TY - THES A1 - Abdel Rahman, Faisal Mirghani T1 - Systematic analysis of genes expressed in the retinal pigment epithelium (RPE) and identification of candidates for genetic susceptibility to age-related macular degeneration (AMD) N2 - Age related macular degeneration (AMD) is the leading cause of visual impairment in the elderly and the major cause of blindness in the developed world. To date, the molecular mechanisms underlying the disease are not well understood although in recent years a primary involvement of the retinal pigment epithelium (RPE) has become evident. The aim of the present study is to systematically analyse genes which are differentially expressed in the RPE, and to assess their possible association with mechanisms and pathways likely to be related to retinal disease, in particular AMD. Towards this goal, 2379 expressed sequence tags (ESTs) were established from an inhouse generated RPE cDNA library. This library was constructed by using the suppression subtraction hybridization (SSH) technique which normalises redundant sequences and ensures enrichment of rare transcripts. In a first phase, 1002 ESTs were sequenced and subjected to comprehensive alignment with public nucleotide and protein databases. A search of the 1002 ESTs against the human genome draft sequence yielded 168 known genes, 51 predicted genes, 15 unknown transcripts and 41 clones with no significant similarity. Reverse Northern blot hybridization was performed for 318 EST clusters to identify abundantly expressed genes in the RPE and to prioritize subsequent analyses. Representative clones were spotted onto a nylon membrane and hybridized with cDNA probes of driver (heart and liver) and tester (RPE) used in the cDNA library construction. Subsequently, 107 EST clusters were subjected to Northern blot hybridizations. These analyses identified 7 RPE-specific, 3 retina-specific, 7 RPE/retina-specific, and 7 tissue restricted transcripts, while 29 EST clusters were ubiquitously expressed, and evaluation was not possible for another 54 EST clusters. Of the 24 transcripts with specific or restricted expression, 16 clones were selected for further characterization. The predicted gene MGC2477 and 2 novel isoforms of the human transient receptor potential cation channel, subfamily M, member 3 (TRPM3) were cloned and further described in detail. In addition, polymorphic variations for these 2 genes as well as for the human MT-Protocadherin gene were determined. For MGC2477, 15 single nucleotide polymorphisms (SNPs) were identified, with 13 having a frequency of the minor allele greater than 20%. 10 of the 15 SNPs have not been reported in so far in public SNP repertoires. Partial assessment of the TRPM3 gene yielded 35 SNPs. Of these, 30 (85.7%) were highly frequent (0.17-0.5%), and 14 (40%) were novel. The MT-Protocadherin gene revealed 35 SNPs, including 28 (80%) with high frequency of the minor allele. 23 (65.7%) were novel SNPs. These SNPs will be used to construct the most common haplotypes. These will be used in case/control association studies in 400 AMD patients and 200 ethnically and aged matched controls to assess a possible contribution of these genes in the etiology of AMD. N2 - Die altersabhängige Makuladegeneration (AMD) ist die häufigste Ursache von gravierenden Einschränkungen des Sehvermögens im fortgeschrittenen Lebensalter. In den Industriestaaten ist die AMD zudem die Hauptursache für Altersblindheit. Die molekularen Mechanismen, die zur Entstehung der AMD führen, sind bisher nur unzureichend bekannt. In den letzten Jahren hat es sich jedoch herausgestellt, dass das retinale Pigmentepithel (RPE) eine primäre Rolle in der Pathogenese der AMD spielt. Ziel dieser Arbeit war die systematische Analyse von Genen, welche im RPE differentiell exprimiert werden. Entsprechende Kandidatengene sollten auf deren mögliche Beteiligung an der Entstehung von Erkrankungen der Retina, insbesondere der AMD, untersucht werden. Zunächst wurden 2379 ESTs aus einer innerhalb der Arbeitsgruppe generierten RPE cDNA Bibliothek definiert. Die dazu verwendete cDNA Bibliothek wurde durch die Suppressions- Subtraktions Hybridisierungs-Technik (SSH) konstruiert. Diese Technik gestattet eine Normalisierung gegenüber redundanten Sequenzen und begünstigt gleichzeitig die Anreicherung von seltenen Transkripten. In einer ersten Phase wurden 1002 ESTs sequenziert und einer umfassenden bioinformatischen Analyse mit Hilfe der verfügbaren DNA- und Protein Datenbanken unterzogen. Der Vergleich der 1002 ESTs mit der Draft Sequenz des menschlichen Genoms ergab den Hinweis auf 168 bereits bekannte Gene, 51 mögliche Gene, 15 völlig unbekannte Transkripte und 41 nicht weiter zuordenbare cDNA Klone. 318 EST Cluster wurden einer reversen Northen-Blot Analyse unterzogen um hochexprimierte Gene zu identifizieren und damit Prioritäten für die weiteren Analysen zu setzen. Im Rahmen der Northern-Analyse wurden repräsentative Klone von 107 EST-Klustern mit cDNA Sonden der ursprünglichen cDNA-Bibliothek hybridisiert. Als Ergebnis dieser Analyse fanden sich 7 RPE-spezifische, 3 Retina-spezifische, 7 sowohl RPE- als auch Retinaspezifische sowie 7 auf einzelne Gewebe limitierte Transkripte. 29 EST Cluster erwiesen sich als ubiquitär exprimiert, und 54 Kluster konnten nicht näher zugeordnet werden. Von den 24 Transkripten mit spezifischer oder zumindest begrenzter Expression wurden 16 Klone zur weiteren Charakterisierung ausgewählt. Aus diesen Material wurden im Rahmen dieser Arbeit das Kandidatengen MGC2477 sowie 2 neue Isoformen des menschlichen TRPM3-Gens kloniert und näher charakterisiert. Weiterhin wurden polymorphe Varianten dieser beiden Isoformen und des menschlichen MTProtocadherin- Gens definiert. Im Gen MGC2477 wurden 15 SNPs identifiziert, wovon die Allelhäufigkeit des selteneren Allels bei 13 der SNPs über 20% lag. Für 10 der insgesamt 15 vii SNPs dieses Gens fanden sich bisher keine Einträge in den entprechenden Datenbanken. Die SNP-Suche wurde auch für das TRPM3-Gen durchgeführt und ergab 35 SNPs, wovon 30 (85,7%) als hochfrequent eingestuft werden konnten. 14 dieser 35 SNPs waren bisher nicht in den Datenbanken verzeichnet. Beim MT-Protocadherin-Gen fanden sich ebenfalls 35 SNPs, wobei 80% eine hohe Frequenz des selteneren Allels aufwiesen. In diesem Fall handelte es sich bei 23 der insgesamt 35 SNPs um bisher unbekannte Allele. Diese SNPs bilden den Ausgangspunkt zur Konstruktion der häufigsten Haplotypen der genannten Gene. Mit der Charakterisierung der Einzel-Nukleotid Polymorphismen der Kandidatengene wurde die Grundlage zur Durchführung von Fall/Kontrollstudien gelegt, in deren Rahmen die Bedeutung der jeweiligen Kandidatengene in der Pathogense der AMD untersucht werden kann. KW - Senile Makuladegeneration / Pigmentepithel / Genexpression KW - RPE KW - AMD KW - RPE specific genes Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-7053 ER - TY - JOUR A1 - Abdel-Latif, Rania A1 - Fathy, Moustafa A1 - Anwar, Hend Ali A1 - Naseem, Muhammad A1 - Dandekar, Thomas A1 - Othman, Eman M. T1 - Cisplatin-induced reproductive toxicity and oxidative stress: ameliorative effect of kinetin JF - Antioxidants N2 - Cisplatin is a commonly used chemotherapeutic agent; however, its potential side effects, including gonadotoxicity and infertility, are a critical problem. Oxidative stress has been implicated in the pathogenesis of cisplatin-induced testicular dysfunction. We investigated whether kinetin use at different concentrations could alleviate gonadal injury associated with cisplatin treatment, with an exploration of the involvement of its antioxidant capacity. Kinetin was administered in different doses of 0.25, 0.5, and 1 mg/kg, alone or along with cisplatin for 10 days. Cisplatin toxicity was induced via a single IP dose of 7 mg/kg on day four. In a dose-dependent manner, concomitant administration of kinetin with cisplatin significantly restored testicular oxidative stress parameters, corrected the distorted sperm quality parameters and histopathological changes, enhanced levels of serum testosterone and testicular StAR protein expression, as well as reduced the up-regulation of testicular TNF-α, IL-1β, Il-6, and caspase-3, caused by cisplatin. It is worth noting that the testicular protective effect of the highest kinetin dose was comparable/more potent and significantly higher than the effects of vitamin C and the lowest kinetin dose, respectively. Overall, these data indicate that kinetin may offer a promising approach for alleviating cisplatin-induced reproductive toxicity and organ damage, via ameliorating oxidative stress and reducing inflammation and apoptosis. KW - cytokinins KW - kinetin KW - cisplatin KW - reproductive toxicity Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-271223 SN - 2076-3921 VL - 11 IS - 5 ER - TY - JOUR A1 - Adam, Alexander A1 - Deimel, Stephan A1 - Pardo-Medina, Javier A1 - García-Martínez, Jorge A1 - Konte, Tilen A1 - Limón, M. Carmen A1 - Avalos, Javier A1 - Terpitz, Ulrich T1 - Protein activity of the \(Fusarium\) \(fujikuroi\) rhodopsins CarO and OpsA and their relation to fungus−plant interaction JF - International Journal of Molecular Sciences N2 - Fungi possess diverse photosensory proteins that allow them to perceive different light wavelengths and to adapt to changing light conditions in their environment. The biological and physiological roles of the green light-sensing rhodopsins in fungi are not yet resolved. The rice plant pathogen Fusarium fujikuroi exhibits two different rhodopsins, CarO and OpsA. CarO was previously characterized as a light-driven proton pump. We further analyzed the pumping behavior of CarO by patch-clamp experiments. Our data show that CarO pumping activity is strongly augmented in the presence of the plant hormone indole-3-acetic acid and in sodium acetate, in a dose-dependent manner under slightly acidic conditions. By contrast, under these and other tested conditions, the Neurospora rhodopsin (NR)-like rhodopsin OpsA did not exhibit any pump activity. Basic local alignment search tool (BLAST) searches in the genomes of ascomycetes revealed the occurrence of rhodopsin-encoding genes mainly in phyto-associated or phytopathogenic fungi, suggesting a possible correlation of the presence of rhodopsins with fungal ecology. In accordance, rice plants infected with a CarO-deficient F. fujikuroi strain showed more severe bakanae symptoms than the reference strain, indicating a potential role of the CarO rhodopsin in the regulation of plant infection by this fungus. KW - fungal rhodopsins KW - CarO KW - OpsA KW - Fusarium fujikuroi KW - Oryza sativa KW - rice–plant infection KW - green light perception KW - indole-3-acetic acid (IAA) KW - bakanae KW - patch-clamp Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285125 SN - 1422-0067 VL - 19 IS - 1 ER - TY - CHAP A1 - Adam, D. A1 - Schartl, A. A1 - Andexinger, S. A1 - Hölter, S. A1 - Wilde, B. A1 - Schartl, Manfred T1 - Genetic factors in tumour formation: The melanoma-inducing gene of Xiphophorus N2 - No abstract available. KW - Humangenetik KW - Tumor KW - Entstehung Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-86388 ER - TY - JOUR A1 - Adam, D. A1 - Wittbrodt, J. A1 - Telling, A. A1 - Schartl, Manfred T1 - RFLP for an EGF-receptor related gene associated with the melanoma oncogene locus of Xiphophorus maculatus N2 - No abstract available KW - Physiologische Chemie Y1 - 1988 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-61822 ER - TY - JOUR A1 - Adam, Dieter A1 - Dimitrijevic, Nicola A1 - Schartl, Manfred T1 - Tumor suppression in Xiphophorus by an accidentally acquired promoter N2 - Melanoma formation in the teleost Xiphophorus is caused by a dominant genetic locus, Tu. This locus includes the Xmrk oncogene, which encodes a receptor tyrosine kinase. Tumor induction is. suppressed in wild-type fish by a tumor suppressor locus, R. Molecular genetic analyses revealed that the Tu locus emerged by nonhomologaus recombination of the Xmrk proto-oncogene with a previously uncharacterized sequence, D. This event generated an additional copy of Xmrk with a new promoter. Suppression of the new Xmrk promoter by R in parental fish and its deregulation in hybrids explain the genetics of melanoma formation in Xiphophorus. KW - Physiologische Chemie Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-61630 ER - TY - JOUR A1 - Adam, Dieter A1 - Maueler, Winfried A1 - Schartl, Manfred T1 - Transcriptional activation of the melanoma inducing Xmrk oncogene in Xiphophorus N2 - The melanoma inducing locus of Xiphophorus encodes a tumorigenic version of a novel putative receptor tyrosine kinase (Xmrk). To elucidate the mechanism of oncogenic activation of Xmrk, we compared the structure and expression of two oncogenic loci with the corresponding proto-oncogene. Only minor structural alterations were found to be specific for the oncogenic Xmrk genes. Marked overexpression of the oncogene transcripts in melanoma, which are approximately 1 kb shorter than the proto-oncogene transcript, correlates with the malignancy of the tumors. The tumor transcripts are derived from an alternative transcription start site that is used only in the oncogenic loci. Thus, oncogenic activation of the melanoma inducing Xmrk gene appears primarily to be due to novel transcriptional control and overexpression. KW - Schwertkärpfling KW - Onkogen KW - Melanom Y1 - 1991 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-87584 ER - TY - JOUR A1 - Adelfinger, Marion A1 - Gentschev, Ivaylo A1 - de Guibert, Julio Grimm A1 - Weibel, Stephanie A1 - Langbein-Laugwitz, Johanna A1 - Härtl, Barbara A1 - Escobar, Hugo Murua A1 - Nolte, Ingo A1 - Chen, Nanhai G. A1 - Aguilar, Richard J. A1 - Yu, Yong A. A1 - Zhang, Qian A1 - Frentzen, Alexa A1 - Szalay, Aladar A. T1 - Evaluation of a New Recombinant Oncolytic Vaccinia Virus Strain GLV-5b451 for Feline Mammary Carcinoma Therapy JF - PLoS ONE N2 - Virotherapy on the basis of oncolytic vaccinia virus (VACV) infection is a promising approach for cancer therapy. In this study we describe the establishment of a new preclinical model of feline mammary carcinoma (FMC) using a recently established cancer cell line, DT09/06. In addition, we evaluated a recombinant vaccinia virus strain, GLV-5b451, expressing the anti-vascular endothelial growth factor (VEGF) single-chain antibody (scAb) GLAF-2 as an oncolytic agent against FMC. Cell culture data demonstrate that GLV-5b451 virus efficiently infected, replicated in and destroyed DT09/06 cancer cells. In the selected xenografts of FMC, a single systemic administration of GLV-5b451 led to significant inhibition of tumor growth in comparison to untreated tumor-bearing mice. Furthermore, tumor-specific virus infection led to overproduction of functional scAb GLAF-2, which caused drastic reduction of intratumoral VEGF levels and inhibition of angiogenesis. In summary, here we have shown, for the first time, that the vaccinia virus strains and especially GLV-5b451 have great potential for effective treatment of FMC in animal model. KW - antibodies KW - cancer treatment KW - carcinomas KW - vaccinia virus KW - oncolytic viruses KW - viral replication KW - cell cultures KW - enzyme-linked immunoassays Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-119387 VL - 9 IS - 8 ER - TY - THES A1 - Adhikari, Bikash T1 - Targeted degradation of Myc-interacting oncoproteins T1 - Gezielte Degradation von mit Myc interagierenden Onkoproteinen N2 - The hallmark oncoprotein Myc is a major driver of tumorigenesis in various human cancer entities. However, Myc’s structural features make it challenging to develop small molecules against it. A promising strategy to indirectly inhibit the function of Myc is by targeting its interactors. Many Myc-interacting proteins have reported scaffolding functions which are difficult to target using conventional occupancy- driven inhibitors. Thus, in this thesis, the proteolysis targeting chimera (PROTAC) approach was used to target two oncoproteins interacting with Myc which promote the oncogenicity of Myc, Aurora-A and WDR5. PROTACs are bifunctional small molecules that bind to the target protein with one ligand and recruit a cellular E3- ligase with the other ligand to induce target degradation via the ubiquitin- proteasome system. So far, the most widely used E3-ligases for PROTAC development are Cereblon (CRBN) and von Hippel–Lindau tumor suppressor (VHL). Furthermore, there are cases of incompatibility between some E3-ligases and proteins to bring about degradation. Hence there is a need to explore new E3- ligases and a demand for a tool to predict degradative E3-ligases for the target protein in the PROTAC field. In the first part, a highly specific mitotic kinase Aurora-A degrader, JB170, was developed. This compound utilized Aurora-A inhibitor alisertib as the target ligand and thalidomide as the E3-ligase CRBN harness. The specificity of JB170 and the ternary complex formation was supported by the interactions between Aurora-A and CRBN. The PROTAC-mediated degradation of Aurora-A induced a distinct S- phase defect rather than mitotic arrest, shown by its catalytic inhibition. The finding demonstrates that Aurora-A has a non-catalytic role in the S-phase. Furthermore, the degradation of Aurora-A led to apoptosis in various cancer cell lines. In the second part, two different series of WDR5 PROTACs based on two protein- protein inhibitors of WDR5 were evaluated. The most efficient degraders from both series recruited VHL as a E3-ligase and showed partial degradation of WDR5. In addition, the degradation efficiency of the PROTACs was significantly affected by the linker nature and length, highlighting the importance of linker length and composition in PROTAC design. The degraders showed modest proliferation defects at best in cancer cell lines. However, overexpression of VHL increased the degradation efficiency and the antiproliferative effect of the PROTACs. In the last part, a rapamycin-based assay was developed to predict the degradative E3-ligase for a target. The assay was validated using the WDR5/VHL and Aurora- A/CRBN pairs. The result that WDR5 is degraded by VHL but not CRBN and Aurora-A is degraded by CRBN, matches observations made with PROTACs. This technique will be used in the future to find effective tissue-specific and essential E3-ligases for targeted degradation of oncoproteins using PROTACs. Collectively, the work presented here provides a strategy to improve PROTAC development and a starting point for developing Aurora-A and WDR5 PROTACs for cancer therapy. N2 - Das Onkoprotein Myc ist ein wichtiger Faktor bei der Tumorentstehung in verschiedenen menschlichen Krebsarten. Die strukturellen Merkmale von Myc machen es jedoch schwierig, kleine Moleküle gegen dieses Protein zu entwickeln. Eine vielversprechende Strategie zur indirekten Hemmung der Funktion von Myc besteht darin, auf seine Interaktoren abzuzielen. Viele Proteine, die mit Myc interagieren, haben Gerüstfunktionen, die mit herkömmlichen Inhibitoren nur schwer zu hemmen sind. Daher wurde in dieser Arbeit der PROTAC-Ansatz (Proteolysis Targeting Chimera) verwendet, um zwei Onkoproteine, die mit Myc interagieren und die Onkogenität von Myc fördern, ins Visier zu nehmen: Aurora-A und WDR5. PROTACs sind bifunktionale kleine Moleküle, die mit einem Liganden an das Zielprotein binden und mit dem anderen Liganden eine zelluläre E3-Ligase rekrutieren, um den Abbau des Zielproteins über das Ubiquitin-Proteasom-System einzuleiten. Die bisher am häufigsten verwendeten E3-Ligasen für die Entwicklung von PROTACs sind Cereblon (CRBN) und der von Hippel-Lindau-Tumorsuppressor (VHL). Außerdem gibt es Fälle von Inkompatibilität zwischen einigen E3-Ligasen und Proteinen, die abgebaut werden sollen. Daher besteht die Notwendigkeit, neue E3-Ligasen zu erforschen und Werkzeuge zur Vorhersage abbauender E3-Ligasen für das Zielprotein zu entwickeln. Im ersten Teil wurde ein hochspezifischer Degrader der mitotischen Kinase Aurora-A, JB170, entwickelt. Bei dieser Verbindung wurde der Aurora-A-Inhibitor Alisertib als Zielligand und Thalidomid als Binder für die E3-Ligase CRBN verwendet. Die Spezifität von JB170 und die ternäre Komplexbildung wurden durch die Wechselwirkungen zwischen Aurora-A und CRBN unterstützt. Der durch PROTAC vermittelte Abbau von Aurora-A führte zu einem deutlichen Defekt in der S-Phase und nicht zu einem mitotischen Stillstand, wie es für dessen katalytische Hemmung beobachtet wurde. Dies zeigt, dass Aurora-A eine nicht-katalytische Funktion in der S-Phase hat. Außerdem führte der Abbau von Aurora-A in verschiedenen Krebszelllinien zur Apoptose. Im zweiten Teil wurden zwei verschiedene Serien von WDR5 PROTACs auf der Grundlage von zwei Protein-Protein-Inhibitoren von WDR5 untersucht. Die effizientesten Degrader aus beiden Serien rekrutierten VHL als E3-Ligase und zeigten einen teilweisen Abbau von WDR5. Darüber hinaus wurde die Abbaueffizienz der PROTACs erheblich von der Art und Länge des Linkers beeinflusst, was die Bedeutung der Linkerlänge und -zusammensetzung bei der Entwicklung von PROTACs unterstreicht. Die Abbauprodukte zeigten bestenfalls bescheidene Proliferationsdefekte in Krebszelllinien. Eine Überexpression von VHL erhöhte jedoch die Abbaueffizienz und den antiproliferativen Effekt der PROTACs. Im letzten Teil wurde ein auf Rapamycin basierender Assay entwickelt, um die abbauende E3-Ligase für ein Target vorherzusagen. Der Assay wurde anhand der Paare WDR5/VHL und Aurora-A/CRBN validiert. Das Ergebnis, dass WDR5 von VHL, aber nicht von CRBN abgebaut wird und Aurora-A von CRBN abgebaut wird, stimmt mit den Beobachtungen überein, die mit PROTACs gemacht wurden. Diese Technik wird in Zukunft eingesetzt werden, um wirksame gewebespezifische und essentielle E3-Ligasen für den gezielten Abbau von Onkoproteinen mit Hilfe von PROTACs zu finden. Insgesamt bieten die hier vorgestellten Arbeiten eine Strategie zur Verbesserung der PROTAC-Entwicklung und einen Ausgangspunkt für die Entwicklung von Aurora-A- und WDR5-PROTACs für die Krebstherapie. KW - Degradation KW - PROTACs KW - Oncoprotein KW - Cancer KW - Onkoprotein Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-317326 ER - TY - JOUR A1 - Adolfi, Mateus C. A1 - Carreira, Ana C. O. A1 - Jesus, Lázaro W. O. A1 - Bogerd, Jan A1 - Funes, Rejane M. A1 - Schartl, Manfred A1 - Sogayar, Mari C. A1 - Borella, Maria I. T1 - Molecular cloning and expression analysis of dmrt1 and sox9 during gonad development and male reproductive cycle in the lambari fish, Astyanax altiparanae JF - Reproductive Biology and Endocrinology N2 - Background The dmrt1 and sox9 genes have a well conserved function related to testis formation in vertebrates, and the group of fish presents a great diversity of species and reproductive mechanisms. The lambari fish (Astyanax altiparanae) is an important Neotropical species, where studies on molecular level of sex determination and gonad maturation are scarce. Methods Here, we employed molecular cloning techniques to analyze the cDNA sequences of the dmrt1 and sox9 genes, and describe the expression pattern of those genes during development and the male reproductive cycle by qRT-PCR, and related to histology of the gonad. Results Phylogenetic analyses of predicted amino acid sequences of dmrt1 and sox9 clustered A. altiparanae in the Ostariophysi group, which is consistent with the morphological phylogeny of this species. Studies of the gonad development revealed that ovary formation occurred at 58 days after hatching (dah), 2 weeks earlier than testis formation. Expression studies of sox9 and dmrt1 in different tissues of adult males and females and during development revealed specific expression in the testis, indicating that both genes also have a male-specific role in the adult. During the period of gonad sex differentiation, dmrt1 seems to have a more significant role than sox9. During the male reproductive cycle dmrt1 and sox9 are down-regulated after spermiation, indicating a role of these genes in spermatogenesis. Conclusions For the first time the dmrt1 and sox9 were cloned in a Characiformes species. We show that both genes have a conserved structure and expression, evidencing their role in sex determination, sex differentiation and the male reproductive cycle in A. altiparanae. These findings contribute to a better understanding of the molecular mechanisms of sex determination and differentiation in fish. KW - spermatogenesis KW - SOX9 KW - DMRT1 KW - sex differentiation KW - teleostei Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-126486 VL - 13 IS - 2 ER - TY - JOUR A1 - Adolfi, Mateus C. A1 - Du, Kang A1 - Kneitz, Susanne A1 - Cabau, Cédric A1 - Zahm, Margot A1 - Klopp, Christophe A1 - Feron, Romain A1 - Paixão, Rômulo V. A1 - Varela, Eduardo S. A1 - de Almeida, Fernanda L. A1 - de Oliveira, Marcos A. A1 - Nóbrega, Rafael H. A1 - Lopez-Roques, Céline A1 - Iampietro, Carole A1 - Lluch, Jérôme A1 - Kloas, Werner A1 - Wuertz, Sven A1 - Schaefer, Fabian A1 - Stöck, Matthias A1 - Guiguen, Yann A1 - Schartl, Manfred T1 - A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas) JF - Scientific Reports N2 - Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGF beta signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes. KW - evolutionary genetics KW - genetic markers KW - genome Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-265672 VL - 11 IS - 1 ER - TY - JOUR A1 - Adolfi, Mateus C. A1 - Herpin, Amaury A1 - Martinez-Bengochea, Anabel A1 - Kneitz, Susanne A1 - Regensburger, Martina A1 - Grunwald, David J. A1 - Schartl, Manfred T1 - Crosstalk Between Retinoic Acid and Sex-Related Genes Controls Germ Cell Fate and Gametogenesis in Medaka JF - Frontiers in Cell and Developmental Biology N2 - Sex determination (SD) is a highly diverse and complex mechanism. In vertebrates, one of the first morphological differences between the sexes is the timing of initiation of the first meiosis, where its initiation occurs first in female and later in male. Thus, SD is intimately related to the responsiveness of the germ cells to undergo meiosis in a sex-specific manner. In some vertebrates, it has been reported that the timing for meiosis entry would be under control of retinoic acid (RA), through activation of Stra8. In this study, we used a fish model species for sex determination and lacking the stra8 gene, the Japanese medaka (Oryzias latipes), to investigate the connection between RA and the sex determination pathway. Exogenous RA treatments act as a stress factor inhibiting germ cell differentiation probably by activation of dmrt1a and amh. Disruption of the RA degrading enzyme gene cyp26a1 induced precocious meiosis and oogenesis in embryos/hatchlings of female and even some males. Transcriptome analyzes of cyp26a1–/–adult gonads revealed upregulation of genes related to germ cell differentiation and meiosis, in both ovaries and testes. Our findings show that germ cells respond to RA in a stra8 independent model species. The responsiveness to RA is conferred by sex-related genes, restricting its action to the sex differentiation period in both sexes. KW - sex determination KW - retinoic acid KW - meiosis KW - gametogenesis KW - medaka Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-222669 SN - 2296-634X VL - 8 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 -