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Optimizing ultracentrifugation conditions for DNA-based stable isotope probing (DNA-SIP)
Journal of Microbiological Methods, 2020DNA-SIP (DNA-based stable isotope probing) is increasingly being employed in soil microbial ecology to identify those microbes assimilating the 13C/15N labelled substrate. Isopycnic gradient centrifugation is the primary experimental process for conducting DNA-SIP. However, diverse centrifugal conditions have been used in various recent studies.
Huaiying Yao
exaly +3 more sources
RNA Stable Isotope Probing (RNA-SIP)
Methods in Molecular Biology, 2019Stable isotope probing is a combined molecular and isotopic technique used to probe the identity and function of uncultivated microorganisms within environmental samples. Employing stable isotopes of common elements such as carbon and nitrogen, RNA-SIP exploits an increase in the buoyant density of RNA caused by the active metabolism and incorporation ...
Benjamin Moreira-Grez +2 more
exaly +3 more sources
Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS
Methods in Molecular Biology, 2019Chip-SIP is a stable isotope probing (SIP) method for linking microbial identity and function in mixed communities and is capable of analyzing multiple isotopes (13C, 15N, and 18O) simultaneously. This method uses a high-density microarray to separate taxon-specific 16S (or 18S) rRNA genes and a high sensitivity magnetic sector secondary ion mass ...
Peter Weber +2 more
exaly +4 more sources
Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP
Methods in Molecular Biology, 2019DNA stable isotope probing (DNA-SIP) allows for the identification of microbes that assimilate isotopically labeled substrates into DNA. Here we describe the analysis of sequencing data using the multiple window high-resolution DNA-SIP method (MW-HR-SIP).
Samuel Barnett +2 more
exaly +4 more sources
Analytical and Bioanalytical Chemistry, 2013
The method of protein-based stable isotope probing (protein-SIP) has previously been shown to allow the modeling of carbon fluxes in microbial communities, thus tackling one of the key questions in microbial ecology. The method allows the analysis of stable isotope distribution in peptides, revealing metabolic activities of the species present in an ...
Jana Seifert +2 more
exaly +4 more sources
The method of protein-based stable isotope probing (protein-SIP) has previously been shown to allow the modeling of carbon fluxes in microbial communities, thus tackling one of the key questions in microbial ecology. The method allows the analysis of stable isotope distribution in peptides, revealing metabolic activities of the species present in an ...
Jana Seifert +2 more
exaly +4 more sources
Water Research, 2018
Stable isotope probing (SIP) is a cultivation-independent approach identifying the functional microbes in their natural habitats, possibly linking their identities to functions. DNA-SIP is well-established but suffers from the shift of 12C-DNA into the heavy DNA (13C-DNA) fraction, which significantly reduces the resolution and accuracy. In this study,
Dayi Zhang, Gan Zhang, Chunling Luo
exaly +3 more sources
Stable isotope probing (SIP) is a cultivation-independent approach identifying the functional microbes in their natural habitats, possibly linking their identities to functions. DNA-SIP is well-established but suffers from the shift of 12C-DNA into the heavy DNA (13C-DNA) fraction, which significantly reduces the resolution and accuracy. In this study,
Dayi Zhang, Gan Zhang, Chunling Luo
exaly +3 more sources
Chemical Engineering Journal, 2018
Abstract The effect of electron acceptors on denitrifying phosphorus (P) removal and its community structures in A2O process treating domestic wastewater was investigated using DNA based stable-isotope probing (DNA-SIP). Stable denitrifying P removal in anoxic zone of A2O process was achieved with an average denitrifying P removal efficiency of 72 ...
Wei Zeng
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Abstract The effect of electron acceptors on denitrifying phosphorus (P) removal and its community structures in A2O process treating domestic wastewater was investigated using DNA based stable-isotope probing (DNA-SIP). Stable denitrifying P removal in anoxic zone of A2O process was achieved with an average denitrifying P removal efficiency of 72 ...
Wei Zeng
exaly +2 more sources
Proteomics, 2011
AbstractThe detection of induced proteins after introduction of specific substrates in culture is of high interest for a comparative description of organisms growing under different conditions. In this study, protein‐based stable isotope probing (Protein‐SIP) is used for a fast and reliable detection of newly synthesized proteins in a substrate shift ...
Frank Schmidt +2 more
exaly +3 more sources
AbstractThe detection of induced proteins after introduction of specific substrates in culture is of high interest for a comparative description of organisms growing under different conditions. In this study, protein‐based stable isotope probing (Protein‐SIP) is used for a fast and reliable detection of newly synthesized proteins in a substrate shift ...
Frank Schmidt +2 more
exaly +3 more sources
Applications of DNA/RNA-stable isotope probing (SIP) in environmental microbiology
Methods in Microbiology, 2021Huaiying Yao
exaly +2 more sources