title: Effect of rotor type on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation.
abstract: Separation of differentially isotope-labeled bacterial RNA by isopycnic density gradient centrifugation is a critical step in RNA-based stable isotope probing analyses, which help to link the structure and function of complex microbial communities. Using isotope-labeled Escherichia coli RNA, we showed that an 8 mL near-vertical rotor performed better than a 2 mL fixed-angle rotor, thereby corroborating current recommendations. Neither increased concentrations of formamide nor urea in the medium improved the separation results using the fixed-angle rotor.
authors.affiliation: a Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology & Hygiene Group, Furtwangen University, Campus Villingen-Schwenningen, Germany.
authors.forename: Elena
authors.initials: E
authors.lastname: Herrmann
authors.affiliation: a Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology & Hygiene Group, Furtwangen University, Campus Villingen-Schwenningen, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Koch
authors.affiliation: b Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany.
authors.forename: Christian U
authors.initials: CU
authors.lastname: Riedel
authors.affiliation: c AgResearch Ltd., Grasslands Research Centre, Palmerston North 4442, New Zealand.
authors.forename: Wayne
authors.initials: W
authors.lastname: Young
authors.affiliation: a Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology & Hygiene Group, Furtwangen University, Campus Villingen-Schwenningen, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Egert
mesh_terms: D002247:Carbon Isotopes / Q000737:chemistry / Q000378:metabolism; D002499:Centrifugation, Density Gradient / Q000295:instrumentation / Q000379:methods*; D002500:Centrifugation, Isopycnic / Q000295:instrumentation / Q000379:methods*; D004926:Escherichia coli / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D007553:Isotope Labeling; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism
chemical_list: D002247:Carbon Isotopes; D012329:RNA, Bacterial
keywords: RNA-SIP; de sondage d’isotopes stables; denaturation; dénaturation; fixed-angle rotor; near-vertical rotor; rotor quasi vertical; rotor à angle fixe; stable isotope probing; ultracentrifugation; « RNA-SIP »