Proteomic analysis of stress responses in Daphnia

Organisms respond to changes in their environment affecting their physiological or ecological optimum by reactions called stress responses. These stress responses may enable the organism to survive by counteracting the consequences of the environ- mental change, the stressor, and usually consist of plastic alterations of traits related to physiology, behaviour, or morphology. In the ecological model species Daphnia, the waterflea, stressors like predators or parasites are known to have an important role in adaptive evolution and have been therefore studied in great detail. However, although various aspects of stress responses in Daphnia have been analysed, molecu- lar mechanisms underlying these traits are not well understood so far. For studying unknown molecular mechanisms, untargeted ‘omics’ approaches are especially suit- able, as they may identify undescribed key players and processes. Recently, ‘omics’ approaches became available for Daphnia. Daphnia is a cosmo- politan distributed fresh water crustacean and has been in research focus for a long time because of its central role in the limnic food web. Furthermore, the responses of this organism to a variety of stressors have been intensively studied e.g. to hypoxic conditions, temperature changes, ecotoxicological relevant substances, parasites or predation. Of these environmental factors, especially predation and interactions with parasites have gained much attention, as both are known to have great influence on the structure of Daphnia populations. In the work presented in this thesis, I characterised the stress responses of Daphnia using proteomic approaches. Proteomics is particularly well suited to analyse bio- logical systems, as proteins are the main effector of nearly all biological processes. However, performing Daphnia proteomics is a challenging task due to high proteolytic activity in the samples, which most probably originate from proteases located in the gut of Daphnia, and are not inhibited by proteomics standard sample pre- paration protocols. Therefore, before performing successful proteomic approaches, I had to optimise the sample preparation step to inhibit proteolytic activity in Daph- nia samples. After succeeding with this task, I was able to analyse stress responses of Daphnia to well-studied stressors like predation and parasites. Furthermore, I stud- ied their response to microgravity exposure, a stressor not well analysed in Daphnia so far. My work on proteins involved in predator-induced phenotypic plasticity is de- scribed in chapter 2 and 3. Daphnia is a textbook example for this phenomenon and is known to show a multitude of inducible defences. For my analysis, I used the system of Daphnia magna and its predator Triops cancriformis. D. magna is known to change its morphology and to increase the stability of its carapace when exposed to the pred- ator, which has been shown to serve as an efficient protection against T. cancriformis predation. In chapter 2, I used a proteomic approach to study predator-induced traits in late-stage D. magna embryos. D. magna neonates are known to be defended against Triops immediately after the release from the brood pouch, if mothers were exposed to the predator. Therefore, the formation of the defensive traits most probably oc- curs during embryonic development. Furthermore, embryos should have reduced protease abundances, as they do not feed inside the brood pouch until release. To study proteins differing in abundance between D. magna exposed to the predator and a control group, I applied a proteomic 2D-DIGE approach, which is a gel based method and therefore enables visual monitoring of protein sample quality. I found differences in traits directly associated with known defences like cuticle proteins and chitin-modifying enzymes most probably involved in carapace stability. In addition, enzymes of the energy metabolism and the yolk protein vitellogenin indicated alterations in energy demand. In chapter 3, I present a subsequent study supporting these results. Here, I analysed responses of adult D. magna to Triops predation at the proteome level using an optimised sample preparation procedure, which was able to generate adult protein samples thereby inhibiting proteolysis. Furthermore, I established a different proteomic approach using a mass-spectrometry based label- free quantification, in which I integrated additional genotypes of D. magna to create a more comprehensive analysis. With this approach, I was able to confirm the results of the embryo study, as similar biological processes indicated by cuticle proteins and vi- tellogenins were involved. Furthermore, additional calcium-binding cuticle proteins and chitin-modifying enzymes and proteins involved in other processes, e.g. protein biosynthesis, could be assigned. Interestingly, I also found evidence for proteins in- volved in a general or a genotype dependent response, with one genotype, which is known to share its habitat with Triops, showing the most distinct responses. Genotype dependent changes in the proteome were also detectable in the study which I present in chapter 4. Here, I analysed molecular mechanisms underlying host-parasite interactions using the well characterised system of D. magna and the bacterial endoparasite Pasteuria ramosa. P. ramosa is known to castrate and kill their host and the infection success is known to depend strongly on the host’s and the para- site’s genotype. I applied a similar proteomic approach as in chapter 3 using label- free quantification, but contrastingly, I did not use whole animal samples but only the freshly shed cuticle. It has been shown, that the genotypic specificity of P. ramosa infection is related to the parasite’s successful attachment to the cuticle of the host and is therefore most probably caused by differences in cuticle composition. Hence, I analysed exuvia proteomes of two different genotypes known to be either suscept- ible to P. ramosa or not. Furthermore, I compared exuvia proteomes of susceptible Daphnia exposed to P. ramosa to a control group for finding proteins involved in the infection process and in the stress response of the host. The proteomes of the different genotypes showed indeed very interesting abundance alterations, connected either to cuticle proteins or matrix metalloproteinases (MMPs). Additionally, the cuticle pro- teins more abundant in the susceptible genotype showed a remarkable increase in predicted glycosylation sites, supporting the hypothesis that P. ramosa attaches to the host’s cuticle by using surface collagen-like proteins to bind to glycosylated cuticle proteins. Most interestingly, in all replicates of the susceptible genotype exposed to P. ramosa, such a collagen-like protein was found in high abundances. Another group of proteins found in higher abundance in the non-susceptible genotype, the MMPs, are also connected to this topic, as they may have collagenolytic characteristics and therefore could interfere with parasite infection. Furthermore, the data indicate that parasite infection may lead to retarded moulting in Daphnia, as moulting is known to reduce the infection success. Contrastingly to the work presented so far, the study described in chapter 5 invest- igated the protein response of Daphnia to a stressor not well studied on other levels, namely microgravity. As gravity is the only environmental parameter which has not changed since life on earth began, organisms usually do not encounter alterations of gravity on earth and cannot adapt to this kind of change. Daphnia has been part of one mission to space, however, responses of the animals to microgravity are not well described so far. In addition, as Daphnia are an interesting candidate organisms for aquatic modules of biological life support systems (BLSS), more information on their response to microgravity is necessary. For this reason, proteomics is an interesting ap- proach, as biological processes not detectable at the morphological or physiological level may become apparent. Therefore, a ground-based method, a 2D-clinostat, was used to simulate microgravity, as studies under real microgravity conditions in space need high technical complexity and financial investment. Subsequently, a proteomic 2D-DIGE approach was applied to compare adult Daphnia exposed to microgravity to a control group. Daphnia showed a strong response to microgravity with abundance alterations in proteins related to the cytoskeleton, protein folding and energy meta- bolism. Most interestingly, this response is very similar to the reactions of a broad range of other organisms to microgravity exposure, indicating that the response to altered gravity conditions in Daphnia follows a general concept. Altogether, the work of my thesis showed a variety of examples of how a proteomic approach may increase the knowledge on stress responses in an organisms not well- established in proteomics. I described both, the analysis of molecular mechanisms underlying well-known traits and the detection of proteins involved in a response not well characterised. Furthermore, I gave examples for highly genotype dependent and also more general stress responses. Therefore, this thesis improves our understanding of the interactions between genotype, phenotype and environment and, moreover, offers interesting starting points for studying the molecular mechanisms underlying stress responses of Daphnia in more detail

In vitro und in vivo Tumoreigenschaften eines kleinzelligen Ovarialkarzinoms vom hyperkalzämischen Typ und mögliche therapeutische Ansätze

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Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses

Background: Phenotypic plasticity in defensive traits occurs in many species when facing heterogeneous predator regimes. The waterflea Daphnia is well-known for showing a variety of these so called inducible defences. However, molecular mechanisms underlying this plasticity are poorly understood so far. We performed proteomic analysis on Daphniamagna exposed to chemical cues of the predator Triops cancriformis. D. magna develops an array of morphological changes in the presence of Triops including changes of carapace morphology and cuticle hardening. Results: Using the 2D-DIGE technique, 1500 protein spots could be matched and quantified. We discovered 179 protein spots with altered intensity when comparing Triops exposed animals to a control group, and 69 spots were identified using nano-LC MS/MS. Kairomone exposure increased the intensity of spots containing muscle proteins, cuticle proteins and chitin-modifying enzymes as well as enzymes of carbohydrate and energy metabolism. The yolk precursor protein vitellogenin decreased in abundance in 41 of 43 spots. Conclusion: Identified proteins may be either directly involved in carapace stability or reflect changes in energy demand and allocation costs in animals exposed to predator kairomones. Our results present promising candidate proteins involved in the expression of inducible defences in Daphnia and enable further in depth analysis of this phenomenon

Developmentally regulated alterations in Polycomb repressive complex 1 proteins on the inactive X chromosome

Polycomb group (PcG) proteins belonging to the polycomb (Pc) repressive complexes 1 and 2 (PRC1 and PRC2) maintain homeotic gene silencing. In Drosophila, PRC2 methylates histone H3 on lysine 27, and this epigenetic mark facilitates recruitment of PRC1. Mouse PRC2 (mPRC2) has been implicated in X inactivation, as mPRC2 proteins transiently accumulate on the inactive X chromosome (Xi) at the onset of X inactivation to methylate histone H3 lysine 27 (H3-K27). In this study, we demonstrate that mPRC1 proteins localize to the Xi, and that different mPRC1 proteins accumulate on the Xi during initiation and maintenance of X inactivation in embryonic cells. The Xi accumulation of mPRC1 proteins requires Xist RNA and is not solely regulated by the presence of H3-K27 methylation, as not all cells that exhibit this epigenetic mark on the Xi show Xi enrichment of mPRC1 proteins. Our results implicate mPRC1 in X inactivation and suggest that the regulated assembly of PcG protein complexes on the Xi contributes to this multistep process

SARS-CoV-2 Transmissibility Within Day Care Centers—Study Protocol of a Prospective Analysis of Outbreaks in Germany

Introduction: Until today, the role of children in the transmission dynamics of SARS-CoV-2 and the development of the COVID-19 pandemic seems to be dynamic and is not finally resolved. The primary aim of this study is to investigate the transmission dynamics of SARS-CoV-2 in child day care centers and connected households as well as transmission-related indicators and clinical symptoms among children and adults. Methods and Analysis: COALA (“Corona outbreak-related examinations in day care centers”) is a day care center- and household-based study with a case-ascertained study design. Based on day care centers with at least one reported case of SARS-CoV-2, we include one- to six-year-old children and staff of the affected group in the day care center as well as their respective households. We visit each child's and adult's household. During the home visit we take from each household member a combined mouth and nose swab as well as a saliva sample for analysis of SARS-CoV-2-RNA by real-time reverse transcription polymerase chain reaction (real-time RT-PCR) and a capillary blood sample for a retrospective assessment of an earlier SARS-CoV-2 infection. Furthermore, information on health status, socio-demographics and COVID-19 protective measures are collected via a short telephone interview in the subsequent days. In the following 12 days, household members (or parents for their children) self-collect the same respiratory samples as described above every 3 days and a stool sample for children once. COVID-19 symptoms are documented daily in a symptom diary. Approximately 35 days after testing the index case, every participant who tested positive for SARS-CoV-2 during the study is re-visited at home for another capillary blood sample and a standardized interview. The analysis includes secondary attack rates, by age of primary case, both in the day care center and in households, as well as viral shedding dynamics, including the beginning of shedding relative to symptom onset and viral clearance. Discussion: The results contribute to a better understanding of the epidemiological and virological transmission-related indicators of SARS-CoV-2 among young children, as compared to adults and the interplay between day care and households.Peer Reviewe

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

The Crowdsourced Replication Initiative: Investigating Immigration and Social Policy Preferences. Executive Report.

In an era of mass migration, social scientists, populist parties and social movements raise concerns over the future of immigration-destination societies. What impacts does this have on policy and social solidarity? Comparative cross-national research, relying mostly on secondary data, has findings in different directions. There is a threat of selective model reporting and lack of replicability. The heterogeneity of countries obscures attempts to clearly define data-generating models. P-hacking and HARKing lurk among standard research practices in this area.This project employs crowdsourcing to address these issues. It draws on replication, deliberation, meta-analysis and harnessing the power of many minds at once. The Crowdsourced Replication Initiative carries two main goals, (a) to better investigate the linkage between immigration and social policy preferences across countries, and (b) to develop crowdsourcing as a social science method. The Executive Report provides short reviews of the area of social policy preferences and immigration, and the methods and impetus behind crowdsourcing plus a description of the entire project. Three main areas of findings will appear in three papers, that are registered as PAPs or in process

Broadband Multi-wavelength Properties of M87 during the 2017 Event Horizon Telescope Campaign

Abstract: In 2017, the Event Horizon Telescope (EHT) Collaboration succeeded in capturing the first direct image of the center of the M87 galaxy. The asymmetric ring morphology and size are consistent with theoretical expectations for a weakly accreting supermassive black hole of mass ∼6.5 × 109 M ⊙. The EHTC also partnered with several international facilities in space and on the ground, to arrange an extensive, quasi-simultaneous multi-wavelength campaign. This Letter presents the results and analysis of this campaign, as well as the multi-wavelength data as a legacy data repository. We captured M87 in a historically low state, and the core flux dominates over HST-1 at high energies, making it possible to combine core flux constraints with the more spatially precise very long baseline interferometry data. We present the most complete simultaneous multi-wavelength spectrum of the active nucleus to date, and discuss the complexity and caveats of combining data from different spatial scales into one broadband spectrum. We apply two heuristic, isotropic leptonic single-zone models to provide insight into the basic source properties, but conclude that a structured jet is necessary to explain M87’s spectrum. We can exclude that the simultaneous γ-ray emission is produced via inverse Compton emission in the same region producing the EHT mm-band emission, and further conclude that the γ-rays can only be produced in the inner jets (inward of HST-1) if there are strongly particle-dominated regions. Direct synchrotron emission from accelerated protons and secondaries cannot yet be excluded

The influence of simulated microgravity on the proteome of Daphnia magna

BACKGROUND: The waterflea Daphnia is an interesting candidate for bioregenerative life support systems (BLSS). These animals are particularly promising because of their central role in the limnic food web and its mode of reproduction. However, the response of Daphnia to altered gravity conditions has to be investigated, especially on the molecular level, to evaluate the suitability of Daphnia for BLSS in space. METHODS: In this study, we applied a proteomic approach to identify key proteins and pathways involved in the response of Daphnia to simulated microgravity generated by a two-dimensional (2D) clinostat. We analyzed five biological replicates using 2D-difference gel electrophoresis proteomic analysis. RESULTS: We identified 109 protein spots differing in intensity (Po0.05). Substantial fractions of these proteins are involved in actin microfilament organization, indicating the disruption of cytoskeletal structures during clinorotation. Furthermore, proteins involved in protein folding were identified, suggesting altered gravity induced breakdown of protein structures in general. In addition, simulated microgravity increased the abundance of energy metabolism-related proteins, indicating an enhanced energy demand of Daphnia. CONCLUSIONS: The affected biological processes were also described in other studies using different organisms and systems either aiming to simulate microgravity conditions or providing real microgravity conditions. Moreover, most of the Daphnia protein sequences are well-conserved throughout taxa, indicating that the response to altered gravity conditions in Daphnia follows a general concept