@phdthesis{Woelke2010,
  author    = {W{\"o}lke, Stefan},
  title     = {Funktionelle Analyse von bakteriellen W-xxx-E Rho GTPasen GEF Mimetika mittels Typ 3 Sekretionssystems von Yersinia enterocolitica},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-55010},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Die zellul{\"a}ren Rho GTPasen kontrollieren und regulieren zentrale elementare Zellvorg{\"a}nge wie Phagozytose, Migration und epitheliale Integrit{\"a}t. Aufgrund ihrer zentralen Stellung, interagiert eine Vielzahl von bakteriellen Cytotoxinen und Modulinen mit den Rho GTPasen und wirken so als Pathogenit{\"a}tsfaktoren. Die zur W-xxx-E Familie geh{\"o}renden Effektoren IpgB1 und IpgB2 von Shigella und Map von E. coli (Pathotypen EHEC und EPEC) werden {\"u}ber ein Typ 3 Sekretionssystem (T3SS) in Wirtszellen injiziert und wirken als Rac1, RhoA bzw. Cdc42 GEF Mimetikum. In der vorliegenden Arbeit wurden die Effektor Funktionen von IpgB1 IpgB2 und Map mit Hilfe des Yersinia (Ysc)-T3SS untersucht, was zur Etablierung der „Yersinia-Toolbox" f{\"u}hrte. Damit k{\"o}nnen heterologe Effektoren isoliert im physiologischen Kontext der Erreger-Zell-Interaktion zellbiologisch untersucht werden unter Vermeidung von simultaner Injektion redundanter oder unbekannter Effektoren. Zur Etablierung der Yersinia-Toolbox wurden zun{\"a}chst die Gene f{\"u}r die Rho GTPasen modulierenden Shigella Effektoren IpgB1 und IpgB2 sowie der E. coli (EHEC)-Effektor Map mit unterschiedlich langen Gensequenzen der N-terminalen Bereiche des Yersinia-Effektorproteins YopE fusioniert (Hybridproteine: YopEi-X:i = 18, 53 bzw. 138 Aminos{\"a}urereste, X = IpgB1, IpgB2 bzw. Map). In der vorliegenden Arbeit wird gezeigt, dass die Hybridproteine YopE53-X und YopE138-X (X=IpgB1, IpgB2, Map) in den Kultur{\"u}berstand sezerniert bzw. in Zielzellen injiziert wurden. In einem weiteren Schritt konnte die zellbiologische Aktivit{\"a}t der heterologen Proteine fluoreszenzmikroskopisch durch Aktinzytoskelettumlagerungen gezeigt werden. So wurden „Membrane Ruffles" (Rac1-Aktivierung) durch YopE138-IpgB1, Stressfasern (RhoA-Aktivierung) durch E138-IpgB2 und „Mikrospikes" (Cdc42-Aktivierung) durch YopE138-Map nachgewiesen. Invasionstudien zeigten, dass YopEi-IpgB1 (i = 53, 138) die Yersinia-Invasion induzierte, wohingegen YopEi-IpgB2 die Invasionsrate der St{\"a}mme WA (pT3SS, pEi-IpgB2) (i=53, 138) verglichen mit dem Stamm WA (pT3SS) reduziert war. Durch Kombination verschiedener Yersinia-Toolbox-St{\"a}mme konnte im Co-Infektionsmodell mit HeLa-Zellen gezeigt werden, dass (1) die YopE138-IpgB1 vermittelte Invasion durch YopE138-IpgB2 signifikant inhibiert werden kann, was auf eine antagonistische Wirkung zwischen IpgB1 und IpgB2 schließen l{\"a}sst, dass (2) YopT ebenfalls die IpgB1 vermittelte Invasionsrate reduziert (inhibitorische Wirkung auf Rac1), und dass (3) YopE als GAP f{\"u}r RhoG/Rac1 (bevorzugt RhoG) praktisch nicht die IpgB1-vermittelte Invasion hemmt. Durch Klonierung der YopE138-IpgB1 und YopE138-IpgB2 kodierenden Fusionsgene in zwei kompatible Plasmidvektoren konnten die Hybridproteine simultan transloziert werden und die Co-Infektionsergebnisse best{\"a}tigt werden. In der Literatur ist beschrieben, dass die Ysc-Translokationspore YopB/YopD Rho-abh{\"a}ngig Membranporen-bedingte Zellsch{\"a}digungen verursacht (LDH-Freisetzung, PI-Kernf{\"a}rbung). Mit der Yersinia-Toolbox konnte mit dem Stamm WA (pT3SS) Zytoplasmamembransch{\"a}digung / Zytotoxizit{\"a}t nachgewiesen werden, nicht aber mit den St{\"a}mmen WA (pE138-X) X = IpgB1, IpgB2 oder Map. Co-Infektionen jedoch zeigen, dass vermehrt LDH bei der Infektion mit WA (pT3SS) + WA (pT3SS, pE138-IpgB1) detektiert wurde, wohingegen dieser Effekt von YopE138-IpgB2 in einer Co-Infektion von WA (pT3SS) + WA (pT3SS, pE138-IpgB2) inhibiert wurde. Auch hier wurde der Antagonismus zwischen IpgB1 und IpgB2 erneut sichtbar. Diese Befunde widersprechen publizierten Daten, die eine RhoA-Aktivierung/Aktinpolymerisierung mit verst{\"a}rkter Porenbildung in einen Zusammenhang bringen. Rho GTPasen sind beteiligt an der Erhaltung der polarisierten Eipthelzellschichtintegrit{\"a}t {\"u}ber Adh{\"a}sionskomplexbildung. Mittels Infektion von polarisierten MDCK-Zellschichten mit verschiedenen Yersinia-St{\"a}mmen und Messung des transepithelialen elektrischen Widerstandes/Resistenz (TER) konnte gezeigt werden, dass die Ysc-T3SS vermittelte Injektion von YopE138-IpgB1 (Rac1-Aktivierung) oder YopE138-Map (Cdc42-Aktivierung) zur Abnahme der TER und damit Sch{\"a}digung der Zellschichtintegrit{\"a}t f{\"u}hrt, wogegen bei YopE138-IpgB2-Injektion der TER-Wert unver{\"a}ndert blieb. Um bakterielle Rho GTPasen-modulierende Effektorproteine detailliert untersuchen zu k{\"o}nnen und um die Rolle von Rho GTPasen im Mausinfektionsmodell mit Yersinia enterocolitica und Salmonellen zu bestimmen, wurden M{\"a}use mit deletierten Genen f{\"u}r RhoA, Rac1 bzw. Cdc42 in Makrophagen hergestellt.},
  subject      = {Actin},
  language  = {de}
}
@article{PoethkeHovestadt2002,
  author    = {Poethke, Hans J. and Hovestadt, Thomas},
  title     = {Evolution of density-and patch-size-dependent dispersal rates},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-49659},
  year      = {2002},
  abstract  = {Based on a marginal value approach, we derive a nonlinear expression for evolutionarily stable (ES) dispersal rates in a metapopulation with global dispersal. For the general case of density-dependent population growth, our analysis shows that individual dispersal rates should decrease with patch capacity and-beyond a certain threshold-increase with population density. We performed a number of spatially explicit, individual-based simulation experiments to test these predictions and to explore further the relevance of variation in the rate of population increase, density dependence, environmental fluctuations and dispersal mortality on the evolution of dispersal rates. They confirm the predictions of our analytical approach. In addition, they show that dispersal rates in metapopulations mostly depend on dispersal mortality and inter-patch variation in population density. The latter is dominantly driven by environmental fluctuations and the rate of population increase. These conclusions are not altered by the introduction of neighbourhood dispersal. With patch capacities in the order of 100 individuals, kin competition seems to be of negligible importance for ES dispersal rates except when overall dispersal rates are low.},
  subject      = {Metapopulation},
  language  = {en}
}
@phdthesis{Knapek2010,
  author    = {Knapek, Stephan},
  title     = {Synapsin and Bruchpilot, two synaptic proteins underlying specific phases of olfactory aversive memory in Drosophila melanogaster},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-49726},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Memory is dynamic: shortly after acquisition it is susceptible to amnesic treatments, gets gradually consolidated, and becomes resistant to retrograde amnesia (McGaugh, 2000). Associative olfactory memory of the fruit fly Drosophila melanogaster also shows these features. After a single associative training where an odor is paired with electric shock (Quinn et al., 1974; Tully and Quinn, 1985), flies form an aversive odor memory that lasts for several hours, consisting of qualitatively different components. These components can be dissociated by mutations, their underlying neuronal circuitry and susceptibility to amnesic treatments (Dubnau and Tully, 1998; Isabel et al., 2004; Keene and Waddell, 2007; Masek and Heisenberg, 2008; Xia and Tully, 2007). A component that is susceptible to an amnesic treatment, i.e. anesthesia-sensitive memory (ASM), dominates early memory, but decays rapidly (Margulies et al., 2005; Quinn and Dudai, 1976). A consolidated anesthesia-resistant memory component (ARM) is built gradually within the following hours and lasts significantly longer (Margulies et al., 2005; Quinn and Dudai, 1976). I showed here that the establishment of ARM requires less intensity of shock reinforcement than ASM. ARM and ASM rely on different molecular and/or neuronal processes: ARM is selectively impaired in the radish mutant, whereas for example the amnesiac and rutabaga genes are specifically required for ASM (Dudai et al., 1988; Folkers et al., 1993; Isabel et al., 2004; Quinn and Dudai, 1976; Schwaerzel et al., 2007; Tully et al., 1994). The latter comprise the cAMP signaling pathway in the fly, with the PKA being its supposed major target (Levin et al., 1992). Here I showed that a synapsin null-mutant encoding the evolutionary conserved phosphoprotein Synapsin is selectively impaired in the labile ASM. Further experiments suggested Synapsin as a potential downstream effector of the cAMP/PKA cascade. Similar to my results, Synapsin plays a role for different learning tasks in vertebrates (Gitler et al., 2004; Silva et al., 1996). Also in Aplysia, PKA-dependent phosphorylation of Synapsin has been proposed to be involved in regulation of neurotransmitter release and short-term plasticity (Angers et al., 2002; Fiumara et al., 2004). Synapsin is associated with a reserve pool of vesicles at the presynapse and is required to maintain vesicle release specifically under sustained high frequency nerve stimulation (Akbergenova and Bykhovskaia, 2007; Li et al., 1995; Pieribone et al., 1995; Sun et al., 2006). In contrast, the requirement of Bruchpilot, which is homologous to the mammalian active zone proteins ELKS/CAST (Wagh et al., 2006), is most pronounced in immediate vesicle release (Kittel et al., 2006). Under repeated stimulation of a bruchpilot mutant motor neuron, immediate vesicle release is severely impaired whereas the following steady-state release is still possible (Kittel et al., 2006). In line with that, knockdown of the Bruchpilot protein causes impairment in clustering of Ca2+ channels to the active zones and a lack of electron-dense projections at presynaptic terminals (T-bars). Thus, less synaptic vesicles of the readily-releasable pool are accumulated to the release sites and their release probability is severely impaired (Kittel et al., 2006; Wagh et al., 2006). First, I showed that Bruchpilot is required for aversive olfactory memory and localized the requirement of Bruchpilot to the Kenyon cells of the mushroom body, the second-order olfactory interneurons in Drosophila. Furthermore, I demonstrated that Bruchpilot selectively functions for the consolidated anesthesia-resistant memory. Since Synapsin is specifically required for the labile anesthesia sensitive memory, different synaptic proteins can dissociate consolidated and labile components of olfactory memory and two different modes of neurotransmission (high- vs. low frequency dependent) might differentiate ASM and ARM.},
  subject      = {Taufliege},
  language  = {en}
}
@phdthesis{Ruchty2010,
  author    = {Ruchty, Markus},
  title     = {Sensory basis of thermal orientation in leaf-cutting ants},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48906},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Leaf-cutting ants have a highly developed thermal sense which the insects use to regulate the own body temperature and also to optimize brood and fungus development. Apart from the already described temperature guided behaviors inside the nest it is unknown to what extent the ants may use their thermal sense outside the nest. As part of the present thesis, the question was addressed whether leaf-cutting ants (Atta vollenweideri) are able to learn the position of a warm object as landmark for orientation during foraging. Using absolute conditioning, it was shown that ten training trials are sufficient to elicit the association be-tween food reward and the temperature stimulus. In the test situation (without reward) a significantly higher amount of ants preferred the heated site compared to the unheated con-trol. Importantly, thermal radiation alone was sufficient to establish the learned association and served as orientation cue during the test situation (chapter IV). Based on the experi-mental design used in the previous chapter, the localization of thermosensitive neurons, which detect the underlying thermal stimuli, is restricted to the head or the antennae of the ants. The antennal sensillum coeloconicum is a potential candidate to detect the thermal stimuli during the orientation behavior. In chapter V the sensillum coeloconicum of Atta vollenweideri was investigated concerning its gross morphology, fine-structure and the phy-siology of the associated thermosensitive neuron. The sensillum is predominantly located on the apical antennal segment (antennal tip) where around 12 sensilla are clustered, and it has a peg-in-pit morphology with a double walled, multiporous peg. The sensory peg is deeply embedded in a cuticular pit, connected to the environment only by a tiny aperture. The sen-sillum houses three receptor neurons of which one is thermosensitive whereas the sensory modality of the other two neurons remains to be shown. Upon stimulation with a drop in temperature, the thermosensitve neuron responds with a phasic-tonic increase in neuronal activity (cold-sensitive neuron) and shows rapid adaptation to prolonged stimulation. In ad-dition, it is shown that thermal radiation is an effective stimulus for the thermosensitive neuron. This is the first evidence that sensilla coeloconica play an important role during the thermal orientation behavior described in chapter IV. During the test situation of the classic-al conditioning paradigm, the ants showed rapid antennal movements, indicating that they scan their environment in order to detect the heated object. Rapid antennal movements will result in rapid discontinuities of thermal radiation that re-quire thermosensitive neurons with outstanding sensitivity and high temporal resolution. In Chapter VI the question was addressed whether the thermosensitive neuron of the sensilla coeloconica fulfils these preconditions. Extracellular recordings revealed that the neuron is extremely sensitive to temperature transients and that, due to the response dynamics, an estimated stimulus frequency of up to 5 Hz can be resolved by the neuron. Already a tem-perature increase of only 0.005 °C leads to a pronounced response of the thermosensitive neuron. Through sensory adaptation, the sensitivity to temperature transients is maintained over a wide range of ambient temperatures. The discovered extreme sensitivity, the high temporal resolution and the pronounced adaptation abilities are further evidence support-ing the idea that sensilla coeloconica receive information of the thermal environment, which the ants may use for orientation. In order to understand how the ants use their thermal environment for orientation, it is ne-cessary to know where and how thermal information is processed in their central nervous system. In Chapter VII the question is addressed where in the brain the thermal information, specifically received by the thermosensitive neuron of sensilla coeloconica, is represented. By selectively staining single sensilla coeloconica, the axons of the receptor neurons could be tracked into the antennal lobe of Atta vollenweideri workers. Each of the three axons termi-nated in a single functional unit (glomerulus) of the antennal lobe. Two of the innervated glomeruli were adjacent to each other and are located lateral, while the third one was clear-ly separate and located medial in the antennal lobe. Using two-photon Ca2+ imaging of an-tennal lobe projection neurons, the general representation of thermal information in the antennal lobe was studied. In 11 investigated antennal lobes up to six different glomeruli responded to temperature stimulation in a single specimen. Both, warm- and cold-sensitive glomeruli could be identified. All thermosensitive glomeruli were located in the medial half of the antennal lobe. Based on the correlative evidence of the general representation of thermal information and the results from the single sensilla stainings, it is assumed that thermal information received by sensilla coeloconica is processed in the medial of the three target glomeruli. This part of the thesis shows the important role of the antennal lobe in temperature processing and links one specific thermosensitive neuron to its target region (a single glomerulus). In chapter V it was shown that the sensilla coeloconica are clustered at the antennal tip and have an extraordinary peg-in-pit morphology. In the last chapter of this thesis (Chapter VIII) the question is addressed whether the morphology of the sensilla coeloconica predicts the receptive field of the thermosensitive neuron during the detection of thermal radiation. The sensory pegs of all sensilla coeloconica in the apical cluster have a similar orientation, which was not constraint by the shape of the antennal tip where the cluster is located. This finding indicates that the sensilla coeloconica function as a single unit. Finally the hypothesis was tested whether a single sensillum could be direction sensitive to thermal radiation based on its eye-catching morphology. By stimulating the thermosensitive neuron from various angles around the sensillum this indeed could be shown. This is the last and most significant evi-dence that the sensilla coeloconica may be adapted to detect spatially distributed heated objects in the environment during the thermal landmark orientation of ants.},
  subject      = {Neurobiologie},
  language  = {en}
}
@article{BonteMaes2008,
  author    = {Bonte, Dries and Maes, Dirk},
  title     = {Trampling affects the distribution of specialised coastal dune arthropods},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48274},
  year      = {2008},
  abstract  = {Abstract: From a conservation point of view, species- tolerances towards disturbance are often generalised and lack reference to spatial scales and underlying processes. In order to investigate how average typical species react to habitat fragmentation and disturbance, we adopted a multi-species approach to address occupancy patterns of five specialised dune arthropods (butterflies Hipparchia semele, Issoria lathonia; grasshopper Oedipoda caerulescens; spiders Alopecosa fabrilis, Xysticus sabulosus) in recently fragmented coastal dune habitats which are subjected to varying levels and modes of local disturbance, i.e. trampling by cattle or people. Occupancy patterns were assessed during two successive years in 133 grey dune fragments of the Flemish coastal dunes (Belgium, France). By treating species as a random factor in our models, emphasis was placed on generalisations rather than documenting species-specific patterns. Our study demonstrates that deteriorating effects of local disturbance on arthropod incidence cannot be interpreted independent of its landscape context, and appear to be more severe when patch area and connectivity decrease. When controlled for patch area and trampling intensity, the probability of species occupancy in poorly connected patches is higher under cattle trampling than under recreation. Incidences additionally decrease with increasing intensity of cattle trampling, but increases with trampling by tourists. This study provides evidence of mode- and landscape-dependent effects of local disturbance on species occupancy patterns. Most importantly, it demonstrates that trampling of sensitive dune fragments will lead to local and metapopulation extinction in landscapes where trampling occurs in a spatially autocorrelated way, but that the outcome (spatial patterns) varies in relation to disturbance mode, indicating that effects of disturbance cannot be generalised.},
  language  = {en}
}
@article{BonteClercqZwertvaegheretal.2009,
  author    = {Bonte, Dries and Clercq, Nele De and Zwertvaegher, Ingrid and Lens, Luc},
  title     = {Repeatability of dispersal behaviour in a common dwarf spider: evidence for different mechanisms behind short- and long-distance dispersal},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48242},
  year      = {2009},
  abstract  = {Abstract: 1. The response of dispersal towards evolution largely depends on its heritability for which upper limits are determined by the trait's repeatability. 2. In the Linyphiid spider E. atra, we were able to separate long- and short-distance dispersal behaviours (respectively ballooning and rappelling) under laboratory conditions. By performing repeated behavioural trials for females, we show that average dispersal trait values decrease with increasing testing days. By comparing mated and unmated individuals during two periods (before and after mating for the mated group, and the same two periods for the unmated group), we show that mating has no effect on the mean displayed dispersal behaviour or its within-individual variation. Repeatabilities were high and consistent for ballooning motivation, but not for rappelling. 3. Ballooning motivation can be regarded as highly individual-specific behaviour, while general pre-dispersal and rappelling behaviours showed more individual variation. Such difference in repeatability between long-and short-distance dispersal suggests that short-and long-distance dispersal events are triggered by different ecological and evolutionary mechanisms.},
  language  = {en}
}
@article{GrosPoethkeHovestadt2009,
  author    = {Gros, Andreas and Poethke, Hans Joachim and Hovestadt, Thomas},
  title     = {Sex-specific spatio-temporal variability in reproductive success promotes the evolution of sex-biased dispersal},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48711},
  year      = {2009},
  abstract  = {Abstract: Inbreeding depression, asymmetries in costs or benefits of dispersal, and the mating system have been identified as potential factors underlying the evolution of sex-biased dispersal. We use individual-based simulations to explore how the mating system and demographic stochasticity influence the evolution of sex-specific dispersal in a metapopulation with females competing over breeding sites, and males over mating opportunities. Comparison of simulation results for random mating with those for a harem system (locally, a single male sires all offspring) reveal that even extreme variance in local male reproductive success (extreme male competition) does not induce male-biased dispersal. The latter evolves if the between-parch variance in reproductive success is larger for males than females. This can emerge due to demographic stochasticity if the habitat patches are small. More generally, members of a group of individuals experiencing higher spatio-temporal variance in fitness expectations may evolve to disperse with greater probability than others.},
  language  = {en}
}
@article{KreftGoebel1974,
  author    = {Kreft, J{\"u}rgen and Goebel, Werner},
  title     = {Complex Co1E1 DNA in Escherichia coli and Proteus mirabilis},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-47044},
  year      = {1974},
  abstract  = {Incubation of the colicinogenic Escherichia coli strain JC 411 (ColE1) at elevated temperatures (47-49°) leads to the accumulation of catenated molecules and replicative intermediates of this plasmid. Mature supercoiled OolE1 DNA molecules synthesized under these conditions have an increased number of tertiary turns as shown by electron microscopy. The monomeric tightly supercoiled molecules possess a slightly slower sedimentation rate and a higher binding capacity for ethidium bromide than supercoiJed monomers synthesized at lower temperatures. Recombination deficient mutants of E. coli recA, recB and recC, which carry the ColE1 plasmid, form about the same amount of catenated molecules at the elevated temperature as a rec+ strain. In addition, we have observed by electron microscopy a small percentage (.--.5\% of the circular DNA molecules) of minicircular DNA molecules in all preparations of JC 411 (CoIE1). They are homogenous in size, with a molecular weight of 1.4 X 106 daltons. Addition of chloramphenicol to a culture of Proteus mirabilis (ColE1) leads to an increased amount of higher multiple circular oligomers and to a stimulated accumulation of catenated OolE1 DNA molecules of varying sizes. ColE1 DNA synthesis is more thermosensitive than chromosomal DNA replication in P. mirabili8. Plasmid replication stops completely at temperatures above 43°C.},
  language  = {en}
}
@article{Kreft1980,
  author    = {Kreft, J{\"u}rgen},
  title     = {Reovirus-specific messenger ribonucleoprotein particles from Hela cells},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-47028},
  year      = {1980},
  abstract  = {When reovirus-infected Hela cells are incubated at 43°C virus-specific messenger RNA is released ~rom the polysomes. It accumulates free in the cytoplasm as messenger ribonucleoprotem partIcles (mRNPs). The:e part~cles have a sedimentati~n rate of about 50S and a buoyant densIty m CsCI of 1.42 g/cm . ReovIrus mRNPs contam, beSIdes all three size classes of reovirus messenger RNA, the same spectrum of proteins found in the polysomal mRNPs from uninfected cells, plus t~o addi~ional pr?teins with molecular masses of 7000~ d and 110000 d, respectively. Electron mIcroscoPIc exammatlOn of the reovIrus mRNP fractIOn reveals specific Y-shaped structures wIth a total mean length ofO.5Ilm.},
  language  = {en}
}
@article{KreftBernhardGoebel1978,
  author    = {Kreft, J{\"u}rgen and Bernhard, K. and Goebel, Werner},
  title     = {Recombinant plasmids capable to replication in B. subtilis and E. coli},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-47000},
  year      = {1978},
  abstract  = {The plasmid pBC16 (4.25 kbases), ongtnally isolated from Bacillus cereus, determines tetracycline resistance and can be transformed into competent cells of B. subtilis. A miniplasmid of pBCl6 (pBCI6-1), 2,7 kb) which has lost an EcoRI fragment of pBCI6 retains the replication functions and the tetracycline resistance. This plasmid which carries only one EcoRI site has been joined in vitro to pBS], a cryptic plasmid previously isolated from B. subtilis and shown to carry also a single EcoRI site (Bernhard et aI., 1978). The recombinant plasmid is unstable and dissociates into the plasmid pBSl61 (8.2 kb) and the smaller plasmid pBS162 (2. I kb). Plasmid pBS161 retains the tetracycline resistance. It possesses a single EcoRI site and 6 HindlII sites. The largest HindIII fragment of pBS161 carries the tetracycline resistance gene and the replication function. After circularization in vitro of this fragment a new plasmid, pBS161-l is generated, which can be used as a HindlII and EcoRI cloning vector in Bacillus suhtilis. Hybrid plasmids consisting of the E. coli plasmids pBR322, p WL 7 or pACl84 and different HindlII fragments of pBSI61 were constructed in vitro. Hybrids containing together with the E. coli plasmid the largest HindlII fragment of pBS161 can replicate in E. coli and B. sublilis. In E. coli only the replicon of the E. coli plasmid part is functioning whereas in B. suhtilis replication of the hybrid plasmid is under the control of the Bacillus replicon. The tetracycline resistance of the B. subtilis plasmid is expressed in E. coli, but several antibiotic resistances of the E. coli plasmids (ampicillin, kanamycin and chloramphenicol) are not expressed in B. suhtilis. The hybrid plasmids seem to be more unstable in B. subtilis than in E. coli.},
  language  = {en}
}
@article{KreftHughes1982,
  author    = {Kreft, J{\"u}rgen and Hughes, Colin},
  title     = {Cloning vectors derived from plasmids and phage of Bacillus},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-47014},
  year      = {1982},
  abstract  = {No abstract available},
  language  = {en}
}
@article{KreftFunkeSchlesingeretal.1989,
  author    = {Kreft, J{\"u}rgen and Funke, D. and Schlesinger, R. and Lottspeich, F. and Goebel, Werner},
  title     = {Purification and characterization of cytolysins from Listeria monocytogenes serovar 4b and Listeria ivanovii},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-47036},
  year      = {1989},
  abstract  = {Several exoproteins from Listeria monocytogenes serovar 4b (NCTC 10527) and Listeria ivanovii (ATCC) 19119, SLCC 2379), respectively, have been purified to homogeneity by thiol-disulfide exchange chromatography and gel filtration. Both strains produce a haemolytic/cytolytic protein of Mr 58 kDa, which has all the properties of a SH-activated cytolysin, the prototype of which is streptolysin 0 (SLO), and this protein has therefore heen termed Iisteriolysin 0 (LLO). In addition a protein of Mr 24 kDa from culture supernatants of L. ivanovii co-purified withLLO. The N-terminal aminoacid sequences of both proteins from L. ivanovii have been determined. By mutagenesis with transposons of Gram-positive origin (Tn916 and TnI545), which have been introduced via conjugation into L. ivanovii, several phenotypic mutants (altered haemolysis on sheep blood agar or lecithinase-negative) were obtained. Results on the properties of these muntants will he presented.},
  language  = {en}
}
@article{KreftHaasGoebel1989,
  author    = {Kreft, J{\"u}rgen and Haas, Albert and Goebel, Werner},
  title     = {Isolation and characterization of genes coding for proteins involved in the cytolysis by Listeria ivanovii},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-46991},
  year      = {1989},
  abstract  = {We established a library of chromosomal DNA of Listeria ivanovii in the pTZ19R plasmid system, using Escherichia coli DH5alpha as the host. One recombinant clone reacted strongly with a polyclonal antiserum raised against the listeriolysin 0 and a second exoprotein (24kDa) of L. ivanovii, which is most probably also involved in cytolytic processes. The recombinant E. coli clone may contain part of the listeriolysin 0 gene of L. ivanovii.},
  language  = {en}
}
@article{BlackenhornPerner1994,
  author    = {Blackenhorn, Wolf U. and Perner, Dirk},
  title     = {Heritability and repeatability of behavioural attributes affecting foraging success and fitness in water striders},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-52496},
  year      = {1994},
  abstract  = {Heritabilities and repeatabilities are presented for various behavioural attributes affecting foraging performance and fitness in Aquarius (Gerris) remigis (Heteroptera: Gerridae) females. These behavioural attributes were patch choice, foraging success, capture accuracy, and measures of mobility, activity, skittishness and aggressiveness. Most heritabilities were not significantly different from zero, which may be related to the low sampIe size. Conclusions as to the potential of direct selection on behaviour in this species were consequently limited. In contrast, with a few exceptions (capture accuracy, foraging success), most repeatabilities were significant and at times high (range=O'22-O'79), indicating consistent, stereotypical individual behaviour. Tbe Iife history or reproductive state of the daughter generation individuals signifieantly affected the magnitude of the repeatabilities as weil as the mean values of many of the variables (notably mobility and aggressiveness), the latter in a manner consistent with field observations. This indicates that the state of the organism affects the general environmental variance, thus contributing to the discrepancies between the repeatabilities and the heritabilities obtained. It is suggested that common physiological proeesses (e.g. hormones) may underlie several of the behavioural attributes examined, resulting in possible pleiotropie effects and eonstraints on selection in a heterogeneous environment. It is further suggested that field studies of selection on behavioural attributes may be a more fruitful approach in this species, whose suitability for genetic analysis is limited.},
  subject      = {Teichl{\"a}ufer},
  language  = {en}
}
@phdthesis{Ondrusch2010,
  author    = {Ondrusch, Nicolai},
  title     = {Der Thiol:Disulfid-Redox Metabolismus und der Blaulichtrezeptor Lmo0799 von Listeria monocytogenes},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-52612},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Der Thiol-Redox-Metabolismus, der in allen lebenden Zellen zu finden ist, wirkt oxidativem Stress entgegen. Des Weiteren dient er auch der Aufrechterhaltung der intrazellul{\"a}ren Thiol:Disulfid-Balance, die wiederum f{\"u}r die Funktion vieler Proteine essentiell ist. Auch stellt er Reduktions{\"a}quivalente f{\"u}r die Produktion von Desoxyribonucleotiden f{\"u}r die DNA-Synthese bereit und hilft oxidierte Proteine zu reparieren. Der Thiol:Disulfid-Redox-Metabolismus (TDRM) unterscheidet sich von anderen metabolischen Netzwerken dadurch, dass keine Kohlenstoff- oder Stickstoffbindungen ver{\"a}ndert werden. In vielen F{\"a}llen beinhaltet er die reversible Oxidation zweier benachbarter Cysteinreste im entsprechenden Protein, was zur Ausbildung von Disulfidbr{\"u}cken f{\"u}hrt. Da ein totaler Ausfall der GSH-Synthese einen geringeren Effekt zu haben schien als ein teilweiser, wurden DNA-Microarray-Transkriptomanalysen der ΔgshF-Mutante durchgef{\"u}hrt. Es wurden rund 750 Gene als signifikant reguliert (p < 0,05, Fold-change <0,5 bzw. >2) identifiziert. Da die am st{\"a}rksten regulierten Gene von besonderem Interesse waren, wurden die Ausschlussgrenzen auf <0,2 bzw. >5 -fach reguliert heraufgesetzt. Diese Parameter trafen auf 92 Gene zu, davon 41 durch GSH-Mangel herauf-regulierte (d.h. die mRNA-Menge war in der Mutante h{\"o}her als im Wildtyp) und 51 herunter-regulierte. Auff{\"a}llig war, dass die Expression vieler Gene, welche durch den Stress-Sigmafaktor SigB reguliert werden, bei Fehlen von GSH ver{\"a}ndert war. Zu den am st{\"a}rksten (sechs- bis elffach) herauf-regulierten Genen z{\"a}hlen lmo0135-7, sie codieren f{\"u}r einen putativen Oligopeptidtransporter. Die Vermutung lag nahe, dass dieser evtl. GSH aus dem Medium in die Zellen transportieren k{\"o}nnte. Man kann also davon ausgehen, dass GSH von Listeria aktiv aus dem Medium aufgenommen wird und dass die Effekte, die im Versuch ohne zus{\"a}tzliches GSH auftreten, direkt auf das Fehlen von GSH zur{\"u}ckzuf{\"u}hren sind. Zusammengefasst zeigte sich, dass ein Ausfall der GSH-Synthese in Listeria keinen auff{\"a}lligen Ph{\"a}notyp zeigt. Es wurden jedoch sehr umfangreiche Ver{\"a}nderungen des Transkriptionsprofils beobachtet, offenbar konnten die Bakterien dadurch eine neue zellul{\"a}re Hom{\"o}ostase erreichen. Physiologische Mengen von GSH im Medium komplementierten den Ausfall der GSH-Synthese fast vollst{\"a}ndig. Im Laufe dieser Analysen fiel das Augenmerk auf ein Gen mit unbekannter Funktion, lmo0799, das in der ΔgshF-Mutante als deutlich heraufreguliert identifiziert worden war. Eine n{\"a}here in-silico-Analyse ergab deutliche Homologien des Lmo0799 Proteins zu einem Blaulicht-photorezeptor, YtvA, von Bacillus subtilis. Da ein Zusammenhang mit dem TDRM aufgrund der Microarray-Analysen mehr als wahrscheinlich schien, richtete sich das Augenmerk verst{\"a}rkt auf die Charakterisierung des putativen Blaulichtrezeptors Lmo0799. Es wurde eine In-Frame-Deletionsmutante in lmo0799 hergestellt, die mit Δlmo0799-Mutante bezeichnet wurde. Darin ist das urspr{\"u}nglich 253 Aminos{\"a}uren (AS) große Genprodukt von lmo0799 auf sieben AS verk{\"u}rzt, ohne den Promotor- oder Terminatorbereich bzw. umliegende Gene zu ver{\"a}ndern. Parallel wurde begonnen, Versuche zum Einfluss von Licht (blau, λ=455nm bzw. rot, λ=625nm) in vivo und in vitro auf L. monocytogenes durchzuf{\"u}hren. Versuche mittels qRT-PCR wurden durchgef{\"u}hrt um die genaue Wirkweise von Lmo0799 n{\"a}her aufzukl{\"a}ren. Dazu wurden Testgene aus verschiedenen Regulons ausgew{\"a}hlt und deren Transkription in Proben von Wildtyp und Δlmo0799-Mutante mit und ohne blauem bzw. rotem Licht sowie mit und ohne Salzstress gemessen. Dabei zeigte sich, dass vor allem die Transkription von Genen des SigB-Regulons, das f{\"u}r die allgemeine Stressantwort in Listerien zust{\"a}ndig ist, durch Licht moduliert wurde. Die Wirkung von Blaulicht hing in hohem Maße von der Anwesenheit von Lmo0799 ab, welches wahrscheinlich eine Komponente des „Stressosoms" von Listeria darstellt. Die Lichtregulation betraf auch die Internaline A und B, deren Transkription durch Belichtung stark erh{\"o}ht wurde. Infektionsversuche mit blau belichteten bzw. dunkel gehaltenen Wildtyp- bzw. Δlmo0799-Bakterien an humanen Caco-2 Enterozyten zeigten, dass wildtypische Listerien nach Bestrahlung mit blauem Licht ihre Invasionsrate verdoppelten, w{\"a}hrend die Δlmo0799-Listerien auf Niveau der Dunkelkontrolle blieben. In der vorliegenden Arbeit konnte erstmals gezeigt werden, dass L. monocytogenes (und wohl auch die anderen Listeria-Arten) in Lmo0799 einen funktionalen Blaulichtrezeptor besitzt, der eine wichtige Rolle in der Vermittlung von Stressreizen via SigB spielt und auch die Motilit{\"a}t und Virulenz moduliert. Weiterhin konnte gezeigt werden, dass auch rotes Licht die Transkription zahlreicher durch Blaulicht regulierter Gene beeinflusst. Der molekulare Mechanismus konnte im Rahmen dieser Arbeit nicht mehr aufgekl{\"a}rt werden.},
  subject      = {Listeria monocytogenes},
  language  = {de}
}
@phdthesis{Salzmann2010,
  author    = {Salzmann, Steffen},
  title     = {Regulation der TNF-Rezeptor Signaltransduktion durch das Zytokin TWEAK},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-52525},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Das pleiotrope Zytokin TNF (tumor necrosis factor) kann an den TNF-Rezeptor 1 (TNFR1) und den TNF-Rezeptor 2 (TNFR2) binden und mit deren Hilfe seine biologischen Funktionen {\"u}ber verschiedene Signalwege, wie z.B. NFB- und MAPK-Aktivierung bzw. Apop¬toseinduktion, vermitteln. In fr{\"u}heren Arbeiten konnte gezeigt werden, dass die Aktivierung des TNFR2 zur proteasomalen Degradation des Adaterproteins TRAF2 f{\"u}hrt und dadurch die TNFR1-induzierte Apoptose verst{\"a}rkt wird. TWEAK (tumor necrosis like weak inducer of apoptosis), das ebenfalls der TNF-Ligandenfamilie angeh{\"o}rt und die Interaktion mit dessen Rezeptor Fn14 (fibroblast growth factor-inducible 14), der wie der TNFR2 zur Untergruppe der TRAF-bindenden Rezeptoren der TNF-Rezeptorfamilie geh{\"o}rt, zeigten in verschiedenen Arbeiten auch eine TRAF2-degradierende Wirkung. In der vorliegenden Arbeit konnte nun gezeigt werden, dass dies auch im Falle des TWEAK/Fn14-Systems mit einem verst{\"a}rkenden Effekt auf die TNFR1-vermittelte Apoptose einhergeht. Dar{\"u}ber hinaus konnte gezeigt werden, dass TWEAK zus{\"a}tzlich auch die TNFR1-induzierte Nekrose verst{\"a}rkt, die den Zelltod durch andere Mechanismen als bei der Apoptose induziert. Von anderen Arbeiten unserer Gruppe war bekannt, dass l{\"o}sliches TWEAK (sTWEAK) und membranst{\"a}ndiges TWEAK (mTWEAK) bez{\"u}glich der TRAF2-Depletion wirkungs¬gleich sind. Da der apoptotische Fn14-TNFR1-„crosstalk" auf der Depletion von TRAF2-Komplexen beruht wurden auch keine signifikanten Unterschiede zwischen sTWEAK und mTWEAK in Bezug auf die Verst{\"a}rkung der TNFR1-induzierten Apoptose beobachtet. Interessanter¬weise zeigte sich in der vorliegenden Arbeit jedoch, dass sTWEAK den klassischen NFB-Signalweg gar nicht bzw. nur schwach aktiviert, wohingegen mTWEAK diesen stark induziert. Bei der Aktivierung des alternativen NFB-Signalweges hingegen ließen sich keine Unterschiede zwischen sTWEAK und mTWEAK erkennen. Die Aktivierung eines Signalweges wird also durch die Oligomerisierung des Liganden nicht moduliert, demgegen{\"u}ber aber erwies sich die Aktivierung eines anderen Signalweges als stark abh{\"a}ngig von der Liganden-Oligomerisierung. Vor dem Hintergrund, dass das Adapterprotein TRAF1 (TNF-receptor-associated factor 1) Heterotrimere mit TRAF2 bildet, wurde weiterhin untersucht, ob dieses Molek{\"u}l einen Einfluss auf die Aktivit{\"a}t der TWEAK-induzierten Signalwege hat. Tats{\"a}chlich zeigte sich in TRAF1-exprimie¬renden Zellen eine Verst{\"a}rkung der TWEAK-induzierten Aktivierung des klassischen NFB-Signalweges Zuk{\"u}nftige Studien m{\"u}ssen nun aufkl{\"a}ren, inwieweit die hier gefundenen Mecha-nismen das Zusammenspiel von TNF und TWEAK in vivo bestimmen.},
  subject      = {Tumor-Nekrose-Faktor},
  language  = {de}
}
@phdthesis{Saverschek2010,
  author    = {Saverschek, Nicole},
  title     = {The influence of the symbiotic fungus on foraging decisions in leaf-cutting ants - Individual behavior and collective patterns},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-52087},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Foraging behavior is a particularly fascinating topic within the studies of social insects. Decisions made by individuals have effects not only on the individual level, but on the colony level as well. Social information available through foraging in a group modulates individual preferences and shapes the foraging pattern of a colony. Identifying parameters influencing foraging behavior in leaf-cutting ants is especially intriguing because they do not harvest for themselves, but for their symbiotic fungus which in turn influences their plant preferences after the incorporation of the substrate. To learn about the substrates' unsuitability for the fungus, ants need to be able to identify the incorporated substrate and associate it with detrimental effects on the fungus. Odor is an important plant characteristic known to be used as recognition key outside the nest in the context of foraging. Chapter 1 shows that foragers are able to recall information about the unsuitability of a substrate through odor alone and consequently reject the substrate, which leads to the conclusion that inside the nest, odor might be enough to indentify incorporated substrate. Identification of plant species is a key factor in the foraging success of leaf-cutting ants as they harvest a multitude of different plant species in a diverse environment and host plant availability and suitability changes throughout the year. Fixed plant preferences of individuals through innate tendencies are therefore only one factor influencing foraging decisions. On the individual as well as the colony level, foraging patterns are flexible and a result of an intricate interplay between the different members involved in the harvesting process: foragers, gardeners and the symbiotic fungus. In chapter 2 I identified several conditions necessary for na{\"i}ve foragers to learn about the unsuitability of substrate inside the nest. In order to exchange of information about the unsuitability of a substrate, the plant in question must be present in the fungus garden. Foragers can learn without own foraging experience and even without experiencing the effects of the substrate on the fungus, solely through the presence of experienced gardeners. The presence of experienced foragers alone on the other hand is not enough to lower the acceptance of substrate by na{\"i}ve foragers in the presence of na{\"i}ve gardeners, even if experienced foragers make up the majority of the workforce inside the nest. Experienced foragers are also able to reverse their previous negative experience and start accepting the substrate again. The individual behavior of foragers and gardeners with different experiential backgrounds in the presence of suitable or unsuitable substrate inside the fungus chamber was investigated in chapter 3 to shed some light on possible mechanisms involved in the flow of information about substrate suitability from the fungus to the ants. Gardeners as well as foragers are involved in the leaf processing and treatment of the applied leaf patches on the fungus. If the plant material is unsuitable, significantly more ants treat the plant patches, but foragers are less active overall. Contacts between workers initiated by either gardeners or foragers occur significantly more frequent and last longer if the substrate is unsuitable. Even though experienced gardeners increase na{\"i}ve foragers' contact rates and duration with other workers in the presence of suitable plant patches, na{\"i}ve foragers show no differences in the handling of the plant patches. This suggests that foragers gain information about plant suitability not only indirectly through the gardening workers, but might also be able to directly evaluate the effects of the substrate on the fungus themselves. Outside the nest, foragers influence each other the trail (chapter 4). Foraging in a group and the presence of social information is a decisive factor in the substrate choice of the individual and leads to a distinct and consentaneous colony response when encountering unfamiliar or unsuitable substrates. As leaf-cutting ants harvest different plant species simultaneously on several trails, foragers gain individual experiences concerning potential host plants. Preferences might vary among individuals of the same colony to the degree that foragers on the same trail perceive a certain substrate as either suitable or unsuitable. If the majority of foragers on the trail perceives one of the currently harvested substrates as unsuitable, na{\"i}ve foragers lower their acceptance within 4 hours. In the absence of a cue in the fungus, na{\"i}ve foragers harvesting by themselves still eventually (within 6 hours) reject the substrate as they encounter experienced gardeners during visits to the nest within foraging bouts. As foraging trails can be up to 100 m long and foragers spend a considerable amount of time away from the nest, learning indirectly from experienced foragers on the trail accelerates the distribution of information about substrate suitability. The level of rejection of a formerly unsuitable substrate after eight hours of foraging by na{\"i}ve foragers correlates with the average percentage of unladen experienced foragers active on the trail. This suggests that unladen experienced foragers might actively contact laden na{\"i}ve workers transmitting information about the unsuitability of the load they carry. Results from experiments were I observed individual laden foragers on their way back to the nest backed up this assumption as individuals were antennated and received bites into the leaf disk they carried. Individuals were contacted significantly more often by nestmates that perceived the carried leaf disk as unsuitable due to previous experience than by nestmates without this experience (chapter 6). Leaf-cutting ants constantly evaluate, learn and re-evaluate the suitability of harvested substrate and adjust their foraging activity accordingly. The importance of the different sources of information within the colony and their effect on the foraging pattern of the colony depend on the presence or absence of each of them as e.g. experienced foragers have a bigger influence on the plant preferences of na{\"i}ve foragers in the absence of a cue in the fungus garden.},
  subject      = {Blattschneiderameisen},
  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}
}
@phdthesis{Laisney2010,
  author    = {Laisney, Juliette Agn{\`e}s Genevi{\`e}ve Claire},
  title     = {Characterisation and regulation of the Egfr/Egfr ligand system in fish models for melanoma},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51369},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Fish of the genus Xiphophorus belong to the oldest animal models in cancer research. The oncogene responsible for the generation of spontaneous aggressive melanoma encodes for a mutated epidermal growth factor receptor (Egfr) and is called xmrk for Xiphophorus melanoma receptor kinase. Xmrk constitutive activation mechanisms and subsequent signaling pathways have already been investigated and charaterized but it is still unknown if Egfr ligands may also play a role in Xmrk-driven melanoma formation. To investigate the potential role of Egfr ligands in Xmrk-driven melanoma, I firstly analyzed the evolution of teleost and tetrapod Egfr/Egfr ligand systems. I especially focused on the analysis on the medaka fish, a closely related species to Xiphophorus, for which the whole genome has been sequenced. I could identify all seven Egfr ligands in medaka and could show that the two teleost-specific Egfr copies of medaka display dissimilar expression patterns in adult tissues together with differential expression of Egfr ligand subsets, arguing for subfunctionalization of receptor functions in this fish. Our phylogenetic and synteny analyses supported the hypothesis that only one gene in the chordate ancestor gave rise to the diversity of Egfr ligands found in vertebrate genomes today. I also could show that the Egfr extracellular subdomains implicated in ligand binding are not evolutionary conserved between tetrapods and teleosts, making the use of heterologous ligands in experiments with fish cells debatable. Despite its well understood and straight-forward process, Xmrk-driven melanomagenesis in Xiphophorus is problematic to further investigate in vivo. Our laboratory recently established a new melanoma animal model by generating transgenic mitf::xmrk medaka fishes, a Xiphophorus closely related species offering many more advantages. These fishes express xmrk under the control of the pigment-cell specific Mitf promoter. During my PhD thesis, I participated in the molecular analysis of the stably transgenic medaka and could show that the Xmrk-induced signaling pathways are similar when comparing Xiphophorus with transgenic mitf::xmrk medaka. These data together with additional RNA expression, protein, and histology analyses showed that Xmrk expression under the control of a pigment cell-specific promoter is sufficient to induce melanoma in the transgenic medaka, which develop very stereotyped tumors, including uveal and extracutaneous melanoma, with early onset during larval stages. To further investigate the potential role of Egfr ligands in Xmrk-driven melanoma, I made use of two model systems. One of them was the above mentioned mitf::xmrk medaka, the other was an in-vitro cell culture system, where the EGF-inducible Xmrk chimera HERmrk is stably expressed in murine melanocytes. Here I could show that HERmrk activation strongly induced expression of amphiregulin (Areg) and heparin-binding EGF-like growth factor (Hbegf) in melanocytes. This regulation was dependent on the MAPK and SRC signaling pathways. Moreover, upregulation of Adam10 and Adam17, the two major sheddases of Egfr ligands, was observed. I also could demonstrate the functionality of the growth factors by invitro analyses. Using the mitf::xmrk medaka model I could also show the upregulation of a subset of ligand genes, namely egf, areg, betacellulin (btc) and epigen (epgn) as well as upregulation of medaka egfrb in tumors from fish with metastatic melanoma. All these results converge to support an Xmrk-induced autocrine Egfr ligand loop. Interestingly, my in-vitro experiments with conditioned supernatant from medaka Egf- and Hbegf-producing cells revealed that not only Xiphophorus Egfrb, but also the pre-activated Xmrk could be further stimulated by the ligands. Altogether, I could show with in-vitro and in-vivo experiments that Xmrk is capable of inducing a functional autocrine Egfr ligand loop. These data confirm the importance of autocrine loops in receptor tyrosine kinase (RTK)-dependent cancer development and show the possibility for a constitutively active RTK to strengthen its oncogenic signaling by ligand binding.},
  subject      = {Schwertk{\"a}rpfling},
  language  = {en}
}
@phdthesis{Vershenya2010,
  author    = {Vershenya, Stanislav},
  title     = {Quantitative and qualitative analyses of in-paralogs},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51358},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {In our analysis I was interested in the gene duplications, with focus on in-paralogs. In-paralogs are gene duplicates which arose after species split. Here I analysed the in-paralogs quantitatively, as well as qualitatively. For quantitative analysis genomes of 21 species were taken. Most of them have vastly different lifestyles with maximum evolutionary distance between them 1100 million years. Species included mammals, fish, insects and worm, plus some other chordates. All the species were pairwised analysed by the Inparanoid software, and in-paralogs matrix were built representing number of in-paralogs in all vs. all manner. Based on the in-paralogs matrix I tried to reconstruct the evolutionary tree using in-paralog numbers as evolutionary distance. If all 21 species were used the resulting tree was very far from real one: a lot of species were misplaced. However if the number was reduced to 12, all of the species were placed correctly with only difference being wrong insect and fish clusters switched. Then to in-paralogs matrix the neighbour-net algorithm was applied. The resulting "net" tree showed the species with fast or slow duplications rates compared to the others. We could identify species with very high or very low duplications frequencies and it correlates with known occurrences of the whole genome duplications. As the next step I built the graphs for every single species showing the correlation between their in-paralogs number and evolutionary distance. As we have 21 species, graph for every species is built using 20 points. Coordinates of the points are set using the evolutionary distance to that particular species and in-paralogs number. In mammals with increasing the distance from speciation the in-paralogs number also increased, however not in linear fashion. In fish and insects the graph close to zero is just the same in mammals' case. However, after reaching the evolutionary distances more than 800 million years the number of inparalogs is beginning to decrease. We also made a simulation of gene duplications for all 21 species and all the splits according to the fossil and molecular clock data from literature. In our simulation duplication frequency was minimal closer to the past and maximum in the near-present time. Resulting curves had the same shape the experimental data ones. In case of fish and insect for simulation the duplication rate coefficient even had to be set negative in order to repeat experimental curve shape. To the duplication rate coefficient in our simulation contribute 2 criteria: gene duplications and gene losses. As gene duplication is stochastical process it should always be a constant. So the changing in the coefficient should be solely explained by the increasing gene loss of old genes. The processes are explained by the evolution model with high gene duplication and loss ratio. The drop in number of in-paralogs is probably due to the BLAST algorithm. It is observed in comparing highly divergent species and BLAST cannot find the orthologs so precisely anymore. In the second part of my work I concentrated more on the specific function of inparalogs. Because such analysis is time-consuming it could be done on the limited number species. Here I used three insects: Drosophila melanogaster (fruit y), Anopheles gambiae (mosquito) and Apis mellifera (honeybee). After Inparnoid analyses and I listed the cluster of orthologs. Functional analyses of all listed genes were done using GO annotations and also KEGG PATHWAY database. We found, that the gene duplication pattern is unique for each species and that this uniqueness is rejected through the differences in functional classes of duplicated genes. The preferences for some classes reject the evolutionary trends of the last 350 million years and allow assumptions on the role of those genes duplications in the lifestyle of species. Furthermore, the observed gene duplications allowed me to find connections between genomic changes and their phenotypic manifestations. For example I found duplications within carbohydrate metabolism rejecting feed pattern adaptation, within photo- and olfactory-receptors indicating sensing adaptation and within troponin indicating adaptations in the development. Despite these species specific differences, found high correlations between the independently duplicated genes between the species. This might hint for a "pool" of genes preferentially duplicated. Taken together, the observed duplication patterns reject the adaptational process and provide us another link to the field of genomic zoology.},
  subject      = {Duplikation},
  language  = {en}
}