Paraneoplastic cerebellar degeneration associated with lymphoepithelial carcinoma of the tonsil

Background: Paraneoplastic cerebellar degeneration (PCD) is a classical tumor-associated, immune-mediated disease typically associated with gynecological malignancies, small-cell lung-cancer or lymphoma. Case presentation: Here we present the case of a 38-year old male with an over 12 months rapidly progressive cerebellar syndrome. Extensive diagnostic workup revealed selective hypermetabolism of the right tonsil in whole-body PET. Histological examination after tonsillectomy demonstrated a lymphoepithelial carcinoma of the tonsil and the tongue base strongly suggesting a paraneoplastic cause of the cerebellar syndrome. To the best of our knowledge this is the first case of an association of a lymphoepithelial carcinoma, a rare pharyngeal tumor, with PCD. Conclusions: In cases of classical paraneoplastic syndromes an extensive search for neoplasms should be performed including whole-body PET to detect tumors early in the course of the disease

Looking beyond stratification: a model-based analysis of the biological drivers of oxygen deficiency in the North Sea

Low oxygen conditions, often referred to as oxy- gen deficiency, occur regularly in the North Sea, a temperate European shelf sea. Stratification represents a major process regulating the seasonal dynamics of bottom oxygen, yet, low- est oxygen conditions in the North Sea do not occur in the regions of strongest stratification. This suggests that stratifi- cation is an important prerequisite for oxygen deficiency, but that the complex interaction between hydrodynamics and the biological processes drives its evolution. In this study we use the ecosystem model HAMSOM- ECOHAM to provide a general characterisation of the dif- ferent zones of the North Sea with respect to oxygen, and to quantify the impact of the different physical and biological factors driving the oxygen dynamics inside the entire sub- thermocline volume and directly above the bottom. With respect to oxygen dynamics, the North Sea can be subdivided into three different zones: (1) a highly produc- tive, non-stratified coastal zone, (2) a productive, season- ally stratified zone with a small sub-thermocline volume, and (3) a productive, seasonally stratified zone with a large sub- thermocline volume. Type 2 reveals the highest susceptibility to oxygen deficiency due to sufficiently long stratification pe- riods (textgreater60 days) accompanied by high surface productivity resulting in high biological consumption, and a small sub- thermocline volume implying both a small initial oxygen in- ventory and a strong influence of the biological consumption on the oxygen concentration. Year-to-year variations in the oxygen conditions are caused by variations in primary production, while spatial dif- ferences can be attributed to differences in stratification and water depth. The large sub-thermocline volume dominates the oxygen dynamics in the northern central and northern North Sea and makes this region insusceptible to oxygen de- ficiency. In the southern North Sea the strong tidal mixing inhibits the development of seasonal stratification which pro- tects this area from the evolution of low oxygen conditions. In contrast, the southern central North Sea is highly suscep- tible to low oxygen conditions (type 2). We furthermore show that benthic diagenetic processes represent the main oxygen consumers in the bottom layer, consistently accounting for more than 50% of the overall consumption. Thus, primary production followed by rem- ineralisation of organic matter under stratified conditions constitutes the main driver for the evolution of oxygen defi- ciency in the southern central North Sea. By providing these valuable insights, we show that ecosystem models can be a useful tool for the interpretation of observations and the es- timation of the impact of anthropogenic drivers on the North Sea oxygen conditions

The impact of intertidal areas on the carbonate system of the southern North Sea

The coastal ocean is strongly affected by ocean acidification because of its shallow water depths, low volume, and the closeness to terrestrial dynamics. Earlier observations of dissolved inorganic carbon (DIC) and total alkalinity (TA) in the southern part of the North Sea, a northwest European shelf sea, revealed lower acidification effects than expected. It has been assumed that anaerobic degradation and subsequent TA release in the adjacent back-barrier tidal areas (Wadden Sea) in summertime is responsible for this phenomenon. In this study the exchange rates of TA and DIC between the Wadden Sea tidal basins and the North Sea and the consequences for the carbonate system in the German Bight are estimated using a 3D ecosystem model. The aim of this study is to differentiate the various sources contributing to observed high summer TA in the southern North Sea. Measured TA and DIC in the Wadden Sea are considered as model boundary conditions. This procedure acknowledges the dynamic behaviour of the Wadden Sea as an area of effective production and decomposition of organic material. According to the modelling results, 39 Gmol TA yr−1 were exported from the Wadden Sea into the North Sea, which is less than a previous estimate but within a comparable range. The interannual variabilities in TA and DIC, mainly driven by hydrodynamic conditions, were examined for the years 2001–2009. Dynamics in the carbonate system are found to be related to specific weather conditions. The results suggest that the Wadden Sea is an important driver for the carbonate system in the southern North Sea. On average 41 % of TA inventory changes in the German Bight were caused by riverine input, 37 % by net transport from adjacent North Sea sectors, 16 % by Wadden Sea export, and 6 % were caused by internal net production of TA. The dominant role of river input for the TA inventory disappears when focusing on TA concentration changes due to the corresponding freshwater fluxes diluting the marine TA concentrations. The ratio of exported TA versus DIC reflects the dominant underlying biogeochemical processes in the Wadden Sea. Whereas aerobic degradation of organic matter played a key role in the North Frisian Wadden Sea during all seasons of the year, anaerobic degradation of organic matter dominated in the East Frisian Wadden Sea. Despite the scarcity of high-resolution field data, it is shown that anaerobic degradation in the Wadden Sea is one of the main contributors of elevated summer TA values in the southern North Sea

Metabolic alkalinity release from large port facilities (Hamburg, Germany) and impact on coastal carbon storage

Metabolic activities in estuaries, especially these of large rivers, profoundly affect the downstream coastal biogeochemistry. Here, we unravel the impacts of large industrial port facilities, showing that elevated metabolic activity in the Hamburg port (Germany) increases total alkalinity (TA) and dissolved inorganic carbon (DIC) runoff to the North Sea. The imports of particulate inorganic carbon, particulate organic carbon, and particulate organic nitrogen (PIC, POC, and PON) from the upstream Elbe River can fuel up to 90 % of the TA generated in the entire estuary via calcium carbonate (CaCO3) dissolution. The remaining at least 10 % of TA generation can be attributed to anaerobic metabolic processes such as denitrification of remineralized PON or other pathways. The Elbe Estuary as a whole adds approximately 15 % to the overall DIC and TA runoff. Both the magnitude and partitioning among these processes appear to be sensitive to climatic and anthropogenic changes. Thus, with increased TA loads, the coastal ocean (in particular) would act as a stronger CO2 sink, resulting in changes to the overall coastal system's capacity to store CO2.</p

Loss spectroscopy of molecular solids: Combining experiment and theory

The nature of the lowest-energy electronic excitations in prototypical molecular solids is studied here in detail by combining electron energy loss spectroscopy (EELS) experiments and state-of-the-art many-body calculations based on the Bethe–Salpeter equation. From a detailed comparison of the spectra in picene, coronene and tetracene we generally find a good agreement between theory and experiment, with an upshift of the main features of the calculated spectrum of 0.1–0.2 eV, which can be considered the error bar of the calculation. We focus on the anisotropy of the spectra, which illustrates the complexity of this class of materials, showing a high sensitivity with respect to the three-dimensional packing of the molecular units in the crystal. The differences between the measured and the calculated spectra are explained in terms of the small differences between the crystal structures of the measured samples and the structural model used in the calculations. Finally, we discuss the role played by the different electron–hole interactions in the spectra. We thus demonstrate that the combination of highly accurate experimental EELS and theoretical analysis is a powerful tool to elucidate and understand the electronic properties of molecular solids

reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells

The combinatorial action of co-localizing chromatin modifications and regulators determines chromatin structure and function. However, identifying co-localizing chromatin features in a high-throughput manner remains a technical challenge. Here we describe a novel reChIP-seq approach and tailored bioinformatic analysis tool, normR that allows for the sequential enrichment and detection of co-localizing DNA-associated proteins in an unbiased and genome-wide manner. We illustrate the utility of the reChIP-seq method and normR by identifying H3K4me3 or H3K27me3 bivalently modified nucleosomes in primary human CD4+ memory T cells. We unravel widespread bivalency at hypomethylated CpG-islands coinciding with inactive promoters of developmental regulators. reChIP-seq additionally uncovered heterogeneous bivalency in the population, which was undetectable by intersecting H3K4me3 and H3K27me3 ChIP- seq tracks. Finally, we provide evidence that bivalency is established and stabilized by an interplay between the genome and epigenome. Our reChIP-seq approach augments conventional ChIP-seq and is broadly applicable to unravel combinatorial modes of action

Mechanisms controlling the air-sea CO2 flux in the North Sea

The mechanisms driving the air–sea exchange of carbon dioxide (CO2CO2) in the North Sea are investigated using the three-dimensional coupled physical–biogeochemical model ECOHAM (ECOlogical-model, HAMburg). We validate our simulations using field data for the years 2001–2002 and identify the controls of the air–sea CO2CO2 flux for two locations representative for the North Sea's biogeochemical provinces. In the seasonally stratified northern region, net CO2CO2 uptake is high (View the MathML source2.06molm-2a-1) due to high net community production (NCP) in the surface water. Overflow production releasing semi-labile dissolved organic carbon needs to be considered for a realistic simulation of the low dissolved inorganic carbon (DIC) concentrations observed during summer. This biologically driven carbon drawdown outcompetes the temperature-driven rise in CO2CO2 partial pressure (pCO2pCO2) during the productive season. In contrast, the permanently mixed southern region is a weak net CO2CO2 source (View the MathML source0.78molm-2a-1). NCP is generally low except for the spring bloom because remineralization parallels primary production. Here, the pCO2pCO2 appears to be controlled by temperature

Mutation spectrum and polygenic score in German patients with familial hypercholesterolemia

Autosomal-dominant familial hypercholesterolemia (FH) is characterized by increased plasma concentrations of low-density lipoprotein cholesterol (LDL-C) and a substantial risk to develop cardiovascular disease. Causative mutations in three major genes are known: the LDL receptor gene (LDLR), the apolipoprotein B gene (APOB) and the proprotein convertase subtilisin/kexin 9 gene (PCSK9). We clinically characterized 336 patients suspected to have FH and screened them for disease causing mutations in LDLR, APOB, and PCSK9. We genotyped six single nucleotide polymorphisms (SNPs) to calculate a polygenic risk score for the patients and 1985 controls. The 117 patients had a causative variant in one of the analyzed genes. Most variants were found in the LDLR gene (84.9%) with 11 novel mutations. The mean polygenic risk score was significantly higher in FH mutation negative subjects than in FH mutation positive patients (P < .05) and healthy controls (P < .001), whereas the score of the two latter groups did not differ significantly. However, the score explained only about 3% of the baseline LDL-C variance. We verified the previously described clinical and genetic variability of FH for German hypercholesterolemic patients. Evaluation of a six-SNP polygenic score recently proposed for clinical use suggests that it is not a reliable tool to classify hypercholesterolemic patients

Advanced sequencing approaches detected insertions of viral and human origin in the viral genome of chronic hepatitis E virus patients

The awareness of hepatitis E virus (HEV) increased significantly in the last decade due to its unexpectedly high prevalence in high-income countries. There, infections with HEV-genotype 3 (HEV-3) are predominant which can progress to chronicity in immunocompromised individuals. Persistent infection and antiviral therapy can select HEV-3 variants; however, the spectrum and occurrence of HEV-3 variants is underreported. To gain in-depth insights into the viral population and to perform detailed characterization of viral genomes, we used a new approach combining long-range PCR with next-generation and third-generation sequencing which allowed near full-length sequencing of HEV-3 genomes. Furthermore, we developed a targeted ultra-deep sequencing approach to assess the dynamics of clinically relevant mutations in the RdRp-region and to detect insertions in the HVR-domain in the HEV genomes. Using this new approach, we not only identified several insertions of human (AHNAK, RPL18) and viral origin (RdRp-derived) in the HVR-region isolated from an exemplary sample but detected a variant containing two different insertions simultaneously (AHNAK- and RdRp-derived). This finding is the first HEV-variant recognized as such showing various insertions in the HVR-domain. Thus, this molecular approach will add incrementally to our current knowledge of the HEV-genome organization and pathogenesis in chronic hepatitis E.Peer Reviewe

Robuste Normalisierung von Next-Generation-Sequencing Datensätzen

I Background 1 The Basics of Molecular Biology 1.1 The Genome and the Readout of Genetic Information 1.1.1 The DNA 1.1.2 The Chromatin 1.1.3 The Readout of Genetic Information 1.2 Measuring the Cell by Next Generation Sequencing 1.2.1 Gene Expression 1.2.2 Chromatin Modifications 2 Mathematical Concepts 2.1 Statistical Prerequisites 2.1.1 Statistical Inference 2.1.2 Multiple Testing Correction and the T Method 2.1.3 The Binomial Distribution 2.1.4 Sampling from Binomial Distributions 2.1.5 Mixture Models 2.2 Model Parameter Estimation 2.2.1 Sufficient Statistics 2.2.2 Maximum Likelihood Estimation 2.2.3 The Expectation-Maximization Algorithm II Normalization of NGS Read Count Data 3 The normR Framework 3.1 Motivation 3.2 The normR Approach 3.2.1 Sequencing is a (Multinomial) Sampling Trial 3.2.2 Deliberations on the Signal-to-Noise Ratio (S/N) 3.2.3 The normR Method 3.2.4 Why Not Use a Negative Binomial or Multinomial Distribution? 3.3 Outlook 4 ChIP-seq Enrichment Calling with enrichR 4.1 Introduction 4.2 Methods 4.2.1 Data Sets 4.2.2 The normR Methods: enrichR 4.2.3 Confidence-Weighted Quantification of DNA-Methylation 4.2.4 Comparison of Enrichment Callers 4.2.5 Correlating enrichR -estimated Enrichment to NCIS and HMD% 4.2.6 Chromatin Segmentation Based on enrichR Enrichment Calls 4.3 Results – Enrichment Calling in High and Low S/N 4.3.1 Systematic Comparison of Available Enrichment Callers 4.3.2 enrichR Normalization Corresponds to Published In Silico as well as In Vitro Normalization Methods 4.3.3 Improved Chromatin Segmentation with an enrichR- chromHMM Hybrid Approach 4.4 Discussion 5 Regime Enrichment Calling with regimeR 5.1 Introduction 5.2 Methods 5.2.1 Data Sets 5.2.2 The normR Methods: regimeR 5.2.3 Validation of regimeR Calls via Sequence Features 5.3 Results - Distinct Heterochromatic Enrichment Regimes 5.3.1 H3K27me3 Peaks Coincide with CpG Islands Bound by EZH2 5.3.2 H3K9me3 Peaks are Found within Repeats Bound by ZNF274 5.3.3 Heterochromatic Peaks Resemble Nucleation Sites for Heterochromatin Embedded within Regions of Broad Enrichment 5.3.4 H3K27me3 and H3K9me3 do Overlap by a Minority within and between Tissues 5.4 Discussion 6 ChIP-seq Difference Calling with diffR 6.1 Introduction 6.2 Methods 6.2.1 Data Sets 6.2.2 The normR Methods: diffR 6.2.3 Gene Ontology Analysis 6.2.4 Comparison of ChIP-seq Difference Callers 6.3 Results 6.3.1 Difference Calling in HepG2 Cells and Primary Human Hepatocytes 6.3.2 Comparison of ChIP-seq Difference Callers 6.4 Discussion III Conclusion Bibliography A Supplementary Figures B Supplementary Tables C Abstract D Zusammenfassung E SelbstständigkeitserklärungMolecular Biology pertains to the molecular basis of the regulation of biomolecular processes in the cell, e.g. gene expression or the genome-wide localization of DNA-associated proteins. These molecular quantities are routinely measured by Next Generation Sequencing (NGS)-based tech- niques due to their genome-wide scalability and cost-efficiency. In order to discern background- regions from genomic loci that harbor a biological relevant signal, i.e. difference calling, the NGS measurements need to be corrected for technical biases with the help of a control, i.e. nor- malization. However, the normalization itself requires the knowledge of background regions and, consequently, difference calling and normalization are inseparable. Here, this problem is solved by the data-driven “normR” framework which models the inter- dependency of NGS mea- surements in background- and signal-regions as a multinomial sampling trial with a binomial mixture model. The robust normR normalization accounts for the effect of signal on the overall measurement statistic by modeling treatment and control simultaneously. In this thesis, I used normR in three studies concerning the inference of DNA-protein binding from ChIP-seq data. Firstly, the two-component “enrichR” model is shown to achieve a more sensitive enrichment calling (AUC≥0.93) than six competitor methods (AUC≤0.86) in low, e.g. H3K36me3, and high, e.g. H3K4me3, signal-to- noise ratio (S/N) ChIP-seq data. enrichR’s enrichment calls augment the resolution and comprehensiveness of chromatin segmentations by chromHMM and its normal- ization improves on present in silico and in vitro ChIP-seq normalization methods. Secondly, the three-component “regimeR” model dissects enrichment into two unprecedented regimes of dif- ferent signal levels. A regimeR-based analysis identified two distinct facultative and constitutive heterochromatic enrichment regimes in H3K27me3 and H3K9me3 ChIP-seq data, respectively. The identified peak regions (high enrichment) resemble nucleation sites for heterochromatin embedded in regions of broad (low) enrichment. Lastly, the three-component “diffR” model calls conditional differences in ChIP-seq enrichment between two conditions. The diffR calls in low (H3K27me3) and high (H3K4me3) S/N ChIP-seq data are confirmed by a systematic compari- son to four difference callers. Overall, normR represents a robust and versatile framework for the comprehensive analysis of ChIP-seq data, yet, it can be readily applied to other NGS-based experiments like ATAC- seq, STARR-seq or RNA-seq.Die Molekulare Biologie studiert die molekulare Basis der Regulierung von biomolekularen Pro- zessen wie der Genexpression und der genomweiten Lokalisation von DNS-bindenden Protei- nen. Die molekularen Größen werden mittels Next Generation Sequencing(NGS)-basierten Me- thoden gemessen, da diese genomweit skalierbar und kosteneffizient sind. Um Hintergrundre- gionen von genomischen Regionen mit einem biologisch relevanten Signal zu unterscheiden (Differenzenbestimmung) müssen technische Verzerrungen in den NGS Messungen mit Hilfe einer Kontrolle normalisiert werden. Jedoch benötigt eine korrekte Normalisierung die Identi- tät der Hintergrundregionen und, somit, sind Differenzenbestimmung und Normalisierung un- trennbar miteinander verbunden. Dieses Problem wird mit dem vorgestellten datenbasierten “normR” Modell gelöst, welches die Wechselbeziehung zwischen Zahlenwerten in Hintergrund- und Signalregionen als eine binomiale Mischverteilung modelliert. Die robuste Normalisierung von normR berücksichtigt durch gleichzeitige Modellierung von Experiment und Kontrolle den Einfluss des Signals auf die Messstatistik. In dieser Arbeit wurde normR in drei Analysen von ChIP-seq Daten verwendet um DNS-Bindestellen von Proteinen zu identifizieren. 1. Das “en- richR” Modell erreicht mit einer Mischverteilung aus zwei Komponenten eine Differenzenbe- stimmung, die sensitiver ist (AUC≥0.93) als bei sechs anderen Programmen (AUC≤0.86). Die identifizierten differentiellen Regionen erweitern die Auflösung und den Umfang von Chroma- tinsegmentierungen durch das chromHMM Programm. Die Normalisierung von enrichR ist bes- ser als bekannte in vitro und in silico Normalisierungsansätze. 2. Das “regimeR” Modell mit drei Komponenten teilt die vom ChIP angereicherten Regionen in zwei Klassen mit unterschiedli- cher Signalintensität. Eine Analyse mit regimeR identifiziert zwei Klassen von Anreicherung in fakultativem und konstitutivem Heterochromatin in H3K27me3 and H3K9me3 ChIP-seq Daten- sätzen. Die Regionen mit hoher Signalintensität sind flankiert von breiten Regionen mit nied- rigem Signal und könnten Keimstellen des Heterochromatins darstellen. 3. Das “diffR” Modell identifiziert Unterschiede zwischen ChIP-seq Messungen in zwei zellulären Bedingungen. Die Ergebnisse von diffR wurden mittels eines systematischen Vergleichs zu vier anderen ChIP-seq Differenzbestimmungsprogrammen validiert. normR ist ein robustes und vielseitiges Programm zur umfassenden Analyse von ChIP-seq Daten und vermag in Zukunft eine sensitive Analyse von anderen NGS Datensätzen wie ATAC-seq, STARR-seq und RNA-seq zu ermöglichen