Differential dynamics of histone H3 methylation at positions K4 and K9 in the mouse zygote

BACKGROUND: In the mouse zygote the paternal genome undergoes dramatic structural and epigenetic changes. Chromosomes are decondensed, protamines replaced by histones and DNA is rapidly and actively demethylated. The epigenetic asymmetry between parental genomes remains at least until the 2-cell stage suggesting functional differences between paternal and maternal genomes during early cleavage stages. RESULTS: Here we analyzed the timing of histone deposition on the paternal pronucleus and the dynamics of histone H3 methylation (H3/K4mono-, H3/K4tri- and H3/K9di-methylation) immediately after fertilization. Whereas maternal chromatin maintains all types of histone H3 methylation throughout the zygotic development, paternal chromosomes acquire new and unmodified histones shortly after fertilization. In the following hours we observe a gradual increase in H3/K4mono-methylation whereas H3/K4tri-methylation is not present before latest pronuclear stages. Histone H3/K9di-methylation is completely absent from the paternal pronucleus, including metaphase chromosomes of the first mitotic stage. CONCLUSION: Parallel to the epigenetic asymmetry in DNA methylation, chromatin modifications are also different between both parental genomes in the very first hours post fertilization. Whereas methylation at H3/K4 gradually becomes similar between both genomes, H3/K9 methylation remains asymmetric

Macroscopic nucleon-nucleon correlations caused by the bounce-off process in energetic collisions of heavy nuclei

Two-particle correlation data are presented for the reaction Ar (800 MeV/ nucleon) + Pb. The experimental results are analyzed in the nuclear fluid dynamical and in a linear cascade model. We demonstrate that the collective hydrodynamical correlations dominate the measured two-particle correlation function for the heavy system studied. We discuss the transition from the early stages of the reaction which are governed by few nucleon correlations, to the later stages with their macroscopic flow which can only be reached using heavy colliding systems. The sensitivity of the correlation data on the underlying compressional dissipative processes is analyzed

When does Christian religion matter for entrepreneurial activity?:the contingent effect of a country’s investments into knowledge

This study furthers scholarship on the religion-entrepreneurship link by proposing that (1) aspects of a country’s religious profile impact individual entrepreneurial activity differently and (2) that a country’s level of investments in knowledge serves as a contingency factor in this milieu. Our cross-level analyses of data from 9,266 individuals and 27 predominantly Christian countries support the second, but not the first suggestion. The study contributes to a more nuanced understanding of religion’s role for entrepreneurship and bridges the literatures on religion and knowledge-based entrepreneurship. Furthermore, the study provides evidence of the effects of religion above and beyond the effects of national culture

Hydrogeologische/Hydrologische Untersuchung einer Prä-Flutungssituation am Beispiel des Gessentals im ehemaligen ostthüringischen Uranbergbaugebiet

Zur Aufnahme und Beschreibung der Prozesse und der Dynamik des bergbauinduzierten Stoffeintrags und -austrags aus einer Uranbergbauhalde während einer Prä-Flutungssituation in ein z.T. entwässertes Talsystem wurden im 30 km² großen Einzugsgebiet des Gessenbaches (Gessental) zwischen 1997 und 2001 hydrologische/hydrogeologische Feld- und Laborarbeiten sowie hydrochemische Modellierungen durchgeführt. Neben den sedimentologischen, geophysikalischen und hydrogeologischen zeigen die hydrogeochemischen prozessorientierten Untersuchungen dieser Arbeit eine Möglichkeit, die Signatur einer definierten Schadstoffquelle über die Vorflut und die Talsedimente zu verfolgen. Das in ein System ohne hydraulische Ankopplung an das hydrogeologische Regime eintretende Haldensickerwasser führt zur Ausbildung von temporären vermutlich metastabilen geochemischen Barrieren , welche den Transport und den Austrag von Schadstoffen verzögern kann. Systeme mit hydraulischer Ankopplung an das Grundwasser weisen eine höhere Transferwirkung auf. Modifikationen der hydrogeologischen Randbedingungen durch die zukünftig austretenden Flutungswässer des Uranbergbaus werden zu einer Veränderung der geochemischen Ausgangsbedingungen führen und die Transferwirkung vermutlich erhöhen. Die Untersuchungen liefern die Eingangsdaten für zukünftige Analysen und Grundwassermodellierungen des Post-Flutungszeitraumes im Gessental bei Ronneburg

Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse

<p>Abstract</p> <p>Background</p> <p>In mammals, imprinted genes are regulated by an epigenetic mechanism that results in parental origin-specific expression. Though allele-specific regulation of imprinted genes has been studied for several individual genes in detail, little is known about their overall tissue-specific expression patterns and interspecies conservation of expression.</p> <p>Results</p> <p>We performed a computational analysis of microarray expression data of imprinted genes in human and mouse placentae and in a variety of adult tissues. For mouse, early embryonic stages were also included. The analysis reveals that imprinted genes are expressed in a broad spectrum of tissues for both species. Overall, the relative tissue-specific expression levels of orthologous imprinted genes in human and mouse are not highly correlated. However, in both species distinctive expression profiles are found in tissues of the endocrine pathways such as adrenal gland, pituitary, pancreas as well as placenta. In mouse, the placental and embryonic expression patterns of imprinted genes are highly similar. Transcription factor binding site (TFBS) prediction reveals correlation of tissue-specific expression patterns and the presence of distinct TFBS signatures in the upstream region of human imprinted genes.</p> <p>Conclusion</p> <p>Imprinted genes are broadly expressed pre- and postnatally and do not exhibit a distinct overall expression pattern when compared to non-imprinted genes. The relative expression of most orthologous gene pairs varies significantly between human and mouse suggesting rapid species-specific changes in gene regulation. Distinct expression profiles of imprinted genes are confined to certain human and mouse hormone producing tissues, and placentae. In contrast to the overall variability, distinct expression profiles and enriched TFBS signatures are found in human and mouse endocrine tissues and placentae. This points towards an important role played by imprinted gene regulation in these tissues.</p

CpG Island Mapping by Epigenome Prediction

CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1) reliance on arbitrary threshold parameters that bear little biological justification, (2) failure to account for widespread heterogeneity among CpG islands, and (3) apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of “CpG island strength” that incorporates epigenetic and functional aspects can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human Chromosomes 21 and 22, we identify informative DNA attributes that correlate with open versus compact chromatin structures. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features, we estimate the inherent CpG island strength for each CpG island in the human genome, i.e., its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted “bona fide” CpG islands. The mapping of CpG islands by epigenome prediction is conceptually superior to identifying CpG islands by widely used sequence criteria since it links CpG island detection to their characteristic epigenetic and functional states. And it is superior to purely experimental epigenome mapping for CpG island detection since it abstracts from specific properties that are limited to a single cell type or tissue. In addition, using computational epigenetics methods we could identify high correlation between the epigenome and characteristics of the DNA sequence, a finding which emphasizes the need for a better understanding of the mechanistic links between genome and epigenome

CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure

CpG island methylation plays an important role in epigenetic gene control during mammalian development and is frequently altered in disease situations such as cancer. The majority of CpG islands is normally unmethylated, but a sizeable fraction is prone to become methylated in various cell types and pathological situations. The goal of this study is to show that a computational epigenetics approach can discriminate between CpG islands that are prone to methylation from those that remain unmethylated. We develop a bioinformatics scoring and prediction method on the basis of a set of 1,184 DNA attributes, which refer to sequence, repeats, predicted structure, CpG islands, genes, predicted binding sites, conservation, and single nucleotide polymorphisms. These attributes are scored on 132 CpG islands across the entire human Chromosome 21, whose methylation status was previously established for normal human lymphocytes. Our results show that three groups of DNA attributes, namely certain sequence patterns, specific DNA repeats, and a particular DNA structure, are each highly correlated with CpG island methylation (correlation coefficients of 0.64, 0.66, and 0.49, respectively). We predicted, and subsequently experimentally examined 12 CpG islands from human Chromosome 21 with unknown methylation patterns and found more than 90% of our predictions to be correct. In addition, we applied our prediction method to analyzing Human Epigenome Project methylation data on human Chromosome 6 and again observed high prediction accuracy. In summary, our results suggest that DNA composition of CpG islands (sequence, repeats, and structure) plays a significant role in predisposing CpG islands for DNA methylation. This finding may have a strong impact on our understanding of changes in CpG island methylation in development and disease

Marine Sciences in Germany: The Restart in Kiel After World War II

The first German paper on oceanography was published in Kiel in 1697 (Kortum, 1994) at the beginning of the country’s long history in ocean science. Following successful development during the nineteenth and early twentieth centuries, culminating in the Atlantic Ocean Expedition of the first research vessel Meteor from 1925 to 1927 (Spiess, 1928), marine sciences almost disappeared from the defeated nation at the end of World War II. Because the country was mostly landlocked, it was not obvious to occupation authorities and German politicians that the country should again develop a strong marine science capacity. Nevertheless, the restart began, mostly at Kiel University and at the newly founded German Hydrographic Office in Hamburg