TY - JOUR A1 - Ademmer, Martin A1 - Horn, Wolfram A1 - Quast, Josefine T1 - Stock market dynamics and the relative importance of domestic, foreign, and common shocks JF - International Journal of Finance & Economics N2 - We quantify the contemporaneous relationships among stock markets in the euro area, the United States, and a group of emerging economies over the period from 2008 to 2017. Exploiting the heteroskedasticity in the stock market data, we identify shocks that originated in the respective domestic markets and shocks that are common to all markets. Our results underline the leading role of the United States in international equity markets, but also point to the importance of indirect spillovers for all economies. Variance decompositions show that while domestic shocks explain the bigger part of the variation in each stock market, a substantial part of the variation in the euro area and the emerging economies can be attributed to foreign shocks. A comparison with a sample covering the pre‐crisis period from 1999 to 2007 suggests a strengthening of the linkages among global stock markets in recent years. In particular, the spillovers from advanced to emerging economies have become more pronounced. KW - financial linkages KW - heteroskedasticity KW - identification KW - spillovers KW - stock markets Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-225729 VL - 27 IS - 4 SP - 3911 EP - 3923 ER - TY - JOUR A1 - Ascierto, Maria Libera A1 - Worschech, Andrea A1 - Yu, Zhiya A1 - Adams, Sharon A1 - Reinboth, Jennifer A1 - Chen, Nanhai G A1 - Pos, Zoltan A1 - Roychoudhuri, Rahul A1 - Di Pasquale, Giovanni A1 - Bedognetti, Davide A1 - Uccellini, Lorenzo A1 - Rossano, Fabio A1 - Ascierto, Paolo A A1 - Stroncek, David F A1 - Restifo, Nicholas P A1 - Wang, Ena A1 - Szalay, Aladar A A1 - Marincola, Francesco M T1 - Permissivity of the NCI-60 cancer cell lines to oncolytic Vaccinia Virus GLV-1h68 JF - BMC Cancer N2 - Background: Oncolytic viral therapy represents an alternative therapeutic strategy for the treatment of cancer. We previously described GLV-1h68, a modified Vaccinia Virus with exclusive tropism for tumor cells, and we observed a cell line-specific relationship between the ability of GLV-1h68 to replicate in vitro and its ability to colonize and eliminate tumor in vivo. Methods: In the current study we surveyed the in vitro permissivity to GLV-1h68 replication of the NCI-60 panel of cell lines. Selected cell lines were also tested for permissivity to another Vaccinia Virus and a vesicular stomatitis virus (VSV) strain. In order to identify correlates of permissity to viral infection, we measured transcriptional profiles of the cell lines prior infection. Results: We observed highly heterogeneous permissivity to VACV infection amongst the cell lines. The heterogeneity of permissivity was independent of tissue with the exception of B cell derivation. Cell lines were also tested for permissivity to another Vaccinia Virus and a vesicular stomatitis virus (VSV) strain and a significant correlation was found suggesting a common permissive phenotype. While no clear transcriptional pattern could be identified as predictor of permissivity to infection, some associations were observed suggesting multifactorial basis permissivity to viral infection. Conclusions: Our findings have implications for the design of oncolytic therapies for cancer and offer insights into the nature of permissivity of tumor cells to viral infection. KW - gene-therapy KW - adenovirus KW - receptor KW - identification KW - infection KW - CD9 KW - panel Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-141503 VL - 11 IS - 451 ER - TY - THES A1 - Bergelt, Steffen T1 - Morphologische und DNA-analytische Untersuchungen am Spurenmaterial Haar T1 - Morphological examinations and forensic DNA-typing of hair samples N2 - In der vorliegenden Arbeit wurde der Versuch unternommen, eine Korrelation zwischen der Morphologie des Spurenmaterials Haar und der molekularbiologischen Untersuchung herzustellen. In der Rechtsmedizin waren Haare lange Zeit wegen der technisch schwierigen und zeitintensiven Untersuchungsmethoden eher von untergeordneter Bedeutung. Erst in den letzten Jahren wurden ausreichende wissenschaftliche Grundlagen geschaffen, um im Rahmen der forensischen Spurenkunde spezielle Fragestellungen anhand von molekularbiologischen Haaranalyseergebnissen mit größter Sicherheit zu beantworten. Humane Kopfhaut wurde aus der occipitalen Region entnommen. Nach ausgewählten Fixationen wurden die Gewebeschnitte mit der Hämatoxylin-Eosin- sowie der Methylgrün-Pyronin-Färbung behandelt. Morphologische Hinweise auf die Existenz von Cytoplasmastrukturen, die mit Nukleinsäuren assoziiert sein könnten, fanden sich nach abgeschlossener Keratinisierung ausschließlich im Bereich der Kutikula. Im Bereich des Markstranges oder anderen Abschnitten des Haares konnten nach den abgeschlossenen Keratinisierungsprozessen keine Strukturen gefunden werden, die auf das Vorhandensein von Nukleinsäuren schließen lassen. Des Weiteren wurden mit geeigneten Verfahren die Extraktion von DNA aus telogenen Haarwurzeln und Haarschäften durchgeführt. Mit der Chelex-100-Extraktionsmethode und der Kombination der anschließenden Reinigung der Extrakte mit Diatomeenerde, war der DNA-Nachweis in mehr als die Hälfte der untersuchten Haarwurzeln möglich. Die Phenol-Chloroform-Extraktionsmethode erlaubte einen erfolgreichen DNA-Nachweis in durchschnittlich 14,3 % der Fälle. Zur Typisierung der genomen DNA wurde die Polymerasen-Ketten-Reaktion (PCR) angewandt. Untersucht wurde dabei zwei in der forensischen Praxis gängige STR-Systeme, zum einen das auf Chromosom 5 lokalisierte System HumACTBP2 (SE33) zum anderen das auf Chromosom 12 gelegene System HumVWA. Zusätzlich wurde das Geschlechtsbestimmungssystem HumAMEL X/Y in die Untersuchung mit einbezogen. Die Ergebnisse lassen zukünftig auf ein gezieltes Vorgehen und die Anwendung spezieller Methoden für die Individualtypisierung am Spurenmaterial Haar hoffen. Da Keratinisierungsprozesse im wachsendem Haar wohl eine Schlüsselrolle über das Schicksal der Zellkerne und der darin enthaltenen Degenerationsgrad der DNA spielen, sollten sich zukünftige Untersuchungen in der Rechtsmedizin verstärkt dieser Thematik widmen. N2 - Because of the technically difficults and time consuming, hairs has been of minor importance in forensic examinations for a long time. The aim of the present study was to establish a correlation between morphological features of hairs and molecular biologic analysis. First of all, human scalp was taken from the occipital region for histologic examinations. After fixation, the slides were stained with methyl green-pyronin method as well as hematoxylin and eosin. Once ceratinisation was completed, morphological evidence of a existance of cytoplasmatic structures, possibly associated with nucleic acids, could be detected only in the cuticular zone. Neither in marrow nor in other zones of the hair, any strucuture indicating the presence of nucleic acids after ceratinisation was completed. Moreover, DNA was extracted from telogen roots of hair and hair shafts. Using the chelex-100-extraction method and a combination of following separation of the extract using diatoms, DNA detection was possible in more than 50 % of the examined roots of hair. The phenol-chloroform-extraction showed successful DNA-detection in a average of 14,3 % of the examined cases. For typing of the obtained DNA, polymerase-chain-reaction (PCR) was used. Thereby two STR-systems, approved in forensic investigation, were studied, including system Hum ACTBP2 (SE33) as well as HumVWA. Additionally the DNA sex test HumAMELX/Y was examined. Since ceratinisation in the growing hair seems to represent a key process concerning the destiny of nucleus and the grade of degeneration of the included DNA, future studies in forensic medicine should investigate this aspect. KW - Haar KW - Identifizierung KW - STR KW - DNA-Typisierung KW - hair KW - identification KW - STR KW - DNA-typing Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-23155 ER - TY - JOUR A1 - De Giorgi, Valeria A1 - Buonaguro, Luigi A1 - Worschech, Andrea A1 - Tornesello, Maria Lina A1 - Izzo, Francesco A1 - Marincola, Francesco M. A1 - Wang, Ena A1 - Buonaguro, Franco M. T1 - Molecular Signatures Associated with HCV-Induced Hepatocellular Carcinoma and Liver Metastasis JF - PLoS ONE N2 - Hepatocellular carcinomas (HCCs) are a heterogeneous group of tumors that differ in risk factors and genetic alterations. In Italy, particularly Southern Italy, chronic hepatitis C virus (HCV) infection represents the main cause of HCC. Using high-density oligoarrays, we identified consistent differences in gene-expression between HCC and normal liver tissue. Expression patterns in HCC were also readily distinguishable from those associated with liver metastases. To characterize molecular events relevant to hepatocarcinogenesis and identify biomarkers for early HCC detection, gene expression profiling of 71 liver biopsies from HCV-related primary HCC and corresponding HCV-positive non-HCC hepatic tissue, as well as gastrointestinal liver metastases paired with the apparently normal peri-tumoral liver tissue, were compared to 6 liver biopsies from healthy individuals. Characteristic gene signatures were identified when normal tissue was compared with HCV-related primary HCC, corresponding HCV-positive non-HCC as well as gastrointestinal liver metastases. Pathway analysis classified the cellular and biological functions of the genes differentially expressed as related to regulation of gene expression and post-translational modification in HCV-related primary HCC; cellular Growth and Proliferation, and Cell-To-Cell Signaling and Interaction in HCV-related non HCC samples; Cellular Growth and Proliferation and Cell Cycle in metastasis. Also characteristic gene signatures were identified of HCV-HCC progression for early HCC diagnosis. Conclusions: A diagnostic molecular signature complementing conventional pathologic assessment was identified. KW - identification KW - hepatitis C virus KW - United States KW - gene expression KW - class I KW - endoplasmic reticulum KW - motile phenotype KW - bladder cancer KW - up-regulation KW - target Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131155 VL - 8 IS - 2 ER - TY - JOUR A1 - Feller, Tatjana A1 - Thom, Pascal A1 - Koch, Natalie A1 - Spiegel, Holger A1 - Addai-Mensah, Otchere A1 - Fischer, Rainer A1 - Reimann, Andreas A1 - Pradel, Gabriele A1 - Fendel, Rolf A1 - Schillberg, Stefan A1 - Scheuermayer, Matthias A1 - Schinkel, Helga T1 - Plant-Based Production of Recombinant Plasmodium Surface Protein Pf38 and Evaluation of its Potential as a Vaccine Candidate JF - PLOS ONE N2 - Pf38 is a surface protein of the malarial parasite Plasmodium falciparum. In this study, we produced and purified recombinant Pf38 and a fusion protein composed of red fluorescent protein and Pf38 (RFP-Pf38) using a transient expression system in the plant Nicotiana benthamiana. To our knowledge, this is the first description of the production of recombinant Pf38. To verify the quality of the recombinant Pf38, plasma from semi-immune African donors was used to confirm specific binding to Pf38. ELISA measurements revealed that immune responses to Pf38 in this African subset were comparable to reactivities to AMA-1 and \(MSP1_{19}\). Pf38 and RFP-Pf38 were successfully used to immunise mice, although titres from these mice were low (on average 1:11.000 and 1:39.000, respectively). In immune fluorescence assays, the purified IgG fraction from the sera of immunised mice recognised Pf38 on the surface of schizonts, gametocytes, macrogametes and zygotes, but not sporozoites. Growth inhibition assays using \(\alpha Pf38\) antibodies demonstrated strong inhibition \((\geq 60 \% ) \) of the growth of blood-stage P. falciparum. The development of zygotes was also effectively inhibited by \(\alpha Pf38\) antibodies, as determined by the zygote development assay. Collectively, these results suggest that Pf38 is an interesting candidate for the development of a malaria vaccine. KW - malaria vaccine KW - balancing selection KW - N-glycans KW - falciparum KW - expression KW - antibodies KW - identification KW - transmission KW - tobacco KW - antigen Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-128221 SN - 1932-6203 VL - 8 IS - 11 ER - TY - THES A1 - Gebhard, Sebastian T1 - DNA-analytische Untersuchungen an frischen und gelagerten Zähnen T1 - DNA-analytical research with fresh and ancient teeth N2 - In dieser Arbeit wurde überprüft, inwieweit sich verschiedene Lagerungsbedingungen von Zähnen auf die Verwertbarkeit von DNA im Zahninneren zur Gewinnung eines genetischen Fingerabdrucks auswirken. Die Untersuchungen an frisch extrahierten Zähnen ließen erkennen, dass die in dieser Arbeit verwendeten Methoden und DNA-Kits für die weitere Analyse der den unterschiedlichen Bedingungen ausgesetzten Zähne geeignet sind. Asensible Zähne weisen bereits bei der Zahnextraktion Zeichen von Degradation auf. Dagegen ist der kariöse Zerstörungsgrad an sich noch kein Ausschlusskriterium. Bei wurzelkanalbehandelten Zähnen konnten nur Systeme mit sehr kurzen Amplifikationsprodukten typisiert werden. Sie waren für eine genetische Identifizierung kaum geeignet. Bei der Analyse im Erdreich vergrabener Zähne nahm die Anzahl der typisierbaren Systeme nach einem Vierteljahr Liegezeit kontinuierlich ab, bis schließlich nach einem Jahr nur noch vereinzelt kleine Systeme detektiert werden konnten. Ein anderes Bild zeigte sich bei den in Wasser gelagerten Zähnen. Bis zu einem halben Jahr nach Versuchsbeginn konnte eine Typisierung aller Systeme durchgeführt werden. Erst nach einem Jahr war die Degradation so weit vorangeschritten, dass große Systeme keine Typisierung mehr erlaubten. Bei Zähnen, die der Sonnenstrahlung einen Monat ausgesetzt waren, war es dagegen problemlos möglich, einen vollständigen genetischen Fingerabdruck zu erfassen. Nach drei Monaten konnten allerdings nur noch vereinzelt sehr kleine Systeme gewonnen werden. Nach einem halben Jahr ergab lediglich der TPOX-vs eine erfolgreiche Typisierung. UV-Strahlung kann Zahnschmelz und –dentin durchdringen und DNA in recht kurzer Zeit degradieren. Die Zähne aus dem Sektionsgut des Instituts für Rechtsmedizin Würzburg lieferten unterschiedliche Ergebnisse, sodass hierzu keine generelle Aussage gemacht werden kann. Bei der Behandlung der Zähne mit Hitze von 200 °C konnte die DNA nur begrenzte Zeit vor Degradation geschützt werden. Bereits nach einer halben Stunde waren große Teile der Multiplex-Kits nicht mehr für eine Typisierung verwertbar. Das STR-System SE33 konnte allerdings noch ermittelt werden. Die Entnahmen zu späteren Zeitpunkten (60 min, 90 min und 120 min) lieferten fast nur noch einzelne STRSysteme. Eine knapp 30-jährige trockene Lagerung von Zähnen in einem Schrank mit Schutz vor Sonneneinstrahlung schadete der DNA-Analysierbarkeit kaum. Ein vollständiger Ausfall aller Systeme musste bei den Zahnproben von der Ausgrabung in Katzwang verzeichnet werden. Die Zähne dieser 380 bis 550 Jahre alten Schädel lieferten kein auswertbares DNA-Material mehr. Ebenso konnte mit diesen Untersuchungsmethoden aus den 2300 bis 2800 Jahre alten Zähnen aus der Dietersberghöhle kein analysierbares DNA-Material gewonnen werden. Es zeigte sich, dass Lagerbedingungen einen entscheidenden Einfluss auf die DNA-Qualität ausüben. Als DNA-schädigende Einflüsse können neben Mikroorganismen und Feuchtigkeit insbesondere UV-Strahlung und Hitze gelten. Der Faktor Zeit spielt bei günstigen Lagerbedingungen eine untergeordnete Rolle. N2 - In this dissertation the possibility of winning a genetic fingerprint out of teeth that have been rested under different conditions was analysed. The examinations of recently extracted teeth showed that the methods and DNA-Kits used in this study are suitable for further analyses of teeth that have been exposed to different conditions. Asensible teeth already showed at time of extraction signs of degradation. However it was possible to get a genetic DNA-typing out of teeth which were destroyed by caries. Teeth with a root canal filling only showed systems with short amplification products. So they were not suitable for a genetic identification. The analysis of teeth which were buried in soil resulted that the number of detectable systems decreased continually after four month. After one year only a few systems were detected. The teeth which were stored in water gave a positive result in all systems after half a year. When the teeth have laid one year in water the degradation had gone so far that the big systems could not be typified anymore. Teeth that were exposed to sunshine for one month gave a complete detection of all analysed systems. Two month later only a few small systems were detected. After six months only the system TPOX-vs was successfully typed. UV-radiation gets through the dentin and the enamel and destroys the DNA very quickly. Two teeth out of the section good of the institute for forensic medicine showed completely different results. In one case the DNA-typing was successful, in the other one it wasn´t. Teeth that were treated in a 200 °C hot oven could protect the DNA for only a few minutes. After 30 minutes half of the analysed systems already were destroyed. After one hour and more only some sporadic systems were detected. The DNA-typing of a genetic fingerprint out of 30 years old teeth was successful. The complete failure of all systems showed examples of 380 to 550 years old teeth from a dig in Katzwang such as examples of 2.300 to 2.800 years old teeth out of the Dietersberg cave. For the DNA-quality it is very important to which conditions the teeth are exposed. DNA-damaging influences among other things are microorganisms, humidity, UV-radiation and heat. The factor time is not so important if the surrounding conditions are optimal. KW - DNA-typing KW - Genetischer Fingerabdruck KW - Zahn KW - Identifikation KW - alt KW - gelagert KW - DNA-typing KW - genetic fingerprint KW - teeth KW - ancient KW - identification Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-46462 ER - TY - THES A1 - Goehtz, Florian T1 - DNA-analytische Identifizierung unter Verwendung von frischem und gelagertem Skelettmaterial T1 - Identification of fresh and ancient bone by DNA-analysis N2 - Der DNA-analytischen Untersuchung von frischem und gelagertem Skelettmaterial kommt bei der Identifikation unbekannter Toter zunehmende Bedeutung zu, insbesondere in Fällen, in denen nur Skelettüberreste einer DNA-Analyse zur Verfügung stehen. Zur Aufklärung der praktischen Durchführbarkeit von Knochen-DNA-Typisierungen im rechtmedizinischen Laboralltag wurden 21 Knochenproben unterschiedlicher Liegezeit analysiert. 14 Knochenproben stammten aus Sektionsgut (Liegezeit von einer Stunde bis 41 Wochen), 7 Proben aus Skelett- bzw. Knochenfunden (geschätzte Liegezeit zwischen 10 und über 200 Jahren). Die DNA-Extraktion wurde mittels reversibler DNA-Bindung an einer Silica-Membran durchgeführt. Die Typisierung erfolgte im Rahmen eines Multiplex-PCR-Ansatzes unter Amplifizierung von neun STR-Loci und dem Amelogenin-Locus. Zusätzlich wurden drei besonders kurze, sog. vs-STRs bestimmt und exemplarisch für zwei Proben Bereiche des mt-Genoms sequenziert. Bei der Multiplex-Analyse ließ sich für 13 der 14 aus Sektionsgut gewonnenen Proben (93 %) ein komplettes, reproduzierbares Allelprofil gewinnen, an einer der Proben konnte nur eine molekulare Geschlechtszuordnung durchgeführt werden. Ebenso konnten alle drei vs-STR-Loci für 13 der 14 Proben reproduzierbar bestimmt werden; eine Probe war in einem der drei vs-STR-Loci typisierbar. Die sieben Proben aus Skelett- bzw. Knochenfunden waren bei der Multiplex-Analyse nicht reproduzierbar typisierbar, die Bestimmung der vs-STR-Loci führte im Fall der ältesten Probe zur Typisierung eines der drei Loci (TPOXvs). Bei zwei Proben, welche im Rahmen der nukleären DNA-Analyse kein reproduzierbares Ergebnis gebracht hatten, erfolgte die mt-DNA-Sequenzierung eines jeweils 234, bzw. 194 Nukleotide langen Segmentes der HV1-Region des mitochondrialen Genoms. Umwelteinflüsse und Lagerungsbedingungen haben mehr Einfluss auf den Erhaltungszustand der DNA in Knochenmaterial, als der Faktor Zeit. Die Analyse und Typisierung von Knochen-DNA hat sich als wichtiges Verfahren zur Identifizierung im rechtsmedizinischen Alltag etabliert, die unverändert unbefriedigenden Typisierungsergebnisse bei der Analyse älteren Knochenmaterials unterstreichen jedoch die Notwendigkeit der Weiterentwicklung zuverlässiger und effektiver Extraktions- und Aufreinigungsverfahren. N2 - In recent years DNA-typing of fresh and ancient bone samples has become increasingly important for the identification of skeletal remains in the forensic context. To assess the efficiency and practicability of forensic DNA-typing 21 bone samples up to 200 years old were analysed. 14 samples were taken from forensic autopsies (post mortem interval 0 to 41 weeks), 7 samples came from accidental finds of skeletal remains (estimated post mortem intervall from 10 years to over 200 years). DNA-extraction was performed with a silica-based method, 9 STR and the Amelogenin-locus were amplified via PCR with a multiplex-kit, additionally 3 very-short-STRs were amplified and analysed. MtDNA-sequencing was carried out for two of the ancient bone samples. With the multiplex-kit 13 out of the 14 autopsy-derived samples (93 %) could be successfully analysed, for one sample only the Amelogenin-locus could be amplified. The 3 vs-STR-loci could be typed for 13 of the 14 samples, one sample only led to a successful analysis of one of the 3 vs-STRs. The 7 samples from accidental finds of skeletal remains yielded no result with the multiplex-kit, for one sample a vs-STR-locus could be analysed. Amplification and sequencing of a 234 and a 194 bp segement of the HV-1-region of the mtDNA could be obtained for two ancient bone samples where STR-loci could not be amplified. There are many factors leading to degradation of DNA in skeletal material, generally environmental conditions have more significance than time. Analysis and typing of bone-DNA has become an important procedure in the forensic routine, yet the results of this study show the need to further develop more efficient DNA-extraction and purification methods of bone samples. KW - Knochen KW - Identifizierung KW - DNA-Typisierung KW - STR KW - mtDNA KW - bone KW - identification KW - DNA-typing . STR KW - mtDNA Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-18205 ER - TY - THES A1 - Grimm, Dorothee T1 - Entwicklung von neuen Nachweismethoden für Legionellen und Amöben und ihre Anwendung in ökologischen Studien T1 - Development and evaluation of novel detection systems specific for legionellae and amoebae and their application in ecological studies N2 - Legionella pneumophila wurde 1976 als Erreger der Legionellose, einer schweren Form von Lungenentzündung, identifiziert. Die inzwischen 42 Arten umfassende Gattung ist weltweit in aquatischen Biotopen verbreitet. Die Bakterien leben vergesellschaftet mit anderen Mikroorganismen in Biofilmen oder intrazellulär in Protozoen. Sie haben ein duales Wirtssystem, das heißt, sie sind in der Lage, sich sowohl in Einzellern als auch in humanen Phagozyten zu vermehren. Für die Erweiterung ihrer Habitate spielen verschiedene Umweltfaktoren eine Rolle. Eine exakte und schnelle Detektion und Identifikation der humanpathogenen Keime ist sowohl für die Lokalisierung der Infektionsquelle als auch für eine rechtzeitige Therapie der Patienten von großer Bedeutung. Die Technik der fluoreszierenden in situ Hybridisierung (FISH) basiert auf der Bindung einer spezifischen, mit einem Fluoreszenzfarbstoff markierten Oligonukleotidsonde an eine komplementäre Zielsequenz der ribosomalen RNA. In der vorliegenden Arbeit wurde für die in situ Hybridisierung eine neue 16S rRNA-gerichtete Sonde LEGPNE1 entwickelt, die spezifisch ist für L. pneumophila. In Versuchsreihen mit verschiedenen Bakterienkulturen wurden die Spezifität und Sensitivität der Gensonde ermittelt. LEGPNE1 erwies sich als artspezifisch und erkannte alle getesteten L. pneumophila-Stämme, ungeachtet ihrer Serogruppe. Nicht-pneumophila-Referenzstämme hybridisierten nicht mit der Sonde, ein einziger Basenaus-tausch in der Sequenz war für diese Unterscheidung ausreichend. Die Anwendung der Sonde wurde auch in Amöben-Infektionsassays und Umweltproben erfolgreich durchgeführt. Unterschiedliche, intrazellulär vorliegende Bakterien wurden von der Sonde spezifisch erkannt. Eine in situ Dokumentation der Infektions- und Vermehrungsrate war damit möglich. Durch die meist fakultativ intrazelluläre Lebensweise der Legionellen ist es wichtig, auch die Wirtszellen der Keime qualitativ zu detektieren und zu identifizieren. Die Entwicklung neuer Gensonden wurde daher auf die beiden bekannten Wirtsamöben Hartmannella und Naegleria ausgedehnt. Basierend auf Sequenzvergleichen wurden die gattungsspezifischen 18S rRNA-gerichteten Sonden HART498 und NAEG1088 konstruiert und in Versuchsreihen mit Referenzstämmen bei steigender Stringenz etabliert. Mit ihrer Hilfe konnten die Ergebnisse der zeit- und arbeitsaufwendigen Determination unbekannter Amöben anhand morphologischer Merkmale bestätigt werden. In situ Hybridisierungen mit einer Kombination von 16S und 18S rRNA-gerichteten Sonden wurden in Amöben-Infektionsassays mit Hartmannella vermiformis und L. pneumophila erfolgreich durchgeführt. Eine Interferenz der Sonden fand nicht statt. Die in situ Untersuchung der Struktur und Funktion komplexer mikrobieller Lebensgemeinschaften erfordert eine kultivierungsunabhängige und hochauflösende Methode, wie sie die fluoreszierende in situ Hybridisierung darstellt. Mit dem Ziel, mögliche Präferenzen der Legionellen für bestimmte Parameter, wie pH, Temperatur, elektrische Leitfähigkeit, Strömungsverhältnisse, zu erkennen und zu definieren, wurden mit Hilfe der neu entwickelten 16S rRNA-gerichteten Sonde 21 verschiedene Kaltwasserhabitate auf die Verbreitung von Legionella untersucht. Die Bakterien zeigten jedoch ein breites Toleranzspektrum gegenüber den gemessenen Parametern. Sie waren in nahezu allen beprobten Gewässern zu finden und ließen sich unabhängig von der Jahreszeit nachweisen. Die neue Sonde LEGPNE1 zeigte sich in in situ Hybridisierungen der Umweltproben als hochspezifisch. Mit ihr konnten auch nicht kultivierbare Legionellen detektiert werden. In drei Legionella-positiven Gewässern wurde außerdem das Vorkommen von Amöben untersucht. Es konnten insgesamt acht Amöbengattungen isoliert, kultiviert und bestimmt werden. Dominierend waren Stämme des nicht humanpathogenen Naegleria gruberi-Komplexes, Echinamoeba spp. und Echinamoeba-like Amöben. In einzelnen Proben wurden Acanthamoeba spp. Gruppe II, Hartmannella spp., Platyamoeba placida, Saccamoeba spp., Thecamoeba quadrilineata und Vexillifera spp. gefunden. Durch in situ Hybridisierung mit den neuen 18S rRNA-gerichteten Sonden HART498 und NAEG1088 konnten die Ergebnisse der morphologischen Bestimmung der Amöben bestätigt werden. Auch die Amöben zeigten keine Präferenzen bezüglich der in den Standorten gemessenen Wasserparameter. Die in situ Hybridisierung mit rRNA-gerichteten Gensonden erlaubt eine Analyse der Struktur und Dynamik von Biozönosen, ermöglicht aber keine Aussage über die speziellen Aktivitäten der nachgewiesenen Bakterien. Eine Lösung hierfür könnte der spezifische in situ Nachweis von mRNA-Molekülen darstellen. Ein Problem hierbei stellt ihre, im Vergleich zu anderen Molekülen wie rRNA, sehr kurze Halbwertszeit und das Vorhandensein von nur wenigen Kopien pro Zelle dar. Daher ist im Anschluss an die in situ Hybridisierung in den meisten Fällen eine Signalamplifikation nötig, um ein detektierbares Signal zu erhalten. In dieser Arbeit sollte die für das iap-Gen in Listeria monocytogenes entwickelte Methode zum Nachweis der mip-mRNA in L. pneumophila etabliert werden. Erste Anwendungen in Dot blot- und in situ Hybridisierungen mit mehrfach DIG-markierten Polyribonukleotidsonden bzw. mit simultan eingesetzten, einfach DIG-markierten Oligonukleotiden zeigten noch nicht die gewünschte Spezifität. Diese Ergebnisse stellen jedoch eine wichtige Grundlage für zukünftige Experimente dar. N2 - Legionella pneumophila was identified in 1976 as the causative agent of a life-threatening atypical pneumonia. Today the genus comprises about 42 species which are spread worldwide in aquatic biotopes. The bacteria live in association with other microorganisms in biofilms as well as intracellularly in protozoa. They have a dual host system which means that they are able to replicate both in protozoans and in human phagocytes. Several environmental factors are known to play a role in their distribution. The ability to quickly detect and to exactly identify these potential human pathogens is important in order to recognize reservoirs for disease as well as to treat patients in due time. Fluorescence in situ hybridization (FISH) is a technique based on the reaction of a specific oligonucleotide, labeled with a fluorescence marker, with the complementary rRNA target region. In this work a new 16S rRNA-targeted oligonucleotide probe LEGPNE1 for in situ hybridization was developed, which is specific for L. pneumophila. The specificity and the sensitivity of the probe were evaluated in experiments with different bacterial cultures. LEGPNE1 was demonstrated to be highly species-specific recognizing all tested strains of L. pneumophila independently of the serogroup. Non-pneumophila reference strains did not hybridize with the probe. Only one mismatch in the sequence was shown to be sufficient for the oligonucleotide to distinguish between complementary and nearly complementary sequences. The probe was also applied successfully to infected amoebal cells and environmental samples. Different bacteria located intracellularly were recognized specifically by the probe. This allows the in situ monitoring of bacterial infection and multiplication rates in amoebae. As legionellae presumably live most of the time as intracellular parasites, it is also important to be able to detect their hosts. Therefore, the design of new probes was extended to cover two known host amoebal genera, Hartmannella and Naegleria. Based on comparative sequence analysis the genus-specific 18S rRNA-targeted probes HART498 and NAEG1088 were constructed. Subsequently they were tested in hybridization series with different reference strains and gradually increasing stringency. Amoebal strains which had been identified previously based on their morphological features could be reconfirmed using in situ hybridization with these new oligonucleotides. In situ hybridization experiments of infection assays with Hartmannella vermiformis and Legionella pneumophila using a combination of 16S and 18S rRNA-targeted probes were done successfully. Interference of the probes with the results of the tests was not observed. For the analysis of the composition of complex microbial communities a culture-independent and highly specific method is required. This can be achieved by the fluorescence in situ hybridization. In order to determine potential preferences of legionellae for water parameters such as pH, temperature, conductivity, or water current, twenty-one different cold water habitats were examined for the presence of Legionella using the newly designed 16S rRNA-targeted oligonucleotide probe. The bacteria were shown to be able to tolerate a broad range of the measured parameters. They could be found in nearly all of the habitats investigated independent of the season. The new probe LEGPNE1 was proved to detect L. pneumophila in environmental samples highly specifically, even if the cells were in a nonculturable state. Three Legionella-positive sampling sites were examined for the presence of amoebae. Using traditional culture methods followed by morphological determination, eight amoebal genera could be isolated and identified. Most abundant were strains of the apathogenic Naegleria gruberi-complex, Echinamoeba spp. and Echinamoeba-like amoebae. Other species including Acanthamoeba spp. (sequence type II), Hartmannella spp., Platyamoeba placida, Saccamoeba spp., Thecamoeba quadrilineata and Vexillifera spp. were found sporadically. In situ hybridization experiments using the new 18S rRNA-targeted oligonucleotide probes HART498 and NAEG1088 confirmed the determinations done by morphological criteria. Concomitant analysis of selected water parameters revealed no preference of the protozoa for certain environmental conditions. In situ hybridization with rRNA-targeted oligonucleotide probes is a powerful tool to analyze structure and dynamics in biocenosis. However, this technique does not provide much information about the in situ function of the detected bacteria. The specific in situ detection of mRNA molecules allows to narrow this gap. One problem in the application of this method is the instability and low copy number of mRNA in each cell compared to other molecules like rRNA. Therefore, a signal amplification posterior to the in situ hybridization is required in most cases in order to generate a detectable signal. In this work the detection of the mRNA of mip in L. pneumophila was to be established using a protocol developed for the detection of iap in Listeria monocytogenes. However, first applications of dot blot and in situ hybridizations using DIG-conjugated polyribonucleotide probes and several DIG-labeled oligonucleotides applied simultaneously did not show the neccessary specificity. This technical approach will be essential for further experiments in this field of research. KW - Legionella pneumophila KW - Freilebende Amöben KW - Nachweis KW - Ökosystem KW - Legionella pneumophila KW - freilebende Süßwasseramöben KW - Nachweis KW - Bestimmung KW - 16S rRNA KW - 18SrRNA KW - fluoreszierende in situ Hybridisierung KW - Legionella pneumophila KW - free-living freshwater amoebae KW - detection KW - identification KW - 16S rRNA KW - 18SrRNA KW - fluorescence in situ hybridization Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-1351 ER - TY - JOUR A1 - Gupta, Shishir K. A1 - Srivastava, Mugdha A1 - Osmanoglu, Oezge A1 - Dandekar, Thomas T1 - Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs JF - Scientific Reports N2 - Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational methods of PPI determination can accelerate biological discovery by identifying the most promising interacting pairs of proteins and by assessing the reliability of identified PPIs. Here we present a first in-depth study describing a global view of the ant Camponotus floridanus interactome. Although several ant genomes have been sequenced in the last eight years, studies exploring and investigating PPIs in ants are lacking. Our study attempts to fill this gap and the presented interactome will also serve as a template for determining PPIs in other ants in future. Our C. floridanus interactome covers 51,866 non-redundant PPIs among 6,274 proteins, including 20,544 interactions supported by domain-domain interactions (DDIs), 13,640 interactions supported by DDIs and subcellular localization, and 10,834 high confidence interactions mediated by 3,289 proteins. These interactions involve and cover 30.6% of the entire C. floridanus proteome. KW - interaction map KW - drosophila KW - identification KW - evolutionary KW - reliability KW - annotation KW - database KW - target KW - cycle Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229406 VL - 10 IS - 1 ER - TY - JOUR A1 - Hoffmann, Linda S A1 - Schmidt, Peter M A1 - Keim, Yvonne A1 - Hoffmann, Carsten A1 - Schmidt, Harald H H W A1 - Stasch, Johannes-Peter T1 - Fluorescence Dequenching Makes Haem-Free Soluble Guanylate Cyclase Detectable in Living Cells JF - PLOS ONE N2 - In cardiovascular disease, the protective NO/sGC/cGMP signalling-pathway is impaired due to a decreased pool of NO-sensitive haem-containing sGC accompanied by a reciprocal increase in NO-insensitive haem-free sGC. However, no direct method to detect cellular haem-free sGC other than its activation by the new therapeutic class of haem mimetics, such as BAY 58-2667, is available. Here we show that fluorescence dequenching, based on the interaction of the optical active prosthetic haem group and the attached biarsenical fluorophor FlAsH can be used to detect changes in cellular sGC haem status. The partly overlap of the emission spectrum of haem and FlAsH allows energy transfer from the fluorophore to the haem which reduces the intensity of FlAsH fluorescence. Loss of the prosthetic group, e. g. by oxidative stress or by replacement with the haem mimetic BAY 58-2667, prevented the energy transfer resulting in increased fluorescence. Haem loss was corroborated by an observed decrease in NO-induced sGC activity, reduced sGC protein levels, and an increased effect of BAY 58-2667. The use of a haem-free sGC mutant and a biarsenical dye that was not quenched by haem as controls further validated that the increase in fluorescence was due to the loss of the prosthetic haem group. The present approach is based on the cellular expression of an engineered sGC variant limiting is applicability to recombinant expression systems. Nevertheless, it allows to monitor sGC's redox regulation in living cells and future enhancements might be able to extend this approach to in vivo conditions. KW - spontaneously hypersensitive-rats KW - nitric-oxide KW - down-regulation KW - energy-transfer KW - cyclic-gmp KW - protein KW - activation KW - identification KW - in-vivo KW - no Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-139631 VL - 6 IS - 8 ER - TY - JOUR A1 - Jellinghaus, K. A1 - Matin, S. A1 - Urban, P. A1 - Bohnert, M. A1 - Jantz, R. T1 - Study of the K-S distance on skulls from different modern populations for sex and ancestry determination JF - Rechtsmedizin N2 - In forensic science determination of the origin and sex of skeletal remains is an important task for identification purposes. In this study we investigated the krotaphion-sphenion distance (K‑S distance) in the pterion region of German, Euro-American, African-American and Rwandan skulls of modern individuals from the nineteenth to the twenty-first century to look for statistically significant differences in sex and ancestry. We found a statistically significant sex-specific difference in the K‑S distance, which was greater in male skulls than in female skulls for both sides of the skull. Our study also showed that there is a statistically significant difference in the K‑S distance between the four populations studied. Landmarks and morphometric parameters measured in our investigations, which were not used for the present examination were provided to the software program Fordisc for its reference data to enhance the range of its usability for identification of unknown skulls or partial skulls of European individuals. N2 - Bei der forensischen Begutachtung zur Identifizierung unbekannter Skelettfunde spielen Herkunftsanlaysen und Geschlechtsbestimmungen eine bedeutende Rolle. In unserer Studie an euroamerikanischen, afroamerikanischen, ruandischen und deutschen Schädeln untersuchte unsere Arbeitsgruppe die sog. Krotaphion-Sphenion-Distanz in der Pterion Region am menschlichen Schädel, um geschlechts- und herkunftsspezifische Unterschiede näher zu beleuchten. Unsere Ergebnisse zeigen einen signifikanten Unterschied in der K‑S-Distanz: Männliche Individuen zeigten auf beiden Seiten des Schädels signifikant größere Werte als weibliche Individuen, des Weiteren waren signifikante Unterschiede unter den vier untersuchten Populationen festzustellen. Die weiteren, im Rahmen der Studie gemessenen, jedoch für die vorliegende Auswertung nicht verwendeten Landmarken und morphometrischen Parameter der Schädel gingen in die Datenbank für die Identifizierungs-Software Fordisc ein, um deren Datengrundlage und damit Nutzbarkeit zur Identifikation unbekannter Schädel oder Schädelteile europäischer Individuen zu verbessern. KW - forensic anthropology KW - forensic osteology KW - identification KW - gender KW - landmarks KW - Forensische Anthropologie KW - Forensische Osteologie KW - Identifizierung KW - Geschlechtsbestimmung KW - Landmarken Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-235185 SN - 0937-9819 VL - 30 ER - TY - JOUR A1 - Kern, Selina A1 - Agarwal, Shruti A1 - Huber, Kilian A1 - Gehring, Andre P. A1 - Strödke, Benjamin A1 - Wirth, Christine C. A1 - Brügl, Thomas A1 - Abodo, Liane Onambele A1 - Dandekar, Thomas A1 - Doerig, Christian A1 - Fischer, Rainer A1 - Tobin, Andrew B. A1 - Alam, Mahmood M. A1 - Bracher, Franz A1 - Pradel, Gabriele T1 - Inhibition of the SR Protein-Phosphorylating CLK Kinases of Plasmodium falciparum Impairs Blood Stage Replication and Malaria Transmission JF - PLOS ONE N2 - Cyclin-dependent kinase-like kinases (CLKs) are dual specificity protein kinases that phosphorylate Serine/Arginine-rich (SR) proteins involved in pre-mRNA processing. Four CLKs, termed PfCLK-1-4, can be identified in the human malaria parasite Plasmodium falciparum, which show homology with the yeast SR protein kinase Sky1p. The four PfCLKs are present in the nucleus and cytoplasm of the asexual blood stages and of gametocytes, sexual precursor cells crucial for malaria parasite transmission from humans to mosquitoes. We identified three plasmodial SR proteins, PfSRSF12, PfSFRS4 and PfSF-1, which are predominantly present in the nucleus of blood stage trophozoites, PfSRSF12 and PfSF-1 are further detectable in the nucleus of gametocytes. We found that recombinantly expressed SR proteins comprising the Arginine/Serine (RS)-rich domains were phosphorylated by the four PfCLKs in in vitro kinase assays, while a recombinant PfSF-1 peptide lacking the RS-rich domain was not phosphorylated. Since it was hitherto not possible to knock-out the pfclk genes by conventional gene disruption, we aimed at chemical knock-outs for phenotype analysis. We identified five human CLK inhibitors, belonging to the oxo-beta-carbolines and aminopyrimidines, as well as the antiseptic chlorhexidine as PfCLK-targeting compounds. The six inhibitors block P. falciparum blood stage replication in the low micromolar to nanomolar range by preventing the trophozoite-to-schizont transformation. In addition, the inhibitors impair gametocyte maturation and gametogenesis in in vitro assays. The combined data show that the four PfCLKs are involved in phosphorylation of SR proteins with essential functions for the blood and sexual stages of the malaria parasite, thus pointing to the kinases as promising targets for antimalarial and transmission blocking drugs. KW - parasite KW - expression KW - mosquito KW - splicing factors KW - lactate dehydrogenase KW - xanthurenic acid KW - in-vitro KW - RNA-SEQ KW - identification KW - culture Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-115405 SN - 1932-6203 VL - 9 IS - 9 ER - TY - JOUR A1 - Krause, Stefan A1 - Weber, Silvana T1 - Lift me up by looking down: social comparison effects of narratives JF - Frontiers in Psychology N2 - Stories are a powerful means to change recipients’ views on themselves by being transported into the story world and by identifying with story characters. Previous studies showed that recipients temporarily change in line with a story and its characters (assimilation). Conversely, assimilation might be less likely when recipients are less identified with story protagonists or less transported into a story by comparing themselves with a story character. This may lead to changes, which are opposite to a story and its characters (contrast). In two experiments, we manipulated transportation and experience taking via two written reviews (Experiment 1; N = 164) and by varying the perspective of the story’s narrator (Experiment 2; N = 79) of a short story about a negligent student. Recipients’ self-ratings in comparison to others, motives, and problem-solving behavior served as dependent variables. However, neither the review nor the perspective manipulation affected transportation or experience taking while reading the story. Against our expectations, highly transported recipients (in Study 1) and recipients with high experience taking (in Study 2) showed more persistency working on an anagram-solving task, even when controlling for trait conscientiousness. Our findings are critically discussed in light of previous research. KW - self KW - self-concept KW - transportation KW - identification KW - experience taking KW - narratives KW - social comparison Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-190624 SN - 1664-1078 VL - 9 ER - TY - JOUR A1 - Krehan, Mario A1 - Heubeck, Christian A1 - Menzel, Nicolas A1 - Seibel, Peter A1 - Schön, Astrid T1 - RNase MRP RNA and RNase P activity in plants are associated with a Pop1p containing complex JF - Nucleic Acids Research N2 - RNase P processes the 5'-end of tRNAs. An essential catalytic RNA has been demonstrated in Bacteria, Archaea and the nuclei of most eukaryotes; an organism-specific number of proteins complement the holoenzyme. Nuclear RNase P from yeast and humans is well understood and contains an RNA, similar to the sister enzyme RNase MRP. In contrast, no protein subunits have yet been identified in the plant enzymes, and the presence of a nucleic acid in RNase P is still enigmatic. We have thus set out to identify and characterize the subunits of these enzymes in two plant model systems. Expression of the two known Arabidopsis MRP RNA genes in vivo was verified. The first wheat MRP RNA sequences are presented, leading to improved structure models for plant MRP RNAs. A novel mRNA encoding the central RNase P/MRP protein Pop1p was identified in Arabidopsis, suggesting the expression of distinct protein variants from this gene in vivo. Pop1p-specific antibodies precipitate RNase P activity and MRP RNAs from wheat extracts. Our results provide evidence that in plants, Pop1p is associated with MRP RNAs and with the catalytic subunit of RNase P, either separately or in a single large complex. KW - enzyme KW - binding KW - sequence KW - cyanelle KW - in vitro KW - partial purification KW - protein subunit KW - ribonuclease-P KW - genes KW - identification Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130648 VL - 40 IS - 16 ER - TY - JOUR A1 - Krämer, Johannes A1 - Bijnens, Bart A1 - Störk, Stefan A1 - Ritter, Christian O. A1 - Liu, Dan A1 - Ertl, Georg A1 - Wanner, Christoph A1 - Weidemann, Frank T1 - Left ventricular geometry and blood pressure as predictors of adverse progression of Fabry cardiomyopathy JF - PLoS ONE N2 - Background In spite of several research studies help to describe the heart in Fabry disease (FD), the cardiomyopathy is not entirely understood. In addition, the impact of blood pressure and alterations in geometry have not been systematically evaluated. Methods In 74 FD patients (mean age 36±12 years; 45 females) the extent of myocardial fibrosis and its progression were quantified using cardiac magnetic-resonance-imaging with late enhancement technique (LE). Results were compared to standard echocardiography complemented by 2D-speckle-tracking, 3D-sphericity-index (SI) and standardized blood pressure measurement. At baseline, no patient received enzyme replacement therapy (ERT). After 51±24 months, a follow-up examination was performed. Results Systolic blood pressure (SBP) was higher in patients with vs. without LE: 123±17 mmHg vs. 115±13 mmHg; P = 0.04. A positive correlation was found between SI and the amount of LE-positive myocardium (r = 0.51; P<0.001) indicating an association of higher SI in more advanced stages of the cardiomyopathy. SI at baseline was positively associated with the increase of LE-positive myocardium during follow-up. The highest SBP (125±19 mmHg) and also the highest SI (0.32±0.05) was found in the subgroup with a rapidly increasing LE (ie, ≥0.2% per year; n = 16; P = 0.04). Multivariate logistic regression analysis including SI, SBP, EF, left ventricular volumes, wall thickness and NT-proBNP adjusted for age and sex showed SI as the most powerful parameter to detect rapid progression of LE (AUC = 0.785; P<0.05). Conclusions LV geometry as assessed by the sphericity index is altered in relation to the stage of the Fabry cardiomyopathy. Although patients with FD are not hypertensive, the SBP has a clear impact on the progression of the cardiomyopathy. KW - cardiovascular magnetic resonance KW - clinical manifestations KW - disease KW - identification KW - fibrosis KW - 2-dimensional speckle tracking KW - myocardial infarction KW - therapy KW - diagnosis KW - impact Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-145131 VL - 10 IS - 11 ER - TY - JOUR A1 - Lando, David A1 - Endesfelder, Ulrike A1 - Berger, Harald A1 - Subramanian, Lakxmi A1 - Dunne, Paul D. A1 - McColl, James A1 - Klenerman, David A1 - Carr, Antony M. A1 - Sauer, Markus A1 - Allshire, Robin C. A1 - Heilemann, Mike A1 - Laue, Ernest D. T1 - Quantitative single-molecule microscopy reveals that CENP-A\(^{Cnp1}\) deposition occurs during G2 in fission yeast JF - Open Biology N2 - The inheritance of the histone H3 variant CENP-A in nucleosomes at centromeres following DNA replication is mediated by an epigenetic mechanism. To understand the process of epigenetic inheritance, or propagation of histones and histone variants, as nucleosomes are disassembled and reassembled in living eukaryotic cells, we have explored the feasibility of exploiting photo-activated localization microscopy (PALM). PALM of single molecules in living cells has the potential to reveal new concepts in cell biology, providing insights into stochastic variation in cellular states. However, thus far, its use has been limited to studies in bacteria or to processes occurring near the surface of eukaryotic cells. With PALM, one literally observes and 'counts' individual molecules in cells one-by-one and this allows the recording of images with a resolution higher than that determined by the diffraction of light (the so-called super-resolution microscopy). Here, we investigate the use of different fluorophores and develop procedures to count the centromere-specific histone H3 variant CENP-A\(^{Cnp1}\) with single-molecule sensitivity in fission yeast (Schizosaccharomyces pombe). The results obtained are validated by and compared with ChIP-seq analyses. Using this approach, CENP-A\(^{Cnp1}\) levels at fission yeast (S. pombe) centromeres were followed as they change during the cell cycle. Our measurements show that CENP-A(Cnp1) is deposited solely during the G2 phase of the cell cycle. KW - nucleosome KW - fission yeast KW - identification KW - propagation KW - CSE4, CENP-A KW - CENP-A KW - schizosaccaromyces-pombe KW - fluorescent protein KW - centomeres KW - superresolution KW - chromatin KW - centromere KW - ingle-molecule microscopy Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134682 VL - 2 IS - 120078 ER - TY - JOUR A1 - Ludwig, K. U. A1 - Sämann, P. A1 - Alexander, M. A1 - Becker, J. A1 - Bruder, J. A1 - Moll, K. A1 - Spieler, D. A1 - Czisch, M. A1 - Warnke, A. A1 - Docherty, S. J. A1 - Davis, O. S. P. A1 - Plomin, R. A1 - Nöthen, M. M. A1 - Landerl, K. A1 - Müller-Myhsok, B. A1 - Hoffmann, P. A1 - Schumacher, J. A1 - Schulte-Körne, G. A1 - Czamara, D. T1 - A common variant in Myosin-18B contributes to mathematical abilities in children with dyslexia and intraparietal sulcus variability in adults JF - Translational Psychiatry N2 - The ability to perform mathematical tasks is required in everyday life. Although heritability estimates suggest a genetic contribution, no previous study has conclusively identified a genetic risk variant for mathematical performance. Research has shown that the prevalence of mathematical disabilities is increased in children with dyslexia. We therefore correlated genome-wide data of 200 German children with spelling disability, with available quantitative data on mathematic ability. Replication of the top findings in additional dyslexia samples revealed that rs133885 was a genome-wide significant marker for mathematical abilities\((P_{comb}=7.71 x 10^{-10}, n=699)\), with an effect size of 4.87%. This association was also found in a sample from the general population (P=0.048, n=1080), albeit with a lower effect size. The identified variant encodes an amino-acid substitution in MYO18B, a protein with as yet unknown functions in the brain. As areas of the parietal cortex, in particular the intraparietal sulcus (IPS), are involved in numerical processing in humans, we investigated whether rs133885 was associated with IPS morphology using structural magnetic resonance imaging data from 79 neuropsychiatrically healthy adults. Carriers of the MYO18B risk-genotype displayed a significantly lower depth of the right IPS. This validates the identified association between rs133885 and mathematical disability at the level of a specific intermediate phenotype. KW - disability KW - sulcal morphology KW - prelevance KW - identification KW - brain KW - cancer KW - association KW - developmental dyscalculia KW - tumor-suppressor gene KW - correlate KW - disorders KW - dyscalculia KW - dyslexia KW - genomic imaging KW - mathematics KW - quantitative trait Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131513 N1 - Supplementary Information accompanies the paper on the Translational Psychiatry website (http://www.nature.com/tp). VL - 3 IS - e229 ER - TY - JOUR A1 - Murakawa, Yasuhiro A1 - Hinz, Michael A1 - Mothes, Janina A1 - Schuetz, Anja A1 - Uhl, Michael A1 - Wyler, Emanuel A1 - Yasuda, Tomoharu A1 - Mastrobuoni, Guido A1 - Friedel, Caroline C. A1 - Dölken, Lars A1 - Kempa, Stefan A1 - Schmidt-Supprian, Marc A1 - Blüthgen, Nils A1 - Backofen, Rolf A1 - Heinemann, Udo A1 - Wolf, Jana A1 - Scheidereit, Claus A1 - Landthaler, Markus T1 - RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-\(\kappa\)B pathway JF - Nature Communications N2 - The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNF\(\alpha\) mRNA decay via a 3'UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ~3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage-induced mRNAs, indicating a role of this RNA-binding protein in the post-transcriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of the NF-\(\kappa\)B pathway regulators such as I\(\kappa\)B\(\alpha\) and A20. RC3H1 uses ROQ and Zn-finger domains to contact a binding site in the A20 3'UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with I\(\kappa\)B kinase and NF-\(\kappa\)B activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-\(\kappa\)B pathway. KW - large gene lists KW - decay KW - identification KW - stress KW - binding protein KW - RQQ domain KW - autoimmunity KW - complex KW - degradation KW - motifs Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-151596 VL - 6 IS - 7367 ER - TY - JOUR A1 - Okoro, Chinyere K. A1 - Barquist, Lars A1 - Connor, Thomas R. A1 - Harris, Simon R. A1 - Clare, Simon A1 - Stevens, Mark P. A1 - Arends, Mark J. A1 - Hale, Christine A1 - Kane, Leanne A1 - Pickard, Derek J. A1 - Hill, Jennifer A1 - Harcourt, Katherine A1 - Parkhill, Julian A1 - Dougan, Gordon A1 - Kingsley, Robert A. T1 - Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa JF - PLoS Neglected Tropical Diseases N2 - Two lineages of Salmonella enterica serovar Typhimurium (S. Typhimurium) of multi-locus sequence type ST313 have been linked with the emergence of invasive Salmonella disease across sub-Saharan Africa. The expansion of these lineages has a temporal association with the HIV pandemic and antibiotic usage. We analysed the whole genome sequence of 129 ST313 isolates representative of the two lineages and found evidence of lineage-specific genome degradation, with some similarities to that observed in S. Typhi. Individual ST313 S. Typhimurium isolates exhibit a distinct metabolic signature and modified enteropathogenesis in both a murine and cattle model of colitis, compared to S. Typhimurium outside of the ST313 lineages. These data define phenotypes that distinguish ST313 isolates from other S. Typhimurium and may represent adaptation to a distinct pathogenesis and lifestyle linked to an-immuno-compromised human population. KW - genome sequence KW - infection KW - pathogenicity KW - children KW - disease KW - adults KW - identification KW - Escherichia coli KW - virulence Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-143779 VL - 9 IS - 3 ER - TY - JOUR A1 - Sass, Andrea M. A1 - Van Acker, Heleen A1 - Förstner, Konrad U. A1 - Van Nieuwerburgh, Filip A1 - Deforce, Dieter A1 - Vogel, Jörg A1 - Coenye, Tom T1 - Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315 JF - BMC Genomics N2 - Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. Methods: RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. Results: Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. Conclusions: Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation. KW - persistence KW - genomic islands KW - pathogen KW - identification KW - bacteria KW - small RNAs KW - translation initiation KW - cepedia complex KW - global gene expression KW - SEQ KW - resistance KW - burkholderia cenocepacia KW - biofilms KW - dRNA-Seq KW - transcription start site KW - antisense RNA Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-139748 VL - 16 IS - 775 ER -