Dominik Jäger

Prospective genome and transcriptome sequencing in advanced-stage neuroendocrine neoplasms

Leonidas Apostolidis, Simon Kreutzfeldt, Małgorzata Oleś, Laura Gieldon et autres

Background: Therapeutic options for neuroendocrine neoplasms (NEN) are limited. Within the NCT/DKTK-MASTER precision oncology trial, we apply prospective whole-genome (WGS), whole-exome (WES), and transcriptome sequencing (TS) in a wide range of solid tumors to evaluate the feasibility of optimizing treatment by deep …

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sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1

Daniela Prasse, Konrad U. Förstner, Dominik Jäger, Rolf Backofen et autres

Trans-encoded sRNA154 is exclusively expressed under nitrogen (N)-deficiency in Methanosarcina mazei strain Gö1. The sRNA154 deletion strain showed a significant decrease in growth under N-limitation, pointing toward a regulatory role of sRNA154 in N-metabolism. Aiming to elucidate its regulatory function we characterized …

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Small regulatory RNAs in Archaea

Julia Babski, Lisa‐Katharina Maier, Ruth Heyer, Katharina Jaschinski et autres

Small regulatory RNAs (sRNAs) are universally distributed in all three domains of life, Archaea, Bacteria, and Eukaryotes. In bacteria, sRNAs typically function by binding near the translation start site of their target mRNAs and thereby inhibit or activate translation. In eukaryotes, miRNAs …

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Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

Dominik Jäger, Konrad U. Förstner, Cynthia M. Sharma, Thomas J. Santangelo et autres

BACKGROUND: Prokaryotes have relatively small genomes, densely-packed with protein-encoding sequences. RNA sequencing has, however, revealed surprisingly complex transcriptomes and here we report the transcripts present in the model hyperthermophilic Archaeon, Thermococcus kodakarensis, under different physiological conditions. RESULTS: Sequencing cDNA libraries, generated from …

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Two CRISPR-Cas systems inMethanosarcina mazeistrain Gö1 display common processing features despite belonging to different types I and III

Lisa Nickel, Katrin Weidenbach, Dominik Jäger, Rolf Backofen et autres

The clustered regularly interspaced short palindromic repeats (CRISPR) system represents a highly adaptive and heritable defense system against foreign nucleic acids in bacteria and archaea. We analyzed the two CRISPR-Cas systems in Methanosarcina mazei strain Gö1. Although belonging to different subtypes (I-B …

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An archaeal sRNA targeting cis - and trans -encoded mRNAs via two distinct domains

Dominik Jäger, Sandy R. Pernitzsch, Andreas S. Richter, Rolf Backofen et autres

We report on the characterization and target analysis of the small (s)RNA(162) in the methanoarchaeon Methanosarcina mazei. Using a combination of genetic approaches, transcriptome analysis and computational predictions, the bicistronic MM2441-MM2440 mRNA encoding the transcription factor MM2441 and a protein of unknown …

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Small RNAs for defence and regulation in archaea

Anita Marchfelder, Susan M. Fischer, Jutta Brendel, Britta Stoll et autres

Non-coding RNAs are key players in many cellular processes within organisms from all three domains of life. The range and diversity of small RNA functions beyond their involvement in translation and RNA processing was first recognized for eukaryotes and bacteria. Since then, …

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Archaea Employ Small RNAs as Regulators

Ruth A. Schmitz, Dominik Jäger, Angelika Jellen-Ritter, Julia Babski et autres

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Establishing a Markerless Genetic Exchange System forMethanosarcina mazeiStrain Gö1 for Constructing Chromosomal Mutants of Small RNA Genes

Claudia Ehlers, Dominik Jäger, Ruth A. Schmitz

A markerless genetic exchange system was successfully established in Methanosarcina mazei strain Gö1 using the hpt gene coding for hypoxanthine phosphoribosyltransferase. First, a chromosomal deletion mutant of the hpt gene was generated conferring resistance to the purine analog 8-aza-2,6-diaminopurine (8-ADP). The nonreplicating …

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Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability

Dominik Jäger, Cynthia M. Sharma, J. Thomsen, Claudia Ehlers et autres

Methanosarcina mazei and related mesophilic archaea are the only organisms fermenting acetate, methylamines, and methanol to methane and carbon dioxide, contributing significantly to greenhouse gas production. The biochemistry of these metabolic processes is well studied, and genome sequences are available, yet little …

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Elastic Registration of Functional MRI Data to Sensorimotor Cortex

Tonio Ball, Isabella Mutschler, Dominik Jäger, M. Otte et autres

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Evaluation of Transgenic Poplars Over‐Expressing Enzymes of Glutathione Synthesis for Phytoremediation of Cadmium

Anna Kopřivová, Stanislav Kopřiva, Dominik Jäger, Britta Will et autres

Abstract: Recently, phytoremediation of soils polluted with heavy metals has received a lot of attention. Since glutathione (GSH) and its derivatives (e.g., phytochelatins) play a major role in plant defence against environmental pollutants, we tested the effects of over‐expression of bacterial genes …

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