How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna

Due to the lack of recombination, asexual organisms are predicted to accumulate mutations and show high levels of within‐individual allelic divergence (heterozygosity); however, empirical evidence for this prediction is largely missing. Instead, evidence of genome homogenization during asexual reproduction is accumulating. Ameiotic crossover recombination is a mechanism that could lead to long genomic stretches of loss of heterozygosity (LOH) and unmasking of mutations that have little or no effect in heterozygous state. Therefore, LOH might be an important force for inducing variation among asexual offspring and may contribute to the limited longevity of asexual lineages. To investigate the genetic consequences of asexuality, here we used high‐throughput sequencing of Daphnia magna for assessing the rate of LOH over a single generation of asexual reproduction. Comparing parthenogenetic daughters with their mothers at several thousand genetic markers generated by restriction site‐associated DNA (RAD) sequencing resulted in high LOH rate estimation that largely overlapped with our estimates for the error rate. To distinguish these two, we Sanger re‐sequenced the top 17 candidate RAD‐loci for LOH, and all of them proved to be false positives. Hence, even though we cannot exclude the possibility that short stretches of LOH occur in genomic regions not covered by our markers, we conclude that LOH does not occur frequently during asexual reproduction in D. magna and ameiotic crossovers are very rare or absent. This finding suggests that clonal lineages of D. magna will remain genetically homogeneous at least over time periods typically relevant for experimental work.

Assessment of parasite virulence in a natural population of a planktonic crustacean

Background

Understanding the impact of disease in natural populations requires an understanding of infection risk and the damage that parasites cause to their hosts (= virulence). However, because these disease traits are often studied and quantified under controlled laboratory conditions and with reference to healthy control hosts, we have little knowledge about how they play out in natural conditions. In the Daphnia–Pasteuria host–parasite system, field assessments often show very low estimates of virulence, while controlled laboratory experiments indicate extremely high virulence.

Results

To examine this discrepancy, we sampled Daphnia magna hosts from the field during a parasite epidemic and recorded disease traits over a subsequent 3-week period in the laboratory. As predicted for chronic disease where infections in older (larger) hosts are also, on average, older, we found that larger D. magna females were infected more often, had fewer offspring prior to the onset of castration and showed signs of infection sooner than smaller hosts. Also consistent with laboratory experiments, infected animals were found in both sexes and in all sizes of hosts. Infected females were castrated at capture or became castrated soon after. As most females in the field carried no eggs in their brood pouch at the time of sampling, virulence estimates of infected females relative to uninfected females were low. However, with improved feeding conditions in the laboratory, only uninfected females resumed reproduction, resulting in very high relative virulence estimates.

Conclusions

Overall, our study shows that the disease manifestation of P. ramosa, as expressed under natural conditions, is consistent with what we know from laboratory experiments. However, parasite induced fecundity reduction of infected, relative to uninfected hosts depended strongly on the environmental conditions. We argue that this effect is particularly strong for castrating parasites, because infected hosts have low fecundity under all conditions.

Mixtures of Aluminum and Indium Induce More than Additive Phenotypic and Toxicogenomic Responses in Daphnia magna

Aquatic systems are contaminated by many metals but their effects as mixtures on organisms are not well understood. Here, we assessed effects of aluminum with fairly well-known modes of actions and indium, an understudied emerging contaminant from electronics, followed by studying equi-effective mixtures thereof. We report acute and adverse phenotypic effects in Daphnia magna adults and global transcriptomic effects employing RNA sequencing in neonates. The mixture induced more than additive activity in mortality and in physiological effects, including growth and reproduction. Similarly, transcriptomic effects were more than additive, as indicated by a markedly higher number of 463 differentially expressed transcripts in the mixture and by distinct classes of genes assigned to several biological functions, including metabolic processes, suggesting depleted energy reserves, which may be responsible for the observed impaired reproduction and growth. A gene set enrichment analysis (GSEA) of a priori known response pathways for aluminum confirmed activation of distinct molecular pathways by indium. Our study is highlighting more than additive effects at the transcriptional and physiological level and is providing a state-of-the art approach to mixture analysis, which is important for risk assessment of these metals and metal mixtures.

Protein profiles of enzymatically isolated rumen epithelium in sheep fed a fibrous diet

BACKGROUND

The rumen wall plays a major role in efficient transfer of digested nutrients in the rumen to peripheral tissues through the portal venous system. Some of these substrates are metabolised in the epithelium during this process. To identify the specific proteins involved in these processes, we used proteomic technologies. Protein extracts were prepared from ventral rumen tissue of six sheep fed a fibrous diet at 1.5× maintenance energy requirements. Using a newly developed method, we were able to enzymatically isolate the epithelial cells from underlying tissue layers, thus allowing cytosol and membrane fractions to be independently analysed using liquid chromatography tandem mass spectrometry (LC MS/MS).

RESULTS

Using our procedure we identified 570 epithelial proteins in the Ovis aries sequence database. Subcellular locations were largely cytosolic (n = 221) and extracellular (n = 85). However, a quarter of the proteins identified were assigned to the plasma membrane or organelle membranes, some of which transport nutrients and metabolites. Of these 91 were transmembrane proteins (TMHMM), 27 had an N-terminal signal peptide (signalP) and TMHMM motif, 13 had a glycosylphosphatidylinositol (GPI) anchor and signalP sequence, 67 had beta (β) strands or 17 β strands and a transit peptide sequence, indicating the identified proteins were integral or peripheral membrane proteins. Subunits of the 5 protein complexes involved in mitochondrial cellular energy production were well represented. Structural proteins (15%), proteins involved in the metabolism of lipids and proteins (26%) and those with steroid or cytokine action were a feature of the proteome.

CONCLUSION

Our research has developed a procedure to isolate rumen epithelium proteins from the underlying tissue layers so that they may be profiled using proteomic technologies. The approach improves the number of proteins that can be profiled that are specific to the epithelium of the rumen wall. It provides new insights into the proteins of structural and nutritional importance in the rumen epithelium, that carry out nutrient transport and metabolism, cell growth and signalling.

Nutrient availability affects the prevalence of a microsporidian parasite

Defining the relationship between nutrients and parasitism is complicated by shifts in host physiology and population density, which can both mediate the effects of host diet on parasites and vice versa. We examined the relationship between nutrient availability and an abundant parasite capable of both horizontal and vertical transmission (Hamiltosporidium tvaerminnensis) of a planktonic crustacean, Daphnia magna, in rock pools on Baltic Sea Skerry islands. We found that the relative availability of nutrients directly affected infection prevalence; parasite prevalence was higher in pools with higher particulate N:P ratios. Infection prevalence was not related to Daphnia population densities. A complementary experiment that examined host responses to an N:P gradient in mesocosms indicated that high N:P ratios can increase spore load in the hosts. We surmise that high N:P food increases Daphnia feeding rate, which increases their contact with parasite spores and leads to higher prevalence and more intense infections. We found no direct evidence that parasite-induced changes in host nutrient use affected nutrient dynamics in pools. However, the relationship between diet N:P and the parasite's prevalence and load is consistent with previously documented patterns of this parasite's effect on host nutrient use. Taken together, this study suggests that high N:P ratios in food may benefit the parasite in multiple ways and could create environments that favour horizontal transmission over vertical transmission for parasites capable of both transmission routes. If so, nutrient limitation could have long-term consequences for host-parasite evolution.

Open questions: what are the genes underlying antagonistic coevolution?

Although the idea of coevolution was first presented 150 years ago, we still only vaguely understand the genetic basis of its workings. Identifying the genes responsible for coevolutionary interactions would enable us to distinguish between fundamentally different models of coevolution and would represent a milestone in population genetics and genomics.

The Combined Effect of Temperature and Host Clonal Line on the Microbiota of a Planktonic Crustacean

Host-associated microbiota vary across host individuals and environmental conditions, but the relative importance of their genetic background versus their environment is difficult to disentangle. We sought to experimentally determine the factors shaping the microbiota of the planktonic Crustacean, Daphnia magna. We used clonal lines from a wide geographic distribution, which had been kept under standardized conditions for over 75 generations. Replicate populations were kept for three generations at 20 and 28 °C. The interaction of the host clonal line and environment (i.e., temperature) influenced microbiota community characteristics, including structure, the relative abundance of common microbial species, and the microbial richness and phylogenetic diversity. We did not find any correlation between host-associated microbiota and the geographic origin of the clones or their temperature tolerance. Our results highlight the prominent effects that host clonal lineage and its interaction with the environment has on host-associated microbiota composition.

Host genotype-specific microbiota do not influence the susceptibility of D. magna to a bacterial pathogen

Host-associated microbiota have been claimed to play a role in hosts' responses to parasitic infections, often protecting the hosts from infection. We tested for such a role in the crustacean Daphnia and the parasitic bacterium Pasteuria ramosa, a widely used model system for host-parasite interactions. We first determined the infection phenotype (i.e., resistotype) of eight clonal D. magna genotypes against four strains of P. ramosa by attachment test, followed by 16 S rDNA amplicon sequencing to determine if their genotype or their parasite resistotype influences the composition of their microbiome. We then reciprocally transplanted the microbiota of two host genotypes with opposite resistotypes to four P. ramosa isolates, followed by a reassessment of their resistotype after transplantation. We found significant differences in microbiome composition and structure between Daphnia genotypes and between Daphnia resistotypes to specific P. ramosa strains. Reciprocal microbiota exchange or making the Daphnia hosts bacteria-free, however, did not influence the resistotypes of the hosts. Thus, in contrary to what has been observed in some taxa, our results suggest that D. magna susceptibility to P. ramosa is strongly dictated by the genetic differences of the hosts and is still dependent on Daphnia's first line of immune defense against the esophageal attachment of P. ramosa, which appears to be uninfluenced by the host's microbiota.

Carbonyl reductases from Daphnia are regulated by redox cycling compounds

Oxidative stress is a major source of reactive carbonyl compounds that can damage cellular macromolecules, leading to so-called carbonyl stress. Aside from endogenously formed carbonyls, including highly reactive short-chain aldehydes and diketones, air pollutants derived from diesel exhaust like 9,10-phenanthrenequinone (PQ) can amplify oxidative stress by redox cycling, causing tissue damage. Carbonyl reductases (CRs), which are inducible in response to ROS, represent a fundamental enzymatic defense mechanism against oxidative stress. While commonly two carbonyl reductases (CBR1 and CBR3) are found in mammalian genomes, invertebrate model organisms like Drosophila melanogaster express no CR but a functional homolog to human CBR1, termed sniffer. The microcrustacean Daphnia is an ideal model organism to investigate the function of CRs because of its unique equipment with even four copies of the CR gene (CR1, CR2, CR3, CR4) in addition to one sniffer gene. Cloning and catalytic characterization of two carbonyl reductases CR1 and CR3 from D. magna and D. pulex arenata revealed that both proteins reductively metabolize aromatic dicarbonyls (e.g., menadione, PQ) and aliphatic α-diketones (e.g., 2,3-hexanedione), while sugar-derived aldehydes (methylglyoxal, glyoxal) and lipid peroxidation products such as acrolein and butanal were poor substrates, indicating no physiological function in the metabolism of short-chain aldehydes. Treatment of D. magna with redox cyclers like menadione and the pesticide paraquat led to an upregulation of CR1 and CR3 mRNA, suggesting a role in oxidative stress defense. Further studies are needed to investigate their potential to serve as novel biomarkers for oxidative stress in Daphnia.

The End of a 60-year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton

The planktonic freshwater crustacean of the genus Daphnia are a model system for biomedical research and, in particular, invertebrate-parasite interactions. Up until now, no virus has been characterized for this system. Here we report the discovery of an iridovirus as the causative agent of White Fat Cell Disease (WFCD) in Daphnia WFCD is a highly virulent disease of Daphnia that can easily be cultured under laboratory conditions. Although it has been studied from sites across Eurasia for more than 60 years, its causative agent had not been described, nor had an iridovirus been connected to WFCD before now. Here we find that an iridovirus-the Daphnia iridescent virus 1 (DIV-1)-is the causative agent of WFCD. DIV-1 has a genome sequence of about 288 kbp, with 39% G+C content and encodes 367 predicted open reading frames. DIV-1 clusters together with other invertebrate iridoviruses but has by far the largest genome among all sequenced iridoviruses. Comparative genomics reveal that DIV-1 has apparently recently lost a substantial number of unique genes but has also gained genes by horizontal gene transfer from its crustacean host. DIV-1 represents the first invertebrate iridovirus that encodes proteins to purportedly cap RNA, and it contains unique genes for a DnaJ-like protein, a membrane glycoprotein and protein of the immunoglobulin superfamily, which may mediate host-pathogen interactions and pathogenicity. Our findings end a 60-year search for the causative agent of WFCD and add to our knowledge of iridovirus genomics and invertebrate-virus interactions.

Daphnia females adjust sex allocation in response to current sex ratio and density

Cyclical parthenogenesis presents an interesting challenge for the study of sex allocation, as individuals' allocation decisions involve both the choice between sexual and asexual reproduction, and the choice between sons and daughters. Male production is therefore expected to depend on ecological and evolutionary drivers of overall investment in sex, and those influencing male reproductive value during sexual periods. We manipulated experimental populations, and made repeated observations of natural populations over their growing season, to disentangle effects of population density and the timing of sex from effects of adult sex ratio on sex allocation in cyclically parthenogenetic Daphnia magna. Male production increased with population density, the major ecological driver of sexual reproduction; however, this response was dampened when the population sex ratio was more male-biased. Thus, in line with sex ratio theory, we show that D. magna adjust offspring sex allocation in response to the current population sex ratio.

Daphnia invest in sexual reproduction when its relative costs are reduced

The timing of sex in facultatively sexual organisms is critical to fitness, due to the differing demographic consequences of sexual versus asexual reproduction. In addition to the costs of sex itself, an association of sex with the production of dormant life stages also influences the optimal use of sex, especially in environments where resting eggs are essential to survive unfavourable conditions. Here we document population dynamics and the occurrence of sexual reproduction in natural populations of Daphnia magna across their growing season. The frequency of sexually reproducing females and males increased with population density and with decreasing asexual clutch sizes. The frequency of sexually reproducing females additionally increased as population growth rates decreased. Consistent with population dynamic models showing that the opportunity cost of sexual reproduction (foregoing contribution to current population growth) diminishes as populations approach carrying capacity, we found that investment in sexual reproduction was highest when asexual population growth was low or negative. Our results support the idea that the timing of sex is linked with periods when the relative cost of sex is reduced due to low potential asexual growth at high population densities. Thus, a combination of ecological and demographic factors affect the optimal timing of sexual reproduction, allowing D. magna to balance the necessity of sex against its costs.

Stents for the Treatment of Aortic Aneurysms

The endovascular treatment of abdominal aortic aneurysms has generated a great deal of interest since the early 1990s, and many different devices are currently available. The procedure of endovascular repair has been evaluated in many institutions and the different devices are compared. The first results were encouraging, but complications like endoleak, dislocation or thrombosis of the graft occurred. By the available devices the stent application is only promising, if the known exclusion criteria are strictly respected. Therefore a careful preinterventional assessment of the patient by different imaging modalities is necessary. As the available results up to now are preliminary and the durability of the devices has to be controlled, multicenter studies are required to improve the devices and observe their long- term success in the exclusion of abdominal aortic aneurysms.

Increased rates of intermittent rhythmic delta and theta activity in the electroencephalographies of adult patients with attention-deficit hyperactivity disorder

INTRODUCTION

Adult attention-deficit hyperactivity disorder (ADHD) is a common neurodevelopmental disorder. In subgroups of patients with a (para)epileptic pathomechanism, this might be due to intermittent rhythmic delta or theta activity (IRDA/IRTA).

PARTICIPANTS AND METHODS

Using a fully data-driven analysis, we compared the IRDA/IRTA rates in the resting electroencephalography (EEG) results of 97 adult patients with ADHD and 30 control subjects. The IRDA/IRTA rates before hyperventilation (HV) and for HV difference (difference between IRDA/IRTA rate after and before HV) were compared between groups using a linear model.

RESULTS

We detected significantly increased rates of IRDA/IRTA before HV (F=4.209, p=0.042) in patients with ADHD but no significant difference between the groups for HV-difference (F=2.46, p=0.119).

DISCUSSION

The increased IRDA/IRTA rates before HV in the group with ADHD might lead to (para)epileptic short-term effects (e.g., impulsivity) via local area network inhibition, and to long-term effects (e.g., cognitive deficits) via connectivistic brain restructuring.

The Evolutionary Consequences of Stepwise Infection Processes

Molecular and cellular studies reveal that the resistance of hosts to parasites and pathogens is a cascade-like process with multiple steps required to be passed for successful infection. By contrast, much of evolutionary reasoning is based on strongly simplified, one- or two-step infection processes with simple genetics or on resistance being a quantitative trait. Here we attempt a conceptual unification of these two perspectives with the aim of cross-fostering research and filling some of the gaps in our concepts of the ecology and evolution of disease. This conceptual unification has a profound impact on the way we understand the genetics and evolution of host resistance, ecological immunity, evolution of virulence, defence portfolios, and host-pathogen coevolution.

THE INFLUENCE OF HOST DEMOGRAPHY ON THE EVOLUTION OF VIRULENCE OF A MICROSPORIDIAN GUT PARASITE

It is predicted that host exploitation should evolve to maximize parasite fitness and that virulence (= parasite-induced host mortality) evolves along with the rate of host exploitation. If the life expectancy of a parasite is short, it is expected to evolve a higher rate of host exploitation and therefore higher virulence because the penalty to the parasite for killing the host is reduced. We tested this hypothesis by keeping for 14 months the horizontally transmitted microsporidian parasite Glugoides intestinalis in mono-clonal host cultures (Daphnia magna) under conditions of high and low host background mortality. High host mortality, and thus parasite mortality, was achieved by replacing weekly 70-80% of all hosts in a culture with uninfected hosts from stock cultures (Replacement lines). In the low-mortality treatment no replacement took place. Contrary to our expectation, parasites from the Replacement lines evolved a lower within-host growth rate and virulence than parasites from the Nonreplacement lines. Across lines we found a strong positive correlation between within-host growth rate and virulence. We did further experiments to answer the question why our data did not support the predictions. Sporophorous vesicles (SVs, spore clusters) were smaller in doubly infected than in singly infected host-gut cells, indicating that competition within cells bears costs for the parasite. Due to our experimental protocol, the average life span of infections had been much higher in the Nonreplacement lines. Since the number of parasites inside a host increases with the time since infection, long-lasting infections led to high frequencies of multiply infected host-gut cells. Therefore, we speculated that within-cell competition was more severe in the Nonreplacement lines and may have led to selection for accelerated within-host growth. SVs in the Nonreplacement lines were indeed significantly larger. Our results point out that single-factor explanations for the evolution of virulence can lead to wrong predictions and that multiple infections are an important factor in virulence evolution.

Reduced flight-to-light behaviour of moth populations exposed to long-term urban light pollution

The globally increasing light pollution is a well-recognized threat to ecosystems, with negative effects on human, animal and plant wellbeing. The most well-known and widely documented consequence of light pollution is the generally fatal attraction of nocturnal insects to artificial light sources. However, the evolutionary consequences are unknown. Here we report that moth populations from urban areas with high, globally relevant levels of light pollution over several decades show a significantly reduced flight-to-light behaviour compared with populations of the same species from pristine dark-sky habitats. Using a common garden setting, we reared moths from 10 different populations from early-instar larvae and experimentally compared their flight-to-light behaviour under standardized conditions. Moths from urban populations had a significant reduction in the flight-to-light behaviour compared with pristine populations. The reduced attraction to light sources of 'city moths' may directly increase these individuals' survival and reproduction. We anticipate that it comes with a reduced mobility, which negatively affects foraging as well as colonization ability. As nocturnal insects are of eminent significance as pollinators and the primary food source of many vertebrates, an evolutionary change of the flight-to-light behaviour thereby potentially cascades across species interaction networks.

Altered Intermittent Rhythmic Delta and Theta Activity in the Electroencephalographies of High Functioning Adult Patients with Autism Spectrum Disorder

Background: Autism spectrum disorder (ASD) is often associated with epilepsy. Previous studies have also shown increased rates of electroencephalographic (EEG) alteration in ASD patients without epilepsy. The aim of this study was to compare the rate of intermittent rhythmic delta and theta activity (IRDA/IRTA) events between high-functioning adult patients with ASD and matched healthy controls.

Materials and Methods: Routine EEG records of 19 ASD patients and 19 matched controls were screened for IRDA/IRTA using a fully data driven analysis with fixed thresholds. IRDA/IRTA rates before and after hyperventilation (HV) as well as the HV-induced difference in IRDA/IRTA rates (HV difference) were analyzed. For inter-group measures, we used the Wilcoxon rank sum test.

Results: Significantly increased HV difference was detected in the ASD group (p = 0.0497). However, the groups showed no difference in IRDA/IRTA rates before HV (p = 0.564) and after HV (p = 0.163).

Conclusions: The lack of any group differences regarding IRDA/IRTA before HV might be related to the fact that we only studied non-secondary high-functioning autism in a small sample of epilepsy-free adult patients. A significantly increased HV difference might be regarded as a marker of subtle neuronal network instability possibly causing short-term disturbances via local area network inhibition and long-term effects via epileptic encephalopathy.

Glutathione metabolism in the prefrontal brain of adults with high-functioning autism spectrum disorder: an MRS study

Background

Autism spectrum disorder (ASD) is a neurodevelopmental disease characterized by difficulties in social communication, unusually restricted, repetitive behavior and interests, and specific abnormalities in language and perception. The precise etiology of ASD is still unknown and probably heterogeneous. In a subgroup of patients, toxic environmental exposure might lead to an imbalance between oxidative stress and anti-oxidant systems. Previous serum and postmortem studies measuring levels of glutathione (GSH), the main cellular free radical scavenger in the brain, have supported the hypothesis that this compound might play a role in the pathophysiology of autism.

Methods

Using the method of single-voxel proton magnetic resonance spectroscopy (MRS), we analyzed the GSH signal in the dorsal anterior cingulate cortex (dACC) and the dorsolateral prefrontal cortex (DLPFC) of 24 ASD patients with normal or above average IQs and 18 matched control subjects. We hypothesized that we would find decreased GSH concentrations in both regions.

Results

We did not find overall group differences in neurometabolites including GSH, neither in the dorsal ACC (Wilks’ lambda test; p = 0.429) nor in the DLPFC (p = 0.288). In the dACC, we found a trend for decreased GSH signals in ASD patients (p = 0.076).

Conclusions

We were unable to confirm our working hypothesis regarding decreased GSH concentrations in the ASD group. Further studies combining MRS, serum, and cerebrospinal fluid measurements of GSH metabolism including other regions of interest or even whole brain spectroscopy are needed.