@article{GoetzEylertEisenreichetal.2010,
  author    = {Goetz, Andreas and Eylert, Eva and Eisenreich, Wolfgang and Goebel, Werner},
  title     = {Carbon Metabolism of Enterobacterial Human Pathogens Growing in Epithelial Colorectal Adenocarcinoma (Caco-2) Cells},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-68555},
  year      = {2010},
  abstract  = {Analysis of the genome sequences of the major human bacterial pathogens has provided a large amount of information concerning their metabolic potential. However, our knowledge of the actual metabolic pathways and metabolite fluxes occurring in these pathogens under infection conditions is still limited. In this study, we analysed the intracellular carbon metabolism of enteroinvasive Escherichia coli (EIEC HN280 and EIEC 4608-58) and Salmonella enterica Serovar Typhimurium (Stm 14028) replicating in epithelial colorectal adenocarcinoma cells (Caco-2). To this aim, we supplied [U-13C6]glucose to Caco-2 cells infected with the bacterial strains or mutants thereof impaired in the uptake of glucose, mannose and/or glucose 6-phosphate. The 13C-isotopologue patterns of protein-derived amino acids from the bacteria and the host cells were then determined by mass spectrometry. The data showed that EIEC HN280 growing in the cytosol of the host cells, as well as Stm 14028 replicating in the Salmonella-containing vacuole (SCV) utilised glucose, but not glucose 6-phosphate, other phosphorylated carbohydrates, gluconate or fatty acids as major carbon substrates. EIEC 4608-58 used C3-compound(s) in addition to glucose as carbon source. The labelling patterns reflected strain-dependent carbon flux via glycolysis and/or the Entner-Doudoroff pathway, the pentose phosphate pathway, the TCA cycle and anapleurotic reactions between PEP and oxaloacetate. Mutants of all three strains impaired in the uptake of glucose switched to C3-substrate(s) accompanied by an increased uptake of amino acids (and possibly also other anabolic monomers) from the host cell. Surprisingly, the metabolism of the host cells, as judged by the efficiency of 13C-incorporation into host cell amino acids, was not significantly affected by the infection with either of these intracellular pathogens.},
  subject      = {Metabolismus},
  language  = {en}
}
@phdthesis{Hacker2010,
  author    = {Hacker, Christian},
  title     = {Beteiligung des Major Vault Proteins an der Kernporenkomplexbildung},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51279},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {In die Kernmembran von Eukaryoten sind Kernporenkomplexe eingelagert. Diese stellen die einzige Verbindung zwischen dem Nukleo- und Zytoplasma dar und vermitteln den gerichteten Transport von Proteinen und Ribonukleoproteinpartikeln {\"u}ber die Kernh{\"u}lle. Durch vorangehende Versuche unserer Arbeitsgruppe konnte gezeigt werden, dass es experimentell m{\"o}glich ist, die Bildung einer kontinuierlichen Doppelmembran von der Insertion der Kernporenkomplexe zu trennen (Ewald et al., 1997). Dabei spielen verschiedene im Extrakt enthaltene Membranfraktionen eine Rolle. Erst k{\"u}rzlich wurden in unserer Arbeitsgruppe zwei unterschiedliche Membranfraktionen aus Xenopus Extrakt isoliert, die aufgrund ihrer Dichte als 40\% und 30\% Membranfraktion benannt wurden. Massenspektrometrische Untersuchungen zeigten, dass sich in der 30\% Membranfraktion, welche f{\"u}r die Kernporenkomplexbildung verantwortlich zu sein scheint, das Major Vault Protein (MVP) befindet. MVP ist Hauptbestandteil der Vault-Komplexe, großer tonnenf{\"o}rmiger Ribonukleoproteinpartikel, denen bislang eine Vielzahl von zellul{\"a}ren Funktionen zugeordnet wurden, die meisten davon jedoch noch stark debattiert. Vaults k{\"o}nnten wom{\"o}glich eine Rolle als Transporter {\"u}ber die Kernporenkomplexe spielen und wurden schon mehrfach mit dem Aufbau einer multiplen Arzneimittelresistenz in Verbindung gebracht. Die Beteiligung von MVP bei der Bildung der Kernporenkomplexe ist eine neue zellul{\"a}re Funktion und sollte deshalb in dieser Arbeit n{\"a}her untersucht werden. In dieser Arbeit wurden zun{\"a}chst die 40\% und 30\% Membranfraktionen auf ihr unterschiedliches Verhalten bei der Bildung der Kernh{\"u}lle separat und in Kombination genauer untersucht. Dabei zeigte sich, dass die 40\% Membranfraktion an Chromatin bindet und eine kontinuierliche Doppelmembran aufbaut. Die 30\% Membranfraktion konnte alleine nicht an Chromatin binden, induzierte aber in der durch die 40\% Membranfraktion gebildeten Doppelmembran den Aufbau von Kernporenkomplexen. Durch Immunfluoreszenzaufnahmen und ultrastrukturelle Untersuchungen wurde belegt, dass das an der 30\% Membranfraktion assoziierte MVP f{\"u}r die Bildung von Kernporenkomplexen verantwortlich war. Ferner konnten wir zeigen, dass sowohl MVP als auch Vault-Partikel die de novo Insertion von Kernporenkomplexen in kontinuierliche Doppelmembranen induzieren konnten. Die molekularen Mechanismen der Kernporenkomplexbildung durch MVP wurden mit Hilfe von artifiziellen Lipidmembranen analysiert. Anhand von unilamellaren Liposomen und elektronenmikroskopischen Aufnahmen konnte gezeigt werden, dass MVP die Lipidstruktur beeinflussen und perforieren kann. Zudem l{\"o}ste MVP die Bildung von Poren in schwarzen Lipidmembranen aus und f{\"u}hrte zur Messung von Str{\"o}men durch Einzelkanalmessungen {\"u}ber die entstandenen Poren. Um die bei dem Prozess der Kernporenkomplexbildung beteiligten Bindungspartner von MVP zu identifizieren, wurden mehrere Protein-Protein-Bindungsstudien durchgef{\"u}hrt. Unter den ermittelten MVP-Bindungspartnern ließen sich keine Nukleoporine mit dem Sequenzmotiv FXFG identifizieren, es ist jedoch nicht auszuschließen, dass MVP bei der Bildung der Kernporenkomplexe mit anderen Nukleoporinen interagiert. Da eine fr{\"u}here Arbeit die Bedeutung von Mikrotubuli bei der Bildung der Kernporenkomplexe aufzeigte (Ewald et al., 2001), wurden in dieser Arbeit die Interaktionen der isolierten 40\% und 30\% Membranfraktionen und von MVP mit dem Mikrotubulinetzwerk n{\"a}her analysiert. Dabei zeigte sich, dass nur die 30\% Membranfraktion mit Mikrotubuli interagierte und eine Inhibition der Mikrotubulipolymerisation durch Colchizin den Einbau von Kernporenkomplexen verhinderte. Im Gegensatz dazu interagierten die 40\% Membranvesikel nicht mit Mikrotubuli und daher hat eine Colchizin-induzierte Inhibition der Mikrotubulipolymerisation keinen Effekt auf den Aufbau einer kontinuierlichen Doppelmembran. Durch immunfluoreszenzmikroskopische Untersuchungen konnte zudem gezeigt werden, dass die Lokalisation von MVP an der Kernh{\"u}lle ebenfalls Abh{\"a}ngig von Mikrotubuli ist. Um zu demonstrieren, dass die MVP-induzierte Kernporenkomplexbildung im zellfreien System abh{\"a}ngig vom Transport von MVP zur Kernh{\"u}lle ist, wurde die Zugabe von MVP zu porenlosen Kernen nach einer Colchizin-Behandlung analysiert. Hierbei konnte belegt werden, dass MVP Mikrotubuli auch ben{\"o}tigt, um die Bildung von Kernporenkomplexen in der Kernmembran zu initiieren. Da Mikrotubulifilamente im zellfreien System mit ihren Plus-Enden gegen die Chromatinoberfl{\"a}che gerichtet sind, sollten f{\"u}r den gerichteten Transport zum Chromatin Motorproteine der Kinesin-Familie eine Rolle spielen. Durch die Inhibition von Mklp2, einem mitotischen Kinesin, konnte der Aufbau der Kernporenkomplexe durch MVP in porenlosen Kernen blockiert werden.},
  subject      = {Ribonucleoproteine},
  language  = {de}
}
@article{StollFeldhaarFraunholzetal.2010,
  author    = {Stoll, Sascha and Feldhaar, Heike and Fraunholz, Martin J. and Gross, Roy},
  title     = {Bacteriocyte dynamics during development of a holometabolous insect, the carpenter ant Camponotus floridanus},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67950},
  year      = {2010},
  abstract  = {Background: The carpenter ant Camponotus floridanus harbors obligate intracellular mutualistic bacteria (Blochmannia floridanus) in specialized cells, the bacteriocytes, intercalated in their midgut tissue. The diffuse distribution of bacteriocytes over the midgut tissue is in contrast to many other insects carrying endosymbionts in specialized tissues which are often connected to the midgut but form a distinct organ, the bacteriome. C.floridanus is a holometabolous insect which undergoes a complete metamorphosis. During pupal stages a complete restructuring of the inner organs including the digestive tract takes place. So far, nothing was known about maintenance of endosymbionts during this life stage of a holometabolous insect. It was shown previously that the number of Blochmannia increases strongly during metamorphosis. This implicates an important function of Blochmannia in this developmental phase during which the animals are metabolically very active but do not have access to external food resources. Previous experiments have shown a nutritional contribution of the bacteria to host metabolism by production of essential amino acids and urease-mediated nitrogen recycling. In adult hosts the symbiosis appears to degenerate with increasing age of the animals. Results: We investigated the distribution and dynamics of endosymbiotic bacteria and bacteriocytes at different stages during development of the animals from larva to imago by confocal laser scanning microscopy. The number of bacteriocytes in relation to symbiont-free midgut cells varied strongly over different developmental stages. Especially during metamorphosis the relative number of bacteria-filled bacteriocytes increased strongly when the larval midgut epithelium is shed. During this developmental stage the midgut itself became a huge symbiotic organ consisting almost exclusively of cells harboring bacteria. In fact, during this phase some bacteria were also found in midgut cells other than bacteriocytes indicating a cell-invasive capacity of Blochmannia. In adult animals the number of bacteriocytes generally decreased. Conclusions: During the life cycle of the animals the distribution of bacteriocytes and of Blochmannia endosymbionts is remarkably dynamic. Our data show how the endosymbiont is retained within the midgut tissue during metamorphosis thereby ensuring the maintenance of the intracellular endosymbiosis despite a massive reorganization of the midgut tissue. The transformation of the entire midgut into a symbiotic organ during pupal stages underscores the important role of Blochmannia for its host in particular during metamorphosis.},
  subject      = {Camponotus floridanus},
  language  = {en}
}
@phdthesis{Vainshtein2010,
  author    = {Vainshtein, Yevhen},
  title     = {Applying microarray-based techniques to study gene expression patterns: a bio-computational approach},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51967},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {The regulation and maintenance of iron homeostasis is critical to human health. As a constituent of hemoglobin, iron is essential for oxygen transport and significant iron deficiency leads to anemia. Eukaryotic cells require iron for survival and proliferation. Iron is part of hemoproteins, iron-sulfur (Fe-S) proteins, and other proteins with functional groups that require iron as a cofactor. At the cellular level, iron uptake, utilization, storage, and export are regulated at different molecular levels (transcriptional, mRNA stability, translational, and posttranslational). Iron regulatory proteins (IRPs) 1 and 2 post-transcriptionally control mammalian iron homeostasis by binding to iron-responsive elements (IREs), conserved RNA stem-loop structures located in the 5'- or 3'- untranslated regions of genes involved in iron metabolism (e.g. FTH1, FTL, and TFRC). To identify novel IRE-containing mRNAs, we integrated biochemical, biocomputational, and microarray-based experimental approaches. Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Methods In this project response to the iron treatment was examined under different conditions using bioinformatical methods. This would improve our understanding of an iron regulatory network. For these purposes we used microarray gene expression data. To identify novel IRE-containing mRNAs biochemical, biocomputational, and microarray-based experimental approaches were integrated. IRP/IRE messenger ribonucleoproteins were immunoselected and their mRNA composition was analysed using an IronChip microarray enriched for genes predicted computationally to contain IRE-like motifs. Analysis of IronChip microarray data requires specialized tool which can use all advantages of a customized microarray platform. Novel decision-tree based algorithm was implemented using Perl in IronChip Evaluation Package (ICEP). Results IRE-like motifs were identified from genomic nucleic acid databases by an algorithm combining primary nucleic acid sequence and RNA structural criteria. Depending on the choice of constraining criteria, such computational screens tend to generate a large number of false positives. To refine the search and reduce the number of false positive hits, additional constraints were introduced. The refined screen yielded 15 IRE-like motifs. A second approach made use of a reported list of 230 IRE-like sequences obtained from screening UTR databases. We selected 6 out of these 230 entries based on the ability of the lower IRE stem to form at least 6 out of 7 bp. Corresponding ESTs were spotted onto the human or mouse versions of the IronChip and the results were analysed using ICEP. Our data show that the immunoselection/microarray strategy is a feasible approach for screening bioinformatically predicted IRE genes and the detection of novel IRE-containing mRNAs. In addition, we identified a novel IRE-containing gene CDC14A (Sanchez M, et al. 2006). The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip, but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls (Vainshtein Y, et al., 2010).},
  subject      = {Microarray},
  language  = {en}
}
@article{SchmidSchindelinCardonaetal.2010,
  author    = {Schmid, Benjamin and Schindelin, Johannes and Cardona, Albert and Longair, Martin and Heisenberg, Martin},
  title     = {A high-level 3D visualization API for Java and ImageJ},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67851},
  year      = {2010},
  abstract  = {Background: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Results: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Conclusions: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.},
  subject      = {Visualisierung},
  language  = {en}
}