Relevant bibliographies by topics / Protein-Based Stable Isotope Probing

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Academic literature on the topic 'Protein-Based Stable Isotope Probing'

Author: Grafiati
Published: 1 July 2021
Last updated: 6 February 2022

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Journal articles on the topic "Protein-Based Stable Isotope Probing"

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Jehmlich, Nico, Frank Schmidt, Martin Taubert, Jana Seifert, Felipe Bastida, Martin von Bergen, Hans-Hermann Richnow, and Carsten Vogt. "Protein-based stable isotope probing." Nature Protocols 5, no. 12 (November 18, 2010): 1957–66. http://dx.doi.org/10.1038/nprot.2010.166.

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Seifert, Jana, Martin Taubert, Nico Jehmlich, Frank Schmidt, Uwe Völker, Carsten Vogt, Hans-Hermann Richnow, and Martin von Bergen. "Protein-based stable isotope probing (protein-SIP) in functional metaproteomics." Mass Spectrometry Reviews 31, no. 6 (March 15, 2012): 683–97. http://dx.doi.org/10.1002/mas.21346.

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Hungate, Bruce A., Rebecca L. Mau, Egbert Schwartz, J. Gregory Caporaso, Paul Dijkstra, Natasja van Gestel, Benjamin J. Koch, et al. "Quantitative Microbial Ecology through Stable Isotope Probing." Applied and Environmental Microbiology 81, no. 21 (August 21, 2015): 7570–81. http://dx.doi.org/10.1128/aem.02280-15.

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ABSTRACTBacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification tostableisotopeprobing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in18O and13C composition after exposure to [18O]water or [13C]glucose. The addition of glucose increased the assimilation of18O into DNA from [18O]water. However, the increase in18O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.
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Jehmlich, Nico, Frank Schmidt, Martin von Bergen, Hans-Hermann Richnow, and Carsten Vogt. "Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures." ISME Journal 2, no. 11 (June 19, 2008): 1122–33. http://dx.doi.org/10.1038/ismej.2008.64.

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Taubert, Martin, Martin von Bergen, and Jana Seifert. "Limitations in detection of 15N incorporation by mass spectrometry in protein-based stable isotope probing (protein-SIP)." Analytical and Bioanalytical Chemistry 405, no. 12 (March 17, 2013): 3989–96. http://dx.doi.org/10.1007/s00216-013-6828-y.

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Jehmlich, Nico, Frank Schmidt, Mathias Hartwich, Martin von Bergen, Hans-Hermann Richnow, and Carsten Vogt. "Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP)." Rapid Communications in Mass Spectrometry 22, no. 18 (September 30, 2008): 2889–97. http://dx.doi.org/10.1002/rcm.3684.

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von Bergen, Martin, Nico Jehmlich, Martin Taubert, Carsten Vogt, Felipe Bastida, Florian-Alexander Herbst, Frank Schmidt, Hans-Hermann Richnow, and Jana Seifert. "Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology." ISME Journal 7, no. 10 (May 16, 2013): 1877–85. http://dx.doi.org/10.1038/ismej.2013.78.

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Bozinovski, Dragana, Steffi Herrmann, Hans-Hermann Richnow, Martin Bergen, Jana Seifert, and Carsten Vogt. "Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing." FEMS Microbiology Ecology 81, no. 1 (March 12, 2012): 134–44. http://dx.doi.org/10.1111/j.1574-6941.2012.01334.x.

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Wang, Juan, Xian Zhang, and Huaiying Yao. "Optimizing ultracentrifugation conditions for DNA-based stable isotope probing (DNA-SIP)." Journal of Microbiological Methods 173 (June 2020): 105938. http://dx.doi.org/10.1016/j.mimet.2020.105938.

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Papp, Katerina, Bruce A. Hungate, and Egbert Schwartz. "Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H218O." Applied and Environmental Microbiology 84, no. 8 (February 9, 2018): e02441-17. http://dx.doi.org/10.1128/aem.02441-17.

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ABSTRACTGrowing bacteria have a high concentration of ribosomes to ensure sufficient protein synthesis, which is necessary for genome replication and cellular division. To elucidate whether metabolic activity of soil microorganisms is coupled with growth, we investigated the relationship between rRNA and DNA synthesis in a soil bacterial community using quantitative stable isotope probing (qSIP) with H218O. Most soil bacterial taxa were metabolically active and grew, and there was no significant difference between the isotopic composition of DNA and RNA extracted from soil incubated with H218O. The positive correlation between18O content of DNA and rRNA of taxa, with a slope statistically indistinguishable from 1 (slope = 0.96; 95% confidence interval [CI], 0.90 to 1.02), indicated that few taxa made new rRNA without synthesizing new DNA. There was no correlation between rRNA-to-DNA ratios obtained from sequencing libraries and the atom percent excess (APE)18O values of DNA or rRNA, suggesting that the ratio of rRNA to DNA is a poor indicator of microbial growth or rRNA synthesis. Our results support the notion that metabolic activity is strongly coupled to cellular division and suggest that nondividing taxa do not dominate soil metabolic activity.IMPORTANCEUsing quantitative stable isotope probing of microbial RNA and DNA with H218O, we show that most soil taxa are metabolically active and grow because their nucleic acids are significantly labeled with18O. A majority of the populations that make new rRNA also grow, which argues against the common paradigm that most soil taxa are dormant. Additionally, our results indicate that relative sequence abundance-based RNA-to-DNA ratios, which are frequently used for identifying active microbial populations in the environment, underestimate the number of metabolically active taxa within soil microbial communities.
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Dissertations / Theses on the topic "Protein-Based Stable Isotope Probing"

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Smyth, Patrick. "Studying the Temporal Dynamics of the Gut Microbiota Using Metabolic Stable Isotope Labeling and Metaproteomics." Thesis, Université d'Ottawa / University of Ottawa, 2021. http://hdl.handle.net/10393/42344.

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The gut microbiome and its metabolic processes are dynamic systems. Surprisingly, our understanding of gut microbiome dynamics is limited. Here we report a metaproteomic workflow that involves protein stable isotope probing (protein-SIP) and identification/quantification of partially labeled peptides. We also developed a package, which we call MetaProfiler, that corrects for false identifications and performs phylogenetic and time series analysis for the study of microbiome dynamics. From the stool sample of five mice that were fed with 15-N hydrolysate from Ralstonia eutropha, we identified 15,297 non-redundant unlabeled peptides of which 10,839 of their heavy counterparts were quantified. These peptides revealed incorporation profiles over time that were different between and within taxa, as well as between and within clusters of orthologous groups (COGs). Our study helps unravel the complex dynamics of protein synthesis and bacterial dynamics in the mouse gut microbiome.
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Wu, Weichao [Verfasser], Kai-Uwe [Akademischer Betreuer] Hinrichs, Kai-Uwe [Gutachter] Hinrichs, and Volker [Gutachter] Thiel. "Microbial activity in marine sediment constrained via lipid-based stable isotope probing / Weichao Wu ; Gutachter: Kai-Uwe Hinrichs, Volker Thiel ; Betreuer: Kai-Uwe Hinrichs." Bremen : Staats- und Universitätsbibliothek Bremen, 2018. http://d-nb.info/1153119420/34.

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Boström, Tove. "High-throughput protein analysis using mass spectrometry-based methods." Doctoral thesis, KTH, Proteinteknologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-154513.

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In the field of proteomics, proteins are analyzed and quantified in high numbers. Protein analysis is of great importance and can for example generate information regarding protein function and involvement in disease. Different strategies for protein analysis and quan- tification have emerged, suitable for different applications. The focus of this thesis lies on protein identification and quantification using different setups and method development has a central role in all included papers. The presented research can be divided into three parts. Part one describes the develop- ment of two different screening methods for His6-tagged recombinant protein fragments. In the first investigation, proteins were purified using immobilized metal ion affinity chro- matography in a 96-well plate format and in the second investigation this was downscaled to nanoliter-scale using the miniaturized sample preparation platform, integrated selective enrichment target (ISET). The aim of these investigations was to develop methods that could work as an initial screening step in high-throughput protein production projects, such as the Human Protein Atlas (HPA) project, for more efficient protein production and purification. In the second part of the thesis, focus lies on quantitative proteomics. Protein fragments were produced with incorporated heavy isotope-labeled amino acids and used as internal standards in absolute protein quantification mass spectrometry experiments. The aim of this investigation was to compare the protein levels obtained using quanti- tative mass spectrometry to mRNA levels obtained by RNA sequencing. Expression of 32 different proteins was studied in six different cell lines and a clear correlation between protein and mRNA levels was observed when analyzing genes on an individual level. The third part of the thesis involves the antibodies generated within the HPA project. In the first investigation a method for validation of antibodies using protein immunoenrichment coupled to mass spectrometry was described. In a second study, a method was developed where antibodies were used to capture tryptic peptides from a digested cell lysate with spiked in heavy isotope-labeled protein fragments, enabling quantification of 20 proteins in a multiplex format. Taken together, the presented research has expanded the pro- teomics toolbox in terms of available methods for protein analysis and quantification in a high-throughput format.

QC 20141022

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Book chapters on the topic "Protein-Based Stable Isotope Probing"

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Jehmlich, Nico, Jana Seifert, Martin Taubert, Frank Schmidt, Carsten Vogt, Hans-Hermann Richnow, and Martin von Bergen. "Protein Stable Isotope Probing." In Stable Isotope Probing and Related Technologies, 73–95. Washington, DC: ASM Press, 2014. http://dx.doi.org/10.1128/9781555816896.ch4.

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Jia, Zhongjun, Weiwei Cao, and Marcela Hernández García. "DNA-Based Stable Isotope Probing." In Methods in Molecular Biology, 17–29. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9721-3_2.

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Jehmlich, Nico, and Martin von Bergen. "Protocol for Performing Protein Stable Isotope Probing (Protein-SIP) Experiments." In Springer Protocols Handbooks, 199–214. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/8623_2016_209.

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Jehmlich, Nico, and Martin von Bergen. "Protein-Based Stable Isotope Probing (Protein-SIP): Applications for Studying Aromatic Hydrocarbon Degradation in Microbial Communities." In Anaerobic Utilization of Hydrocarbons, Oils, and Lipids, 1–8. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-33598-8_17-1.

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Jehmlich, Nico, and Martin von Bergen. "Protein-Based Stable Isotope Probing (Protein-SIP): Applications for Studying Aromatic Hydrocarbon Degradation in Microbial Communities." In Anaerobic Utilization of Hydrocarbons, Oils, and Lipids, 277–84. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-319-50391-2_17.

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Lueders, Tillmann. "DNA- and RNA-Based Stable Isotope Probing of Hydrocarbon Degraders." In Springer Protocols Handbooks, 181–97. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/8623_2015_74.

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Weis, Severin, Sylvia Schnell, and Markus Egert. "RNA-Based Stable Isotope Probing (RNA-SIP) in the Gut Environment." In Methods in Molecular Biology, 221–31. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9721-3_17.

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Jameson, Eleanor, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J. Colin Murrell, Josh D. Neufeld, and Marc G. Dumont. "DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms." In Methods in Molecular Biology, 57–74. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6691-2_5.

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Rasche, Frank, Michael Schloter, Tillmann Lüders, and Angela Sessitsch. "DNA-Based Stable Isotope Probing for Identifying Active Bacterial Endophytes in Potato." In Molecular Microbial Ecology of the Rhizosphere, 413–21. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118297674.ch38.

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Liu, Bin, David S. Barber, and Stanley M. Stevens. "Stable Isotope Labeling with Amino Acids in Cell Culture-Based Proteomic Analysis of Ethanol-Induced Protein Expression Profiles in Microglia." In Methods in Molecular Biology, 551–65. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-458-2_35.

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