCK), a peptide that is distributed widely throughout the gastrointestinal tract and the central nervous system, has a number of physiological effects including the stimulation of gallbladder contraction and pancreatic and gastric acid secretion, slowing of gastric emptying and suppression of energy intake. This review focuses on current knowledge relating to (i) the effects of CCK on energy intake; (ii) the role for CCK in the pathophysiology of obesity; and (iii) the therapeutic potential for strategies which modulate the action or secretion of CCK in the management of obesity. While CCK plays a role in the acute regulation of appetite and energy intake, there is little evidence to suggest that specific CCK receptor agonists, or modulation of the actions of endogenous CCK by dietary manipulation, have sustainable inhibitory effects on energy intake. Hence, it appears unlikely that manipulating the pathways by which CCK modulates energy intake will prove to be an effective strategy in the long term management of obesity.

Temporal patterns of genetic variation for resistance and infectivity in a Daphnia-microparasite system

Theoretical studies have indicated that the population genetics of host-parasite interactions may be highly dynamic. with parasites perpetually adapting to common host genotypes and hosts evolving resistance to common parasite genotypes. The present study examined temporal variation in resistance of hosts and infectivity of parasites within three populations of Daphnia magna infected with the sterilizing bacterium Pasteuria ramosa. Parasite isolates and host clones were collected in each of two years (1997, 1998) from one population; in two other populations, hosts were collected from both years, but parasites from only the first year. We then performed infection experiments (separately for each population) that exposed hosts to parasites from the same year or made combinations involving hosts and parasites from different years. In two populations, patterns were consistent with the evolution of host resistance: either infectivity or the speed with which parasites sterilized hosts declined from 1997 to 1998. In another population, infectivity, virulence, and parasite spore production did not vary among host-year or parasite-year. For this population, we also detected strong within-population genetic variation for resistance. Thus, in this case, genetic variability for fitness-related traits apparently did not translate into evolutionary change. We discuss a number of reasons why genetic change may not occur as expected in parasite-host systems, including negative correlations between resistance and other traits, gene flow, or that the dynamic process itself may obscure the detection of gene frequency changes.

Genetic variation in a host-parasite association: potential for coevolution and frequency-dependent selection

Models of host-parasite coevolution assume the presence of genetic variation for host resistance and parasite infectivity, as well as genotype-specific interactions. We used the freshwater crustacean Daphnia magna and its bacterial microparasite Pasteuria ramosa to study genetic variation for host susceptibility and parasite infectivity within each of two populations. We sought to answer the following questions: Do host clones differ in their susceptibility to parasite isolates? Do parasite isolates differ in their ability to infect different host clones? Are there host clone-parasite isolate interactions? The analysis revealed considerable variation in both host resistance and parasite infectivity. There were significant host clone-parasite isolate interactions, such that there was no single host clone that was superior to all other clones in the resistance to every parasite isolate. Likewise, there was no parasite isolate that was superior to all other isolates in infectivity to every host clone. This form of host clone-parasite isolate interaction indicates the potential for coevolution based on frequency-dependent selection. Infection success of original host clone-parasite isolate combinations (i.e., those combinations that were isolated together) was significantly higher than infection success of novel host clone-parasite isolate combinations (i.e., those combinations that were created in the laboratory). This finding is consistent with the idea that parasites track specific host genotypes under natural conditions. In addition, correspondence analysis revealed that some host clones, although distinguishable with neutral genetic markers, were susceptible to the same set of parasite isolates and thus probably shared resistance genes.

The cause of parasitic infection in natural populations of Daphnia (Crustacea: Cladocera): the role of host genetics

Disease patterns in nature may be determined by genetic variation for resistance or by factors, genetic or environmental, which influence the host-parasite encounter rate. Elucidating the cause of natural infection patterns has been a major pursuit of parasitologists, but it also matters for evolutionary biologists because host resistance genes must influence the expression of disease if parasite-mediated selection is to occur. We used a model system in order to disentangle the strict genetic component from other causes of infection in the wild. Using the crustacean Daphnia magna and its sterilizing bacterial parasite Pasteuria ramosa, we tested whether genetic variation for resistance, as determined under controlled conditions, accounted for the distribution of infections within natural populations. Specifically, we compared whether the clonally produced great-granddaughters of those individuals that were infected in field samples (but were subsequently 'cured' with antibiotics) were more susceptible than were the great-granddaughters of those individuals that were healthy in field samples. High doses of parasite spores led to increased infection in all four study populations, indicating the importance of encounter rate. Host genetics appeared to be irrelevant to natural infection patterns in one population. However, in three other populations hosts that were healthy in the field had greater genetic-based resistance than hosts that were infected in the field, unambiguously showing the effect of host genetic factors on the expression of disease in the wild.

Sex, linkage disequilibrium and patterns of parasitism in three species of cyclically parthenogenetic Daphnia (Cladocera: Crustacea)

To gain insight into genetic variation for resistance to parasites, this study assayed clonal variation in cyclically parthenogenetic Daphnia magna with respect to parasitic infection. Samples were collected from natural populations, and the allozyme phenotypes of infected hosts were compared to those of uninfected hosts. Differences between the clonal composition of the infected and uninfected class were evident in only two of 16 populations examined. This result stands in contrast to a study of species in the D. pulex and D. longispina species complexes, where clonal variation for infection was found in 12 of 25 populations (Little & Ebert, 1999). Considering all populations from both studies, associations between host genotype and infection were typically evident only in populations that showed low genotypic diversity and evidence of genetic disequilibria, with D. magna showing the least amount of disequilibria. This pattern is compatible with at least two possibly overlapping hypotheses. First, it may be that those populations lacking clonal variation for infection experienced weaker parasite-mediated selection. We can not rule out variation in selection pressure as an explanation, but found no evidence that the prevalence or intensity of parasitism differed either among species, or between those populations which showed clonal variation for infection and those that did not. Second, it could be that some populations, especially those of D. magna, have more frequent sexual recruitment than others. Sexual recombination breaks up gene combinations which are in linkage disequilibrium, and our method to detect clonal variation for resistance relies on linkage between genetic markers (allozymes) and resistance loci. Past work on Daphnia has shown that the level of sexual recruitment (which is in turn mediated by habitat permanency) is indeed commonly linked to the occurrence of genetic disequilibria. Our results may thus underestimate the prevalence of clonal variation for infection (especially for D. magna), because most of the populations analysed appeared to have high levels of sexual recruitment and therefore lacked the linkage disequilibrium that underlies associations between allozymes and susceptibility.

Partial sequence of the mitochondrial genome of the crustacean Daphnia pulex

A 4062-nucleotide (nt) fragment of the mitochondrial genome of the crustacean Daphnia pulex was sequenced and found to contain the complete genes for eight tRNAs and five proteins (ATP6, ATP8, COII, COIII, ND3) and the partial sequence of COI. In combination with data described previously, approximately 50% of the D. pulex mitochondrial genome has been sequenced. The gene order in this half of the genome is identical to that of Drosophila yakuba which differs from that of the other completely sequenced crustacean mitochondrial genome, Artemia franciscana. Comparison of seven mitochondrial proteins among D. pulex, A. franciscana, D. yakuba, Anopheles gambiae, Locusta migratoria and Apis mellifera showed that, with one exception, the D. pulex proteins are most similar in length and sequence to the proteins of the dipteran insects. Conversely, patterns of nucleotide bias at third codon positions in fourfold degenerate codon families are very similar in the two crustaceans but differed substantially from the insects.