@article{ShityakovDandekar2010,
  author    = {Shityakov, Sergey and Dandekar, Thomas},
  title     = {Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67824},
  year      = {2010},
  abstract  = {Indinavir (Crivaxan®) is a potent inhibitor of the HIV (human immunodeficiency virus) protease. This enzyme has an important role in viral replication and is considered to be very attractive target for new antiretroviral drugs. However, it becomes less effective due to highly resistant new viral strains of HIV, which have multiple mutations in their proteases. For this reason, we used a lead expansion method to create a new set of compounds with a new mode of action to protease binding site. 1300 compounds chemically diverse from the initial hit were generated and screened to determine their ability to interact with protease and establish their QSAR properties. Further computational analyses revealed one unique compound with different protease binding ability from the initial hit and its role for possible new class of protease inhibitors is discussed in this report.},
  subject      = {Proteasen},
  language  = {en}
}
@article{KellerFoersterMuelleretal.2010,
  author    = {Keller, Alexander and Foerster, Frank and Mueller, Tobias and Dandekar, Thomas and Schultz, Joerg and Wolf, Matthias},
  title     = {Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67832},
  year      = {2010},
  abstract  = {Background: In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results: This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions: Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers: This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Open peer review: Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.},
  subject      = {Phylogenie},
  language  = {en}
}
@phdthesis{Tyagi2012,
  author    = {Tyagi, Anu},
  title     = {Role of SWI/SNF in regulating pre-mRNA processing in Drosophila melanogaster},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-72253},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2012},
  abstract  = {ATP dependent chromatin remodeling complexes are multifactorial complexes that utilize the energy of ATP to rearrange the chromatin structure. The changes in chromatin structure lead to either increased or decreased DNA accessibility. SWI/SNF is one of such complex. The SWI/SNF complex is involved in both transcription activation and transcription repression. The ATPase subunit of SWI/SNF is called SWI2/SNF2 in yeast and Brahma, Brm, in Drosophila melanogaster. In mammals there are two paralogs of the ATPase subunit, Brm and Brg1. Recent studies have shown that the human Brm is involved in the regulation of alternative splicing. The aim of this study was to investigate the role of Brm in pre-mRNA processing. The model systems used were Chironomus tentans, well suited for in situ studies and D. melanogaster, known for its full genome information. Immunofluorescent staining of the polytene chromosome indicated that Brm protein of C. tentans, ctBrm, is associated with several gene loci including the Balbiani ring (BR) puffs. Mapping the distribution of ctBrm along the BR genes by both immuno-electron microscopy and chromatin immunoprecipitation showed that ctBrm is widely distributed along the BR genes. The results also show that a fraction of ctBrm is associated with the nascent BR pre-mRNP. Biochemical fractionation experiments confirmed the association of Brm with the RNP fractions, not only in C. tentans but also in D. melanogaster and in HeLa cells. Microarray hybridization experiments performed on S2 cells depleted of either dBrm or other SWI/SNF subunits show that Brm affects alternative splicing and 3´ end formation. These results indicated that BRM affects pre-mRNA processing as a component of SWI/SNF complexes. 1},
  subject      = {Taufliege},
  language  = {en}
}
@article{SebaldMachleidtOtto1973,
  author    = {Sebald, Walter and Machleidt, W. and Otto, J.},
  title     = {Products of mitochondrial protein synthesis in Neurospora crassa. Determination of equimolar amounts of three products in cytochrome oxidase on the basis of amino-acid analysis},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-62827},
  year      = {1973},
  abstract  = {Cytochrome oxidase isolated from N eurospora crassa was resolved into seven protein eomponents by eleetrophoresis in polyaerylamide gels eontaining sodium dodeeylsulfate. The apparent molecular weights were determined tobe 41000, 28500, 21000, 16000, 14000, 11500 and 10000 for the eomponents 1, 2, 3, 4, 5, 6, and 7, respectively. The components 1, 2 and 3 are synthesized on mitochondrial ribosomes as shown by the incorporation of radioactive amino aeids in the presenee of cyeloheximide. Amino-acidanalysis of the isolated components 1, 2 and 3 revealed a high content of apolar amino acids and a low eontent of basic amino aeids compared to an average amino-aeid eomposition of components 4-7. Components 1, 2 and 3 eontribute 27.9°/0, 18°/0 and 14.2°/0 to the whole eytoehrome oxidase protein. This was calculated from the contributions of the single eomponents to the totalleueine eontent of the enzyme and the leueine eontents (nmol leueine per mg protein) of the single eomponents as determined by amino-aeid analysis. Equimolar relations of the components 1, 2 and 3 are found by dividing the amounts of protein by their apparent molecular weights. A stoichiometry of 1:1:1 results assuming a minimal molecular weight of 150000 for the whole cytochrome oxidase protein. On the basis of the heme a content a molecular weight of about 70000 per heme group was determined, using an absorption coeffieient L1e605 (redueed minus oxidized) of 12 mM-1 cm-1• It is concluded that the smallest structural unit of eytochrome oxidase contains two heme groups.},
  subject      = {Biochemie},
  language  = {en}
}
@article{WeissSebaldSchwabetal.1973,
  author    = {Weiss, H. and Sebald, Walter and Schwab, A. J. and Kleinow, W. and Lorenz, B.},
  title     = {Contribution of mitochondrial and cytoplasmic protein synthesis to the formation of cytochrome b and cytochrome aa\(_3\)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-62835},
  year      = {1973},
  abstract  = {A cytochrome b preparation from Neurospora crassa mitochondria is found to consist of three polypeptides (apparent molecular weight 10 000, 11 000 and 32 000), a cytochrome aa3 preparation of six to seven polypeptides (apparent molecular weight 8 000, 11 000, 13 000, 18 000, 28 000 and 36 000). Selective incorporation of radioactive amino acids by eilher mitochondrial protein synthesis when the cytoplasmic one is blocked or by the cytoplasmic protein synthesis, when the mitochondrial one is blocked, indicates that one cytochrome b polypeptide (mw 32 000) and one to three cytochrome aa3 polypeptides (mw 36 000, 28 000 and 18 000) are mitochondrial translation products, the other cytochrome b and cytochrome aa3 polypeptides cytoplasmic translation products. The delayed appearance of labeling in the cytochrome b and cytochrome aa3 polypeptides compared to the average cell protein after a pulse of <~H leueine revealed that these polypeptides are derived from separate pools of precursor polypeptides. The pool sizes range from 2 p. cent to 25 p. cent of the amount of the corresponding polypeptide present in the cytochromes. The 32 000 molecular weight polypeptide of cytochrome band at least the 18 000 molecular weight polypeptide of cytochrome aa\(_3\) are mitochondrial translation products as well in the fungus Neurospora crassa as in the insect Locusta migratoria. So, despite the fact that the size of mitochondrial DNA and mitochondrial ribosomes is reduced in insects, the products have maintained their characteristics.},
  subject      = {Biochemie},
  language  = {en}
}
@article{SchwabSebaldWeiss1972,
  author    = {Schwab, A. J. and Sebald, Walter and Weiss, H.},
  title     = {Different pool sizes of the precursor polypeptides of cytochrome oxidase from Neurospora crassa.},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-62841},
  year      = {1972},
  abstract  = {Pulse-labelling experiments with growing Neurospora crassa revealed that the polypeptides composing the protein moiety of a cytochrome oxidase preparation are derived from at least four independent pools of precursor polypeptides. The pool sizes range from 2 ° f 0 to 25 °/0 of the amount of the corresponding polypeptide present in cytochrome oxidase. The smallest pool is assigned to a polypeptide of mitochondrial origm. Serial pools were found for one of the polypeptides.},
  subject      = {Biochemie},
  language  = {en}
}
@article{SebaldWeissJackl1972,
  author    = {Sebald, Walter and Weiss, H. and Jackl, G.},
  title     = {Inhibition of the assembly of cytochrome oxidase in Neurospora crassa by chloramphenicol},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-62852},
  year      = {1972},
  abstract  = {Cytochrome oxidasewas prepared from Neurospora crassa by chromatography on oleyl polymethacrylic acid resin and separated into seven polypeptides by polyacrylamide gel electrophoresis in the presence of sodium dodecylsulfate. Incorporation oflabelled amino acids into the single polypeptideswas investigated after a pulse labelling in the absence and presence of chloramphenicol, and afterwashing out the inhibitor. Chloramphenicol (4 mg/ml) inhibited amino acid incorporation into all polypeptides 90-95\%• while labeHing of the whole membrane protein was inhibited only 30\%• Mter washing out the inhibitor and further growth of the cells. the four smaller polypeptides were highly labelled, whereas the other polypeptides showed only a. small increase in radioactivity. It is concluded that the four small-sized polypeptides of cytochrome oxidase are synthesized but not integrated into the functional enzyme under the action of chloramphenicol.},
  subject      = {Biochemie},
  language  = {en}
}
@article{WeissSebaldBuecher1971,
  author    = {Weiss, H. and Sebald, Walter and B{\"u}cher, T.},
  title     = {Cycloheximide resistant incorporation of amino acids into a polypeptide of the cytochrome oxidase of Neurospora crassa},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-62866},
  year      = {1971},
  abstract  = {Radioaetive leueine was ineorporated by N eurospora crassa mitoehondria in vivo in the presence of cyeloheximide. When the membrane protein of these mitochondria was ehromatographieally separated on oleyl polymethaerylie aeid resin, \& nurober of fraetions were obtained whieh differ with respeet to their eontents of radioaetivity and eytoehromes. The highest speeifie radioaetivity was found in the fraction eontaining eytoehrome aa3• This fraetion proved to be a pure and enzymatically aetive cytoehrome oxidase. Its ratio of absorbanee at 280 nm (ox)/ 443 nm (red.) was 2.1. By means of sodium dodeeylsulfate gel-electrophoresis, this enzymewas separated into five polypeptides with molecular weights of 30000, 20000, 13000, 10000, and 8000. Only the polypeptide with the molecular weight 20000 displayed a high specific radioaetivity.},
  subject      = {Biochemie},
  language  = {en}
}
@article{SebaldNeupertBirkmayer1970,
  author    = {Sebald, Walter and Neupert, W. and Birkmayer, G. D.},
  title     = {Internal and external contributions to the biogenesis of mitochondrial proteins},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-62876},
  year      = {1970},
  abstract  = {No abstract available},
  subject      = {Biochemie},
  language  = {en}
}
@article{NeupertSebaldSchwabetal.1969,
  author    = {Neupert, W. and Sebald, Walter and Schwab, A. J. and Massinger, P. and B{\"u}cher, T.},
  title     = {Incorporation in vivo of \(^{14}\)C-labelled amino acids into the proteins of mitochondrial ribosomes from Neurospora crassa sensitive to cycloheximide and insensitive to Chloramphenicol},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-62884},
  year      = {1969},
  abstract  = {Radioactive amino acids were incorporated in vivo into N eurospora crassa cells, and the mitochondrial ribosomes were isolated. The incorporation of radioactivity into the proteins of these ribosomes was inhibited by cycloheximide, but not by chloramphenicol. It is therefore concluded that these proteins are synthesized on the cycloheximide sensitive and chloramphenicol insensitive cytoplasmic ribosomes.},
  subject      = {Biochemie},
  language  = {en}
}
@misc{Fiala1990,
  author    = {Fiala, Brigitte},
  title     = {Extrafloral nectaries versus ant-Homoptera mutualisms : a comment on Becerra and Venable},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-32948},
  year      = {1990},
  abstract  = {No abstract available},
  subject      = {Nektarium},
  language  = {en}
}
@phdthesis{Heinecke2010,
  author    = {Heinecke, Kai},
  title     = {Die Dynamik der prim{\"a}ren Erkennungsschritte von BMP-Rezeptoren},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-49257},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Bone Morphogenetic Proteins (BMPs) bilden zusammen mit den Activinen, Growth and Differentiation Factors (GDFs) und Transforming Growth Factor \&\#946; (TGF-\&\#946;) die Transforming Growth Factor \&\#946;-Superfamilie von sekretierten Signalproteinen. Sie spielen eine wichtige Rolle in der Entwicklung, Erhaltung und Regeneration von Geweben und Organen. Die Signalvermittlung dieser Proteine erfolgt durch die Bindung von zwei verschiedenen Typen von Serin-/Threonin-Kinaserezeptoren, die als Typ-I- und Typ-II-Rezeptoren bezeichnet werden. Im ersten Schritt erfolgt die Bindung an den hochaffinen Rezeptor (im Fall von BMP-2 der Typ-I-Rezeptor), im n{\"a}chsten Schritt wird der niederaffine Rezeptor in den Komplex rekrutiert. Bis heute sind lediglich sieben Typ-I- und f{\"u}nf Typ-II-Rezeptoren bekannt, was auf eine Promiskuit{\"a}t in der Liganden-Rezeptor-Interaktion schließen l{\"a}sst. Die Architektur beider Rezeptorsubtypen ist dabei relativ {\"a}hnlich. Beide bestehen aus einer ligandenbindenden extrazellul{\"a}ren Dom{\"a}ne, einer Transmembrandom{\"a}ne sowie einer intrazellul{\"a}ren Kinasedom{\"a}ne. Eine nacheinander ablaufende Transphosphorylierung der intrazellul{\"a}ren Dom{\"a}nen f{\"u}hrt zu einer Phosphorylierung von SMAD-Proteinen, die dann als nachgeschaltete Vermittler fungieren und die Transkription regulierter Gene ausl{\"o}sen. Im Hauptteil dieser Arbeit wurden die initialen Schritte der Rezeptorkomplexformierung sowie die Mobilit{\"a}t der Rezeptoren mit Hilfe von fluoreszenzmikroskopischen Methoden untersucht. Dabei konnte festgestellt werden, dass f{\"u}r die Bildung eines Signalkomplexes eine bestimmte Schwellenkonzentration des Liganden n{\"o}tig ist und dass der Mechanismus nach einem Alles-oder-Nichts-Prinzip wie ein Schalter funktioniert. Außerdem konnten Unterschiede in der Nutzung der gleichen Rezeptoren durch verschiedene Liganden festgestellt werden. Die anderen Teile der Arbeit befassen sich mit der Funktionalit{\"a}t der verschiedenen Rezeptordom{\"a}nen in der Signal{\"u}bermittlung, der Analyse von hoch- und niederaffinen Ligandenbindestellen auf ganzen Zellen sowie dem Einfluss des SMAD- und des MAPK-Signalwegs auf die Induktion der Alkalischen Phosphatase. Dabei konnte gezeigt werden, dass die Art der SMAD-Phosphorylierung allein vom Typ der Kinasedom{\"a}ne abh{\"a}ngig ist, dass auf einer Zelle verschiedene Rezeptorpopulationen existieren, welche von unterschiedlichen Ligandenkonzentrationen angesprochen werden, und dass die Induktion der Alkalischen Phosphatase stark vom zeitlichen Verlauf der SMAD- und MAPK-Aktivierung abh{\"a}ngig ist.},
  subject      = {Knochen-Morphogenese-Proteine},
  language  = {de}
}
@phdthesis{Breher2009,
  author    = {Breher, Stephanie},
  title     = {Die kardiale Funktion von Popdc1 in der Maus: Vom Gen zum Ph{\"a}n},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-37283},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Die Popeye domain containing (Popdc)-Gene bilden eine evolution{\"a}r stark konservierte Genfamilie mit pr{\"a}ferenzieller Expression im Herzen und in der Skelettmuskulatur. In dieser Arbeit konnte gezeigt werden, dass Popdc1 in kardialen Myozyten in Glanzstreifen, lateralen Membranen und im T-Tubuli-System exprimiert wird und mit Ionenkan{\"a}len und anderen myozyt{\"a}ren Membranproteinen wie Cav1.2, Caveolin 3 und NCX1 kolokalisiert ist. Im ventrikul{\"a}ren Reizleitungssystem ist die Expression von Popdc1 gegen{\"u}ber dem ventrikul{\"a}ren Arbeitsmyokard erh{\"o}ht, w{\"a}hrend Atrium und Sinusknoten nahezu {\"a}quivalente Expressionsdom{\"a}nen aufweisen. Mithilfe von elektrophysiologischen Untersuchungen konnte bei den Popdc1-Nullmutanten eine stressinduzierte Sinusbradykardie festgestellt werden, die altersabh{\"a}ngig auftritt und auf Sinuspausen zur{\"u}ckzuf{\"u}hren ist. Histologische Untersuchungen, unter Zuhilfenahme des Sinusknotenmarkers HCN4, zeigten einen Zellverlust im inferioren Teil des Sinusknotens. Popdc1 ist ein Transmembranprotein, das eine 150 Aminos{\"a}ure umfassende, stark konservierte Popeye-Dom{\"a}ne aufweist. F{\"u}r diese Dom{\"a}ne konnte auf struktureller Ebene eine Homologie zu zyklischen Nukleotid-Bindungsdom{\"a}nen vorhergesagt und eine Bindung an cAMP und cGMP experimentell demonstriert werden. Es handelt sich bei den Popdc-Proteinen um einen neuen Zweig der Bindungsproteine f{\"u}r zyklische Nukleotidmonophosphate (cNMP). Die Bindungssequenz weist signifikante Unterschiede zu anderen bereits identifizierten cNMP-Bindungsproteinen auf. Weiterhin wurde die Interaktion von Popdc1 mit TREK1, einem Mitglied der Tandemporenkan{\"a}le untersucht. Es zeigte sich, dass Popdc1 nach Koexpression in Froschoozyten, den TREK1-Strom erh{\"o}ht und dass die \&\#946;-adrenerge Inhibition des TREK1 Kanals durch Popdc1 verst{\"a}rkt wird. Im Arbeitsmyokard, im kardialen Reizleitungssystem und in kotransfizierten Cos7-Zellen werden beide Proteine {\"u}berlappend exprimiert. Diese Daten zeigen, dass Popdc1 eine wichtige Funktion bei der Regulation der Schrittmacheraktivit{\"a}t, der Aufrechterhaltung der Sinusknotenmorphologie und der Modulation von Ionenkan{\"a}len aufweist. Interessanterweise wurden von unserer Arbeitsgruppe bereits die gleichen Ph{\"a}notypen f{\"u}r die Popdc2 Maus beschrieben, sodass die Popdc Genfamilie {\"u}berlappende und redundante Funktionen aufweist.},
  subject      = {Sinusknoten},
  language  = {de}
}
@article{HeisswolfGablerObermaieretal.2007,
  author    = {Heisswolf, Annette and Gabler, Dirk and Obermaier, Elisabeth and M{\"u}ller, Caroline},
  title     = {Olfactory versus contact cues in host plant recognition of a monophagous chrysomelid beetle},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-49475},
  year      = {2007},
  abstract  = {The importance of olfactory versus contact cues for host plant recognition was investigated in the tortoise beetle Cassida canaliculata Laich. (Coleoptera: Chrysomelidae), which is strictly monophagous on meadow sage. The reaction of adult beetles to olfactory and contact host cues was tested using three bioassays (locomotion compensator, six-chamber-olfactometer, stem arena') to account for different behavioral contexts. Bioassay-guided fractionation of plant extracts was elaborated to characterize the nature of contact stimuli. The beetles were only slightly attracted to odors from small amounts of leaf material. However, when contact cues were provided additionally, the beetles showed strong preferences for samples of their host plant over controls. Bioassay-guided fractionation led to isolation of at least two non-polar contact stimuli acting in concert that are sufficient for host plant identification in C. canaliculata.},
  subject      = {Insekt},
  language  = {en}
}
@phdthesis{Wang2011,
  author    = {Wang, Huiqiang},
  title     = {Enhanced Replication of Vaccinia Virus GLV-1h68 in Cancer Stem-like Cells of Human Breast Cancer Cell Preparations},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-64750},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {There is more and more evidence for the cancer stem cell hypothesis which believes that cancers are driven by a cellular subcomponent that has stem cell properties which is self-renewal, tumorigenicity and multilineage differentiation capacity. Cancer stem cells have been connected to the initiation of tumors and are even found to be responsible for relapses after apparently curative therapies have been undertaken. This hypothesis changes our conceptual approach of oncogenesis and shall have implications in breast cancer prevention, detection and treatment, especially in metastatic breast cancer for which no curative treatment exists. Given the specific stem cell features, novel therapeutic pathways can be targeted. Since the value of vaccinia virus as a vaccination virus against smallpox was discovered by E. Jenner at 18th century, it plays an important role in human medicine and molecular biology. After smallpox was successfully eradicated, vaccinia virus is mainly used as a viral vector in molecular biology and increasingly in cancer therapy. The outstanding capability to specifically target and destroy cancer cells makes it a perfect agent for oncolytic virotherapy. Furthermore, the virus can easily be modified by inserting genes which encode therapeutic or diagnostic proteins to be expressed when a tumor is infected. The emphasis in this study was the establishment of methods for the enrichment of human breast cancer stem-like cells from cancer cell lines and characterization of those cancer stem-like cells in vitro and in vivo. Furthermore, by using the Genelux Corporation vaccinia virus strain GLV-1h68, the isolated cancer stem-like cells can be targeted not only in vitro but also in vivo more efficiently. Side-population (SP) cells within cancers and cell lines are rare cell populations known to be enriched cancer stem-like cells. In this study, we used Hoechst 33342 staining and flow cytometry to identify SP cells from the human breast cancer cell lines MCF-7 and GI-101A as models for cancer stem-like cells. Considering the cytotoxicity of Hoechst dye and the restriction of instrument, we did not carry out further studies by this method. Utilizing in vitro and in vivo experimental systems, we showed that human breast cancer cell line GI-101A with aldehyde dehydrogenase activity (ALDH) have stemlike properties. Higher ALDH activity identifies the tumorigenic cell fraction which is capable of self-renewal and of generating tumors that could recapitulate the heterogeneity of the parental tumor. Furthermore, the cells with higher ALDH activity display significant resistance to chemotherapy and ionizing radiation, which proves their stem-like properties again. The cells which have higher ALDH activity also are more invasive compared to cells which have lower ALDH activity, which connects the cancer stem-like cells with cancer metastases. By analyzing the popular human breast cancer stem cells surface markers CD44, CD49f and CD24, it was discovered that the cells with higher ALDH activity have stronger CD44 and CD49f expression than in those cells with lower ALDH activity, which further confirms their stem-like properties. Finally, the cells with higher ALDH activity and lower ALDH activity were infected in vitro and used in virotherapy in a mouse xenograft model was performed. The results indicated that the vaccinia virus GLV-1h68 can replicate in cells with higher ALDH activity more efficiently than cells with lower ALDH activity. GLV-1h68 also can selectively target and eradicate the xenograft tumors which were derived from cells with higher ALDH activity. The epithelial-mesenchymal transition (EMT) is a key developmental program that is often activated during cancer invasion and metastases. EMT was induced in immortalized human mammary epithelial cells (HMLEs) and in GI-101A cells, which results in the acquisition of mesenchymal traits and in the expression of stem cell markers. Furthermore, the EMT-induced GI-101A cells showed resistance to chemotherapy and invasion capacity. CD44+/CD24- cells were enriched during the EMT induction. Following flow cytometry sorting by using CD44, CD24 and ESA surface marker, the sorted cells were tested in a mouse model regarding tumorigenicity. Unexpectedly, we found that CD44+/CD24+/ESA+ cells could initiate tumors more efficiently rather than CD44+/CD24-/ESA+ and other fractions in EMTinduced GI-101A cells. We also infected the CD44+/CD24+/ESA+ and CD44+/CD24- /ESA+ cells in vitro and performed virotherapy in a mouse xenograft model. The results indicated that the vaccinia virus GLV-1h68 is able to replicate in CD44+/CD24+/ESA+ cells more efficiently than in CD44+/CD24-/ESA+ cells. GLV-1h68 was also capable to selectively target and eradicate the xenograft tumors which derived from CD44+/CD24+/ESA+ cells. Moreover, CD44- cells have much lower tumorigenicity in the mouse model and CD44- cells derived-tumors are not responsive to vaccinia virotherapy. In summary, we have successfully established an in vitro and in vivo system for the identification, characterization and isolation of cancer stem-like cells from the human breast cancer cell line GI-101A by using the ALDEFLUOR assay. The vaccinia virus GLV-1h68 was able to efficiently target and eradicate the higher ALDH activity cells and tumors derived from those cells. Although contrary to the current assumption, CD44+/CD24+/ESA+ cells in the EMT-induced GI-101A cell line showed stem-like properties and GLV-1h68 was able to efficiently target and eradicate the CD44+/CD24+/ESA+ cells and tumors which derived from those cells. Finally, improved understanding of cancer stem cells may have tremendous relevance for how cancer should be treated. It is menacing that cancer stem cells are resistant to almost all anti-tumor approaches which have already been established for the treatment of metastatic diseases such as ionizing radiation, hormonal therapy, chemotherapy, and small molecular inhibitors. Therefore, it is promising that our results suggest that these cancer stem cells may be susceptible to treatment with oncolytic vaccinia virus.},
  subject      = {Vaccinia Virus},
  language  = {en}
}
@phdthesis{Kirchmaier2010,
  author    = {Kirchmaier, Bettina Carmen},
  title     = {Characterization of the Popeye domain containing gene family in zebrafish},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-49413},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {The Popeye domain containing (Popdc) gene family of membrane proteins is predominantly expressed in striated and smooth muscle tissues and has been shown to act as novel cAMP-binding proteins. In mice, loss of Popdc1 and Popdc2, respectively, affects sinus node function in the postnatal heart in an age and stress-dependent manner. In this thesis, I examined gene expression pattern and function of the Popdc gene family during zebrafish development with an emphasis on popdc2. Expression of the zebrafish popdc2 was exclusively present in cardiac and skeletal muscle during cardiac development, whereas popdc3 was expressed in striated muscle tissue and in distinct regions of the brain. In order to study the function of these genes, an antisense morpholino-based knockdown approach was used. Knockdown of popdc2 resulted in aberrant development of facial and tail musculature. In the heart, popdc2 morphants displayed irregular ventricular contractions with 2:1 and 3:1 ventricular pauses. Recordings of calcium transients using a transgenic indicator line Tg(cmlc2:gCaMP)s878 and selective plane illumination microscopy (SPIM) revealed the presence of an atrioventricular (AV) block in popdc2 morphants as well as a complete heart block. Interestingly, preliminary data revealed that popdc3 morphants developed a similar phenotype. In order to find a morphological correlate for the observed AV conduction defect, I studied the structure of the AV canal in popdc2 morphants using confocal analysis of hearts of the transgenic line Tg(cmlc2:eGFP-ras)s883, which outlines individual cardiac myocytes with the help of membrane-localized GFP. However, no evidence for morphological alterations was obtained. To ensure that the observed arrhythmia phenotype in the popdc2 morphant was based on a myocardial defect and not caused by defective valve development, live imaging was performed revealing properly formed valves. Thus, in agreement with the data obtained in knockout mice, popdc2 and popdc3 genes in zebrafish are involved in the regulation of cardiac electrical activity. However, both genes are not required for cardiac pacemaking, but they play essential roles in AV conduction. In order to elucidate the biological importance of cAMP-binding, wild type Popdc1 as well as mutants with a significant reduction in binding affinity for cAMP in vitro were overexpressed in zebrafish embryos. Expression of wild type Popdc1 led to a cardiac insufficiency phenotype characterized by pericardial edema and venous blood retention. Strikingly, the ability of the Popdc1 mutants to induce a cardiac phenotype correlated with the binding affinity for cAMP. These data suggest that cAMP-binding represents an important biological property of the Popdc protein family.},
  subject      = {Zebrab{\"a}rbling},
  language  = {en}
}
@phdthesis{Goeb2011,
  author    = {G{\"o}b, Eva},
  title     = {Die Kernh{\"u}lle in Keimzellen: Strukturelle Besonderheiten, dynamische Prozesse und die Umgestaltung des Zellkerns w{\"a}hrend der Spermatogenese der Maus},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-56839},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {Die Kernh{\"u}lle umgibt als geschlossenes Membransystem einen jeden Zellkern und ist damit ein gemeinsames Merkmal aller eukaryotischen Zellen. Sie besteht aus einer inneren und einer {\"a}ußeren Kernmembran sowie der nukleoplasmatischen Kernlamina, die aufgrund zahlreicher assoziierter Proteine in enger Wechselbeziehung mit der inneren Kernmembran steht. Neben der rein r{\"a}umlichen Trennung nukle{\"a}rer und zytoplasmatischer Strukturen hat die Kernh{\"u}lle bedeutenden regulatorischen Einfluss auf die gesamte Zelle. So ist sie unter anderem an der Steuerung der genomischen Aktivit{\"a}t, an der nukleo- und zytoplasmatischen Signal{\"u}bertragung und in hohem Maße an der Positionierung und Formerhaltung des Zellkerns beteiligt. Es mehren sich die Hinweise, dass die Kernh{\"u}lle auch w{\"a}hrend der Gametogenese, der Differenzierung befruchtungsf{\"a}higer Keimzellen, eine zentrale Rolle einnimmt und folglich auch mit bislang ungekl{\"a}rten Ursachen humaner Infertilit{\"a}t in Kontext stehen k{\"o}nnte. Um die Bedeutung der Kernh{\"u}lle f{\"u}r die Keimbahn der S{\"a}uger generell besser verstehen zu k{\"o}nnen, wurden in dieser Arbeit ausgew{\"a}hlte Bestandteile der Keimzellkernh{\"u}lle untersucht. Dadurch sollte der Kenntnisstand erweitert werden, in welcher Weise die Kernh{\"u}lle dynamische, morphologische und vor allem f{\"u}r die Keimbahn essentielle Prozesse beeinflusst; insbesondere w{\"a}hrend der meiotischen und der postmeiotischen Differenzierungsphase bei m{\"a}nnlichen M{\"a}usen. Im Mittelpunkt stand dabei einerseits Lamin C2, ein meiosespezifisches A-Typ Lamin, dessen Verlust zu einer schwer gesch{\"a}digten Meiose und infolgedessen zu vollst{\"a}ndiger m{\"a}nnlicher Infertilit{\"a}t f{\"u}hrt. Es zeigte sich, dass Lamin C2-defiziente m{\"a}nnliche M{\"a}use schwerwiegende Defekte bei der Paarung und Synapsis der homologen Chromosomen in der meiotischen Prophase I aufweisen und aufgrund apoptotischer Spermatocyten keine reifen Spermien bilden k{\"o}nnen. Es wird angenommen, dass die Assoziation homologer Chromosomen bzw. die Abstoßung nicht-homologer durch gerichtete Telomerbewegungen entlang der Kernh{\"u}llenperipherie vorangetrieben bzw. verhindert wird. Da Lamin C2 seinerseits diese Wanderung der Telomere durch eine Flexibilisierung der Spermatocytenkernh{\"u}lle vereinfachen soll, ist es durchaus vorstellbar, dass sein Verlust verlangsamte Telomerbewegungen, eine gest{\"o}rte Homologenfindung und folglich Fehlpaarungen zur Folge hat. Ein weiteres zentrales Thema war die Erforschung potentieller LINC-Komplexe w{\"a}hrend der Differenzierungs- und morphologischen Umgestaltungsphase postmeiotischer Keimzellen. LINC-Komplexe sind kernh{\"u}llendurchspannende Proteingebilde aus SUN-Proteinen in der inneren und Nesprinen in der {\"a}ußeren Kernmembran, die nukle{\"a}re Strukturen an das Zytoskelett binden. Da sie aufgrund dieser strukturellen Eigenschaft die Kernmorphologie beeinflussen k{\"o}nnen, erscheinen sie als {\"a}ußerst geeignet, an der Formierung des Spermienkopfes beteiligt zu sein. Die detaillierte Untersuchung spermiogeneserelevanter LINC-Komplex-Bestandteile ergab, dass w{\"a}hrend der Spermiogenese tats{\"a}chlich zwei neue, strukturell einzigartige LINC-Komplexe gebildet werden, die dar{\"u}ber hinaus auf den entgegengesetzten Seiten differenzierender Spermatiden polarisieren. Da sie den Kern dort an jeweils spezielle Zytoskelettelemente binden k{\"o}nnten, wurde in dieser Arbeit das Modell der LINC-Komplex vermittelten Umformung des Spermienkopfes aufgestellt. Insgesamt tr{\"a}gt diese Arbeit durch die funktionelle Analyse von Lamin C2 und die Identifizierung neuer LINC-Komplexe dazu bei, die Wichtigkeit der Kernh{\"u}lle f{\"u}r die Spermatogenese zu vertiefen und auszuweiten.},
  subject      = {Spermatogenese},
  language  = {de}
}
@phdthesis{Shityakov2011,
  author    = {Shityakov, Sergey},
  title     = {Molecular modelling and simulation of retroviral proteins and nanobiocomposites},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-56960},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {Molecular modelling and simulation are powerful methods in providing important in-formation on different biological systems to elucidate their structural and functional proper-ties, which cannot be determined in experiment. These methods are applied to analyse versa-tile biological systems: lipid membrane bilayers stabilized by an intercalated single wall carbon nanotube and retroviral proteins such as HIV protease and integrase. HIV-1 integrase has nuclear localization signals (NLS) which play a crucial role in nuclear import of viral preintegration complex (PIC). However, the detailed mechanisms of PIC formation and its nuclear transport are not known. Previously it was shown that NLSs bind to the cell transport machinery e.g. proteins of nuclear pore complex such as transportins. I investigated the interaction of this viral protein HIV-1 integrase with proteins of the nuclear pore complex such as transportin-SR2 (Shityakov et al., 2010). I showed that the transportin-SR2 in nuclear import is required due to its interaction with the HIV-1 integrase. I analyzed key domain interaction, and hydrogen bond formation in transportin-SR2. These results were discussed in comparison to other retroviral species such as foamy viruses to better understand this specific and efficient retroviral trafficking route. The retroviral nuclear import was next analyzed in experiments regarding the retroviral ability to infect nondividing cells. To accomplish the gene transfer task successfully, ret-roviruses must efficiently transduce different cell cultures at different phases of cell cycle. However, promising and safe foamy viral vectors used for gene transfer are unable to effi-ciently infect quiescent cells. This drawback was due to their inability to create a preintegra-tion complex (PIC) for nuclear import of retroviral DNA. On the contrary, the lentiviral vec-tors are not dependant on cell cycle. In the course of reverse transcription the polypurine tract (PPT) is believed to be crucial for PIC formation. In this thesis, I compared the transduction frequencies of PPT modified FV vectors with lentiviral vectors in nondividing and dividing alveolar basal epithelial cells from human adenocarcinoma (A549) by using molecular cloning, transfection and transduction techniques and several other methods. In contrast to lentiviral vectors, FV vectors were not able to effi-ciently transduce nondividing cell (Shityakov and Rethwilm, unpublished data). Despite the findings, which support the use of FV vectors as a safe and efficient alternative to lentiviral vectors, major limitation in terms of foamy-based retroviral vector gene transfer in quiescent cells still remains. Many attempts have been made recently to search for the potential molecules as pos-sible drug candidates to treat HIV infection for over decades now. These molecules can be retrieved from chemical libraries or can be designed on a computer screen and then synthe-sized in a laboratory. Most notably, one could use the computerized structure as a reference to determine the types of molecules that might block the enzyme. Such structure-based drug design strategies have the potential to save off years and millions of dollars compared to a more traditional trial-and-error drug development process. After the crystal structure of the HIV-encoded protease enzyme had been elucidated, computer-aided drug design played a pivotal role in the development of new compounds that inhibit this enzyme which is responsible for HIV maturation and infectivity. Promising repre-sentatives of these compounds have recently found their way to patients. Protease inhibitors show a powerful sustained suppression of HIV-1 replication, especially when used in combi-nation therapy regimens. However, these drugs are becoming less effective to more resistant HIV strains due to multiple mutations in the retroviral proteases. In computational drug design I used molecular modelling methods such as lead ex-pansion algorithm (Tripos®) to create a virtual library of compounds with different binding affinities to protease binding site. In addition, I heavily applied computer assisted combinato-rial chemistry approaches to design and optimize virtual libraries of protease inhibitors and performed in silico screening and pharmacophore-similarity scoring of these drug candidates. Further computational analyses revealed one unique compound with different protease bind-ing ability from the initial hit and its role for possible new class of protease inhibitors is dis-cussed (Shityakov and Dandekar, 2009). A number of atomistic models were developed to elucidate the nanotube behaviour in lipid bilayers. However, none of them provided useful information for CNT effect upon the lipid membrane bilayer for implementing all-atom models that will allow us to calculate the deviations of lipid molecules from CNT with atomistic precision. Unfortunately, the direct experimental investigation of nanotube behaviour in lipid bilayer remains quite a tricky prob-lem opening the door before the molecular simulation techniques. In this regard, more de-tailed multi-scale simulations are needed to clearly understand the stabilization characteristics of CNTs in hydrophobic environment. The phenomenon of an intercalated single-wall carbon nanotube in the center of lipid membrane was extensively studied and analyzed. The root mean square deviation and root mean square fluctuation functions were calculated in order to measure stability of lipid mem-branes. The results indicated that an intercalated carbon nanotube restrains the conformational freedom of adjacent lipids and hence has an impact on the membrane stabilization dynamics (Shityakov and Dandekar, 2011). On the other hand, different lipid membranes may have dissimilarities due to the differing abilities to create a bridge formation between the adherent lipid molecules. The results derived from this thesis will help to develop stable nanobiocom-posites for construction of novel biomaterials and delivery of various biomolecules for medi-cine and biology.},
  subject      = {Kohlenstoff},
  language  = {en}
}
@phdthesis{Hauber2011,
  author    = {Hauber, Melanie Erika},
  title     = {Description and Improvement of the 'Whedo'-Aquaculture-System in Malanville (North of Benin)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-57711},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {This work delves into the recently developed 'Whedo'-aquaculture-system in the rural community of Malanville (North Benin)and aims on providing a closer insight on this - for the area--recent system including the ecological but also the sociological and economical aspects in order to develop this extensive traditional fishery to a more productive semi-intensive aquaculture system. With the retreat of the flood 'Whedos' usually become infested with numerous hydato-and tenagophytes, while the presence and density of the free-floating macrophytes were positively related to the nutrient content of the 'Whedo'. Extensive plant infestation also affects water quality through the decomposition of organic material and its accumulation in thick mud layers on the pond bottom as well as through the nocturnal oxygen consumption. Unfavourable water quality, especially low dissolved oxygen as well as high conductivity and nitrite levels, was identified to be the main factor determining which fish species were able to survive the harsh conditions prevailing in the 'Whedos' during the dry season. With the deteriorating water quality with advancing dry season, fish diversity decreased significantly leaving only species that are highly adapted to such unfavourable conditions. The most abundant species were Clarias gariepinus, Heterotis niloticus, Oreochromis niloticus L., Hemichromis c.f. letourneauxi, Polypterus senegalus and Epiplatys spilargyreius. Besides, the investigations also concentrated on the fish diversity of the rivers Niger and Sota with the results that for three species distribution gaps could be closed and for further three species their already known distribution could be expanded. But otherwise it could also be detected that some economically important species that were abundant in the past. In regard to the 'Whedo'-management, the investigations showed that the owners lack most of the knowledge on appropriate management strategies, e.g. the feeding and stocking regime. The exploitation period depends on the extent of the previous annual flood and the location of the 'Whedo' within the floodplain, but the main season is from February to April. The biomass harvested on a hectare basis separated for each of the 'Whedos' averaged 17 tons/ha in 2008 and 8.6 tons/ha in 2009. However, 72 percent of the total biomass of Clarias only had an average weight of 40 grams. Therefore, two separated feeding trials were conducted and in total 6 supplementary feeds were tested on Clarias gariepinus. Groundnut cake, fish trash, rice bran, blood meal and azolla meal were used in different combination and rations to formulate the experimental diets. Diet containing 19 percent blood meal resulted in the best economical benefits showing that the use of high quality feed ingredients such as groundnut cake is not recommendable because local fish prices are too low to compensate the additional feeding costs. Instead of high quality feed farmers should focus on ingredients that are free of charge and easy to process. The supplementation based on 19 percent blood meal resulted in the doubling of the net profit compared to the income based on feeding only rice bran, thus provided higher additional income, enhancing the livelihood of the fish farmers. Concluding, the 'Whedo'-aquaculture system is still in its infancy but nevertheless is an attractive system for the rural population because of existing knowledge of post-flood wetland fisheries as well as the low investment needed for its installation. Additionally, the local fish supply will increase and hence not only contribute to a better provision of protein-rich food and reduced pressure on the wild fish stocks but might also prevent fish prices to increase in a way that the poor won't be able anymore to afford their most important source of animal protein. But fish farmers need more knowledge on appropriate management strategies and thus should be provided with technical support to guarantee a successful development and not to discourage the owners as a consequence of avoidable failures. Furthermore, the use of supplementary feed offers a cheap and effective means to increase the biomass production and thus enhance the extensive fishery to a semi-intensive aquaculture system.},
  subject      = {Aquakultur},
  language  = {en}
}
@phdthesis{Weiss2011,
  author    = {Weiß, Sabine},
  title     = {Function of the Spir actin nucleators in intracellular vesicle transport processes},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-64589},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {Spir proteins are the founding members of the novel class of WH2-actin nucleators. A C-terminal modified FYVE zinc finger motif is necessary to target Spir proteins towards intracellular membranes. The function and regulation of the Spir actin organizers at vesicular membranes is almost unknown. Live cell imaging analyses performed in this study show that Spir-2 is localized at tubular vesicles. Cytoplasmic Spir-2-associated vesicles branch and form protrusions, which can make contacts to the microtubule network, where the Spir-2 vesicles stretch and slide along the microtubule filaments. The analysis of living HeLa cells expressing eGFP-tagged Spir-2, Spir-2-ΔKIND and Spir-2-ΔKW (lacking the 4 WH2 domains and the KIND domain) showed Spir-2-associated tubular structures which differ in their length and motility. Throughout the course of that study it could be shown that the tail domain of the actin motor protein myosin Vb, as a force-generating molecule, is colocalizing and co-immunoprecipitating with Spir-2-ΔKW. By using the tail domain of myosin Vb as a dominant negative mutant for myosin Vb-dependent vesicle transport processes it could be shown that Spir-2-ΔKW/MyoVb-cc-tail- associated vesicles exhibit an increased elongation. Moreover, using the microtubule depolymerizing drug nocodazole it could be shown that the elongation and the motility of Spir-2-ΔKW-associated vesicles depends on an intact microtubule cytoskeleton. Motility and morphological dynamics of Spir-2-associated vesicles is therefore dependent on actin, actin motorproteins and microtubule filaments. These results propose a model in which myosin/F-actin forces mediate vesicle branching, allowing the vesicles to move to and in between the microtubule filaments and thereby providing a new degree of freedom in vesicular motility. To determine the exact subcellular localization of Spir-2, colocalization studies were performed. It could be shown that Spir-2 shows a partial colocalization to Rab11a-positive compartments. Furthermore, Spir-2 exhibits an almost identical localization to Arf1 and the Arf1 small G protein but not Rab11a could be immunoprecipitated with Spir-2-ΔKW. This suggests, that Arf1 recruits Spir-2 to Arf1/Rab11a-positive membranes. Another important function of the Spir-2 C-terminus is the membrane targeting by the FYVE domain. By performing a protein-lipid overlay assay, it has been shown that purified GST- and 6xHis-tagged Spir-2-ΔKW bind phosphatidic acid suggesting a mechanism in which Spir-2 is recruited to phosphatidic acid-enriched membranes. To further elucidate the mechanism in which Spir-2 membrane-targeting could be regulated, interaction studies of C-terminal parts of Spir-2 revealed that the Spir-2 proteins interact directly.},
  subject      = {Aktin},
  language  = {en}
}