@phdthesis{Mahnkopf2005,
  author    = {Mahnkopf, Sven},
  title     = {Photonic crystal based widely tunable laser diodes and integrated optoelectronic components},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13860},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {In a first aspect of this work, the development of photonic crystal based widely tunable laser diodes and their monolithic integration with photonic crystal based passive waveguide and coupler structures is explored theoretically and experimentally. In these devices, the photonic crystal is operated in the photonic bandgap which can be used for the realization of effective reflectors and waveguide structures. Such tunable light sources are of great interest for the development of optical network systems that are based on wavelength division multiplexing. In a second aspect of this work, the operation of a photonic crystal block near the photonic band edge is investigated with respect to the so-called superprism effect. After a few introductory remarks that serve to motivate this work, chapter 3 recapitulates some aspects of semiconductor lasers and photonic crystals that are essential for the understanding of this work so that the reader should be readily equipped with the tools to appreciate the results presented in this work.},
  subject      = {Laserdiode},
  language  = {en}
}
@phdthesis{FernandezMora2005,
  author    = {Fern{\´a}ndez-Mora, Eugenia},
  title     = {Analysis of the maturation of Rhodococcus equi-containing vacuoles in macrophages},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-14049},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {Rhodococcus equi is a Gram-positive intracellular pathogen which can cause severe bronchopneumonia in foals. In recent years, the role of this bacterium as human pathogen has been noted, as R.equi infections in humans have increase in frequency. This increase is associated with the rise in immunosupressed individuals, specially AIDS patients, where infection leads to symptoms and pathology similar to those seen in foals with a high mortality rate. Due to its capability to survive and multiply in murine and equine macrophages, R.equi has been classified as a facultative intracellular bacterium. R.equi is found frequently in macrophages in alveolar infiltrate from infected animals. The pathogenicity of R.equi depends on its ability to exist and multiply inside macrophages and has been associated with the presence of virulence plasmids. It has been observed that, inside foal alveolar macrophages, R.equi-containing vacuoles (RCVs) do not mature into phagolysosomes. However, most of the intracellular events during R.equi infection have not been investigated in detail. The aim of this study was to elucidate the intracellular compartmentation of R.equi and the mechanism by which the bacteria avoid destruction in host macrophages. The importance of the virulence-associated plasmids of R.equi for the establishment of RCVs was also evaluated. Furthermore, the intracellular fate of viable and non-viable R.equi was compared in order to study whether viability of R.equi influeciantes the establishment of RCVs. In this study, the RCV was characterized by using a variety of endocytic markers to follow the path of the bacteria trhough murine macropages. Transmission electron microscopy-base analysis showed that R.equi was found equally frequently in phagosomes with loosely or thightly apposed membranes, and RCV often contains numerous membranous vesicles. Laser scanning microscopy of infected macrophages showed that the majority of phagosomes containing R.equi acquired transiently the early endosomal markers Rab5, Ptlns3P, and EEA-1, suggesting initially undisturbed phagosome maturation. Although the RCV acquired some late endosomal markers, such as Rab7, LAMP-1, and Lamp-2, they did not acquired vATPase, did not interact with pre-labeled lysosomes, and failed to acidify. These data clearly suggest that the RCV is a compartment which has left vacuoles that resemble multivesicular body compartments (MVB), which are transport intermediates between early and late endosomes and display internal vesicles very similar to the ones observed within RCVs. Analyisis of several R.equi strains containing either VapA- or VapB-expressing plasmids or neither demonstrated that the possession of the virulence-associated plasmids does not affect phagosome trafficking over a two hour period of infection. The finding that non-viable R.equi was still able to inhibit phagosome maturation (although not to the same extent as viable R.equi did) suggests that heat-insensitive factors, such as cell periphery lipids, may play a major role in inhibition of phagosome maturation, although heat-sensitive factors may also be involved.},
  subject      = {Rhodococcus equi},
  language  = {en}
}
@phdthesis{Maksimenka2005,
  author    = {Maksimenka, Raman},
  title     = {Techniques in frequency conversion and time-resolved spectroscopy with nonlinear optical processes in the femtosecond regime},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-14087},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {Nichtlineare Frequenzumsetzung der niederenergetischen femtosekunden Laserpulsen wurde in den Festk{\"o}rpermitteln nachgeforscht. Ramanumwandlung im weiss-Licht-freien Regime des impulsiven stimulierten Raman Streuungs wurde erzielt, indem man KGW-Kristall mit den Bessel-Lichtstrahl pumpte. Leistungs-f{\"a}higes Superkontinuumerzeugung wurde f{\"u}r die sub-microjule Pulse demonstriert, die in Mikrostrukturfaser fokussiert wurden. Anwendung von Vier-Wellen-Mischung Techniken zur {\"U}berwachung der Aufregenzustandsdynamik in den mehratomigen Molek{\"u}len wurde demonstriert. Zeitkonstanten der Prozesse, die auf Schwingungsenergiewiederverteilung nach dem ursprunglichen Photoanregung von Stilben-3 bezogen wurden, wurden mittels der Pump-CARS Technik festgestellt, in der CARS-Prozess als wirkungsvoller Modus-vorgew{\"a}hlter Filter diente. Spektrale sowie zeitliche Eigenschaften der elektronischen Entspannungbahnen in den Azulenderivats wurden erforscht, indem man verg{\"a}nglichen-Bev{\"o}lkerungs-Gittern und Pump-Probe verg{\"a}nglichen Absorptions Techniken verwendete.},
  subject      = {Frequenzumsetzung},
  language  = {en}
}
@phdthesis{Joshi2005,
  author    = {Joshi, Sanjeev},
  title     = {Preparation and characterization of CdS nanoparticles},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13395},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {Zusammenfassung CdS-Nanoteilchen mit Gr{\"o}ßen zwischen 1.1 und 4.2 nm wurden in {\"A}thanol und mit Thioglycerol (TG)-H{\"u}lle synthetisiert. Es wurde gezeigt, dass die nass-chemische Synthese ohne Wasser und die Verwendung von TG als H{\"u}lle folgende Vorteile bieten: Es konnten kleinere Teilchen hergestellt und eine schmalere Gr{\"o}ßenverteilung erzielt werden. Zus{\"a}tzlich wird dem Altern der Teilchen vorgebeugt, und die Ergebnisse sind besser reproduzierbar. Hochaufgel{\"o}ste Photoemissions-Messungen an kleinen CdS-Teilchen (1.1, 1.4, 1.7, 1.8; 1.8 nm mit Glutathion-H{\"u}lle) ergaben Beitr{\"a}ge von f{\"u}nf verschiedenen Schwefelatom-Typen zum S 2p-Gesamt Signal. Außerdem wurde beobachtet, dass Nanoteilchen unterschiedlicher Gr{\"o}ße und/oder mit unterschiedlichen H{\"u}llen-Substanzen verschiedene Photoemissionsspektren zeigen und verschieden starke Strahlensch{\"a}den aufweisen. Bei den 1.4 nm großen CdS-Teilchen entsprechen die Komponenten des S 2p-Signals entweder Schwefelatomen mit unterschiedlichen Cd-Nachbarn, Thiol-Schwefelatomen oder teilweise oxidiertem Schwefel. Die jeweilige Zuweisung der Schwefeltypen erfolgte {\"u}ber Intensit{\"a}ts-{\"A}nderungen der einzelnen S 2p-Komponenten als Funktion der Photonenenergie und des Strahlenschadens. Die Daten der 1.4 nm großen CdS-Teilchen wurden mit PES-Intensit{\"a}ts-Rechnungen verglichen, die auf einem neuen Strukturmodell-Ansatz basieren. Von den drei verwendeten CdS-Strukturmodellen konnte nur ein Modell mit 33 S-Atomen die Variation der experimentellen Intensit{\"a}ten richtig wieder geben. Modelle von gr{\"o}ßeren Nanoteilchen mit beispielsweise 53 S-Atomen zeigen Abweichungen von den experimentellen Daten der 1.4 nm-Teilchen. Auf diese Weise kann indirekt auf die Gr{\"o}ße der gemessenen Teilchen geschlossen werden. Die Intensit{\"a}tsrechnungen wurden zum einen „per Hand" zur groben Absch{\"a}tzung durchgef{\"u}hrt, zum anderen wurden exaktere Berechnungen mit einem von L. Weinhardt und O. Fuchs entwickelten Programm angestellt. Diese best{\"a}tigen die Ergebnisse der Absch{\"a}tzung. Zudem wurde festgestellt, dass die inelastische freie Wegl{\"a}nge \&\#955; keinen signifikanten Einfluss auf die Modellrechnungen hat. Die gemessenen Intensit{\"a}ts-{\"A}nderungen konnten zwar mit mehreren leicht verchiedenen Modellen erkl{\"a}rt werden, allerdings f{\"u}hrte nur ein kugelf{\"o}rmiges Teilchen-Modell auch zu den richtigen Intensit{\"a}tsverh{\"a}ltnissen der einzelnen S 2p-Komponenten. Weiterhin konnte beobachtet werden, dass die elektronische Bandl{\"u}cke gr{\"o}ßer ist als die optische Bandl{\"u}cke. Bei den PES-Messungen wurden einige wichtige Einfl{\"u}sse sichtbar. So spielen strahlenbedingte Effekte eine große Rolle. Kenntnisse {\"u}ber die Zeitskala solcher Effekte erm{\"o}glichen PES-Aufnahmen mit guter Signal-Qualit{\"a}t und erlauben eine Extraploation zur Situation ohne Strahlenschaden. Auch die D{\"u}nnschicht-Pr{\"a}paration beeinflusst die Spektren. Beispielsweise zeigten mit Elektrophorese hergestellte Filme Hinweise auf Agglomeration. Schichten, die per Tropfen-Deposition erzeugt wurden, weisen spektrale {\"A}nderungen am Rand der Probe auf, und Filme aus Nanoteilchen-Pulver waren nicht homogen. Mikro-Raman Experimente, die in Kollaboration mit Dr. M. Schmitt und Prof. W. Kiefer durchgef{\"u}hrt wurden, ließen große Unterschiede in den Spektren von Nanoteilchen und TG in L{\"o}sung erkennen. Dies wurde vor allem auf das Fehlen von S - H -Bindungen zur{\"u}ckgef{\"u}hrt und zeigt damit, dass alle TG-Molek{\"u}le verwertet oder ausgewaschen wurden.},
  subject      = {Cadmiumsulfid},
  language  = {en}
}
@phdthesis{Bera2005,
  author    = {Bera, Holger},
  title     = {Halfsandwich tungsten complexes with a silanol-functionalized cyclopentadienyl ligand : synthesis and reactivity},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13778},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {Within the studies concerning metallo-silanols, halfsandwich-tungsten complexes have been silanol-functionalized at the cyclopentadienyl ligand. The stability and the condensation behavior have been investigated. Thus, it was shown that these complexes are stable enough for isolation but they are reactiv enough for time-effective condensation reactions with diverse chlorosilanes, chlorostannanes or metalhalogenides. These processes are characterized by an increased reactivity in contrast to metallo-silanols with a direct metal-bonded silanol group and proves that the separation of the silanol group has to be regarded as a successful manipulation. In addition, this modification allows a wide variation of the ligand sphere of the metal which was shown by H/Cl exchange, methylation, silylation or phosphine substitution. These changes evoke a small but significant influence on the silanol group. For example leads an introduced phosphine to an enhanced stability of the silanol function. A further separation of the silanol group from the metal by an additional alkylidene spacer leads to the complete lost of the stabilizing effect of the metal fragment and generates silanols which show a condensation behavior very similar to those of ordinary organosilanols.},
  subject      = {Wolframkomplexe},
  language  = {en}
}
@phdthesis{Na2005,
  author    = {Na, Shin-Young},
  title     = {PKB/Akt : a critical regulator of lymphocyte, development and function},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13755},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {Protein kinase B (PKB), a serine threonine kinase, is highly involved in the regulation of cellular proliferation and survival. To characterize PKB's function in lymphocyte development and activation, transgenic (tg) mice that express a membrane targeted constitutively active form of PKBa (myr PKB) in T and B cells were analysed. Thymocytes from myr PKB tg mice showed enhanced proliferation after T cell receptor (TCR) engagement compared to wild type (wt) mice. Astonishingly, myr PKB tg thymocytes were capable to proliferate in response to PMA only and were also less sensitive to inhibition by the calcineurin inhibitors CsA or FK506, which indicates the proliferative response of myr PKB tg T cells is relatively independent of calcium mobilisation and calcineurin activity. In addition, when TCR signalling was inhibited by the MEKinase inhibitor PD98059 or the Srckinase inhibitor PP1 myr PKB tg thymocytes again were more resistant to inhibition. Western blot analysis revealed myr PKB enhances activation of the kinases Lck, Raf and Erk after TCR/CD3 stimulation. Thus, myr PKB renders proliferative responses of thymocytes more sensitive to TCR signals by positive regulation of the Lck-Raf-MEK-Erk signalling pathway. Studies on the cellular location of the tg protein showed myr PKB is located in membrane socalled "lipid rafts". Furthermore, we found that after TCR/CD3 ligation endogenous cytoplasmic PKB moves into "lipid rafts", which highlights PKB as a crucial mediator of TCR proximal signalling events. Analysing three different TCR tg model systems for positive and negative selection of immature precursors in the thymus, we found myr PKB promotes positive selection of CD4+ but not CD8+ T cells. This most likely results from PKB's positive cross-talk on Lck-Raf-Erk signalling, which is known to influence thymocyte selection and CD4/CD8-lineage choice. Furthermore, myr PKB enhances phosphorylation of glycogen synthase kinase 3 (GSK3), a negative regulator of the transcription factor NFAT (nuclear factor of activated T cells) and T cell activation, and of the adapter protein c-Cbl. Concerning negative selection, myr PKB enhanced (OT1 mice), reduced (HY mice) or had no influence (OT2 mice) on negative selection. Thus, myr PKB's effect on negative selection strongly depends on the model system analysed and this most likely results from differences in TCR affinity/avidity and TCR specificity for MHC. 106 Peripheral CD4+ T cells from myr PKB tg mice showed enhanced production of both Th1 and Th2 cytokines. Furthermore, after TCR/CD3 stimulation in the presence of TGF-b1, wt CD4+ T cells showed a drastic inhibition of proliferation, whereas myr PKB tg CD4+ T cells proliferated even better, i.e. they were resistant to the inhibitory TGF-b1 signals. Expression of myr PKB in B cells leads to reduced Ca2+ flux and proliferation after BCR stimulation, but activation of Lyn, SLP-65, c-Cbl and GSK-3 were enhanced. When we analysed B cell subsets in myr PKB tg mice, a decrease in immature and mature B cells became obvious, whereas cell numbers for marginal zone (MZ) B cells were normal. In aged myr PKB tg mice we detected a very strong reduction of pro/pre and immature B cell populations in the bone marrow, indicating PKB is very important for maintenance of B cell development. Furthermore, myr PKB also lead to a strong reduction of peritoneal B-1 cells. However, expression of NFATc1, which is required for B-1 cell development, was comparable between wt and myr PKB tg B-1 cells. To analyse the effect of myr PKB on immunoglobulin production, mice were immunized with thymus dependent (TD) and independent (TI) antigens. In both cases, B cell responses were strongly elevated in myr PKB tg mice. Finally, RT-PCR analyses of in vitro expanded B cells revealed increased Blimp-1 and Notch3 expression in myr PKB tg B cells, which might be primary candidates involved in their enhanced effector function. In summary, this study clearly shows an important cross-talk between PKB and various critical signalling molecules downstream of the TCR and BCR. Thereby active PKB modulates and regulates the thresholds for thymocyte selection and T cell activation as well as for B cell development and function.},
  subject      = {Proteinkinase B},
  language  = {en}
}
@phdthesis{Zhou2005,
  author    = {Zhou, Qingchun},
  title     = {Molecular analysis of the sex-determining region of the Y chromosome in the platyfish Xiphophorus maculatus},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13827},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {A large variety of sex determination systems have been described in fish. However, almost no information is available about sex determination in the classical fish models, the zebrafish Danio rerio and the pufferfish Takifugu rubripes. A DNA-binding protein gene called dmrt1bY (or DMY) has been recently described as an outstanding candidate for the primary sex-determining gene in the medaka fish Oryzias latipes. But this gene is not the universal master sex-determining gene in teleost fish, since dmrt1bY is not found in most other fishes. Hence, other fish models need to be examined including the platyfish Xiphophorus maculatus. Xiphophorus maculatus has three types of sex chromosomes (X, Y and W; females are XX, WX or WY; males are XY or YY). Its gonosomes are at an early stage of differentiation. The sex-determining locus on the sex chromosomes is flanked by two receptor tyrosine kinase genes, the Xmrk oncogene and its protooncogenic progenitor gene egfrb, which both delimit a region of about 0.6 centiMorgans. This situation should allow the positional cloning of the sex-determining gene (SD) of the platyfish. For this purpose, Bacterial Artificial Chromosome (BAC) contigs were assembled from a BAC library of XY males constructed in our laboratory, using the oncogene Xmrk, egfrb, as well as a Y-specific pseudogene called ps-criptY as starting points. The ps-criptY sequence was found to be closely linked to the SD gene, since no recombination was observed between SD and ps-criptY in more than 400 individuals tested. Two major BAC contigs for the X chromosome (about 2.5 Mb) and three major BAC contigs for the Y chromosome (about 3.5 Mb) were built up and analyzed by strategic sequencing. These are some of the largest contigs ever assembled for the sex chromosomes of a non-mammalian vertebrate species. The molecular analysis of the ps-criptY contig was the major objective of this work. The Y-specific ps-criptY contig has been extended over 1 Mb in this work with 58 identified molecular markers. Approximatively 700 kb of non-redundant sequences has been obtained from this contig by strategic sequencing. Numerous Y-linked markers from the contig including ps-criptY were also detected on the X chromosome. Nevertheless, major structural differences were observed between the X and Y chromosomes. Particularly, a large region, which is present at one copy on the X chromosome and contains several candidate genes, was found to be duplicated on the Y chromosome. Evidence for an inversion in the sex-determining region and for the Y-specific accumulation of a repeated sequence called XIR was also obtained. Such events might correspond to an initiation of differentiation between both types of gonosomes. Accumulation of transposable elements was also observed in the ps-criptY contig. A DNA transposable element, helitron, was isolated from the sex-determining region of X. maculatus. Three copies of helitron are located on the ps-criptY contig and one copy on the X-linked contig (helitron has roughly 15 copies per haploid genome). No in-frame stop codon, truncation or intron was found in these four copies, which present high nucleotide identities to each other. This suggests that helitron elements might be active or have been recently active in X. maculatus. A consensus open reading frame of helitron was also assembled from medaka (Oryzias latipes) genomic sequences. Two candidate genes from the ps-criptY contig are also located on the W chromosome in the X. maculatus Usumacinta strain (heterogamety). These markers show the relationship between the different types of gonosomes and allow to compare the male and female heterogameties in the platyfish. Several gene candidates were identified in the ps-criptY contig. However, some of them such as msh2, cript, igd and acr probably correspond to pseudogenes. Interestingly, a novel gene, called swimy, is exclusively expressed in spermatogonia of the adult testis. Swimy is a gene encoding a DNA-binding protein with several putative DNA-binding domains. The data suggest that swimy is a very promising candidate for the master SD gene. Another novel gene, which is called fredi and encodes a novel helix-turn-helix protein, is predominately expressed in the adult testis and currently under scrutiny. There is no doubt that the master SD gene of X. maculatus will be identified by positional cloning. Further molecular analysis of the contigs built in this work will shed new light on the molecular mechanism of sex determination and the evolution of sex chromosomes in fish.},
  subject      = {Platy},
  language  = {en}
}
@phdthesis{Stojic2005,
  author    = {Stojic, Jelena},
  title     = {Cloning and functional characterization of novel genes expressed preferentially in the human retina},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13746},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {The human retina is a multi-layered neuronal tissue specialized for the reception and processing of visual information. The retina is composed of a great diversity of neuronal cell types including rod and cone photoreceptors, bipolar cells, ganglion cells, amacrine cells, horizontal cells and M{\"u}ller glia. In response to light, a coordinated series of molecular events, the so-called phototransduction cascade, is triggered in photoreceptor cells and the signals from the photoreceptors are further processed by the bipolar and ganglion cells to the higher centers of the brain. The retina as highly complex system may be greatly susceptible to genetic defects which can lead to a wide range of disease phenotypes. Therefore, isolation and characterisation of the genes active in the human retina will facilitate our deeper understanding of retinal physiology and mechanisms underlying retinal degeneration and provide novel candidates for the retinal disease genes. To identify novel genes that are specifically or predominantly expressed in the human retina, a cDNA library enriched for retina specific transcripts was generated using suppression subtractive hybridization (SSH) technique. In total, 1113 clones were randomly isolated from the retina SSH cDNA library and partially sequenced. On the basis of BLASTN algorithm analysis these clones were classified into four categories including those with I) significant homology to known human genes (766/1113), II) significant homology to partial transcripts and hypothetical gene predictions (162/1113), III) no homology to known mRNAs (149/1113), and IV) vector sequences and clones derived from mitochondrial genes (36/1113). After correcting for redundancy, category I represented 234 known human genes and category II a total of 92unknown transcripts. Clones from category I, were selected for expression analysis by RT-PCR in a great number of human tissues. This resulted in the identification of 16 genes which were expressed exclusively in the retina, 13 which were highly expressed in the retina compared to other tissues, 12 genes which were specifically expressed in neuronal tissues and 48 ubiquitously expressed genes. Thus, our expression analysis resulted in the identification of 29 genes exclusively or abundantly transcribed in the human retina. Of those, retina specific genes L25,L33, L35, L37, L38 and L40 were selected for further analysis. To characterize the complete mRNA sequences of these transcripts a full-length human retina cDNA library was constructed. The analysis of the L25 gene revealed three splicing variants of the ABCC5 gene, consequently named ABCC5_SV1 (SV1), ABCC5_SV2 (SV2) and ABCC5_SV3 (SV3).These isoforms comprise the first five exons of ABCC5 and additional novel exons named 5a, 5b and 5c, generated by differential exon usage. The determined lengths of the three transcripts are 2039 bp, 1962 bp, and 1887 bp in size, respectively. RT-PCR, real-time PCR and Northern blot analysis of ABCC5 as well as the isoforms SV1, SV2 and SV3demonstrated high levels of expression for all transcripts in the retina compared to other tissues. Analysis of their nucleotide sequences revealed that inclusion of exon 5a in splicing variant SV1 produced a frame shift and premature termination codon (PTC). Our data show that this splice variant is the target of nonsense mediated mRNA decay (NMD). This was shown by inhibition of protein synthesis with antibiotics puromycin and anisomycin in human cell lines A-RPE 19 and Y79. Our analysis resulted in an increase of the PTC containing transcript and a decrease of the ABCC5 transcript. Conversely, the amount of both transcripts (SV1 and ABCC5) returned to pre-treatment levels after removal of the inhibitors. Together, our results suggest that alternative splicing of the ubiquitously expressed ABCC5 gene in addition to NMD is involved in retina-specific transcriptional regulation of the mRNA level of ABCC5. In contrast, additional experiments demonstrated that the levels of expression ofSV2 and SV3 isoforms do not appear to influence ABCC5 transcription. Several of the cloned genes were selected for additional genotyping of single nucleotide polymorphisms (SNPs) in order to construct their SNP maps which are going to be used for future association studies of complex disease AMD. Thus, identification of novel retinal genes and their functional characterization will further our elucidation of retinal physiology in general and in the diseased state in particular, by providing candidate retinal disease genes.},
  subject      = {Netzhaut},
  language  = {en}
}
@phdthesis{Volkmann2004,
  author    = {Volkmann, Thorsten},
  title     = {Lattice gas models and simulations of epitaxial growth},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13812},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2004},
  abstract  = {In this PhD thesis, we develop models for the numerical simulation of epitaxial crystal growth, as realized, e.g., in molecular beam epitaxy (MBE). The basic idea is to use a discrete lattice gas representation of the crystal structure, and to apply kinetic Monte Carlo (KMC) simulations for the description of the growth dynamics. The main advantage of the KMC approach is the possibility to account for atomistic details and at the same time cover MBE relevant time scales in the simulation. In chapter 1, we describe the principles of MBE, pointing out relevant physical processes and the influence of experimental control parameters. We discuss various methods used in the theoretical description of epitaxial growth. Subsequently, the underlying concepts of the KMC method and the lattice gas approach are presented. Important aspects concerning the design of a lattice gas model are considered, e.g. the solid-on-solid approximation or the choice of an appropriate lattice topology. A key element of any KMC simulation is the selection of allowed events and the evaluation of Arrhenius rates for thermally activated processes. We discuss simplifying schemes that are used to approximate the corresponding energy barriers if detailed knowledge about the barriers is not available. Finally, the efficient implementation of the MC kinetics using a rejection-free algorithm is described. In chapter 2, we present a solid-on-solid lattice gas model which aims at the description of II-VI(001) semiconductor surfaces like CdTe(001). The model accounts for the zincblende structure and the relevant surface reconstructions of Cd- and Te-terminated surfaces. Particles at the surface interact via anisotropic nearest and next nearest neighbor interactions, whereas interactions in the bulk are isotropic. The anisotropic surface interactions reflect known properties of CdTe(001) like the small energy difference between the c(2x2) and (2x1) vacancy structures of Cd-terminated surfaces. A key element of the model is the presence of additional Te atoms in a weakly bound Te* state, which is motivated by experimental observations of Te coverages exceeding one monolayer at low temperatures and high Te fluxes. The true mechanism of binding excess Te to the surface is still unclear. Here, we use a mean-field approach assuming a Te* reservoir with limited occupation. In chapter 3, we perform KMC simulations of atomic layer epitaxy (ALE) of CdTe(001). We study the self-regulation of the ALE growth rate and demonstrate how the interplay of the Te* reservoir occupation with the surface kinetics results in two different regimes: at high temperatures the growth rate is limited to one half layer of CdTe per ALE cycle, whereas at low enough temperatures each cycle adds a complete layer. The temperature where the transition between the two regimes occurs depends mainly on the particle fluxes. The temperature dependence of the growth rate and the flux dependence of the transition temperature are in good qualitative agreement with experimental results. Comparing the macroscopic activation energy for Te* desorption in our model with experimental values we find semiquantitative agreement. In chapter 4, we study the formation of nanostructures with alternating stripes during submonolayer heteroepitaxy of two different adsorbate species on a given substrate. We evaluate the influence of two mechanisms: kinetic segregation due to chemically induced diffusion barriers, and strain relaxation by alternating arrangement of the adsorbate species. KMC simulations of a simple cubic lattice gas with weak inter-species binding energy show that kinetic effects are sufficient to account for stripe formation during growth. The dependence of the stripe width on control parameters is investigated. We find an Arrhenius temperature dependence, in agreement with experimental investigations of phase separation in binary or ternary material systems. Canonical MC simulations show that the observed stripes are not stable under equilibrium conditions: the adsorbate species separate into very large domains. Off-lattice simulations which account for the lattice misfit of the involved particle species show that, under equilibrium conditions, the competition between binding and strain energy results in regular stripe patterns with a well-defined width depending on both misfit and binding energies. In KMC simulations, the stripe-formation and the experimentally reported ramification of adsorbate islands are reproduced. To clarify the origin of the island ramification, we investigate an enhanced lattice gas model whose parameters are fitted to match characteristic off-lattice diffusion barriers. The simulation results show that a satisfactory explanation of experimental observations within the lattice gas framework requires a detailed incorporation of long-range elastic interactions. In the appendix we discuss supplementary topics related to the lattice gas simulations in chapter 4.},
  subject      = {Kristallwachstum},
  language  = {en}
}
@phdthesis{Engelhardt2004,
  author    = {Engelhardt, Catherine Marie},
  title     = {Identification and characterisation of the Spred protein family},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-11456},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2004},
  abstract  = {The subject of this thesis was the cloning and the initial biochemical and functional characterisation of novel human proteins with an N-terminal Ena-VASP homology (EVH)-1 domain and a C-terminal Sprouty homologous region (SPR), which are related to the Drosophila AE33 protein. During the course of this work, three mouse homologues of the AE33 fly protein have been reported and termed Sprouty-related protein with an EVH-1 domain 1, 2 and 3 (Spred-1, -2, -3)(Wakioka et al, 2001; Kato et al, 2003). Spred-1, -2 and -3 are membrane associated substrates of receptor tyrosine kinases and they act as negative regulators of the Ras pathway during growth factor stimulation. As the Spred-family members seem to exert similar functions, the specific function of each member remains enigmatic. Therefore, we investigated the mRNA and protein expression patterns of the two murine protein family members Spred-1 and Spred-2 on the whole organ level. Furthermore, we focussed on the cellular localisation and the role of human and murine Spred-2 in the organism. The expression patterns of Spred-1 and Spred-2 differed markedly among various tissues and cell types. In mouse, Spred-1 is abundantly expressed in adult brain, cerebellum, and fetal tissues, whereas Spred-2 was ubiquitously expressed. In humans, Spred-2 was found to be strongly expressed in glandular epithelia and in invasive cytotrophoblasts, and at the subcellular level its immunoreactivity was associated with secretory vesicles and was found to colocalise with Rab11 GTPase. The new human Spred gene family was investigated in detail. Cloning of the fulllength form of human Spred-2 resulted in an 1254 bp coding sequence, corresponding to a 418 amino-acids protein. Immunoblotting with a set of affinitypurified antibodies confirmed the expression of a 47 kDa protein and suggested the presence of additional differently sized variants. Cloning of various shortened Spred- 2 mRNAs and identification of 2 additional human Spred genes (localised on different chromosomes) with their respective EST (expressed sequence tag) revealed that the new human Spred gene family displays extensive splicing, leading to the generation of short and long Spred proteins. All protein isoforms and splicing variants contain an EVH1-domain located at the N-terminus of the protein. The full-length forms ("a" forms) comprised the SPR, another functional domain localised at the C-terminus whereas the short variants (Spred-1b, 2 c-e, 3 c) lack the entire C-terminal SPR domain or part of it. The existence of short and long splicing variants of Spred-1, -2 and -3 revealed a common principle of organisation and splicing pattern in the Spred family. Functional analyses of the 5 cloned Spred-2 splicing variants revealed differential subcellular localisation and differential regulation of serum- and EGF- mediated ERK activation in HEK-293 cells. Taken together, these results indicate a highly specific expression pattern of Spred-1 and Spred-2 in various tissues suggesting a specific physiological role for the individual Spred isoform in these tissues. For example, Spred-2 appears to be involved in regulating secretory pathways. Furthermore, the human Spred family contains three genes, which are subject to extensive alternative splicing resulting in at least 8 different proteins with differential subcellular localisation and differential regulatory potential of the MAPK pathways during growth factor stimulation.},
  subject      = {Spred Protein},
  language  = {en}
}