@phdthesis{Schlossarek2023,
  author    = {Schlossarek, Dennis},
  title     = {Identification of dynamic protein-metabolite complexes in saccharomyces cerevisiae using co-fractionation mass spectrometry},
  doi       = {10.25932/publishup-58282},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-582826},
  school      = {Universit{\"a}t Potsdam},
  pages     = {123},
  year      = {2023},
  abstract  = {Cells are built from a variety of macromolecules and metabolites. Both, the proteome and the metabolome are highly dynamic and responsive to environmental cues and developmental processes. But it is not their bare numbers, but their interactions that enable life. The protein-protein (PPI) and protein-metabolite interactions (PMI) facilitate and regulate all aspects of cell biology, from metabolism to mitosis. Therefore, the study of PPIs and PMIs and their dynamics in a cell-wide context is of great scientific interest. In this dissertation, I aim to chart a map of the dynamic PPIs and PMIs across metabolic and cellular transitions. As a model system, I study the shift from the fermentative to the respiratory growth, known as the diauxic shift, in the budding yeast Saccharomyces cerevisiae. To do so, I am applying a co-fractionation mass spectrometry (CF-MS) based method, dubbed protein metabolite interactions using size separation (PROMIS). PROMIS, as well as comparable methods, will be discussed in detail in chapter 1. Since PROMIS was developed originally for Arabidopsis thaliana, in chapter 2, I will describe the adaptation of PROMIS to S. cerevisiae. Here, the obtained results demonstrated a wealth of protein-metabolite interactions, and experimentally validated 225 previously predicted PMIs. Applying orthogonal, targeted approaches to validate the interactions of a proteogenic dipeptide, Ser-Leu, five novel protein-interactors were found. One of those proteins, phosphoglycerate kinase, is inhibited by Ser-Leu, placing the dipeptide at the regulation of glycolysis. In chapter 3, I am presenting PROMISed, a novel web-tool designed for the analysis of PROMIS- and other CF-MS-datasets. Starting with raw fractionation profiles, PROMISed enables data pre-processing, profile deconvolution, scores differences in fractionation profiles between experimental conditions, and ultimately charts interaction networks. PROMISed comes with a user-friendly graphic interface, and thus enables the routine analysis of CF-MS data by non-computational biologists. Finally, in chapter 4, I applied PROMIS in combination with the isothermal shift assay to the diauxic shift in S. cerevisiae to study changes in the PPI and PMI landscape across this metabolic transition. I found a major rewiring of protein-protein-metabolite complexes, exemplified by the disassembly of the proteasome in the respiratory phase, the loss of interaction of an enzyme involved in amino acid biosynthesis and its cofactor, as well as phase and structure specific interactions between dipeptides and enzymes of central carbon metabolism. In chapter 5, I am summarizing the presented results, and discuss a strategy to unravel the potential patterns of dipeptide accumulation and binding specificities. Lastly, I recapitulate recently postulated guidelines for CF-MS experiments, and give an outlook of protein interaction studies in the near future.},
  language  = {en}
}
@phdthesis{Bishop2022,
  author    = {Bishop, Christopher Allen},
  title     = {Influence of dairy intake on odd-chain fatty acids and energy metabolism},
  doi       = {10.25932/publishup-56154},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-561541},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xii, 104, xv},
  year      = {2022},
  abstract  = {As of late, epidemiological studies have highlighted a strong association of dairy intake with lower disease risk, and similarly with an increased amount of odd-chain fatty acids (OCFA). While the OCFA also demonstrate inverse associations with disease incidence, the direct dietary sources and mode of action of the OCFA remain poorly understood. The overall aim of this thesis was to determine the impact of two main fractions of dairy, milk fat and milk protein, on OCFA levels and their influence on health outcomes under high-fat (HF) diet conditions. Both fractions represent viable sources of OCFA, as milk fats contain a significant amount of OCFA and milk proteins are high in branched chain amino acids (BCAA), namely valine (Val) and isoleucine (Ile), which can produce propionyl-CoA (Pr-CoA), a precursor for endogenous OCFA synthesis, while leucine (Leu) does not. Additionally, this project sought to clarify the specific metabolic effects of the OCFA heptadecanoic acid (C17:0). Both short-term and long-term feeding studies were performed using male C57BL/6JRj mice fed HF diets supplemented with milk fat or C17:0, as well as milk protein or individual BCAA (Val; Leu) to determine their influences on OCFA and metabolic health. Short-term feeding revealed that both milk fractions induce OCFA in vivo, and the increases elicited by milk protein could be, in part, explained by Val intake. In vitro studies using primary hepatocytes further showed an induction of OCFA after Val treatment via de novo lipogenesis and increased α-oxidation. In the long-term studies, both milk fat and milk protein increased hepatic and circulating OCFA levels; however, only milk protein elicited protective effects on adiposity and hepatic fat accumulation—likely mediated by the anti-obesogenic effects of an increased Leu intake. In contrast, Val feeding did not increase OCFA levels nor improve obesity, but rather resulted in glucotoxicity-induced insulin resistance in skeletal muscle mediated by its metabolite 3-hydroxyisobutyrate (3-HIB). Finally, while OCFA levels correlated with improved health outcomes, C17:0 produced negligible effects in preventing HF-diet induced health impairments. The results presented herein demonstrate that the beneficial health outcomes associated with dairy intake are likely mediated through the effects of milk protein, while OCFA levels are likely a mere association and do not play a significant causal role in metabolic health under HF conditions. Furthermore, the highly divergent metabolic effects of the two BCAA, Leu and Val, unraveled herein highlight the importance of protein quality.},
  language  = {en}
}
@phdthesis{Herpich2021,
  author    = {Herpich, Catrin},
  title     = {Fibroblast growth factor 21 and its association with nutritional stimuli in older age},
  school      = {Universit{\"a}t Potsdam},
  pages     = {75},
  year      = {2021},
  abstract  = {Fibroblast growth differentiation factor 21 (FGF21) is known as a pivotal regulator of the glucose and lipid metabolism. As such, it is considered beneficial and has even been labelled a longevity hormone. Nevertheless, recent observational studies have shown that FGF21 is increased in higher age with possible negative effects such as loss of lean and bone mass as well as decreased survival. Hepatic FGF21 secretion can be induced by various nutritional stimuli such as starvation, high carbohydrate and fat intake as well as protein deficiency.. So far it is still unclear whether the FGF21 response to different macronutrients is altered in older age. An altered response would potentially contribute to explain the higher FGF21 concentrations found in older age. In this publication-based doctoral dissertation, a cross-sectional study as well as a dietary challenge were conducted to investigate the influence of nutrition on FGF21 concentrations and response in older age. In a cross-sectional study, FGF21 concentrations were assessed in older patients with and without cachexia anorexia syndrome anorexia syndrome compared to an older community-dwelling control group. Cachexia anorexia syndrome is a multifactorial syndrome frequently occurring in old age or in the context of an underlying disease. It is characterized by a severe involuntary weight loss, loss of appetite (anorexia) and reduced food intake, therefore representing a state of severe nutrient deficiency, in some aspects similar to starvation. The highest FGF21 concentrations were found in patients with cachexia anorexia syndrome. Moreover, FGF21 was positively correlated with weight loss and loss of appetite. In addition, cachexia anorexia syndrome itself was associated with FGF21 independent of sex, age and body mass index. As cachectic patients presumably exhibit protein malnutrition and FGF21 has been proposed a marker for protein insufficiency, the higher levels of FGF21 in patients with cachexia anorexia syndrome might be partly explained by insufficient protein intake. In order to investigate the acute response of FGF21 to different nutritional stimuli, a dietary challenge with a parallel group design was conducted. Here, healthy older (65-85 years) and younger (18-35 years) adults were randomized to one of four test meals: a dextrose drink, a high carbohydrate, high fat or high protein meal. Over the course of four hours, postprandial FGF21 concentrations (dynamics) were assessed and the FGF21 response (incremental area under the curve) to each test meal was examined.. In a sub-group of older and younger women, also the adiponectin response was investigated, as adiponectin is a known mediator of FGF21 effects on glucose and lipid metabolism. The dietary meal challenge revealed that dextrose and high carbohydrate intake result in higher FGF21 concentrations after four hours in older adults. This was partly explained by higher postprandial glucose concentrations in the old. For high fat ingestion no age differences were found. For the first time, acute FGF21 response to high protein intake was shown. Here, protein ingestion resulted in lower FGF21 concentrations in younger compared to older adults. Furthermore, sufficient protein intake, according to age-dependent recommendations, of the previous day, was associated with lower FGF21 concentrations in both age groups. The higher FGF21 response to dextrose ingestion resulted in a higher adiponectin response in older women, independent of fat mass, insulin resistance, triglyceride concentrations, inflammation and oxidative stress. Following the high fat meal, adiponectin concentrations declined in older women. Adiponectin response was not affected by meal composition in younger women. In summary, this thesis showed a positive association of FGF21 and cachexia anorexia syndrome with concomitant anorexia in older patients. Regarding the acute FGF21 response, a higher response following dextrose and carbohydrate ingestion was found in older compared with younger subjects. This might be attributed to a higher glucose response in older age. Furthermore, it was shown that the higher FGF21 response after dextrose ingestion possibly contributes to a higher adiponectin response in older women, independent of potential metabolic and inflammatory confounders. Acute protein ingestion resulted in a significant decrease in FGF21 concentrations. Moreover, protein intake of the previous day was inversely associated with fasting FGF21 concentrations. This might explain why FGF21 concentrations are higher in cachexia anorexia syndrome. These results therefore support the role of FGF21 as a sensor of protein restriction.},
  language  = {en}
}
@phdthesis{Banerjee2020,
  author    = {Banerjee, Pallavi},
  title     = {Glycosylphosphatidylinositols (GPIs) and GPI-anchored proteins tethered to lipid bilayers},
  doi       = {10.25932/publishup-48956},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-489561},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xv, 141},
  year      = {2020},
  abstract  = {Glycosylphosphatidylinositols (GPIs) are highly complex glycolipids that serve as membrane anchors to a large variety of eukaryotic proteins. These are covalently attached to a group of peripheral proteins called GPI-anchored proteins (GPI-APs) through a post-translational modification in the endoplasmic reticulum. The GPI anchor is a unique structure composed of a glycan, with phospholipid tail at one end and a phosphoethanolamine linker at the other where the protein attaches. The glycan part of the GPI comprises a conserved pseudopentasaccharide core that could branch out to carry additional glycosyl or phosphoethanolamine units. GPI-APs are involved in a diverse range of cellular processes, few of which are signal transduction, protein trafficking, pathogenesis by protozoan parasites like the malaria- causing parasite Plasmodium falciparum. GPIs can also exist freely on the membrane surface without an attached protein such as those found in parasites like Toxoplasma gondii, the causative agent of Toxoplasmosis. These molecules are both structurally and functionally diverse, however, their structure-function relationship is still poorly understood. This is mainly because no clear picture exists regarding how the protein and the glycan arrange with respect to the lipid layer. Direct experimental evidence is rather scarce, due to which inconclusive pictures have emerged, especially regarding the orientation of GPIs and GPI-APs on membrane surfaces and the role of GPIs in membrane organization. It appears that computational modelling through molecular dynamics simulations would be a useful method to make progress. In this thesis, we attempt to explore characteristics of GPI anchors and GPI-APs embedded in lipid bilayers by constructing molecular models at two different resolutions - all-atom and coarse-grained. First, we show how to construct a modular molecular model of GPIs and GPI-anchored proteins that can be readily extended to a broad variety of systems, addressing the micro-heterogeneity of GPIs. We do so by creating a hybrid link to which GPIs of diverse branching and lipid tails of varying saturation with their optimized force fields, GLYCAM06 and Lipid14 respectively, can be attached. Using microsecond simulations, we demonstrate that GPI prefers to "flop-down" on the membrane, thereby, strongly interacting with the lipid heads, over standing upright like a "lollipop". Secondly, we extend the model of the GPI core to carry out a systematic study of the structural aspects of GPIs carrying different side chains (parasitic and human GPI variants) inserted in lipid bilayers. Our results demonstrate the importance of the side branch residues as these are the most accessible, and thereby, recognizable epitopes. This finding qualitatively agrees with experimental observations that highlight the role of the side branches in immunogenicity of GPIs and the specificity thereof. The overall flop-down orientation of the GPIs with respect to the bilayer surface presents the side chain residues to face the solvent. Upon attaching the green fluorescent protein (GFP) to the GPI, it is seen to lie in close proximity to the bilayer, interacting both with the lipid heads and glycan part of the GPI. However the orientation of GFP is sensitive to the type of GPI it is attached to. Finally, we construct a coarse-grained model of the GPI and GPI-anchored GFP using a modified version of the MARTINI force-field, using which the timescale is enhanced by at least an order of magnitude compared to the atomistic system. This study provides a theoretical perspective on the conformational behavior of the GPI core and some of its branched variations in presence of lipid bilayers, as well as draws comparisons with experimental observations. Our modular atomistic model of GPI can be further employed to study GPIs of variable branching, and thereby, aid in designing future experiments especially in the area of vaccines and drug therapies. Our coarse-grained model can be used to study dynamic aspects of GPIs and GPI-APs w.r.t plasma membrane organization. Furthermore, the backmapping technique of converting coarse-grained trajectory back to the atomistic model would enable in-depth structural analysis with ample conformational sampling.},
  language  = {en}
}
@phdthesis{Markova2016,
  author    = {Markova, Mariya},
  title     = {Metabolic and molecular effects of two different isocaloric high protein diets in subjects with type 2 diabetes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-394310},
  school      = {Universit{\"a}t Potsdam},
  pages     = {x, 127},
  year      = {2016},
  abstract  = {Ern{\"a}hrung stellt ein wichtiger Faktor in der Pr{\"a}vention und Therapie von Typ-2-Diabetes dar. Fr{\"u}here Studien haben gezeigt, dass Hochproteindi{\"a}ten sowohl positive als auch negative Effekte auf den Metabolismus hervorrufen. Jedoch ist unklar, ob die Herkunft des Proteins dabei eine Rolle spielt. In der LeguAN-Studie wurden die Effekte von zwei unterschiedlichen Hochproteindi{\"a}ten, entweder tierischer oder pflanzlicher Herkunft, bei Typ-2-Diabetes Patienten untersucht. Beide Di{\"a}ten enthielten 30 EN\% Proteine, 40 EN\% Kohlenhydrate und 30 EN\% Fette. Der Anteil an Ballaststoffen, der glyk{\"a}mischer Index und die Fettkomposition waren in beiden Di{\"a}ten {\"a}hnlich. Die Proteinaufnahme war h{\"o}her, w{\"a}hrend die Fettaufnahme niedriger im Vergleich zu den fr{\"u}heren Ern{\"a}hrungsgewohnheiten der Probanden war. Insgesamt f{\"u}hrten beide Di{\"a}tinterventionen zu einer Verbesserung der glyk{\"a}mischen Kontrolle, der Insulinsensitivit{\"a}t, des Leberfettgehalts und kardiovaskul{\"a}rer Risikomarkern ohne wesentliche Unterschiede zwischen den Proteintypen. In beiden Interventionsgruppen wurden die n{\"u}chternen Glukosewerte zusammen mit Indizes von Insulinresistenz in einem unterschiedlichen Ausmaß, jedoch ohne signifikante Unterschiede zwischen beiden Di{\"a}ten verbessert. Die Reduktion von HbA1c war ausgepr{\"a}gter in der pflanzlichen Gruppe, w{\"a}hrend sich die Insulinsensitivit{\"a}t mehr in der tierischen Gruppe erh{\"o}hte. Die Hochproteindi{\"a}ten hatten nur einen geringf{\"u}gigen Einfluss auf den postprandialen Metabolismus. Dies zeigte sich durch eine leichte Verbesserung der Indizes f{\"u}r Insulinsekretion, -sensitivit{\"a}t und -degradation sowie der Werte der freien Fetts{\"a}uren. Mit Ausnahme des Einflusses auf die GIP-Sekretion riefen die tierische und die pflanzliche Testmahlzeit {\"a}hnliche metabolische und hormonelle Antworten, trotz unterschiedlicher Aminos{\"a}urenzusammensetzung. Die tierische Hochproteindi{\"a}t f{\"u}hrte zu einer selektiven Zunahme der fettfreien Masse und Abnahme der Fettmasse, was nicht signifikant unterschiedlich von der pflanzlichen Gruppe war. Dar{\"u}ber hinaus reduzierten die Hochproteindi{\"a}ten den Leberfettgehalt um durchschnittlich 42\%. Die Reduktion des Leberfettgehaltes ging mit einer Verminderung der Lipogenese, der Lipolyse und des freien Fetts{\"a}ure Flux einher. Beide Interventionen induzierten einen moderaten Abfall von Leberenzymen im Blut. Die Reduktion des Leberfetts war mit einer verbesserten Glukosehom{\"o}ostase und Insulinsensitivit{\"a}t assoziiert. Blutlipide sanken in allen Probanden, was eventuell auf die niedrigere Fettaufnahme zur{\"u}ckzuf{\"u}hren war. Weiterhin waren die Spiegel an Harns{\"a}ure und Inflammationsmarkern erniedrigt unabh{\"a}ngig von der Proteinquelle. Die Werte des systolischen und diastolischen Blutdrucks sanken nur in der pflanzlichen Gruppe, was auf eine potentielle Rolle von Arginin hinweist. Es wurden keine Hinweise auf eine beeintr{\"a}chtigte Nierenfunktion durch die 6-w{\"o}chige Hochproteindi{\"a}ten beobachtet unabh{\"a}ngig von der Herkunft der Proteine. Serumkreatinin war nur in der pflanzlichen Gruppe signifikant reduziert, was eventuell an dem geringen Kreatingehalt der pflanzlichen Nahrungsmittel liegen k{\"o}nnte. Jedoch sind l{\"a}ngere Studien n{\"o}tig, um die Sicherheit von Hochproteindi{\"a}ten vollkommen aufkl{\"a}ren zu k{\"o}nnen. Des Weiteren verursachte keine der Di{\"a}ten eine Induktion des mTOR Signalwegs weder im Fettgewebe noch in Blutzellen. Die Verbesserung der Ganzk{\"o}rper-Insulinsensitivit{\"a}t deutete auch auf keine Aktivierung von mTOR und keine Verschlechterung der Insulinsensitivit{\"a}t im Skeletmuskel hin. Ein nennenswerter Befund war die erhebliche Reduktion von FGF21, einem wichtigen Regulator metabolischer Prozesse, um ungef{\"a}hr 50\% bei beiden Proteinarten. Ob hepatischer ER-Stress, Ammoniumniveau oder die Makron{\"a}hrstoffpr{\"a}ferenz hinter dem paradoxen Ergebnis stehen, sollte weiter im Detail untersucht werden. Entgegen der anf{\"a}nglichen Erwartung und der bisherigen Studienlage zeigte die pflanzlich-betonte Hochproteindi{\"a}t keine klaren Vorteile gegen{\"u}ber der tierischen Di{\"a}t. Der ausgepr{\"a}gte g{\"u}nstige Effekt des tierischen Proteins auf Insulinhom{\"o}ostase trotz des hohen BCAA-Gehaltes war sicherlich unerwartet und deutet darauf hin, dass bei dem l{\"a}ngeren Verzehr andere komplexe metabolische Adaptationen stattfinden. Einen weiteren Aspekt stellt der niedrigere Fettverzehr dar, der eventuell auch zu den Verbesserungen in beiden Gruppen beigetragen hat. Zusammenfassend l{\"a}sst sich sagen, dass eine 6-w{\"o}chige Di{\"a}t mit 30 EN\% Proteinen (entweder pflanzlich oder tierisch), 40 EN\% Kohlenhydraten und 30 EN\% Fetten mit weniger ges{\"a}ttigten Fetten zu metabolischen Verbesserungen bei Typ-2-Diabetes Patienten unabh{\"a}ngig von Proteinherkunft f{\"u}hrt.},
  language  = {en}
}
@phdthesis{Ulaganathan2016,
  author    = {Ulaganathan, Vamseekrishna},
  title     = {Molecular fundamentals of foam fractionation},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94263},
  school      = {Universit{\"a}t Potsdam},
  pages     = {ix, 136},
  year      = {2016},
  abstract  = {Foam fractionation of surfactant and protein solutions is a process dedicated to separate surface active molecules from each other due to their differences in surface activities. The process is based on forming bubbles in a certain mixed solution followed by detachment and rising of bubbles through a certain volume of this solution, and consequently on the formation of a foam layer on top of the solution column. Therefore, systematic analysis of this whole process comprises of at first investigations dedicated to the formation and growth of single bubbles in solutions, which is equivalent to the main principles of the well-known bubble pressure tensiometry. The second stage of the fractionation process includes the detachment of a single bubble from a pore or capillary tip and its rising in a respective aqueous solution. The third and final stage of the process is the formation and stabilization of the foam created by these bubbles, which contains the adsorption layers formed at the growing bubble surface, carried up and gets modified during the bubble rising and finally ends up as part of the foam layer. Bubble pressure tensiometry and bubble profile analysis tensiometry experiments were performed with protein solutions at different bulk concentrations, solution pH and ionic strength in order to describe the process of accumulation of protein and surfactant molecules at the bubble surface. The results obtained from the two complementary methods allow understanding the mechanism of adsorption, which is mainly governed by the diffusional transport of the adsorbing protein molecules to the bubble surface. This mechanism is the same as generally discussed for surfactant molecules. However, interesting peculiarities have been observed for protein adsorption kinetics at sufficiently short adsorption times. First of all, at short adsorption times the surface tension remains constant for a while before it decreases as expected due to the adsorption of proteins at the surface. This time interval is called induction time and it becomes shorter with increasing protein bulk concentration. Moreover, under special conditions, the surface tension does not stay constant but even increases over a certain period of time. This so-called negative surface pressure was observed for BCS and BLG and discussed for the first time in terms of changes in the surface conformation of the adsorbing protein molecules. Usually, a negative surface pressure would correspond to a negative adsorption, which is of course impossible for the studied protein solutions. The phenomenon, which amounts to some mN/m, was rather explained by simultaneous changes in the molar area required by the adsorbed proteins and the non-ideality of entropy of the interfacial layer. It is a transient phenomenon and exists only under dynamic conditions. The experiments dedicated to the local velocity of rising air bubbles in solutions were performed in a broad range of BLG concentration, pH and ionic strength. Additionally, rising bubble experiments were done for surfactant solutions in order to validate the functionality of the instrument. It turns out that the velocity of a rising bubble is much more sensitive to adsorbing molecules than classical dynamic surface tension measurements. At very low BLG or surfactant concentrations, for example, the measured local velocity profile of an air bubble is changing dramatically in time scales of seconds while dynamic surface tensions still do not show any measurable changes at this time scale. The solution's pH and ionic strength are important parameters that govern the measured rising velocity for protein solutions. A general theoretical description of rising bubbles in surfactant and protein solutions is not available at present due to the complex situation of the adsorption process at a bubble surface in a liquid flow field with simultaneous Marangoni effects. However, instead of modelling the complete velocity profile, new theoretical work has been started to evaluate the maximum values in the profile as characteristic parameter for dynamic adsorption layers at the bubble surface more quantitatively. The studies with protein-surfactant mixtures demonstrate in an impressive way that the complexes formed by the two compounds change the surface activity as compared to the original native protein molecules and therefore lead to a completely different retardation behavior of rising bubbles. Changes in the velocity profile can be interpreted qualitatively in terms of increased or decreased surface activity of the formed protein-surfactant complexes. It was also observed that the pH and ionic strength of a protein solution have strong effects on the surface activity of the protein molecules, which however, could be different on the rising bubble velocity and the equilibrium adsorption isotherms. These differences are not fully understood yet but give rise to discussions about the structure of protein adsorption layer under dynamic conditions or in the equilibrium state. The third main stage of the discussed process of fractionation is the formation and characterization of protein foams from BLG solutions at different pH and ionic strength. Of course a minimum BLG concentration is required to form foams. This minimum protein concentration is a function again of solution pH and ionic strength, i.e. of the surface activity of the protein molecules. Although at the isoelectric point, at about pH 5 for BLG, the hydrophobicity and hence the surface activity should be the highest, the concentration and ionic strength effects on the rising velocity profile as well as on the foamability and foam stability do not show a maximum. This is another remarkable argument for the fact that the interfacial structure and behavior of BLG layers under dynamic conditions and at equilibrium are rather different. These differences are probably caused by the time required for BLG molecules to adapt respective conformations once they are adsorbed at the surface. All bubble studies described in this work refer to stages of the foam fractionation process. Experiments with different systems, mainly surfactant and protein solutions, were performed in order to form foams and finally recover a solution representing the foamed material. As foam consists to a large extent of foam lamella - two adsorption layers with a liquid core - the concentration in a foamate taken from foaming experiments should be enriched in the stabilizing molecules. For determining the concentration of the foamate, again the very sensitive bubble rising velocity profile method was applied, which works for any type of surface active materials. This also includes technical surfactants or protein isolates for which an accurate composition is unknown.},
  language  = {en}
}
@phdthesis{Schroeder2015,
  author    = {Schr{\"o}der, Christine},
  title     = {Identifizierung und Charakterisierung der Isoflavon-umsetzenden Enzyme aus dem humanen Darmbakterium Slackia isoflavoniconvertens},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-80065},
  school      = {Universit{\"a}t Potsdam},
  pages     = {X, 129},
  year      = {2015},
  abstract  = {Aufgrund ihrer potenziell gesundheitsf{\"o}rdernden Wirkung sind die polyphenolischen Isoflavone f{\"u}r die menschliche Ern{\"a}hrung von großem Interesse. Eine Vielzahl an experimentellen und epidemiologischen Studien zeigen f{\"u}r die in Soja enthaltenen Isoflavone Daidzein und Genistein eine pr{\"a}ventive Wirkung bez{\"u}glich hormon-abh{\"a}ngiger und altersbedingter Erkrankungen, wie Brust- und Prostatakrebs, Osteoporose, Herz-Kreislauf-Erkrankungen sowie des menopausalen Syndroms. Die Metabolisierung und Bioaktivierung dieser sekund{\"a}ren Pflanzenstoffe durch die humane intestinale Darmmikrobiota ist individuell unterschiedlich. Nur in einem geringen Teil der westlichen Bev{\"o}lkerung wird der Daidzein-Metabolit Equol durch spezifische Darmbakterien gebildet. Ein isoliertes Equol-produzierendes Bakterium des menschlichen Darmtrakts ist Slackia isoflavoniconvertens. Anhand dieser Spezies sollten die bislang unbekannten, an der Umsetzung von Daidzein und Genistein beteiligten Enzyme identifiziert und charakterisiert werden. Fermentationsexperimente mit S. isoflavoniconvertens zeigten, dass die Gene der Daidzein und Genistein-umsetzenden Enzyme nicht konstitutiv exprimiert werden, sondern induziert werden m{\"u}ssen. Mit Hilfe der zweidimensionalen differentiellen Gelelektrophorese wurden sechs Proteine detektiert, welche in einer S. isoflavoniconvertens-Kultur in Anwesenheit von Daidzein induziert wurden. Auf Grundlage einzelner Peptidsequenzen erfolgte die Sequenzierung eines Genkomplexes mit den in gleicher Orientierung angeordneten Genen der durch Daidzein induzierten Proteine. Sequenzvergleiche identifizierten zudem {\"a}quivalente Genprodukte zu den Proteinen von S. isoflavoniconvertens in anderen Equolproduzierenden Bakterien. Nach der heterologen Expression in Escherichia coli wurden drei dieser Gene durch enzymatische Aktivit{\"a}tstests als Daidzein-Reduktase (DZNR), Dihydrodaidzein-Reduktase (DHDR) und Tetrahydrodaidzein-Reduktase (THDR) identifiziert. Die Kombination der E. coli-Zellextrakte f{\"u}hrte zur vollst{\"a}ndigen Umsetzung von Daidzein {\"u}ber Dihydrodaidzein zu Equol. Neben Daidzein setzte die DZNR auch Genistein zu Dihydrogenistein um. Dies erfolgte mit einer gr{\"o}ßeren Umsatzgeschwindigkeit im Vergleich zur Reduktion von Daidzein zu Dihydrodaidzein. Enzymatische Aktivit{\"a}tstests mit dem Zellextrakt von S. isoflavoniconvertens zeigten ebenfalls eine schnellere Umsetzung von Genistein. Die Kombination der rekombinanten DHDR und THDR f{\"u}hrte zur Umsetzung von Dihydrodaidzein zu Equol. Der korrespondierende Metabolit 5-Hydroxyequol konnte als Endprodukt des Genistein-Metabolismus nicht detektiert werden. Zur Reinigung der drei identifizierten Reduktasen wurden diese genetisch an ein Strep-tag fusioniert und mittels Affinit{\"a}tschromatographie gereinigt. Die {\"u}brigen durch Daidzein induzierten Proteine IfcA, IfcBC und IfcE wurden ebenfalls in E. coli exprimiert und als Strep-Fusionsproteine gereinigt. Vergleichende Aktivit{\"a}tstests identifizierten das induzierte Protein IfcA als Dihydrodaidzein-Racemase. Diese katalysierte die Umsetzung des (R)- und (S)-Enantiomers von Dihydrodaidzein und Dihydrogenistein zum korrespondierenden Racemat. Neben dem Elektronentransfer-Flavoprotein IfcBC wurden auch die THDR, DZNR und IfcE als FAD-haltige Flavoproteine identifiziert. Zudem handelte es sich bei IfcE um ein Eisen-Schwefel-Protein. Nach Induktion der f{\"u}r die Daidzein-Umsetzung kodierenden Gene wurden mehrere verschieden lange mRNA-Transkripte gebildet. Dies zeigte, dass die Transkription des durch Daidzein induzierten Genkomplexes in S. isoflavoniconvertens nicht in Form eines einzelnen Operonsystems erfolgte. Auf Grundlage der identifizierten Daidzein-umsetzenden Enzyme kann der Mechanismus der bakteriellen Umsetzung von Isoflavonen durch S. isoflavoniconvertens eingehend erforscht werden. Die ermittelten Gensequenzen der durch Daidzein induzierten Proteine sowie die korrespondierenden Gene weiterer Equol-produzierender Bakterien bieten zudem die M{\"o}glichkeit der mikrobiellen Metagenomanalyse im humanen Darmtrakt.},
  language  = {de}
}
@phdthesis{Wettstein2015,
  author    = {Wettstein, Christoph},
  title     = {Cytochrome c-DNA and cytochrome c-enzyme interactions for the construction of analytical signal chains},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-78367},
  school      = {Universit{\"a}t Potsdam},
  pages     = {120},
  year      = {2015},
  abstract  = {Electron transfer (ET) reactions play a crucial role in the metabolic pathways of all organisms. In biotechnological approaches, the redox properties of the protein cytochrome c (cyt c), which acts as an electron shuttle in the respiratory chain, was utilized to engineer ET chains on electrode surfaces. With the help of the biopolymer DNA, the redox protein assembles into electro active multilayer (ML) systems, providing a biocompatible matrix for the entrapment of proteins. In this study the characteristics of the cyt c and DNA interaction were defined on the molecular level for the first time and the binding sites of DNA on cyt c were identified. Persistent cyt c/DNA complexes were formed in solution under the assembly conditions of ML architectures, i.e. pH 5.0 and low ionic strength. At pH 7.0, no agglomerates were formed, permitting the characterization of the NMR spectroscopy. Using transverse relaxation-optimized spectroscopy (TROSY)-heteronuclear single quantum coherence (HSQC) experiments, DNAs' binding sites on the protein were identified. In particular, negatively charged AA residues, which are known interaction sites in cyt c/protein binding were identified as the main contact points of cyt c and DNA. Moreover, the sophisticated task of arranging proteins on electrode surfaces to create functional ET chains was addressed. Therefore, two different enzyme types, the flavin dependent fructose dehydrogenase (FDH) and the pyrroloquinoline quinone dependent glucose dehydrogenase (PQQ-GDH), were tested as reaction partners of freely diffusing cyt c and cyt c immobilized on electrodes in mono- and MLs. The characterisation of the ET processes was performed by means of electrochemistry and the protein deposition was monitored by microgravimetric measurements. FDH and PQQ-GDH were found to be generally suitable for combination with the cyt c/DNA ML system, since both enzymes interact with cyt c in solution and in the immobilized state. The immobilization of FDH and cyt c was achieved with the enzyme on top of a cyt c monolayer electrode without the help of a polyelectrolyte. Combining FDH with the cyt c/DNA ML system did not succeed, yet. However, the basic conditions for this protein-protein interaction were defined. PQQ-GDH was successfully coupled with the ML system, demonstrating that that the cyt c/DNA ML system provides a suitable interface for enzymes and that the creation of signal chains, based on the idea of co-immobilized proteins is feasible. Future work may be directed to the investigation of cyt c/DNA interaction under the precise conditions of ML assembly. Therefore, solid state NMR or X-ray crystallography may be required. Based on the results of this study, the combination of FDH with the ML system should be addressed. Moreover, alternative types of enzymes may be tested as catalytic component of the ML assembly, aiming on the development of innovative biosensor applications.},
  language  = {en}
}
@phdthesis{Suetterlin2013,
  author    = {S{\"u}tterlin, Martin},
  title     = {New inverse hydogel opals as protein responsive sensors},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70179},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {In this work, the development of temperature- and protein-responsive sensor materials based on biocompatible, inverse hydrogel opals (IHOs) is presented. With these materials, large biomolecules can be specifically recognised and the binding event visualised. The preparation of the IHOs was performed with a template process, for which monodisperse silica particles were vertically deposited onto glass slides as the first step. The obtained colloidal crystals with a thickness of 5 μm displayed opalescent reflections because of the uniform alignment of the colloids. As a second step, the template was embedded in a matrix consisting of biocompatible, thermoresponsive hydrogels. The comonomers were selected from the family of oligo(ethylene glycol)methacrylates. The monomer solution was injected into a polymerisation mould, which contained the colloidal crystals as a template. The space in-between the template particles was filled with the monomer solution and the hydrogel was cured via UV-polymerisation. The particles were chemically etched, which resulted in a porous inner structure. The uniform alignment of the pores and therefore the opalescent reflection were maintained, so these system were denoted as inverse hydrogel opals. A pore diameter of several hundred nanometres as well as interconnections between the pores should facilitate a diffusion of bigger (bio)molecules, which was always a challenge in the presented systems until now. The copolymer composition was chosen to result in a hydrogel collapse over 35 °C. All hydrogels showed pronounced swelling in water below the critical temperature. The incorporation of a reactive monomer with hydroxyl groups ensured a potential coupling group for the introduction of recognition units for analytes, e.g. proteins. As a test system, biotin as a recognition unit for avidin was coupled to the IHO via polymer-analogous Steglich esterification. The amount of accessible biotin was quantified with a colorimetric binding assay. When avidin was added to the biotinylated IHO, the wavelength of the opalescent reflection was significantly shifted and therefore the binding event was visualised. This effect is based on the change in swelling behaviour of the hydrogel after binding of the hydrophilic avidin, which is amplified by the thermoresponsive nature of the hydrogel. A swelling or shrinking of the pores induces a change in distance of the crystal planes, which are responsible for the colour of the reflection. With these findings, the possibility of creating sensor materials or additional biomolecules in the size range of avidin is given.},
  language  = {en}
}
@phdthesis{Buller2013,
  author    = {Buller, Jens},
  title     = {Entwicklung neuer stimuli-sensitiver Hydrogelfilme als Plattform f{\"u}r die Biosensorik},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66261},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Diese Arbeit befasst sich mit der Synthese und der Charakterisierung von thermoresponsiven Polymeren und ihrer Immobilisierung auf festen Oberfl{\"a}chen als nanoskalige d{\"u}nne Schichten. Dabei wurden thermoresponsive Polymere vom Typ der unteren kritischen Entmischungstemperatur (engl.: lower critical solution temperature, LCST) verwendet. Sie sind bei niedrigeren Temperaturen im L{\"o}sungsmittel gut und nach Erw{\"a}rmen oberhalb einer bestimmten kritischen Temperatur nicht mehr l{\"o}slich; d. h. sie weisen bei einer bestimmten Temperatur einen Phasen{\"u}bergang auf. Als Basismaterial wurden verschiedene thermoresponsive und biokompatible Polymere basierend auf Diethylenglykolmethylethermethacrylat (MEO2MA) und Oligo(ethylenglykol)methylethermethacrylat (OEGMA475, Mn = 475 g/ mol) {\"u}ber frei radikalische Copolymerisation synthetisiert. Der thermoresponsive Phasen{\"u}bergang der Copolymere wurde in w{\"a}ssriger L{\"o}sung und in gequollenen vernetzten d{\"u}nnen Schichten beobachtet. Außerdem wurde untersucht, inwiefern eine selektive Proteinbindung an geeignete funktionalisierte Copolymere die Phasen{\"u}bergangstemperatur beeinflusst. Die thermoresponsiven Copolymere wurden {\"u}ber photovernetzbare Gruppen auf festen Oberfl{\"a}chen immobilisiert. Die n{\"o}tigen lichtempfindlichen Vernetzereinheiten wurden mittels des polymerisierbaren Benzophenonderivates 2 (4 Benzoylphenoxy)ethylmethacrylat (BPEM) in das Copolymer integriert. D{\"u}nne Filme der Copolymere mit ca. 100 nm Schichtdicke wurden {\"u}ber Rotationsbeschichtung auf Siliziumwafer aufgeschleudert und anschließend durch Bestrahlung mit UV Licht vernetzt und auf der Oberfl{\"a}che immobilisiert. Die Filme sind stabiler je gr{\"o}ßer der Vernetzeranteil und je gr{\"o}ßer die Molmasse der Copolymere ist. Bei einem Waschprozess nach der Vernetzung wird beispielsweise aus einem Film mit moderater Molmasse und geringem Vernetzeranteil mehr unvernetztes Copolymer ausgewaschen als bei einem h{\"o}hermolekularen Copolymer mit hohem Vernetzeranteil. Die Quellbarkeit der Polymerschichten wurde mit Ellipsometrie untersucht. Sie ist gr{\"o}ßer je geringer der Vernetzeranteil in den Copolymeren ist. Schichten aus thermoresponsiven OEG Copolymeren zeigen einen Volumenphasen{\"u}bergang vom Typ der LCST. Der thermoresponsive Kollaps der Schichten ist komplett reversibel, die Kollapstemperatur kann {\"u}ber die Zusammensetzung der Copolymere eingestellt werden. F{\"u}r einen Vergleich dieser Eigenschaften mit dem gut charakterisierten und derzeit wohl am h{\"a}ufigsten untersuchten thermoresponsiven Polymer Poly(N-isopropylacrylamid) (PNIPAM) wurden zus{\"a}tzlich photovernetzte Schichten aus PNIPAM hergestellt und ebenfalls ellipsometrisch vermessen. Im Vergleich zu PNIPAM verl{\"a}uft der Phasen{\"u}bergang der Schichten aus den Copolymeren mit Oligo(ethylenglykol)-seitenketten (OEG Copolymere) {\"u}ber einen gr{\"o}ßeren Temperaturbereich. Mit Licht einer Wellenl{\"a}nge > 300 nm wurden die photosensitiven Benzophenongruppen selektiv angeregt. Bei der Verwendung kleinerer Wellenl{\"a}ngen vernetzten die Copolymerschichten auch ohne die Anwesenheit der lichtempfindlichen Benzophenongruppen. Dieser Effekt ließ sich zur kontrollierten Immobilisierung und Vernetzung der OEG Copolymere einsetzen. Als weitere Methode zur Immobilisierung der Copolymere wurde die Anbindung {\"u}ber Amidbindungen untersucht. Dazu wurden OEG Copolymere mit dem carboxylgruppenhaltigen 2 Succinyloxyethylmethacrylat (MES) auf mit 3 Aminopropyldimethylethoxysilan (APDMSi) silanisierte Siliziumwafer rotationsbeschichtet, und mit dem oligomeren α, ω Diamin Jeffamin® ED 900 vernetzt. Die Vernetzungsreaktion erfolgte ohne weitere Zus{\"a}tze durch Erhitzen der Proben. Die Hydrogelschichten waren anschließend stabil und zeigten neben thermoresponsivem auch pH responsives Verhalten. Um zu untersuchen, ob die Phasen{\"u}bergangstemperatur durch eine Proteinbindung beeinflusst werden kann, wurde ein polymerisierbares Biotinderivat 2 Biotinyl-aminoethylmethacrylat (BAEMA) in das thermoresponsive Copolymer eingebaut. Der Einfluss des biotinbindenen Proteins Avidin auf das thermoresponsive Verhalten des Copolymers in L{\"o}sung wurde untersucht. Die spezifische Bindung von Avidin an das biotinylierte Copolymer verschob die {\"U}bergangstemperatur deutlich zu h{\"o}heren Temperaturen. Kontrollversuche zeigten, dass dieses Verhalten auf eine selektive Proteinbindung zur{\"u}ckzuf{\"u}hren ist. Thermoresponsive OEG Copolymere mit photovernetzbaren Gruppen aus BPEM und Biotingruppen aus BAEMA wurden {\"u}ber Rotationsbeschichtung auf Gold- und auf Siliziumoberfl{\"a}chen aufgetragen und durch UV Strahlung vernetzt. Die spezifische Bindung von Avidin an die Copolymerschicht wurde mit Oberfl{\"a}chenplasmonenresonanz und Ellipsometrie untersucht. Die Bindungskapazit{\"a}t der Schichten war umso gr{\"o}ßer, je kleiner der Vernetzeranteil, d. h. je gr{\"o}ßer die Maschenweite des Netzwerkes war. Die Quellbarkeit der Schichten wurde durch die Avidinbindung erh{\"o}ht. Bei hochgequollenen Systemen verursachte eine Mehrfachbindung des tetravalenten Avidins allerdings eine zus{\"a}tzliche Quervernetzung des Polymernetzwerkes. Dieser Effekt wirkt der erh{\"o}hten Quellbarkeit durch die Avidinbindung entgegen und l{\"a}sst die Polymernetzwerke schrumpfen.},
  language  = {de}
}