@phdthesis{Franke2019,
  author    = {Franke, Christian},
  title     = {Advancing Single-Molecule Localization Microscopy: Quantitative Analyses and Photometric Three-Dimensional Imaging},
  doi       = {10.25972/OPUS-15635},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-156355},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2019},
  abstract  = {Since its first experimental implementation in 2005, single-molecule localization microscopy (SMLM) emerged as a versatile and powerful imaging tool for biological structures with nanometer resolution. By now, SMLM has compiled an extensive track-record of novel insights in sub- and inter- cellular organization.\\ Moreover, since all SMLM techniques rely on the analysis of emission patterns from isolated fluorophores, they inherently allocate molecular information \$per\$ \$definitionem\$.\\ Consequently, SMLM transitioned from its origin as pure high-resolution imaging instrument towards quantitative microscopy, where the key information medium is no longer the highly resolved image itself, but the raw localization data set.\\ The work presented in this thesis is part of the ongoing effort to translate those \$per\$ \$se\$ molecular information gained by SMLM imaging to insights into the structural organization of the targeted protein or even beyond. Although largely consistent in their objectives, the general distinction between global or segmentation clustering approaches on one side and particle averaging or meta-analyses techniques on the other is usually made.\\ During the course of my thesis, I designed, implemented and employed numerous quantitative approaches with varying degrees of complexity and fields of application.\\ \\ In my first major project, I analyzed the localization distribution of the integral protein gp210 of the nuclear pore complex (NPC) with an iterative \textit{k}-means algorithm. Relating the distinct localization statistics of separated gp210 domains to isolated fluorescent signals led, among others, to the conclusion that the anchoring ring of the NPC consists of 8 homo-dimers of gp210.\\ This is of particular significance, both because it answered a decades long standing question about the nature of the gp210 ring and it showcased the possibility to gain structural information well beyond the resolution capabilities of SMLM by crafty quantification approaches.\\ \\ The second major project reported comprises an extensive study of the synaptonemal complex (SNC) and linked cohesin complexes. Here, I employed a multi-level meta-analysis of the localization sets of various SNC proteins to facilitate the compilation of a novel model of the molecular organization of the major SNC components with so far unmatched extend and detail with isotropic three-dimensional resolution.\\ In a second venture, the two murine cohesin components SMC3 and STAG3 connected to the SNC were analyzed. Applying an adapted algorithm, considering the disperse nature of cohesins, led to the realization that there is an apparent polarization of those cohesin complexes in the SNC, as well as a possible sub-structure of STAG3 beyond the resolution capabilities of SMLM.\\ \\ Other minor projects connected to localization quantification included the study of plasma membrane glycans regarding their overall localization distribution and particular homogeneity as well as the investigation of two flotillin proteins in the membrane of bacteria, forming clusters of distinct shapes and sizes.\\ \\ Finally, a novel approach to three-dimensional SMLM is presented, employing the precise quantification of single molecule emitter intensities. This method, named TRABI, relies on the principles of aperture photometry which were improved for SMLM.\\ With TRABI it was shown, that widely used Gaussian fitting based localization software underestimates photon counts significantly. This mismatch was utilized as a \$z\$-dependent parameter, enabling the conversion of 2D SMLM data to a virtual 3D space. Furthermore it was demonstrated, that TRABI can be combined beneficially with a multi-plane detection scheme, resulting in superior performance regarding axial localization precision and resolution.\\ Additionally, TRABI has been subsequently employed to photometrically characterize a novel dye for SMLM, revealing superior photo-physical properties at the single-molecule level.\\ Following the conclusion of this thesis, the TRABI method and its applications remains subject of diverse ongoing research.},
  subject      = {Einzelmolek{\"u}lmikroskopie},
  language  = {en}
}
@article{FrankeVilnedaCostaetal.2015,
  author    = {Franke, Katharina and Vilne, Baiba and da Costa, Olivia Prazeres and Rudelius, Martina and Peschel, Christian and Oostendorp, Robert A. J. and Keller, Ulrich},
  title     = {In vivo hematopoietic Myc activation directs a transcriptional signature in endothelial cells within the bone marrow microenvironment},
  series = {Oncotarget},
  volume    = {6},
  journal   = {Oncotarget},
  number    = {26},
  doi       = {10.18632/oncotarget.5217},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-145844},
  pages     = {21827 -- 21839},
  year      = {2015},
  abstract  = {Cancer pathogenesis involves tumor-intrinsic genomic aberrations and tumor-cell extrinsic mechanisms such as failure of immunosurveillance and structural and functional changes in the microenvironment. Using Myc as a model oncogene we established a conditional mouse bone marrow transduction/transplantation model where the conditional activation of the oncoprotein Myc expressed in the hematopoietic system could be assessed for influencing the host microenvironment. Constitutive ectopic expression of Myc resulted in rapid onset of a lethal myeloproliferative disorder with a median survival of 21 days. In contrast, brief 4-day Myc activation by means of the estrogen receptor (ER) agonist tamoxifen did not result in gross changes in the percentage/frequency of hematopoietic lineages or hematopoietic stem/progenitor cell (HSPC) subsets, nor did Myc activation significantly change the composition of the non-hematopoietic microenvironment defined by phenotyping for CD31, ALCAM, and Sca-1 expression. Transcriptome analysis of endothelial CD45-Ter119-cells from tamoxifen-treated MycER bone marrow graft recipients revealed a gene expression signature characterized by specific changes in the Rho subfamily pathway members, in the transcription-translation-machinery and in angiogenesis. In conclusion, intra-hematopoietic Myc activation results in significant transcriptome alterations that can be attributed to oncogene-induced signals from hematopoietic cells towards the microenvironment, e. g. endothelial cells, supporting the idea that even pre-leukemic HSPC highjack components of the niche which then could protect and support the cancer-initiating population.},
  language  = {en}
}
@article{SchneiderKleinMielichSuessetal.2015,
  author    = {Schneider, Johannes and Klein, Teresa and Mielich-S{\"u}ss, Benjamin and Koch, Gudrun and Franke, Christian and Kuipers, Oskar P. and Kov{\´a}cs, {\´A}kos T. and Sauer, Markus and Lopez, Daniel},
  title     = {Spatio-temporal Remodeling of Functional Membrane Microdomains Organizes the Signaling Networks of a Bacterium},
  series = {PLoS Genetics},
  volume    = {11},
  journal   = {PLoS Genetics},
  number    = {4},
  doi       = {10.1371/journal.pgen.1005140},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-125577},
  pages     = {e1005140},
  year      = {2015},
  abstract  = {Lipid rafts are membrane microdomains specialized in the regulation of numerous cellular processes related to membrane organization, as diverse as signal transduction, protein sorting, membrane trafficking or pathogen invasion. It has been proposed that this functional diversity would require a heterogeneous population of raft domains with varying compositions. However, a mechanism for such diversification is not known. We recently discovered that bacterial membranes organize their signal transduction pathways in functional membrane microdomains (FMMs) that are structurally and functionally similar to the eukaryotic lipid rafts. In this report, we took advantage of the tractability of the prokaryotic model Bacillus subtilis to provide evidence for the coexistence of two distinct families of FMMs in bacterial membranes, displaying a distinctive distribution of proteins specialized in different biological processes. One family of microdomains harbors the scaffolding flotillin protein FloA that selectively tethers proteins specialized in regulating cell envelope turnover and primary metabolism. A second population of microdomains containing the two scaffolding flotillins, FloA and FloT, arises exclusively at later stages of cell growth and specializes in adaptation of cells to stationary phase. Importantly, the diversification of membrane microdomains does not occur arbitrarily. We discovered that bacterial cells control the spatio-temporal remodeling of microdomains by restricting the activation of FloT expression to stationary phase. This regulation ensures a sequential assembly of functionally specialized membrane microdomains to strategically organize signaling networks at the right time during the lifespan of a bacterium.},
  language  = {en}
}
@article{MarenholzEsparzaGordilloRueschendorfetal.2015,
  author    = {Marenholz, Ingo and Esparza-Gordillo, Jorge and R{\"u}schendorf, Franz and Bauerfeind, Anja and Strachan, David P. and Spycher, Ben D. and Baurecht, Hansj{\"o}rg and Magaritte-Jeannin, Patricia and S{\"a}{\"a}f, Annika and Kerkhof, Marjan and Ege, Markus and Baltic, Svetlana and Matheson, Melanie C. and Li, Jin and Michel, Sven and Ang, Wei Q. and McArdle, Wendy and Arnold, Andreas and Homuth, Georg and Demenais, Florence and Bouzigon, Emmanuelle and S{\"o}derh{\"a}ll, Cilla and Pershagen, G{\"o}ran and de Jongste, Johan C. and Postma, Dirkje S. and Braun-Fahrl{\"a}nder, Charlotte and Horak, Elisabeth and Ogorodova, Ludmila M. and Puzyrev, Valery P. and Bragina, Elena Yu and Hudson, Thomas J. and Morin, Charles and Duffy, David L. and Marks, Guy B. and Robertson, Colin F. and Montgomery, Grant W. and Musk, Bill and Thompson, Philip J. and Martin, Nicholas G. and James, Alan and Sleiman, Patrick and Toskala, Elina and Rodriguez, Elke and F{\"o}lster-Holst, Regina and Franke, Andre and Lieb, Wolfgang and Gieger, Christian and Heinzmann, Andrea and Rietschel, Ernst and Keil, Thomas and Cichon, Sven and N{\"o}then, Markus M. and Pennel, Craig E. and Sly, Peter D. and Schmidt, Carsten O. and Matanovic, Anja and Schneider, Valentin and Heinig, Matthias and H{\"u}bner, Norbert and Holt, Patrick G. and Lau, Susanne and Kabesch, Michael and Weidinger, Stefan and Hakonarson, Hakon and Ferreira, Manuel A. R. and Laprise, Catherine and Freidin, Maxim B. and Genuneit, Jon and Koppelman, Gerard H. and Mel{\´e}n, Erik and Dizier, Marie-H{\´e}l{\`e}ne and Henderson, A. John and Lee, Young Ae},
  title     = {Meta-analysis identifies seven susceptibility loci involved in the atopic march},
  series = {Nature Communications},
  volume    = {6},
  journal   = {Nature Communications},
  number    = {8804},
  doi       = {10.1038/ncomms9804},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139835},
  year      = {2015},
  abstract  = {Eczema often precedes the development of asthma in a disease course called the 'atopic march'. To unravel the genes underlying this characteristic pattern of allergic disease, we conduct a multi-stage genome-wide association study on infantile eczema followed by childhood asthma in 12 populations including 2,428 cases and 17,034 controls. Here we report two novel loci specific for the combined eczema plus asthma phenotype, which are associated with allergic disease for the first time; rs9357733 located in EFHC1 on chromosome 6p12.3 (OR 1.27; P = 2.1 x 10(-8)) and rs993226 between TMTC2 and SLC6A15 on chromosome 12q21.3 (OR 1.58; P = 5.3 x 10(-9)). Additional susceptibility loci identified at genome-wide significance are FLG (1q21.3), IL4/KIF3A (5q31.1), AP5B1/OVOL1 (11q13.1), C11orf30/LRRC32 (11q13.5) and IKZF3 (17q21). We show that predominantly eczema loci increase the risk for the atopic march. Our findings suggest that eczema may play an important role in the development of asthma after eczema.},
  language  = {en}
}
@article{Freitag‐WolfMunzJungeetal.2021,
  author    = {Freitag-Wolf, Sandra and Munz, Matthias and Junge, Olaf and Graetz, Christian and Jockel-Schneider, Yvonne and Staufenbiel, Ingmar and Bruckmann, Corinna and Lieb, Wolfgang and Franke, Andre and Loos, Bruno G. and Jepsen, S{\o}ren and Dommisch, Henrik and Schaefer, Arne S.},
  title     = {Sex-specific genetic factors affect the risk of early-onset periodontitis in Europeans},
  series = {Journal of Clinical Periodontology},
  volume    = {48},
  journal   = {Journal of Clinical Periodontology},
  number    = {11},
  doi       = {10.1111/jcpe.13538},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-262445},
  pages     = {1404 -- 1413},
  year      = {2021},
  abstract  = {Aims Various studies have reported that young European women are more likely to develop early-onset periodontitis compared to men. A potential explanation for the observed variations in sex and age of disease onset is the natural genetic variation within the autosomal genomes. We hypothesized that genotype-by-sex (G × S) interactions contribute to the increased prevalence and severity. Materials and methods Using the case-only design, we tested for differences in genetic effects between men and women in 896 North-West European early-onset cases, using imputed genotypes from the OmniExpress genotyping array. Population-representative 6823 controls were used to verify that the interacting variables G and S were uncorrelated in the general population. Results In total, 20 loci indicated G × S associations (P < 0.0005), 3 of which were previously suggested as risk genes for periodontitis (ABLIM2, CDH13, and NELL1). We also found independent G × S interactions of the related gene paralogs MACROD1/FLRT1 (chr11) and MACROD2/FLRT3 (chr20). G × S-associated SNPs at CPEB4, CDH13, MACROD1, and MECOM were genome-wide-associated with heel bone mineral density (CPEB4, MECOM), waist-to-hip ratio (CPEB4, MACROD1), and blood pressure (CPEB4, CDH13). Conclusions Our results indicate that natural genetic variation affects the different heritability of periodontitis among sexes and suggest genes that contribute to inter-sex phenotypic variation in early-onset periodontitis.},
  language  = {en}
}
@article{PhilippAbbrederisHerrmannKnopetal.2015,
  author    = {Philipp-Abbrederis, Kathrin and Herrmann, Ken and Knop, Stefan and Schottelius, Margret and Eiber, Matthias and L{\"u}ckerath, Katharina and Pietschmann, Elke and Habringer, Stefan and Gerngroß, Carlos and Franke, Katharina and Rudelius, Martina and Schirbel, Andreas and Lapa, Constantin and Schwamborn, Kristina and Steidle, Sabine and Hartmann, Elena and Rosenwald, Andreas and Kropf, Saskia and Beer, Ambros J and Peschel, Christian and Einsele, Hermann and Buck, Andreas K and Schwaiger, Markus and G{\"o}tze, Katharina and Wester, Hans-J{\"u}rgen and Keller, Ulrich},
  title     = {In vivo molecular imaging of chemokine receptor CXCR4 expression in patients with advanced multiple myeloma},
  series = {EMBO Molecular Medicine},
  volume    = {7},
  journal   = {EMBO Molecular Medicine},
  number    = {4},
  doi       = {10.15252/emmm.201404698},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148738},
  pages     = {477-487},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@article{BrevikvanDonkelaarWeberetal.2016,
  author    = {Brevik, Erlend J and van Donkelaar, Marjolein M. J. and Weber, Heike and S{\´a}nchez-Mora, Cristina and Jacob, Christian and Rivero, Olga and Kittel-Schneider, Sarah and Garcia-martinez, Iris and Aebi, Marcel and van Hulzen, Kimm and Cormand, Bru and Ramos-Quiroga, Josep A and Lesch, Klaus-Peter and Reif, Andreas and Ribases, Marta and Franke, Barbara and Posserud, Maj-Britt and Johansson, Stefan and Lundervold, Astri J. and Haavik, Jan and Zayats, Tetyana},
  title     = {Genome-wide analyses of aggressiveness in attention-deficit hyperactivity disorder},
  series = {American Journal of Medical Genetics Part B-Neuropsychiatric Genetics},
  volume    = {171B},
  journal   = {American Journal of Medical Genetics Part B-Neuropsychiatric Genetics},
  number    = {5},
  organization    = {IMAGE Consortium},
  doi       = {10.1002/ajmg.b.32434},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188116},
  pages     = {733-747},
  year      = {2016},
  abstract  = {Aggressiveness is a behavioral trait that has the potential to be harmful to individuals and society. With an estimated heritability of about 40\%, genetics is important in its development. We performed an exploratory genome-wide association (GWA) analysis of childhood aggressiveness in attention deficit hyperactivity disorder (ADHD) to gain insight into the underlying biological processes associated with this trait. Our primary sample consisted of 1,060 adult ADHD patients (aADHD). To further explore the genetic architecture of childhood aggressiveness, we performed enrichment analyses of suggestive genome-wide associations observed in aADHD among GWA signals of dimensions of oppositionality (defiant/vindictive and irritable dimensions) in childhood ADHD (cADHD). No single polymorphism reached genome-wide significance (P<5.00E-08). The strongest signal in aADHD was observed at rs10826548, within a long noncoding RNA gene (beta = -1.66, standard error (SE) = 0.34, P = 1.07E-06), closely followed by rs35974940 in the neurotrimin gene (beta = 3.23, SE = 0.67, P = 1.26E-06). The top GWA SNPs observed in aADHD showed significant enrichment of signals from both the defiant/vindictive dimension (Fisher's P-value = 2.28E-06) and the irritable dimension in cADHD (Fisher's P-value = 0.0061). In sum, our results identify a number of biologically interesting markers possibly underlying childhood aggressiveness and provide targets for further genetic exploration of aggressiveness across psychiatric disorders.},
  language  = {en}
}
@phdthesis{Franke2023,
  author    = {Franke, Christian},
  title     = {Gelenkknorpelintegration im Tissue Engineering: Untersuchung von Polyethylenglykol- und Hyalurons{\"a}ure-Komponenten f{\"u}r ein Adh{\"a}sivum und Etablierung eines biomechanischen Versuchsmodells},
  doi       = {10.25972/OPUS-32337},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-323375},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Gelenkknorpel besitzt aufgrund seiner avaskul{\"a}ren Natur und der fehlenden mitotischen Aktivit{\"a}t der Chondrozyten bei Sch{\"a}den kaum Potential zur Selbstheilung. Traumatische L{\"a}sionen und degenerative Ver{\"a}nderungen m{\"u}nden im Krankheitsbild der Osteoarthrose, welches mit dem Untergang des Gelenkknorpels einhergeht. Ein neuerer Therapieansatz ist das Tissue Engineering von Gelenkknorpel, wobei jedoch die laterale Integration der Implantate mit dem nativen Knorpelgewebe problematisch bleibt. Ein Adh{\"a}sivum kann neben einer ad{\"a}quaten Sofortadh{\"a}sion die Langzeitintegration f{\"o}rdern. In dieser Arbeit wurden verschiedene Polyethylenglykol (PEG)-basierte Zweikomponentenkleber, ausgehend vom kommerziell erh{\"a}ltlichen Gewebekleber CoSeal™, auf ihre Eignung f{\"u}r Gelenkknorpel untersucht. Dabei wurde Hyalurons{\"a}ure (HA) als physiologischer Bestandteil von Gelenkknorpel in thiolierter Form (HA-SH) als Komponente verwendet und auf seine prointegrativen Eigenschaften untersucht. Der den CoSeal™-Komponenten entsprechende 4-Succinimidyl-Glutarat/4-Thiol-PEG (4SG/4T-PEG)-Kleber hatte sich trotz seiner hohen Sofortadh{\"a}sionskraft auch nach der Substitution des 4T-PEG mit HA-SH als zu schnell in fl{\"u}ssiger Umgebung degradierend gezeigt, um eine suffiziente Langzeitintegration zu erreichen. Durch die Verwendung der langsamer degradierenden funktionellen 4-Succinimidyl-Carbonat-PEG (4C-PEG)-Komponente konnte die Langzeitadh{\"a}sionskraft in Kombination mit 4-Amin-PEG (4A-PEG) durch die stabilere Amid-Bindung zum einen und in Kombination mit HA-SH zum anderen signifikant gesteigert werden. Immunhistochemisch konnten bei beiden HA-haltigen Klebern Zeichen von Knorpelintegration nachgewiesen werden, w{\"a}hrend der 4C/4A-PEG-Kleber keine Integrationszeichen aufwies. Im 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium Bromid (MTT)-Assay war bei keinem Adh{\"a}sivum eine zytotoxische Wirkung zu erkennen. Insgesamt bieten die untersuchten PEG-basierten Adh{\"a}siva im Vergleich zu den weitverbreiteten Fibrinklebern eine deutlich h{\"o}here Sofortadh{\"a}sion, welche vergleichbar mit glutaraldehydbasierten Klebern ist. Allerdings k{\"o}nnen die initialen adh{\"a}siven Kr{\"a}fte, trotz histologisch nachweisbaren Integrationszeichen bei Inkorporation von HA, nicht langfristig aufrechterhalten werden, so dass Fibrinkleber weiterhin die Spitzengruppe in Sachen Langzeitadh{\"a}sion bilden. Da PEG eine ausgezeichnete Biokompatibilit{\"a}t, einfache Anwendbarkeit und zahlreiche weitere chemische Anpassungsm{\"o}glichkeiten zur Feinabstimmung der Degradationseigenschaften bietet, ist in Zukunft ein erfolgreicher Einsatz auch im Bereich von Gelenkknorpel denkbar. F{\"u}r die experimentelle Untersuchung von Adh{\"a}siva und Gelenkknorpel werden biomechanische Versuchsmodelle ben{\"o}tigt. Der Tensile-Test des Sandwich-Modells konnte im Rahmen dieser Arbeit erfolgreich etabliert und ein Protokoll festgelegt werden. In einem vergleichenden Versuch mit dem Push-Out-Test des Disc-Ring-Modells, welches als Referenzmodell dient, konnte in Bezug auf die Reproduzierbarkeit und Qualit{\"a}t der Messergebnisse die Gleichwertigkeit gezeigt werden. Insgesamt bietet er eine gute Alternative zum Push-Out-Test, um weiterf{\"u}hrende Fragestellung, wie z.B. extrinsische Kraftwirkungen auf das Konstrukt, zu untersuchen.},
  subject      = {Knorpel},
  language  = {de}
}