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Approaches to the Analysis of Proteomics and Transcriptomics Data based on Statistical Methodology
(2014)
Recent developments in genomics and molecular biology led to the generation of an enormous amount of complex data of different origin. This is demonstrated by a number of published results from microarray experiments in Gene Expression Omnibus. The number was growing in exponential pace over the last decade. The challenge of interpreting these vast amounts of data from different technologies led to the development of new methods in the fields of computational biology and bioinformatics. Researchers often want to represent biological phenomena in the most detailed and comprehensive way. However, due to the technological limitations and other factors like limited resources this is not always possible. On one hand, more detailed and comprehensive research generates data of high complexity that is very often difficult to approach analytically, however, giving bioinformatics a chance to draw more precise and deeper conclusions. On the other hand, for low-complexity tasks the data distribution is known and we can fit a mathematical model. Then, to infer from this mathematical model, researchers can use well-known and standard methodologies. In return for using standard methodologies, the biological questions we are answering might not be unveiling the whole complexity of the biological meaning. Nowadays it is a standard that a biological study involves generation of large amounts of data that needs to be analyzed with a statistical inference. Sometimes data challenge researchers with low complexity task that can be performed with standard and popular methodologies as in Proteomic analysis of mouse oocytes reveals 28 candidate factors of the "reprogrammome". There, we established a protocol for proteomics data that involves preprocessing of the raw data and conducting Gene Ontology overrepresentation analysis utilizing hypergeometric distribution. In cases, where the data complexity is high and there are no published frameworks a researcher could follow, randomization can be an approach to exploit. In two studies by The mouse oocyte proteome escapes maternal aging and CellFateScout - a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction we showed how randomization can be performed for distinct complex tasks. In The mouse oocyte proteome escapes maternal aging we constructed a random sample of semantic similarity score between oocyte transcriptome and random transcriptome subset of oocyte proteome size. Therefore, we could calculate whether the proteome is representative of the trancriptome. Further, we established a novel framework for Gene Ontology overrepresentation that involves randomization testing. Every Gene Ontology term is tested whether randomly reassigning all gene labels of belonging to or not belonging to this term will decrease the overall expression level in this term. In CellFateScout - a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction we validated CellFateScout against other well-known bioinformatics tools. We stated the question whether our plugin is able to predict small molecule effects better in terms of expression signatures. For this, we constructed a protocol that uses randomization testing. We assess here if the small molecule effect described as a (set of) active signaling pathways, as detected by our plugin or other bioinformatics tools, is significantly closer to known small molecule targets than a random path.
Purines of exogenous and endogenous sources are degraded to uric acid in human beings. Concentrations >6.8 mg uric acid/dl serum cause hyperuricemia and its symptoms. Pharmaceuticals and the reduction of the intake of purine-rich food are used to control uric acid levels. A novel approach to the latter proposition is the enzymatic reduction of the purine content of food by purine-degrading enzymes. Here we describe the production of recombinant guanine deaminase by the yeast Arxula adeninivorans LS3 and its application in food. In media supplemented with nitrogen sources hypoxanthine or adenine, guanine deaminase (AGDA) gene expression is induced and intracellular accumulation of guanine deaminase (Agdap) protein occurs. The characteristics of the guanine deaminase isolated from wild-type strain LS3 and a transgenic strain expressing the AGDA gene under control of the strong constitutive TEF1 promoter were determined and compared. Both enzymes were dimeric and had temperature optima of 55°C with high substrate specificity for guanine and localisation in both the cytoplasm and vacuole of yeast. The enzyme was demonstrated to reduce levels of guanine in food. A mixture of guanine deaminase and other purine degradation enzymes will allow the reduction of purines in purine-rich foods.
The dentate gyrus (DG) of the hippocampus is one of the stem cell housing niches in the adult mammalian brain. Canonical Wingless-type (Wnt) signals provided by the microenvironment are one of the major niche factors that regulate the differentiation of adult neural stem cells (aNSCs) towards the neuronal lineage. Wnts are part of a complex and diverse set of signaling pathways with a wide range of possible interactions. It remains unknown whether different canonical and non-canonical Wnt signals act in a stage-specific manner to regulate distinctive steps of adult hippocampal neurogenesis. Using in vitro assays on adult hippocampal NSCs, we identified an attenuation of canonical Wnt/ß-Catenin signaling responsiveness in the course of neuronal differentiation, while non-canonical Wnt/Planar Cell Polarity (PCP) signaling events progressively increased. Single-cell genetic manipulations were performed by using retroviral vectors to target dividing progenitor cells in the murine hippocampus. Retrovirus-mediated knockdown of ATP6AP2, a recently discovered core protein involved in both Wnt signaling pathways, revealed that the dual role of this adaptor protein is dependent on the signaling context that is present. We were able to confirm its dual role in neurogenic Wnt signaling in cultured adult hippocampal progenitors (AHPs) for both canonical Wnt signaling in proliferating AHPs and non-canonical Wnt signaling in differentiating AHPs. Specific knockdown of ATP6AP2 in neural progenitor cells in vivo resulted in a decreased induction of neuronal cell fate and severe morphological defects of newborn neurons, likely via altering both canonical and non-canonical Wnt signaling. Furthermore, in vivo knockdown of PCP core proteins CELSR1-3 and FZD3 mimicked the maturational defects of ATP6AP2-deficient neuroblasts but did not affect granule cell fate. In summary, the data presented here characterize a transition of Wnt signaling responsiveness from Wnt/ß-Catenin signaling to non-canonical Wnt/PCP signaling in the course of granule cell fate that was confirmed in a human pluripotent stem cell (hPSC)-based model of dentate granule neurogenesis. Our findings suggest that these pathways show stage-dependent activities and regulate distinct steps of adult dentate granule cell neurogenesis. Conclusively, we provide evidence for a stage-specific regulation of fate determination through the Wnt/ß-Catenin pathway and granule cell morphogenesis through the Wnt/PCP signaling pathway, including the FZD3-CELSR1-3 system. Additionally, the Wnt adaptor protein ATP6AP2 is involved in earlier and later stages of adult neurogenesis and its knockdown in vivo resembles all phenotypic features of both canonical and Wnt/PCP signaling mutants.
Background: Alcohol dependence is among the most severely stigmatized mental disorders. We examine whether negative stereotypes and illness beliefs related to alcohol dependence have changed between 1990 and 2011. Methods: We used data from two population surveys with identical methodology that were conducted among German citizens aged ≥18 years, living in the ‘old' German states. They were conducted in 1990 and 2011, respectively. In random subsamples (1990: n = 1,022, and 2011: n = 1,167), identical questions elicited agreement with statements regarding alcohol dependence, particularly with regard to the illness definition of alcohol dependence and blame. Results: Overall, agreement with negative stereotypes did not change in the course of 2 decades. About 55% of the respondents agreed that alcohol dependence is an illness like any other, >40% stated that it was a weakness of character and 30% endorsed that those affected are themselves to blame for their problems. Conclusions: It is apparent that promoting an illness concept of alcohol dependence has not been an easy solution to the problem of stigma. We discuss how the normative functions of alcohol dependence stigma might have prevented a reduction of negative stereotypes.
During pregnancy, the maternal immune system faces a double dilemma: tolerate the growing semi-allogeneic fetus and at the same time protect the mother and the progeny against pathogens. This requires a fine and extremely regulated equilibrium between immune activation and tolerance. As professional antigen presenting cells, B cells and in particular B-1a B cells, can activate or tolerize T cells and thus participate in the generation or regulation of the immune response. B-1a B cells were involved in the humoral immune response leading to pre-eclampsia, one of the main medical complications during pregnancy. Here we demonstrated that B-1a B cells are additionally involved in cellular immune mechanisms associated with pregnancy complications. Using a mouse model of pregnancy disturbances, we showed that B-1a B cells from animals suffering pregnancy disturbances but not from those developing normal pregnancies induce the differentiation of naïve T cells into Th17 and Th1 cells. This differential role of B-1a B cells during pregnancy seems to be associated with the co-stimulatory molecule CD86 as normal pregnant mice showed lower percentages of CD86 expressing B-1a B cells as compared to pregnant mice developing pregnancy disturbances or to non-pregnant animals. Our data bring to light a new and not explored role of B-1a B cells in the context of pregnancy.
Heparin is an anticoagulant drug. It is important in the treatment of deep vein thrombosis,pulmonary embolism and during surgeries. Heparin-induced thrombocytopenia (HIT) is a severe adverse reaction caused by the formation of ultralarge complexes of platelet factor 4 (PF4) with unfractionated heparin (UFH). It can lead to limb loss or fatal events like stroke, myocardial infarction or pulmonary embolism. HIT has an incidence of about 3% in patients receiving anticoagulative heparin treatment. PF4 is a tetrameric protein, released from the α-granules of platelets upon activation. PF4 is known to form antigenic complexes with UFH accompanied by structural changes of PF4. In this thesis, the size and size distribution of PF4 and PF4/heparin complexes were analyzed using asymmetrical flow field-flow-fractionation (AF4), photon correlation spectroscopy (PCS) and atomic force microscopy (AFM). PF4 tends to form auto-aggregates and to adsorb to different surfaces, including regenerated cellulose, polyethersulfone, quartz and glass. The aggregates are less pronounced in solutions at isotonic NaCl concentration. Arginine and Tween 20 were identified as possible ingredients to hinder the auto-aggregation of PF4. Also, it is shown by combining circular dichroism (CD) spectroscopy, atomic force microscopy (AFM) and isothermal titration calorimetry (ITC) with UFH and defined chain length (16-, 8-, 6-, 5-mer) heparins that structural changes (i.e., increase in β-sheets) alone are not sufficient to induce antigenicity. While UFH, 16-, 8-, and 6-mer heparins all induced an increase in the antiparallel β-sheet content to > 30% (as determined by CD spectroscopy), complex antigenicity as measured by anti-PF4/heparin antibody binding in an enzyme-linked immunosorbent assay (EIA) was only induced by UFH and 16-mer heparin. Fondaparinux (5-mer heparin), which forms in vitro non-antigenic complexes with PF4, did not induce structural changes of PF4. Interestingly, the structural changes induced by antigenic UFH and 16-mer heparin but not by non-antigenic shorter heparins were reversible at higher heparin concentrations. Furthermore, the complexes formed by PF4 with longer heparins were larger than those formed with shorter heparins as shown by atomic force microscopy (AFM). UFH, HO16 and HO08 are able to form ultralarge multimolecular complexes with PF4. ITC data indicated strong electrostatic interactions and energetically unfavorable conformational changes of PF4 with longer heparins, while for the short heparins, favorable conformational changes in the structure of PF4 are induced. This explains the reversibility of the structural changes seen for UFH and HO16 upon addition of an over-saturating amount of heparin. Finally, using differential scanning calorimetry (DSC) the thermal stability of PF4 and PF4/heparin complexes was assessed. Despite its tendency to form auto-aggregates, PF4 is a heat-stable protein. This stability is, length dependently, even increased in complex with heparins. This work shows important differences in the binding between PF4 and heparins of different chain length and might be relevant for the understanding of other biological functions of heparins (e.g., involvement in allergic and inflammatory reactions).
Chemistry and biology of Phenolics isolated from Myricaria germanica (L.) Desv. (Tamaricaceae)
(2014)
In accordance with the recent worldwide interest in plant phenolics, which emerges from their broad range of biological activities, particular emphasis has been focused, in the present thesis, on the constitutive phenolics of the extract of Myricaria germanica (L.) Desv. (Tamaricaceae). During the current thesis twenty phenolics (1 – 20) were isolated and identified from the aqueous/ethanol extract of the whole Myricaria germanica plant. The isolates include four hitherto unknown natural phenolics (2, 10, 12 and 20). Also, the cytotoxic activities of M. germanica extract, column fractions, and one new natural isolate against three different solid tumor cell lines, namely, breast cancer (MCF-7), prostate (PC-3), and liver (Huh-7) cancer cell using SRB viability assay have been investigated and first insights into mode of action have been obtained.
Congenital hyperinsulinism (CHI) causes hypoglycemia due to irregular insulin secretion. In infants, a rapid diagnosis and appropriate management to avoid severe hypoglycemia is mandatory. CHI is a heterogeneous condition at the clinical and genetic level, and disease-causing genes have been identified in about half of the patients. The majority of mutations have been identified in the ABCC8 and KCNJ11 genes encoding subunits of the K<sub>ATP</sub> channel responsible for two distinct histological forms. The diffuse form is caused by autosomal recessive or dominant inherited mutations, whereas the focal form is caused by a paternally transmitted recessive mutation and a second somatic event. We report on an unselected cohort of 136 unrelated patients from the German CHI registry. Mutations in either the ABCC8 or KCNJ11 gene were identified in 61 of these patients (45%). In total, 64 different mutations including 38 novel ones were detected in this cohort. We observed biparental (recessive) inheritance in 34% of mutation-positive patients, dominant inheritance in 11% and paternal transmission of a mutation associated with a focal CHI type in 38%. In addition, we observed inheritance patterns that do not exactly follow the classical recessive or dominant mode, further adding to the genetic complexity of this disease.
Transcriptional repression of regulated structural genes in eukaryotes often depends on pleiotropic corepressor complexes. A well-known corepressor conserved from yeast to mammalian systems is Sin3. In addition to Sin3, yeast Cyc8/Tup1 corepressor complex also regulates a diverse set of genes. Both corepressors can be recruited to target genes via interaction with specific DNA-binding proteins, leading to down-regulation of a large number of unrelated structural genes by associated histone deacetylases (HDACs). In vitro interaction studies performed in this work by GST pull-down assays showed that various repressor proteins (such as Whi5, Stb1, Gal80, Rfx1, Ure2, Rdr1, Xbp1, Yhp1, Rox1, Yox1, Dal80 and Mot3) are indeed able to bind pleiotropic corepressors Sin3 and/or Cyc8/Tup1. All repressors interacting with Sin3 contact its paired amphipathic helix domains PAH1 and/or PAH2. Mapping experiments allowed the characterization of minimum repressor domains and to derive a sequence pattern which may be important for repressor interaction with Cyc8 or Sin3. Interactions for some pathway-specific repressors such as Cti6 and Fkh1 have been studied comprehensively; minimal domains of Cti6 and Fkh1 required for interaction with Sin3 have been mapped and subsequently investigated by mutational analysis. In vitro interaction studies could show that amino acids 350-506 of Cti6 bind PAH2 of Sin3. To analyze this Cti6-Sin3 interaction domain (CSID) in more detail, selected amino acids within CSID were replaced by alanine. It turned out that hydrophobic amino acids V467, L481 and L491 L492 L493 are important for Cti6-Sin3 binding. The results of this work also suggest that repression is not executed entirely via Sin3, but rather CSID is also important for contacting pleiotropic corepressor Cyc8. In addition to PAH2 of Sin3, CSID also binds to tetratricopeptide repeats (TPR) of Cyc8. Furthermore, in vitro mapping studies revealed that Fkh1 also binds PAH2 of corepressor Sin3 via its N-terminal domain (aa 51-125). Binding studies with mutagenized Fkh1-Sin3 interaction domain (FSID) showed that Fkh151-125 variants L74A and I78A were unable to bind PAH2 of Sin3. Confirming in vitro studies, Cti6350-506 and Fkh151-125 also displayed in vivo interaction with PAH2 of Sin3 by using the “yeast two -hybrid” system. Chromatin immunoprecipitation (ChIP) analyses have demonstrated Cti6 recruitment to promoters of genes such as RNR3 and SMF3 containing iron responsive elements (IRE). Importantly, Sin3 was also recruited to these promoters but only in the presence of functional Cti6. Similarly, recruitment of Fkh1 and Sin3 to promoters of cell-cycle regulated genes CLB2 and SWI5 was shown. Recruitment of Sin3 was completely Fkh1-dependent. Additional findings of this work shed light on the fact that not only repressor proteins may contact Sin3 but also activator proteins not yet considered for interaction, e. g. specific activators such as Pho4 and Ino2. These findings indicate that Sin3 may fulfill functions beyond acting as a corepressor. In vitro studies on Sin3-Pho4 interaction showed that aa 156-208 of Pho4 are able to bind both PAH1 and PAH2 of Sin3, while an internal region of Ino2 comprising amino acids 119-212 binds to both Sin3 and Cyc8.