@article{AdemmerHornQuast2022,
  author    = {Ademmer, Martin and Horn, Wolfram and Quast, Josefine},
  title     = {Stock market dynamics and the relative importance of domestic, foreign, and common shocks},
  series = {International Journal of Finance \& Economics},
  volume    = {27},
  journal   = {International Journal of Finance \& Economics},
  number    = {4},
  doi       = {10.1002/ijfe.2194},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-225729},
  pages     = {3911 -- 3923},
  year      = {2022},
  abstract  = {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.},
  language  = {en}
}
@article{AsciertoWorschechYuetal.2011,
  author    = {Ascierto, Maria Libera and Worschech, Andrea and Yu, Zhiya and Adams, Sharon and Reinboth, Jennifer and Chen, Nanhai G and Pos, Zoltan and Roychoudhuri, Rahul and Di Pasquale, Giovanni and Bedognetti, Davide and Uccellini, Lorenzo and Rossano, Fabio and Ascierto, Paolo A and Stroncek, David F and Restifo, Nicholas P and Wang, Ena and Szalay, Aladar A and Marincola, Francesco M},
  title     = {Permissivity of the NCI-60 cancer cell lines to oncolytic Vaccinia Virus GLV-1h68},
  series = {BMC Cancer},
  volume    = {11},
  journal   = {BMC Cancer},
  number    = {451},
  doi       = {10.1186/1471-2407-11-451},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-141503},
  pages     = {1-14},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Bergelt2007,
  author    = {Bergelt, Steffen},
  title     = {Morphologische und DNA-analytische Untersuchungen am Spurenmaterial Haar},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-23155},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2007},
  abstract  = {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 gr{\"o}ßter Sicherheit zu beantworten. Humane Kopfhaut wurde aus der occipitalen Region entnommen. Nach ausgew{\"a}hlten Fixationen wurden die Gewebeschnitte mit der H{\"a}matoxylin-Eosin- sowie der Methylgr{\"u}n-Pyronin-F{\"a}rbung behandelt. Morphologische Hinweise auf die Existenz von Cytoplasmastrukturen, die mit Nukleins{\"a}uren assoziiert sein k{\"o}nnten, 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 Nukleins{\"a}uren schließen lassen. Des Weiteren wurden mit geeigneten Verfahren die Extraktion von DNA aus telogenen Haarwurzeln und Haarsch{\"a}ften durchgef{\"u}hrt. Mit der Chelex-100-Extraktionsmethode und der Kombination der anschließenden Reinigung der Extrakte mit Diatomeenerde, war der DNA-Nachweis in mehr als die H{\"a}lfte der untersuchten Haarwurzeln m{\"o}glich. Die Phenol-Chloroform-Extraktionsmethode erlaubte einen erfolgreichen DNA-Nachweis in durchschnittlich 14,3 \% der F{\"a}lle. Zur Typisierung der genomen DNA wurde die Polymerasen-Ketten-Reaktion (PCR) angewandt. Untersucht wurde dabei zwei in der forensischen Praxis g{\"a}ngige STR-Systeme, zum einen das auf Chromosom 5 lokalisierte System HumACTBP2 (SE33) zum anderen das auf Chromosom 12 gelegene System HumVWA. Zus{\"a}tzlich wurde das Geschlechtsbestimmungssystem HumAMEL X/Y in die Untersuchung mit einbezogen. Die Ergebnisse lassen zuk{\"u}nftig auf ein gezieltes Vorgehen und die Anwendung spezieller Methoden f{\"u}r die Individualtypisierung am Spurenmaterial Haar hoffen. Da Keratinisierungsprozesse im wachsendem Haar wohl eine Schl{\"u}sselrolle {\"u}ber das Schicksal der Zellkerne und der darin enthaltenen Degenerationsgrad der DNA spielen, sollten sich zuk{\"u}nftige Untersuchungen in der Rechtsmedizin verst{\"a}rkt dieser Thematik widmen.},
  language  = {de}
}
@article{DeGiorgiBuonaguroWorschechetal.2013,
  author    = {De Giorgi, Valeria and Buonaguro, Luigi and Worschech, Andrea and Tornesello, Maria Lina and Izzo, Francesco and Marincola, Francesco M. and Wang, Ena and Buonaguro, Franco M.},
  title     = {Molecular Signatures Associated with HCV-Induced Hepatocellular Carcinoma and Liver Metastasis},
  series = {PLoS ONE},
  volume    = {8},
  journal   = {PLoS ONE},
  number    = {2},
  doi       = {10.1371/journal.pone.0056153},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131155},
  pages     = {e56153},
  year      = {2013},
  abstract  = {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.},
  language  = {en}
}
@article{FellerThomKochetal.2013,
  author    = {Feller, Tatjana and Thom, Pascal and Koch, Natalie and Spiegel, Holger and Addai-Mensah, Otchere and Fischer, Rainer and Reimann, Andreas and Pradel, Gabriele and Fendel, Rolf and Schillberg, Stefan and Scheuermayer, Matthias and Schinkel, Helga},
  title     = {Plant-Based Production of Recombinant Plasmodium Surface Protein Pf38 and Evaluation of its Potential as a Vaccine Candidate},
  series = {PLOS ONE},
  volume    = {8},
  journal   = {PLOS ONE},
  number    = {11},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0079920},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-128221},
  pages     = {e79920},
  year      = {2013},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Gebhard2009,
  author    = {Gebhard, Sebastian},
  title     = {DNA-analytische Untersuchungen an frischen und gelagerten Z{\"a}hnen},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-46462},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {In dieser Arbeit wurde {\"u}berpr{\"u}ft, inwieweit sich verschiedene Lagerungsbedingungen von Z{\"a}hnen auf die Verwertbarkeit von DNA im Zahninneren zur Gewinnung eines genetischen Fingerabdrucks auswirken. Die Untersuchungen an frisch extrahierten Z{\"a}hnen ließen erkennen, dass die in dieser Arbeit verwendeten Methoden und DNA-Kits f{\"u}r die weitere Analyse der den unterschiedlichen Bedingungen ausgesetzten Z{\"a}hne geeignet sind. Asensible Z{\"a}hne weisen bereits bei der Zahnextraktion Zeichen von Degradation auf. Dagegen ist der kari{\"o}se Zerst{\"o}rungsgrad an sich noch kein Ausschlusskriterium. Bei wurzelkanalbehandelten Z{\"a}hnen konnten nur Systeme mit sehr kurzen Amplifikationsprodukten typisiert werden. Sie waren f{\"u}r eine genetische Identifizierung kaum geeignet. Bei der Analyse im Erdreich vergrabener Z{\"a}hne 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 Z{\"a}hnen. Bis zu einem halben Jahr nach Versuchsbeginn konnte eine Typisierung aller Systeme durchgef{\"u}hrt werden. Erst nach einem Jahr war die Degradation so weit vorangeschritten, dass große Systeme keine Typisierung mehr erlaubten. Bei Z{\"a}hnen, die der Sonnenstrahlung einen Monat ausgesetzt waren, war es dagegen problemlos m{\"o}glich, einen vollst{\"a}ndigen 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 Z{\"a}hne aus dem Sektionsgut des Instituts f{\"u}r Rechtsmedizin W{\"u}rzburg lieferten unterschiedliche Ergebnisse, sodass hierzu keine generelle Aussage gemacht werden kann. Bei der Behandlung der Z{\"a}hne mit Hitze von 200 °C konnte die DNA nur begrenzte Zeit vor Degradation gesch{\"u}tzt werden. Bereits nach einer halben Stunde waren große Teile der Multiplex-Kits nicht mehr f{\"u}r eine Typisierung verwertbar. Das STR-System SE33 konnte allerdings noch ermittelt werden. Die Entnahmen zu sp{\"a}teren Zeitpunkten (60 min, 90 min und 120 min) lieferten fast nur noch einzelne STRSysteme. Eine knapp 30-j{\"a}hrige trockene Lagerung von Z{\"a}hnen in einem Schrank mit Schutz vor Sonneneinstrahlung schadete der DNA-Analysierbarkeit kaum. Ein vollst{\"a}ndiger Ausfall aller Systeme musste bei den Zahnproben von der Ausgrabung in Katzwang verzeichnet werden. Die Z{\"a}hne dieser 380 bis 550 Jahre alten Sch{\"a}del lieferten kein auswertbares DNA-Material mehr. Ebenso konnte mit diesen Untersuchungsmethoden aus den 2300 bis 2800 Jahre alten Z{\"a}hnen aus der Dietersbergh{\"o}hle kein analysierbares DNA-Material gewonnen werden. Es zeigte sich, dass Lagerbedingungen einen entscheidenden Einfluss auf die DNA-Qualit{\"a}t aus{\"u}ben. Als DNA-sch{\"a}digende Einfl{\"u}sse k{\"o}nnen neben Mikroorganismen und Feuchtigkeit insbesondere UV-Strahlung und Hitze gelten. Der Faktor Zeit spielt bei g{\"u}nstigen Lagerbedingungen eine untergeordnete Rolle.},
  subject      = {DNA-typing},
  language  = {de}
}
@phdthesis{Goehtz2006,
  author    = {Goehtz, Florian},
  title     = {DNA-analytische Identifizierung unter Verwendung von frischem und gelagertem Skelettmaterial},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-18205},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2006},
  abstract  = {Der DNA-analytischen Untersuchung von frischem und gelagertem Skelettmaterial kommt bei der Identifikation unbekannter Toter zunehmende Bedeutung zu, insbesondere in F{\"a}llen, in denen nur Skelett{\"u}berreste einer DNA-Analyse zur Verf{\"u}gung stehen. Zur Aufkl{\"a}rung der praktischen Durchf{\"u}hrbarkeit 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 (gesch{\"a}tzte Liegezeit zwischen 10 und {\"u}ber 200 Jahren). Die DNA-Extraktion wurde mittels reversibler DNA-Bindung an einer Silica-Membran durchgef{\"u}hrt. Die Typisierung erfolgte im Rahmen eines Multiplex-PCR-Ansatzes unter Amplifizierung von neun STR-Loci und dem Amelogenin-Locus. Zus{\"a}tzlich wurden drei besonders kurze, sog. vs-STRs bestimmt und exemplarisch f{\"u}r zwei Proben Bereiche des mt-Genoms sequenziert. Bei der Multiplex-Analyse ließ sich f{\"u}r 13 der 14 aus Sektionsgut gewonnenen Proben (93 \%) ein komplettes, reproduzierbares Allelprofil gewinnen, an einer der Proben konnte nur eine molekulare Geschlechtszuordnung durchgef{\"u}hrt werden. Ebenso konnten alle drei vs-STR-Loci f{\"u}r 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 f{\"u}hrte im Fall der {\"a}ltesten Probe zur Typisierung eines der drei Loci (TPOXvs). Bei zwei Proben, welche im Rahmen der nukle{\"a}ren 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. Umwelteinfl{\"u}sse 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 unver{\"a}ndert unbefriedigenden Typisierungsergebnisse bei der Analyse {\"a}lteren Knochenmaterials unterstreichen jedoch die Notwendigkeit der Weiterentwicklung zuverl{\"a}ssiger und effektiver Extraktions- und Aufreinigungsverfahren.},
  language  = {de}
}
@phdthesis{Grimm2000,
  author    = {Grimm, Dorothee},
  title     = {Entwicklung von neuen Nachweismethoden f{\"u}r Legionellen und Am{\"o}ben und ihre Anwendung in {\"o}kologischen Studien},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1351},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2000},
  abstract  = {Legionella pneumophila wurde 1976 als Erreger der Legionellose, einer schweren Form von Lungenentz{\"u}ndung, identifiziert. Die inzwischen 42 Arten umfassende Gattung ist weltweit in aquatischen Biotopen verbreitet. Die Bakterien leben vergesellschaftet mit anderen Mikroorganismen in Biofilmen oder intrazellul{\"a}r 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. F{\"u}r die Erweiterung ihrer Habitate spielen verschiedene Umweltfaktoren eine Rolle. Eine exakte und schnelle Detektion und Identifikation der humanpathogenen Keime ist sowohl f{\"u}r die Lokalisierung der Infektionsquelle als auch f{\"u}r 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 komplement{\"a}re Zielsequenz der ribosomalen RNA. In der vorliegenden Arbeit wurde f{\"u}r die in situ Hybridisierung eine neue 16S rRNA-gerichtete Sonde LEGPNE1 entwickelt, die spezifisch ist f{\"u}r L. pneumophila. In Versuchsreihen mit verschiedenen Bakterienkulturen wurden die Spezifit{\"a}t und Sensitivit{\"a}t der Gensonde ermittelt. LEGPNE1 erwies sich als artspezifisch und erkannte alle getesteten L. pneumophila-St{\"a}mme, ungeachtet ihrer Serogruppe. Nicht-pneumophila-Referenzst{\"a}mme hybridisierten nicht mit der Sonde, ein einziger Basenaus-tausch in der Sequenz war f{\"u}r diese Unterscheidung ausreichend. Die Anwendung der Sonde wurde auch in Am{\"o}ben-Infektionsassays und Umweltproben erfolgreich durchgef{\"u}hrt. Unterschiedliche, intrazellul{\"a}r vorliegende Bakterien wurden von der Sonde spezifisch erkannt. Eine in situ Dokumentation der Infektions- und Vermehrungsrate war damit m{\"o}glich. Durch die meist fakultativ intrazellul{\"a}re 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 Wirtsam{\"o}ben Hartmannella und Naegleria ausgedehnt. Basierend auf Sequenzvergleichen wurden die gattungsspezifischen 18S rRNA-gerichteten Sonden HART498 und NAEG1088 konstruiert und in Versuchsreihen mit Referenzst{\"a}mmen bei steigender Stringenz etabliert. Mit ihrer Hilfe konnten die Ergebnisse der zeit- und arbeitsaufwendigen Determination unbekannter Am{\"o}ben anhand morphologischer Merkmale best{\"a}tigt werden. In situ Hybridisierungen mit einer Kombination von 16S und 18S rRNA-gerichteten Sonden wurden in Am{\"o}ben-Infektionsassays mit Hartmannella vermiformis und L. pneumophila erfolgreich durchgef{\"u}hrt. Eine Interferenz der Sonden fand nicht statt. Die in situ Untersuchung der Struktur und Funktion komplexer mikrobieller Lebensgemeinschaften erfordert eine kultivierungsunabh{\"a}ngige und hochaufl{\"o}sende Methode, wie sie die fluoreszierende in situ Hybridisierung darstellt. Mit dem Ziel, m{\"o}gliche Pr{\"a}ferenzen der Legionellen f{\"u}r bestimmte Parameter, wie pH, Temperatur, elektrische Leitf{\"a}higkeit, Str{\"o}mungsverh{\"a}ltnisse, 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 gegen{\"u}ber den gemessenen Parametern. Sie waren in nahezu allen beprobten Gew{\"a}ssern zu finden und ließen sich unabh{\"a}ngig 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 Gew{\"a}ssern wurde außerdem das Vorkommen von Am{\"o}ben untersucht. Es konnten insgesamt acht Am{\"o}bengattungen isoliert, kultiviert und bestimmt werden. Dominierend waren St{\"a}mme des nicht humanpathogenen Naegleria gruberi-Komplexes, Echinamoeba spp. und Echinamoeba-like Am{\"o}ben. 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 Am{\"o}ben best{\"a}tigt werden. Auch die Am{\"o}ben zeigten keine Pr{\"a}ferenzen bez{\"u}glich der in den Standorten gemessenen Wasserparameter. Die in situ Hybridisierung mit rRNA-gerichteten Gensonden erlaubt eine Analyse der Struktur und Dynamik von Bioz{\"o}nosen, erm{\"o}glicht aber keine Aussage {\"u}ber die speziellen Aktivit{\"a}ten der nachgewiesenen Bakterien. Eine L{\"o}sung hierf{\"u}r k{\"o}nnte der spezifische in situ Nachweis von mRNA-Molek{\"u}len darstellen. Ein Problem hierbei stellt ihre, im Vergleich zu anderen Molek{\"u}len 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 F{\"a}llen eine Signalamplifikation n{\"o}tig, um ein detektierbares Signal zu erhalten. In dieser Arbeit sollte die f{\"u}r 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 gew{\"u}nschte Spezifit{\"a}t. Diese Ergebnisse stellen jedoch eine wichtige Grundlage f{\"u}r zuk{\"u}nftige Experimente dar.},
  subject      = {Legionella pneumophila},
  language  = {de}
}
@article{GuptaSrivastavaOsmanogluetal.2020,
  author    = {Gupta, Shishir K. and Srivastava, Mugdha and Osmanoglu, Oezge and Dandekar, Thomas},
  title     = {Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs},
  series = {Scientific Reports},
  volume    = {10},
  journal   = {Scientific Reports},
  number    = {1},
  doi       = {10.1038/s41598-020-59344-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229406},
  year      = {2020},
  abstract  = {Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational methods of PPI determination can accelerate biological discovery by identifying the most promising interacting pairs of proteins and by assessing the reliability of identified PPIs. Here we present a first in-depth study describing a global view of the ant Camponotus floridanus interactome. Although several ant genomes have been sequenced in the last eight years, studies exploring and investigating PPIs in ants are lacking. Our study attempts to fill this gap and the presented interactome will also serve as a template for determining PPIs in other ants in future. Our C. floridanus interactome covers 51,866 non-redundant PPIs among 6,274 proteins, including 20,544 interactions supported by domain-domain interactions (DDIs), 13,640 interactions supported by DDIs and subcellular localization, and 10,834 high confidence interactions mediated by 3,289 proteins. These interactions involve and cover 30.6\% of the entire C. floridanus proteome.},
  language  = {en}
}
@article{HoffmannSchmidtKeimetal.2011,
  author    = {Hoffmann, Linda S and Schmidt, Peter M and Keim, Yvonne and Hoffmann, Carsten and Schmidt, Harald H H W and Stasch, Johannes-Peter},
  title     = {Fluorescence Dequenching Makes Haem-Free Soluble Guanylate Cyclase Detectable in Living Cells},
  series = {PLOS ONE},
  volume    = {6},
  journal   = {PLOS ONE},
  number    = {8},
  doi       = {10.1371/journal.pone.0023596},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139631},
  pages     = {e23596},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@article{JellinghausMatinUrbanetal.2020,
  author    = {Jellinghaus, K. and Matin, S. and Urban, P. and Bohnert, M. and Jantz, R.},
  title     = {Study of the K-S distance on skulls from different modern populations for sex and ancestry determination},
  series = {Rechtsmedizin},
  volume    = {30},
  journal   = {Rechtsmedizin},
  issn      = {0937-9819},
  doi       = {10.1007/s00194-020-00426-9},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-235185},
  pages     = {451-457},
  year      = {2020},
  abstract  = {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.},
  language  = {en}
}
@article{KernAgarwalHuberetal.2014,
  author    = {Kern, Selina and Agarwal, Shruti and Huber, Kilian and Gehring, Andre P. and Str{\"o}dke, Benjamin and Wirth, Christine C. and Br{\"u}gl, Thomas and Abodo, Liane Onambele and Dandekar, Thomas and Doerig, Christian and Fischer, Rainer and Tobin, Andrew B. and Alam, Mahmood M. and Bracher, Franz and Pradel, Gabriele},
  title     = {Inhibition of the SR Protein-Phosphorylating CLK Kinases of Plasmodium falciparum Impairs Blood Stage Replication and Malaria Transmission},
  series = {PLOS ONE},
  volume    = {9},
  journal   = {PLOS ONE},
  number    = {9},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0105732},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-115405},
  pages     = {e105732},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{KrauseWeber2018,
  author    = {Krause, Stefan and Weber, Silvana},
  title     = {Lift me up by looking down: social comparison effects of narratives},
  series = {Frontiers in Psychology},
  volume    = {9},
  journal   = {Frontiers in Psychology},
  issn      = {1664-1078},
  doi       = {10.3389/fpsyg.2018.01889},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-190624},
  year      = {2018},
  abstract  = {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.},
  language  = {en}
}
@article{KrehanHeubeckMenzeletal.2012,
  author    = {Krehan, Mario and Heubeck, Christian and Menzel, Nicolas and Seibel, Peter and Sch{\"o}n, Astrid},
  title     = {RNase MRP RNA and RNase P activity in plants are associated with a Pop1p containing complex},
  series = {Nucleic Acids Research},
  volume    = {40},
  journal   = {Nucleic Acids Research},
  number    = {16},
  doi       = {10.1093/nar/gks476},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-130648},
  pages     = {7956- 7966},
  year      = {2012},
  abstract  = {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.},
  language  = {en}
}
@article{KraemerBijnensStoerketal.2015,
  author    = {Kr{\"a}mer, Johannes and Bijnens, Bart and St{\"o}rk, Stefan and Ritter, Christian O. and Liu, Dan and Ertl, Georg and Wanner, Christoph and Weidemann, Frank},
  title     = {Left ventricular geometry and blood pressure as predictors of adverse progression of Fabry cardiomyopathy},
  series = {PLoS ONE},
  volume    = {10},
  journal   = {PLoS ONE},
  number    = {11},
  doi       = {10.1371/journal.pone.0140627},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-145131},
  pages     = {e0140627},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@article{LandoEndesfelderBergeretal.2012,
  author    = {Lando, David and Endesfelder, Ulrike and Berger, Harald and Subramanian, Lakxmi and Dunne, Paul D. and McColl, James and Klenerman, David and Carr, Antony M. and Sauer, Markus and Allshire, Robin C. and Heilemann, Mike and Laue, Ernest D.},
  title     = {Quantitative single-molecule microscopy reveals that CENP-A\(^{Cnp1}\) deposition occurs during G2 in fission yeast},
  series = {Open Biology},
  volume    = {2},
  journal   = {Open Biology},
  number    = {120078},
  doi       = {10.1098/rsob.120078},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134682},
  year      = {2012},
  abstract  = {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.},
  language  = {en}
}
@article{LudwigSaemannAlexanderetal.2013,
  author    = {Ludwig, K. U. and S{\"a}mann, P. and Alexander, M. and Becker, J. and Bruder, J. and Moll, K. and Spieler, D. and Czisch, M. and Warnke, A. and Docherty, S. J. and Davis, O. S. P. and Plomin, R. and N{\"o}then, M. M. and Landerl, K. and M{\"u}ller-Myhsok, B. and Hoffmann, P. and Schumacher, J. and Schulte-K{\"o}rne, G. and Czamara, D.},
  title     = {A common variant in Myosin-18B contributes to mathematical abilities in children with dyslexia and intraparietal sulcus variability in adults},
  series = {Translational Psychiatry},
  volume    = {3},
  journal   = {Translational Psychiatry},
  number    = {e229},
  doi       = {10.1038/tp.2012.148},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131513},
  year      = {2013},
  abstract  = {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.},
  language  = {en}
}
@article{MurakawaHinzMothesetal.2015,
  author    = {Murakawa, Yasuhiro and Hinz, Michael and Mothes, Janina and Schuetz, Anja and Uhl, Michael and Wyler, Emanuel and Yasuda, Tomoharu and Mastrobuoni, Guido and Friedel, Caroline C. and D{\"o}lken, Lars and Kempa, Stefan and Schmidt-Supprian, Marc and Bl{\"u}thgen, Nils and Backofen, Rolf and Heinemann, Udo and Wolf, Jana and Scheidereit, Claus and Landthaler, Markus},
  title     = {RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-\(\kappa\)B pathway},
  series = {Nature Communications},
  volume    = {6},
  journal   = {Nature Communications},
  number    = {7367},
  doi       = {10.1038/ncomms8367},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151596},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@article{OkoroBarquistConnoretal.2015,
  author    = {Okoro, Chinyere K. and Barquist, Lars and Connor, Thomas R. and Harris, Simon R. and Clare, Simon and Stevens, Mark P. and Arends, Mark J. and Hale, Christine and Kane, Leanne and Pickard, Derek J. and Hill, Jennifer and Harcourt, Katherine and Parkhill, Julian and Dougan, Gordon and Kingsley, Robert A.},
  title     = {Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa},
  series = {PLoS Neglected Tropical Diseases},
  volume    = {9},
  journal   = {PLoS Neglected Tropical Diseases},
  number    = {3},
  doi       = {10.1371/journal.pntd.0003611},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143779},
  pages     = {e0003611},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@article{SassVanAckerFoerstneretal.2015,
  author    = {Sass, Andrea M. and Van Acker, Heleen and F{\"o}rstner, Konrad U. and Van Nieuwerburgh, Filip and Deforce, Dieter and Vogel, J{\"o}rg and Coenye, Tom},
  title     = {Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315},
  series = {BMC Genomics},
  volume    = {16},
  journal   = {BMC Genomics},
  number    = {775},
  doi       = {10.1186/s12864-015-1993-3},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139748},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}