@article{SchmidtDenkWiegering2020,
  author    = {Schmidt, Stefanie and Denk, Sarah and Wiegering, Armin},
  title     = {Targeting protein synthesis in colorectal cancer},
  series = {Cancers},
  volume    = {12},
  journal   = {Cancers},
  number    = {5},
  issn      = {2072-6694},
  doi       = {10.3390/cancers12051298},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-206014},
  year      = {2020},
  abstract  = {Under physiological conditions, protein synthesis controls cell growth and survival and is strictly regulated. Deregulation of protein synthesis is a frequent event in cancer. The majority of mutations found in colorectal cancer (CRC), including alterations in the WNT pathway as well as activation of RAS/MAPK and PI3K/AKT and, subsequently, mTOR signaling, lead to deregulation of the translational machinery. Besides mutations in upstream signaling pathways, deregulation of global protein synthesis occurs through additional mechanisms including altered expression or activity of initiation and elongation factors (e.g., eIF4F, eIF2α/eIF2B, eEF2) as well as upregulation of components involved in ribosome biogenesis and factors that control the adaptation of translation in response to stress (e.g., GCN2). Therefore, influencing mechanisms that control mRNA translation may open a therapeutic window for CRC. Over the last decade, several potential therapeutic strategies targeting these alterations have been investigated and have shown promising results in cell lines, intestinal organoids, and mouse models. Despite these encouraging in vitro results, patients have not clinically benefited from those advances so far. In this review, we outline the mechanisms that lead to deregulated mRNA translation in CRC and highlight recent progress that has been made in developing therapeutic strategies that target these mechanisms for tumor therapy.},
  language  = {en}
}
@article{KannKunzHansenetal.2020,
  author    = {Kann, Simone and Kunz, Meik and Hansen, Jessica and Sievertsen, J{\"u}rgen and Crespo, Jose J. and Loperena, Aristides and Arriens, Sandra and Dandekar, Thomas},
  title     = {Chagas disease: detection of Trypanosoma cruzi by a new, high-specific real time PCR},
  series = {Journal of Clinical Medicine},
  volume    = {9},
  journal   = {Journal of Clinical Medicine},
  number    = {5},
  issn      = {2077-0383},
  doi       = {10.3390/jcm9051517},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-205746},
  year      = {2020},
  abstract  = {Background: Chagas disease (CD) is a major burden in Latin America, expanding also to non-endemic countries. A gold standard to detect the CD causing pathogen Trypanosoma cruzi is currently not available. Existing real time polymerase chain reactions (RT-PCRs) lack sensitivity and/or specificity. We present a new, highly specific RT-PCR for the diagnosis and monitoring of CD. Material and Methods: We analyzed 352 serum samples from Indigenous people living in high endemic CD areas of Colombia using three leading RT-PCRs (k-DNA-, TCZ-, 18S rRNA-PCR), the newly developed one (NDO-PCR), a Rapid Test/enzyme-linked immuno sorbent assay (ELISA), and immunofluorescence. Eighty-seven PCR-products were verified by sequence analysis after plasmid vector preparation. Results: The NDO-PCR showed the highest sensitivity (92.3\%), specificity (100\%), and accuracy (94.3\%) for T. cruzi detection in the 87 sequenced samples. Sensitivities and specificities of the kDNA-PCR were 89.2\%/22.7\%, 20.5\%/100\% for TCZ-PCR, and 1.5\%/100\% for the 18S rRNA-PCR. The kDNA-PCR revealed a 77.3\% false positive rate, mostly due to cross-reactions with T. rangeli (NDO-PCR 0\%). TCZ- and 18S rRNA-PCR showed a false negative rate of 79.5\% and 98.5\% (NDO-PCR 7.7\%), respectively. Conclusions: The NDO-PCR demonstrated the highest specificity, sensitivity, and accuracy compared to leading PCRs. Together with serologic tests, it can be considered as a reliable tool for CD detection and can improve CD management significantly.},
  language  = {en}
}
@article{GrundMuellerRuedenauerSpaetheetal.2020,
  author    = {Grund-Mueller, Nils and Ruedenauer, Fabian A. and Spaethe, Johannes and Leonhardt, Sara D.},
  title     = {Adding amino acids to a sucrose diet is not sufficient to support longevity of adult bumble bees},
  series = {Insects},
  volume    = {11},
  journal   = {Insects},
  number    = {4},
  issn      = {2075-4450},
  doi       = {10.3390/insects11040247},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-203866},
  year      = {2020},
  abstract  = {Dietary macro-nutrients (i.e., carbohydrates, protein, and fat) are important for bee larval development and, thus, colony health and fitness. To which extent different diets (varying in macro-nutrient composition) affect adult bees and whether they can thrive on nectar as the sole amino acid source has, however, been little investigated. We investigated how diets varying in protein concentration and overall nutrient composition affected consumption, longevity, and breeding behavior of the buff-tailed bumble bee, Bombus terrestris (Hymenoptera: Apidae). Queenless micro-colonies were fed either natural nutrient sources (pollen), nearly pure protein (i.e., the milk protein casein), or sucrose solutions with low and with high essential amino acid content in concentrations as can be found in nectar. We observed micro-colonies for 110 days. We found that longevity was highest for pure pollen and lowest for pure sucrose solution and sucrose solution supplemented with amino acids in concentrations as found in the nectar of several plant species. Adding higher concentrations of amino acids to sucrose solution did only slightly increase longevity compared to sucrose alone. Consequently, sucrose solution with the applied concentrations and proportions of amino acids or other protein sources (e.g., casein) alone did not meet the nutritional needs of healthy adult bumble bees. In fact, longevity was highest and reproduction only successful in micro-colonies fed pollen. These results indicate that, in addition to carbohydrates and protein, adult bumble bees, like larvae, need further nutrients (e.g., lipids and micro-nutrients) for their well-being. An appropriate nutritional composition seemed to be best provided by floral pollen, suggesting that pollen is an essential dietary component not only for larvae but also for adult bees.},
  language  = {en}
}
@article{GrubbsSurupBiedermannetal.2020,
  author    = {Grubbs, Kirk J. and Surup, Frank and Biedermann, Peter H. W. and McDonald, Bradon R. and Klassen, Jonathan L. and Carlson, Caitlin M. and Clardy, Jon and Currie, Cameron R.},
  title     = {Cycloheximide-Producing Streptomyces Associated With Xyleborinus saxesenii and Xyleborus affinis Fungus-Farming Ambrosia Beetles},
  series = {Frontiers in Microbiology},
  volume    = {11},
  journal   = {Frontiers in Microbiology},
  doi       = {10.3389/fmicb.2020.562140},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212449},
  year      = {2020},
  abstract  = {Symbiotic microbes help a myriad of insects acquire nutrients. Recent work suggests that insects also frequently associate with actinobacterial symbionts that produce molecules to help defend against parasites and predators. Here we explore a potential association between Actinobacteria and two species of fungus-farming ambrosia beetles, Xyleborinus saxesenii and Xyleborus affinis. We isolated and identified actinobacterial and fungal symbionts from laboratory reared nests, and characterized small molecules produced by the putative actinobacterial symbionts. One 16S rRNA phylotype of Streptomyces (XylebKG-1) was abundantly and consistently isolated from the galleries and adults of X. saxesenii and X. affinis nests. In addition to Raffaelea sulphurea, the symbiont that X. saxesenii cultivates, we also repeatedly isolated a strain of Nectria sp. that is an antagonist of this mutualism. Inhibition bioassays between Streptomyces griseus XylebKG-1 and the fungal symbionts from X. saxesenii revealed strong inhibitory activity of the actinobacterium toward the fungal antagonist Nectria sp. but not the fungal mutualist R. sulphurea. Bioassay guided HPLC fractionation of S. griseus XylebKG-1 culture extracts, followed by NMR and mass spectrometry, identified cycloheximide as the compound responsible for the observed growth inhibition. A biosynthetic gene cluster putatively encoding cycloheximide was also identified in S. griseus XylebKG-1. The consistent isolation of a single 16S phylotype of Streptomyces from two species of ambrosia beetles, and our finding that a representative isolate of this phylotype produces cycloheximide, which inhibits a parasite of the system but not the cultivated fungus, suggests that these actinobacteria may play defensive roles within these systems.},
  language  = {en}
}
@article{FathyOkabeOthmanetal.2020,
  author    = {Fathy, Moustafa and Okabe, Motonori and Othman, Eman M. and Saad Eldien, Heba M. and Yoshida, Toshiko},
  title     = {Preconditioning of adipose-derived mesenchymal stem-like cells with eugenol potentiates their migration and proliferation in vitro and therapeutic abilities in rat hepatic fibrosis},
  series = {Molecules},
  volume    = {25},
  journal   = {Molecules},
  number    = {9},
  issn      = {1420-3049},
  doi       = {10.3390/molecules25092020},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-203662},
  year      = {2020},
  abstract  = {Mesenchymal stem cells (MSCs) have considerable therapeutic abilities in various disorders, including hepatic fibrosis. They may be affected with different culture conditions. This study investigated, on molecular basics, the effect of pretreatment with eugenol on the characteristics of adipose tissue-derived MSCs (ASCs) in vitro and the implication of eugenol preconditioning on the in vivo therapeutic abilities of ASCs against CCl\(_4\)-induced hepatic fibrosis in rats. The effect of eugenol on ASCs was assessed using viability, scratch migration and sphere formation assays. Expressions of genes and proteins were estimated by immunofluorescence or qRT-PCR. For the in vivo investigations, rats were divided into four groups: the normal control group, fibrotic (CCl\(_4\)) group, CCl\(_4\)+ASCs group and CCl\(_4\) + eugenol-preconditioned ASCs (CCl\(_4\)+E-ASCs) group. Eugenol affected the viability of ASCs in a concentration- and time-dependent manner. Eugenol improved their self-renewal, proliferation and migration abilities and significantly increased their expression of c-Met, reduced expression 1 (Rex1), octamer-binding transcription factor 4 (Oct4) and nanog genes. Furthermore, E-ASCs showed more of a homing ability than ASCs and improved the serum levels of ALT, AST, albumin, total bilirubin and hyaluronic acid more efficient than ASCs in treating CCl\(_4\)-induced hepatic fibrosis, which was confirmed with histopathology. More interestingly, compared to the CCl\(_4\)+ASCs group, CCl\(_4\)+E-ASCs group showed a lower expression of inducible nitric oxide synthase (iNOS), monocyte chemoattractant protein-1 (MCP-1), cluster of differentiation 163 (CD163) and tumor necrosis factor-α (TNF-α) genes and higher expression of matrix metalloproteinase (MMP)-9 and MMP-13 genes. This study, for the first time, revealed that eugenol significantly improved the self-renewal, migration and proliferation characteristics of ASCs, in vitro. In addition, we demonstrated that eugenol-preconditioning significantly enhanced the therapeutic abilities of the injected ASCs against CCl\(_4\)-induced hepatic fibrosis.},
  language  = {en}
}
@article{BiltuevaProkopovRomanenkoetal.2020,
  author    = {Biltueva, Larisa S. and Prokopov, Dmitry Yu. and Romanenko, Svetlana A. and Interesova, Elena A. and Schartl, Manfred and Trifonov, Vladimir A.},
  title     = {Chromosome distribution of highly conserved tandemly arranged repetitive DNAs in the Siberian sturgeon (Acipenser baerii)},
  series = {Genes},
  volume    = {11},
  journal   = {Genes},
  number    = {11},
  issn      = {2073-4425},
  doi       = {10.3390/genes11111375},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-219371},
  year      = {2020},
  abstract  = {Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.},
  language  = {en}
}
@phdthesis{Thelen2020,
  author    = {Thelen, David},
  title     = {Erstellung eines genregulatorischen Netzwerkes zur Simulation der Entstehung von Zahnhartsubstanz},
  doi       = {10.25972/OPUS-20406},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-204068},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {In this dissertation, the author describes the creation of a basic bioinformatic model of human enamel maturation. Supported by the interactions found in the KEGG Pathway database, we were able to establish a gene regulatory network (GRN) that focuses primarily on the signal transduction pathways apoptosis, cell cycle, hedgehog signaling pathway, MAP kinase pathway, mTOR signaling pathway, Notch signaling pathway, TGF-β signaling pathway and Wnt signaling pathway. We extended this through further verified interactions and implicated the tooth-specific genes AMELX, AMELY, AMBN, ENAM and DSPP. In the subsequent simulation of the network by the simulation tool Jimena, six stable states could be identified. These are examined in more detail and juxtaposed with results of a GEO dataset. The long-term goal is to draw conclusions about the odontogenesis of humans through consistent optimization of the bioinformatics network.},
  subject      = {Universit{\"a}t W{\"u}rzburg. Lehrstuhl f{\"u}r Bioinformatik},
  language  = {de}
}
@article{KochHoernerMuenchetal.2020,
  author    = {Koch, Rebecca-Diana and H{\"o}rner, Eva-Maria and M{\"u}nch, Nadine and Maier, Elke and Kozjak-Pavlovic, Vera},
  title     = {Modulation of Host Cell Death and Lysis Are Required for the Release of Simkania negevensis},
  series = {Frontiers in Cellular and Infection Microbiology},
  volume    = {10},
  journal   = {Frontiers in Cellular and Infection Microbiology},
  issn      = {2235-2988},
  doi       = {10.3389/fcimb.2020.594932},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-215158},
  year      = {2020},
  abstract  = {Simkania negevensis is a Chlamydia-like bacterium and emerging pathogen of the respiratory tract. It is an obligate intracellular bacterium with a biphasic developmental cycle, which replicates in a wide range of host cells. The life cycle of S. negevensis has been shown to proceed for more than 12 days, but little is known about the mechanisms that mediate the cellular release of these bacteria. This study focuses on the investigation of host cell exit by S. negevensis and its connection to host cell death modulation. We show that Simkania-infected epithelial HeLa as well as macrophage-like THP-1 cells reduce in number during the course of infection. At the same time, the infectivity of the cell culture supernatant increases, starting at the day 3 for HeLa and day 4 for THP-1 cells and reaching maximum at day 5 post infection. This correlates with the ability of S. negevensis to block TNFα-, but not staurosporin-induced cell death up to 3 days post infection, after which cell death is boosted by the presence of bacteria. Mitochondrial permeabilization through Bax and Bak is not essential for host cell lysis and release of S. negevensis. The inhibition of caspases by Z-VAD-FMK, caspase 1 by Ac-YVAD-CMK, and proteases significantly reduces the number of released infectious particles. In addition, the inhibition of myosin II by blebbistatin also strongly affects Simkania release, pointing to a possible double mechanism of exit through host cell lysis and potentially extrusion.},
  language  = {en}
}
@article{HardulakMoriniereHausmannetal.2020,
  author    = {Hardulak, Laura A. and Morini{\`e}re, J{\´e}r{\^o}me and Hausmann, Axel and Hendrich, Lars and Schmidt, Stefan and Doczkal, Dieter and M{\"u}ller, J{\"o}rg and Hebert, Paul D. N. and Haszprunar, Gerhard},
  title     = {DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species},
  series = {Molecular Ecology Resources},
  volume    = {20},
  journal   = {Molecular Ecology Resources},
  number    = {6},
  doi       = {10.1111/1755-0998.13212},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-217812},
  pages     = {1542 -- 1557},
  year      = {2020},
  abstract  = {DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6\% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.},
  language  = {en}
}
@phdthesis{Beliu2020,
  author    = {Beliu, Gerti},
  title     = {Bioorthogonale Tetrazin-Farbstoffe f{\"u}r die Lebendzell-Markierung und hochaufgel{\"o}ste Fluoreszenzmikroskopie},
  doi       = {10.25972/OPUS-18962},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189628},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Der genetische Code beschreibt die Ver- und Entschl{\"u}sselung der Erb-information f{\"u}r das universelle Prinzip der Proteinbiosynthese aus einzelnen Aminos{\"a}uren. Durch Erweiterung des genetischen Codes lassen sich unna-t{\"u}rliche Aminos{\"a}uren (uAA) mit einzigartigen biophysikalischen Eigenschaf-ten ortsspezifisch in Proteine einf{\"u}hren und erm{\"o}glichen die spezifische Ma-nipulation von Proteinen. Die Click-Reaktion zwischen der unnat{\"u}rlichen Aminos{\"a}ure TCO*-Lysin und Tetrazin besitzt eine außergew{\"o}hnliche Reaktionskinetik (≥800 M-1s-1) und erm{\"o}glicht eine spezifische und bioorthogonale Markierung von Bio- ¬molek{\"u}len unter physiologischen Bedingungen. Im Fokus dieser Arbeit stand zun{\"a}chst die Markierung von Membran- ¬rezeptoren durch Click-Chemie in lebenden Zellen sowie die Untersuchung der Wechselwirkung 22 bekannter und neuartiger Tetrazin-Farbstoff- Konjugate. Dar{\"u}ber hinaus wurde die Anwendbarkeit von bioorthogonalen Click-Reaktionen f{\"u}r die hochaufl{\"o}sende Fluoreszenzmikroskopie untersucht. Durch Erweiterung des genetischen Codes in Proteine aus der Klasse der ionotropen Glutamatrezeptoren (iGluR), TNF-Rezeptoren oder Mikrotubu-li-assoziierten Proteinen (MAP) wurde ortspezifisch die unnat{\"u}rliche Amino-s{\"a}ure TCO*-Lysin eingef{\"u}hrt und dadurch die Fluoreszenzmarkierung durch Tetrazin-Farbstoffe erm{\"o}glicht. Die direkte chemische Kopplung von TCO an Liganden wie Phalloidin und Docetaxel, welche spezifisch das Aktin-Zytoskelett bzw. Mikrotubuli-Filamente binden k{\"o}nnen, erm{\"o}glichte zudem die Click-F{\"a}rbungen von fixierten und lebenden Zellen ohne genetische Ver-{\"a}nderungen der Zielproteine. Des Weiteren wurden die spektroskopischen Eigenschaften von 22 Tetrazin-Farbstoffen, verteilt {\"u}ber den gesamten sichtbaren Wellenl{\"a}ngenbereich, untersucht. Ein charakteristisches Kennzeichen der Click-Reaktion mit Tet-razin-Farbstoffen ist dabei ihre Fluorogenit{\"a}t. Das Tetrazin fungiert nicht nur als reaktive Gruppe w{\"a}hrend der Click-Reaktion mit Alkenen, sondern f{\"u}hrt in vielen Tetrazin-Farbstoff-Konjugaten zur Fluoreszenzl{\"o}schung. W{\"a}hrend bei gr{\"u}n-absorbierenden Farbstoffe vor allem FRET-basierte L{\"o}schprozesse dominieren, konnte photoinduzierter Elektronentransfer (PET) vom angeregten Farbstoff zum Tetrazin als Hauptl{\"o}schmechanismus bei rot-absorbierenden Oxazin- und Rhodamin-Derivaten identifiziert werden. Die effiziente und spezifische Markierung aller untersuchten Tetrazin- Farbstoffe erm{\"o}glichte die Visualisierung von Aktin-Filamenten, Mikrotubuli und Membranrezeptoren sowohl durch konventionelle Fluoreszenzmikrosko-pie als auch durch hochaufl{\"o}sende Verfahren, wie z.B. dSTORM, auf Ein-zelmolek{\"u}lebene. Die unterschiedliche Zellpermeabilit{\"a}t von Tetrazin-Farbstoffen kann dabei vorteilhaft f{\"u}r die spezifische intra- und extrazellul{\"a}re Markierung von Proteinen in fixierten und lebenden Zellen genutzt werden.},
  subject      = {Hochaufgel{\"o}ste Fluoreszenzmikroskopie},
  language  = {de}
}
@article{Biedermann2020,
  author    = {Biedermann, Peter H. W.},
  title     = {Cooperative Breeding in the Ambrosia Beetle Xyleborus affinis and Management of Its Fungal Symbionts},
  series = {Frontiers in Ecology and Evolution},
  volume    = {8},
  journal   = {Frontiers in Ecology and Evolution},
  issn      = {2296-701X},
  doi       = {10.3389/fevo.2020.518954},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-215662},
  year      = {2020},
  abstract  = {Fungus-farming is known from attine ants, macrotermites, and ambrosia beetles (Scolytinae, Platypodinae). Farming ant and termite societies are superorganismal and grow fungal cultivars in monocultures. Social organization of ambrosia beetle groups and their farming systems are poorly studied, because of their enigmatic life within tunnel systems inside of wood. Ambrosia beetle-fungus symbioses evolved many times independently in both the beetles and their fungal cultivars. Observations suggest that there is evolutionary convergence between these lineages, but also a high variation in the degree of sociality and the modes of fungiculture. Using a laboratory observation technique, I here tried to give insights into the social system and fungus symbiosis of the sugar-cane borer, Xyleborus affinis Eichhoff (Scolytinae: Curculionidae), a currently poorly studied ambrosia beetle. The study revealed a cooperatively breeding system characterized by delayed dispersal of adult daughters, alloparental brood care by larvae and adults, and about half of the totipotent adult daughters laying eggs within the natal nest. Most interesting, there was a tendency of egg-laying females to engage more commonly in mutually beneficial behaviors than non-egg-layers. Fungus gardens covering gallery walls composed of five different filamentous fungi. A Raffaelea isolate was predominant and together with an unidentified fungus likely served as the main food for adults and larvae. Three isolates, a Mucor, a Fusarium and a Phaeoacremonium isolate were most abundant in the oldest gallery part close to the entrance; Mucor, Fusarium and the Raffaelea isolate in diseased individuals. Additionally, there was correlative evidence for some fungal isoaltes influencing beetle feeding and hygienic behaviors. Overall, X. affinis is now the second ambrosia beetle that can be classified as a cooperative breeder with division of labor among and between adults and larvae.},
  language  = {en}
}
@article{SolgerKunzFinketal.2020,
  author    = {Solger, Franziska and Kunz, Tobias C. and Fink, Julian and Paprotka, Kerstin and Pfister, Pauline and Hagen, Franziska and Schumacher, Fabian and Kleuser, Burkhard and Seibel, J{\"u}rgen and Rudel, Thomas},
  title     = {A Role of Sphingosine in the Intracellular Survival of Neisseria gonorrhoeae},
  series = {Frontiers in Cellular and Infection Microbiology},
  volume    = {10},
  journal   = {Frontiers in Cellular and Infection Microbiology},
  issn      = {2235-2988},
  doi       = {10.3389/fcimb.2020.00215},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-204111},
  year      = {2020},
  abstract  = {Obligate human pathogenic Neisseria gonorrhoeae are the second most frequent bacterial cause of sexually transmitted diseases. These bacteria invade different mucosal tissues and occasionally disseminate into the bloodstream. Invasion into epithelial cells requires the activation of host cell receptors by the formation of ceramide-rich platforms. Here, we investigated the role of sphingosine in the invasion and intracellular survival of gonococci. Sphingosine exhibited an anti-gonococcal activity in vitro. We used specific sphingosine analogs and click chemistry to visualize sphingosine in infected cells. Sphingosine localized to the membrane of intracellular gonococci. Inhibitor studies and the application of a sphingosine derivative indicated that increased sphingosine levels reduced the intracellular survival of gonococci. We demonstrate here, that sphingosine can target intracellular bacteria and may therefore exert a direct bactericidal effect inside cells.},
  language  = {en}
}
@phdthesis{Stelzner2020,
  author    = {Stelzner, Kathrin},
  title     = {Identification of factors involved in Staphylococcus aureus- induced host cell death},
  doi       = {10.25972/OPUS-18899},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188991},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Staphylococcus aureus is a Gram-positive commensal bacterium, that asymptomatically colonizes human skin and mucosal surfaces. Upon opportune conditions, such as immunodeficiency or breached barriers of the host, it can cause a plethora of infections ranging from local, superficial infections to life-threatening diseases. Despite being regarded as an extracellular pathogen, S. aureus can invade and survive within non-phagocytic and phagocytic cells. Eventually, the pathogen escapes from the host cell resulting in killing of the host cell, which is associated with tissue destruction and spread of infection. However, the exact molecular mechanisms underlying S. aureus-induced host cell death remain to be elucidated. In the present work, a genome-wide haploid genetic screen was performed to identify host cell genes crucial for S. aureus intracellular cytotoxicity. A mutant library of the haploid cell line HAP1 was infected with the pathogen and cells surviving the infection were selected. Twelve genes were identified, which were significantly enriched when compared to an infection with a non-cytotoxic S. aureus strain. Additionally, characteristics of regulated cell death pathways and the role of Ca2+ signaling in S. aureus-infected cells were investigated. Live cell imaging of Ca2+ reporter cell lines was used to analyze single cells. S. aureus-induced host cell death exhibited morphological features of apoptosis and activation of caspases was detected. Cellular H2O2 levels were elevated during S. aureus intracellular infection. Further, intracellular S. aureus provoked cytosolic Ca2+ overload in epithelial cells. This resulted from Ca2+ release from endoplasmic reticulum and Ca2+ influx via the plasma membrane and led to mitochondrial Ca2+ overload. The final step of S. aureus-induced cell death was plasma membrane permeabilization, a typical feature of necrotic cell death. In order to identify bacterial virulence factors implicated in S. aureus-induced host cell killing, the cytotoxicity of selected mutants was investigated. Intracellular S. aureus employs the bacterial cysteine protease staphopain A to activate an apoptosis-like cell death characterized by cell contraction and membrane bleb formation. Phagosomal escape represents a prerequisite staphopain A-induced cell death, whereas bacterial intracellular replication is dispensable. Moreover, staphopain A contributed to efficient colonization of the lung in a murine pneumonia model. In conclusion, this work identified at least two independent cell death pathways activated by intracellular S. aureus. While initially staphopain A mediates S. aureus-induced host cell killing, cytosolic Ca2+-overload follows later and leads to the final demise of the host cell.},
  subject      = {Staphylococcus aureus},
  language  = {en}
}
@phdthesis{Hartlieb2020,
  author    = {Hartlieb, Heiko},
  title     = {Functional analysis of Mushroom body miniature's RGG-box and its role in neuroblast proliferation in Drosophila melanogaster},
  doi       = {10.25972/OPUS-19967},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-199674},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Development of the central nervous system in Drosophila melanogaster relies on neural stem cells called neuroblasts. Neuroblasts divide asymmetrically to give rise to a new neuroblast as well as a small daughter cell which eventually generates neurons or glia cells. Between each division, neuroblasts have to re-grow to be able to divide again. In previous studies, it was shown that neuroblast proliferation, cell size and the number of progeny cells is negatively affected in larvae carrying a P-element induced disruption of the gene mushroom body miniature (mbm). This mbm null mutation called mbmSH1819 is homozygously lethal during pupation. It was furthermore shown that the nucleolar protein Mbm plays a role in the processing of ribosomal RNA (rRNA) as well as the translocation of ribosomal protein S6 (RpS6) in neuroblasts and that it is a transcriptional target of Myc. Therefore, it was suggested that Mbm might regulate neuroblast proliferation through a role in ribosome biogenesis. In the present study, it was attempted to further elucidate these proposed roles of Mbm and to identify the protein domains that are important for those functions. Mbm contains an arginine/glycine rich region in which a di-RG as well as a di-RGG motif could be found. Together, these two motifs were defined as Mbm's RGG-box. RGG-boxes can be found in many proteins of different families and they can either promote or inhibit protein-RNA as well as protein-protein interactions. Therefore, Mbm's RGG-box is a likely candidate for a domain involved in rRNA binding and RpS6 translocation. It could be shown by deletion of the RGG-box, that MbmdRGG is unable to fully rescue survivability and neuroblast cell size defects of the null mutation mbmSH1819. Furthermore, Mbm does indeed rely on its RGG-box for the binding of rRNA in vitro and in mbmdRGG as well as mbmSH1819 mutants RpS6 is partially delocalized. Mbm itself also seems to depend on the RGG-box for correct localization since MbmdRGG is partially delocalized to the nucleus. Interestingly, protein synthesis rates are increased in mbmdRGG mutants, possibly induced by an increase in TOR expression. Therefore, Mbm might possess a promoting function in TOR signaling in certain conditions, which is regulated by its RGG-box. Moreover, RGG-boxes often rely on methylation by protein arginine methyltransferases (in Drosophila: Darts - Drosophila arginine methyltransferases) to fulfill their functions. Mbm might be symmetrically dimethylated within its RGG-box, but the results are very equivocal. In any case, Dart1 and Dart5 do not seem to be capable of Mbm methylation. Additionally, Mbm contains two C2HC type zinc-finger motifs, which could be involved in rRNA binding. In an earlier study, it was shown that the mutation of the zinc-fingers, mbmZnF, does not lead to changes in neuroblast cell size, but that MbmZnF is delocalized to the cytoplasm. In the present study, mbmZnF mutants were included in most experiments. The results, however, are puzzling since mbmZnF mutant larvae exhibit an even lower viability than the mbm null mutants and MbmZnF shows stronger binding to rRNA than wild-type Mbm. This suggests an unspecific interaction of MbmZnF with either another protein, DNA or RNA, possibly leading to a dominant negative effect by disturbing other interaction partners. Therefore, it is difficult to draw conclusions about the zinc-fingers' functions. In summary, this study provides further evidence that Mbm is involved in neuroblast proliferation as well as the regulation of ribosome biogenesis and that Mbm relies on its RGG-box to fulfill its functions.},
  subject      = {Taufliege},
  language  = {en}
}
@phdthesis{Lehmann2020,
  author    = {Lehmann, Julian},
  title     = {Hochaufl{\"o}sende Fluoreszenzmikroskopie beleuchtet den Oligomerisierungsstatus pflanzlicher Membranproteine},
  doi       = {10.25972/OPUS-21176},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-211762},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {SLAC/SLAH Anionenkan{\"a}le, die zur Familie der langsamen Anionenkan{\"a}le geh{\"o}ren, repr{\"a}sentieren Schl{\"u}sselproteine in der pflanzlichen Stressantwort. Neben ihrer Aufgabe in Stresssituationen, ist eine Untergruppe der Kan{\"a}le f{\"u}r die Beladung der Leitgef{\"a}ße mit Nitrat und Chlorid in der Stele der Pflanzenwurzeln verantwortlich. Biophysikalische und pflanzenphysiologische Studien stellten heraus, dass vor Allem der Anionenkanal SLAH3 f{\"u}r die Beladung der Xylem Leitgef{\"a}ße mit Nitrat und Chlorid verantwortlich ist. Ihm zur Seite gestellt werden noch die elektrisch inaktiven Homologe SLAH1 und SLAH4 in der Wurzel exprimiert. Sie steuern die Aktivit{\"a}t von SLAH3 durch die Assemblierung zu SLAH1/SLAH3 oder SLAH3/SLAH4 Heteromeren. Neben der Kontrolle durch Heteromerisierungsereignisse, werden SLAH3 Homomere sehr spezifisch und schnell durch zytosolische Ans{\"a}uerung aktiviert. Obwohl bereits die Kristallstruktur des bakteriellen Homologs HiTehA zu pflanzlichen SLAC/SLAH Anionenkan{\"a}len bekannt ist, welche HiTehA als Trimer charakterisiert, sind die St{\"o}chiometrie und der Polymerisierungsgrad der pflanzlichen SLAC/SLAHs bisher noch unbekannt. Die Fluoreszenzmikroskopie umfasst viele etablierte Anwendungsmethoden, wie die konfokale Laserrastermikroskopie (CLSM), Techniken mit verbesserter Aufl{\"o}sung, wie die Mikroskopie mit strukturierter Beleuchtung (SIM) und hochaufl{\"o}sende Methoden, welche durch die Lokalisationsmikroskopie (z.B. dSTORM und PALM) oder die Expansionsmikroskopie (ExM) vertreten werden. Diese unterschiedlichen Mikroskopie-methoden erm{\"o}glichen neue Einblicke in die Organisation von Proteinen in biologischen Systemen, die bis auf die molekulare Ebene hinunterreichen. Insbesondere im Bereich der hochaufl{\"o}senden Fluoreszenzmikroskopie sind im Gegensatz zu tierischen Frage-stellungen bisher jedoch nur wenige Untersuchungen in pflanzlichen Geweben durchgef{\"u}hrt worden. Die Lokalisationsmikroskopie erm{\"o}glicht die Quantifizierung einzelner Molek{\"u}le in nativen Systemen und l{\"a}sst {\"u}berdies R{\"u}ckschl{\"u}sse auf den Polymerisierungsgrad von Proteinen zu. Da Poly- und Heteromerisierung von Proteinen oftmals mit der Funktionalit{\"a}t eines entsprechenden Proteins einhergeht, wie es bei den SLAC/SLAH Anionenkan{\"a}len der Fall ist, wurden in dieser Arbeit PALM Messungen zur Untersuchung des Polymerisierungsgrades und Interaktionsmuster der Anionenkan{\"a}le angewendet. Ferner wurden Expressionsmuster der SLAC/SLAHs untersucht und zudem Mikroskopieanwendungen im Pflanzengewebe etabliert und verbessert. In Bezug auf die Mikroskopieanwendungen konnten wir in Arabidopsis thaliana (At) Wurzeln die polare Verteilung von PIN Proteinen mittels SIM best{\"a}tigen und die gruppierte Verteilung in der Plasmamembran am Zellpol aufl{\"o}sen. In Wurzel-querschnitten war es m{\"o}glich, Zellw{\"a}nde zu vermessen, den Aufbau der Pflanzenwurzel mit den verschiedenen Zelltypen zu rekonstruieren und diesen in Zusammenhang mit Zellwanddicken zu bringen. Anhand dieser Aufnahmen ließ sich die Aufl{\"o}sungsgrenze eines SIM-Mikroskops bestimmen, weshalb diese Probe als Modellstruktur f{\"u}r Aufl{\"o}sungsanalysen, zur Kontrolle f{\"u}r die korrekte Bildverarbeitung bei hochaufl{\"o}sender Bildgebung und andere Fragestellungen empfohlen werden kann. F{\"u}r die Expansionsmikroskopie in pflanzlichen Proben konnten ein enzym- und ein denaturierungsbasiertes Pr{\"a}parationsprotokoll etabliert werden. Dabei wurden ganze At Setzlinge, Wurzelabschnitte und Blattst{\"u}cke gef{\"a}rbt, expandiert und mit zwei bis drei Mal verbesserter Aufl{\"o}sung bildlich dargestellt. In diesem Zusammenhang waren Aufnahmen ganzer Wurzel- und Blattproben mit beeindruckender Eindringtiefe und extrem geringem Hintergrundsignal m{\"o}glich. Zudem wurden die Daten kritisch betrachtet, Probleme aufgezeigt, gewebespezifische Ver{\"a}nderungen dargestellt und limitierende Faktoren f{\"u}r die ExM in Pflanzenproben thematisiert. Im Fokus dieser Arbeit stand die Untersuchung der SLAC/SLAH Proteine. SLAH2 wird in den Wurzeln vornehmlich in Endodermis- und Perizykelzellen exprimiert, was anhand verschiedener At SLAH2 YFP Mutanten untersucht werden konnte. Dies unterst{\"u}tzt die Annahme, dass SLAH2 bei der Beladung der Leitgef{\"a}ße mit Nitrat maßgeblich beteiligt ist. Es ist denkbar, dass SLAH2 ebenfalls eine wachstumsbeeinflussende Funktion {\"u}ber die Regulation von Nitratkonzentrationen zugeschrieben werden kann. Darauf deuten vor allem die verst{\"a}rkte Expression von SLAH2 im Bereich der Seitenwurzeln und die heterogene Expression in der Elongations-, Differenzierungs- und meristematischen Zone hin. Die Membranst{\"a}ndigkeit von SLAH4 konnte nachgewiesen werden und FRET FLIM Untersuchungen zeigten eine hohe Affinit{\"a}t von SLAH4 zu SLAH3, was die beiden Homologe als Interaktionspartner identifiziert. F{\"u}r die Bestimmung des Oligomerisierungsgrades mittels PALM wurden die pflanzlichen Anionenkan{\"a}le in tierischen COS7-Zellen exprimiert. Die elektrophysiologische Funktionalit{\"a}t der mEOS2-SLAC/SLAH-Konstrukte wurde mit Hilfe von Patch-Clamp-Versuchen in COS7-Zellen {\"u}berpr{\"u}ft. Um Expressionslevel, Membranst{\"a}ndigkeit und die Verteilung {\"u}ber die Membran der SLAC/SLAHs zu verifizieren, wurden dSTORM-Aufnahmen herangezogen Schließlich erm{\"o}glichten PALM-Aufnahmen die Bestimmung des Polymerisierungs-grades der SLAC/SLAH Anionenkan{\"a}le, die st{\"o}chiometrischen Ver{\"a}nderungen bei Heteromerisierung von SLAH3 mit SLAH1 oder SLAH4 und auch der Einfluss einer zytosolischer Ans{\"a}uerung auf den Polymerisierungsgrad von SLAH3 Homomeren. Zudem weisen die Oligomerisierungsanalysen von SLAH3 Mutanten darauf hin, dass die Aminos{\"a}uren Histidin His330 und His454 entscheidend an der pH sensitiven Regulierung von SLAH3 beteiligt sind. Durch die erhobenen Daten konnten also entscheidende, neue Erkenntnisse {\"u}ber die Regulationsmechanismen von pflanzlichen Anionenkan{\"a}len auf molekularer Ebene gewonnen werden: Unter Standardbedingungen liegen SLAC1, SLAH2 und SLAH3 haupts{\"a}chlich als Dimer vor. Auf eine zytosolische Ans{\"a}uerung reagiert ausschließlich SLAH3 mit einer signifikanten st{\"o}chiometrischen Ver{\"a}nderung und liegt im aktiven Zustand vor Allem als Monomer vor. Der Oligomerisierungsgrad von SLAC1 und SLAH2 bleibt hingegen bei einer zytosolischen Ans{\"a}uerung unver{\"a}ndert. Ferner kommt es bei der Interaktion von SLAH3 mit SLAH1 oder SLAH4 zur Formierung eines Heterodimers, welches unbeeinflusst durch den zytosolischen pH bleibt. Im Gegensatz dazu bleiben die elektrisch inaktiven Untereinheiten SLAH1 und SLAH4 monomerisch und assemblieren ganz spezifisch nur mit SLAH3. Die hochaufl{\"o}sende Fluoreszenz-mikroskopie, insbesondere PALM erlaubt es also Heteromerisierungsereignisse und {\"A}nderungen im Poylmerisierungsgrad von Membranproteinen wie den SLAC/SLAHs auf molekularer Ebene zu untersuchen und l{\"a}sst so R{\"u}ckschl{\"u}sse auf physiologische Ereignisse zu.},
  subject      = {Fluoreszenzmikroskopie},
  language  = {de}
}
@article{LichthardtWagnerLoebetal.2020,
  author    = {Lichthardt, Sven and Wagner, Johanna and L{\"o}b, Stefan and Matthes, Niels and Kastner, Caroline and Anger, Friedrich and Germer, Christoph-Thomas and Wiegering, Armin},
  title     = {Pathological complete response due to a prolonged time interval between preoperative chemoradiation and surgery in locally advanced rectal cancer: analysis from the German StuDoQ|Rectalcarcinoma registry},
  series = {BMC Cancer},
  volume    = {20},
  journal   = {BMC Cancer},
  number    = {1},
  doi       = {10.1186/s12885-020-6538-8},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229334},
  year      = {2020},
  abstract  = {Background Preoperative chemoradiotherapy is the recommended standard of care for patients with local advanced rectal cancer. However, it remains unclear, whether a prolonged time interval to surgery results in an increased perioperative morbidity, reduced TME quality or better pathological response. Aim of this study was to determine the time interval for best pathological response and perioperative outcome compared to current recommended interval of 6 to 8 weeks. Methods This is a retrospective analysis of the German StuDoQ|Rectalcarcinoma registry. Patients were grouped for the time intervals of "less than 6 weeks", "6 to 8 weeks", "8 to 10 weeks" and "more than 10 weeks". Primary endpoint was pathological response, secondary endpoint TME quality and complications according to Clavien-Dindo classification. Results Due to our inclusion criteria (preoperative chemoradiation, surgery in curative intention, M0), 1.809 of 9.560 patients were suitable for analysis. We observed a trend for increased rates of pathological complete response (pCR: ypT0ypN0) and pathological good response (pGR: ypT0-1ypN0) for groups with a prolonged time interval which was not significant. Ultimately, it led to a steady state of pCR (16.5\%) and pGR (22.6\%) in "8 to 10" and "more than 10" weeks. We were not able to observe any differences between the subgroups in perioperative morbidity, proportion of rectal extirpation (for cancer of the lower third) or difference in TME quality. Conclusion A prolonged time interval between neoadjuvant chemoradiation can be performed, as the rate of pCR seems to be increased without influencing perioperative morbidity.},
  language  = {en}
}
@phdthesis{Seibold2020,
  author    = {Seibold, Marcel},
  title     = {Funktionelle Charakterisierung des Ras family small GTP binding protein RAL im Multiplen Myelom},
  doi       = {10.25972/OPUS-20800},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-208003},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Die monoklonale Proliferation maligner Plasmazellen im Knochenmark ist charakteristisch f{\"u}r das multiple Myelom (MM) und kann bei Erkrankten zu St{\"o}rungen in der H{\"a}matopoese sowie zu Knochenl{\"a}sionen und Niereninsuffizienz f{\"u}hren. Die Weiterentwicklung und der Einsatz neuer Therapieoptionen konnten das {\"U}berleben von MM-Patienten zwar erheblich verbessern, jedoch gilt diese Krankheit weiterhin als unheilbar. Onkogene Mutationen und das Knochenmarkmikromilieu f{\"u}hren in MM-Zellen zur Entstehung eines onkogenen Signalnetzwerks, das das Wachstum und {\"U}berleben der Zellen aufrechterh{\"a}lt. Mutationen der GTPase RAS treten bei bis zu 50 \% der MM-Patienten auf und tragen zum {\"U}berleben von MM-Zellen bei. Trotz der H{\"a}ufigkeit und Bedeutsamkeit von onkogenem RAS, auch in anderen Tumorentit{\"a}ten, ist die GTPase nach wie vor therapeutisch nicht angreifbar. Die GTPase RAL aus der Familie der RAS-GTPasen wird als Downstream-Effektor von RAS angesehen, der damit ebenfalls zur Aufrechterhaltung des Tumorzell{\"u}berlebens beitragen k{\"o}nnte. In einigen Tumorentit{\"a}ten konnte bisher gezeigt werden, dass eine {\"U}berexpression von RAL in den Tumorzellen vorliegt und die Proliferation und Apoptose von Tumorzellen durch RAL beeinflusst wird. Daher stellte sich die Frage, ob RAL im MM ebenfalls das {\"U}berleben von Tumorzellen beeinflusst und ob eine direkte Verbindung zwischen onkogenem RAS und RAL besteht. In dieser Arbeit wurde die funktionelle Rolle von RAL sowie dessen Zusammenhang mit onkogenem RAS im MM untersucht. Hierbei konnte eine {\"U}berexpression von RAL in MM-Zellen im Vergleich zu MGUS oder normalen Plasmazellen beobachtet werden. In Knockdown-Analysen wurde gezeigt, dass RAL {\"u}berlebensnotwendig f{\"u}r MM-Zellen ist. Dabei wurde in Western Blot-Analysen festgestellt, dass diese {\"U}berlebenseffekte unabh{\"a}ngig von MAPK/ERK-Signaling vermittelt werden. Es konnte teilweise jedoch eine Abh{\"a}ngigkeit von der AKT-Aktivit{\"a}t beobachtet werden. Da RAL-Knockdown Einfluss auf das {\"U}berleben von MM-Zellen hat, wurde eine pharmakologische Inhibition von RAL durch den Inhibitor RBC8 untersucht. RBC8 zeigte in h{\"o}heren Dosen nur bei einem Teil der MM-Zelllinien eine Wirkung auf das Zell{\"u}berleben sowie auf die RAL-Aktivierung. Die Weiterentwicklung potenter RAL-Inhibitoren ist daher f{\"u}r eine klinische Translation einer RAL-Inhibition von großer Bedeutung. Zur Untersuchung des Zusammenhangs zwischen onkogenem RAS und der RAL-Aktivierung wurden RAL-Pulldown-Analysen nach Knockdown von onkogenem RAS durchgef{\"u}hrt. In diesen Experimenten wurde keine Abh{\"a}ngigkeit der RAL-Aktivierung von onkogenem RAS festgestellt. Dar{\"u}ber hinaus zeigten Genexpressionsanalysen nach RAS- bzw. RAL-Knockdown unterschiedliche Genexpressionsprofile. In Massenspektrometrie-Analysen wurden m{\"o}gliche Effektoren, die mit RAL an der Beeinflussung des Zell{\"u}berlebens beteiligt sein k{\"o}nnten, untersucht. Hierbei wurden die Komponenten des Exozyst-Komplexes EXO84 und SEC5 als Interaktionspartner von RAL identifiziert. Nachdem gezeigt wurde, dass RAL ausschlaggebend f{\"u}r das {\"U}berleben von MM-Zellen ist, wurde eine Kombination von RAL-Knockdown mit klinisch relevanten Wirkstoffen analysiert. Diese zeigte bei der Kombination mit PI3K oder AKT-Inhibitoren verst{\"a}rkte Effekte auf das Zell{\"u}berleben der MM-Zellen. Zusammenfassend wurde die Bedeutung von RAL f{\"u}r das {\"U}berleben von Tumorzellen im MM gezeigt und RAL als potentielles therapeutisches Target im MM beschrieben, welches unabh{\"a}ngig von onkogenem RAS reguliert wird.},
  subject      = {Kleine GTP-bindende Proteine},
  language  = {de}
}
@phdthesis{Spindler2020,
  author    = {Spindler, Marie-Christin},
  title     = {Molecular architecture of meiotic multiprotein complexes},
  doi       = {10.25972/OPUS-21210},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212105},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Sexually reproducing organisms depend on meiosis for the generation of haploid, genetically diverse gametes to maintain genome stability and the potential to adapt to changing environments. Haploidization is achieved through two successive rounds of cell division after a single initial pre-meiotic DNA replication. Meiosis I segregates the homologous chromosomes, followed by the segregation of the sister chromatids in meiosis II. Genetic diversity is achieved through the process of recombination that de-scribes the exchange of genetic material between the maternal and paternal homolog. Recombination and the initial steps of haploidization are executed already early on in prophase I. Both essential processes depend on a variety of multiprotein complexes, such as the linker of nucleo- and cytoplasm (LINC) complex and the synaptonemal complex (SC). The structure of multiprotein complexes is adjusted according to their function, environment, and the forces they are subjected to. Coiled-coil domains typical in load-bearing proteins characterize the meiotic mechanotransducing LINC complexes. SCs resemble ladder-like structures that are highly conserved amongst eukaryotes, while the primary sequence of the proteins that form the complex display very little if any sequence homology. Despite the apparent significance of the structure to their function, little quantitative and topological data existed on the LINC complexes and the SC within their morphological context prior to the present work. Here, the molecular architecture of the meiotic telomere attachment site where LINC complexes reside and the SC have been analyzed in depth, mainly on the basis of electron microscope tomography derived 3D models complemented by super-resolution light microscopic acquisitions of the respective protein components.},
  subject      = {Meiose},
  language  = {en}
}
@phdthesis{Lu2020,
  author    = {Lu, Yunzhi},
  title     = {Kinetics of mouse and human muscle type nicotinic receptor channels},
  doi       = {10.25972/OPUS-19268},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-192688},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Acetylcholine (ACh) mediates transmission at vertebrate neuromuscular junctions and many other synapses. The postsynaptic ACh receptors at neuromuscular junctions are of the nicotinic subtype (nAChRs). They are among the best studied receptor channels and often serve as models or receptor prototypes. Despite a wealth of information on muscle type nAChRs so far little is known about species specific functional differences. In this work, mouse and human adult muscle type nAChRs are investigated. Cell attached recordings in the HEK293T heterologous expression system provided evidence that the ACh affinity of recombinant mouse and human adult muscle type nAChRs are different. To clarify this, I compared these receptors in outside-out patches employing a system for fast agonist application. Thus, the individual membrane patches with receptors can be exposed to various ligand concentrations. In response to 10 and 30 µM ACh normalized peak currents ({\^i}) were significantly larger and current rise-time (tr) shorter in human than in mouse receptors. Analyzing dose-response curves of {\^i} and tr and fitting them with a two-step equivalent binding-site kinetic mechanism revealed a two-fold higher ACh association rate constant in human compared to mouse receptors. Furthermore, human nAChRs were blocked faster in outside-out patches by superfusion of 300 nM α-Bungarotoxin (α-Bgtx) than mouse nAChRs. Finally, human nAChRs in outside-out patches showed higher affinity at 3 µM ACh than chimeric receptors consisting of mouse α- and human β-, γ- and ε-subunits. The higher affinity of human than mouse receptors for ACh and α-Bgtx is thus at least in part due to sequence difference in their α-subunits.},
  subject      = {Nicotinischer Acetylcholinrezeptor},
  language  = {en}
}
@phdthesis{Becker2020,
  author    = {Becker, Mira Caroline},
  title     = {Principles of olfactory-visual integration to form a common percept in honeybees},
  doi       = {10.25972/OPUS-19919},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-199190},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {The honeybee is a well studied and important organism in neuroethology. The possibility to train them with a classical conditioning paradigm and their miniature brain provide a perfect requisite to investigate the neuronal principles of learning and memory. Honeybees use visual and olfactory cues to detect flowers during their foraging trips. Hence, the reward association of a nectar source is a multi-modal construct, which has at least two major components - olfactory and visual cues. It is still an open question, how both sensory components are converged in the mushroom body, which represent the multi-modal integration centre of the honeybee brain. The main goal of this study, is to investigate the processing of multiple modalities and how a reward association is formed. This includes, how and wether both sensory modalities interfere during learning. Thus, in this study stimulation with UV, blue and green light was used to evoke distinct photoreceptor activities in the compound eye. Furthermore, three different odours (Geraniol, Citronellol and Farnesol) were used. These stimuli were tested in three different experimental series. The first experiment involved classical differential conditioning of the single modalities - odour and colour. Honeybees showed high learning performances in differentiating olfactory stimuli and also reliable responses for visual conditioning. Furthermore, a temporal discrepancy in the stimulus length for best learning in the olfatcoty and visual cues was found. In the second series, it was tested how multi-modal compounds are perceived. This includes, unique cues (configural processing) or the sum of the single components of a compound (elemen- tal processing). This was tested by combining single odour components with monochromatic light in a positive (PP) and negative patterning (NP) experiment. During PP, the olfactory- visual compound was rewarded, whereas the single components were unrewarded. In contrast, during NP the single components were reinforced, but the compound was not. In addition, the ability to distinguish between two different light stimuli presented as a part of an olfactory-visual compound with the same odour component during acquisition was tested. In a memory test, the light stimuli were presented again as a compound and in addition as the single components. The results revealed that bees used elemental processing with compounds containing green and blue light. In contrast, when UV light was presented the bees used configural processing. Finally, a third experiment was conducted at the neuronal level. Multi-unit recordings were established to provide a suitable method to analyse extrinsic neurons at the mushroom body output region, the so called ventral lobe of the pedunculus. Here, three different odours (Geran- iol, Farnesol and Citronellol), two colours (green and blue) and two combined stimuli (colour + odour) were chosen as stimuli, to search for possible variations in processing stimuli with different modalities. Two units could be detected that responded mainly to visual stimuli.},
  language  = {en}
}
@phdthesis{HornneeBunz2020,
  author    = {Horn [n{\´e}e Bunz], Melanie},
  title     = {The impact of Drosophila melanogaster`s endogenous clock on fitness: Influence of day length, humidity and food composition},
  doi       = {10.25972/OPUS-21141},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-211415},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {We are living in a system that underlies permanent environmental changes due to the rotation of our planet. These changes are rhythmic with the most prominent one having a period of about 24 hours, but also shorter and longer rhythms characterize our environment. To cope with the ever-changing environmental conditions, it is thought to be beneficial if an organism can track and anticipate these changes. The so called endogenous clocks enable this and might provide a fitness advantage. To investigate and unravel the mechanism of endogenous clocks Chronobiologists have used different model organisms. In this thesis Drosophila melanogaster was used as model organism with its about 150 clock neurons representing the main endogenous clock of the fly in the central brain. The molecular mechanisms and the interlocked feedback loops with the main circadian key players like period, timeless, clock or cycle are under investigation since the 1970s and are characterized quite well so far. But the impact of a functional endogenous clock in combination with diverse factors and the resulting fitness advantages were analysed in only a few studies and remains for the most part unknown. Therefore the aim of this thesis was to unravel the impact of Drosophila melanogaster`s endogenous clock on the fitness of the fly. To achieve this goal different factors - like day length, humidity and food composition - were analyzed in wild type CS and three different period mutants, namely perL, perS and per01, that carry a point mutation altering or abolishing the free-running period of the fruit fly as well as a second arrhythmic strain, clkAR. In competition assay experiments wild type and clock mutant flies competed for up to 63 generations under a normal 24 hour rhythm with 12 hours light/day and 12 hours darkness/night (LD12:12) or T-cycles with 19 or 29 hours, according to the mutants free-running period, or constant light (LL) in case of the arrhythmic mutant as well as under natural-like outdoor conditions in two consecutive years. Overall the wild type CS strain was outcompeting the clock mutant strains independent of the environmental conditions. As the perL fly strain elongated their free-running period, the competition experiments were repeated with naturally cantonized new fly strains. With these experiments it could be shown that the genetic background of the fly strains - which are kept for decades in the lab, with backcrosses every few years - is very important and influences the fitness of flies. But also the day length impacts the fitness of the flies, enabling them to persist in higher percentage in a population under competition. Further factors that might influence the survival in a competing population were investigated, like e.g. mating preferences and locomotor activity of homo- and heterozygous females or sperm number of males transferred per mating. But these factors can still not explain the results in total and play no or only minor roles and show the complexity of the whole system with still unknown characteristics. Furthermore populations of flies were recorded to see if the flies exhibit a common locomotor activity pattern or not and indeed a population activity pattern could be recorded for the first time and social contact as a Zeitgeber could be verified for Drosophila melanogaster. In addition humidity and its impact on the flies´ fitness as well as a potential Zeitgeber was examined in this thesis. The flies experienced different relative humidities for eclosion and wing expansion and humidity cycle phase shifting experiments were performed to address these two different questions of fitness impact and potential Zeitgeber. The fruit fly usually ecloses in the morning hours when the relative humidity is quite high and the general assumption was that they do so to prevent desiccation. The results of this thesis were quite clear and demonstrate that the relative humidity has no great effect on the fitness of the flies according to successful eclosion or wing expansion and that temperature might be the more important factor. In the humidity cycle phase shifting experiments it could be revealed that relative humidity cannot act as a Zeitgeber for Drosophila melanogaster, but it influences and therefore masks the activity of flies by allowing or surpressing activity at specific relative humidity values. As final experiments the lifespan of wild type and clock mutant flies was investigated under different day length and with different food qualities to unravel the impact of these factors on the fitness and therefore survival of the flies on the long run. As expected the flies with nutrient-poor minimum medium died earlier than on the nutrient-rich maximum medium, but a small effect of day length could also be seen with flies living slightly longer when they experience environmental day length conditions resembling their free-running period. The experiments also showed a fitness advantage of the wild type fly strain against the clock mutant strains for long term, but not short term (about the first 2-3 weeks). As a conclusion it can be said that genetic variation is important to be able to adapt to changing environmental conditions and to optimize fitness and therefore survival. Having a functional endogenous clock with a free-running period of about 24 hours provides fitness advantages for the fruit fly, at least under competition. The whole system is very complex and many factors - known and unknown ones - play a role in this system by interacting on different levels, e.g. physiology, metabolism and/or behavior.},
  subject      = {Taufliege},
  language  = {en}
}
@article{GoetzPanzerTrinksetal.2020,
  author    = {G{\"o}tz, Ralph and Panzer, Sabine and Trinks, Nora and Eilts, Janna and Wagener, Johannes and Turr{\`a}, David and Di Pietro, Antonio and Sauer, Markus and Terpitz, Ulrich},
  title     = {Expansion Microscopy for Cell Biology Analysis in Fungi},
  series = {Frontiers in Microbiology},
  volume    = {11},
  journal   = {Frontiers in Microbiology},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2020.00574},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-202569},
  year      = {2020},
  abstract  = {Super-resolution microscopy has evolved as a powerful method for subdiffraction-resolution fluorescence imaging of cells and cellular organelles, but requires sophisticated and expensive installations. Expansion microscopy (ExM), which is based on the physical expansion of the cellular structure of interest, provides a cheap alternative to bypass the diffraction limit and enable super-resolution imaging on a conventional fluorescence microscope. While ExM has shown impressive results for the magnified visualization of proteins and RNAs in cells and tissues, it has not yet been applied in fungi, mainly due to their complex cell wall. Here we developed a method that enables reliable isotropic expansion of ascomycetes and basidiomycetes upon treatment with cell wall degrading enzymes. Confocal laser scanning microscopy (CLSM) and structured illumination microscopy (SIM) images of 4.5-fold expanded sporidia of Ustilago maydis expressing fluorescent fungal rhodopsins and hyphae of Fusarium oxysporum or Aspergillus fumigatus expressing either histone H1-mCherry together with Lifeact-sGFP or mRFP targeted to mitochondria, revealed details of subcellular structures with an estimated spatial resolution of around 30 nm. ExM is thus well suited for cell biology studies in fungi on conventional fluorescence microscopes.},
  language  = {en}
}
@article{VikukFuchsKrischkeetal.2020,
  author    = {Vikuk, Veronika and Fuchs, Benjamin and Krischke, Markus and Mueller, Martin J. and Rueb, Selina and Krauss, Jochen},
  title     = {Alkaloid Concentrations of Lolium perenne Infected with Epichlo{\"e} festucae var. lolii with Different Detection Methods—A Re-Evaluation of Intoxication Risk in Germany?},
  series = {Journal of Fungi},
  volume    = {6},
  journal   = {Journal of Fungi},
  number    = {3},
  issn      = {2309-608X},
  doi       = {10.3390/jof6030177},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213171},
  year      = {2020},
  abstract  = {Mycotoxins in agriculturally used plants can cause intoxication in animals and can lead to severe financial losses for farmers. The endophytic fungus Epichlo{\"e} festucae var. lolii living symbiotically within the cool season grass species Lolium perenne can produce vertebrate and invertebrate toxic alkaloids. Hence, an exact quantitation of alkaloid concentrations is essential to determine intoxication risk for animals. Many studies use different methods to detect alkaloid concentrations, which complicates the comparability. In this study, we showed that alkaloid concentrations of individual plants exceeded toxicity thresholds on real world grasslands in Germany, but not on the population level. Alkaloid concentrations on five German grasslands with high alkaloid levels peaked in summer but were also below toxicity thresholds on population level. Furthermore, we showed that alkaloid concentrations follow the same seasonal trend, regardless of whether plant fresh or dry weight was used, in the field and in a common garden study. However, alkaloid concentrations were around three times higher when detected with dry weight. Finally, we showed that alkaloid concentrations can additionally be biased to different alkaloid detection methods. We highlight that toxicity risks should be analyzed using plant dry weight, but concentration trends of fresh weight are reliable.},
  language  = {en}
}
@article{OsmanStigloherMuelleretal.2020,
  author    = {Osman, Mohamed and Stigloher, Christian and Mueller, Martin J. and Waller, Frank},
  title     = {An improved growth medium for enhanced inoculum production of the plant growth-promoting fungus Serendipita indica},
  series = {Plant Methods},
  volume    = {16},
  journal   = {Plant Methods},
  doi       = {10.1186/s13007-020-00584-7},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229186},
  year      = {2020},
  abstract  = {Background The plant endophytic fungus Serendipita indica colonizes roots of a wide range of plant species and can enhance growth and stress resistance of these plants. Due to its ease of axenic cultivation and its broad host plant range including the model plant Arabidopsis thaliana and numerous crop plants, it is widely used as a model fungus to study beneficial fungus-root interactions. In addition, it was suggested to be utilized for commercial applications, e.g. to enhance yield in barley and other species. To produce inoculum, S. indica is mostly cultivated in a complex Hill-Kafer medium (CM medium), however, growth in this medium is slow, and yield of chlamydospores, which are often used for plant root inoculation, is relatively low. Results We tested and optimized a simple vegetable juice-based medium for an enhanced yield of fungal inoculum. The described vegetable juice (VJ) medium is based on commercially available vegetable juice and is easy to prepare. VJ medium was superior to the currently used CM medium with respect to biomass production in liquid medium and hyphal growth on agar plates. Using solid VJ medium supplemented with sucrose (VJS), a high amount of chlamydospores developed already after 8 days of cultivation, producing significantly more spores than on CM medium. Use of VJ medium is not restricted to S. indica, as it also supported growth of two pathogenic fungi often used in plant pathology experiments: the ascomycete Fusarium graminearum, the causal agent of Fusarium head blight disease on wheat and barley, and Verticillium longisporum, the causal agent of verticillium wilt. Conclusions The described VJ medium is recommended for streamlined and efficient production of inoculum for the plant endophytic fungus Serendipita indica and might prove superior for the propagation of other fungi for research purposes.},
  language  = {en}
}
@article{ShityakovBencurovaFoersteretal.2020,
  author    = {Shityakov, Sergey and Bencurova, Elena and F{\"o}rster, Carola and Dandekar, Thomas},
  title     = {Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches},
  series = {BMC Bioinformatics},
  volume    = {2020},
  journal   = {BMC Bioinformatics},
  doi       = {10.1186/s12859-020-3461-6},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229169},
  year      = {2020},
  abstract  = {Background Processing and analysis of DNA sequences obtained from next-generation sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinformatics approaches. However, algorithms based on NGS perform inefficiently due to the generation of long DNA fragments, the difficulty of assembling them and the complexity of the used genomes. On the other hand, the Sanger DNA sequencing method is still considered to be the most reliable; it is a reliable choice for virtual modeling to build all possible consensus sequences from smaller DNA fragments. Results In silico and in vitro experiments were conducted: (1) to implement and test our novel sequencing algorithm, using the standard cloning vectors of different length and (2) to validate experimentally virtual shotgun sequencing using the PCR technique with the number of cycles from 1 to 9 for each reaction. Conclusions We applied a novel algorithm based on Sanger methodology to correctly predict and emphasize the performance of DNA sequencing techniques as well as in de novo DNA sequencing and its further application in synthetic biology. We demonstrate the statistical significance of our results.},
  language  = {en}
}
@article{SeitzvanEngelsdorpLeonhardt2020,
  author    = {Seitz, Nicola and vanEngelsdorp, Dennis and Leonhardt, Sara D.},
  title     = {Are native and non-native pollinator friendly plants equally valuable for native wild bee communities?},
  series = {Ecology and Evolution},
  volume    = {10},
  journal   = {Ecology and Evolution},
  number    = {23},
  doi       = {10.1002/ece3.6826},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-218439},
  pages     = {12838-12850},
  year      = {2020},
  abstract  = {Bees rely on floral pollen and nectar for food. Therefore, pollinator friendly plantings are often used to enrich habitats in bee conservation efforts. As part of these plantings, non-native plants may provide valuable floral resources, but their effects on native bee communities have not been assessed in direct comparison with native pollinator friendly plantings. In this study, we performed a common garden experiment by seeding mixes of 20 native and 20 non-native pollinator friendly plant species at separate neighboring plots at three sites in Maryland, USA, and recorded flower visitors for 2 years. A total of 3,744 bees (120 species) were collected. Bee abundance and species richness were either similar across plant types (midseason and for abundance also late season) or lower at native than at non-native plots (early season and for richness also late season). The overall bee community composition differed significantly between native and non-native plots, with 11 and 23 bee species being found exclusively at one plot type or the other, respectively. Additionally, some species were more abundant at native plant plots, while others were more abundant at non-natives. Native plants hosted more specialized plant-bee visitation networks than non-native plants. Three species out of the five most abundant bee species were more specialized when foraging on native plants than on non-native plants. Overall, visitation networks were more specialized in the early season than in late seasons. Our findings suggest that non-native plants can benefit native pollinators, but may alter foraging patterns, bee community assemblage, and bee-plant network structures.},
  language  = {en}
}
@phdthesis{Vikuk2020,
  author    = {Vikuk, Veronika},
  title     = {Epichlo{\"e} endophyte-grass symbioses in Germany - Infection rates, alkaloid concentrations and possible intoxication risks},
  doi       = {10.25972/OPUS-21389},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213895},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Endophytes live in partial symbiosis inside a plant and have been detected in all tested plants. They belong to the group of fungi or bacteria and their ecological function is mostly unknown. The fungal endophytes of the genus Epichlo{\"e} belong to a special group of endophytes. Epichlo{\"e} endophytes live symbiotically inside cool season grass species and some of them are able to produce alkaloids toxic to vertebrates and insects. Their symbiosis is seen as mutualistic for the following reasons: the fungus provides the plant herbivore resistance by producing alkaloids, and it increases the plant's drought tolerance as well as its biomass production. In return, the grass provides the fungus shelter, nutrients and dispersal. Epichlo{\"e} endophytes are host specific and the ability to produce alkaloids differs between species. In order to estimate intoxication risks in grasslands, it is necessary to detect infection rates of different grass species with Epichlo{\"e} endophytes, and to determine the genotypes and chemotypes of the Epichlo{\"e} species as well as the produced alkaloid concentrations. Factors like land-use intensity or season may have an influence on infection rates and alkaloid concentrations. Also, different methodological approaches may lead to different results. In this doctoral thesis my general aim was to evaluate intoxication risks in German grasslands caused by Epichlo{\"e} endophytes. For that I investigated infection rates of different grass species and the genotypes and chemotypes of their Epichlo{\"e} endophytes in German grasslands (Chapter II). Furthermore, I compared alkaloid concentrations detected with dry and fresh plant weight and different analytical methods. I also detected possible changes on the influence of season or land-use intensity (Chapter III). Additionally, I examined infections with Epichlo{\"e} endophytes and alkaloid concentrations in commercially available grass seed mixtures and determined how that influences the intoxication risk of grazing animals in Europe (Chapter IV). It is of agricultural interest to estimate intoxication risks for grazing livestock on German grasslands due to Epichlo{\"e} infected grass species. Therefore, it is important to investigate which grasses are infected with the Epichlo{\"e} endophyte, if the endophytes have the ability to produce vertebrate and invertebrate toxic alkaloids and if the alkaloids are indeed produced. I showed that Epichlo{\"e} festucae var. lolii infecting agriculturally important Lolium perenne lacked the starting gene for ergovaline biosynthesis. Hence, vertebrate toxic ergovaline was not detected in the majority of the collected L. perenne plants. The detection of alkaloid concentrations is an important tool to estimate intoxication risk for vertebrates, but also invertebrates. My studies showed that the usage of dry plant material is crucial to quantify the correct alkaloid concentrations, and that alkaloid concentrations can vary depending on the detection method. Hence, the usage of validated, similar detection methods is important to be able to compare alkaloid concentrations from different studies. Nevertheless, the trends of seasonal changes and the influence of land-use intensity stayed the same, regardless if dry or fresh plant weight was used. Also, alkaloid concentrations were below toxicity thresholds on population level, regardless of the method used. Two commercially available forage grass and two commercially available turf grass seed mixtures were infected with Epichlo{\"e} endopyhtes and alkaloids were detected. This might contribute to the spreading of Epichlo{\"e} endopyhtes in Germany, therefore seed mixtures should be tested for Epichlo{\"e} infections. My results indicate that the intoxication risk is generally low in Germany at the moment, although that might change due to climate change, an increase of monocultural land-use, or the seeding of Epichlo{\"e} infected grass seeds.},
  subject      = {Endophytische Pilze},
  language  = {en}
}
@article{BowlerBjorkmanDornelasetal.2020,
  author    = {Bowler, Diana E. and Bjorkman, Anne D. and Dornelas, Maria and Myers-Smith, Isla H. and Navarro, Laetitia M. and Niamir, Aidin and Supp, Sarah R. and Waldock, Conor and Winter, Marten and Vellend, Mark and Blowes, Shane A. and B{\"o}hning-Gaese, Katrin and Bruelheide, Helge and Elahi, Robin and Ant{\~a}o, Laura H. and Hines, Jes and Isbell, Forest and Jones, Holly P. and Magurran, Anne E. and Cabral, Juliano Sarmento and Bates, Amanda E.},
  title     = {Mapping human pressures on biodiversity across the planet uncovers anthropogenic threat complexes},
  series = {People and Nature},
  volume    = {2},
  journal   = {People and Nature},
  number    = {2},
  doi       = {10.1002/pan3.10071},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213634},
  pages     = {380 -- 394},
  year      = {2020},
  abstract  = {Climate change and other anthropogenic drivers of biodiversity change are unequally distributed across the world. Overlap in the distributions of different drivers have important implications for biodiversity change attribution and the potential for interactive effects. However, the spatial relationships among different drivers and whether they differ between the terrestrial and marine realm has yet to be examined. We compiled global gridded datasets on climate change, land-use, resource exploitation, pollution, alien species potential and human population density. We used multivariate statistics to examine the spatial relationships among the drivers and to characterize the typical combinations of drivers experienced by different regions of the world. We found stronger positive correlations among drivers in the terrestrial than in the marine realm, leading to areas with high intensities of multiple drivers on land. Climate change tended to be negatively correlated with other drivers in the terrestrial realm (e.g. in the tundra and boreal forest with high climate change but low human use and pollution), whereas the opposite was true in the marine realm (e.g. in the Indo-Pacific with high climate change and high fishing). We show that different regions of the world can be defined by Anthropogenic Threat Complexes (ATCs), distinguished by different sets of drivers with varying intensities. We identify 11 ATCs that can be used to test hypotheses about patterns of biodiversity and ecosystem change, especially about the joint effects of multiple drivers. Our global analysis highlights the broad conservation priorities needed to mitigate the impacts of anthropogenic change, with different priorities emerging on land and in the ocean, and in different parts of the world.},
  language  = {en}
}
@article{GuptaSrivastavaOsmanogluetal.2020,
  author    = {Gupta, Shishir K. and Srivastava, Mugdha and Osmanoglu, Oezge and Dandekar, Thomas},
  title     = {Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs},
  series = {Scientific Reports},
  volume    = {10},
  journal   = {Scientific Reports},
  number    = {1},
  doi       = {10.1038/s41598-020-59344-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229406},
  year      = {2020},
  abstract  = {Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational methods of PPI determination can accelerate biological discovery by identifying the most promising interacting pairs of proteins and by assessing the reliability of identified PPIs. Here we present a first in-depth study describing a global view of the ant Camponotus floridanus interactome. Although several ant genomes have been sequenced in the last eight years, studies exploring and investigating PPIs in ants are lacking. Our study attempts to fill this gap and the presented interactome will also serve as a template for determining PPIs in other ants in future. Our C. floridanus interactome covers 51,866 non-redundant PPIs among 6,274 proteins, including 20,544 interactions supported by domain-domain interactions (DDIs), 13,640 interactions supported by DDIs and subcellular localization, and 10,834 high confidence interactions mediated by 3,289 proteins. These interactions involve and cover 30.6\% of the entire C. floridanus proteome.},
  language  = {en}
}
@article{DeLiraRamanSchulzeetal.2020,
  author    = {De Lira, Maria Nathalia and Raman, Sudha Janaki and Schulze, Almut and Schneider-Schaulies, Sibylle and Avota, Elita},
  title     = {Neutral Sphingomyelinase-2 (NSM 2) Controls T Cell Metabolic Homeostasis and Reprogramming During Activation},
  series = {Frontiers in Molecular Biosciences},
  volume    = {7},
  journal   = {Frontiers in Molecular Biosciences},
  issn      = {2296-889X},
  doi       = {10.3389/fmolb.2020.00217},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-211311},
  year      = {2020},
  abstract  = {Neutral sphingomyelinase-2 (NSM2) is a member of a superfamily of enzymes responsible for conversion of sphingomyelin into phosphocholine and ceramide at the cytosolic leaflet of the plasma membrane. Upon specific ablation of NSM2, T cells proved to be hyper-responsive to CD3/CD28 co-stimulation, indicating that the enzyme acts to dampen early overshooting activation of these cells. It remained unclear whether hyper-reactivity of NSM2-deficient T cells is supported by a deregulated metabolic activity in these cells. Here, we demonstrate that ablation of NSM2 activity affects metabolism of the quiescent CD4\(^+\) T cells which accumulate ATP in mitochondria and increase basal glycolytic activity. This supports enhanced production of total ATP and metabolic switch early after TCR/CD28 stimulation. Most interestingly, increased metabolic activity in resting NSM2-deficient T cells does not support sustained response upon stimulation. While elevated under steady-state conditions in NSM2-deficient CD4\(^+\) T cells, the mTORC1 pathway regulating mitochondria size, oxidative phosphorylation, and ATP production is impaired after 24 h of stimulation. Taken together, the absence of NSM2 promotes a hyperactive metabolic state in unstimulated CD4\(^+\) T cells yet fails to support sustained T cell responses upon antigenic stimulation.},
  language  = {en}
}
@article{VogelGossnerMergneretal.2020,
  author    = {Vogel, Sebastian and Gossner, Martin M. and Mergner, Ulrich and M{\"u}ller, J{\"o}rg and Thorn, Simon},
  title     = {Optimizing enrichment of deadwood for biodiversity by varying sun exposure and tree species: An experimental approach},
  series = {Journal of Applied Ecology},
  volume    = {57},
  journal   = {Journal of Applied Ecology},
  number    = {10},
  doi       = {10.1111/1365-2664.13648},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214614},
  pages     = {2075 -- 2085},
  year      = {2020},
  abstract  = {The enrichment of deadwood is essential for the conservation of saproxylic biodiversity in managed forests. However, existing strategies focus on a cost-intensive increase of deadwood amount, while largely neglecting increasing deadwood diversity. Deadwood objects, that is logs and branches, from six tree species were experimentally sun exposed, canopy shaded and artificially shaded for 4 years, after which the alpha-, beta- and gamma-diversity of saproxylic beetles, wood-inhabiting fungi and spiders were analysed. Analyses of beta-diversity included the spatial distance between exposed deadwood objects. A random-drawing procedure was used to identify the combination of tree species and sun exposure that yielded the highest gamma-diversity at a minimum of exposed deadwood amount. In sun-exposed plots, species numbers in logs were higher than in shaded plots for all taxa, while in branches we observed the opposite for saproxylic beetles. Tree species affected the species numbers only of saproxylic beetles and wood-inhabiting fungi. The beta-diversity of saproxylic beetles and wood-inhabiting fungi among logs was influenced by sun exposure and tree species, but beta-diversity of spiders by sun exposure only. For all saproxylic taxa recorded in logs, differences between communities increased with increasing spatial distance. A combination of canopy-shaded Carpinus logs and sun-exposed Populus logs resulted in the highest species numbers of all investigated saproxylic taxa among all possible combinations of tree species and sun-exposure treatments. Synthesis and applications. We recommend incorporating the enrichment of different tree species and particularly the variation in sun exposure into existing strategies of deadwood enrichment. Based on the results of our study, we suggest to combine the logs of softwood broadleaf tree species (e.g. Carpinus, Populus), hardwood broadleaf tree species (e.g. Quercus) and coniferous tree species (e.g. Pinus) under different conditions of sun exposure and distribute them spatially in a landscape to maximize the beneficial effects on overall diversity.},
  language  = {en}
}
@article{MuellerUlyshenSeiboldetal.2020,
  author    = {M{\"u}ller, J{\"o}rg and Ulyshen, Mike and Seibold, Sebastian and Cadotte, Marc and Chao, Anne and B{\"a}ssler, Claus and Vogel, Sebastian and Hagge, Jonas and Weiß, Ingmar and Baldrian, Petr and Tl{\´a}skal, Vojtěch and Thorn, Simon},
  title     = {Primary determinants of communities in deadwood vary among taxa but are regionally consistent},
  series = {Oikos},
  volume    = {129},
  journal   = {Oikos},
  number    = {10},
  doi       = {10.1111/oik.07335},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-228201},
  pages     = {1579 -- 1588},
  year      = {2020},
  abstract  = {The evolutionary split between gymnosperms and angiosperms has far-reaching implications for the current communities colonizing trees. The inherent characteristics of dead wood include its role as a spatially scattered habitat of plant tissue, transient in time. Thus, local assemblages in deadwood forming a food web in a necrobiome should be affected not only by dispersal ability but also by host tree identity, the decay stage and local abiotic conditions. However, experiments simultaneously manipulating these potential community drivers in deadwood are lacking. To disentangle the importance of spatial distance and microclimate, as well as host identity and decay stage as drivers of local assemblages, we conducted two consecutive experiments, a 2-tree species and 6-tree species experiment with 80 and 72 tree logs, respectively, located in canopy openings and under closed canopies of a montane and a lowland forest. We sampled saproxylic beetles, spiders, fungi and bacterial assemblages from logs. Variation partitioning for community metrics based on a unified framework of Hill numbers showed consistent results for both studies: host identity was most important for sporocarp-detected fungal assemblages, decay stage and host tree for DNA-detected fungal assemblages, microclimate and decay stage for beetles and spiders and decay stage for bacteria. Spatial distance was of minor importance for most taxa but showed the strongest effects for arthropods. The contrasting patterns among the taxa highlight the need for multi-taxon analyses in identifying the importance of abiotic and biotic drivers of community composition. Moreover, the consistent finding of microclimate as the primary driver for saproxylic beetles compared to host identity shows, for the first time that existing evolutionary host adaptions can be outcompeted by local climate conditions in deadwood.},
  language  = {en}
}
@article{SchaeblerAmatobiHornetal.2020,
  author    = {Sch{\"a}bler, Stefan and Amatobi, Kelechi M. and Horn, Melanie and Rieger, Dirk and Helfrich‑F{\"o}rster, Charlotte and Mueller, Martin J. and Wegener, Christian and Fekete, Agnes},
  title     = {Loss of function in the Drosophila clock gene period results in altered intermediary lipid metabolism and increased susceptibility to starvation},
  series = {Cellular and Molecular Life Sciences},
  volume    = {77},
  journal   = {Cellular and Molecular Life Sciences},
  issn      = {1420-682X},
  doi       = {10.1007/s00018-019-03441-6},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-232432},
  pages     = {4939-4956},
  year      = {2020},
  abstract  = {The fruit fly Drosophila is a prime model in circadian research, but still little is known about its circadian regulation of metabolism. Daily rhythmicity in levels of several metabolites has been found, but knowledge about hydrophobic metabolites is limited. We here compared metabolite levels including lipids between period\(^{01}\) (per\(^{01}\)) clock mutants and Canton-S wildtype (WT\(_{CS}\)) flies in an isogenic and non-isogenic background using LC-MS. In the non-isogenic background, metabo-lites with differing levels comprised essential amino acids, kynurenines, pterinates, glycero(phospho)lipids, and fatty acid esters. Notably, detectable diacylglycerols (DAG) and acylcarnitines (AC), involved in lipid metabolism, showed lower levels in per\(^{01}\) mutants. Most of these differences disappeared in the isogenic background, yet the level differences for AC as well as DAG were consistent for fly bodies. AC levels were dependent on the time of day in WTCS in phase with food consumption under LD conditions, while DAGs showed weak daily oscillations. Two short-chain ACs continued to cycle even in constant darkness. per\(^{01}\) mutants in LD showed no or very weak diel AC oscillations out of phase with feeding activity. The low levels of DAGs and ACs in per\(^{01}\) did not correlate with lower total food consumption, body mass or weight. Clock mutant flies showed higher sensitivity to starvation independent of their background-dependent activity level. Our results suggest that neither feeding, energy storage nor mobilisation is significantly affected in per\(^{01}\) mutants, but point towards impaired mitochondrial activity, supported by upregulation of the mitochondrial stress marker 4EBP in the clock mutants},
  language  = {en}
}
@article{TrinklKaluzaWallaceetal.2020,
  author    = {Trinkl, Moritz and Kaluza, Benjamin F. and Wallace, Helen and Heard, Tim A. and Keller, Alexander and Leonhardt, Sara D.},
  title     = {Floral Species Richness Correlates with Changes in the Nutritional Quality of Larval Diets in a Stingless Bee},
  series = {Insects},
  volume    = {11},
  journal   = {Insects},
  number    = {2},
  issn      = {2075-4450},
  doi       = {10.3390/insects11020125},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-200605},
  pages     = {125},
  year      = {2020},
  abstract  = {Bees need food of appropriate nutritional quality to maintain their metabolic functions. They largely obtain all required nutrients from floral resources, i.e., pollen and nectar. However, the diversity, composition and nutritional quality of floral resources varies with the surrounding environment and can be strongly altered in human-impacted habitats. We investigated whether differences in plant species richness as found in the surrounding environment correlated with variation in the floral diversity and nutritional quality of larval provisions (i.e., mixtures of pollen, nectar and salivary secretions) composed by the mass-provisioning stingless bee Tetragonula carbonaria (Apidae: Meliponini). We found that the floral diversity of larval provisions increased with increasing plant species richness. The sucrose and fat (total fatty acid) content and the proportion and concentration of the omega-6 fatty acid linoleic acid decreased, whereas the proportion of the omega-3 fatty acid linolenic acid increased with increasing plant species richness. Protein (total amino acid) content and amino acid composition did not change. The protein to fat (P:F) ratio, known to affect bee foraging, increased on average by more than 40\% from plantations to forests and gardens, while the omega-6:3 ratio, known to negatively affect cognitive performance, decreased with increasing plant species richness. Our results suggest that plant species richness may support T. carbonaria colonies by providing not only a continuous resource supply (as shown in a previous study), but also floral resources of high nutritional quality.},
  language  = {en}
}
@phdthesis{Vollmuth2021,
  author    = {Vollmuth, Nadine},
  title     = {Role of the proto-oncogene c-Myc in the development of Chlamydia trachomatis},
  doi       = {10.25972/OPUS-20365},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-203655},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Chlamydia trachomatis, an obligate intracellular human pathogen, is the world's leading cause of infection related blindness and the most common, bacterial sexually transmitted disease. In order to establish an optimal replicative niche, the pathogen extensively interferes with the physiology of the host cell. Chlamydia switches in its complex developmental cycle between the infectious non-replicative elementary bodies (EBs) and the non-infectious replicative reticulate bodies (RBs). The transformation to RBs, shortly after entering a host cell, is a crucial process in infection to start chlamydial replication. Currently it is unknown how the transition from EBs to RBs is initiated. In this thesis, we could show that, in an axenic media approach, L glutamine uptake by the pathogen is crucial to initiate the EB to RB transition. L-glutamine is converted to amino acids which are used by the bacteria to synthesize peptidoglycan. Peptidoglycan inturn is believed to function in separating dividing Chlamydia. The glutamine metabolism is reprogrammed in infected cells in a c-Myc-dependent manner, in order to accomplish the increased requirement for L-glutamine. Upon a chlamydial infection, the proto-oncogene c-Myc gets upregulated to promote host cell glutaminolysis via glutaminase GLS1 and the L-glutamine transporter SLC1A5/ASCT2. Interference with this metabolic reprogramming leads to limited growth of C. trachomatis. Besides the active infection, Chlamydia can persist over a long period of time within the host cell whereby chronic and recurrent infections establish. C. trachomatis acquire a persistent state during an immune attack in response to elevated interferon-γ (IFN-γ) levels. It has been shown that IFN-γ activates the catabolic depletion of L-tryptophan via indoleamine 2,3-dioxygenase (IDO), resulting in the formation of non-infectious atypical chlamydial forms. In this thesis, we could show that IFN-γ depletes the key metabolic regulator c-Myc, which has been demonstrated to be a prerequisite for chlamydial development and growth, in a STAT1-dependent manner. Moreover, metabolic analyses revealed that the pathogen de routs the host cell TCA cycle to enrich pyrimidine biosynthesis. Supplementing pyrimidines or a-ketoglutarate helps the bacteria to partially overcome the persistent state. Together, the results indicate a central role of c-Myc induced host glutamine metabolism reprogramming and L-glutamine for the development of C. trachomatis, which may provide a basis for anti-infectious strategies. Furthermore, they challenge the longstanding hypothesis of L-tryptophan shortage as the sole reason for IFN-γ induced persistence and suggest a pivotal role of c-Myc in the control of the C. trachomatis dormancy.},
  language  = {en}
}
@phdthesis{Gruendl2021,
  author    = {Gr{\"u}ndl, Marco},
  title     = {Biochemical characterization of the MMB-Hippo crosstalk and its physiological relevance for heart development},
  doi       = {10.25972/OPUS-21332},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213328},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {The Myb-MuvB (MMB) complex plays an essential role in the time-dependent transcriptional activation of mitotic genes. Recently, our laboratory identified a novel crosstalk between the MMB-complex and YAP, the transcriptional coactivator of the Hippo pathway, to coregulate a subset of mitotic genes (Pattschull et al., 2019). Several genetic studies have shown that the Hippo-YAP pathway is essential to drive cardiomyocyte proliferation during cardiac development (von Gise et al., 2012; Heallen et al., 2011; Xin et al., 2011). However, the exact mechanisms of how YAP activates proliferation of cardiomyocytes is not known. This doctoral thesis addresses the physiological role of the MMB-Hippo crosstalk within the heart and characterizes the YAP-B-MYB interaction with the overall aim to identify a potent inhibitor of YAP. The results reported in this thesis indicate that complete loss of the MMB scaffold protein LIN9 in heart progenitor cells results in thinning of ventricular walls, reduced cardiomyocyte proliferation and early embryonic lethality. Moreover, genetic experiments using mice deficient in SAV1, a core component of the Hippo pathway, and LIN9-deficient mice revealed that the correct function of the MMB complex is critical for proliferation of cardiomyocytes due to Hippo-deficiency. Whole genome transcriptome profiling as well as genome wide binding studies identified a subset of Hippo-regulated cell cycle genes as direct targets of MMB. By proximity ligation assay (PLA), YAP and B-MYB were discovered to interact in embryonal cardiomyocytes. Biochemical approaches, such as co-immunoprecipitation assays, GST-pulldown assays, and µSPOT-based peptide arrays were employed to characterize the YAP-B-MYB interaction. Here, a PY motif within the N-terminus of B-MYB was found to directly interact with the YAP WW-domains. Consequently, the YAP WW-domains were important for the ability of YAP to drive proliferation in cardiomyocytes and to activate MMB target genes in differentiated C2C12 cells. The biochemical information obtained from the interaction studies was utilized to develop a novel competitive inhibitor of YAP called MY-COMP (Myb-YAP competition). In MY-COMP, the protein fragment of B-MYB containing the YAP binding domain is fused to a nuclear localization signal. Co-immunoprecipitation studies as well as PLA revealed that the YAP-B-MYB interaction is robustly blocked by expression of MY-COMP. Adenoviral overexpression of MY-COMP in embryonal cardiomyocytes suppressed entry into mitosis and blocked the pro-proliferative function of YAP. Strikingly, characterization of the cellular phenotype showed that ectopic expression of MY-COMP led to growth defects, nuclear abnormalities and polyploidization in HeLa cells. Taken together, the results of this thesis reveal the mechanism of the crosstalk between the Hippo signaling pathway and the MMB complex in the heart and form the basis for interference with the oncogenic activity of the Hippo coactivator YAP.},
  subject      = {Zellzyklus},
  language  = {en}
}
@phdthesis{Ruedenauer2021,
  author    = {R{\"u}denauer, Fabian},
  title     = {Nutrition facts of pollen: nutritional quality and how it affects reception and perception in bees},
  doi       = {10.25972/OPUS-21254},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212548},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Nutrients belong to the key elements enabling life and influencing an organism's fitness. The intake of nutrients in the right amounts and ratios can increase fitness; strong deviations from the optimal intake target can decrease fitness. Hence, the ability to assess the nutritional profile of food would benefit animals. To achieve this, they need the according nutrient receptors, the ability to interpret the receptor information via perceptive mechanisms, and the ability to adjust their foraging behavior accordingly. Additionally, eventually existing correlations between the nutrient groups and single nutrient compounds in food could help them to achieve this adjustment. A prominent interaction between food and consumer is the interaction between flowering plants (angiosperms) and animal pollinators. Usually both of the interacting partners benefit from this mutualistic interaction. Plants are pollinated while pollinators get a (most of the times) nutritional reward in form of nectar and/or pollen. As similar interactions between plants and animals seem to have existed even before the emergence of angiosperms, these interactions between insects and angiosperms very likely have co-evolved right from their evolutionary origin. Therefore, insect pollinators with the ability to assess the nutritional profile may have shaped the nutritional profile of plant species depending on them for their reproduction via selection pressure. In Chapter I of this thesis the pollen nutritional profile of many plant species was analyzed in the context of their phylogeny and their dependence on insect pollinators. In addition, correlations between the nutrients were investigated. While the impact of phylogeny on the pollen protein content was little, the mutual outcome of both of the studies included in this chapter is that protein content of pollen is mostly influenced by the plant's dependence on insect pollinators. Several correlations found between nutrients within and between the nutrient groups could additionally help the pollinators to assess the nutrient profile of pollen. An important prerequisite for this assessment would be that the pollinators are able to differentiate between pollen of different plant species. Therefore, in Chapter II it was investigated whether bees have this ability. Specifically, it was investigated whether honeybees are able to differentiate between pollen of two different, but closely related plant species and whether bumblebees prefer one out of three pollen mixes, when they were fed with only one of them as larvae. Honeybees indeed were able to differentiate between the pollen species and bumblebees preferred one of the pollen mixes to the pollen mix they were fed as larvae, possibly due to its nutritional content. Therefore, the basis for pollen nutrient assessment is given in bees. However, there also was a slight preference for the pollen fed as larvae compared to another non-preferred pollen mix, at least hinting at the retention of larval memory in adult bumblebees. Chapter III looks into nutrient perception of bumblebees more in detail. Here it was shown that they are principally able to perceive amino acids and differentiate between them as well as different concentrations of the same amino acid. However, they do not seem to be able to assess the amino acid content in pollen or do not focus on it, but instead seem to focus on fatty acids, for which they could not only perceive concentration differences, but also were able to differentiate between. These findings were supported by feeding experiments in which the bumblebees did not prefer any of the pollen diets containing less or more amino acids but preferred pollen with less fatty acids. In no choice feeding experiments, bumblebees receiving a diet with high fatty acid content accepted undereating other nutrients instead of overeating fat, leading to increased mortality and the inability to reproduce. Hence, the importance of fat in pollen needs to be looked into further. In conclusion, this thesis shows that the co-evolution of flowering plants and pollinating insects could be even more pronounced than thought before. Insects do not only pressure the plants to produce high quality nectar, but also pressure those plants depending on insect pollination to produce high quality pollen. The reason could be the insects' ability to receive and perceive certain nutrients, which enables them to forage selectively leading to a higher reproductive success of plants with a pollinator-suitable nutritional pollen profile.},
  subject      = {Pollen},
  language  = {en}
}
@phdthesis{Krimmer2021,
  author    = {Krimmer, Elena},
  title     = {Agri-environment schemes and ecosystem services: The influence of different sown flower field characteristics on pollination, natural pest control and crop yield},
  doi       = {10.25972/OPUS-20657},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-206577},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Insects are responsible for the major part of the ecosystem services pollination and natural pest control. If insects decline, these ecosystem services can not longer be reliably delivered. Agricultural intensification and the subsequent loss and fragmentation of habitats has among others been identified to cause insect decline. Ecological intensification aims to promote alternative and sustainable management practices in agricultural farming, for example to decrease the use of external inputs such as pesticides. Agri-environment schemes make amends for farmers if they integrate ecologically beneficial measures into their farming regime and can therefore promote ecological intensification. There is a wide variety of agri-environment schemes, but the implementation of sown flower fields on crop fields is often included. Flower fields offer foraging resources as well as nesting sites for many different insect species and should be able to support insect populations as well as to increase ecosystem services to adjacent fields. However, the potential of flower fields to exhibit these effects is depending on many factors. Among others, the age and size of the flower field can influence if and how different insects profit from the measure. Additionally, the complexity of the surrounding landscape and therefore the existing biodiversity is influencing the potential of flower fields to increase ecosystem services locally. The goal of this study is to disentangle to which degree these factors influence the ecosystem services pollination and natural pest control and if these factors interact with each other. Furthermore, it will be examined if and how flower fields and ecosystem services influence crop yield. Additional factors examined in this study are distance decay and pesticide use. The abundance of beneficial insects can decrease strongly with increasing distance to suitable habitats. Pesticide use in turn could abrogate positive effects of flower fields on beneficial insects. To examine these different aspects and to be able to make recommendations for flower field implementation, field experiments were conducted on differently composed sown flower fields and adjacent oilseed rape fields. Flower fields differed in their age and continuity as well as in their size. Additionally, flower and oilseed rape fields were chosen in landscapes with different amounts of semi-natural habitat. Oilseed rape fields adjacent to calcareous grasslands and conventional crop fields served as controls. Pollinator observations and pollen beetle and parasitism surveys were conducted in the oilseed rape fields. Additionally, different yield parameters of the oilseed rape plants were recorded. Observations were conducted and samples taken in increasing distance to the flower fields to examine distance decay functions. Spray windows were established to inspect the influence of pesticides on ecosystem services and crop yields. Linear mixed models were used for statistical analysis. The results show, that newly established flower fields with high amounts of flower cover are very attractive for pollinators. If the flower fields reached a certain size (> 1.5ha), the pollinators tended to stay in these fields and did not distribute into the surroundings. High amounts of semi-natural habitat in the surrounding landscape increased the value of small flower fields as starting points for pollinators and their subsequent spillover into crop fields. Additionally, high amounts of semi-natural habitat decreased the decay of pollinators with increasing distance to the flower fields. Based on these results, it can be recommended to establish many small flower fields in landscapes with high amounts of semi-natural habitat and large flower fields in landscapes with low amounts of semi-natural habitat. However, it is mentionable that flower fields are no substitute for perennial semi-natural habitats. These still must be actively conserved to increase pollination to crop fields. Furthermore, the lowest amount of pollen beetle infestation was found on oilseed rape fields adjacent to continuous flower fields aged older than 6 years. Flower fields and calcareous grasslands in general increased pollen beetle parasitism in adjacent oilseed rape fields compared to conventional crop fields. The threshold for effective natural pest control could only be reached in the pesticide free areas in the oilseed rape fields adjacent to continuous flower fields and calcareous grasslands. Parasitism and superparasitism declined with increasing distance to the adjacent fields in pesticide treated areas of the oilseed rape fields. However, they remained on a similar level in spray windows without pesticides. Large flower fields increased parasitism and superparasitism more than small flower fields. Flower fields generally have the potential to increase pollen beetle parasitism rates, but pesticides can abrogate these positive effects of flower fields on natural pest control. Last but not least, effects of flower fields and ecosystem services on oilseed rape yield were examined. No positive effects of pollination on oilseed rape yield could be found. Old and continuous flower fields increased natural pest control in oilseed rape fields, which in turn increased seed set and total seed weight of oilseed rape plants. The pesticide treatment had negative effects on natural pest control, but positive effects on crop yield. Pollination and natural pest control decreased with increasing distance to the field edge, but fruit set slightly increased. The quality of the field in terms of soil and climatic conditions did not influence the yield parameters examined in this study. Yield formation in oilseed rape plants is a complex process with many factors involved, and it is difficult to disentangle indirect effects of flower fields on yield. However, perennial flower fields can promote ecological intensification by increasing crop yield via natural pest control. This study contributes to a better understanding of the effects of differently composed flower fields on pollination, natural pest control and oilseed rape yield.},
  subject      = {{\"O}kologie},
  language  = {en}
}
@phdthesis{Schuster2021,
  author    = {Schuster, Sarah},
  title     = {Analysis of \(Trypanosoma\) \(brucei\) motility and the infection process in the tsetse fly vector},
  doi       = {10.25972/OPUS-19269},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-192691},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {African trypanosomes are protist pathogens that are infective for a wide spectrum of mammalian hosts. Motility has been shown to be essential for their survival and represents an important virulence factor. Trypanosoma brucei is transmitted by the bite of the bloodsucking tsetse fly, the only vector for these parasites. The voyage through the fly is complex and requires several migration, proliferation and differentiation steps, which take place in a defined order and in specific fly tissues. The first part of this doctoral thesis deals with the establishment of the trypanosome tsetse system as a new model for microswimmer analysis. There is an increasing interdisciplinary interest in microbial motility, but a lack of accessible model systems. Therefore, this work introduces the first enclosed in vivo host parasite system that is suitable for analysis of diverse microswimmer types in specific microenvironments. Several methods were used and adapted to gain unprecedented insights into trypanosome motion, the fly´s interior architecture and the physical interaction between host and parasite. This work provides a detailed overview on trypanosome motile behavior as a function of development in diverse host surroundings. In additional, the potential use of artificial environments is shown. This can be used to partly abstract the complex fly architecture and analyze trypanosome motion in defined nature inspired geometries. In the second part of the thesis, the infection of the tsetse fly is under investigation. Two different trypanosome forms exist in the blood: proliferative slender cells and cell cycle arrested stumpy cells. Previous literature states that stumpy cells are pre adapted to survive inside the fly, whereas slender cells die shortly after ingestion. However, infection experiments in our laboratory showed that slender cells were also potentially infective. During this work, infections were set up so as to minimize the possibility of stumpy cells being ingested, corroborating the observation that slender cells are able to infect flies. Using live cell microscopy and fluorescent reporter cell lines, a comparative analysis of the early development following infection with either slender or stumpy cells was performed. The experiments showed, for the first time, the survival of slender trypanosomes and their direct differentiation to the procyclic midgut stage, contradicting the current view in the field of research. Therefore, we can shift perspectives in trypanosome biology by proposing a revised life cycle model of T. brucei, where both bloodstream stages are infective for the vector.},
  subject      = {Motilit{\"a}t},
  language  = {en}
}
@phdthesis{Heiby2021,
  author    = {Heiby, Julia},
  title     = {Insight into molecular mechanisms of folding and self-association of spider silk protein domains},
  doi       = {10.25972/OPUS-19345},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-193455},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Spider silk is a biomaterial of extraordinary toughness paired with elasticity. The assembly of silk proteins, so-called spidroins (from "spider" and "fibroin"), generates the silk threads we typically see in our garden or the corners of our houses. Although spider webs from different species vary considerably in geometry and size, many sections of spidroin sequences are conserved. Highly conserved regions, found in all spidroins, relate to the terminal domains of the protein, i.e., the N-terminal (NTD) and C-terminal domains (CTD). Both have an essential function in the silk fibre association and polymerisation. The NTD is a 14 kDa five-helix bundle, which self-associates via a pH-driven mechanism. This process is critical for starting the polymerisation of the fibre. However, detailed insights into how conserved this mechanism is in different species and the quantitative thermodynamic comparison between homologous NTDs was missing. For this reason, four homologous NTDs of the major ampullate gland (MaSp) from spider species Euprosthenops australis, Nephila clavipes, Latrodectus hesperus, and Latrodectus geometricus were investigated. I analysed and quantified equilibrium thermodynamics, kinetics of folding, and self-association. Methods involved dynamic light scattering (MALS), stopped-flow fluorescence and circular dichroism spectroscopy in combination with thermal and chemical denaturation experiments. The results showed conserved, cooperative two-state folding on a sub-millisecond time scale. All homologous NTDs showed a similarly fast association in the order of 10^9 M^-1 s^-1, while the resulting equilibrium dissociation constants were in the low nanomolar range. Electrostatic forces were found to be of great importance for protein association. Monomeric protein stability increased with salt concentration while enhancing its folding speed. However, due to Debye-H{\"u}ckel effects, we found intermolecular electrostatics to be shielded, which reduced the NTDs association capacity significantly at high ionic strength. Altogether, the energetics and kinetics of the NTD dimerisation was conserved for all analysed homologs. Comparable to the NTD, the spider silks CTD is also a α-helix bundle, which covalently links two spidroins. The orientation of the domains predetermines the future fibre geometry. Here again, the detailed quantitative characterisation of the folding and dimerisation was missing. Therefore, the CTD from the E. australis was analysed in-depth. The protein folded via a three-state mechanism and was placed in the family of knotted proteins. By analysing the amino acid composition of the NTD of the MaSp1 of the Euprosthenops australis, we found an unusually high content of methionine residues (Met). To elucidate why this protein exhibits so many Met residues, I mutated all core Mets simultaneously to leucine (Leu). Results revealed a dramatically stabilised NTD, which now folded 50 times faster. After solving the tertiary structure of the mutant by NMR (nuclear magnetic resonance) spectroscopy, the structure of the monomeric mutant was found to be identical with the wild-type protein. However, when probing the dimerisation of the NTD, I could show that the association capacity was substantially impaired for the mutant. Our findings lead to the conclusion that Met provides the NTD with enhanced conformational dynamics and thus mobilises the protein, which results in tightly associated dimers. In additional experiments, I first re-introduced new Met residues into the Met-depleted protein at sequence positions containing native Leu. Hence, the mutated NTD protein was provided with the same number of Leu, which were previously removed by mutation. However, the protein did not regain wild-type characteristics. The functionality was not restored, but its stability was decreased as expected. To probe our hypothesis gained from the MaSp NTD, I transferred the experiment to another protein, namely the Hsp90 chaperone. Therefore, I incorporated methionine residues in the protein, which resulted in a slight improvement of its function. Finally, trial experiments were performed aiming at the synthesis of shortened spidroin constructs containing less repetitive middle-segments than the wild-type protein. The objective was to study the findings of the terminal domains in the context of an intact spidroin. The synthesis of these engineered spidroins was challenging. Nevertheless, preliminary results encourage the assumption that the characteristics observed in the isolated domains hold true in the context of a full-length spidroin.},
  subject      = {Spinnenseide},
  language  = {en}
}
@phdthesis{Markert2021,
  author    = {Markert, Sebastian Matthias},
  title     = {Enriching the understanding of synaptic architecture from single synapses to networks with advanced imaging techniques},
  doi       = {10.25972/OPUS-18993},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189935},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Because of its complexity and intricacy, studying the nervous system is often challenging. Fortunately, the small nematode roundworm Caenorhabditis elegans is well established as a model system for basic neurobiological research. The C. elegans model is also the only organism with a supposedly complete connectome, an organism-wide map of synaptic connectivity resolved by electron microscopy, which provides some understanding of how the nervous system works as a whole. However, the number of available data-sets is small and the connectome contains errors and gaps. One example of this concerns electrical synapses. Electrical synapses are formed by gap junctions and difficult to map due to their often ambiguous morphology in electron micrographs, leading to misclassification or omission. On the other hand, chemical synapses are more easily mapped, but many aspects of their mode of operation remain elusive and their role in the C. elegans connectome is oversimplified. A comprehensive understanding of signal transduction of neurons between each other and other cells will be indispensable for a comprehensive understanding of the nervous system. In this thesis, I approach these challenges with a combination of advanced light and electron microscopy techniques. First, this thesis describes a strategy to increase synaptic specificity in connectomics. Specifically, I classify gap junctions with a high degree of confidence. To achieve this, I utilized array tomography (AT). In this thesis, AT is adapted for high-pressure freezing to optimize for structure preservation and for super-resolution light microscopy; in this manner, I aim to bridge the gap between light and electron microscopy resolutions. I call this adaptation super-resolution array tomography (srAT). The srAT approach made it possible to clearly identify and map gap junctions with high precision and accuracy. The results from this study showcased the feasibility of incorporating electrical synapses into connectomes in a systematic manner, and subsequent studies have used srAT for other models and questions. As mentioned above, the C. elegans connectomic model suffers from a shortage of datasets. For most larval stages, including the special dauer larval stage, connectome data is completely missing up to now. To obtain the first partial connectome data-set of the C. elegans dauer larva, we used focused ion-beam scanning electron microscopy (FIB-SEM). This technique offers an excellent axial resolution and is useful for acquiring large volumes for connectomics. Together with our collaborators, I acquired several data-sets which enable the analysis of dauer stage-specific "re-wiring" of the nervous system and thus offer valuable insights into connectome plasticity/variability. While chemical synapses are easy to map relative to electrical synapses, signal transduction via chemical transmitters requires a large number of different proteins and molecular processes acting in conjunction in a highly constricted space. Because of the small spatial scale of the synapse, investigating protein function requires very high resolution, which electron tomography provides. I analyzed electron tomograms of a worm-line with a mutant synaptic protein, the serine/threonine kinase SAD-1, and found remarkable alterations in several architectural features. My results confirm and re-contextualize previous findings and provide new insight into the functions of this protein at the chemical synapse. Finally, I investigated the effectiveness of our methods on "malfunctioning," synapses, using an amyotrophic lateral sclerosis (ALS) model. In the putative synaptopathy ALS, the mechanisms of motor neuron death are mostly unknown. However, mutations in the gene FUS (Fused in Sarcoma) are one known cause of the disease. The expression of the mutated human FUS in C. elegans was recently shown to produce an ALS-like phenotype in the worms, rendering C. elegans an attractive disease model for ALS. Together with our collaboration partners, I applied both srAT and electron tomography methods to "ALS worms" and found effects on vesicle docking. These findings help to explain electrophysiological recordings that revealed a decrease in frequency of mini excitatory synaptic currents, but not amplitudes, in ALS worms compared to controls. In addition, synaptic endosomes appeared larger and contained electron-dense filaments in our tomograms. These results substantiate the idea that mutated FUS impairs vesicle docking and also offer new insights into further molecular mechanisms of disease development in FUS-dependent ALS. Furthermore, we demonstrated the broader applicability of our methods by successfully using them on cultured mouse motor neurons. Overall, using the C. elegans model and a combination of light and electron microscopy methods, this thesis helps to elucidate the structure and function of neuronal synapses, towards the aim of obtaining a comprehensive model of the nervous system.},
  subject      = {Caenorhabditis elegans},
  language  = {en}
}
@phdthesis{Auer2021,
  author    = {Auer, Daniela},
  title     = {Impact of the chlamydial deubiquitinase ChlaDUB1 on host cell defense},
  doi       = {10.25972/OPUS-17846},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178462},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {The human pathogen Chlamydia trachomatis is the main cause of sexually transmitted infections worldwide. The obligate intracellular bacteria are the causative agent of several diseases that reach from conjunctivitis causing trachoma and blindness as well as salpingitis and urethritis which can lead to infertility if left untreated. In order to gain genetically engineered Chlamydia that inducible knock down specific gene expression, the CRISPRi system was established in C. trachomatis. In a proof of principle experiment it was shown that C. trachomatis pCRISPRi:gCdu1III target ChlaDUB1 expression and reduce the protein amount up to 50 \%. Knock-down of the DUB did not influence protein levels of anti-apoptotic Mcl-1 and did not make cells susceptible for apoptosis. However, reduced dCas9 protein size, bacterial growth impairment and off target effects interfering with the GFP signal, form obstacles in CRISPRi system in Chlamydia. For routinely use of the CRISPRi method in C. trachomatis further investigation is needed. Since the bacterial life cycle includes two morphological and functional distinct forms, it is essential for chlamydial spread to complete the development cycle and form infectious progeny. Therefore, Chlamydia has evolved strategies to evade the host immune system in order to stay undetected throughout the developmental cycle. The bacteria prevent host cell apoptosis via stabilization of anti-apoptotic proteins like Mcl-1, Survivin and HIF-1α and activate pro-survival pathways, inhibiting invasion of immune cells to the site of infection. The host cell itself can destroy intruders via cell specific defense systems that involve autophagy and recruitment of professional immune cells. In this thesis the role of the chlamydial deubiuqitinase ChlaDUB1 upon immune evasion was elucidated. With the mutant strain Ctr Tn-cdu1 that encodes for a truncated DUB due to transposon insertion, it was possible to identify ChlaDUB1 as a potent opponent of the autophagic system. Mutant inclusions were targeted by K48 and K63 chain ubiquitination. Subsequently the inclusion was recognized by autophagic receptors like p62, NBR1 and NDP52 that was reversed again by complementation with the active DUB. Xenophagy was promoted so far as LC3 positive phagosomes formed around the inclusion of Ctr Tn-cdu1, which did not fuse with the lysosome. The detected growth defect in human primary cells of Chlamydia missing the active DUB was not traced back to autophagy, but was due to impaired development and replication. It was possible to identify Ankib1, the E3 ligase, that ubiquitinates the chlamydial inclusion in a siRNA based screen. The activating enzyme Ube1 and the conjugating enzyme Ube2L3 are also essential in this process. Chlamydia have a reduced genome and depend on lipids and nutrients that are translocated from the host cell to the inclusion to proliferate. Recruitment of fragmented Golgi stacks to the inclusion surface was prevented when ChlaDUB1 was inactive, probably causing diminished bacterial growth. Additionally, the modification of the inclusion by Ankib1 and subsequent decoration by autophagic markers was not only present in human but also murine cells. Comparison of other Chlamydia strains and species revealed Ankib1 to be located at the proximity of the inclusion in C. trachomatis strains only but not in C. muridarum or C. pneumoniae, indicating that Ankib1 is specifically the E3 ligase of C. trachomatis. Moreover, the role of ChlaDUB1 in infected tissue was of interest, since ChlaDUB1 protein was also found in early EB stage and so might get in contact with invading immune cells after cell lysis. While bacteria spread and infect new host cells, Chlamydia can also infect immune cells. Infection of human neutrophils with Ctr Tn-cdu1 shows less bacterial survival and affirms the importance of the DUB for bacterial fitness in these cells.},
  subject      = {Chlamydia},
  language  = {en}
}
@phdthesis{daCruzGueerisoli2021,
  author    = {da Cruz G{\"u}erisoli, Irene Maria},
  title     = {Investigating the murine meiotic telomere complex TERB1-TERB2-MAJIN: spatial organization and evolutionary history},
  doi       = {10.25972/OPUS-21056},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-210562},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Einess der faszinierenden Merkmale der meiotischen Prophase I sind die hochkonservierten kr{\"a}ftigen Bewegungen homologer Chromosomen. Diese Bewegungen sind entscheidend f{\"u}r den Erfolg von Schl{\"u}sselereignissen wie die Ausrichtung, Paarung und Rekombination der homologen Chromosomen. Mehrere bisher untersuchte Organismen, darunter S{\"a}ugetiere, W{\"u}rmer, Hefen und Pflanzen, erreichen diese Bewegungen, indem sie die Chromosomenenden an spezialisierten Stellen in der Kernh{\"u}lle verankern. Diese Verankerung erfordert Telomer-Adapterproteine, die bisher in der Spalthefe und der Maus identifiziert wurden. Die meiosespezifischen Telomer-Adapterproteine der Maus, TERB1, TERB2 und MAJIN, sind an der Verankerung des ubiquit{\"a}ren Telomer-Shelterin-protein an den LINC-Komplex beteiligt, mit einem analogen Mechanismus, wie er die Spalthefe beschrieben wird. Obgleich die meiose-spezifischen TelomerAdapterproteine eine wesentliche Rolle spielen, ist der genaue Mechanismus der Verankerung der Telomere an die Kernh{\"u}lle sowie ihre evolution{\"a}re Geschichte bisher noch wenig verstanden. Das Hauptziel dieser Arbeit ist daher die Untersuchung der Organisation des meiosespezifischen TelomerAdapterkomplexes TERB1-TERB2-MAJIN der Maus und dessen Evolutionsgeschichte. Im ersten Teil dieser Arbeit wurde die Organisation des TERB1-TERB2-MAJIN Komplexes mittels hochaufl{\"o}sender Mikroskopie (SIM), an Mausspermatozyten untersucht, sowie die Lokalisation in Bezug auf TRF1 des Telomer-ShelterinKomplexes und die telomerische DNA analysiert. In den Stadien Zygot{\"a}n und Pachyt{\"a}n zeigten die Fluoreszenzsignale eine starke {\"U}berlappung der Verteilung der meiotischen Telomer-Komplex-Proteine, wobei die Organisation von TERB2 an den Chromosomenenden heterogener war als die von TERB1 und MAJIN. Außerdem konnte die TRF1-Lokalisation an den Enden der Lateralelemente (LEs) mit einer griffartigen Anordnung um die TERB1- und MAJIN-Signale im Zygot{\"a}n- und Pachyt{\"a}n-Stadium gezeigt werden. Interessanterweise erwies sich die telomerische DNA als lateral verteilt und teilweise {\"u}berlappend mit der zentralen Verteilung der meiotischen Telomer-Komplex-Proteine an den Enden der LEs. Die Kombination dieser Ergebnisse erlaubte die Beschreibung eines alternativen Modells der Verankerung der Telomer an die Kernh{\"u}lle w{\"a}hrend der meiotischen Prophase I. Der zweite Teil dieser Arbeit analysiert die Evolutionsgeschichte der Mausproteine von TERB1, TERB2 und MAJIN. Die fehlende {\"U}bereinstimmung zwischen den Meiose-spezifische Telomer-Adapteproteinen der Maus und der Spalthefe hat die Frage nach dem evolutionsbedingten Ursprung dieses spezifischen Komplexes aufgeworfen. Um vermeintliche Orthologen der Mausproteinevon TERB1, TERB2 und MAJIN {\"u}ber Metazoen hinweg zu identifizieren, wurden computergest{\"u}tzte Verfahren und phylogenetische Analysen durchgef{\"u}hrt. Dar{\"u}ber hinaus wurden Expressionsstudien implementiert, um ihre potenzielle Funktion w{\"a}hrend der Meiose zu testen. Die Analysen haben ergeben, dass der Meiose-spezifische Telomer-Komplex der Maus sehr alt ist, da er bereits in den Eumetazoen entstand, was auf einen einzigen Ursprung hindeutet. Das Fehlen jeglicher Homologen des meiosespezifischen Telomerkomplexes in Nematoden und die einigen wenigen in Arthropoden nachgewiesenen Kandidaten, deuten darauf hin, dass die Telomer-Adapterproteine in diesen Abstammungslinien verloren/ersetzt oder stark diversifiziert worden sind. Bemerkenswerterweise zeigten Proteindom{\"a}nen von TERB1, TERB2 und MAJIN, die an der Bildung des Komplexes sowie an der Interaktion mit dem Telomer-Shelterin-Protein und den LINC-Komplexen beteiligt sind, eine hohe Sequenz{\"a}hnlichkeit {\"u}ber alle Kladen hinweg. Abschließend lieferte die Genexpression im Nesseltier Hydra vulgaris den Beweis, dass der TERB1-TERB2-MAJIN-Komplex selektiv in der Keimbahn exprimiert wird, was auf die Konservierung meiotischer Funktionen {\"u}ber die gesamte Metazoen-Evolution hinweg hindeutet. Zusammenfassend bietet diese Arbeit bedeutende neue Erkenntnisse hinsichtlich des Meiose-spezifischen Telomer-Adapterkomplex, seines Mechanismus zur Verankerung der Telomer an die Kernh{\"u}lle und die Entschl{\"u}sselung seines Ursprungs in den Metazoen.},
  language  = {en}
}
@phdthesis{Roeschert2021,
  author    = {R{\"o}schert, Isabelle},
  title     = {Aurora-A prevents transcription-replication conflicts in MYCN-amplified neuroblastoma},
  doi       = {10.25972/OPUS-24303},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-243037},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Neuroblastoma is the most abundant, solid, extracranial tumor in early childhood and the leading cause of cancer-related childhood deaths worldwide. Patients with high-risk neuroblastoma often show MYCN-amplification and elevated levels of Aurora-A. They have a low overall survival and despite multimodal therapy options a poor therapeutic prognosis. MYCN-amplified neuroblastoma cells depend on Aurora-A functionality. Aurora-A stabilizes MYCN and prevents it from proteasomal degradation by competing with the E3 ligase SCFFBXW7. Interaction between Aurora-A and MYCN can be observed only in S phase of the cell cycle and activation of Aurora-A can be induced by MYCN in vitro. These findings suggest the existence of a profound interconnection between Aurora-A and MYCN in S phase. Nevertheless, the details remain elusive and were investigated in this study. Fractionation experiments show that Aurora-A is recruited to chromatin in S phase in a MYCN-dependent manner. Albeit being unphosphorylated on the activating T288 residue, Aurora-A kinase activity was still present in S phase and several putative, novel targets were identified by phosphoproteomic analysis. Particularly, eight phosphosites dependent on MYCN-activated Aurora-A were identified. Additionally, phosphorylation of serine 10 on histone 3 was verified as a target of this complex in S phase. ChIP-sequencing experiments reveal that Aurora-A regulates transcription elongation as well as histone H3.3 variant incorporation in S phase. 4sU-sequencing as well as immunoblotting demonstrated that Aurora-A activity impacts splicing. PLA measurements between the transcription and replication machinery revealed that Aurora-A prevents the formation of transcription-replication conflicts, which activate of kinase ATR. Aurora-A inhibitors are already used to treat neuroblastoma but display dose-limiting toxicity. To further improve Aurora-A based therapies, we investigated whether low doses of Aurora-A inhibitor combined with ATR inhibitor could increase the efficacy of the treatment albeit reducing toxicity. The study shows that the combination of both drugs leads to a reduction in cell growth as well as an increase in apoptosis in MYCN-amplified neuroblastoma cells, which is not observable in MYCN non-amplified neuroblastoma cells. This new approach was also tested by a collaboration partner in vivo resulting in a decrease in tumor burden, an increase in overall survival and a cure of 25\% of TH-MYCN mice. These findings indicate indeed a therapeutic window for targeting MYCN-amplified neuroblastoma.},
  subject      = {Neuroblastom},
  language  = {en}
}
@phdthesis{Aydinli2021,
  author    = {Aydinli, Muharrem},
  title     = {Software unterst{\"u}tzte Analyse von regulatorischen Elementen in Promotoren mittels AIModules},
  doi       = {10.25972/OPUS-24802},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-248025},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Die Regulation der Genexpression steht am Anfang vieler zellbiologischer Prozesse wie beispielsweise dem Zellwachstum oder der Differenzierung. Gene werden an Promotoren transkribiert, wobei ein Promotor selbst aus vielen logischen Einheiten aufgebaut ist, den Transkriptionsfaktorbindestellen (TFBSs). Diese k{\"o}nnen sehr nah beieinander liegen, aber auch weit entfernt voneinander sein. Sie werden spezifisch von Transkriptionsfaktoren (TFs) gebunden, die die Transkritptionsrate z.B. verst{\"a}rken (Enhancer) oder schw{\"a}chen (Silencer) k{\"o}nnen. Zwei oder mehr dieser TFBSs mit bestimmtem Abstand werden als "Module" zusammengefasst, die {\"u}ber Spezies hinweg konserviert sein k{\"o}nnen. Typischerweise findet man Module in Zellen mit einem Zellkern. Spezies mit gemeinsamen Modulen k{\"o}nnen ein Hinweis auf die gemeinsame phylogenetische Abstammung darstellen, aber auch gemeinsame Funktionsmechanismen von TFs {\"u}ber Gene hinweg aufdecken. Heutzutage sind verschiedene Anwendungen verf{\"u}gbar, mit denen nach TFBSs in DNA gesucht werden kann. Zum Zeitpunkt des Verfassens dieser Arbeit sind aber nur zwei kommerzielle Produkte bekannt, die nicht nur TFBSs, sondern auch Module erkennen. Deshalb stellen wir hier die freie und quelloffene L{\"o}sung "AIModules" vor, die diese L{\"u}cke f{\"u}llt und einen Webservice zur Verf{\"u}gung stellt, der es erlaubt nach TFBSs sowie nach Modulen auf DNA- und auf RNA-Abschnitten zu suchen. F{\"u}r die Motivesuche werden entweder Matrizen aus der Jaspar Datenbank oder Matrizen vom Anwender verwendet. Dar{\"u}berhinaus zeigen wir, dass unser Tool f{\"u}r die TF Suche nur Sekunden ben{\"o}tigt, wohingegen conTraV3 mindestens eine Stunde f{\"u}r dieselbe Analyse braucht. Zus{\"a}tzlich kann der Anwender bei unserem Tool den Grad der Konserviertheit f{\"u}r TFs mit angeben und wir zeigen, dass wir mit unserer L{\"o}sung, die die Jaspar Datenbank heranzieht, mehr Module finden, als ein kommerziell verf{\"u}gbares Produkt. Weiterhin kann mit unserer L{\"o}sung auch auf RNA-Sequenzen nach regulatorischen Motiven gesucht werden, wenn der Anwender die daf{\"u}r n{\"o}tigen Matrizen liefert. Wir zeigen dies am Beispiel von Polyadenylierungsstellen. Zusammenfassend stellen wir ein Werkzeug vor, das erstens frei und quelloffen ist und zweitens entweder auf Servern ver{\"o}ffentlicht werden kann oder On-Site auf einem Notebook l{\"a}uft. Unser Tool erlaubt es Promotoren zu analysieren und nach konservierten Modulen sowie TFBSs in Genfamilien sowie nach regulatorischen Elementen in mRNA wie z.B. Polyadenylierungsstellen oder andere regulatorische Elemente wie beispielsweise Enhancern oder Silencern in genomischer DNA zu suchen.},
  subject      = {Genregulation},
  language  = {de}
}
@phdthesis{Boegelein2021,
  author    = {B{\"o}gelein, Anna},
  title     = {Einfluss systemischer Therapeutika auf die CXCR4-Expression von Myelomzellen},
  doi       = {10.25972/OPUS-24174},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-241746},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Im Zuge der Bem{\"u}hungen um neue, tumorspezifische Therapieans{\"a}tze f{\"u}r die Myelomerkrankung hat sich der C-X-C-Chemokinrezeptor 4 (CXCR4) aufgrund seiner zentralen Rolle in der Tumorgenese als vielversprechender Angriffspunkt hervorgetan. Im Sinne eines theranostischen Konzepts wird der Rezeptor mithilfe eines radioaktiv markierten Liganden quantifiziert und anschließend von rezeptorspezifischen Radiotherapeutika als Zielstruktur genutzt. Die CXCR4-Expression ist allerdings ein h{\"o}chst dynamischer Prozess mit großer inter- und intraindividueller Heterogenit{\"a}t, der u.a. durch eine begleitende Chemotherapie beeinflusst werden kann. Ob sich therapieinduzierte Ver{\"a}nderungen der Rezeptorexpression gezielt nutzen lassen, um die CXCR4-Expression zu optimieren und so die Effektivit{\"a}t der CXCR4-gerichteten Strategien zu steigern, wurde bislang nicht untersucht. Vor diesem Hintergrund wurden in der vorliegenden Arbeit verschiedene, in der Myelomtherapie etablierte Substanzen sowohl einzeln als auch in Kombination hinsichtlich ihres Einflusses auf die CXCR4-Expression von MM-Zelllinien und prim{\"a}ren MM-Zellen unter in vitro Bedingungen analysiert. In den durchgef{\"u}hrten Experimenten zeigte sich eine hohe Variabilit{\"a}t der CXCR4-Expression der MM-Zellen nach Therapieinduktion, die sich als substanz-, dosis- und zeitabh{\"a}ngig herausstellte. Die Ergebnisse best{\"a}tigten das große Potenzial der therapieinduzierten Modulation der CXCR4-Expression. Im weiteren Verlauf sind translationale Forschungsans{\"a}tze gerechtfertigt, die die {\"U}bertragbarkeit der in vitro gewonnenen Ergebnisse auf die komplexen Vorg{\"a}nge im lebenden Organismus {\"u}berpr{\"u}fen. Langfristiges Ziel ist der Entwurf eines patientenzentrierten, multimodalen Therapiekonzepts, welches das CXCR4-gerichtete theranostische Konzept mit einer individuell angepassten, medikament{\"o}sen MM-Therapie kombiniert.},
  subject      = {Plasmozytom},
  language  = {de}
}
@article{ScheinerLimMeixneretal.2021,
  author    = {Scheiner, Ricarda and Lim, Kayun and Meixner, Marina D. and Gabel, Martin S.},
  title     = {Comparing the appetitive learning performance of six European honeybee subspecies in a common apiary},
  series = {Insects},
  volume    = {12},
  journal   = {Insects},
  number    = {9},
  issn      = {2075-4450},
  doi       = {10.3390/insects12090768},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-245180},
  year      = {2021},
  abstract  = {The Western honeybee (Apis mellifera L.) is one of the most widespread insects with numerous subspecies in its native range. How far adaptation to local habitats has affected the cognitive skills of the different subspecies is an intriguing question that we investigate in this study. Naturally mated queens of the following five subspecies from different parts of Europe were transferred to Southern Germany: A. m. iberiensis from Portugal, A. m. mellifera from Belgium, A. m. macedonica from Greece, A. m. ligustica from Italy, and A. m. ruttneri from Malta. We also included the local subspecies A. m. carnica in our study. New colonies were built up in a common apiary where the respective queens were introduced. Worker offspring from the different subspecies were compared in classical olfactory learning performance using the proboscis extension response. Prior to conditioning, we measured individual sucrose responsiveness to investigate whether possible differences in learning performances were due to differential responsiveness to the sugar water reward. Most subspecies did not differ in their appetitive learning performance. However, foragers of the Iberian honeybee, A. m. iberiensis, performed significantly more poorly, despite having a similar sucrose responsiveness. We discuss possible causes for the poor performance of the Iberian honeybees, which may have been shaped by adaptation to the local habitat.},
  language  = {en}
}
@unpublished{Dandekar2021,
  author    = {Dandekar, Thomas},
  title     = {Our universe may have started by Qubit decoherence},
  doi       = {10.25972/OPUS-23918},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239181},
  pages     = {54},
  year      = {2021},
  abstract  = {Our universe may have started by Qubit decoherence: In quantum computers, qubits have all their states undefined during calculation and become defined as output ("decoherence"). We study the transition from an uncontrolled, chaotic quantum vacuum ("before") to a clearly interacting "real world". In such a cosmology, the Big Bang singularity is replaced by a condensation event of interacting strings. This triggers a crystallization process. This avoids inflation, not fitting current observations: increasing long-range interactions limit growth and crystal symmetries ensure the same laws of nature and basic symmetries over the whole crystal. Tiny mis-arrangements provide nuclei of superclusters and galaxies and crystal structure allows arrangement of dark (halo regions) and normal matter (galaxy nuclei) for galaxy formation. Crystals come and go: an evolutionary cosmology is explored: entropic forces from the quantum soup "outside" of the crystal try to dissolve it. This corresponds to dark energy and leads to a "big rip" in 70 Gigayears. Selection for best growth and condensation events over generations of crystals favors multiple self-organizing processes within the crystal including life or even conscious observers in our universe. Philosophically this theory shows harmony with nature and replaces absurd perspectives of current cosmology. Independent of cosmology, we suggest that a "real world" (so our everyday macroscopic world) happens only inside a crystal. "Outside" there is wild quantum foam and superposition of all possibilities. In our crystallized world the vacuum no longer boils but is cooled down by the crystallization event, space-time exists and general relativity holds. Vacuum energy becomes 10**20 smaller, exactly as observed in our everyday world. We live in a "solid" state, within a crystal, the n quanta which build our world have all their different m states nicely separated. There are only nm states available for this local "multiverse". The arrow of entropy for each edge of the crystal forms one fate, one world-line or clear development of our world, while layers of the crystal are different system states. Mathematical leads from loop quantum gravity (LQG) point to required interactions and potentials. Interaction potentials for strings or loop quanta of any dimension allow a solid, decoherent state of quanta challenging to calculate. However, if we introduce here the heuristic that any type of physical interaction of strings corresponds just to a type of calculation, there is already since 1898 the Hurwitz theorem showing that then only 1D, 2D, 4D and 8D (octonions) allow complex or hypercomplex number calculations. No other hypercomplex numbers and hence dimensions or symmetries are possible to allow calculations without yielding divisions by zero. However, the richest solution allowed by the Hurwitz theorem, octonions, is actually the observed symmetry of our universe, E8. Standard physics such as condensation, crystallization and magnetization but also solid-state physics and quantum computing allow us to show an initial mathematical treatment of our new theory by LQG to describe the cosmological state transformations by equations, and, most importantly, point out routes to parametrization of free parameters looking at testable phenomena, experiments and formulas that describe processes of crystallization, protein folding, magnetization, solid-state physics and quantum computing. This is presented here for LQG, for string theory it would be more elegant but was too demanding to be shown here. Note: While my previous Opus server preprint "A new cosmology of a crystallization process (decoherence) from the surrounding quantum soup provides heuristics to unify general relativity and quantum physics by solid state physics" (https://doi.org/10.25972/OPUS-23076) deals with the same topics and basic formulas, this new version is improved: clearer in title, better introduction, more stringent in its mathematics and improved discussion of the implications including quantum computing, hints for parametrization and connections to LQG and other current cosmological efforts. This 5th of June 2021 version is again an OPUS preprint, but this will next be edited for Archives https://arxiv.org.},
  language  = {en}
}
@phdthesis{Goos2021,
  author    = {Goos, Carina},
  title     = {Nuclear periphery granules of trypanosomes - A characterization of composition and function},
  doi       = {10.25972/OPUS-23436},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-234368},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {The nuclear envelope serves as important mRNA surveillance system. In yeast and humans, several control mechanisms act in parallel to prevent nuclear export of unprocessed mRNAs. However, trypanosomes lack homologues to most of the proteins involved. In addition, gene expression in trypanosomes relies almost completely on post-transcriptional regulation as they transcribe mRNAs as long polycistrons, which are subsequently processed into individual mRNA molecules by trans-splicing. As trans-splicing is not error-free, unspliced mRNAs may be recognized and prevented from reaching the cytoplasm by a yet unknown mechanism. When trans-splicing is inhibited in trypanosomes, the formation of a novel RNA granule type at the cytoplasmic periphery of the nucleus, so called nuclear periphery granules (NPGs) was previously observed. To identify potential regulators of nuclear export control, changes in protein localization which occur when trans-splicing is inhibited, were globally analyzed during this work. For this, trypanosome nuclei were purified under conditions maintaining NPG attachment to the nucleus, in the absence and presence of trans-splicing. Mass spectrometry analyses identified 128 proteins which are specifically enriched in nuclear preparations of cells inhibited for trans-splicing. Amongst them are proteins, which change their localization to the nucleus or to the nuclear pores as well as many proteins that move into NPGs. Some of these proteins are promising candidates for nuclear export control proteins, as the changes in localization (to the nucleus or nuclear pores) were specific to the accumulation of unspliced mRNAs. The NPG proteome almost exclusively contains proteins involved in mRNA metabolism, mostly unique to trypanosomes, notably major translation initiation factors were absent. These data indicate that NPGs are RNP complexes which have started or completed nuclear export, but not yet entered translation. As a byproduct of these proteomic studies, a high-quality dataset of the yet unknown T. brucei nuclear proteome is provided, closing an important gap in knowledge to study trypanosome biology, in particular nuclear related processes. NPGs were characterized in more detail by microscopy. The granules are cytoplasmic and present in at least two different trypanosome life cycle stages. There are at least two distinct granule subsets, with differences in protein composition. A closer analysis of NPGs by electron microscopy revealed that the granules are electron dense structures, which are connected to nuclear pores by string-like structures. In order to approach the function of NPGs, on the one hand, the hypothesis that NPGs might be related to perinuclear germ granules of adult gonads of C. elegans was tested: we found no relation between the two granule types. On the other hand, initial single molecule mRNA FISH experiments performed in trypanosomes showed no accumulation of unspliced transcripts in NPGs, arguing against an involvement of the granules in mRNA quality control.},
  subject      = {Trypanosoma brucei},
  language  = {en}
}
@phdthesis{Classen2021,
  author    = {Claßen, Alexandra},
  title     = {The ERK-cascade in the pathophysiology of cardiac hypertrophy},
  doi       = {10.25972/OPUS-22966},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229664},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {ERK1/2 are known key players in the pathophysiology of heart failure, but the members of the ERK cascade, in particular Raf1, can also protect the heart from cell death and ischemic injury. An additional autophosphorylation (ERK1 at Thr208, ERK2 at Thr188) empowers ERK1/2 translocation to the nucleus and phosphorylation of nuclear targets which take part in the development of cardiac hypertrophy. Thereby, targeting this additional phosphorylation is a promising pharmacological approach. In this thesis, an in silico model of ERK cascade in the cardiomyocyte is introduced. The model is a semi-quantitive model and its behavior was tested with different softwares (SQUAD and CellNetAnalyzer). Different phosphorylation states of ERK1/2 as well as different stimuli can be reproduced. The different types of stimuli include hypertrophic as well as non-hypertrophic stimuli. With the introduced in-silico model time courses and synergistic as well as antagonistic receptor stimuli combinations can be predicted. The simulated time courses were experimentally validated. SQUAD was mainly used to make predictions about time courses and thresholds, whereas CNA was used to analyze steady states and feedback loops. Furthermore, new targets of ERK1/2 which partially contribute, also in the formation of cardiac hypertrophy, were identified and the most promising of them were illuminated. Important further targets are Caspase 8, GAB2, Mxi-2, SMAD2, FHL2 and SPIN90. Cardiomyocyte gene expression data sets were analyzed to verify involved components and to find further significantly altered genes after induced hypertrophy with TAC (transverse aortic constriction). Changes in the ultrastructure of the cardiomyocyte are the final result of induced hypertrophy.},
  subject      = {Herzhypertrophie},
  language  = {en}
}