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- Noguchi, S, et al.
(author)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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In: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Journal article (peer-reviewed)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 3. |
- Banhart, S., et al.
(author)
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Identification of a new Association between Genogroup G10557 (G7072) and Cefixime Resistance by means of molecular Typing of Neisseria gonorrhoeae Isolates in Germany (2014-2017)
- 2021
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In: Der Hautarzt. - : Springer. - 0017-8470 .- 1432-1173. ; 72:Suppl. 1, s. S8-S9
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Journal article (other academic/artistic)abstract
- Hintergrund/Fragestellung: Die Behandlung von Neisseria gonorrhoeae-Infektionen ist aufgrund sich neu entwickelnder Antibiotikaresistenzen gefährdet. Folglich sind Surveillance-Programme zur Beschreibung der antimikrobiellen Resistenz (AMR) und molekularen Epidemiologie bei Gonokokken auf nationaler und internationaler Ebene dringend erfor-derlich. In Deutschland wurde hierfür im Jahr 2013 das Gonokokken-Resistenznetzwerk (GORENET) etabliert. Unser Ziel war es, die geneti-sche Diversität von N. gonorrhoeae-Isolaten in Deutschland von 2014 bis 2017 mittels NG-MAST (N. gonorrhoeae multi-antigen sequence typing) zu beschreiben.Methoden: N. gonorrhoeae-Isolate aus den Jahren 2014–2017 (n=1220; 106 aus 2014, 122 aus 2015, 511 aus 2016 und 481 aus 2017) wurden deutschlandweit eingesandt und mittels AMR-Testung und NG-MAST charakterisiert.Ergebnisse: 88,4% aller Isolate stammten von Männern, 11,2% von Frauen. Das mediane Alter lag bei 32 Jahren (Interquartalsabstand; IQA: 25–44 Jahre). Insgesamt wurden 432 verschiedene NG-MAST-Sequenztypen (STs) einschließlich 146 neuer STs detektiert. Daraus resultieren 17 verschiedene Genogruppen, welche 59,2% aller Isolate beinhalten. Genogruppen G1407 und G10557 (G7072) waren signifikant mit Cefixim-Resistenz assoziiert. Dabei sank der Anteil dieser Genogruppen von 2014–2017 von 14,2 auf 6,2% (G1407) bzw. von 6,6 auf 3,1% (G10557 (G7072)),wohingegen der Anteil mehrerer Cefixim-empfindlicher Genogruppen (G11461, von 0,0 auf 5,6%; G17420, von 0,0 auf 5,0%; und G5441, von 0,9 und 4,8%) im gleichen Zeitraum anstieg.Schlussfolgerungen: In dieser Arbeit beschreiben wir Neisseria gonorrhoeae in Deutschland als eine genetisch diverse und variable Population und identifizieren eine neue Assoziation zwischen Genogruppe G10557 (G7072) und Cefixim-Resistenz. Diese Ergebnisse unterstreichen die Bedeutung der AMR-Überwachung auf der detaillierten Ebene molekularer Typisierung. Darüber hinaus deuten unsere Daten darauf hin, dass es mit Einführung einer dualen Therapie aus Ceftriaxon und Azithromycin und dem konsekutiv verminderten Einsatz von Cefixim zu einem Rückgang von Cefixim-resistenten Stämmen gekommen ist.
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| 5. |
- Talavera-Lopez, C, et al.
(author)
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Repeat-Driven Generation of Antigenic Diversity in a Major Human Pathogen, Trypanosoma cruzi
- 2021
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In: Frontiers in cellular and infection microbiology. - : Frontiers Media SA. - 2235-2988. ; 11, s. 614665-
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Journal article (peer-reviewed)abstract
- Trypanosoma cruzi, a zoonotic kinetoplastid protozoan parasite, is the causative agent of American trypanosomiasis (Chagas disease). Having a very plastic, repetitive and complex genome, the parasite displays a highly diverse repertoire of surface molecules, with pivotal roles in cell invasion, immune evasion and pathogenesis. Before 2016, the complexity of the genomic regions containing these genes impaired the assembly of a genome at chromosomal level, making it impossible to study the structure and function of the several thousand repetitive genes encoding the surface molecules of the parasite. We here describe the genome assembly of the Sylvio X10/1 genome sequence, which since 2016 has been used as a reference genome sequence for T. cruzi clade I (TcI), produced using high coverage PacBio single-molecule sequencing. It was used to analyze deep Illumina sequence data from 34 T. cruzi TcI isolates and clones from different geographic locations, sample sources and clinical outcomes. Resolution of the surface molecule gene distribution showed the unusual duality in the organization of the parasite genome, a synteny of the core genomic region with related protozoa flanked by unique and highly plastic multigene family clusters encoding surface antigens. The presence of abundant interspersed retrotransposons in these multigene family clusters suggests that these elements are involved in a recombination mechanism for the generation of antigenic variation and evasion of the host immune response on these TcI strains. The comparative genomic analysis of the cohort of TcI strains revealed multiple cases of such recombination events involving surface molecule genes and has provided new insights into T. cruzi population structure.
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| 6. |
- Zheng, Jia, et al.
(author)
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Iridium-catalysed enantioselective formal deoxygenation of racemic alcohols via asymmetric hydrogenation
- 2019
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In: NATURE CATALYSIS. - : NATURE PUBLISHING GROUP. - 2520-1158. ; 2:12, s. 1093-1100
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Journal article (peer-reviewed)abstract
- Asymmetric hydrogenation of alkenes is one of the most powerful tools for the preparation of optically active compounds. However, to achieve high enantioselectivity, the starting olefin in most cases needs to be isomerically pure in either the cis or the trans form. Generally, most olefination protocols provide olefins as isomeric mixtures that are difficult to separate, and in many cases also generate lots of waste. In contrast, the synthesis of racemic alcohols is straightforward and highly atom-efficient, with products that are easier to purify. Here, we describe a strategy that enables rapid access to chiral alkanes via enantioconvergent formal deoxygenation of racemic alcohols. Mechanistic studies indicate an Ir-mediated elimination of water and subsequent in situ hydrogenation. This approach allows rapid and efficient assembly of chiral intermediates and is exemplified in the total synthesis of antidepressant sertraline and sigma(2) receptor PB 28.
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