Name: concentration of metabolites from low-density planktonic communities for environmental metabolomics using nuclear magnetic resonance spectroscopy
Uploaded: 2012-04-07T14:00:00
Description: Watch this Scientific Journal Video about Concentration of Metabolites from Low-density Planktonic Communities for Environmental Metabolomics using Nuclear Magnetic Resonance Spectroscopy at JoVE.com

इस शोध में भाग द्वारा समर्थित किया गया अनुदान सहायता में शिक्षा, संस्कृति, खेल, विज्ञान मंत्रालय से खोजपूर्ण (जे), अनुसंधान और वैज्ञानिक अनुसंधान (ए) (जे और एस) को चुनौती देने के लिए वैज्ञानिक अनुसंधान के लिए, और प्रौद्योगिकी, जापान . एक आरआईकेईएन fpr फैलोशिप (RCE) अतिरिक्त सहायता प्रदान की है. लेखकों डीआरएस के प्रति अपनी कृतज्ञता व्यक्त करते हैं. Eisuke Chikayama, Yasuyo Sekiyama और एनएमआर और सांख्यिकीय विश्लेषण के साथ तकनीकी सहायता के लिए ममी Okamoto.

1. फिल्टर करने के लिए तैयार extractables निकालें <ol><li> 25 मिमी व्यास .22 माइक्रोन ताकना आकार Durapore PVDF हाइड्रोफिलिक फिल्टर (Millipore) का प्रयोग करें. चिमटी का उपयोग कर एक स्वच्छ 500 मिलीलीटर Pyrex बीकर में जगह फिल्टर. आसुत जल के साथ ?...

<ol>
	<li>Bundy, J. G., Davey, M. P., Viant, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Environmental+metabolomics:+a+critical+review+and+future+perspectives.">Environmental metabolomics: a critical review and future perspectives.</a> Metabolomics. 5, 3-21 (2008).</li><li>Chikayama, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Statistical+indices+for+simultaneous+large-scale+metabolite+detections+for+a+single+NMR+spectrum.">Statistical indices for simultaneous large-scale metabolite detections for a single NMR spectrum.</a> Anal. Chem. 82, 1653-1658 (2010).</li><li>Lewis, I. A., Schommer, S. C., Markley, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=rNMR:+open+source+software+for+identifying+and+quantifying+metabolites+in+NMR+spectra.">rNMR: open source software for identifying and quantifying metabolites in NMR spectra.</a> Magn. Reson. Chem. 47, S123-S126 (2009).</li><li>Li, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Symbiotic+gut+microbes+modulate+human+metabolic+phenotypes.">Symbiotic gut microbes modulate human metabolic phenotypes.</a> Proc. Natl. Acad. Sci. U.S.A. 105, 2117-2122 (2008).</li><li>Mochida, K., Furuta, T., Ebana, K., Shinozaki, K., Kikuchi, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Correlation+exploration+of+metabolic+and+genomic+diversity+in+rice.">Correlation exploration of metabolic and genomic diversity in rice.</a> BMC Genomics. 10, 568 (2009).</li><li>Fukuda, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bifidobacteria+can+protect+from+enteropathogenic+infection+through+production+of+acetate.">Bifidobacteria can protect from enteropathogenic infection through production of acetate.</a> Nature. 469, 543-547 (2011).</li><li>Kikuchi, J., Hirayama, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Practical+aspects+of+stable+isotope+labeling+of+higher+plants+for+a+hetero-nuclear+multi-dimensional+NMR-based+metabolomics.">Practical aspects of stable isotope labeling of higher plants for a hetero-nuclear multi-dimensional NMR-based metabolomics.</a> Methods Mol. Biol. 358, 273-286 (2007).</li><li>Martin, F. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+top-down+systems+biology+view+of+microbiome-mammalian+metabolic+interactions+in+a+mouse+model.">A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model.</a> Mol. Syst. Biol. 3, 112 (2007).</li><li>Mahrous, E. A., Lee, R. B., Lee, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+rapid+approach+to+lipid+profiling+of+mycobacteria+using+2D+HSQC+NMR+maps.">A rapid approach to lipid profiling of mycobacteria using 2D HSQC NMR maps.</a> J. Lipid Res. 49, 455-463 (2008).</li><li>Fukuda, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+and+characterization+of+bacterial+metabolic+dynamics+with+a+novel+profiling+technique,+real-time+metabolotyping.">Evaluation and characterization of bacterial metabolic dynamics with a novel profiling technique, real-time metabolotyping.</a> PloS ONE. 4, e4893 (2009).</li><li>Date, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+monitoring+approach+for+metabolic+dynamics+in+microbial+ecosystems+using+stable-isotope-labeling+technologies.">New monitoring approach for metabolic dynamics in microbial ecosystems using stable-isotope-labeling technologies.</a> J. Biosci. Bioeng. 110, 87-93 (2010).</li><li>Nakanishi, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+omics+approach+identifies+nutrition-mediated+microbial+interactions.">Dynamic omics approach identifies nutrition-mediated microbial interactions.</a> J. Proteome Res. 10, 824-836 (2011).</li><li>Falkowski, P., Barber, R., Smetacek, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biogeochemical+controls+and+feedbacks+on+ocean+primary+production.">Biogeochemical controls and feedbacks on ocean primary production.</a> Science. 281, 200-207 (1998).</li><li>Viant, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolomics+of+aquatic+organisms:+the+new+'omics'+on+the+block.">Metabolomics of aquatic organisms: the new 'omics' on the block.</a> Mar. Ecol. Prog. Ser. 332, 301-306 (2007).</li><li>Sekiyama, Y., Chikayama, E., Kikuchi, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+a+semipolar+solvent+system+as+a+step+toward+heteronuclear+multidimensional+NMR-based+metabolomics+for+13C-labeled+bacteria,+plants,+and+animals.">Evaluation of a semipolar solvent system as a step toward heteronuclear multidimensional NMR-based metabolomics for 13C-labeled bacteria, plants, and animals.</a> Anal. Chem. 83, 719-726 (2011).</li><li>Delaglio, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NMRPipe:+A+multidimensional+spectral+processing+system+based+on+UNIX+pipes.">NMRPipe: A multidimensional spectral processing system based on UNIX pipes.</a> J. Biomol. NMR. 6, 277-293 (1995).</li><li>Wang, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automics:+an+integrated+platform+for+NMR-based+metabonomics+spectral+processing+and+data+analysis.">Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis.</a> BMC Bioinformatics. 10, 83 (2009).</li><li>Eldon, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BioMagResBank.">BioMagResBank.</a> Nucleic Acids Res. 36, D402-D408 (2007).</li><li>Sekiyama, Y., Chikayama, E., Kikuchi, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Profiling+polar+and+semipolar+plant+metabolites+throughout+extraction+processes+using+a+combined+solution-state+and+high-resolution+magic+angle+spinning+NMR+approach.">Profiling polar and semipolar plant metabolites throughout extraction processes using a combined solution-state and high-resolution magic angle spinning NMR approach.</a> Anal. Chem. 82, 1643-1652 (2011).</li></ol>

निस्पंदन और metabolite निष्कर्षण विधि यहाँ का प्रदर्शन माइक्रोबियल planktonic बायोमास के लिए पर्याप्त राशि के में एनएमआर metabolomics के लिए एकत्र होने की अनुमति देता है. जबकि जलीय घुलनशील चयापचयों का उपयोग कर KPI और 1D 1 ?...

<table border="1"><tbody><tr><td> अभिकर्मक का नाम </td><td> कंपनी </td><td> सूचीपत्र संख्या </td><td> टिप्पणियाँ </td></tr><tr><td> 0.22 माइक्रोन हाइड्रोफिलिक Durapore PVDF फिल्टर, 25 मिमी </td><td> Millipore </td><td> GVWP02500 </td><td></td></tr><tr><td> Microanalysis फ़िल्टर धारक, 25 मिमी, कांच समर्थन fritted </td><td> Millipore </td><td> XX1002500 </td><td></td></tr><tr><td> 3 जगह कई गुना, 47 मिमी, स्टेनलेस स्टील </td><td> Millipore </td><td> XX2504735 </td><td></td></tr><tr><td> 2 के.एच. पीओ 4 </td><td> Wako </td><td> 169-04,245 </td><td></td></tr><tr><td> 2 कश्मीर HPO 4 </td><td> Wako </td><td> 164-04,295 </td><td></td></tr><tr><td> ड्यूटिरियम ऑक्साइड, एच 2&gt; 90% </td><td> Campridge आइसोटोप Laboratoties </td><td> DLM - 4 </td><td></td<html> &gt; </tr><tr><td> इस के बारे </td><td> Fluka </td><td> 92,754 </td><td></td></tr><tr><td> Automill </td><td> Tokken </td><td> टी - AM4 </td><td> स्टेनलेस स्टील crushers </td></tr><tr><td> Thermomixer आराम </td><td> Eppendorf </td><td> 5355 000.011 </td><td></td></tr><tr><td> Bioruptor </td><td> Diagenode </td><td> शिक्षक - 200 </td><td></td></tr><tr><td> निर्वात बाष्पीकरण </td><td> EYELA </td><td> CVE-3100 </td><td></td></tr><tr><td> एनएमआर </td><td> Bruker </td><td> 5 मिमी TXI जांच के साथ DRX-500 </td><td></td></tr><tr><td> वर्णक्रमीय binning उपकरण </td><td> मूल रूप से विकसित </td><td> FT2DB </td><td> <a href="https://database.riken.jp/ecomics/">https://database.riken.jp/ecomics/</a> </td></tr><tr><td> Metabolite एनोटेशन उपकरण और डेटाबेस </td><td> मूल रूप से विकसित </td><td> SpinAssign </td><td>, = Nmr_search &quot;&gt; http://prime.psc.riken.jp/?action=nmr_search </td></tr></tbody></table>

concentration of metabolites from low-density planktonic communities for environmental metabolomics using nuclear magnetic resonance spectroscopy

Environmental metabolomics is an emerging field that is promoting new understanding in how organisms respond to and interact with the environment and each other at the biochemical level1. Nuclear magnetic resonance (NMR) spectroscopy is one of several technologies, including gas chromatography&#x2013;mass spectrometry (GC-MS), with considerable promise for such studies. Advantages of NMR are that it is suitable for untargeted analyses, provides structural information and spectra can be queried in quantitative and statistical manners against recently available databases of individual metabolite spectra2,3. In addition, NMR spectral data can be combined with data from other omics levels (e.g. transcriptomics, genomics) to provide a more comprehensive understanding of the physiological responses of taxa to each other and the environment4,5,6. However, NMR is less sensitive than other metabolomic techniques, making it difficult to apply to natural microbial systems where sample populations can be low-density and metabolite concentrations low compared to metabolites from well-defined and readily extractable sources such as whole tissues, biofluids or cell-cultures. Consequently, the few direct environmental metabolomic studies of microbes performed to date have been limited to culture-based or easily defined high-density ecosystems such as host-symbiont systems, constructed co-cultures or manipulations of the gut environment where stable isotope labeling can be additionally used to enhance NMR signals7,8,9,10,11,12. Methods that facilitate the concentration and collection of environmental metabolites at concentrations suitable for NMR are lacking. Since recent attention has been given to the environmental metabolomics of organisms within the aquatic environment, where much of the energy and material flow is mediated by the planktonic community13,14, we have developed a method for the concentration and extraction of whole-community metabolites from planktonic microbial systems by filtration. Commercially available hydrophilic poly-1,1-difluoroethene (PVDF) filters are specially treated to completely remove extractables, which can otherwise appear as contaminants in subsequent analyses. These treated filters are then used to filter environmental or experimental samples of interest. Filters containing the wet sample material are lyophilized and aqueous-soluble metabolites are extracted directly for conventional NMR spectroscopy using a standardized potassium phosphate extraction buffer2. Data derived from these methods can be analyzed statistically to identify meaningful patterns, or integrated with other omics levels for comprehensive understanding of community and ecosystem function.

Watch this Scientific Journal Video about Concentration of Metabolites from Low-density Planktonic Communities for Environmental Metabolomics using Nuclear Magnetic Resonance Spectroscopy at JoVE.com

Concentration of Metabolites from Low-density Planktonic Communities for Environmental Metabolomics using Nuclear Magnetic Resonance Spectroscopy

माइक्रोबियल planktonic समुदायों से metabolite का निष्कर्षण के लिए एक विधि प्रस्तुत किया है. पूरे समुदाय के नमूने निस्पंदन द्वारा विशेष रूप से तैयार फिल्टर पर हासिल की है. Lyophilization के बाद, जलीय घुलनशील चयापचयों निकाले जाते हैं. इस दृष्टिकोण से पर्यावरण metabolomics की प्राकृतिक या प्रयोगात्मक सूक्ष्म समुदायों के पार omics जांच करने के लिए आवेदन के लिए अनुमति देता है.

चयापचयों की परमाणु चुंबकीय अनुनाद स्पेक्ट्रोस्कोपी का उपयोग पर्यावरण Metabolomics के लिए कम घनत्व planktonic समुदाय से एकाग्रता

Environmental metabolomics is an emerging field that is promoting new understanding in how organisms respond to and interact with the environment and each ...

Research

JoVE Journal

Biology

Microbial Communities in Nature and Laboratory - Interview

प्रकृति और प्रयोगशाला में माइक्रोबियल समुदाय - साक्षात्कार

In vitro Labeling of Human Embryonic Stem Cells for Magnetic Resonance Imaging

चुंबकीय अनुनाद इमेजिंग के लिए मानव भ्रूण स्टेम कोशिकाओं की इन विट्रो लेबल में

Human embryonic stem cells (hESC) have demonstrated the ability to restore the injured myocardium. Magnetic resonance imaging (MRI) has emerged as one of ...

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics

समुद्री माइक्रोबियल पर्यावरण Transcriptomics का उपयोग कर समुदाय से जीन एक्सप्रेशन विश्लेषण

Analogous to metagenomics, environmental transcriptomics (metatranscriptomics) retrieves and sequences environmental mRNAs from a microbial assemblage ...

Detection of Nitric Oxide and Superoxide Radical Anion by Electron Paramagnetic Resonance Spectroscopy from Cells using Spin Traps

नाइट्रिक ऑक्साइड और कोशिकाओं से superoxide इलेक्ट्रॉन paramagnetic अनुनाद स्पेक्ट्रोस्कोपी द्वारा कट्टरपंथी आयनों की जांच स्पिन जाल का उपयोग

Reactive nitrogen/oxygen species (ROS/RNS) at low concentrations play an important role in regulating cell function, signaling, and immune response but in ...

Preparation, Purification, and Characterization of Lanthanide Complexes for Use as Contrast Agents for Magnetic Resonance Imaging

तैयारी, शोधन, चुंबकीय अनुनाद इमेजिंग के लिए और कंट्रास्ट एजेंटों के रूप में उपयोग के लिए Lanthanide परिसर की विशेषता

Polyaminopolycarboxylate-based ligands are commonly used to chelate lanthanide ions, and the resulting complexes are 
useful as contrast agents for ...

Quantifying Mixing using Magnetic Resonance Imaging

मिश्रण बढ़ाता चुंबकीय अनुनाद इमेजिंग का उपयोग

Mixing is a unit operation that combines two or more components into a homogeneous mixture.  This work involves mixing two viscous liquid streams using an ...

Purification of Transcripts and Metabolites from Drosophila Heads

Purification of Transcripts and Metabolites from Drosophila Heads

देखिए और चयापचयों से शुद्धिकरण<em&gt; ड्रोसोफिला</em&gt; प्रमुखों

For the last decade, we have tried to understand the molecular and cellular mechanisms of neuronal degeneration using Drosophila as a model organism. ...

Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside

जमे हुए कोर के बाहरी हिस्से से Exogenous सामग्री को हटाने प्राचीन जैविक समुदायों शरण के अंदर जांच करने के लिए

The cryosphere offers access to preserved organisms that persisted under past environmental conditions. In fact, these frozen materials could reflect ...

Experimental Protocol for Using Drosophila As an Invertebrate Model System for Toxicity Testing in the Laboratory

Experimental Protocol for Using Drosophila As an Invertebrate Model System for Toxicity Testing in the Laboratory

प्रयोगशाला में विषाक्तता परीक्षण के लिए एक Invertebrate मॉडल प्रणाली के रूप में Drosophila का उपयोग करने के लिए प्रायोगिक प्रोटोकॉल

Emergent properties and external factors (population-level and ecosystem-level interactions, in particular) play important roles in mediating ...

Co-immunoprecipitation Assay Using Endogenous Nuclear Proteins from Cells Cultured Under Hypoxic Conditions

सह immunoprecipitation परख कोशिकाओं से अंतर्जात परमाणु प्रोटीन का उपयोग Hypoxic शर्तों के तहत संस्कृति

Low oxygen levels (hypoxia) trigger a variety of adaptive responses with the Hypoxia-inducible factor 1 (HIF-1) complex acting as a master regulator. ...