Mitochondrial DNA in yeast recombination and subsequent modification following mating between a grande and a suppressive petite

Summary The fluorinated pyrimidines 5-fluorouracil (5FU) and 5-fluorocytosine (5FC) induce the cytoplasmic petite mutation in the yeastSaccharomyces cerevisiae with high efficiency. It was found that in order to induce the mutation, 5FC must first be deaminated to 5FU. However, mutagenesis does not depend on the further conversion of 5FU to its deoxyriboside (5FUDR) and subsequent blockade of intracellular thymidine synthesis, since 5FUDR itself was found not to be mutagenic, and 5FU-induced mutagenesis was not antagonised by supplying thymidine monophosphate (dTMP) to a dTMP permeable strain. In any case, observations of the molecular changes accompanying petite induction in log phase cells ruled out the possibility that mutagenesis resulted simply from the dilution out of replication-blocked mitDNA molecules, since the appearance of mutants coincided with the synthesis of altered mitDNA molecules. In different strains, the resulting defective molecules were either maintained, giving rise to suppressive ^– petites, or completely degraded, to give pure clones of neutral ⁰ mutants. It is suggested that this degradative process was a consequence of the incorporation of 5FU into RNA.     

Virus population extinction via ecological traps

Populations are at risk of extinction when unsuitable or when sink habitat exceeds a threshold frequency in the environment. Sinks that present cues associated with high-quality habitats, termed ecological traps, have especially detrimental effects on net population growth at metapopulation scales. Ecological traps for viruses arise naturally, or can be engineered, via the expression of viral-binding sites on cells that preclude viral reproduction. We present a model for virus population growth in a heterogeneous host community, parameterized with data from populations of the RNA bacteriophage Φ6 presented with mixtures of suitable host bacteria and either neutral or trap cells. We demonstrate that viruses can sustain high rates of population growth in the presence of neutral non-hosts as long as some host cells are present, whereas trap cells dramatically reduce viral fitness. In addition, we demonstrate that the efficacy of traps for viral elimination is frequency dependent in spatially structured environments such that population viability is a nonlinear function of habitat loss in dispersal-limited virus populations. We conclude that the ecological concepts applied to species conservation in altered landscapes can also contribute to the development of trap cell therapies for infectious human viruses.     

Experimental evidence that source genetic variation drives pathogen emergence

A pathogen can readily mutate to infect new host types, but this does not guarantee successful establishment in the new habitat. What factors, then, dictate emergence success? One possibility is that the pathogen population cannot sustain itself on the new host type (i.e. host is a sink), but migration from a source population allows adaptive sustainability and eventual emergence by delivering beneficial mutations sampled from the source''s standing genetic variation. This idea is relevant regardless of whether the sink host is truly novel (host shift) or whether the sink is an existing or related, similar host population thriving under conditions unfavourable to pathogen persistence (range expansion). We predicted that sink adaptation should occur faster under range expansion than during a host shift owing to the effects of source genetic variation on pathogen adaptability in the sink. Under range expansion, source migration should benefit emergence in the sink because selection acting on source and sink populations is likely to be congruent. By contrast, during host shifts, source migration is likely to disrupt emergence in the sink owing to uncorrelated selection or performance tradeoffs across host types. We tested this hypothesis by evolving bacteriophage populations on novel host bacteria under sink conditions, while manipulating emergence via host shift versus range expansion. Controls examined sink adaptation when unevolved founding genotypes served as migrants. As predicted, adaptability was fastest under range expansion, and controls did not adapt. Large, similar and similarly timed increases in fitness were observed in the host-shift populations, despite declines in mean fitness of immigrants through time. These results suggest that source populations are the origin of mutations that drive adaptive emergence at the edge of a pathogen''s ecological or geographical range.     

Viral ecology and the maintenance of novel host use

Viruses can occasionally emerge by infecting new host species. However, the early phases of emergence can hinge upon ecological sustainability of the virus population, which is a product of both within-host population growth and between-host transmission. Insufficient growth or transmission can force virus extinction before the latter phases of emergence, where genetic adaptations that improve host use may occur. We examined the early phase of emergence by studying the population dynamics of RNA phages in replicated laboratory environments containing native and novel host bacteria. To predict the breadth of transmission rates allowing viral persistence on each species, we developed a simple model based on in vitro data for phage growth rate over a range of initial population densities on both hosts. Validation of these predictions using serial passage experiments revealed a range of transmission rates for which the native host was a source and the novel host was a sink. In this critical range of transmission rates, periodic exposure to the native host was sufficient for the maintenance of the viral population on the novel host. We argue that this effect should facilitate adaptation by the virus to utilize the novel host--often crucial in subsequent phases of emergence.     

Bacteriophage Migration via Nematode Vectors: Host-Parasite-Consumer Interactions in Laboratory Microcosms

Pathogens vectored by nematodes pose serious agricultural, economic, and health threats; however, little is known of the ecological and evolutionary aspects of pathogen transmission by nematodes. Here we describe a novel model system with two trophic levels, bacteriophages and nematodes, each of which competes for bacteria. We demonstrate for the first time that nematodes are capable of transmitting phages between spatially distinct patches of bacteria. This model system has considerable advantages, including the ease of maintenance and manipulation at the laboratory bench, the ability to observe many generations in short periods, and the capacity to freeze evolved strains for later comparison to their ancestors. More generally, experimental studies of complex multispecies interactions, host-pathogen coevolution, disease dynamics, and the evolution of virulence may benefit from this model system because current models (e.g., chickens, mosquitoes, and malaria parasites) are costly to maintain, are difficult to manipulate, and require considerable space. Our initial explorations centered on independently assessing the impacts of nematode, bacterium, and phage population densities on virus migration between host patches. Our results indicated that virus transmission increases with worm density and host bacterial abundance; however, transmission decreases with initial phage abundance, perhaps because viruses eliminate available hosts before migration can occur. We discuss the microbial growth dynamics that underlie these results, suggest mechanistic explanations for nematode transmission of phages, and propose intriguing possibilities for future research.     

Genotype imputation in the domestic dog

Application of imputation methods to accurately predict a dense array of SNP genotypes in the dog could provide an important supplement to current analyses of array-based genotyping data. Here, we developed a reference panel of 4,885,283 SNPs in 83 dogs across 15 breeds using whole genome sequencing. We used this panel to predict the genotypes of 268 dogs across three breeds with 84,193 SNP array-derived genotypes as inputs. We then (1) performed breed clustering of the actual and imputed data; (2) evaluated several reference panel breed combinations to determine an optimal reference panel composition; and (3) compared the accuracy of two commonly used software algorithms (Beagle and IMPUTE2). Breed clustering was well preserved in the imputation process across eigenvalues representing 75 % of the variation in the imputed data. Using Beagle with a target panel from a single breed, genotype concordance was highest using a multi-breed reference panel (92.4 %) compared to a breed-specific reference panel (87.0 %) or a reference panel containing no breeds overlapping with the target panel (74.9 %). This finding was confirmed using target panels derived from two other breeds. Additionally, using the multi-breed reference panel, genotype concordance was slightly higher with IMPUTE2 (94.1 %) compared to Beagle; Pearson correlation coefficients were slightly higher for both software packages (0.946 for Beagle, 0.961 for IMPUTE2). Our findings demonstrate that genotype imputation from SNP array-derived data to whole genome-level genotypes is both feasible and accurate in the dog with appropriate breed overlap between the target and reference panels.     

Evaluation of artificial selection in Standard Poodles using whole-genome sequencing

Identifying regions of artificial selection within dog breeds may provide insights into genetic variation that underlies breed-specific traits or diseases—particularly if these traits or disease predispositions are fixed within a breed. In this study, we searched for runs of homozygosity (ROH) and calculated the d _i statistic (which is based upon F _ST) to identify regions of artificial selection in Standard Poodles using high-coverage, whole-genome sequencing data of 15 Standard Poodles and 49 dogs across seven other breeds. We identified consensus ROH regions ≥1 Mb in length and common to at least ten Standard Poodles covering 0.6 % of the genome, and d _i regions that most distinguish Standard Poodles from other breeds covering 3.7 % of the genome. Within these regions, we identified enriched gene pathways related to olfaction, digestion, and taste, as well as pathways related to adrenal hormone biosynthesis, T cell function, and protein ubiquitination that could contribute to the pathogenesis of some Poodle-prevalent autoimmune diseases. We also validated variants related to hair coat and skull morphology that have previously been identified as being under selective pressure in Poodles, and flagged additional polymorphisms in genes such as ITGA2B, CBX4, and TNXB that may represent strong candidates for other common Poodle disorders.     

Synchrony's double edge: transient dynamics and the Allee effect in stage structured populations

In populations subject to positive density dependence, individuals can increase their fitness by synchronizing the timing of key life history events. However, phenological synchrony represents a perturbation from a population's stable stage structure and the ensuing transient dynamics create troughs of low abundance that can promote extinction. Using an ecophysiological model of a mass-attacking pest insect, we show that the effect of synchrony on local population persistence depends on population size and adult lifespan. Results are consistent with a strong empirical pattern of increased extinction risk with decreasing initial population size. Mortality factors such as predation on adults can also affect transient dynamics. Throughout the species range, the seasonal niche for persistence increases with the asynchrony of oviposition. Exposure to the Allee effect after establishment may be most likely at northern range limits, where cold winters tend to synchronize spring colonization, suggesting a role for transient dynamics in the determination of species distributions.     

Reproductive Experience and the Response of Female Sprague�CDawley Rats to Fear and Stress

The present work examines the relationship between reproductive experience (comprising breeding, parturition, and lactation) and the behavioral and hormonal processes of fear and stress in the female laboratory rat. Previous research has indicated that reproductive experience functions to decrease the female''s stress response in potentially harmful environments, thereby providing her with numerous survival benefits, including decreased fearfulness, increased aggression, and refined hunting skills. This study was designed to determine how nulliparous (no reproductive experience), primiparous (1 reproductive experience) and multiparous (at least 2 reproductive experiences) rats respond to a Pavlovian paradigm of learned fear, involving the pairing of a neutral stimulus (conditioned stimulus) with an aversive stimulus (unconditioned stimulus). We report evidence that reproductive experience is linked with fear-response and anxiety-like behaviors. Our findings indicate that reproductive experience has an additive effect: primiparous mothers showed a different response to the paradigm of conditioned fear not only compared with those of nulliparous rats as well as multiparous mothers. Assessing the complex interconnections among the behavioral and physiologic measures recorded in this study, multidimensional scaling confirmed a clear separation among the 3 groups of rats in terms of the behavioral and physiologic responses to the experimental paradigm, supporting the conclusion that reproductive experience influences the maternal mind.Stress, fear, and lack of adequate stimuli can constitute a serious problem for laboratory animals. Although several studies have investigated various social and environmental changes to improve the health of laboratory animals, the literature on husbandry regimen and reproductive experience is scarce.^{3,23,44,56,58} Pregnancy and lactation represent the quintessence of change in mammals.^13,38 Reproduction entails high physiologic costs, especially in small mammals like rodents, including increased energy and nutrient demands, making the connection between husbandry and health in laboratory rats even more compelling.⁴⁹ Extensive neuroendocrine and behavioral modifications ensure mothers the flexibility to meet their own survival needs with the survival of their offspring in most environmental contingencies.^30,46 The long-term effects of these changes on the somatic and psychologic development of infants are well-known and pervasive in most mammals: from immediate infant survival to the ability to cope with stress during adulthood.^5,7,22,26,43 Several studies have indicated that the long-term consequences on mothers themselves are as compelling. Although some authors have found a significant decrease in cell proliferation in the dentate gyrus of the hippocampus in primiparous and multiparous rats during the postpartum period, associated with temporary impaired learning skills,¹⁵ others have found that motherhood can improve spatial cognition, learning and memory,^9,27,33,42 through mechanisms based on increased glucocorticoid production.^31,41 The combination of improved behavioral performances and increased physiologic stress in mothers is hardly surprising considering that the sequence of modifications during pregnancy involves, as a cascade of events, the whole body and shapes the inherently plastic central nervous system to cope with the extra challenges of providing for offspring. At the pinnacle of its fruition, the maternal brain is responsible for a complex set of behaviors that mold mothers in every aspect of their life.^28,29 In this scenario, we expect that empirical examinations of laboratory female rats with differential reproductive experience would yield significant differences in both the fear and stress response of maternal and virgin rats. Because stress and fear can impair the health of research animals and, if not controlled for, confound results obtained in experimental data, it is important to evaluate how reproductive experience can modify both stress and fear responses. Previous studies have indicated that, when confronted with a stressful stimulus, maternal rats display fewer stress-related behaviors than do nonmaternal rats.^32,57One common method of examining the animal''s reaction to a threatening environment is to use a Pavlovian model of learned fear. The neural circuitry of learned fear, involving the association of a conditioned stimulus or context with an unconditioned stimulus, is of particular interest because learned fear processes involve multiple cognitive functions including predicting, representing, and defining relationships between events.⁴⁵ The literature discussing the neural correlates of learned fear is vast and, further, agrees that the amygdala is the central brain structure responsible for learned fear. In fact, bilateral damage to the amygdala seriously impairs Pavlovian fear conditioning.^8,53 Studies conducted in developing rats revealed that different nuclei of the amygdala process sensory information of different modalities, mediate unconditioned freezing behavior, and may be involved in developmental changes in the fear response in young rats.¹⁴ Research elucidating a relationship or lack thereof between reproductive experience and changes in fear response is limited presently.^19,55 Examinations of unconditioned fear and maternal experience have suggested that an attenuated stress response and an overall decrease in fearfulness provides numerous survival benefits, such as enhanced and increased hunting and gathering skills, exploration, social awareness, and aggression, to the female rat.^21,37,50,51 Because survivability is dependent upon the prediction and appropriate response to threatening stimuli, this research paradigm can provide pertinent information about the animal''s fitness, thus providing critical information on both the health of animals and the quality of experimental data.Pregnancy, lactation, and the complex behavioral repertoire comprising maternal care constitute an expensive metabolic and genetic investment that is pivotal to species survival.^11,52 Alterations of the female brain due to occurrences of several cycles of pup exposure are reflected in many aspects of maternal life, including fear responses, activation of the hypothalamic–pituitary–adrenal axis, and anxiety.¹⁰ In the present work, we assessed whether reproductive experience plays a specific role on fear response and how this response activates the hypothalamic–pituitary–adrenal axis and interacts with anxiety-related behaviors in rats. We also assessed whether these effects are additive, that is, whether multiparous mothers (2 or more pregnancies) have a different fear response than do primiparous mothers (only 1 pregnancy). On the basis of information provided by previous studies, we hypothesized that during the retention–testing trials of the conditioning model, maternal subjects (primiparous and multiparous groups) would express fewer fear-related (freezing) behaviors than would nonmaternal subjects (nulliparous group). We further hypothesized that the maternal groups would express anxiety-related behaviors less frequently than would the nonmaternal group during the retention–testing trials. In addition, we speculated that the nulliparous group would exhibit significantly higher activation of the hypothalamic–pituitary–adrenal axis than would the reproductive groups (primiparous and multiparous), as measured by corticosterone concentrations after the fear-conditioning training trials.