@phdthesis{Zhu2015, author = {Zhu, Ana Cheng}, title = {Metagenomic analysis of genetic variation in human gut microbial species}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-113890}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {Microbial species (bacteria and archaea) in the gut are important for human health in various ways. Not only does the species composition vary considerably within the human population, but each individual also appears to have its own strains of a given species. While it is known from studies of bacterial pan-genomes, that genetic variation between strains can differ considerably, such as in Escherichia coli, the extent of genetic variation of strains for abundant gut species has not been surveyed in a natural habitat. This is mainly due to the fact that most of these species cannot be cultured in the laboratory. Genetic variation can range from microscale genomic rearrangements such as small nucleotide polymorphism (SNP) to macroscale large genomic rearrangements like structural variations. Metagenomics offers an alternative solution to study genetic variation in prokaryotes, as it involves DNA sequencing of the whole community directly from the environment. However, most metagenomic studies to date only focus on variation in gene abundance and hence are not able to characterize genetic variation (in terms of presence or absence of SNPs and genes) of gut microbial strains of individuals. The aim of my doctorate studies was therefore to study the extent of genetic variation in the genomic sequence of gut prokaryotic species and its phenotypic effects based on: (1) the impact of SNP variation in gut bacterial species, by focusing on genes under selective pressure and (2) the gene content variation (as a proxy for structural variation) and their effect on microbial species and the phenotypic traits of their human host. In the first part of my doctorate studies, I was involved in a project in which we created a catalogue of 10.3 million SNPs in gut prokaryotic species, based on metagenomes. I used this to perform the first SNP-based comparative study of prokaryotic species evolution in a natural habitat. Here, I found that strains of gut microbial species in different individuals evolve at more similar rates than the strains within an individual. In addition, I found that gene evolution can be uncoupled from the evolution of its originating species, and that this could be related to selective pressure such as diet, exemplified by galactokinase gene (galK). Despite the individuality (i.e. uniqueness of each individual within the studied metagenomic dataset) in the SNP profile of the gut microbiota that we found, for most cases it is not possible to link SNPs with phenotypic differences. For this reason I also used gene content as a proxy to study structural variation in metagenomes. In the second part of my doctorate studies, I developed a methodology to characterize the variability of gene content in gut bacterial species, using metagenomes. My approach is based on gene deletions, and was applied to abundant species (demonstrated using a set of 11 species). The method is sufficiently robust as it captures a similar range of gene content variability as has been detected in completely sequenced genomes. Using this procedure I found individuals differ by an average of 13\% in their gene content of gut bacterial strains within the same species. Interestingly no two individuals shared the same gene content across bacterial species. However, this variation corresponds to a lower limit, as it is only accounts for gene deletion and not insertions. This large variation in the gene content of gut strain was found to affect important functions, such as polysaccharide utilization loci (PULs) and capsular polysaccharide synthesis (CPS), which are related with digestion of dietary fibers. In summary, I have shown that metagenomics based approaches can be robust in characterizing genetic variation in gut bacterial species. I also illustrated, using examples both for SNPs and gene content (galK, PULs and CPS), that this genetic variation can be used to predict the phenotypic characteristics of the microbial species, as well as predicting the phenotype of their human host (for example, their capacity to digest different food components). Overall, the results of my thesis highlight the importance of characterizing the strains in the gut microbiome analogous to the emerging variability and importance of human genomics.}, subject = {Darmflora}, language = {en} } @phdthesis{Zhou2005, author = {Zhou, Qingchun}, title = {Molecular analysis of the sex-determining region of the Y chromosome in the platyfish Xiphophorus maculatus}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13827}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2005}, abstract = {A large variety of sex determination systems have been described in fish. However, almost no information is available about sex determination in the classical fish models, the zebrafish Danio rerio and the pufferfish Takifugu rubripes. A DNA-binding protein gene called dmrt1bY (or DMY) has been recently described as an outstanding candidate for the primary sex-determining gene in the medaka fish Oryzias latipes. But this gene is not the universal master sex-determining gene in teleost fish, since dmrt1bY is not found in most other fishes. Hence, other fish models need to be examined including the platyfish Xiphophorus maculatus. Xiphophorus maculatus has three types of sex chromosomes (X, Y and W; females are XX, WX or WY; males are XY or YY). Its gonosomes are at an early stage of differentiation. The sex-determining locus on the sex chromosomes is flanked by two receptor tyrosine kinase genes, the Xmrk oncogene and its protooncogenic progenitor gene egfrb, which both delimit a region of about 0.6 centiMorgans. This situation should allow the positional cloning of the sex-determining gene (SD) of the platyfish. For this purpose, Bacterial Artificial Chromosome (BAC) contigs were assembled from a BAC library of XY males constructed in our laboratory, using the oncogene Xmrk, egfrb, as well as a Y-specific pseudogene called ps-criptY as starting points. The ps-criptY sequence was found to be closely linked to the SD gene, since no recombination was observed between SD and ps-criptY in more than 400 individuals tested. Two major BAC contigs for the X chromosome (about 2.5 Mb) and three major BAC contigs for the Y chromosome (about 3.5 Mb) were built up and analyzed by strategic sequencing. These are some of the largest contigs ever assembled for the sex chromosomes of a non-mammalian vertebrate species. The molecular analysis of the ps-criptY contig was the major objective of this work. The Y-specific ps-criptY contig has been extended over 1 Mb in this work with 58 identified molecular markers. Approximatively 700 kb of non-redundant sequences has been obtained from this contig by strategic sequencing. Numerous Y-linked markers from the contig including ps-criptY were also detected on the X chromosome. Nevertheless, major structural differences were observed between the X and Y chromosomes. Particularly, a large region, which is present at one copy on the X chromosome and contains several candidate genes, was found to be duplicated on the Y chromosome. Evidence for an inversion in the sex-determining region and for the Y-specific accumulation of a repeated sequence called XIR was also obtained. Such events might correspond to an initiation of differentiation between both types of gonosomes. Accumulation of transposable elements was also observed in the ps-criptY contig. A DNA transposable element, helitron, was isolated from the sex-determining region of X. maculatus. Three copies of helitron are located on the ps-criptY contig and one copy on the X-linked contig (helitron has roughly 15 copies per haploid genome). No in-frame stop codon, truncation or intron was found in these four copies, which present high nucleotide identities to each other. This suggests that helitron elements might be active or have been recently active in X. maculatus. A consensus open reading frame of helitron was also assembled from medaka (Oryzias latipes) genomic sequences. Two candidate genes from the ps-criptY contig are also located on the W chromosome in the X. maculatus Usumacinta strain (heterogamety). These markers show the relationship between the different types of gonosomes and allow to compare the male and female heterogameties in the platyfish. Several gene candidates were identified in the ps-criptY contig. However, some of them such as msh2, cript, igd and acr probably correspond to pseudogenes. Interestingly, a novel gene, called swimy, is exclusively expressed in spermatogonia of the adult testis. Swimy is a gene encoding a DNA-binding protein with several putative DNA-binding domains. The data suggest that swimy is a very promising candidate for the master SD gene. Another novel gene, which is called fredi and encodes a novel helix-turn-helix protein, is predominately expressed in the adult testis and currently under scrutiny. There is no doubt that the master SD gene of X. maculatus will be identified by positional cloning. Further molecular analysis of the contigs built in this work will shed new light on the molecular mechanism of sex determination and the evolution of sex chromosomes in fish.}, subject = {Platy}, language = {en} } @article{ZhangSiPahl2012, author = {Zhang, Shaowu and Si, Aung and Pahl, Mario}, title = {Visually guided decision making in foraging honeybees}, series = {Frontiers in Neuroscience}, volume = {6}, journal = {Frontiers in Neuroscience}, number = {88}, doi = {10.3389/fnins.2012.00088}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124228}, year = {2012}, abstract = {Honeybees can easily be trained to perform different types of discrimination tasks under controlled laboratory conditions. This review describes a range of experiments carried out with free-flying forager honeybees under such conditions. The research done over the past 30 or so years suggests that cognitive abilities (learning and perception) in insects are more intricate and flexible than was originally imagined. It has become apparent that honeybees are capable of a variety of visually guided tasks, involving decision making under challenging situations: this includes simultaneously making use of different sensory modalities, such as vision and olfaction, and learning to use abstract concepts such as "sameness" and "difference." Many studies have shown that decision making in foraging honeybees is highly flexible. The trained animals learn how to solve a task, and do so with a high accuracy, but when they are presented with a new variation of the task, they apply the learnt rules from the earlier setup to the new situation, and solve the new task as well. Honeybees therefore not only feature a rich behavioral repertoire to choose from, but also make decisions most apt to the current situation. The experiments in this review give an insight into the environmental cues and cognitive resources that are probably highly significant for a forager bee that must continually make decisions regarding patches of resources to be exploited.}, language = {en} } @article{ZhanStanciauskasStigloheretal.2014, author = {Zhan, Hong and Stanciauskas, Ramunas and Stigloher, Christian and Dizon, Kevin K. and Jospin, Maelle and Bessereau, Jean-Luis and Pinaud, Fabien}, title = {In vivo single-molecule imaging identifies altered dynamics of calcium channels in dystrophin-mutant C. elegans}, series = {Nature Communications}, volume = {5}, journal = {Nature Communications}, number = {4974}, doi = {10.1038/ncomms5974}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121125}, year = {2014}, abstract = {Single-molecule (SM) fluorescence microscopy allows the imaging of biomolecules in cultured cells with a precision of a few nanometres but has yet to be implemented in living adult animals. Here we used split-GFP (green fluorescent protein) fusions and complementation-activated light microscopy (CALM) for subresolution imaging of individual membrane proteins in live Caenorhabditis elegans (C. elegans). In vivo tissue-specific SM tracking of transmembrane CD4 and voltage-dependent Ca(2+) channels (VDCC) was achieved with a precision of 30 nm within neuromuscular synapses and at the surface of muscle cells in normal and dystrophin-mutant worms. Through diffusion analyses, we reveal that dystrophin is involved in modulating the confinement of VDCC within sarcolemmal membrane nanodomains in response to varying tonus of C. elegans body-wall muscles. CALM expands the applications of SM imaging techniques beyond the petri dish and opens the possibility to explore the molecular basis of homeostatic and pathological cellular processes with subresolution precision, directly in live animals.}, language = {en} } @article{ZentgrafTrendelenburgSpringetal.1979, author = {Zentgraf, Hanswalter and Trendelenburg, Michael F. and Spring, Herbert and Scheer, Ulrich and Franke, Werner W. and M{\"u}ller, Ulrike and Drury, Kenneth C. and Rungger, Duri}, title = {Mitochondrial DNA arranged into chromatin-like structures after injection into amphibian oocyte nuclei}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-33174}, year = {1979}, abstract = {Purified mitochondrial DNA (mitDNA) from ovaries ofXenopus lae vis was injected into the nuclei (germinal vesicles) of large viteUogenic oocytes of the same organism and examined by electron microscopy ofthe spread nuclear contents. Normally located nuclei of untreated oocytes as weil as peripherally translocated nuclei of centrifuged oocytes were used. In addition, oocyte nuclei isolated and incubated under liquid paraffin oil were injected with DNA. The integrity oftranscriptional structures of endogenous chromosomal (Iampbrush chromosomes) and extrachromosomal (nucleoli) genes of the injected nuclei was demonstrated. Microinjected mitDN A was identified as circles of chromatin exhibiting polynucleosome-like organization and a me an contour length of 2.6 J.Lm, corresponding to a compaction ratio of the mitDN A of about 2 : I. This DNA packing ratio is similar to that observed after preparation of various kinds of native chromatin in low salt buffers. The chromatin circles formed from injected mitDNA only very rarely exhibited lateral fibrils suggestive of transcriptional activity. These results suggest that purified mitDNA can be transformed to normally structured chromatin when exposed to oocyte nuclear contents but is rarely , if at all , transcribed in this form and in this environment.}, language = {en} } @article{ZentgrafScheerFranke1975, author = {Zentgraf, Hanswalter and Scheer, Ulrich and Franke, Werner W.}, title = {Characterization and localization of the RNA synthesized in mature avian erythrocytes}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-32410}, year = {1975}, abstract = {No abstract available}, language = {en} } @inproceedings{ZentgrafScheerFranke1976, author = {Zentgraf, Hanswalter and Scheer, Ulrich and Franke, Werner W.}, title = {On the existence of arrested transcriptional machinery in late stages of avian erythropoiesis}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-33696}, year = {1976}, abstract = {No abstract available}, language = {de} } @article{ZentgrafMuellerScheeretal.1981, author = {Zentgraf, H. and M{\"u}ller, U. and Scheer, Ulrich and Franke, W. W.}, title = {Evidence for the existence of globular units in the supranucleosomal organization of chromatin}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-34123}, year = {1981}, abstract = {No abstract available}, language = {en} } @phdthesis{Zeeshan2012, author = {Zeeshan, Ahmed}, title = {Bioinformatics Software for Metabolic and Health Care Data Management}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-73926}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {Computer Science approaches (software, database, management systems) are powerful tools to boost research. Here they are applied to metabolic modelling in infections as well as health care management. Starting from a comparative analysis this thesis shows own steps and examples towards improvement in metabolic modelling software and health data management. In section 2, new experimental data on metabolites and enzymes induce high interest in metabolic modelling including metabolic flux calculations. Data analysis of metabolites, calculation of metabolic fluxes, pathways and their condition-specific strengths is now possible by an advantageous combination of specific software. How can available software for metabolic modelling be improved from a computational point of view? A number of available and well established software solutions are first discussed individually. This includes information on software origin, capabilities, development and used methodology. Performance information is obtained for the compared software using provided example data sets. A feature based comparison shows limitations and advantages of the compared software for specific tasks in metabolic modeling. Often found limitations include third party software dependence, no comprehensive database management and no standard format for data input and output. Graphical visualization can be improved for complex data visualization and at the web based graphical interface. Other areas for development are platform independency, product line architecture, data standardization, open source movement and new methodologies. The comparison shows clearly space for further software application development including steps towards an optimal user friendly graphical user interface, platform independence, database management system and third party independence especially in the case of desktop applications. The found limitations are not limited to the software compared and are of course also actively tackled in some of the most recent developments. Other improvements should aim at generality and standard data input formats, improved visualization of not only the input data set but also analyzed results. We hope, with the implementation of these suggestions, metabolic software applications will become more professional, cheap, reliable and attractive for the user. Nevertheless, keeping these inherent limitations in mind, we are confident that the tools compared can be recommended for metabolic modeling for instance to model metabolic fluxes in bacteria or metabolic data analysis and studies in infection biology. ...}, subject = {Stoffwechsel}, language = {en} } @article{Zeeshan2010, author = {Zeeshan, Ahmed}, title = {Towards Performance Measurement and Metrics Based Analysis of PLA Applications}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-68188}, year = {2010}, abstract = {This article is about a measurement analysis based approach to help software practitioners in managing the additional level complexities and variabilities in software product line applications. The architecture of the proposed approach i.e. ZAC is designed and implemented to perform preprocessesed source code analysis, calculate traditional and product line metrics and visualize results in two and three dimensional diagrams. Experiments using real time data sets are performed which concluded with the results that the ZAC can be very helpful for the software practitioners in understanding the overall structure and complexity of product line applications. Moreover the obtained results prove strong positive correlation between calculated traditional and product line measures.}, subject = {Programmierbare logische Anordnung}, language = {en} }