The role of Dnmts and Tets in shaping the DNA methylation landscape of mouse embryonic stem cells

DNA methylation is an important epigenetic mark, which is set and maintained by DNA methyltransferases (Dnmts) and removed via passive or active mechanisms involving Ten eleven translocation enzyme (Tet) mediated oxidation. Stable cell type specific methylation patterns can only be achieved if methylation and demethylation events are in balance. Yet, the genome wide regulation of Dnmt and Tet activity is still not fully understood. The present studies use novel hairpin sequencing techniques coupled with oxidative bisul te sequencing, which permits the simultaneous and strand speci c detection of 5- methylcytosine and 5-hydroxymethylcytosine. Application of HMM models then facilitates the estimation of enzyme efficiencies for Dnmts and Tets. Furthermore, spatial modelling of hairpin bisulfite data allows the investigation of how Dnmts interpret preexisting methylation patterns. Taken together, the results of the presented studies show that methylation and hydroxylation are antagonistic, but not mutual exclusive events. In this context, the data shows that Tet efficiency is highest at open and accessible chromatin. Furthermore, the absence of Tets leads to a considerable misregulation of Dnmts, resulting in an increase in both maintenance and de novo methylation efficiency. Lastly, the spatial analysis of methylation patterns reveals that the de novo methyltransferases Dnmt3a and 3b depend in their activity on pre-existing neighbouring CpG methylation.DNA Methylierung is eine epigenetische Modifikation, welche durch DNA Methyltransferasen (Dnmts) gesetzt und beibehalten wird. Entfernt wird DNA Methylierung durch aktive oder passive Mechanismen welche die Oxidation von DNA Methylierung durch Ten- Eleven Translocation Enzyme (Tets) involviert. Stabile, Zelltyp-spezifische Methylierungsmuster können nur erreicht werden, wenn Methylierungs- und Demethylierungsvorgänge im Gleichgewicht sind. Dennoch ist die genomweite Regulation von Dnmts und Tets nicht vollständig geklärt. Die hier gezeigten Studien verwenden neue Hairpin-Sequenzierungs-Verfahren, gekoppelt mit oxidativer Bisulfit-Sequenzierung, was eine simultane und strangspezifische Analyse von 5-Methylcytosin und 5-Hydroxymethylcytosin erlaubt. Die Anwendung von hid- den Markov Modellen erlaubt im Anschluss die Berechnung von Enzymeeffizienzen für Dnmts und Tets. Darüber hinaus erlaubt eine räumliche Modellierung von Methylierungsmustern die Untersuchung, wie Dnmts bereits bestehende Methylierung interpretieren. Die Ergebnisse zeigen, dass Methylierung und Hydroxylierung antagonistische, aber keinesfalls sich ausschließende Ereignisse sind. Dabei zeigen Tets ihre stärkste Aktivität an offenem und zugänglichem Chromatin. Zudem führt der Verlust von Tets zu einer deutlichen Missregulation von Dnmts, welche sich durch eine Zunahme der Maintenance und de novo-Methylierungseffizienz äußert. Schließlich zeigt die räumliche Modellierung, dass die de novo-Methyltransferasen bei ihrer Aktivität abhängig von bereits bestehender DNA Methylierung sind

The importance of direct fitness for helpers in advanced social societies

Social insect societies are characterized by a caste determined reproductive and non-reproductive division of labor. Usually, queens stay in the safe surrounding of the nest and produce offspring, while workers refrain from reproduction and care for the brood, forage or defend the nest. However, workers of many social insect species are principally capable of laying unfertilized eggs, which can develop into males. In cooperatively breeding birds or mammals, helpers forgo early reproduction to benefit from brood care experience or nest inheritance and thus, gain an increased direct fitness later in life. However, workers in highly social insect species as in many ants, bees and wasps, generally cannot inherit the nest and replace a fully fertile queen due to physiological restrictions, and the importance of direct fitness benefits for workers has long been neglected. Referring to Hamilton (1964b), it is assumed that ant workers refrain from direct fitness (their own produced offspring) to benefit from indirect fitness the offspring produced by the queen due to their help) and thereby, increase their inclusive fitness. Questions arose whether this is sufficient to explain a lifetime resignation from reproduction in social insect workers. Indeed, several studies report selfish behaviors like worker policing, egg dumping or the refusal of costly tasks, possibly to increase the chance for future direct fitness in individual workers. Here, we studied the importance of direct fitness for workers in the monogynous, monandrous ant Temnothorax crassispinus. We examined the reproductive success of workers by ovary dissections and genotyping workers and males from natural queenless and queenright colonies (chapter 2), and monitored the survival and productivity of queenless and queenright colonies for four years in captivity (chapter 3). We compared fitness traits of queen- and worker-produced males under near-natural and standardized conditions (chapter 4) and investigated whether males produced by workers in the absence of a queen, are accepted in queenright colonies during colony reunification before hibernation (chapter 5). Moreover, we hypothesized that the reproductive potential of young workers might induce selfishness and limit behavioral flexibility under pathogen threat (chapter 6) and examined the effect of selfish reproduction on sanitary behavior of the workers (chapter 7). Our studies show, that queen presence or absence, respectively did not affect ovary development in workers and that around 30% of the genotyped males were not produced by the estimated queen in natural colonies. Most males that were not produced by the queen, were produced by workers not related to the colony. Accordingly, the reproductive success of workers related to the queen seemed to be comparably low in nature but increased under laboratory conditions. Workers seem to be capable of increasing their direct fitness by the expulsion or killing of the queen and a reinforced reproduction afterwards. Queenless colonies were highly productive and persistent and sperm traits of worker-produced males varied only little from that of queen-produced males. Furthermore, larvae produced in queenless colony fragments could be readily integrated in queenright laboratory colonies during colony reunification before hibernation, and contributed considerably to male production in queenright colonies. However, the prospect of future reproductive success did not affect altruistic self-removal in health compromised workers, but microbiota growth seemed to be encouraged in queenless colonies when sanitary behavior is neglected

Queen execution in a monogynous ant

Workers in many species of social insects are capable of laying unfertilized eggs, which can develop into haploid males. This causes a conflict about male parentage between queens and workers. In a few species, this may result in matricide, that is, workers kill the colony's queen. Queen killing has so far been observed mainly in multi‐queen colonies or in annual species, when the queen's fecundity declines at the end of the reproductive period. Here, we report queen expulsion and matricide in a monogynous, monandrous ant with perennial societies. Workers were seen to aggressively expel both related and unrelated queens from their nest shortly after the end of hibernation. Queen expulsion and matricide led to a significant decrease in the number of workers and brood, but eventually increased the direct fitness of workers through significant male production. Long‐term observations revealed a short lifespan of queens, while workers in orphaned colonies survived and produced male offspring over several years

Ant queens increase their reproductive efforts after pathogen infection

Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect

Tindak Tutur Direktif Dalam Novel Pukat Karya Tere-liye

This article was written based on (a) to describe the type of directive speech acts, (b) the strategy told the directive speech act, (c) the context of the use of directive speech acts, and (d) the effect of the use of linguistic politeness strategies recalled toin the novelPukat created by Tere-Liye.The data of this study is the speech acts of the figures contained in the novel Pukat created by Tere-Liye.The data source of this research is the novelPukat created by Tere-Liye.Data collected by reading and noting directive speech acts contained therein. Data were analyzed with the following steps: (1) identify the data and classifies data based on type, recalled strategy, context, and tells of the effects of linguistic politeness strategies in the directive speech act, (2) connecting the data with the data of the other, (3 ) conducted a study of data inference.The findings of this study are as follows. First, there are 5 types of directive speech acts, that is telling, asking, advising, challenging, and suggest. Second, there are 3 strategies recalled, that tells directly without further ado, instantly recalled with niceties positive politeness, recalled instantly with niceties negative politeness. Third, the strategy of direct recalled without further ado tends to be used in the context of the directive speech act hearer smaller, intimate, and speech do both. Fourth, the use of recalled strategy directly without further ado hearer in the context of smaller, intimate, and the speech made ​​two decent effect

A Continual Learning Approach for Cross-Domain White Blood Cell Classification

Accurate classification of white blood cells in peripheral blood is essential for diagnosing hematological diseases. Due to constantly evolving clinical settings, data sources, and disease classifications, it is necessary to update machine learning classification models regularly for practical real-world use. Such models significantly benefit from sequentially learning from incoming data streams without forgetting previously acquired knowledge. However, models can suffer from catastrophic forgetting, causing a drop in performance on previous tasks when fine-tuned on new data. Here, we propose a rehearsal-based continual learning approach for class incremental and domain incremental scenarios in white blood cell classification. To choose representative samples from previous tasks, we employ exemplar set selection based on the model's predictions. This involves selecting the most confident samples and the most challenging samples identified through uncertainty estimation of the model. We thoroughly evaluated our proposed approach on three white blood cell classification datasets that differ in color, resolution, and class composition, including scenarios where new domains or new classes are introduced to the model with every task. We also test a long class incremental experiment with both new domains and new classes. Our results demonstrate that our approach outperforms established baselines in continual learning, including existing iCaRL and EWC methods for classifying white blood cells in cross-domain environments.Comment: Accepted for publication at workshop on Domain Adaptation and Representation Transfer (DART) in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023

Worker ants promote outbreeding by transporting young queens to alien nests

Choosing the right mating partner is one of the most critical decisions in the life of a sexually reproducing organism and is the basis of sexual selection. This choice is usually assumed to be made by one or both of the sexual partners. Here, we describe a system in which a third party – the siblings – promote outbreeding by their sisters: workers of the tiny ant Cardiocondyla elegans carry female sexuals from their natal nest over several meters and drop them in the nest of another, unrelated colony to promote outbreeding with wingless, stationary males. Workers appear to choose particular recipient colonies into which they transfer numerous female sexuals. Assisted outbreeding and indirect female choice in the ant C. elegans are comparable to human matchmaking and suggest a hitherto unknown aspect of natural history – third party sexual selection. Our study highlights that research at the intersection between social evolution and reproductive biology might reveal surprising facets of animal behavior

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs.

Mouse embryonic stem cells are dynamic and heterogeneous. For example, rare cells cycle through a state characterized by decondensed chromatin and expression of transcripts, including the Zscan4 cluster and MERVL endogenous retrovirus, which are usually restricted to preimplantation embryos. Here, we further characterize the dynamics and consequences of this transient cell state. Single-cell transcriptomics identified the earliest upregulated transcripts as cells enter the MERVL/Zscan4 state. The MERVL/Zscan4 transcriptional network was also upregulated during induced pluripotent stem cell reprogramming. Genome-wide DNA methylation and chromatin analyses revealed global DNA hypomethylation accompanying increased chromatin accessibility. This transient DNA demethylation was driven by a loss of DNA methyltransferase proteins in the cells and occurred genome-wide. While methylation levels were restored once cells exit this state, genomic imprints remained hypomethylated, demonstrating a potential global and enduring influence of endogenous retroviral activation on the epigenome