המחברים מבקשים להודות לכל חברי המעבדות של ד&quot;ר Barletta וד&quot;ר פאוורס על הערות תוך פיתוח הפרוטוקול. אנו מודים לנדים אוסטין לדיונים מועילים והגהה של כתב היד. העבודה המתוארת בכתב היד הזה מומנה על ידי מענקי טייס זרעים לכל אחד מחוקרים המפורטים לעיל מאוניברסיטת ביולוגית מרכז חיזור נברסקה לינקולן (הורה המענק # NCRR 2P20RR 017675, ד &#39;בקר, PI). בנוסף, אנו מבקשים להודות לד&quot;ר אופליה צ&#39;אקון למתן כספים ממענק R21 (1R21AI087561-01A1) לתמיכת המשכורת החלקית של מר Halouska לתקנן שיטות תמ&quot;ג כלול בפרסום זה מחקר ואספקה.

<ol>
	<li>Larsen, M. H., Biermann, K., Tandberg, S., Hsu, T., Jacobs, W. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+Manipulation+of+Mycobacterium+tuberculosis.">Genetic Manipulation of Mycobacterium tuberculosis.</a> Curr. Protoc. Microbiol. Chapter 10, 2 (2007).</li><li>Larsen, M. H., Biermann, K., Jacobs, W. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laboratory+Maintenance+of+Mycobacterium+tuberculosis.">Laboratory Maintenance of Mycobacterium tuberculosis.</a> Curr. Protoc. Microbiol. Chapter 10, 1 (2007).</li><li>Clarridge, J. E., Shawar, R. M., Shinnick, T. M., Plikaytis, B. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+use+of+polymerase+chain+reaction+for+detection+of+Mycobacterium+tuberculosis+in+a+routine+mycobacteriology+laboratory.">Large-scale use of polymerase chain reaction for detection of Mycobacterium tuberculosis in a routine mycobacteriology laboratory.</a> J. Clin. Microbiol. 31, 2049-2056 (1993).</li><li>Nguyen, B. D., Meng, X., Donovan, K. J., Shaka, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SOGGY:+solvent-optimized+double+gradient+spectroscopy+for+water+suppression.+A+comparison+with+some+existing+techniques.">SOGGY: solvent-optimized double gradient spectroscopy for water suppression. A comparison with some existing techniques.</a> J. Magn. Reson. 184, 263-274 (2007).</li><li>Cui, Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolite+identification+via+the+Madison+Metabolomics+Consortium+Database.">Metabolite identification via the Madison Metabolomics Consortium Database.</a> Nat. Biotechnol. 26, 162-164 (2008).</li><li>Ulrich, E. L. <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, 402-408 (2008).</li><li>Wishart, D. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HMDB:+the+Human+Metabolome+Database.">HMDB: the Human Metabolome Database.</a> Nucleic Acids Res. 35, 521-526 (2007).</li><li>Kanehisa, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=KEGG+for+linking+genomes+to+life+and+the+environment.">KEGG for linking genomes to life and the environment.</a> Nucleic Acids Res. 36, 480-484 (2008).</li><li>Karp, P. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expansion+of+the+BioCyc+collection+of+pathway/genome+databases+to+160+genomes.">Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.</a> Nucleic Acids Res. 33, 6083-6089 (2005).</li><li>Halouska, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+NMR+metabolomics+to+analyze+the+targets+of+D-cycloserine+in+mycobacteria:+role+of+D-alanine+racemase.">Use of NMR metabolomics to analyze the targets of D-cycloserine in mycobacteria: role of D-alanine racemase.</a> J. Proteome. Res. 6, 4608-4614 (2007).</li><li>Boshoff, H. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+transcriptional+responses+of+Mycobacterium+tuberculosis+to+inhibitors+of+metabolism:+novel+insights+into+drug+mechanisms+of+action.">The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action.</a> J. Biol. Chem. 279, 40174-40184 (2004).</li><li>Mehaffy, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Descriptive+proteomic+analysis+shows+protein+variability+between+closely+related+clinical+isolates+of+Mycobacterium+tuberculosis.">Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis.</a> Proteomics. 10, 1966-1984 (2010).</li><li>Schnappinger, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcriptional+Adaptation+of+Mycobacterium+tuberculosis+within+Macrophages:+Insights+into+the+Phagosomal+Environment.">Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment.</a> J. Exp. Med. 198, 693-704 (2003).</li><li>Schnappinger, D., Schoolnik, G. K., Ehrt, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+profiling+of+host+pathogen+interactions:+how+Mycobacterium+tuberculosis+and+the+macrophage+adapt+to+one+another.">Expression profiling of host pathogen interactions: how Mycobacterium tuberculosis and the macrophage adapt to one another.</a> Microbes. Infect. 8, 1132-1140 (2006).</li><li>Shui, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+proteomic+profiling+of+host-pathogen+interactions:+the+macrophage+response+to+Mycobacterium+tuberculosis+lipids.">Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids.</a> J. Proteome. Res. 8, 282-289 (2009).</li><li>Talaat, A. M., Lyons, R., Howard, S. T., Johnston, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+temporal+expression+profile+of+Mycobacterium+tuberculosis+infection+in+mice.">The temporal expression profile of Mycobacterium tuberculosis infection in mice.</a> Proc. Natl. Acad. Sci. U.S.A. 101, 4602-4607 (2004).</li><li>Forgue, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NMR+metabolic+profiling+of+Aspergillus+nidulans+to+monitor+drug+and+protein+activity.">NMR metabolic profiling of Aspergillus nidulans to monitor drug and protein activity.</a> J. Proteome Res. 5, 1916-1923 (2006).</li><li>Goodacre, R., Vaidyanathan, S., Dunn, W. B., Harrigan, G. G., Kell, D. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolomics+by+numbers:+acquiring+and+understanding+global+metabolite+data.">Metabolomics by numbers: acquiring and understanding global metabolite data.</a> Trends Biotechnol. 22, 245-252 (2004).</li><li>Shin, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NMR-based+Metabolomic+Profiling+in+Mice+Infected+with+Mycobacterium+tuberculosis.">NMR-based Metabolomic Profiling in Mice Infected with Mycobacterium tuberculosis.</a> J. Proteome Res. 10, 2238-2247 (2011).</li><li>Jaki, B. U., Franzblau, S. G., Cho, S. H., Pauli, G. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+an+extraction+method+for+mycobacterial+metabolome+analysis.">Development of an extraction method for mycobacterial metabolome analysis.</a> J. Pharm. Biomed. Anal. 41, 196-200 (2006).</li><li>de Carvalho, L. P. <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+Mycobacterium+tuberculosis+reveals+compartmentalized+co-catabolism+of+carbon+substrates.">Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates.</a> Chem. Biol. 17, 1122-1131 (2010).</li><li>de Carvalho, L. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activity-based+metabolomic+profiling+of+enzymatic+function:+identification+of+Rv1248c+as+a+mycobacterial+2-hydroxy-3-oxoadipate+synthase.">Activity-based metabolomic profiling of enzymatic function: identification of Rv1248c as a mycobacterial 2-hydroxy-3-oxoadipate synthase.</a> Chem. Biol. 17, 323-332 (2010).</li><li>Marrero, J., Rhee, K. Y., Schnappinger, D., Pethe, K., Ehrt, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gluconeogenic+carbon+flow+of+tricarboxylic+acid+cycle+intermediates+is+critical+for+Mycobacterium+tuberculosis+to+establish+and+maintain+infection.">Gluconeogenic carbon flow of tricarboxylic acid cycle intermediates is critical for Mycobacterium tuberculosis to establish and maintain infection.</a> Proc. Natl. Acad. Sci. U.S.A. 107, 9819-9824 (2010).</li><li>Tang, Y. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Central+metabolism+in+Mycobacterium+smegmatis+during+the+transition+from+O2-rich+to+O2-poor+conditions+as+studied+by+isotopomer-assisted+metabolite+analysis.">Central metabolism in Mycobacterium smegmatis during the transition from O2-rich to O2-poor conditions as studied by isotopomer-assisted metabolite analysis.</a> Biotechnol. Lett. 31, 1233-1240 (2009).</li><li>Kweon, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+polyomic+approach+to+elucidate+the+fluoranthene-degradative+pathway+in+Mycobacterium+vanbaalenii+PYR-1.">A polyomic approach to elucidate the fluoranthene-degradative pathway in Mycobacterium vanbaalenii PYR-1.</a> J. Bacteriol. 189, 4635-4647 (2007).</li><li>Hasan, M. R., Rahman, M., Jaques, S., Purwantini, E., Daniels, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Glucose+6-phosphate+accumulation+in+mycobacteria:+implications+for+a+novel+F420-dependent+anti-oxidant+defense+system.">Glucose 6-phosphate accumulation in mycobacteria: implications for a novel F420-dependent anti-oxidant defense system.</a> J. Biol. Chem. 285, 19135-19144 (2010).</li><li>Soga, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+metabolome+analysis+using+capillary+electrophoresis+mass+spectrometry.">Quantitative metabolome analysis using capillary electrophoresis mass spectrometry.</a> J. Proteome Res. 2, 488-494 (2003).</li><li>Metz, T. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+future+of+liquid+chromatography-mass+spectrometry+(LC-MS)+in+metabolic+profiling+and+metabolomic+studies+for+biomarker+discovery.">The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery.</a> Biomark Med. 1, 159-185 (2007).</li><li>Ludwig, C., 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=Two-dimensional+J-resolved+NMR+spectroscopy:+review+of+a+key+methodology+in+the+metabolomics+toolbox.">Two-dimensional J-resolved NMR spectroscopy: review of a key methodology in the metabolomics toolbox.</a> Phytochem. Anal. 21, 22-32 (2010).</li><li>Simpson, R. J., Inglis, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Proteins and Proteomics: A Laboratory Manual. , 425-595 (2003).</li><li>Beste, D. J., McFadden, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=System-level+strategies+for+studying+the+metabolism+of+Mycobacterium+tuberculosis.">System-level strategies for studying the metabolism of Mycobacterium tuberculosis.</a> Mol. Biosyst. 6, 2363-2372 (2010).</li><li>Rhee, K. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Central+carbon+metabolism+in+Mycobacterium+tuberculosis:+an+unexpected+frontier.">Central carbon metabolism in Mycobacterium tuberculosis: an unexpected frontier.</a> Trends Microbiol. , (2011).</li><li>Who. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Health+Organization.">Health Organization.</a> Anti-tuberculosis Drug Resistance in the World: Report No. 4. , (2008).</li><li>Jassal, M., Bishai, W. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extensively+drug-resistant+tuberculosis.">Extensively drug-resistant tuberculosis.</a> Lancet Infect Dis. 9, 19-30 (2009).</li></ol>

אין ניגודי האינטרסים הכריזו.

מספר לא מבוטל של מחקרים נתח את פרופילי transcriptomic וproteomic של מ &#39; שחפת תחת מגוון במבחנה בתנאי vivo. 11-16 סופו של דבר, שינויים בביטוי גנים ופעילות אנזים יובילו לשינויים בריכוזים של מולקולות קטנות משקל מולקולריות. התיאור המלא של תרכובות אלו מהווה metabolome. לכן, יכו...

<table border="1" style=";text-align:right;direction:rtl"><tbody><tr><td> שם המגיב / הציוד </td><td> חברה </td><td> מספר קטלוגים </td><td> תגובות </td></tr><tr><td> העשרת ADC </td><td> BD BBL מידלברוק </td><td> 212352 </td><td></td></tr><tr><td> BACS-120 מחליף לדוגמה </td><td> ברוקר </td><td></td><td></td></tr><tr><td> הברוקר Avance NMR </td><td> ברוקר </td><td></td><td> 500 MHz </td></tr><tr><td> שור הסרום אלבומין </td><td> הפישר סיינטיפיק </td><td> BP1600-100 </td><td> החלק V </td></tr><tr><td> סרכזת </td><td> Beckman Coulter </td><td> אלגרה X-15R </td><td> Benchtop </td></tr><tr><td> צינורות צנטריפוגות </td><td> קורנינג </td><td> 430291 </td><td> פוליפרופילן 50 המ&quot;ל סטרילי </td></tr><tr><td> בקבוקוני קריוגני </td><td> קורנינג </td><td> 430488 </td><td> פוליפרופילן סטרילי 2.0 מ&quot;ל </td></tr><tr><td> Cycloheximide </td><td> AG מדעית </td><td> C-1189 </td><td> רעיל </td></tr><tr><td> D (+) - גלוקוז </td><td> Acros </td><td> 41095-0010 </td><td></td></tr><tr><td> אוקסיד דאוטריום </td><td> סיגמה אולדריץ </td><td> 617385 </td><td></td></tr><tr><td> Flask Erlenmeyer </td><td> VWR </td><td> 89095-266 </td><td> , בסיס שטוח סטרילי, פוליקרבונט, כובע 0.22 מיקרומטר PTFE קרום פרק </td></tr><tr><td> Flask ההקפאה פלאש </td><td> VWR </td><td> 82018-226 </td><td> 750 מ&quot;ל </td></tr><tr><td> הקפא מייבש </td><td> VWR </td><td> 82019-038 </td><td> 4.5 הליטר Benchtop </td></tr><tr><td> גליצרול </td><td> GibcoBRL </td><td> 15514-029 </td><td></td></tr><tr><td> מדגרה </td><td> ניו ברונסוויק </td><td> Innova 40 </td><td> Benchtop ייקר </td></tr><tr><td> Lysing מטריקס B </td><td> Biomedicals MP </td><td> 6911-100 </td><td></td></tr><tr><td> מכונת תמוגה </td><td> Biomedicals MP </td><td> FastPrep-24 </td><td></td></tr><tr><td> Microcentrifuge </td><td> אפנדורף </td><td> 5415D </td><td> Benchtop </td></tr><tr><td> Microcentrifuge </td><td> Beckman Coulter </td><td> Microfuge 22R </td><td> Benchtop </td></tr><tr><td> מידלברוק 7H9 מרק </td><td> Difco </td><td> 271310 </td><td></td></tr><tr><td> NMR צינורות </td><td> Norell </td><td> ST500-7 </td><td> 5mm </td></tr><tr><td> העשרת OADC </td><td> BD BBL מידלברוק </td><td> 212351 </td><td></td></tr><tr><td> חומצה אולאית </td><td> סיגמא </td><td> O1008 </td><td></td></tr><tr><td> אשלגן זרח Dibasic </td><td> VWR </td><td> BDH0266 </td><td></td></tr><tr><td> אשלגן זרח Monobasic </td><td> VWR </td><td> BDH0268 </td><td></td></tr><tr><td> רוטור - Microfuge 22R </td><td> Beckman Coulter </td><td> F241.5P </td><td> אטום ופוליפרופילן </td></tr><tr><td> רוטור - אלגרה X-15R</td><td> Beckman Coulter </td><td> SX4750 </td><td> עם כיסויים יו מוסמכים </td></tr><tr><td> כלוריד הנתרן </td><td> הפישר סיינטיפיק </td><td> S271-3 </td><td></td></tr><tr><td> נתרן-3-trimethylsilylpropionate-2 ,2,3,3-D4 </td><td> קיימברידג&#39; איזוטופ </td><td> DLM-48 </td><td></td></tr><tr><td> ספקטרופוטומטר </td><td> Beckman Coulter </td><td> DU-530 </td><td></td></tr><tr><td> Cuvettes ספקטרופוטומטר </td><td> עורק חיים </td><td> LS-2410 </td><td> פוליסטירן מ&quot;ל 1.5, 2 צדדים ברורים </td></tr><tr><td> מזרק </td><td> הקיטון דיקינסון </td><td> 309585 </td><td> סטרילי, 3 מ&quot;ל luer-Lok </td></tr><tr><td> מזרק סינון </td><td> Nalgene </td><td> 190-2520 </td><td> יצטט תאית סטרילי 0.2 מיקרומטר </td></tr><tr><td> Tween 80 </td><td> הפישר סיינטיפיק </td><td> BP338-500 </td><td></td></tr></tbody></table>

sample preparation of mycobacterium tuberculosis extracts for nuclear magnetic resonance metabolomic studies

Mycobacterium tuberculosis הוא אחד גורמים עיקריים לתמותה בבני אדם בקנה מידה גלובלי. ההופעה של שניהם רבים-(MDR) ונרחבים-(XDR) זנים עמידים לתרופות מאיימת להרוס את תהליך בקרת מחלות נוכחיות. לפיכך, יש צורך דחוף לפתח תרופות וחיסונים שיעילים יותר מאלה הזמינים כיום. הגנום של מ &#39; שחפת ידועה כבר יותר מ 10 שנים, עדיין קיימים פערים בידע חשוב של תפקוד גן והחיוניות שלנו. מחקרים רבים בשימוש מאז ניתוח ביטוי גנים בשתי רמות transcriptomic וproteomic כדי לקבוע את ההשפעות של תרופות, חמצון, ותנאי גידול על הדפוסים הגלובליים של ביטוי גנים. סופו של דבר, התשובה הסופית של שינויים אלה בא לידי ביטוי בהרכב המטבולי של החיידק כולל כמה אלף כימיקלי משקל מולקולריים קטנים. השוואה בין פרופילים מטבוליים מהסוג פרוע וזנים מוטנטים, גם ללא טיפול או treated עם תרופה מסוימת, יכול למעשה מאפשר זיהוי המטרה, ועלול להוביל להתפתחות של מעכבים חדשים עם פעילות אנטי שחפת. כמו כן, את ההשפעות של שני תנאים או יותר על metabolome יכולות גם להיות מוערכות. תהודה מגנטית גרעינית (NMR) היא טכנולוגיה רבה עצמה המשמשת לזיהוי ולכמת ביניים מטבוליים. בפרוטוקול זה, נהלים להכנתו של מ &#39; תמציות סלולריות חפת לניתוח metabolomic NMR מתוארות. תרביות תאים גדלות בתנאים מתאימים ו3 בלימה ברמת בטיחות הביולוגית הנדרשת, 1 נקטפו, ונתונים לתמוגה מכאנית תוך שמירה על טמפרטורות נמוכות על מנת למקסם את השימור של מטבוליטים. lysates הסלולרי הם התאוששו, מסוננים מעוקרים, ומאוחסנים בטמפרטורות נמוכות במיוחד. Aliquots מתמציות תאים אלה מצופים באגר 7H9 מידלברוק ליחידות מושבה להרכיב כדי לוודא היעדר תאי קיימא. לאחר חודשים של דגירה ב 37 ° C, אם לא viמושבות מסוגלות הם נצפו, דגימות יוסרו ממתקן הבלימה לעיבוד במורד זרם. תמציות הנן lyophilized, resuspended במאגר deuterated ומוזרק במכשיר NMR, לכידת נתונים ספקטרוסקופיות אז זה נתון לניתוח סטטיסטי. ההליכים המתוארים יכולים להיות מיושמים גם לממד יחיד-(1D) H NMR 1 ודו ממדי 1 (2D) H-13 C ניתוחי NMR. מתודולוגיה זו מספקת זיהוי אמין יותר קטן משקל מולקולרי מטבוליט וניתוחים כמותיים אמינים ורגישים יותר של יצירות מטבוליות תמצית סלולרית מאשר שיטות chromatographic. וריאציות של ההליך מתוארת בעקבות צעד תמוגה התא יכול גם להיות מותאם לניתוח proteomic מקביל.

Watch this Scientific Journal Video about Sample Preparation of Mycobacterium tuberculosis Extracts for Nuclear Magnetic Resonance Metabolomic Studies at JoVE.com

Sample Preparation of Mycobacterium tuberculosis Extracts for Nuclear Magnetic Resonance Metabolomic Studies

הפרופיל של metabolomic<em&gt; Mycobacterium tuberculosis</em&gt; נקבע לאחר צמיחה בתרבויות ציר מרק. תנאים יכולים להיות מגוונים כדי לבדוק את ההשפעות של תוספי תזונה, חמצון, וסוכנים נגד שחפת על הפרופיל המטבולי של מיקרואורגניזם זה. נוהל להכנת תמצית היא ישים עבור שניהם 1D<sup&gt; 1</sup&gt; H ו2D<sup&gt; 1</sup&gt; H-<sup&gt; 13</sup&gt; C ניתוחי NMR.

לדוגמא הכנה של<em&gt; Mycobacterium tuberculosis</em&gt; תמציות ללימודי metabolomic תהודה מגנטיים גרעיניים

Mycobacterium tuberculosis is a major cause of mortality in human beings on a global scale. The emergence of both multi- (MDR) and extensively-(XDR) ...

sample-preparation-mycobacterium-tuberculosis-extracts-for-nuclear

Research

Education

JoVE Core

JoVE Journal

Analytical Chemistry

Immunology and Infection

Unit 1

Sample Preparation of Mycobacterium tuberculosis Extracts for Nuclear Magnetic Resonance Metabolomic Studies

Principles of Nuclear Magnetic Resonance

SCIENTISTS IN ACTION

15.3K Views.  University of Nebraska-Lincoln. הפרופיל של metabolomic Mycobacterium tuberculosis נקבע לאחר צמיחה בתרבויות ציר מרק. תנאים יכולים להיות מגוונים כדי לבדוק את ההשפעות של תוספי תזונה, חמצון, וסוכנים נגד שחפת על הפרופיל המטבולי של מיקרואורגניזם זה. נוהל להכנת תמצית היא ישים עבור שניהם 1D 1 H ו2D 1

Video: Sample Preparation of Mycobacterium tuberculosis Extracts for Nuclear Magnetic Resonance Metabolomic Studies

Growth of Mycobacterium tuberculosis Biofilms

Mycobacterium tuberculosis, the etiologic agent of human tuberculosis, has an extraordinary ability to survive against environmental stresses including antibiotics. Although stress tolerance of M. tuberculosis is one of the likely contributors to the 6-month long chemotherapy of tuberculosis 1, the molecular mechanisms underlying this characteristic phenotype of the pathogen remain unclear. Many microbial species have evolved to survive in stressful environments by self-assembling in highly organized, surface attached, and matrix encapsulated structures called biofilms 2-4. Growth in communities appears to be a preferred survival strategy of microbes, and is achieved through genetic components that regulate surface attachment, intercellular communications, and synthesis of extracellular polymeric substances (EPS) 5,6. The tolerance to environmental stress is likely facilitated by EPS, and perhaps by the physiological adaptation of individual bacilli to heterogeneous microenvironments within the complex architecture of biofilms 7.
In a series of recent papers we established that M. tuberculosis and Mycobacterium smegmatis have a strong propensity to grow in organized multicellular structures, called biofilms, which can tolerate more than 50 times the minimal inhibitory concentrations of the anti-tuberculosis drugs isoniazid and rifampicin 8-10. M. tuberculosis, however, intriguingly requires specific conditions to form mature biofilms, in particular 9:1 ratio of headspace: media as well as limited exchange of air with the atmosphere 9. Requirements of specialized environmental conditions could possibly be linked to the fact that M. tuberculosis is an obligate human pathogen and thus has adapted to tissue environments. In this publication we demonstrate methods for culturing M. tuberculosis biofilms in a bottle and a 12-well plate format, which is convenient for bacteriological as well as genetic studies. We have described the protocol for an attenuated strain of M. tuberculosis, mc27000, with deletion in the two loci, panCD and RD1, that are critical for in vivo growth of the pathogen 9. This strain can be safely used in a BSL-2 containment for understanding the basic biology of the tuberculosis pathogen thus avoiding the requirement of an expensive BSL-3 facility. The method can be extended, with appropriate modification in media, to grow biofilm of other culturable mycobacterial species.
Overall, a uniform protocol of culturing mycobacterial biofilms will help the investigators interested in studying the basic resilient characteristics of mycobacteria. In addition, a clear and concise method of growing mycobacterial biofilms will also help the clinical and pharmaceutical investigators to test the efficacy of a potential drug.

Growth of Mycobacterium tuberculosis Biofilms

Mycobacterium tuberculosis forms drug tolerant biofilms when cultured in certain conditions. Here we describe methods for culturing M. tuberculosis biofilms and determining the frequency of drug tolerant persisters. These protocols will be useful for further studies into the mechanisms of drug tolerance in M. tuberculosis.

גידול של שחפת Mycobacterium Biofilms

Mycobacterium tuberculosis, the etiologic agent of human tuberculosis, has an extraordinary ability to survive against environmental stresses including ...

Monitoring Dendritic Cell Migration using 19F / 1H Magnetic Resonance Imaging

Continuous advancements in noninvasive imaging modalities such as magnetic resonance imaging (MRI) have greatly improved our ability to study physiological or pathological processes in living organisms. MRI is also proving to be a valuable tool for capturing transplanted cells in vivo. Initial cell labeling strategies for MRI made use of contrast agents that influence the MR relaxation times (T1, T2, T2*) and lead to an enhancement (T1) or depletion (T2*) of signal where labeled cells are present. T2* enhancement agents such as ultrasmall iron oxide agents (USPIO) have been employed to study cell migration and some have also been approved by the FDA for clinical application. A drawback of T2* agents is the difficulty to distinguish the signal extinction created by the labeled cells from other artifacts such as blood clots, micro bleeds or air bubbles. In this article, we describe an emerging technique for tracking cells in vivo that is based on labeling the cells with fluorine (19F)-rich particles. These particles are prepared by emulsifying perfluorocarbon (PFC) compounds and then used to label cells, which subsequently can be imaged by 19F MRI. Important advantages of PFCs for cell tracking in vivo include (i) the absence of carbon-bound 19F in vivo, which then yields background-free images and complete cell selectivityand(ii) the possibility to quantify the cell signal by 19F MR spectroscopy.

Monitoring Dendritic Cell Migration using 19F / 1H Magnetic Resonance Imaging

Tracking of cells using MRI has gained remarkable attention in the past years. This protocol describes the labeling of dendritic cells with fluorine (19F)-rich particles, the in vivo application of these cells, and monitoring the extent of their migration to the draining lymph node with 19F/1H MRI and 19F MRS.

נדידת תאים דנדריטים ניטור באמצעות<sup&gt; 19</sup&gt; F /<sup&gt; 1</sup&gt; H דימות תהודה מגנטית

Continuous  advancements in noninvasive imaging modalities such as magnetic resonance  imaging (MRI) have greatly improved our ability to study ...

An Experimental Model to Study Tuberculosis-Malaria Coinfection upon Natural Transmission of Mycobacterium tuberculosis and Plasmodium berghei

Coinfections naturally occur due to the geographic overlap of distinct types of pathogenic organisms. Concurrent infections most likely modulate the respective immune response to each single pathogen and may thereby affect pathogenesis and disease outcome. Coinfected patients may also respond differentially to anti-infective interventions. Coinfection between tuberculosis as caused by mycobacteria and the malaria parasite Plasmodium, both of which are coendemic in many parts of sub-Saharan Africa, has not been studied in detail. In order to approach the challenging but scientifically and clinically highly relevant question how malaria-tuberculosis coinfection modulate host immunity and the course of each disease, we established an experimental mouse model that allows us to dissect the elicited immune responses to both pathogens in the coinfected host. Of note, in order to most precisely mimic naturally acquired human infections, we perform experimental infections of mice with both pathogens by their natural routes of infection, i.e. aerosol and mosquito bite, respectively.

An Experimental Model to Study Tuberculosis-Malaria Coinfection upon Natural Transmission of Mycobacterium tuberculosis and Plasmodium berghei

Tuberculosis and malaria are two of the most prevalent infections in humans and major causes of morbidity and mortality in impoverished populations in the tropics. We established an experimental model system to study outcome of malaria-tuberculosis coinfection in mice after challenge with both pathogens via their natural route of infection.

מודל ניסיוני לחקר המלריה שחפת-coinfection על הילוכים טבעיים של חפת Mycobacterium ו Berghei Plasmodium</i

Coinfections naturally occur due to the geographic overlap of distinct types of pathogenic organisms. Concurrent infections most likely modulate the ...

Demonstrating a Multi-drug Resistant Mycobacterium tuberculosis Amplification Microarray

Simplifying microarray workflow is a necessary first step for creating MDR-TB microarray-based diagnostics that can be routinely used in lower-resource environments. An amplification microarray combines asymmetric PCR amplification, target size selection, target labeling, and microarray hybridization within a single solution and into a single microfluidic chamber. A batch processing method is demonstrated with a 9-plex asymmetric master mix and low-density gel element microarray for genotyping multi-drug resistant Mycobacterium tuberculosis (MDR-TB). The protocol described here can be completed in 6 hr and provide correct genotyping with at least 1,000 cell equivalents of genomic DNA. Incorporating on-chip wash steps is feasible, which will result in an entirely closed amplicon method and system. The extent of multiplexing with an amplification microarray is ultimately constrained by the number of primer pairs that can be combined into a single master mix and still achieve desired sensitivity and specificity performance metrics, rather than the number of probes that are immobilized on the array. Likewise, the total analysis time can be shortened or lengthened depending on the specific intended use, research question, and desired limits of detection. Nevertheless, the general approach significantly streamlines microarray workflow for the end user by reducing the number of manually intensive and time-consuming processing steps, and provides a simplified biochemical and microfluidic path for translating microarray-based diagnostics into routine clinical practice.

Demonstrating a Multi-drug Resistant Mycobacterium tuberculosis Amplification Microarray

An amplification microarray combines asymmetric PCR amplification and microarray hybridization into a single chamber, which significantly streamlines microarray workflow for the end user. Simplifying microarray workflow is a necessary first step for creating microarray-based diagnostics that can be routinely used in lower-resource environments.

הוכחת סמים רבים עמידים<em&gt; חפת Mycobacterium</em&gt; Microarray ההגברה

Simplifying microarray workflow is a necessary first step for creating MDR-TB microarray-based diagnostics that can be routinely used in lower-resource ...

A 3D Human Lung Tissue Model for Functional Studies on Mycobacterium tuberculosis Infection

Tuberculosis (TB) still holds a major threat to the health of people worldwide, and there is a need for cost-efficient but reliable models to help us understand the disease mechanisms and advance the discoveries of new treatment options. In vitro cell cultures of monolayers or co-cultures lack the three-dimensional (3D) environment and tissue responses. Herein, we describe an innovative in vitro model of a human lung tissue, which holds promise to be an effective tool for studying the complex events that occur during infection with Mycobacterium tuberculosis (M. tuberculosis). The 3D tissue model consists of tissue-specific epithelial cells and fibroblasts, which are cultured in a matrix of collagen on top of a porous membrane. Upon air exposure, the epithelial cells stratify and secrete mucus at the apical side. By introducing human primary macrophages infected with M. tuberculosis to the tissue model, we have shown that immune cells migrate into the infected-tissue and form early stages of TB granuloma. These structures recapitulate the distinct feature of human TB, the granuloma, which is fundamentally different or not commonly observed in widely used experimental animal models. This organotypic culture method enables the 3D visualization and robust quantitative analysis that provides pivotal information on spatial and temporal features of host cell-pathogen interactions. Taken together, the lung tissue model provides a physiologically relevant tissue micro-environment for studies on TB. Thus, the lung tissue model has potential implications for both basic mechanistic and applied studies. Importantly, the model allows addition or manipulation of individual cell types, which thereby widens its use for modelling a variety of infectious diseases that affect the lungs.

A 3D Human Lung Tissue Model for Functional Studies on Mycobacterium tuberculosis Infection

Human tuberculosis infection is a complex process, which is difficult to model in vitro. Here we describe a novel 3D human lung tissue model that recapitulates the dynamics that occur during infection, including the migration of immune cells and early granuloma formation in a physiological environment.

דגם רקמות 3D ריאות אדם ללימודים פונקציונליים ב<em&gt; חפת Mycobacterium</em&gt; זיהום

Tuberculosis (TB) still holds a major threat to the health of people worldwide, and there is a need for cost-efficient but reliable models to help us ...

System for Efficacy and Cytotoxicity Screening of Inhibitors Targeting Intracellular Mycobacterium tuberculosis

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a leading cause of morbidity and mortality worldwide. With the increased spread of multi drug-resistant TB (MDR-TB), there is a real urgency to develop new therapeutic strategies against M. tuberculosis infections. Traditionally, compounds are evaluated based on their antibacterial activity under in vitro growth conditions in broth; however, results are often misleading for intracellular pathogens like M. tuberculosis since in-broth phenotypic screening conditions are significantly different from the actual disease conditions within the human body. Screening for inhibitors that work inside macrophages has been traditionally difficult due to the complexity, variability in infection, and slow replication rate of M. tuberculosis. In this study, we report a new approach to rapidly assess the effectiveness of compounds on the viability of M. tuberculosis in a macrophage infection model. Using a combination of a cytotoxicity assay and an in-broth M. tuberculosis viability assay, we were able to create a screening system that generates a comprehensive analysis of compounds of interest. This system is capable of producing quantitative data at a low cost that is within reach of most labs and yet is highly scalable to fit large industrial settings.

System for Efficacy and Cytotoxicity Screening of Inhibitors Targeting Intracellular Mycobacterium tuberculosis

We have developed a modular high-throughput screening system for discovering novel compounds against Mycobacterium tuberculosis, targeting intracellular and in-broth growing bacteria as well as cytotoxicity against the mammalian host cell.

מערכת לסינון יעילות Cytotoxicity של מעכבי מיקוד תאי<em&gt; שחפת Mycobacterium</em

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a leading cause of morbidity and mortality worldwide. With the increased spread ...

A High-throughput Compatible Assay to Evaluate Drug Efficacy against Macrophage Passaged Mycobacterium tuberculosis

The early drug development process for anti-tuberculosis drugs is hindered by the inefficient translation of compounds with in vitro activity to effectiveness in the clinical setting. This is likely due to a lack of consideration for the physiologically relevant cellular penetration barriers that exist in the infected host. We recently established an alternative infection model that generates large macrophage aggregate structures containing densely packed M. tuberculosis (Mtb) at its core, which was suitable for drug susceptibility testing. This infection model is inexpensive, rapid, and most importantly BSL-2 compatible. Here, we describe the experimental procedures to generate Mtb/macrophage aggregate structures that would produce macrophage-passaged Mtb for drug susceptibility testing. In particular, we demonstrate how this infection system could be directly adapted to the 96-well plate format showing throughput capability for the screening of compound libraries against Mtb. Overall, this assay is a valuable addition to the currently available Mtb drug discovery toolbox due to its simplicity, cost effectiveness, and scalability.

A High-throughput Compatible Assay to Evaluate Drug Efficacy against Macrophage Passaged Mycobacterium tuberculosis

New models and assays that would improve the early drug development process for next-generation anti-tuberculosis drugs are highly desirable. Here, we describe a quick, inexpensive, and BSL-2 compatible assay to evaluate drug efficacy against Mycobacterium tuberculosis that can be easily adapted for high-throughput screening.

Assay תואם תפוקה גבוהה כדי להעריך יעילות התרופה נגד Macrophage passaged<em&gt; שחפת Mycobacterium</em

The early drug development process for anti-tuberculosis drugs is hindered by the inefficient translation of compounds with in vitro activity to ...

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates

Mycobacterium tuberculosis remains the number one infectious agent in the world today. With the emergence of antibiotic resistant strains, new clinically relevant methods are needed that evaluate the disease process and screen for potential antibiotic and vaccine treatments. Positron Emission Tomography/Computed Tomography (PET/CT) has been established as a valuable tool for studying a number of afflictions such as cancer, Alzheimer&#39;s disease, and inflammation/infection. Outlined here are a number of strategies that have been employed to evaluate PET/CT images in cynomolgus macaques that are infected intrabronchially with low doses of M. tuberculosis. Through evaluation of lesion size on CT and uptake of 18F-fluorodeoxyglucose (FDG) in lesions and lymph nodes in PET images, these described methods show that PET/CT imaging can predict future development of active versus latent disease and the propensity for reactivation from a latent state of infection. Additionally, by analyzing the overall level of lung inflammation, these methods determine antibiotic efficacy of drugs against M. tuberculosis in the most clinically relevant existing animal model. These image analysis methods are some of the most powerful tools in the arsenal against this disease as not only can they evaluate a number of characteristics of infection and drug treatment, but they are also directly translatable to a clinical setting for use in human studies.

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates

Here, we present a protocol to describe the analysis of 18F-FDG PET/CT imaging in non-human primates that have been infected with M. tuberculosis to study disease process, drug treatment, and disease reactivation.

ניתוח של 18FDG PET/CT הדמיה ככלי לימודי שחפת Mycobacterium זיהום וטיפול פרימטים לא אנושית

Mycobacterium tuberculosis remains the number one infectious agent in the world today. With the emergence of antibiotic resistant strains, new clinically ...

Imaging Mycobacterium tuberculosis in Mice with Reporter Enzyme Fluorescence

Reporter enzyme fluorescence (REF) utilizes substrates that are specific for enzymes present in target organisms of interest for imaging or detection by fluorescence or bioluminescence. We utilize BlaC, an enzyme expressed constitutively by all M. tuberculosis strains. REF allows rapid quantification of bacteria in lungs of infected mice. The same group of mice can be imaged at many time points, greatly reducing costs, enumerating bacteria more quickly, allowing novel observations in host-pathogen interactions, and increasing statistical power, since more animals per group are readily maintained. REF is extremely sensitive due to the catalytic nature of the BlaC enzymatic reporter and specific due to the custom flourescence resonance energy transfer (FRET) or fluorogenic substrates used. REF does not require recombinant strains, ensuring normal host-pathogen interactions. We describe the imaging of M. tuberculosis infection using a FRET substrate with maximal emission at 800 nm. The wavelength of the substrate allows sensitive deep tissue imaging in mammals. We will outline aerosol infection of mice with M. tuberculosis, anesthesia of mice, administration of the REF substrate, and optical imaging. This method has been successfully applied to evaluating host-pathogen interactions and efficacy of antibiotics targeting M. tuberculosis.

Imaging Mycobacterium tuberculosis in Mice with Reporter Enzyme Fluorescence

We describe the optical imaging of mice infected with Mycobacterium tuberculosis (M. tuberculosis) using reporter enzyme fluorescence (REF). This protocol facilitates the sensitive and specific detection of M. tuberculosis in pre-clinical animal models for pathogenesis, therapeutics and vaccine research.

הדמיה שחפת Mycobacterium בעכברים עם הכתב אנזים קרינה פלואורסצנטית

Reporter enzyme fluorescence (REF) utilizes substrates that are specific for enzymes present in target organisms of interest for imaging or detection by ...

Modeling Tuberculosis in Mycobacterium marinum Infected Adult Zebrafish

Mycobacterium tuberculosis is currently the deadliest human pathogen causing 1.7 million deaths and 10.4 million infections every year. Exposure to this bacterium causes a wide disease spectrum in humans ranging from a sterilized infection to an actively progressing deadly disease. The most common form is the latent tuberculosis, which is asymptomatic, but has the potential to reactivate into a fulminant disease. Adult zebrafish and its natural pathogen Mycobacterium marinum have recently proven to be an applicable model to study the wide disease spectrum of tuberculosis. Importantly, spontaneous latency and reactivation as well as adaptive immune responses in the context of mycobacterial infection can be studied in this model. In this article, we describe methods for the experimental infection of adult zebrafish, the collection of internal organs for the extraction of nucleic acids for the measurement of mycobacterial loads and host immune responses by quantitative PCR. The in-house-developed, M. marinum-specific qPCR assay is more sensitive than the traditional plating methods as it also detects DNA from non-dividing, dormant or recently dead mycobacteria. As both DNA and RNA are extracted from the same individual, it is possible to study the relationships between the diseased state, and the host and pathogen gene-expression. The adult zebrafish model for tuberculosis thus presents itself as a highly applicable, non-mammalian in vivo system to study host-pathogen interactions.

Modeling Tuberculosis in Mycobacterium marinum Infected Adult Zebrafish

Here, we present a protocol to model human tuberculosis in an adult zebrafish using its natural pathogen Mycobacterium marinum. Extracted DNA and RNA from the internal organs of infected zebrafish can be used to reveal the total mycobacterial loads in the fish and the host&#39;s immune responses with qPCR.

מידול שחפת ב דג נגוע זברה בוגרת התחממות עולמית

Mycobacterium tuberculosis is currently the deadliest human pathogen causing 1.7 million deaths and 10.4 million infections every year. Exposure to this ...