TY - JOUR A1 - Buchheim, Mark A. A1 - Keller, Alexander A1 - Koetschan, Christian A1 - Förster, Frank A1 - Merget, Benjamin A1 - Wolf, Matthias T1 - Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life JF - PLoS ONE N2 - Background: Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta. Methodology/Principal Findings: Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses. Conclusions/Significance: Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages. KW - RBCL Gene-sequences KW - Colonial volvocales chlorophyta KW - 26S RDNA Data KW - Land plants KW - Molecular systematics KW - Secondary structure KW - Nuclear RDNA KW - DNA KW - Barcodes KW - Dasycladales chlorophyta KW - Profile distances Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-140866 VL - 6 IS - 2 ER - TY - JOUR A1 - Iyengar, Sudha K. A1 - Sedor, John R. A1 - Freedman, Barry I. A1 - Kao, W. H. Linda A1 - Kretzler, Matthias A1 - Keller, Benjamin J. A1 - Abboud, Hanna E. A1 - Adler, Sharon G. A1 - Best, Lyle G. A1 - Bowden, Donald W. A1 - Burlock, Allison A1 - Chen, Yii-Der Ida A1 - Cole, Shelley A. A1 - Comeau, Mary E. A1 - Curtis, Jeffrey M. A1 - Divers, Jasmin A1 - Drechsler, Christiane A1 - Duggirala, Ravi A1 - Elston, Robert C. A1 - Guo, Xiuqing A1 - Huang, Huateng A1 - Hoffmann, Michael Marcus A1 - Howard, Barbara V. A1 - Ipp, Eli A1 - Kimmel, Paul L. A1 - Klag, Michael J. A1 - Knowler, William C. A1 - Kohn, Orly F. A1 - Leak, Tennille S. A1 - Leehey, David J. A1 - Li, Man A1 - Malhotra, Alka A1 - März, Winfried A1 - Nair, Viji A1 - Nelson, Robert G. A1 - Nicholas, Susanne B. A1 - O’Brien, Stephen J. A1 - Pahl, Madeleine V. A1 - Parekh, Rulan S. A1 - Pezzolesi, Marcus G. A1 - Rasooly, Rebekah S. A1 - Rotimi, Charles N. A1 - Rotter, Jerome I. A1 - Schelling, Jeffrey R. A1 - Seldin, Michael F. A1 - Shah, Vallabh O. A1 - Smiles, Adam M. A1 - Smith, Michael W. A1 - Taylor, Kent D. A1 - Thameem, Farook A1 - Thornley-Brown, Denyse P. A1 - Truitt, Barbara J. A1 - Wanner, Christoph A1 - Weil, E. Jennifer A1 - Winkler, Cheryl A. A1 - Zager, Philip G. A1 - Igo, Jr, Robert P. A1 - Hanson, Robert L. A1 - Langefeld, Carl D. T1 - Genome-wide association and trans-ethnic meta-analysis for advanced diabetic kidney disease: Family Investigation of Nephropathy and Diabetes (FIND) JF - PLoS Genetics N2 - Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10\(^{−9}\)). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10\(^{−8}\)), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD. KW - diabetic kidney disease KW - genome-wide association study KW - Family Investigation of Nephropathy and Diabetes Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-180545 VL - 11 IS - 8 ER - TY - JOUR A1 - Koetschan, Christian A1 - Foerster, Frank A1 - Keller, Alexander A1 - Schleicher, Tina A1 - Ruderisch, Benjamin A1 - Schwarz, Roland A1 - Mueller, Tobias A1 - Wolf, Matthias A1 - Schultz, Joerg T1 - The ITS2 Database III-sequences and structures for phylogeny N2 - The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps .biozentrum.uni-wuerzburg.de) which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version, we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline. This allowed the identification of more than 160 000 correct full ength and more than 50 000 partial structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses. KW - Biologie Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-68390 ER - TY - GEN A1 - Keller, Matthias T1 - Kampfpreisstrategien - Aktuelle Entwicklungen im Lichte des More Economic Approach: Von AKZO über Tetra Pak und Wanadoo Interactive bis hin zur Prioritätenmitteilung T1 - Predatory Pricing - Current Developments in the Light of More Economic Approach: From AKZO to Tetra Pak and Wanadoo Interactive to the Guidance on Enforcement Priorities N2 - Die vorliegende Arbeit ist dem sogenannten Kampfpreismissbrauch im ökonomisierten Unionskartellrecht gewidmet. Sie befasst sich mit den Fragen, inwieweit missbräuchliche – d. h. nicht kostendeckende – Kampfpreisstrategien von erwünschten Preissenkungen im Rahmen des zulässigen Leistungswettbewerbs plausibel abgegrenzt werden können und welche Kriterien zu einer entsprechenden Unterscheidung heranzuziehen sind. Thematisiert und kritisch durchleuchtet wird dabei der aktuelle Reformprozess der Kommission, welcher prinzipiell für ein stärker ökonomisiertes Verständnis des Kartellrechts steht ("More Economic Approach"). Als elementare Grundlage dient in diesem Zusammenhang neben dem im Dezember 2005 erschienenen Diskussionspapier insbesondere die im Februar 2009 veröffentlichte Prioritätenmitteilung. Anhand konkreter Beispiele aus der europäischen Fallpraxis soll außerdem aufgezeigt werden, in welchem Maße die europäischen Gerichte bereit sind, den stärker ökonomisierten Ansatz mitzutragen. Ziel ist es, die von Kommission und EuGH entwickelten Rechtsgrundsätze im Bereich des strategischen Kampfpreismissbrauchs darzustellen und zu bewerten. Dabei gilt es vor allem die ökonomischen Aspekte des "More Economic Approach" herauszustellen, auf systematische Grenzen einzugehen und etwaige Umsetzungsprobleme zu diskutieren. Neben den ökonomischen Auslegungen werden stets auch die rechtlichen Ansprüche an Rechtssicherheit und Nachweisbarkeit ins Kalkül miteinbezogen. T3 - Würzburger Arbeiten zum Wirtschaftsrecht - 2 KW - Behinderungsmissbrauch KW - Kampfpreisstrategie KW - Kampfpreismissbrauch KW - Verdrängungswettbewerb KW - Predatory Pricing Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-70569 ER - TY - JOUR A1 - Keller, Alexander A1 - Foerster, Frank A1 - Mueller, Tobias A1 - Dandekar, Thomas A1 - Schultz, Joerg A1 - Wolf, Matthias T1 - Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees N2 - Background: In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results: This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions: Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers: This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Open peer review: Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers’ comments section. KW - Phylogenie KW - phylogenetics Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-67832 ER - TY - JOUR A1 - Ramachandran, Sarada Devi A1 - Schirmer, Katharina A1 - Münst, Bernhard A1 - Heinz, Stefan A1 - Ghafoory, Shahrouz A1 - Wölfl, Stefan A1 - Simon-Keller, Katja A1 - Marx, Alexander A1 - Øie, Cristina Ionica A1 - Ebert, Matthias P. A1 - Walles, Heike A1 - Braspenning, Joris A1 - Breitkopf-Heinlein, Katja T1 - In Vitro Generation of Functional Liver Organoid-Like Structures Using Adult Human Cells JF - PLoS One N2 - In this study we used differentiated adult human upcyte (R) cells for the in vitro generation of liver organoids. Upcyte (R) cells are genetically engineered cell strains derived from primary human cells by lenti-viral transduction of genes or gene combinations inducing transient proliferation capacity (upcyte (R) process). Proliferating upcyte (R) cells undergo a finite number of cell divisions, i.e., 20 to 40 population doublings, but upon withdrawal of proliferation stimulating factors, they regain most of the cell specific characteristics of primary cells. When a defined mixture of differentiated human upcyte (R) cells (hepatocytes, liver sinusoidal endothelial cells (LSECs) and mesenchymal stem cells (MSCs)) was cultured in vitro on a thick layer of Matrigel\(^{TM}\), they self-organized to form liver organoid-like structures within 24 hours. When further cultured for 10 days in a bioreactor, these liver organoids show typical functional characteristics of liver parenchyma including activity of cytochromes P450, CYP3A4, CYP2B6 and CYP2C9 as well as mRNA expression of several marker genes and other enzymes. In summary, we hereby describe that 3D functional hepatic structures composed of primary human cell strains can be generated in vitro. They can be cultured for a prolonged period of time and are potentially useful ex vivo models to study liver functions. KW - adults KW - enzyme metabolism KW - albumins KW - primary cells KW - induction KW - expression KW - human heptocytes KW - mesenchymal stem cells KW - oragnoids KW - heptaocytes KW - drug metabolism Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-139552 VL - 10 IS - 10 ER - TY - JOUR A1 - Philipp-Abbrederis, Kathrin A1 - Herrmann, Ken A1 - Knop, Stefan A1 - Schottelius, Margret A1 - Eiber, Matthias A1 - Lückerath, Katharina A1 - Pietschmann, Elke A1 - Habringer, Stefan A1 - Gerngroß, Carlos A1 - Franke, Katharina A1 - Rudelius, Martina A1 - Schirbel, Andreas A1 - Lapa, Constantin A1 - Schwamborn, Kristina A1 - Steidle, Sabine A1 - Hartmann, Elena A1 - Rosenwald, Andreas A1 - Kropf, Saskia A1 - Beer, Ambros J A1 - Peschel, Christian A1 - Einsele, Hermann A1 - Buck, Andreas K A1 - Schwaiger, Markus A1 - Götze, Katharina A1 - Wester, Hans-Jürgen A1 - Keller, Ulrich T1 - In vivo molecular imaging of chemokine receptor CXCR4 expression in patients with advanced multiple myeloma JF - EMBO Molecular Medicine N2 - CXCR4 is a G-protein-coupled receptor that mediates recruitment of blood cells toward its ligand SDF-1. In cancer, high CXCR4 expression is frequently associated with tumor dissemination andpoor prognosis. We evaluated the novel CXCR4 probe [\(^{68}\)Ga]Pentixafor for invivo mapping of CXCR4 expression density in mice xenografted with human CXCR4-positive MM cell lines and patients with advanced MM by means of positron emission tomography (PET). [\(^{68}\)Ga]Pentixafor PET provided images with excellent specificity and contrast. In 10 of 14 patients with advanced MM [\(^{68}\)Ga]Pentixafor PET/CT scans revealed MM manifestations, whereas only nine of 14 standard [\(^{18}\)F]fluorodeoxyglucose PET/CT scans were rated visually positive. Assessment of blood counts and standard CD34\(^{+}\) flow cytometry did not reveal significant blood count changes associated with tracer application. Based on these highly encouraging data on clinical PET imaging of CXCR4 expression in a cohort of MM patients, we conclude that [\(^{68}\)Ga]Pentixafor PET opens a broad field for clinical investigations on CXCR4 expression and for CXCR4-directed therapeutic approaches in MM and other diseases. KW - FDG PET/CT KW - cells KW - CXCR4/SDF-1 KW - CXCR4 KW - multiple myeloma KW - positron emission tomography KW - chemokine receptor KW - in vivo imaging KW - malignancies KW - involvement KW - microenvironment KW - survival KW - cancer KW - autologous transplantation KW - bone disease Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148738 VL - 7 IS - 4 ER - TY - JOUR A1 - Hornick, Thomas A1 - Richter, Anett A1 - Harpole, William Stanley A1 - Bastl, Maximilian A1 - Bohlmann, Stephanie A1 - Bonn, Aletta A1 - Bumberger, Jan A1 - Dietrich, Peter A1 - Gemeinholzer, Birgit A1 - Grote, Rüdiger A1 - Heinold, Bernd A1 - Keller, Alexander A1 - Luttkus, Marie L. A1 - Mäder, Patrick A1 - Motivans Švara, Elena A1 - Passonneau, Sarah A1 - Punyasena, Surangi W. A1 - Rakosy, Demetra A1 - Richter, Ronny A1 - Sickel, Wiebke A1 - Steffan‐Dewenter, Ingolf A1 - Theodorou, Panagiotis A1 - Treudler, Regina A1 - Werchan, Barbora A1 - Werchan, Matthias A1 - Wolke, Ralf A1 - Dunker, Susanne T1 - An integrative environmental pollen diversity assessment and its importance for the Sustainable Development Goals JF - Plants, People, Planet N2 - Societal Impact Statement Pollen relates to many aspects of human and environmental health, which protection and improvement are endorsed by the United Nations Sustainable Development Goals. By highlighting these connections in the frame of current challenges in monitoring and research, we discuss the need of more integrative and multidisciplinary pollen research related to societal needs, improving health of humans and our ecosystems for a sustainable future. Summary Pollen is at once intimately part of the reproductive cycle of seed plants and simultaneously highly relevant for the environment (pollinators, vector for nutrients, or organisms), people (food safety and health), and climate (cloud condensation nuclei and climate reconstruction). We provide an interdisciplinary perspective on the many and connected roles of pollen to foster a better integration of the currently disparate fields of pollen research, which would benefit from the sharing of general knowledge, technical advancements, or data processing solutions. We propose a more interdisciplinary and holistic research approach that encompasses total environmental pollen diversity (ePD) (wind and animal and occasionally water distributed pollen) at multiple levels of diversity (genotypic, phenotypic, physiological, chemical, and functional) across space and time. This interdisciplinary approach holds the potential to contribute to pressing human issues, including addressing United Nations Sustainable Development Goals, fostering social and political awareness of these tiny yet important and fascinating particles. KW - aerobiology KW - allergy KW - diversity KW - environmental monitoring KW - food safety KW - paleoecology KW - palynology KW - pollination Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-276487 VL - 4 IS - 2 SP - 110 EP - 121 ER -