Sēfer Ḥiddûšê tôrā : we-ze šemô ašer yiqre'û lô Berît Šālôm û-vô derûšîm neḥmādîm ...

ašer îzzēn ḥîbbēr we-tîqqēn ... Pinḥās .... Ben- ... Pelṭā

Miqrâ Tôrã, nevî'îm u-_ketûvîm : enthaltend: Den heiligen Urtext, die deutsche Übertragung, die allgemeine, ausführliche Erläuterung mit mehr als 500 englischen Holzschnitten

hrsg. von Ludwig Philippson

Novel Imaging-Based Techniques Reveal a Role for PD-1/PD-L1 in Tumor Immune Surveillance in the Lung

The binding of immune inhibitory receptor Programmed Death 1 (PD-1) on T cells to its ligand PD-L1 has been implicated as a major contributor to tumor induced immune suppression. Clinical trials of PD-L1 blockade have proven effective in unleashing therapeutic anti-tumor immune responses in a subset of patients with advanced melanoma, yet current response rates are low for reasons that remain unclear. Hypothesizing that the PD-1/PD-L1 pathway regulates T cell surveillance within the tumor microenvironment, we employed intravital microscopy to investigate the in vivo impact of PD-L1 blocking antibody upon tumor-associated immune cell migration. However, current analytical methods of intravital dynamic microscopy data lack the ability to identify cellular targets of T cell interactions in vivo, a crucial means for discovering which interactions are modulated by therapeutic intervention. By developing novel imaging techniques that allowed us to better analyze tumor progression and T cell dynamics in the microenvironment; we were able to explore the impact of PD-L1 blockade upon the migratory properties of tumor-associated immune cells, including T cells and antigen presenting cells, in lung tumor progression. Our results demonstrate that early changes in tumor morphology may be indicative of responsiveness to anti-PD-L1 therapy. We show that immune cells in the tumor microenvironment as well as tumors themselves express PD-L1, but immune phenotype alone is not a predictive marker of effective anti-tumor responses. Through a novel method in which we quantify T cell interactions, we show that T cells are largely engaged in interactions with dendritic cells in the tumor microenvironment. Additionally, we show that during PD-L1 blockade, non-activated T cells are recruited in greater numbers into the tumor microenvironment and engage more preferentially with dendritic cells. We further show that during PD-L1 blockade, activated T cells engage in more confined, immune synapse-like interactions with dendritic cells, as opposed to more dynamic, kinapse-like interactions with dendritic cells when PD-L1 is free to bind its receptor. By advancing the contextual analysis of anti-tumor immune surveillance in vivo, this study implicates the interaction between T cells and tumor-associated dendritic cells as a possible modulator in targeting PD-L1 for anti-tumor immunotherapy.

RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION

My dissertation focuses on two aspects of RNA sequencing technology. The first is the methodology for modeling the overdispersion inherent in RNA-seq data for differential expression analysis. This aspect is addressed in three sections. The second aspect is the application of RNA-seq data to identify the CpG island methylator phenotype (CIMP) by integrating datasets of mRNA expression level and DNA methylation status. Section 1: The cost of DNA sequencing has reduced dramatically in the past decade. Consequently, genomic research increasingly depends on sequencing technology. However it remains elusive how the sequencing capacity influences the accuracy of mRNA expression measurement. We observe that accuracy improves along with the increasing sequencing depth. To model the overdispersion, we use the beta-binomial distribution with a new parameter indicating the dependency between overdispersion and sequencing depth. Our modified beta-binomial model performs better than the binomial or the pure beta-binomial model with a lower false discovery rate. Section 2: Although a number of methods have been proposed in order to accurately analyze differential RNA expression on the gene level, modeling on the base pair level is required. Here, we find that the overdispersion rate decreases as the sequencing depth increases on the base pair level. Also, we propose four models and compare them with each other. As expected, our beta binomial model with a dynamic overdispersion rate is shown to be superior. Section 3: We investigate biases in RNA-seq by exploring the measurement of the external control, spike-in RNA. This study is based on two datasets with spike-in controls obtained from a recent study. We observe an undiscovered bias in the measurement of the spike-in transcripts that arises from the influence of the sample transcripts in RNA-seq. Also, we find that this influence is related to the local sequence of the random hexamer that is used in priming. We suggest a model of the inequality between samples and to correct this type of bias. Section 4: The expression of a gene can be turned off when its promoter is highly methylated. Several studies have reported that a clear threshold effect exists in gene silencing that is mediated by DNA methylation. It is reasonable to assume the thresholds are specific for each gene. It is also intriguing to investigate genes that are largely controlled by DNA methylation. These genes are called “L-shaped” genes. We develop a method to determine the DNA methylation threshold and identify a new CIMP of BRCA. In conclusion, we provide a detailed understanding of the relationship between the overdispersion rate and sequencing depth. And we reveal a new bias in RNA-seq and provide a detailed understanding of the relationship between this new bias and the local sequence. Also we develop a powerful method to dichotomize methylation status and consequently we identify a new CIMP of breast cancer with a distinct classification of molecular characteristics and clinical features.

1.2 Ma stacked benthic foraminiferal carbon isotope record

Pleistocene stable carbon isotope (d13C) records from surface and deep dwelling foraminifera in all major ocean basins show two distinct long-term carbon isotope fluctuations since 1.00 Ma. The first started around 1.00 Ma and was characterised by a 0.35 per mil decrease in d13C values until 0.90 Ma, followed by an increase of 0.60 per mil lasting until 0.50 Ma. The subsequent fluctuation started with a 0.40 per mil decrease between 0.50 and 0.25 Ma, followed by an increase of 0.30 per mil between 0.25 and 0.10 Ma. Here, we evaluate existing evidence and various hypotheses for these global Pleistocene d13C fluctuations and present an interpretation, where the fluctuations most likely resulted from concomitant changes in the burial fluxes of organic and inorganic carbon due to ventilation changes and/or changes in the production and export ratio. Our model indicates that to satisfy the long-term 'stability' of the Pleistocene lysocline, the ratio between the amounts of change in the organic and inorganic carbon burial fluxes would have to be close to a 1:1 ratio, as deviations from this ratio would lead to sizable variations in the depth of the lysocline. It is then apparent that the mid-Pleistocene climate transition, which, apart from the glacial cycles, represents the most fundamental change in the Pleistocene climate, was likely not associated with a fundamental change in atmospheric pCO2. While recognising that high frequency glacial/interglacial cycles are associated with relatively large (100 ppmv) changes in pCO2, our model scenario (with burial changes close to a 1:1 ratio) produces a maximum long-term variability of only 20 ppmv over the fluctuation between 1.00 and 0.50 Ma.

(Table 1) Chemical composition of buried manganese noduls and host sediments of ODP Hole 138-854C

Two manganese (Mn) nodules were found in upper Miocene sediments in Hole 854C at a depth of 32.12 mbsf (Samples 138-854C-5H-1,0-2 cm, and -6H-1, 2-4 cm). In structure and composition, the lower nodule is similar to the Pleistocene surface nodules associated with radiolarian ooze from the Clarion-Clipperton Nodule Province. The upper nodule resembles those occurring on pelagic clay from the northern margin of that province.

Mineral composition of 0.1-0.05 mm grain size fraction from the surface layer of bottom sediments in the West European province of the Atlantic Ocean

Rock material sampled from the Mir manned deep-sea submersibles and by dradges, grabs, and sediment cores over a vast area of the North Atlantic was analyzed to show that this material is of continental origin, unlike original rocks of the ocean floor. It is proved to be related to iceberg rafting during Quaternary glaciations. Independent data on distribution and composition of sandy and silty grains in sediment cores also support this relation to the recent glaciation. New criteria for identification of iceberg rock matter in pelagic sediments are presented on the base of analysis of all available data.

(Table 1) Chemical composition of magmatic rocks from a submarine seamount

Petrography of magmatic rocks collected from a submarine seamount on the Mid-Pacific Rise is briefly characterized. Variety of petrographic types of effusive rocks and xenoliths contained in them indicates complexity of geologic development and distinctive structure of the oceanic crust in the area under study.