TY - THES A1 - Altrock, Stefanie T1 - Genetische Organisation und Transkription eines Virulenz-assoziierten, instabilen Chromosomenabschnitts von Listeria ivanovii T1 - Genetic organisation and transcription of a virulence-associated, instable chromosomal region of Listeria ivanovii N2 - Unter den sechs Arten der Gattung Listeria finden sich nur zwei pathogene Spezies. L. monocytogenes ist pathogen für Mensch und Tier, L. ivanovii nur tierpathogen. Beide Arten besitzen ein Virulenzgencluster, das auch als Pathogenitätsinsel LIPI-1 bezeichnet wird. Pathogenitätsinseln (PAIs) sind bei gram-negativen Bakterien weit verbreitet, wurden bei gram-positiven Pathogenen bisher jedoch nur selten beschrieben. In L. ivanovii wurde nun ein weiterer Virulenz-assoziierter, instabiler Chromosomenabschnitt entdeckt, der in einem Teilbereich Eigenschaften einer Pathogenitätsinsel besitzt. Ausgehend von einem spontanen, aber reproduzierbaren Deletionsereignis eines großen Genomabschnitts, der einige schon bekannte Virulenz-assoziierte Gene umfasst (i-inlE, i-inlF, smcL), wurden in Zusammenarbeit mit den Kooperationspartnern an der "Universidad Complutense de Madrid", insbesondere mit G. Domínguez-Bernal die komplette deletierte Region sowie flankierende Genombereiche genauer analysiert. Im Rahmen dieser Arbeit konnten rechts von dem bereits charakterisierten Gen smcL 13 neue Open Reading Frames (ORFs) bzw. Gene (ydeI, rnaH, norA) von L. ivanovii identifiziert werden, die größtenteils in der Deletionsmutante L. ivanovii GD-3 deletiert waren. Für die meisten Open Reading Frames konnten Homologien zu ORFs in den Genomsequenzen von L. monocytogenes und der apathogenen Art L. innocua gefunden werden. Eigene experimentelle Analysen zeigten zudem, dass diese ORFs in ähnlicher Anordnung auch in den apathogenen Arten L. seeligeri und L. welshimeri vorhanden sind, was wahrscheinlich macht, dass sie nicht an der Virulenz von Listerien beteiligt sind. G. Domínguez-Bernal fand im links von smcL liegenden Bereich eine Reihe neuer Internalingene, die alle spezifisch für L. ivanovii sind. Für die Gene i-inlE, i-inlF und smcL ist bereits bekannt, dass diese Virulenz-assoziiert sind. Dies führte zur Definition einer neuen, LIPI-2 genannten Pathogenitätsinsel in L. ivanovii, die außer smcL und i-inlFE alle neu gefundenen Internalingene umfasst. In dieser Arbeit durchgeführte Untersuchungen der LIPI-2 flankierenden Bereiche zeigten, dass diese in L. monocytogenes und auch den apathogenen Arten L. innocua, L. seeligeri und L. welshimeri bemerkenswert konserviert sind. Durch Transkriptionsuntersuchungen mittels RT-PCR wurde die Expression der neu identifizierten Gene analysiert. Hierbei wurden verschiedene Kulturbedingungen untersucht sowie die Transkription nach Infektion mehrerer Zelllinien bestimmt. Bei der Sequenzanalyse wurde für fast alle Internalingene eine PrfA-Box identifiziert und es bestätigte sich in dieser Arbeit, dass die meisten der Internalingene PrfA-abhängig exprimiert werden. Allerdings wiesen die einzelnen Gene kein einheitliches Transkriptionsprofil unter verschiedenen in vitro-Bedingungen auf. Eine Analyse der Genexpression nach Infektion verschiedener Zelllinien zeigte schließlich, dass die Internalingene während einer Infektion differentiell transkribiert werden und möglicherweise am Infektionsgeschehen beteiligt sind. Das Expressionsmuster der zu LIPI-2 benachbarten Open Reading Frames bestätigte, dass diese Gene PrfA-unabhängig und unter verschiedenen Bedingungen konstitutiv exprimiert werden. Das Expressionsmuster dieser Gene läßt den Schluss zu, dass sie vermutlich nicht zur Virulenz von L. ivanovii beitragen. Die Untersuchung der Virulenzclustergene in LIPI-1 schließlich zeigte eine deutliche PrfA-Abhängigkeit der Genexpression. Es konnte bestätigt werden, dass deren Transkription unter PrfA-induzierenden Bedingungen verstärkt wird. Zudem fand sich auch nach Infektion eine deutliche Expression dieser Gene. N2 - Among the six species of Listeria only two are pathogenic. Whereas L. monocytogenes is pathogenic for men and animals, L. ivanovii only causes Listeriosis in animals. Both pathogenic species possess a virulence gene cluster, which is also designated as pathogenicity island LIPI-1. Pathogenicity islands (PAIs) are widespread among gram-negative bacteria, but so far have rarely been described for gram-positive pathogens. In L. ivanovii, an additional virulence-associated unstable part of the chromosome has recently been discovered, parts of which have some characteristics of a pathogenicity island. Starting from a spontaneous but reproducible deletion event of a big part of the genome which carries some known virulence associated genes (i-inlE, i-inlF, smcL), the complete deleted area plus flanking regions were analyzed in co-operation with G. Domínguez-Bernal from the "Universidad Complutense de Madrid". Within this work 13 new open reading frames (ORFs) resp. genes (ydeI, rnaH, norA) on the right side of the smcL gene could be identified in L. ivanovii. Most of them were deleted in the deletion mutant L ivanovii GD-3. Most of the open reading frames show homologies to ORFs also found in the genome sequences of L. monocytogenes and the apathogenic species L. innocua. Own experimental analyses showed, that the genes identified in this work are also present in the apathogenic species L. seeligeri and L. welshimeri. From this it can be concluded that they presumably are not involved in L. ivanovii virulence. G. Domínguez-Bernal discovered several new internalin genes on the left side of the smcL gene. All these genes are specific for L. ivanovii. For i-inlE, i-inlF and smcL it has already been shown that they are virulence associated. This lead to the definition of a new pathogenicity island (LIPI-2) in L. ivanovii, which, in addition to smcL and i-inlFE, comprises all newly found internalin genes. Study of the regions flanking LIPI-2 showed that these are considerably conserved in L. monocytogenes as well as in the apathogenic species L. innocua, L. seeligeri and L. welshimeri. By means of RT-PCR the expression of the new identified genes was analyzed. For this, different culture conditions and transcription after infection of several cell lines were examined. By sequence analysis, a PrfA-box has been identified in front of almost all internalin genes. This work confirmed, that the expression of most internalin genes is PrfA-dependent. However, the transcription pattern was not uniform under different in vitro conditions. Finally, the analysis of gene expression after infection of several cell lines showed, that the internalin genes are transcribed differentially during infection. From this it can be concluded that they may have a role in the infection process. The expression pattern of the open reading frames flanking LIPI-2 confirmed, that these genes are transcribed PrfA independently and constitutively in vitro. This suggests that they do not contribute to virulence of L. ivanovii. Examination of the virulence cluster genes finally showed, that there is a strong PrfA dependency in gene expression. It could be confirmed, that the transcription of these genes is increased under PrfA inducing conditions. In addition, after infection also a strong expression could be detected. KW - Listeria ivanovii KW - Virulenz KW - Molekulargenetik KW - Listeria KW - Listeria ivanovii KW - LIPI-2 KW - Pathogenitätsinsel KW - Internaline KW - ydeI KW - rnaH KW - norA KW - Genexpression KW - Listeria KW - Listeria ivanovii KW - LIPI-2 KW - pathogenicity island KW - internalins KW - ydeI KW - rnaH KW - norA KW - gene expression Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-3303 ER - TY - JOUR A1 - Alsheimer, Manfred A1 - Link, Jana A1 - Leubner, Monika A1 - Schmitt, Johannes A1 - Göb, Eva A1 - Benavente, Ricardo A1 - Jeang, Kuan-Teh A1 - Xu, Rener T1 - Analysis of Meiosis in SUN1 Deficient Mice Reveals a Distinct Role of SUN2 in Mammalian Meiotic LINC Complex Formation and Function N2 - LINC complexes are evolutionarily conserved nuclear envelope bridges, composed of SUN (Sad-1/UNC-84) and KASH (Klarsicht/ANC-1/Syne/homology) domain proteins. They are crucial for nuclear positioning and nuclear shape determination, and also mediate nuclear envelope (NE) attachment of meiotic telomeres, essential for driving homolog synapsis and recombination. In mice, SUN1 and SUN2 are the only SUN domain proteins expressed during meiosis, sharing their localization with meiosis-specific KASH5. Recent studies have shown that loss of SUN1 severely interferes with meiotic processes. Absence of SUN1 provokes defective telomere attachment and causes infertility. Here, we report that meiotic telomere attachment is not entirely lost in mice deficient for SUN1, but numerous telomeres are still attached to the NE through SUN2/KASH5-LINC complexes. In Sun12/2 meiocytes attached telomeres retained the capacity to form bouquetlike clusters. Furthermore, we could detect significant numbers of late meiotic recombination events in Sun12/2 mice. Together, this indicates that even in the absence of SUN1 telomere attachment and their movement within the nuclear envelope per se can be functional. Author summary: Correct genome haploidization during meiosis requires tightly regulated chromosome movements that follow a highly conserved choreography during prophase I. Errors in these movements cause subsequent meiotic defects, which typically lead to infertility. At the beginning of meiotic prophase, chromosome ends are tethered to the nuclear envelope (NE). This attachment of telomeres appears to be mediated by well-conserved membrane spanning protein complexes within the NE (LINC complexes). In mouse meiosis, the two main LINC components SUN1 and SUN2 were independently described to localize at the sites of telomere attachment. While SUN1 has been demonstrated to be critical for meiotic telomere attachment, the precise role of SUN2 in this context, however, has been discussed controversially in the field. Our current study was targeted to determine the factual capacity of SUN2 in telomere attachment and chromosome movements in SUN1 deficient mice. Remarkably, although telomere attachment is impaired in the absence of SUN1, we could find a yet undescribed SUN1-independent telomere attachment, which presumably is mediated by SUN2 and KASH5. This SUN2 mediated telomere attachment is stable throughout prophase I and functional in moving telomeres within the NE. Thus, our results clearly indicate that SUN1 and SUN2, at least partially, fulfill redundant meiotic functions. KW - telomeres KW - spermatocytes KW - Oocytes KW - meiosis KW - protein domains KW - cytoskeleton KW - synapsis KW - homologous chromosomes Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-111355 ER - TY - JOUR A1 - Alsheimer, Manfred A1 - Link, Jana A1 - Jahn, Daniel A1 - Schmitt, Johannes A1 - Göb, Eva A1 - Baar, Johannes A1 - Ortega, Sagrario A1 - Benavente, Ricardo T1 - The Meiotic Nuclear Lamina Regulates Chromosome Dynamics and Promotes Efficient Homologous Recombination in the Mouse JF - PLoS Genetics N2 - The nuclear lamina is the structural scaffold of the nuclear envelope and is well known for its central role in nuclear organization and maintaining nuclear stability and shape. In the past, a number of severe human disorders have been identified to be associated with mutations in lamins. Extensive research on this topic has provided novel important clues about nuclear lamina function. These studies have contributed to the knowledge that the lamina constitutes a complex multifunctional platform combining both structural and regulatory functions. Here, we report that, in addition to the previously demonstrated significance for somatic cell differentiation and maintenance, the nuclear lamina is also an essential determinant for germ cell development. Both male and female mice lacking the short meiosis-specific A-type lamin C2 have a severely defective meiosis, which at least in the male results in infertility. Detailed analysis revealed that lamin C2 is required for telomere-driven dynamic repositioning of meiotic chromosomes. Loss of lamin C2 affects precise synapsis of the homologs and interferes with meiotic double-strand break repair. Taken together, our data explain how the nuclear lamina contributes to meiotic chromosome behaviour and accurate genome haploidization on a mechanistic level. KW - homologous chromosomes KW - homologous recombination KW - lamins KW - Oocytes KW - spermatocytes KW - synapsis KW - telomeres KW - testes Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-96285 ER - TY - JOUR A1 - Alnusaire, Taghreed S. A1 - Sayed, Ahmed M. A1 - Elmaidomy, Abeer H. A1 - Al-Sanea, Mohammad M. A1 - Albogami, Sarah A1 - Albqmi, Mha A1 - Alowaiesh, Bassam F. A1 - Mostafa, Ehab M. A1 - Musa, Arafa A1 - Youssif, Khayrya A. A1 - Refaat, Hesham A1 - Othman, Eman M. A1 - Dandekar, Thomas A1 - Alaaeldin, Eman A1 - Ghoneim, Mohammed M. A1 - Abdelmohsen, Usama Ramadan T1 - An in vitro and in silico study of the enhanced antiproliferative and pro-oxidant potential of Olea europaea L. cv. Arbosana leaf extract via elastic nanovesicles (spanlastics) JF - Antioxidants N2 - The olive tree is a venerable Mediterranean plant and often used in traditional medicine. The main aim of the present study was to evaluate the effect of Olea europaea L. cv. Arbosana leaf extract (OLE) and its encapsulation within a spanlastic dosage form on the improvement of its pro-oxidant and antiproliferative activity against HepG-2, MCF-7, and Caco-2 human cancer cell lines. The LC-HRESIMS-assisted metabolomic profile of OLE putatively annotated 20 major metabolites and showed considerable in vitro antiproliferative activity against HepG-2, MCF-7, and Caco-2 cell lines with IC\(_{50}\) values of 9.2 ± 0.8, 7.1 ± 0.9, and 6.5 ± 0.7 µg/mL, respectively. The encapsulation of OLE within a (spanlastic) nanocarrier system, using a spraying method and Span 40 and Tween 80 (4:1 molar ratio), was successfully carried out (size 41 ± 2.4 nm, zeta potential 13.6 ± 2.5, and EE 61.43 ± 2.03%). OLE showed enhanced thermal stability, and an improved in vitro antiproliferative effect against HepG-2, MCF-7, and Caco-2 (IC\(_{50}\) 3.6 ± 0.2, 2.3 ± 0.1, and 1.8 ± 0.1 µg/mL, respectively) in comparison to the unprocessed extract. Both preparations were found to exhibit pro-oxidant potential inside the cancer cells, through the potential inhibitory activity of OLE against glutathione reductase and superoxide dismutase (IC\(_{50}\) 1.18 ± 0.12 and 2.33 ± 0.19 µg/mL, respectively). These inhibitory activities were proposed via a comprehensive in silico study to be linked to the presence of certain compounds in OLE. Consequently, we assume that formulating such a herbal extract within a suitable nanocarrier would be a promising improvement of its therapeutic potential. KW - olive KW - metabolomic profiling KW - antiproliferative KW - pro-oxidant KW - encapsulation KW - spanlastic KW - nanocarrier KW - docking KW - molecular dynamics simulation KW - Olea Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-250064 SN - 2076-3921 VL - 10 IS - 12 ER - TY - JOUR A1 - Alizadehrad, Davod A1 - Krüger, Timothy A1 - Engstler, Markus A1 - Stark, Holger T1 - Simulating the complex cell design of Trypanosoma brucei and its motility JF - PLOS Computational Biology N2 - The flagellate Trypanosoma brucei, which causes the sleeping sickness when infecting a mammalian host, goes through an intricate life cycle. It has a rather complex propulsion mechanism and swims in diverse microenvironments. These continuously exert selective pressure, to which the trypanosome adjusts with its architecture and behavior. As a result, the trypanosome assumes a diversity of complex morphotypes during its life cycle. However, although cell biology has detailed form and function of most of them, experimental data on the dynamic behavior and development of most morphotypes is lacking. Here we show that simulation science can predict intermediate cell designs by conducting specific and controlled modifications of an accurate, nature-inspired cell model, which we developed using information from live cell analyses. The cell models account for several important characteristics of the real trypanosomal morphotypes, such as the geometry and elastic properties of the cell body, and their swimming mechanism using an eukaryotic flagellum. We introduce an elastic network model for the cell body, including bending rigidity and simulate swimming in a fluid environment, using the mesoscale simulation technique called multi-particle collision dynamics. The in silico trypanosome of the bloodstream form displays the characteristic in vivo rotational and translational motility pattern that is crucial for survival and virulence in the vertebrate host. Moreover, our model accurately simulates the trypanosome's tumbling and backward motion. We show that the distinctive course of the attached flagellum around the cell body is one important aspect to produce the observed swimming behavior in a viscous fluid, and also required to reach the maximal swimming velocity. Changing details of the flagellar attachment generates less efficient swimmers. We also simulate different morphotypes that occur during the parasite's development in the tsetse fly, and predict a flagellar course we have not been able to measure in experiments so far. KW - multiparticle collision dynamics KW - human african trypanosomiasis KW - biology KW - cytoskeleton KW - flow KW - flagellar motility KW - tsetse fly KW - propulsion KW - cytokinesis KW - parasites Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-144610 VL - 11 IS - 1 ER - TY - THES A1 - Alcantarino Menescal, Luciana T1 - In vivo characterization of genetic factors involved in Xmrk driven melanoma formation in Medaka (Oryzias latipes): a closer look at braf, Stat5 and c-myc T1 - In vivo Charakterisierung genetischer Faktoren mit Einfluss auf Xmrk induzierte Melanome in Medaka (Oryzias latipes): Untersuchung von braf, Stat5 und c-myc. N2 - Melanoma arises from the malignant transformation of melanocytes and is one of the most aggressive forms of human cancer. In fish of the genus Xiphophorus, melanoma development, although very rarely, happens spontaneously in nature and can be induced by interspecific crossing. The oncogenic receptor tyrosine kinase, Xmrk, is responsible for melanoma formation in these fishes. Since Xiphophorus are live-bearing fishes and therefore not compatible with embryonic manipulation and transgenesis, the Xmrk melanoma model was brought to the medaka (Oryzias latipes) system. Xmrk expression under the control of the pigment cell specific mitf promoter leads to melanoma formation with 100% penetrance in medaka. Xmrk is an orthologue of the human epidermal growth factor receptor (EGFR) and activates several downstream signaling pathways. Examples of these pathways are the direct phosphorylation of BRAF and Stat5, as well as the enhanced transcription of C-myc. BRAF is a serine-threonine kinase which is found mutated at high frequencies in malignant melanomas. Stat5 is a transcription factor known to be constitutively activated in fish melanoma. C-myc is a transcription factor that is thought to regulate the expression of approximately 15% of all human genes and is involved in cancer progression of a large number of different tumors. To gain new in vivo information on candidate factors known to be involved in melanoma progression, I identified and analysed BRAF, Stat5 and C-myc in the laboratory fish model system medaka. BRAF protein motifs are highly conserved among vertebrates and the results of this work indicate that its function in the MAPK signaling is maintained in medaka. Transgenic medaka lines carrying a constitutive active version of BRAF (V614E) showed more pigmented skin when compared to wild type. Also, some transiently expressing BRAF V614E fishes showed a disrupted eye phenotype. In addition, I was able to identify two Stat5 copies in medaka, named Stat5ab/a and Stat5ab/b. Sequence analysis revealed a higher similarity between both Stat5 sequences when compared to either human Stat5a or Stat5b. This suggests that the two Stat5 copies in medaka arose by an independent duplication processes. I cloned these two Stat5 present in medaka, produced constitutive active and dominant negative gene versions and successfully established transgenic lines carrying each version under the control of the MITF promoter. These lines will help to elucidate questions that are still remaining in Stat5 biology and its function in melanoma progression, like the role of Stat5 phosphorylation on tumor invasiveness. In a third project during my PhD work, I analysed medaka C-myc function and indentified two copies of this gene in medaka, named c-myc17 and c-myc20, according to the chromosome where they are located. I produced conditional transgenic medaka lines carrying the c-myc17 gene coupled to the hormone binding domain of the estrogen receptor to enable specific transgene activation at a given time point. Comparable to human C-myc, medaka C-myc17 is able to induce proliferation and apoptosis in vivo after induction. Besides that, C-myc17 long-term activation led to liver hyperplasia. In summary, the medaka models generated in this work will be important to bring new in vivo information on genes involved in cancer development. Also, the generated transgenic lines can be easily crossed to the melanoma developing Xmrk medaka lines, thereby opening up the possibility to investigate their function in melanoma progression. Besides that, the generated medaka fishes make it possible to follow the whole development of melanocytes, since the embryos are transparent and can be used for high throughput chemical screens. N2 - Melanome entstehen durch die krankhafte Transformation von Melanozyten und sind eine der aggressivsten Krebsarten beim Menschen. In Fischen der Gattung Xiphophorus können, wenn auch sehr selten, spontan Melanome entstehen oder durch spezielle Artenkreuzungen induziert werden. Grundlage für das Entstehen der Melanome in diesen Fischen ist die Rezeptortyrosinkinase Xmrk. Da alle Xiphophorus-Arten lebendgebärend sind und keine Manipulationen an Embryonen vorgenommen werden können, wurde ein Xmrk Melanommodel für Medaka (Oryzias latipes) etabliert. Die Expression von Xmrk in Pigmentzellen dieser Fischart resultiert mit 100%iger Penetranz in Melanomen. Das Xmrk ist ein Ortholog des menschlichen „epidermal growth factor“ (EGFR) und aktiviert verschiedene nachgeschaltete Signalwege. Beispiele für diese Aktivierungen sind die Phosphorylierung von BRAF, Stat5 und die erhöhte Expression von c-myc. BRAF ist eine Serin-Threoninkinase, welche oft in malignen Melanomen mutiert ist. Stat5 ist ein Transkriptionsfaktor, welcher dauerhaft in Fischtumoren aktiviert ist. C-myc ist ein Transkriptionsfaktor, welcher etwa 15% aller menschlichen Gene sowie die Entstehung vieler menschlicher Tumore reguliert. Um neue Einsichten in die Funktion der Kanidatengene im Prozess der Melanomentstehung in vivo zu erlangen, habe ich Orthologe von BRAF, Stat5 und C-myc bei Medaka identifiziert und analysiert. Die Domänen des BRAF Proteins sind hoch konserviert in allen Vertebraten. Weiterhin deuten die Ergebnisse meiner Arbeit auf eine Beibehaltung der Funktionen im MAPK Signalweg hin. Transgene Medakalinien, welche eine dauerhaft aktive Version des BRAF Gens (V614E) exprimieren, weisen einerseits eine stärkere Hautpigmentierung auf. Weiterhin treten in diesen Fischen Veränderungen der Augen auf. In einem weiteren Projekt meiner Arbeit gelang es mir, zwei Kopien des Stat5 Gens im Medaka zu identifizieren, Stat5ab/a und Stat5ab/b. Sequenzanalysen zeigten eine höhere Übereinstimmung zwischen den beiden Genkopien, als zwischen denen von Medaka und Menschen. Dieses Ergebnis deutet darauf hin, dass die beiden Medaka Gene durch eine unabhängige Duplikation entstanden. In meiner Arbeit habe ich beide Gene des Medakas kloniert und jeweils eine konstitutiv aktive und eine dominant negative Version der Gene hergestellt. Weiterhin konnte ich erfolgreich für jede Genversion eine transgene Medakalinie etablieren, welche die verschiedenen Genvarianten unter der Kontrolle des pigmentzellspezifischen Promoters des mitf Gens exprimieren. Diese Linien werden in Zukunft helfen, den Einfluss von Stat5 Signalen auf den Prozess der Melanomverbreitung und dessen Invasivität zu erklären. In einem dritten Projekt meiner Doktorarbeit untersuchte ich das Vorkommen und die Funktion der C-myc Gene des Medakas. Ich konnte zwei Genkopien identifizieren, c-myc17 und c-myc20, welche auf unterschiedlichen Chromosomen lokalisiert sind. Ich konnte induzierbare, stabil transgene Linien herstellen, welche ein Fusionsprotein aus C-myc17 und der Hormonbindungsdomäne des Östrogenrezeptors von Maus exprimiert. Diese Linie ermöglichte eine induzierbare Aktivität des Transgens. Vergleichbar zum menschlichen MYC ist C-myc17 fähig, nach Aktivierung Proliferation und Apoptose in vivo auszulösen. Dauerhafte Aktivierung über einen längeren Zeitraum führt in diesen Linien zu Hyperplasie in Leber. Die verschiedenen Fischmodelle, die während dieser Arbeit generiert wurden, werden essentiell sein, um neue Einsichten in die Rolle diese Faktoren während der Krebsentwicklung in vivo zu erlangen. Weiterhin ermöglichen diese transgenen Linien durch einfaches Auskreuzen auf Xmrk Linien, deren Einfluss auf die Verbreitung von Melanomen zu untersuchen. Letztendlich sind mit diesen Linien auch Untersuchungen der Entwicklung von Pigmentzellen über Zeit möglich, da die Embryonen transparent sind und sich für chemisches Hochdurchsatz-Screening eignen. KW - Japankärpfling KW - Melanom KW - Myc KW - Molekulargenetik KW - melanoma KW - medaka KW - BRAF KW - Stat5 KW - c-myc KW - melanoma KW - medaka KW - BRAF KW - Stat5 KW - c-myc Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-70762 ER - TY - JOUR A1 - Albrecht, Marco A1 - Sharma, Cynthia M. A1 - Reinhardt, Richard A1 - Vogel, Joerg A1 - Rudel, Thomas T1 - Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome N2 - Chlamydia trachomatis is an obligate intracellular pathogenic bacterium that has been refractory to genetic manipulations. Although the genomes of several strains have been sequenced, very little information is available on the gene structure of these bacteria. We used deep sequencing to define the transcriptome of purified elementary bodies (EB) and reticulate bodies (RB) of C. trachomatis L2b, respectively. Using an RNAseq approach, we have mapped 363 transcriptional start sites (TSS) of annotated genes. Semiquantitative analysis of mapped cDNA reads revealed differences in the RNA levels of 84 genes isolated from EB and RB, respectively. We have identified and in part confirmed 42 genome- and 1 plasmid-derived novel non-coding RNAs. The genome encoded non-coding RNA, ctrR0332 was one of the most abundantly and differentially expressed RNA in EB and RB, implying an important role in the developmental cycle of C. trachomatis. The detailed map of TSS in a thus far unprecedented resolution as a complement to the genome sequence will help to understand the organization, control and function of genes of this important pathogen. KW - Biologie Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-68389 ER - TY - JOUR A1 - Albrecht, Marco A1 - Sharma, Cynthia M. A1 - Dittrich, Marcus T. A1 - Müller, Tobias A1 - Reinhardt, Richard A1 - Vogel, Jörg A1 - Rudel, Thomas T1 - The Transcriptional Landscape of Chlamydia pneumoniae N2 - Background: Gene function analysis of the obligate intracellular bacterium Chlamydia pneumoniae is hampered by the facts that this organism is inaccessible to genetic manipulations and not cultivable outside the host. The genomes of several strains have been sequenced; however, very little information is available on the gene structure and transcriptome of C. pneumoniae. Results: Using a differential RNA-sequencing approach with specific enrichment of primary transcripts, we defined the transcriptome of purified elementary bodies and reticulate bodies of C. pneumoniae strain CWL-029; 565 transcriptional start sites of annotated genes and novel transcripts were mapped. Analysis of adjacent genes for cotranscription revealed 246 polycistronic transcripts. In total, a distinct transcription start site or an affiliation to an operon could be assigned to 862 out of 1,074 annotated protein coding genes. Semi-quantitative analysis of mapped cDNA reads revealed significant differences for 288 genes in the RNA levels of genes isolated from elementary bodies and reticulate bodies. We have identified and in part confirmed 75 novel putative non-coding RNAs. The detailed map of transcription start sites at single nucleotide resolution allowed for the first time a comprehensive and saturating analysis of promoter consensus sequences in Chlamydia. Conclusions: The precise transcriptional landscape as a complement to the genome sequence will provide new insights into the organization, control and function of genes. Novel non-coding RNAs and identified common promoter motifs will help to understand gene regulation of this important human pathogen. KW - Chlamydia pneumoniae Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-69116 ER - TY - JOUR A1 - Albrecht, Jörg A1 - Classen, Alice A1 - Vollstädt, Maximilian G.R. A1 - Mayr, Antonia A1 - Mollel, Neduvoto P. A1 - Schellenberger Costa, David A1 - Dulle, Hamadi I. A1 - Fischer, Markus A1 - Hemp, Andreas A1 - Howell, Kim M. A1 - Kleyer, Michael A1 - Nauss, Thomas A1 - Peters, Marcell K. A1 - Tschapka, Marco A1 - Steffan-Dewenter, Ingolf A1 - Böhning-Gaese, Katrin A1 - Schleuning, Matthias T1 - Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient JF - Nature Communications N2 - Species' functional traits set the blueprint for pair-wise interactions in ecological networks. Yet, it is unknown to what extent the functional diversity of plant and animal communities controls network assembly along environmental gradients in real-world ecosystems. Here we address this question with a unique dataset of mutualistic bird-fruit, bird-flower and insect-flower interaction networks and associated functional traits of 200 plant and 282 animal species sampled along broad climate and land-use gradients on Mt. Kilimanjaro. We show that plant functional diversity is mainly limited by precipitation, while animal functional diversity is primarily limited by temperature. Furthermore, shifts in plant and animal functional diversity along the elevational gradient control the niche breadth and partitioning of the respective other trophic level. These findings reveal that climatic constraints on the functional diversity of either plants or animals determine the relative importance of bottom-up and top-down control in plant-animal interaction networks. KW - Traits-Environment Relationships KW - Species Traits KW - Ecological Networks KW - 4TH-Corner Problem KW - Multiple Traits KW - Bottom-up KW - Biodiversity KW - Community ecology KW - Ecological networks KW - Ecology KW - Ecosystem ecology Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-221056 VL - 9 ER - TY - JOUR A1 - Albert, Štefan A1 - Spaethe, Johannes A1 - Grübel, Kornelia A1 - Rössler, Wolfgang T1 - Royal jelly-like protein localization reveals differences in hypopharyngeal glands buildup and conserved expression pattern in brains of bumblebees and honeybees N2 - Royal jelly proteins (MRJPs) of the honeybee bear several open questions. One of them is their expression in tissues other than the hypopharyngeal glands (HGs), the site of royal jelly production. The sole MRJP-like gene of the bumblebee, Bombus terrestris (BtRJPL), represents a pre-diversification stage of the MRJP gene evolution in bees. Here we investigate the expression of BtRJPL in the HGs and the brain of bumblebees. Comparison of the HGs of bumblebees and honeybees revealed striking differences in their morphology with respect to sex- and caste-specific appearance, number of cells per acinus, and filamentous actin (F-actin) rings. At the cellular level, we found a temporary F-actin-covered meshwork in the secretory cells, which suggests a role for actin in the biogenesis of the end apparatus in HGs. Using immunohistochemical localization, we show that BtRJPL is expressed in the bumblebee brain, predominantly in the Kenyon cells of the mushroom bodies, the site of sensory integration in insects, and in the optic lobes. Our data suggest that a dual glandbrain function preceded the multiplication of MRJPs in the honeybee lineage. In the course of the honeybee evolution, HGs dramatically changed their morphology in order to serve a food-producing function. KW - Hypopharyngeal glands KW - Bumblebee KW - Bombus KW - Brain KW - Labial glands KW - Immunohistochemistry KW - Kenyon cells KW - Mushroom bodies KW - Honeybee Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-112733 ER - TY - THES A1 - Albers, Christine T1 - Reinigung und Charakterisierung der alpha-Methylacyl-CoA-Racemase aus menschlicher Leber T1 - Purification and characterisation of alpha-Methylacyl-CoA-Racemase from human liver N2 - Im Katabolismus methylverzweigter Fettsäuren spielt die alpha-Methylacyl-CoA-Racemase eine wichtige Rolle, indem sie die (R)- und (S)-Isomere von alpha-methylverzweigten Fettsäuren als Coenzym A Thioester racemisiert. Methylverzweigte Fettsäuren entstehen beim Abbau von Isoprenoiden und werden darüber hinaus auch von vielen Organismen, wie z.B. Mycobakterien, synthetisiert. Die Hauptaufgabe der Racemase ist aber vermutlich in der Biosynthese von Gallensäuren zu sehen. Das Ziel der vorliegenden Arbeit war es, die alpha-Methylacyl-CoA-Racemase aus humanem Gewebe zu reinigen und zu charakterisieren sowie ihre physiologische Rolle im Katabolismus verzweigtkettiger Fettsäuren und der Gallensäurebiosynthese zu untersuchen. Die alpha-Methylacyl-CoA-Racemase wurde aus humanem Gewebe zur Homogenität gereinigt, umfassend biochemisch charakterisiert und zur genauen molekularbiologischen Analyse in E.coli kloniert. Die Aktivität der Racemase wurde anhand der [³H]H2O-Freisetzung aus [alpha-³H]-a-Methylacyl-CoAs bestimmt. Die humane Racemase ist in der aktiven Form ein monomeres Protein und besteht aus 382 Aminosäuren. Als Substrate akzeptiert das Enzym ein breites Spektrum von alpha-Methylacyl-CoAs. Neben den Coenzym A-Thioestern alpha-methylverzweigter Fettsäuren, wie Pristansäure, werden auch CoA-Ester von Steroidderivaten, z.B. des Gallensäureintermediats Trihydroxycoprostansäure, und aromatischen Phenylpropionsäuren, wie dem Analgetikum Ibuprofen, umgesetzt. Freie Fettsäuren, geradkettige oder beta-methylverzweigte Acyl-CoAs werden nicht racemisiert. Die alpha-Methylacyl-CoA-Racemase ist im Menschen zu ca. 80 Prozent auf die Peroxisomen und ca. 20 Prozent auf die Mitochondrien verteilt, wobei entsprechende peroxisomale (PTS 1) und mitochondriale (MTS) Transportsignale die Lokalisation bestimmen. Die vollständige cDNA-Sequenz der humanen a-Methylacyl-CoA-Racemase hat eine Gesamtlänge von 2039 Basenpaaren mit einem offenen Leseraster von 89 - 1237 bp. Das Startcodon ATG ist in eine klassische Kozak-Sequenz zum Translationsstart eingebettet. Die Protein endet am C-Terminus mit dem Sequenzmotiv –KASL, das dem peroxisomalen Transportsignal (PTS I) einiger Säugetierkatalasen entspricht. Aufgrund alternativer Polyadenylierung sind in allen untersuchten menschlichen Geweben Transkripte von 1,6 kb bzw. 2,0 kb zu finden. Es liegt keine gewebsabhängige Polyadenylierung vor, die Racemase wird aber gewebsspezifisch exprimiert (besonders stark in Leber und Niere). Das humane Racemasegen liegt auf dem kurzen Arm des Chromosoms 5 nahe am Centromer (5p1.3), im Intervall von D5S651 (46,6 cM) und D5S634 (59.9 cM). N2 - Racemization is an essential step for bile acid synthesis and it is important for degradation of alpha-methyl branched-chain fatty acids. The (R)- and (S)-isomers of alpha-methyl-branched chain fatty acids were shown to be interconverted as coenzyme A thioesters by an alpha-methylacyl-CoA racemase. Various branched-chain fatty acids arise in the catabolism of isoprenoids and are also synthesized by a variety of organisms, particularly mycobacteria. The aim of this work was to purify and to characterize the racemase from human tissue and to analyse the physiological role in the degradation of branched-chain fatty acids and the bile acid synthesis. The alpha-methylacyl-CoA racemase was purified from human liver to apparent homogeneity. The enzyme was exhaustively characterized by methods of biochemistry and protein chemistry. The cDNA coding for human racemase was cloned in E. coli and sequenced. A radiometric assay with 2-methyl[2-³H]acyl-CoAs as substrates was used routinely for monitoring purification procedure. The active form of the enzyme is a monomeric protein comprising 382 amino acids. The enzyme accepts a wide range of alpha-methylacyl-CoAs, including pristanoyl-CoA, trihydroxycoprostanoyl-CoA (an intermediate in bile acid synthesis) as substrates. Also arylpropionyl-CoAs such as the anti-inflammatory drug ibuprofen are accepted, but neither free fatty acids, beta-methyl-branched nor linear-chain acyl-CoAs. In human tissues 80 - 90 Prozent of the racemase activity is found in peroxisomes and 10 - 20 Prozent in mitochondria. Degradation of branched chain fatty acids is located in both compartments, so the enzyme has to be distributed between peroxisomes and mitochondria. No evidence was found for the existence of isoenzymes or different transcription products. It appears that only one mRNA is transcribed from one gene and that also only one protein is synthesized. The different recognition of peroxisomal (PTS 1) and mitochondrial targeting signals (MTS) may determine the subcellular distribution. The complete cDNA sequence has an overall length of 2039 base pairs, with a open reading frame between 89 - 1237 bp. The ATG start codon is embedded in a classical Kozak sequence for translation start. The C-Terminus of the protein is –KASL, which is very similar to the peroxisomal targeting signals (PTS 1) of many mammalian catalases. In all human tissues analysed in this work two different transcripts of racemase with sizes of 1,6 kb and 2,0 kb have been found and show alternate polyadenylation. Polyadenylation of racemase is not tissue-dependent but its expression is tissue-specific (strong activity is found in liver and kidney). The human racemase gene is localized on the short arm of chromosome 5, near the centromer (region 5p1.3) and between the markers D5S651 (46,6 cM) and D5S634 (59.9 cM). KW - Alpha-Methylacyl-CoA racemase KW - Mensch KW - Leber KW - Molekularbiologie KW - Racemase KW - human KW - Enzym KW - Reinigung KW - Charakterisierung KW - Peroxisom KW - alpha-Methylacyl-CoA KW - Racemase KW - human KW - enzyme KW - purification KW - characterisation KW - peroxisome KW - alpha-Methylacyl-CoA Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-770 ER - TY - JOUR A1 - Al-Warhi, Tarfah A1 - Elmaidomy, Abeer H. A1 - Maher, Sherif A. A1 - Abu-Baih, Dalia H. A1 - Selim, Samy A1 - Albqmi, Mha A1 - Al-Sanea, Mohammad M. A1 - Alnusaire, Taghreed S. A1 - Ghoneim, Mohammed M. A1 - Mostafa, Ehab M. A1 - Hussein, Shaimaa A1 - El-Damasy, Ashraf K. A1 - Saber, Entesar Ali A1 - Elrehany, Mahmoud A. A1 - Sayed, Ahmed M. A1 - Othman, Eman M. A1 - El-Sherbiny, Mohamed A1 - Abdelmohsen, Usama Ramadan T1 - The wound-healing potential of Olea europaea L. Cv. Arbequina leaves extract: an integrated in vitro, in silico, and in vivo investigation JF - Metabolites N2 - Olea europaea L. Cv. Arbequina (OEA) (Oleaceae) is an olive variety species that has received little attention. Besides our previous work for the chemical profiling of OEA leaves using LC–HRESIMS, an additional 23 compounds are identified. An excision wound model is used to measure wound healing action. Wounds are provided with OEA (2% w/v) or MEBO\(^®\) cream (marketed treatment). The wound closure rate related to vehicle-treated wounds is significantly increased by OEA. Comparing to vehicle wound tissues, significant levels of TGF-β in OEA and MEBO\(^®\) (p < 0.05) are displayed by gene expression patterns, with the most significant levels in OEA-treated wounds. Proinflammatory TNF-α and IL-1β levels are substantially reduced in OEA-treated wounds. The capability of several lignan-related compounds to interact with MMP-1 is revealed by extensive in silico investigation of the major OEA compounds (i.e., inverse docking, molecular dynamics simulation, and ΔG calculation), and their role in the wound-healing process is also characterized. The potential of OEA as a potent MMP-1 inhibitor is shown in subsequent in vitro testing (IC\(_{50}\) = 88.0 ± 0.1 nM). In conclusion, OEA is introduced as an interesting therapeutic candidate that can effectively manage wound healing because of its anti-inflammatory and antioxidant properties. KW - olive KW - LC–HRESIMS KW - wound KW - Olea KW - TNF-α KW - virtual docking KW - TGF-β KW - MMP-1 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-286150 SN - 2218-1989 VL - 12 IS - 9 ER - TY - THES A1 - Akimzhanov, Askar M. T1 - Epigenetic repression of the NFATc1 transcription factor in human lymphomas T1 - Epigenetische Repression des NFATc1 Transkriptionsfakors in menschlichen Lymphomen N2 - We examined the regulation of NFATc1 in different lymphomas and observed an inversed correlation between the methylation status and expression of NFATc1. Our data demonstrate that aberrant DNA methylation associated with chromatin remodeling within nfatc1 locus is a major mechanism for the repression of NFATc1 expression, suggesting that the DNA methylation-mediated transcriptional silencing of NFATc1 may be a critical event in the tumorogenesis of ALCLs and cHLs. Furthermore, the DNA methylation of human nfatc1 promoter region could be used as a novel biomarker of tumor progression. Our results indicate a close link between the loss of immunoreceptor signaling and NFATc1 expression in human lymphomas. For both ALCLs and cHLs, defects in immunoreceptor signaling have been described which result in a loss of receptor-mediated gene expression programs (Schwering et al., 2003; Bonzheim et al., 2004; Marafioti et al., 2004). In T cells, one indicator gene of these programs appears to be the nfatc1 gene whose expression is controlled by TCR signals (Chuvpilo et al., 2002a). In contrast, in T cells NFATc1 expression is unaffected by TCR signals, and NFATc2 was found to be expressed at normal levels in ALCLs and cHLs (L.K., unpubl. data). Moreover, the activity of NF-kappaB factors which can bind to certain NFAT binding sites and share a distantly-related DNA binding domain with NFATs is strongly elevated in cHL cells (Bargou et al., 1997; Hinz et al., 2001; Hinz et al., 2002) suggesting that NFATs and NF-kappaBs exert very different effects on generation and maintenance of Hodgkin’s lymhomas. However, it should be mentioned that in Burkitt’s and further B cell lymphomas in which NFATc1 proteins are strongly expressed and controlled by receptor signals (Kondo et al., 2003), they could exert a promoting function in tumor development. The genes of p53 family members p63 and p73 are prominent examples for mammalian genes whose products can act both as oncoproteins and tumor suppressor genes (Hibi et al., 2000; Stiewe and Putzer, 2002), and it is likely that more genes exist which encode both tumor suppressors and oncoproteins. It remains to be shown whether the nfatc1 gene is one of them. N2 - Wir haben die Regulation von NFATc1 in verschiedenen Lymphomen untersucht und beobachteten eine umgekehrte Korrelation zwischen dem Ausmaß an Methylierung und der Expression von NFATc1. Unsere Daten demonstrieren, dass eine aberrante DNA-Methylierung, die mit veränderter Chromatinstruktur innerhalb des nfatc1 Lokus assoziiert ist, der Hauptmechanismus für die Repression der NFATc1-Expression ist. Es wäre zu vermuten, dass die durch DNA-Methylierung verursachte transkriptionelle Abschaltung von NFATc1 der kritische Schritt bei der Tumorgenese von ALCLs und cHLs ist. Des weiteren könnte das Ausmaß der DNA-Methylierung in der humanen nfatc1-Promotorregion als neuer Biomarker für Tumorprogression genutzt werden. Unsere Daten indizieren eine enge Verbindung zwischen dem Verlust von Immunrezeptorsignalen und der NFATc1-Expression in humanen Lymphomen. Für sowohl ALCLs als auch cHLs wurden Defekte in der Immunrezeptorsignalgebung beschrieben, welche sich im Verlust des Rezeptor vermittelten Genexpressionsprogramms niederschlagen (Schwering et al., 2003; Bonzheim et al., 2004; Marafioti et al., 2004). In T-Zellen scheint das nfatc1-Gen eins der Indikatorgene dieses Programms zu sein, dessen Expression durch TCR-Signale kontrolliert wird (Chuvpilo et al., 2002a). Im Gegensatz dazu bleibt die NFATc2-Expression in T-Zellen unbeeinflusst von TCR-Signalen, weshalb NFATc2 in ALCLs und cHLs auch in normalem Ausmaß exprimiert wird (L.K., unpubl. data). Andererseits ist die Aktivität der NF-kappaB-Faktoren, die auch an bestimmte NFAT-Bindungsstellen binden können und deren DNA-Bindungsdomäne entfernt mit der der NFATs verwandt ist, in cHL-Zellen stark erhöht (Bargou et al., 1997; Hinz et al., 2001; Hinz et al., 2002). Das lässt vermuten, dass NFATc1 und die NF-kappa-Faktoren eine sehr unterschiedliche Rolle bei der Entstehung und dem Erhalt der Hodgkinlymphome spielen. Es sollte aber erwähnt werden, dass in Burkitts und anderen B-Zelllymphomen, in denen NFATc1-Proteine stark exprimiert und darüber hinaus durch Rezeptorsignale kontrolliert sind (Kondo et al., 2003), diese eine Tumor fördernde Funktion ausüben könnten. Die Gene der p53-Familienmitglieder p63 und p73 sind prominente Beispiele für Säugergene, deren Produkte sowohl als Onkoproteine als auch als Tumorsuppressoren fungieren können (Hibi et al., 2000; Stiewe and Putzer, 2002), und es ist wahrscheinlich, dass es noch weitere Gene gibt, die beide Funktionen ausüben. Es wird zu zeigen sein, ob das nfatc1-Gen eins von ihnen ist. KW - Lymphom KW - T-Lymphozyt KW - Transkriptionsfaktor KW - Methylierung KW - Epigenese KW - NFATc1 KW - Lymphome KW - Epigenetik KW - Methylierung KW - NFATc1 KW - Lymphoma KW - Epigenetics KW - Methylation Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-12921 ER - TY - JOUR A1 - Akhoon, Bashir A. A1 - Singh, Krishna P. A1 - Varshney, Megha A1 - Gupta, Shishir K. A1 - Shukla, Yogeshwar A1 - Gupta, Shailendra K. T1 - Understanding the Mechanism of Atovaquone Drug Resistance in Plasmodium falciparum Cytochrome b Mutation Y268S Using Computational Methods JF - PLOS ONE N2 - The rapid appearance of resistant malarial parasites after introduction of atovaquone (ATQ) drug has prompted the search for new drugs as even single point mutations in the active site of Cytochrome b protein can rapidly render ATQ ineffective. The presence of Y268 mutations in the Cytochrome b (Cyt b) protein is previously suggested to be responsible for the ATQ resistance in Plasmodium falciparum (P. falciparum). In this study, we examined the resistance mechanism against ATQ in P. falciparum through computational methods. Here, we reported a reliable protein model of Cyt bc1 complex containing Cyt b and the Iron-Sulphur Protein (ISP) of P. falciparum using composite modeling method by combining threading, ab initio modeling and atomic-level structure refinement approaches. The molecular dynamics simulations suggest that Y268S mutation causes ATQ resistance by reducing hydrophobic interactions between Cyt bc1 protein complex and ATQ. Moreover, the important histidine contact of ATQ with the ISP chain is also lost due to Y268S mutation. We noticed the induced mutation alters the arrangement of active site residues in a fashion that enforces ATQ to find its new stable binding site far away from the wild-type binding pocket. The MM-PBSA calculations also shows that the binding affinity of ATQ with Cyt bc1 complex is enough to hold it at this new site that ultimately leads to the ATQ resistance. KW - molecular-dynamics simulations KW - HIV-1 protease KW - structure prediction KW - saccharomyces cerevisiae KW - I-tasser KW - inhibitors KW - binding KW - malaria KW - complex KW - protein-protein interactions Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-114882 VL - 9 IS - 10 ER - TY - JOUR A1 - Akhoon, Bashir A. A1 - Gupta, Shishir K. A1 - Tiwari, Sudeep A1 - Rathor, Laxmi A1 - Pant, Aakanksha A1 - Singh, Nivedita A1 - Gupta, Shailendra K. A1 - Dandekar, Thomas A1 - Pandey, Rakesh T1 - C. elegans protein interaction network analysis probes RNAi validated pro-longevity effect of nhr-6, a human homolog of tumor suppressor Nr4a1 JF - Scientific Reports N2 - Protein-protein interaction (PPI) studies are gaining momentum these days due to the plethora of various high-throughput experimental methods available for detecting PPIs. Proteins create complexes and networks by functioning in harmony with other proteins and here in silico network biology hold the promise to reveal new functionality of genes as it is very difficult and laborious to carry out experimental high-throughput genetic screens in living organisms. We demonstrate this approach by computationally screening C. elegans conserved homologs of already reported human tumor suppressor and aging associated genes. We select by this nhr-6, vab-3 and gst-23 as predicted longevity genes for RNAi screen. The RNAi results demonstrated the pro-longevity effect of these genes. Nuclear hormone receptor nhr-6 RNAi inhibition resulted in a C. elegans phenotype of 23.46% lifespan reduction. Moreover, we show that nhr-6 regulates oxidative stress resistance in worms and does not affect the feeding behavior of worms. These findings imply the potential of nhr-6 as a common therapeutic target for aging and cancer ailments, stressing the power of in silico PPI network analysis coupled with RNAi screens to describe gene function. KW - Computer modelling KW - Embryonic induction KW - RNAi Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-202666 VL - 9 ER - TY - THES A1 - Aichinger, Eric T1 - Risikoberechnung bei der Muskeldystrophie Duchenne und der Muskeldystrophie Becker T1 - Risk estimation in families with Duchenne muscular dystrophy or Becker muscular dystrophy N2 - Risikoberechnung in Familien mit Muskeldystrophie Duchenne oder Muskeldystrophie Becker. Unter Berücksichtigung eines Keimzellmosaiks, heterogener Neumutationsraten und der Möglichkeit homozygot betroffener Frauen. N2 - Risk estimation in families with Duchenne muscular dystrophy or Becker muscular dystrophy. Regarding germline mosaicism, specific mutation rates and homozygote affected women. KW - Risikoberechnung KW - Duchenne KW - Becker KW - Keimzellmosaik KW - Mutationsrate KW - Risk estimation KW - Duchenne KW - Becker KW - germline mosaicism KW - mutation rate Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-27000 ER - TY - JOUR A1 - Ahmed, Zeeshan A1 - Zeeshan, Saman A1 - Huber, Claudia A1 - Hensel, Michael A1 - Schomburg, Dietmar A1 - Münch, Richard A1 - Eylert, Eva A1 - Eisenreich, Wolfgang A1 - Dandekar, Thomas T1 - ‘Isotopo’ a database application for facile analysis and management of mass isotopomer data JF - Database N2 - The composition of stable-isotope labelled isotopologues/isotopomers in metabolic products can be measured by mass spectrometry and supports the analysis of pathways and fluxes. As a prerequisite, the original mass spectra have to be processed, managed and stored to rapidly calculate, analyse and compare isotopomer enrichments to study, for instance, bacterial metabolism in infection. For such applications, we provide here the database application ‘Isotopo’. This software package includes (i) a database to store and process isotopomer data, (ii) a parser to upload and translate different data formats for such data and (iii) an improved application to process and convert signal intensities from mass spectra of \(^{13}C\)-labelled metabolites such as tertbutyldimethylsilyl-derivatives of amino acids. Relative mass intensities and isotopomer distributions are calculated applying a partial least square method with iterative refinement for high precision data. The data output includes formats such as graphs for overall enrichments in amino acids. The package is user-friendly for easy and robust data management of multiple experiments. KW - stable-isotope Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120102 VL - 2014 IS - bau077 ER - TY - JOUR A1 - Ahmed, Zeeshan A1 - Zeeshan, Saman A1 - Dandekar, Thomas T1 - Mining biomedical images towards valuable information retrieval in biomedical and life sciences JF - Database - The Journal of Biological Databases and Curation N2 - Biomedical images are helpful sources for the scientists and practitioners in drawing significant hypotheses, exemplifying approaches and describing experimental results in published biomedical literature. In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems. In this review, we summarize technologies related to data mining of figures. We describe and compare the potential of different approaches in terms of their developmental aspects, used methodologies, produced results, achieved accuracies and limitations. Our comparative conclusions include current challenges for bioimaging software with selective image mining, embedded text extraction and processing of complex natural language queries. KW - humans KW - software KW - image processing KW - animals KW - computer-assisted KW - data mining/methods KW - natural language processing Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-162697 VL - 2016 ER - TY - JOUR A1 - Agoston, Zsuzsa A1 - Li, Naixin A1 - Haslinger, Anja A1 - Wizenmann, Andrea A1 - Schulte, Dorothea T1 - Genetic and physical interaction of Meis2, Pax3 and Pax7 during dorsal midbrain development JF - BMC Developmental Biology N2 - Background: During early stages of brain development, secreted molecules, components of intracellular signaling pathways and transcriptional regulators act in positive and negative feed-back or feed-forward loops at the mid-hindbrain boundary. These genetic interactions are of central importance for the specification and subsequent development of the adjacent mid-and hindbrain. Much less, however, is known about the regulatory relationship and functional interaction of molecules that are expressed in the tectal anlage after tectal fate specification has taken place and tectal development has commenced. Results: Here, we provide experimental evidence for reciprocal regulation and subsequent cooperation of the paired-type transcription factors Pax3, Pax7 and the TALE-homeodomain protein Meis2 in the tectal anlage. Using in ovo electroporation of the mesencephalic vesicle of chick embryos we show that (i) Pax3 and Pax7 mutually regulate each other's expression in the mesencephalic vesicle, (ii) Meis2 acts downstream of Pax3/7 and requires balanced expression levels of both proteins, and (iii) Meis2 physically interacts with Pax3 and Pax7. These results extend our previous observation that Meis2 cooperates with Otx2 in tectal development to include Pax3 and Pax7 as Meis2 interacting proteins in the tectal anlage. Conclusion: The results described here suggest a model in which interdependent regulatory loops involving Pax3 and Pax7 in the dorsal mesencephalic vesicle modulate Meis2 expression. Physical interaction with Meis2 may then confer tectal specificity to a wide range of otherwise broadly expressed transcriptional regulators, including Otx2, Pax3 and Pax7. KW - dosage KW - quali-chick chimeras KW - drosophila embryo KW - neural crest KW - transcription activation KW - hindbrain boundary KW - isthmic oragnizer KW - sonic hedghog KW - expression KW - induction Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-132626 VL - 12 IS - 10 ER - TY - JOUR A1 - Adolfi, Mateus C. A1 - Herpin, Amaury A1 - Regensburger, Martina A1 - Sacquegno, Jacopo A1 - Waxman, Joshua S. A1 - Schartl, Manfred T1 - Retinoic acid and meiosis induction in adult versus embryonic gonads of medaka JF - Scientific Reports N2 - In vertebrates, one of the first recognizable sex differences in embryos is the onset of meiosis, known to be regulated by retinoic acid (RA) in mammals. We investigated in medaka a possible meiotic function of RA during the embryonic sex determination (SD) period and in mature gonads. We found RA mediated transcriptional activation in germ cells of both sexes much earlier than the SD stage, however, no such activity during the critical stages of SD. In adults, expression of the RA metabolizing enzymes indicates sexually dimorphic RA levels. In testis, RA acts directly in Sertoli, Leydig and pre-meiotic germ cells. In ovaries, RA transcriptional activity is highest in meiotic oocytes. Our results show that RA plays an important role in meiosis induction and gametogenesis in adult medaka but contrary to common expectations, not for initiating the first meiosis in female germ cells at the SD stage. KW - developmental biology KW - molecular biology Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147843 VL - 6 ER -