@phdthesis{PradaSalcedo2018,
  author    = {Prada Salcedo, Juan Pablo},
  title     = {Image Processing and other bioinformatic tools for Neurobiology},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157721},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Neurobiology is widely supported by bioinformatics. Due to the big amount of data generated from the biological side a computational approach is required. This thesis presents four different cases of bioinformatic tools applied to the service of Neurobiology. The first two tools presented belong to the field of image processing. In the first case, we make use of an algorithm based on the wavelet transformation to assess calcium activity events in cultured neurons. We designed an open source tool to assist neurobiology researchers in the analysis of calcium imaging videos. Such analysis is usually done manually which is time consuming and highly subjective. Our tool speeds up the work and offers the possibility of an unbiased detection of the calcium events. Even more important is that our algorithm not only detects the neuron spiking activity but also local spontaneous activity which is normally discarded because it is considered irrelevant. We showed that this activity is determinant in the calcium dynamics in neurons and it is involved in important functions like signal modulation and memory and learning. The second project is a segmentation task. In our case we are interested in segmenting the neuron nuclei in electron microscopy images of c.elegans. Marking these structures is necessary in order to reconstruct the connectome of the organism. C.elegans is a great study case due to the simplicity of its nervous system (only 502 neurons). This worm, despite its simplicity has taught us a lot about neuronal mechanisms. There is still a lot of information we can extract from the c.elegans, therein lies the importance of reconstructing its connectome. There is a current version of the c.elegans connectome but it was done by hand and on a single subject which leaves a big room for errors. By automatizing the segmentation of the electron microscopy images we guarantee an unbiased approach and we will be able to verify the connectome on several subjects. For the third project we moved from image processing applications to biological modeling. Because of the high complexity of even small biological systems it is necessary to analyze them with the help of computational tools. The term in silico was coined to refer to such computational models of biological systems. We designed an in silico model of the TNF (Tumor necrosis factor) ligand and its two principal receptors. This biological system is of high relevance because it is involved in the inflammation process. Inflammation is of most importance as protection mechanism but it can also lead to complicated diseases (e.g. cancer). Chronic inflammation processes can be particularly dangerous in the brain. In order to better understand the dynamics that govern the TNF system we created a model using the BioNetGen language. This is a rule based language that allows one to simulate systems where multiple agents are governed by a single rule. Using our model we characterized the TNF system and hypothesized about the relation of the ligand with each of the two receptors. Our hypotheses can be later used to define drug targets in the system or possible treatments for chronic inflammation or lack of the inflammatory response. The final project deals with the protein folding problem. In our organism proteins are folded all the time, because only in their folded conformation are proteins capable of doing their job (with some very few exceptions). This folding process presents a great challenge for science because it has been shown to be an NP problem. NP means non deterministic Polynomial time problem. This basically means that this kind of problems cannot be efficiently solved. Nevertheless, somehow the body is capable of folding a protein in just milliseconds. This phenomenon puzzles not only biologists but also mathematicians. In mathematics NP problems have been studied for a long time and it is known that given the solution to one NP problem we could solve many of them (i.e. NP-complete problems). If we manage to understand how nature solves the protein folding problem then we might be able to apply this solution to many other problems. Our research intends to contribute to this discussion. Unfortunately, not to explain how nature solves the protein folding problem, but to explain that it does not solve the problem at all. This seems contradictory since I just mentioned that the body folds proteins all the time, but our hypothesis is that the organisms have learned to solve a simplified version of the NP problem. Nature does not solve the protein folding problem in its full complexity. It simply solves a small instance of the problem. An instance which is as simple as a convex optimization problem. We formulate the protein folding problem as an optimization problem to illustrate our claim and present some toy examples to illustrate the formulation. If our hypothesis is true, it means that protein folding is a simple problem. So we just need to understand and model the conditions of the vicinity inside the cell at the moment the folding process occurs. Once we understand this starting conformation and its influence in the folding process we will be able to design treatments for amyloid diseases such as Alzheimer's and Parkinson's. In summary this thesis project contributes to the neurobiology research field from four different fronts. Two are practical contributions with immediate benefits, such as the calcium imaging video analysis tool and the TNF in silico model. The neuron nuclei segmentation is a contribution for the near future. A step towards the full annotation of the c.elegans connectome and later for the reconstruction of the connectome of other species. And finally, the protein folding project is a first impulse to change the way we conceive the protein folding process in nature. We try to point future research in a novel direction, where the amino code is not the most relevant characteristic of the process but the conditions within the cell.},
  subject      = {Bildverarbeitung},
  language  = {en}
}
@phdthesis{Andlauer2013,
  author    = {Andlauer, Till Felix Malte},
  title     = {Structural and Functional Diversity of Synapses in the Drosophila CNS},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-85018},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {Large-scale anatomical and functional analyses of the connectivity in both invertebrate and mammalian brains have gained intense attention in recent years. At the same time, the understanding of synapses on a molecular level still lacks behind. We have only begun to unravel the basic mechanisms of how the most important synaptic proteins regulate release and reception of neurotransmitter molecules, as well as changes of synaptic strength. Furthermore, little is known regarding the stoichiometry of presynaptic proteins at different synapses within an organism. An assessment of these characteristics would certainly promote our comprehension of the properties of different synapse types. Presynaptic proteins directly influence, for example, the probability of neurotransmitter release as well as mechanisms for short-term plasticity. We have examined the strength of expression of several presynaptic proteins at different synapse types in the central nervous system of Drosophila melanogaster using immunohistochemistry. Clear differences in the relative abundances of the proteins were obvious on different levels: variations in staining intensities appeared from the neuropil to the synaptic level. In order to quantify these differences, we have developed a ratiometric analysis of antibody stainings. By application of this ratiometric method, we could assign average ratios of presynaptic proteins to different synapse populations in two central relays of the olfactory pathway. In this manner, synapse types could be characterized by distinct fingerprints of presynaptic protein ratios. Subsequently, we used the method for the analysis of aberrant situations: we reduced levels of Bruchpilot, a major presynaptic protein, and ablated different synapse or cell types. Evoked changes of ratio fingerprints were proportional to the modifications we had induced in the system. Thus, such ratio signatures are well suited for the characterization of synapses. In order to contribute to our understanding of both the molecular composition and the function of synapses, we also characterized a novel synaptic protein. This protein, Drep-2, is a member of the Dff family of regulators of apoptosis. We generated drep-2 mutants, which did not show an obvious misregulation of apoptosis. By contrast, Drep-2 was found to be a neuronal protein, highly enriched for example at postsynaptic receptor fields of the input synapses of the major learning centre of insects, the mushroom bodies. Flies mutant for drep-2 were viable but lived shorter than wildtypes. Basic synaptic transmission at both peripheral and central synapses was in normal ranges. However, drep-2 mutants showed a number of deficiencies in adaptive behaviours: adult flies were locomotor hyperactive and hypersensitive towards ethanol-induced sedation. Moreover, the mutant animals were heavily impaired in associative learning. In aversive olfactory conditioning, drep-2 mutants formed neither short-term nor anaesthesia-sensitive memories. We could demonstrate that Drep-2 is required in mushroom body intrinsic neurons for normal olfactory learning. Furthermore, odour-evoked calcium transients in these neurons, a prerequisite for learning, were reduced in drep-2 mutants. The impairment of the mutants in olfactory learning could be fully rescued by pharmacological application of an agonist to metabotropic glutamate receptors (mGluRs). Quantitative mass spectrometry of Drep-2 complexes revealed that the protein is associated with a large number of translational repressors, among them the fragile X mental retardation protein FMRP. FMRP inhibits mGluR-mediated protein synthesis. Lack of this protein causes the fragile X syndrome, which constitutes the most frequent monogenic cause of autism. Examination of the performance of drep-2 mutants in courtship conditioning showed that the animals were deficient in both short- and long-term memory. Drep-2 mutants share these phenotypes with fmrp and mGluR mutants. Interestingly, drep-2; fmrp double mutants exhibited normal memory. Thus, we propose a model in which Drep-2 antagonizes FMRP in the regulation of mGluR-dependent protein synthesis. Our hypothesis is supported by the observation that impairments in synaptic plasticity can arise if mGluR signalling is imbalanced in either direction. We suggest that Drep-2 helps in establishing this balance.},
  subject      = {Taufliege},
  language  = {en}
}
@phdthesis{Streinzer2013,
  author    = {Streinzer, Martin},
  title     = {Sexual dimorphism of the sensory systems in bees (Hymenoptera, Apoidea) and the evolution of sex-specific adaptations in the context of mating behavior},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-78689},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {Bees have had an intimate relationship with humans for millennia, as pollinators of fruit, vegetable and other crops and suppliers of honey, wax and other products. This relationship has led to an extensive understanding of their ecology and behavior. One of the most comprehensively understood species is the Western honeybee, Apis mellifera. Our understanding of sex-specific investment in other bees, however, has remained superficial. Signals and cues employed in bee foraging and mating behavior are reasonably well understood in only a handful of species and functional adaptations are described in some species. I explored the variety of sensory adaptations in three model systems within the bees. Females share a similar ecology and similar functional morphologies are to be expected. Males, engage mainly in mating behavior. A variety of male mating strategies has been described which differ in their spatiotemporal features and in the signals and cues involved, and thus selection pressures. As a consequence, males' sensory systems are more diverse than those of females. In the first part I studied adaptations of the visual system in honeybees. I compared sex and caste-specific eye morphology among 5 species (Apis andreniformis, A. cerana, A. dorsata, A. florea, A. mellifera). I found a strong correlation between body size and eye size in both female castes. Queens have a relatively reduced visual system which is in line with the reduced role of visual perception in their life history. Workers differed in eye size and functional morphology, which corresponds to known foraging differences among species. In males, the eyes are conspicuously enlarged in all species, but a disproportionate enlargement was found in two species (A. dorsata, A. florea). I further demonstrate a correlation between male visual parameters and mating flight time, and propose that light intensities play an important role in the species-specific timing of mating flights. In the second study I investigated eye morphology differences among two phenotypes of drones in the Western honeybee. Besides normal-sized drones, smaller drones are reared in the colony, and suffer from reduced reproductive success. My results suggest that the smaller phenotype does not differ in spatial resolution of its visual system, but suffers from reduced light and contrast sensitivity which may exacerbate the reduction in reproductive success caused by other factors. In the third study I investigated the morphology of the visual system in bumblebees. I explored the association between male eye size and mating behavior and investigated the diversity of compound eye morphology among workers, queens and males in 11 species. I identified adaptations of workers that correlate with distinct foraging differences among species. Bumblebee queens must, in contrast to honeybees, fulfill similar tasks as workers in the first part of their life, and correspondingly visual parameters are similar among both female castes. Enlarged male eyes are found in several subgenera and have evolved several times independently within the genus, which I demonstrate using phylogenetic informed statistics. Males of these species engage in visually guided mating behavior. I find similarities in the functional eye morphology among large-eyed males in four subgenera, suggesting convergent evolution as adaptation to similar visual tasks. In the remaining species, males do not differ significantly from workers in their eye morphology. In the fourth study I investigated the sexual dimorphism of the visual system in a solitary bee species. Males of Eucera berlandi patrol nesting sites and compete for first access to virgin females. Males have enlarged eyes and better spatial resolution in their frontal eye region. In a behavioral study, I tested the effect of target size and speed on male mate catching success. 3-D reconstructions of the chasing flights revealed that angular target size is an important parameter in male chasing behavior. I discuss similarities to other insects that face similar problems in visual target detection. In the fifth study I examined the olfactory system of E. berlandi. Males have extremely long antennae. To investigate the anatomical grounds of this elongation I studied antennal morphology in detail in the periphery and follow the sexual dimorphism into the brain. Functional adaptations were found in males (e.g. longer antennae, a multiplication of olfactory sensilla and receptor neurons, hypertrophied macroglomeruli, a numerical reduction of glomeruli in males and sexually dimorphic investment in higher order processing regions in the brain), which were similar to those observed in honeybee drones. The similarities and differences are discussed in the context of solitary vs. eusocial lifestyle and the corresponding consequences for selection acting on males.},
  subject      = {Biene},
  language  = {en}
}
@phdthesis{Bartl2012,
  author    = {Bartl, Jasmin},
  title     = {Impairment of insulin signaling pathway in Alzheimer's disease},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-74197},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2012},
  abstract  = {The neurodegenerative disorder Alzheimer's disease (AD) is the cause of approximately 60\% of the world's 35 million patients suffering from dementia. Current research focuses here are on association with other diseases such as diabetes type 2 (T2DM), possible genetic markers, specific signal transduction pathways within the brain and potential protein modification, because the pathogenesis and etiology of AD are still not fully understood. Specifically association of T2DM with AD came to the focus with the so-called "Rotterdam study" in 1999, indicating that T2DM doubles the risk of developing AD. In the meantime, it is known that the prevalence rate in patients with T2DM is 30\%. Drugs commonly used in the treatment of T2DM such as peroxisome proliferator-activated receptors gamma (PPARγ) agonists show improvement of the cognitive abilities in patients with early stage of dementia, with potential therapeutically relevance. Therefore it is important not only to investigate a link between these diseases, but also to investigate the insulin signaling pathway in the brain of AD patients. In order to investigate this complex issue in more details and demonstrate additional links between T2DM and AD, the present study used several basic biological methods to clarify the question: "Is impaired insulin signaling pathway within the brain crucial for the development of AD?" from several points of view. The methods used in this work have been i) an analysis of single nucleotide (SNP) polymorphism of the insulin-degrading enzyme gene (IDE) in relation to risk of AD and / or of T2DM, ii) post-mortem histochemical studies of brain tissue of patients with only AD, with AD combined with T2DM and with only T2DM compared with an age-matched control group, and iii.) investigations of neurochemical pathways and gene/protein expression changes of a human cell culture as a consequences of amyloid β (Aβ) treatment. After analysis of the IDE SNP polymorphism in the selected VITA (Vienna Trans Danube Aging) cohort disease-specific effects were discovered. The upstream polymorphism (IDE2) was found to influence AD risk in a protective manner, while the downstream polymorphism (IDE7) modified the T2DM risk. Based on the SNP results, the presented study delineate the model that IDE promoter and 3‟ untranslated region/downstream variation can have different effects on IDE expression, maybe a relevant endophenotype with disorder-specific effects on AD and T2DM susceptibility. Furthermore, the human post-mortem studies could show that both AD as well as T2DM patients had a significantly lower density of the insulin receptor (IR) in the hippocampus, whereas a significantly increased density of inactive phosphorylated PPARγ has been found and this persisted even in patients with both diseases. Summarizing the histological study, it was possible to reveal common histological features of AD and T2DM, but no direct connection between the two diseases. Although AD is nowadays not only characterized by amyloid-containing plaque deposits and by the hyperphosphorylation of tau protein, the excessive Aβ42 presence in the brains of AD patients is still playing a key role. Up to date it is still not entirely clear which physical form of Aβ42 is responsible for the development of AD. The present work investigated, what impact has the state of aggregation of Aβ42 on genes and proteins of the insulin signaling pathway and the amyloid cascade. It could be shown that the oligomeric variant enhanced specifically the gene and protein expression of glycogen synthase kinase (GSK) 3β and also the enzyme activity was significantly increased, but has in turn strongly inhibited the IR gene and protein expression. Additionally, the effect of Aβ42 on monoamine oxidase B (MAO-B) was examined. An effect of both aggregated forms of Aβ42 had on enzyme activity was discovered. However, the fibrillar variants led to significantly increased activity of MAO-B while the oligomeric variants inhibited the enzyme activity. Several previous studies have demonstrated the involvement of increased MAO-B activity in AD, but the present work provides for the first time a direct link between the states of aggregation of Aβ42 to enzyme activity. Finally the results of the presented thesis can be summarized to following conclusion: Although AD and T2DM sharing some degrees of common features, still there is a lack of direct association, and therefore the diseases must be considered more independent rather than linked. But the impaired cerebral insulin signaling pathway seems to be another manifested hallmark of AD.},
  subject      = {Alzheimer-Krankheit},
  language  = {en}
}
@article{Siren1982,
  author    = {Sir{\´e}n, Anna-Leena},
  title     = {Differences in central actions of arachidonic acid and prostaglandin F\(_{2\alpha}\) between spontaneously hypertensive and normotensive rats},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-63324},
  year      = {1982},
  abstract  = {Prostag1andin F\(_{2\alpha}\) (PGF\(_{2\alpha}\)) is one of the most common metabo1ites of arachidonic acid (M) in rat brain. When administered intracerebroventricularly (i.c.v.) to rats, both AA and PGFal exert dose-related hypertensive, tachycardic and hyperthermic effects. Metabolie alterations in the endogenaus formation of some prostaglandins in the brain-stem of spontaneously hypertensive rats (SHR) have been reported. Therefore the central effects of AA and PGF \(_{2\alpha}\) on blood pressure, heart rate and body temperature were studied both in SHR and nonootensive Wistar rats (NR) under urethane-anaesthesia. The hypertensive effect of AA i.c.v. (0.01-100 \(\mu\)g/rat) was larger in magni tude in SHR than in NR, but there was no significant difference in the M-induced changes of heart rate and body temperature between the groups. Pretreatment of NR wi th soditm1 :meclofenamate (1 mg/rat i.c.v.) antagonised the central effects of M indicating that these effects are not due to M itself but to its conversion to prostaglandins. Unlike the effects of AA, the central hypertensive, tachycardic and hyperthennic responses to PGF\(_{2\alpha}\) (0.5-50 l-lg/rat i.c.v .) were significantly attenuated in SHR. The present results obtained with M are conpatible with the previous assumption that the synthesis of prostaglandins in the brain of SHR might differ from that in NR. The results also demonstrate that the central effects of PGF\(_{2\alpha}\) are reduced in SHR.},
  subject      = {Neurobiologie},
  language  = {en}
}
@article{EimerlSirenFeuerstein1986,
  author    = {Eimerl, J. and Sir{\´e}n, Anna-Leena and Feuerstein, G.},
  title     = {Systemic and regional hemodynamic effects of leukotrienes D\(_4\) and E\(_4\) in the conscious rat},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-63317},
  year      = {1986},
  abstract  = {No abstract available},
  subject      = {Neurobiologie},
  language  = {en}
}
@article{SirenFeuersteinLabrooetal.1986,
  author    = {Sir{\´e}n, Anna-Leena and Feuerstein, G. and Labroo, V. M. and Coleen, L. A. and Lozovsky, D.},
  title     = {Effect of thyrotropin releasing hormone and some of its histidine analogs on the cardiovascular system and prolactin release in the conscious rat},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-63307},
  year      = {1986},
  abstract  = {The cardiovascular and endocrine activity of three analogs of thyrotropin releasing hor.mone (TRH), 4-nitro-imidazole TRH (4-nitroTRH), 2-trifluoro-methyl-imidazole TRH (2-TFM-TRH) and 4-trifluoromethyl- imidazole TRH (4-TFM-TRH), was compared to TRH in conscious rats. Injection of TRH or the three analogs (1 mg/kg or 5 mg/kg) into the arterial line induced increases in mean arterial pressure, pulse pressure and heart rate and raised plasma prolactin (PRL). None of the analogs were more potent than TRH in inducing cardiovascular changes. The 4-TFM-TRH was significantly less potent than the 2-TFM-TRH in increasing blood pressure, while the nitro-TRH was more potent than the 2-TFM-TRH in producing tachycardia. TRH induced a two-fold increase in PRL at the 5 mg/kg dose, while both the fluorinated analogs elici ted a 4 to 5 fold increase in PRL at the higher dose. The present results suggest that the receptors for TRH-elicited PRL release differ from TRH-receptors involved in its cardiovascular actions.},
  subject      = {Neurobiologie},
  language  = {en}
}
@article{SirenFeuerstein1986,
  author    = {Sir{\´e}n, Anna-Leena and Feuerstein, G.},
  title     = {Effect of T-2 toxin on regional blood flow and vascular resistance in the conscious rat},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-63293},
  year      = {1986},
  abstract  = {The acute effect ofT-2 toxemia on local blood flow and vascular resistance in hindquarter. mesenteric. and renal vascular beds was continuously measured by the directional pulsed Doppler technique in conscious, male Sprague-Dawley rats. Intravenous injection ofT-2 toxin (I mg/kg) in the conscious rat reduced blood flow and increased vascular resistance in all blood vessels studied but had no significant effect on mean arterial pressure or heart rate. The blood flow in hindquarters gradually decreased to a minimum of -77 ± 9\% (mean ±SE) 6 hr after the toxin injection. The hindquarter vascular resistance concomitantly increased to a maximum value of + 323 ± 69\% above thc resistance before toxin administration. Mesenteric and renal blood flow initially increased (slightly) and then gradually decreased. The maximum drop of blood flow, -90 ± 13\% and -76 ± 13\% for the mesenteric and renal vascular beds, respectively, was achieved 4 hr after T-2 toxin injection and the blood flow values remained low for up to 6 hr. Simultaneously with the impairment of},
  subject      = {Neurobiologie},
  language  = {en}
}
@article{SirenPowellFeuerstein1986,
  author    = {Sir{\´e}n, Anna-Leena and Powell, E. and Feuerstein, G.},
  title     = {Thyrotropin releasing hormone in hypovolemia: a hemodynamic evaluation in the rat},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-63288},
  year      = {1986},
  abstract  = {ln the present study the effects of thyrotropin releasing hormone (TRH) and its stable analogue, CG3703, on cardiac output (thermodilution, Cardiomax) and regional blood flow (BF; directional pulsed Doppler technique) were investigated in hypovolemic hypotension in the rat. In urethan-anesthetized rats TRH (0.5 or 2 mg/ kg ia) or CG3703 (0.05 or 0.5 mg/kg ia) reversed the bleeding (27\% of the blood volume)-induced decreases in mean arterial ...},
  subject      = {Neurobiologie},
  language  = {en}
}
@article{PaakkariNurminenSiren1986,
  author    = {Paakkari, I. and Nurminen, M-L. and Sir{\´e}n, Anna-Leena},
  title     = {Cardioventilatory effects of TRH in anesthetized rats: role of the brainstem},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-63277},
  year      = {1986},
  abstract  = {Cardioventilator responses were studied in anaesthetized rats after injections of TRH into either the lateral (i.c.v. lat) or the fourth (i.c.v. IV) cerebral ventricles. TRH induced a morerapid hypertensive effect i.c.v. IV than i.c.v. lat. Blocking of the cerebral aqueduct abolished the hypertensive and tachypnoeic effects of TRH i.c.v. lat but not those of TRH i.c.v. IV. It is concluded that TRH increased blood pressure and ventilation rate via brain stem structures close to the fourtli ventricle.},
  subject      = {Neurobiologie},
  language  = {en}
}