No / N/A

In den letzten Jahren hat sich das gemeinhin gültige Bild von Thrombozyten, in dem die Blutplättchen eine eher passive Rolle als Bestandteil der Koagulations-Kaskade inne hatten, hin zu einem Modell gewandelt, in dem ihnen eine aktive Rolle zugeschrieben wird. Diese ist von besonderer Bedeutung in Hinblick auf die Produktion humoraler Faktoren, die sowohl die Bildung von Blutgerinnseln als auch Entzündungsvorgänge potenzieren. Letzteres ist von besonderer Relevanz bei kardiovaskulären Erkrankungen, wie Myokardinfarkt, Schlaganfall und peripherer arterieller Verschlusskrankheit. Darüber hinaus wurden mittlerweile neue Eigenschaften der Thrombozyten beobachtet, die auf deren Beteiligung bei Krebserkrankungen, Infektionen und Morbus Alzheimer schließen lassen. In der Forschung – und im weitesten Sinne auch in klinischen Anwendungen – werden heute zur näheren Erforschung der Thrombozyten sowohl das Proteom betreffende Analysemethoden, als auch auf PCR basierende Techniken, wie SAGE und qRT-PCR eingesetzt. Für diese Techniken ist die Reinheit der verwendeten Thrombozyten-Präparationen von besonderer Wichtigkeit. Im Rahmen dieser Arbeit, entwickelte ich eine neue, effektive und effiziente Technik zur Aufreinigung humaner Thrombozyten. Ich erzielte hochreine Thrombozyten- Präparationen mit weniger als 1,5 kontaminierenden Leukozyten pro 108 Blutplättchen. Überdies erwiesen sich die aufgereinigten Thrombozyten-Präparationen als frei von kontaminierenden Erythrozyten und Plasma Proteinen. Zudem konnte die Funktionalität der auf der Oberfläche der hochreinen Blutplättchen vorhandenen Membranrezeptoren (z. B. P2Y12 und PGI2 Rezeptoren) mittels FACS Analyse bestätigt werden (Birschmann*, Mietner* et al. 2008). Zwei verschiedene Anwendungen dieser hochreinen Plättchen wurden im Rahmen dieser Arbeit gezeigt. Zum einen wurden sie in einer Studie zur Aufklärung der unterschiedlichen Beschaffenheit der in Thrombozyten vorkommenden Membrantypen verwendet. Hierzu wurden nach Lyse und Dichtegradienten der Plättchen zwei Fraktionen erhalten, welche anschließend sowohl anhand von Western-Blot- als auch durch Lipid-Analysen („Lipidomics“) charakterisiert wurden. Dabei stellte sich heraus, dass es sich bei einer Fraktion um Plasmamembranfragmente handelte und bei der anderen Fraktion um eine Anreicherung von Membranen des kanalikulären Systems. In Verbindung mit Genomics und Proteomics werden diese Techniken der Lipidomics dazu beitragen, die Lipidfunktionen in biologischen Systemen besser zu verstehen. Außerdem können sie einflussreiche Werkzeug für die Aufklärung des Mechanismus von lipid-basierenden Erkrankungen, für die Überwachung biologisch relevanter Lipide und für die pharmakologische Therapiekontrolle sein. Eine weitere Anwendung fanden die hochreinen Plättchen in Interaktions-Studien von Thrombozytenproteinen. In Zusammenarbeit mit dem Lehrstuhl für Bioinformatik wurde unter Verwendung von Proteom- und SAGE-Daten ein Protein-Interaktom erstellt. Daraus stellten wir ein Subnetzwerk mit dem IPP-Komplex (ILK-PINCHParvin) als Mittelpunkt dar. Dieser ternäre Komplex fungiert über eine Interaktion mit dem Aktin-Zytoskelett als eine Signalplattform für Integrine. Ausgehend von den einzelnen Proteinen ILK und PINCH ist es im Modell möglich, eine vollständige Signalkaskade zu erstellen, die die Aktin-Polymerisation zur Folge hat. Im Labor konnten wichtige Interaktionen in Thrombozyten mittels Immunopräzipitation und anschließender Western-Blot Analyse erstmals nachgewiesen werden. Das erstellte Thrombozyten-Interaktom kann somit effektiv für ein systematisches „target screening“ genutzt werden. Auf diese Weise wäre es möglich neue Rezeptoren, Proteine oder ganze Signalkaskaden zu identifizieren. Somit legt das Interaktom die Basis für die Generierung von komplexeren Modellen durch das Einbeziehen von neuen Daten. Dies ist auch in Zukunft von besonderer Wichtigkeit, wenn man die entscheidende Bedeutung dieser Interaktionen für die Signaltransduktionswege während der Hämostase in Thrombozyten berücksichtigt. / In recent years the role of platelets has changed from one of passive participation in the coagulation cascade, to one of active production of humoral factors that potentiate both clot formation and inflammation. In addition to platelet functions in cardiovascular disorders like myocardial infarction, stroke and peripheral vascular disease, new functions have been observed which play a role in cancer, infection and Alzheimers disease. For research and also for clinical applications proteomic methods as well as PCR-based techniques such as SAGE and qRT-PCR are mostly used today, especially in high-throughput analysis. For these methods the purity of the platelet sample is of significant importance.

The objectives of this study were to determine fatty acid composition and acrosome status from bull sperm with different freezabilities (n = 12). We hypothesized that lipid fractions had differentiated fatty acid compositions and such differences influence sperm freezability and the sperm acrosome. Fatty acids were extracted from fresh frozen sperm and fractionated by solid-phase extraction. Thirtyour fatty acids were quantified. Saturated fatty acids were predominant, accounting for 71 to 80% of fatty acids in both fractions. Differences in composition between fractions existed (P < 0.001). Branched chain fatty acid concentrations (15 to 18 µg) were almost twice that of polyunsaturated fatty acid concentrations found in the polar fractions (8 to 9 µg; P < 0.001). Sperm with differentiated freezabilities had few differences in 22:0, 18:1 cis 9, and 14:0 13-methyl fatty acids (P ≤ 0.011). Analyses of acrosome status of sperm revealed that acrosomes were affected differently among bulls.

Thesis advisor: Jeffrey H. Chuang / The field of lipidomics has rapidly progressed since its inception only a decade ago. Technological revolutions in mass spectrometry, chromatography, and computational biology now enables high-throughput high-accuracy quantification of the cellular lipidome. One significant improvement of these technologies is that lipids can now be identified and quantified as individual molecular species. Lipidomics provides an additional layer of information to genomics and proteomics and opens a new opportunity for furthering our understanding of cellular signaling networks and physiology, which have broad therapeutic values. As with other 'omics sciences, these new technologies are producing vast amounts of lipidomic data, which require sophisticated statistical and computational approaches for analysis and interpretation. However, computational tools for utilizing such data are sparse. The complexity of lipid metabolic systems and the fact that lipid enzymes remain poorly understood also present challenges to computational lipidomics. The focus of my dissertation has been the development of novel computational methods for systematic study of lipid metabolism in cellular function and human diseases using lipidomic data. In this dissertation, I first present a mathematical model describing cardiolipin molecular species distribution in steady state and its relationship with fatty acid chain compositions. Knowledge of this relationship facilitates determination of isomeric species for complex lipids, providing more detailed information beyond current limits of mass spectrometry technology. I also correlate lipid species profiles with diseases and predict potential therapeutics. Second, I present statistical studies of mechanisms influencing phosphatidylcholine and phosphatidylethanolamine molecular architectures, respectively. I describe a statistical approach to examine dependence of sn1 and sn2 acyl chain regulatory mechanisms. Third, I describe a novel network inference approach and illustrate a dynamic model of ethanolamine glycerophospholipid acyl chain remodeling. The model is the first that accurately and robustly describes lipid species changes in pulse-chase experiments. A key outcome is that the deacylation and reacylation rates of individual acyl chains can be determined, and the resulting rates explain the well-known prevalence of sn1 saturated chains and sn2 unsaturated chains. Lastly, I summarize and remark on future studies for lipidomics. / Thesis (PhD) — Boston College, 2012. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Die Phosphoglykolat-Phosphatase PGP (früher auch als AUM bezeichnet) wurde in unserem Labor als Mitglied der HAD-Typ-Phosphatasen identifiziert. Die genetische Inaktivierung des Enzyms im gesamten Mausorganismus führt ab E8.5 zu einer Wachstumsverzögerung muriner Embryonen und bis E12.5 schließlich zu deren Tod. Im Gegensatz dazu sind Mäuse mit einer PGP-Inaktivierung in hämatopoetischen Zellen und im Endothel lebensfähig und phänotypisch unauffällig. Neue Erkenntnisse schreiben dem Enzym neben einer Aktivität gegenüber Phosphoglykolat auch Aktivitäten gegenüber Glycerin-3-phosphat (G3P), P-Erythronat und P-Lactat zu. Da diese Phosphatase-Aktivitäten Auswirkungen auf den Lipidstoffwechsel nahelegen, wurde in der vorliegenden Arbeit mittels massenspektrometrischer Methoden der Einfluss der Phosphoglykolat-Phosphatase auf den Metabolismus von Signal-, Membran- und Speicherlipiden in murinen Embryonen und Lymphozyten untersucht. Nach Inaktivierung der PGP im gesamten Organismus wurden in E8.5-Embryonen erhöhte Diacylglycerin (DG)-, Triacylglycerin (TG)- und Sphingomyelin (SM)-Spiegel gemessen, während niedrigere Phosphatidylcholin (PC)-Level vorlagen. In PGP-inaktivierten Lymphozyten waren G3P-, DG-, TG-, PC- und SM-Level nicht verändert. Dafür kam es zu signifikanten Erhöhungen der Phosphatidylglycerol (PG*)- und Cardiolipin (CL)-Spiegel. Zusammenfassend konnte gezeigt werden, dass die PGP in unterschiedlichen Geweben differenzielle Effekte auf die Spiegel verschiedener Lipide hat. Dies deckt neue Funktionen der PGP für die Regulation des Lipidmetabolismus auf. Die vorliegende Arbeit stellt somit die Grundlage für weitere Untersuchungen über die genauen Ursachen und Folgen dieser Regulation dar und lässt auf eine wichtige Rolle der PGP als metabolische Phosphatase im Organismus schließen. / Our laboratory has previously identified the mammalian phosphoglycolate phosphatase PGP (also referred to as AUM) as a member of the HAD-type superfamily of hydrolases. Whole-body PGP inactivation led to an intrauterine growth defect with developmental delay after E8.5, resulting in a gradual deterioration and death of PgpD34N/D34N embryos until E12.5. In contrast, mice with a deficiency of PGP activity in endothelial and hematopoietic cells were viable and phenotypically normal. Recent findings demonstrate catalytic activities of the PGP towards phosphoglycolate, glycerol-3-phosphate (G3P), P-erythronate and P-lactate. Since these catalytic activities suggest implications for the lipid metabolism, this thesis examined the PGP-dependent formation of signal-, membrane- and storage lipids in E8.5 embryos and adult lymphocytes of mice by means of mass spectrometry. Following whole-body inactivation of PGP increased diacylglycerol (DG)-, triacylglycerol (TG)- and sphingomyeline (SM)-levels were detected in E8.5 embryos, whereas lower phosphatidylcholine (PC)-levels were present. In PGP-deficient lymphocytes G3P-, DG-, TG-, PC- and SM-level were unaltered. However, levels of phosphatidylglycerol (PG*) and cardiolipine (CL) were significantly increased. Taken together this thesis reveals new and tissue-dependent functions of PGP in the regulation of the lipid metabolism and indicates an important role of PGP as a metabolic phosphatase. It constitutes the basis for further studies on the exact roots and the physiological effects of the metabolic regulation by PGP.

Developing cultivation methods that yield chemically and isotopically defined fatty acid (FA) compositions within bacterial cytoplasmic membranes establishes an in vivo experimental platform to study membrane biophysics and cell membrane regulation using novel approaches. Yet before fully realizing the potential of this method, it is prudent to understand the systemic changes in cells induced by the labeling procedure itself. In this work, analysis of cellular membrane compositions was paired with proteomics to assess how the proteome changes in response to the directed incorporation of exogenous FAs into the membrane of Bacillus subtilis. Key findings from this analysis include an alteration in lipid headgroup distribution, with an increase in phosphatidylglycerol lipids and decrease in phosphatidylethanolamine lipids, possibly providing a fluidizing effect on the cell membrane in response to the induced change in membrane composition. Changes in the abundance of enzymes involved in FA biosynthesis and degradation are observed; along with changes in abundance of cell wall enzymes and isoprenoid lipid production. The observed changes may influence membrane organization, and indeed the well-known lipid raft-associated protein flotillin was found to be substantially down-regulated in the labeled cells – as was the actin-like protein MreB. Taken as a whole, this study provides a greater depth of understanding for this important cell membrane experimental platform and presents a number of new connections to be explored in regard to modulating cell membrane FA composition and its effects on lipid headgroup and raft/cytoskeletal associated proteins.

Master of Science / Department of Statistics / Gary L. Gadbury / This report presents an analysis of data resulting from a lipidomics experiment. The experiment sought to determine the changes in the lipidome of big bluestem prairie grass when exposed to stressors. The two stressors were drought (versus a watered condition) and a rust infection (versus no infection), and were whole plot treatments arranged in a 2 by 2 factorial. A split plot treatment factor was the position on a sampled leaf (top half versus bottom half). In addition, samples were analyzed at different times, representing a blocking factor. A total of 110 samples were used and, for each sample, concentrations of 137 lipids were obtained. Many lipids were not detected for certain samples and, in some cases, a lipid was not detected in most samples. Thus, each lipid was analyzed separately using a modeling strategy that involved a combination of mixed effects linear models and a categorical analysis technique, with the latter used for certain lipids to determine if a pattern of observed zeros was associated with the treatment condition(s). In addition, p-values from tests of fixed effects in a mixed effect model were computed three different ways and compared. Results in general show that the drought condition has the greatest effect on the concentrations of certain lipids, followed by the effect of position on the leaf. Of least effect on lipid concentrations was the rust condition.

Master of Science / Department of Statistics / Gary L. Gadbury / Discerning the metabolic or enzymatic role of a particular gene product, in the absence of information indicating sequence homology to known gene products, is a difficult task. One approach is to compare the levels of metabolites in a wild-type organism to those in an organism with a mutation that causes loss of function of the gene. The goal of this project was to develop an approach to analyze metabolite data on wild-type and mutant organisms for the purpose of identifying the function of a mutated gene. To develop and test statistical approaches to analysis of metabolite data for identification of gene function, levels of 141 lipid metabolites were measured in leaves of wild-type Arabidopsis thaliana plants and in leaves of Arabidopsis thaliana plants with known mutations in genes involved in lipid metabolism. The mutations were primarily in fatty acid desaturases, which are enzymes that catalyze reactions in which double bonds are added to fatty acids. When these enzymes are mutated, leaf lipid composition is altered, and the altered levels of specific lipid metabolites can be detected by a mass spectrometry. A randomization P-Value and other metrics were calculated for all potential reactant product pairs, which included all lipid metabolite pairs. An algorithm was developed to combine these data and rank the results for each pair as to likelihood of being the actual reactant-product pair. This method was designed and tested on data collected on mutants in genes with known functions, fad2 (Okuley et al., 1994), fad3 (Arondel et al., 1992), fad4, fad5 (Mekhedov et al., 2000), fad6 (Falcone et al., 1994), and fad7 (Iba et al., 1993 and Gibson et al., 1994). Application of the method to three additional genes produced by random mutagenesis, sfd1, sfd2, and sfd3, indicated that the significant pairs for fad6 and sfd3 were similar. Consistent with this, genetic evidence has indicated that sfd3 is a mutation in the FAD6 gene. The methods provide a list of putative reactions for an enzyme encoded by an unknown mutant gene. The output lists for unknown genes and known genes can be compared to provide evidence for similar biochemical activities. However, the strength of the current method is that the list of candidate chemical reactions for an enzyme encoded by a mutant gene can be produced without data other than the metabolite profile of the wild-type and mutant organisms, i.e., known gene analysis is not a requirement to obtain the candidate reaction list.

Depression is highly prevalent in coronary artery disease (CAD) and confers an increased risk of morbidity and mortality, yet mechanisms are unknown. Platelet activating factor (PAF) lipids are associated not only with CAD but also with inflammation, oxidative/nitrosative stress, vascular endothelial dysfunction and platelet reactivity which are proposed etiopathological mechanisms for depression. This study investigated the relationship between PAF species and depressive symptoms in 20 CAD patients. Plasma analyses were performed using electrospray ionization mass spectrometry (precursor ion scan). Primary analysis revealed no association between the potent pro-inflammatory PAF PC(O-16:0/2:0) and depressive symptoms measured by the Hamilton Depression Rating Scale [HAM-D] (F=0.405, p=0.533) or Beck Depression Inventory [BDI]-II (F=0.120, p=0.733) in a linear regression. Exploratory analyses revealed potential associations between greater PC(O-18:1/0:0) and greater HAM-D score and greater PC(O-22:6/2:0) concentrations with a greater BDI-II score. This study suggests that specific PAFs might be biomarkers for depressive symptoms in CAD patients.

Depression is highly prevalent in coronary artery disease (CAD) and confers an increased risk of morbidity and mortality, yet mechanisms are unknown. Platelet activating factor (PAF) lipids are associated not only with CAD but also with inflammation, oxidative/nitrosative stress, vascular endothelial dysfunction and platelet reactivity which are proposed etiopathological mechanisms for depression. This study investigated the relationship between PAF species and depressive symptoms in 20 CAD patients. Plasma analyses were performed using electrospray ionization mass spectrometry (precursor ion scan). Primary analysis revealed no association between the potent pro-inflammatory PAF PC(O-16:0/2:0) and depressive symptoms measured by the Hamilton Depression Rating Scale [HAM-D] (F=0.405, p=0.533) or Beck Depression Inventory [BDI]-II (F=0.120, p=0.733) in a linear regression. Exploratory analyses revealed potential associations between greater PC(O-18:1/0:0) and greater HAM-D score and greater PC(O-22:6/2:0) concentrations with a greater BDI-II score. This study suggests that specific PAFs might be biomarkers for depressive symptoms in CAD patients.