The able technical assistance of Anthony Thomas is gratefully acknowledged.

Procedure for Processing Urine Samples
<ol>
 <li>Thaw the urine sample in a 37&deg; C water bath. Decant into a new container if the original is compromised.</li>
 <li>Take a maximum aliquot of 13 ml of sample and store it at -20&deg; C in a labeled conical centrifuge tube.</li>
 <li>Measure and record the optical density of the sample by placing a couple of drops of urine in the refractometer.</li>
 <li>Filter the sample through a 0.2 um filter.</li>
 <li>Measure out the volume of sample below according to the optical density
 <table border="0">
 <tbody>
 <tr>
 <td>1.000-1.009</td>
 <td>1.00 ml</td>
 </tr>
 <tr>
 <td>1.010-1.019</td>
 <td>0.50 ml</td>
 </tr>
 <tr>
 <td>1.020-1.050</td>
 <td>0.25 ml + 0.25 ml H2O</td>
 </tr>
 </tbody>
 </table>
 </li>
 <li>The specified volume is then transferred to a Reactivial containing the following internal standards: 500 nanomoles (nmoles) 3 Creatine; 10 nmoles d3 Methylmalonic acid; 100 nmoles each of the following 13C3 lactate, 13C3 pyruvate, 13C2 15N glycine, d3 serine, d5 phenylalanine, d11 hexanoylglycine,15N2 orotate, d4 sebacic acid, 13C6 glucose, d6 inositol and d5 tryptophan.</li>
 <li>20 microliters (&mu;l) of a 7.5 Units/&mu;l solution of urease (Calzyme Laboratories catalog no. 116A0100) is added to the sample, which is then flushed and sealed under CO2 through an inert septum.</li>
 <li>The sample is held at 37&deg;C for 30 minutes with more carbon dioxide gas added at 15 minute intervals to maintain pressure.</li>
 <li>20 &mu;l more of the urease solution is added, the vial is flushed with carbon dioxide, and the sample maintained at 37&deg;C for another 15 minutes.</li>
 <li>500 &mu;l of 30:70 acetone : methanol is added, the rubber septum is replaced with a Teflon coated septum, and the sample is chilled at -20&deg; C for 15 minutes.</li>
 <li>Solids are removed by centrifugation at 1500 rpm x 10 minutes then decanted into a clean 2.0 cc Reactivial (Supelco/Sigma)</li>
 <li>Add triethylammonium trifluoroacetate (TEA/TFA) (Sigma) as follows:
 <ul>
 <li>20 &mu;l for 1.00 ml samples</li>
 <li>40 &mu;l for 0.5 ml, or less, samples</li>
 </ul>
 </li>
 <li>Top off with acetonitrile and place under a nitrogen stream at 70&deg; C until constant volume is achieved (TEA/TFA will remain) (~ 15 minutes).</li>
 <li>Repeat step 13, up to 4 times until a precipitate forms (~ 10 minutes each).</li>
 <li>Let cool for about 2 minutes. Top off with methylene chloride, being careful of boil over, and dry (~ 4:00 minutes).</li>
 <li>Repeat step 15.</li>
 <li>Add MSTFA (N-methyl-N-trimethylsilyltrifluoroacetamide) (Thermal Scientific) at the following rates:
 <ul>
 <li>150 &mu;l for 1.00 ml samples</li>
 <li>200 &mu;l for 0.50 ml, or less, samples</li>
 </ul>
 </li>
 <li>Cap under a nitrogen atmosphere and incubate at 70&deg; C for 1 hour.</li>
 <li>Transfer to microvials, under a nitrogen atmosphere, for analysis on gas chromatograph /mass spectrometer.</li>
 <li>Place microvials for automated injection by the Agilent 5975 GC/MS: Instrument temperatures are: injector 200&deg; C, interface 250&deg; C, oven 80&deg; C for 1 minute; ramp at 4&deg; C/minute 80-130&deg; C, ramp at 6&deg; C/ minute 130-200&deg; C, ramp at 12&deg; C/ minute 200-285&deg; C, hold for 10 minutes. Column: 25 m, 320 micron ID, 0.5 micron film thickness DB-5. Mass Spec: source 230&deg; C, quad 150&deg; C, Scan 50-650 amu at 2.46 scans/sec. Solvent delay 3.5 minutes.</li>
</ol>
Representative Results
Please <a href="https://www.jove.com/files/ftp_upload/2014/ShoemakerResultHawkinsinuria.pdf">click here</a> to see the representative results.

<ol>
	<li>Shoemaker, J. D., Elliott, W. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+screening+of+urine+samples+for+carbohydrates,+organic+and+amino+acids+after+treatment+with+urease.">Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease.</a> J. Chromatogr. 562 (1-2), 125-138 (1991).</li><li>Kuhara, T., Shinka, T., Inoue, Y., Ohse, M., Zhen-wei, X., Yoshida, I., Inokuchi, T., Yamaguchi, S., Takayanagi, M., Matsumoto, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pilot+study+of+gas+chromatographic-mass+spectrometric+screening+of+newborn+urine+for+inborn+errors+of+metabolism+after+treatment+with+urease.">Pilot study of gas chromatographic-mass spectrometric screening of newborn urine for inborn errors of metabolism after treatment with urease.</a> J Chromatogr B Biomed Sci Appl. 731 (1), 141-147 (1999).</li><li>Fu, X., Iga, M., Kimura, M., Yamaguchi, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simplified+screening+for+organic+acidemia+using+GC/MS+and+dried+urine+filter+paper:+a+study+on+neonatal+mass+screening.">Simplified screening for organic acidemia using GC/MS and dried urine filter paper: a study on neonatal mass screening.</a> Early Hum Dev. 58 (1), 41-55 (2000).</li><li>Kuhara, T., Ohdoi, C., Ohse, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+gas+chromatographic-mass+spectrometric+procedure+for+diagnosing+pyrimidine+degradation+defects+for+prevention+of+severe+anticancer+side+effects.">Simple gas chromatographic-mass spectrometric procedure for diagnosing pyrimidine degradation defects for prevention of severe anticancer side effects.</a> J Chromatogr B Biomed Sci Appl. 758 (1), 61-74 (2001).</li><li>Kuhara, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diagnosis+of+inborn+errors+of+metabolism+using+filter+paper+urine,+urease+treatment,+isotope+dilution+and+gas+chromatography-mass+spectrometry.">Diagnosis of inborn errors of metabolism using filter paper urine, urease treatment, isotope dilution and gas chromatography-mass spectrometry.</a> J Chromatogr B Biomed Sci Appl. 758, 3-25 (2001).</li><li>Iga, M., Kimura, M., Ohura, T., Kikawa, Y., Yamaguchi, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid,+simplified+and+sensitive+method+for+screening+fructose-1,6-diphosphatase+deficiency+by+analyzing+urinary+metabolites+in+urease/direct+preparations+and+gas+chromatography-mass+spectrometry+in+the+selected-ion+monitoring+mode.">Rapid, simplified and sensitive method for screening fructose-1,6-diphosphatase deficiency by analyzing urinary metabolites in urease/direct preparations and gas chromatography-mass spectrometry in the selected-ion monitoring mode.</a> J Chromatogr B Biomed Sci Appl. 746 (1), 75-82 (2000).</li><li>Kuhara, T., Ohse, M., Ohdoi, C., Ishida, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differential+diagnosis+of+homocystinuria+by+urease+treatment,+isotope+dilution+and+gas+chromatography-mass+spectrometry.">Differential diagnosis of homocystinuria by urease treatment, isotope dilution and gas chromatography-mass spectrometry.</a> J Chromatogr B Biomed Sci Appl. 742 (1), 59-70 (2000).</li><li>Young, V., Lo, S., Shoemaker, J., Thomas, A., Rhead, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Validation+and+Extension+of+the+Urease+Method+for+Urine+Organic+and+Amino+Acid+Analysis.">Validation and Extension of the Urease Method for Urine Organic and Amino Acid Analysis.</a> , (2008).</li><li>Smith, E. M., Hoi, J. T., Eissenberg, J. C., Shoemaker, J. D., Neckameyer, W. S., Ilvarsonn, A. M., Harshman, L. G., Schlegel, V. L., Zempleni, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Feeding+Drosophila+a+biotin-deficient+diet+for+multiple+generations+increases+stress+resistance+and+lifespan+and+alters+gene+expression+and+histone+biotinylation+patterns.">Feeding Drosophila a biotin-deficient diet for multiple generations increases stress resistance and lifespan and alters gene expression and histone biotinylation patterns.</a> J Nutr. 137 (9), 2006-2012 (2007).</li><li>Brown, S. M., Shoemaker, J. D., Lodge, J. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Importance+of+NADP+-Dependent+Isocitrate+Dehydrogenase+in+Resistance+to+Nitrosative+Stress+and+the+Inessentiality+of+Glucose-6-Phosphate+Dehydrogenase+for+Oxidative+Stress+Resistance+in+Cryptococcus+neoformans.">The Importance of NADP+-Dependent Isocitrate Dehydrogenase in Resistance to Nitrosative Stress and the Inessentiality of Glucose-6-Phosphate Dehydrogenase for Oxidative Stress Resistance in Cryptococcus neoformans.</a> Eukaryotic Cell. , (2010).</li><li>Shoemaker, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nutritional+Screening+in+Humans+by+Gas+Chromatography-Mass+Spectrometry+of+Urine+Metabolites+After+Substrate+Loading.">Nutritional Screening in Humans by Gas Chromatography-Mass Spectrometry of Urine Metabolites After Substrate Loading.</a> , (1992).</li><li>Baggot, P. J., Kalamarides, J. A., Shoemaker, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Valproate-induced+biochemical+abnormalities+in+pregnancy+corrected+by+vitamins:+A+Case+Report.">Valproate-induced biochemical abnormalities in pregnancy corrected by vitamins: A Case Report.</a> Epilepsia. 40 (44), 512-515 (1999).</li><li>Baggot, P. J., Eliseo, A. J., Kalamarides, J. A., Shoemaker, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+folate-dependent+metabolite+in+amniotic+fluid+from+pregnancies+with+normal+or+trisomy+21+chromosomes.">A folate-dependent metabolite in amniotic fluid from pregnancies with normal or trisomy 21 chromosomes.</a> Fetal Diagn Ther. 21 (1), 148-152 (2006).</li><li>Baggot, P. J., Eliseo, A. J., DeNicola, N. G., Kalamarides, J. A., Shoemaker, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organic+acid+concentrations+in+amniotic+fluid+found+in+normal+and+Down+syndrome+pregnancies.">Organic acid concentrations in amniotic fluid found in normal and Down syndrome pregnancies.</a> Fetal Diagn Ther. 23 (3), 245-248 (2008).</li><li>Baggot, P. J., Eliseo, A. J., DeNicola, N. G., Kalamarides, J. A., Shoemaker, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pyridoxine-related+metabolite+concentrations+in+normal+and+Down+syndrome+amniotic+fluid.">Pyridoxine-related metabolite concentrations in normal and Down syndrome amniotic fluid.</a> Fetal Diagn Ther. 23 (4), 254-257 (2008).</li></ol>

The Metabolic Screening Lab is a CLIA-licensed clinical laboratory owned by Saint Louis University, a non-profit corporation. Dr. Shoemaker does not directly profit from laboratory revenues, but may benefit indirectly from laboratory productivity. None of the methods, techniques, results, normal ranges, macros, software, libraries or conclusions are considered proprietary and are freely available to interested parties.

The urease method (1) has been cited 62 times in the medical literature with various modifications. Matsumoto's group (2,3) simplified the procedure for high-throughput neonatal screening and reported the results from 16000 patients. Kuhara and others (4-7) have reported the use of the method in several cases of inborn error diagnosis and follow-up. Rhead (8) also confirmed the method's utility for clinical diagnosis and follow-up of inborn errors. The method has been applied to urine of bears, knock-out mice, elephants and homogenates of whole fruit flies and their larvae (9). Culture media from Cryptococcus before and after site-directed mutagenesis were also analyzed, without the urease step (10). The method has been applied to human nutritional assessment in medical students, Down syndrome patients and demented elderly veterans after loading the subjects with oral doses of the amino acids tryptophan, methionine and isoleucine (11). All eight B-vitamins were assessed by quantifying the breakdown products of the three amino acids which, among them, require all 8 vitamins at some point in their degradation. The toxic effects of pharmaceuticals and their mitigation by vitamin supplementation has been reported (12). Amniotic fluid samples from normal and Down syndrome pregnancies were analyzed and reported (13-15).

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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">	
		
		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>MSD 5975</td>
<td>&nbsp;</td>
<td>Agilent</td>
<td>&nbsp;</td>
<td>GC/MS/Computer</td>
</tr>
<tr>
<td>MSD 5973</td>
<td>&nbsp;</td>
<td>Agilent</td>
<td>&nbsp;</td>
<td>GC/MS/Computer</td>
</tr>
<tr>
<td>Urease</td>
<td>&nbsp;</td>
<td>Calzyme</td>
<td>116A0100</td>
<td>Also Sigma C3</td>
</tr>
<tr>
<td>Stable Isotope Standards</td>
<td>&nbsp;</td>
<td>CDN Isotopes, Isotec, Cambridge Isotope Lab</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Solvents</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Analytes</td>
<td>&nbsp;</td>
<td>Sigma, Universidad Autonoma de Madrid, Ernesto Brunet</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>GC Columns</td>
<td>&nbsp;</td>
<td>J&amp;W Scientific</td>
<td>123-5026</td>
<td>&nbsp;</td>
<tr>
<td>TEA/TFA</td>
<td>&nbsp;</td>
<td>Fluka/Sigma</td>
<td>09747</td>
<td>&nbsp;</td>
<tr>
<td>Vials</td>
<td>&nbsp;</td>
<td>Supelco/Sigma</td>
<td>Z115088/12EA</td>
<td>&nbsp;</td>
<tr>
<td>Merlin Microseal</td>
<td>&nbsp;</td>
<td>Agilent</td>
<td>5181-8815</td>
<td>&nbsp;</td>
<tr>
<td>MSTFA</td>
<td>&nbsp;</td>
<td>Thermal Scientific</td>
<td>48913</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

one-step metabolomics: carbohydrates, organic and amino acids quantified in a single procedure

Every infant born in the US is now screened for up to 42 rare genetic disorders called "inborn errors of metabolism". The screening method is based on tandem mass spectrometry and quantifies acylcarnitines as a screen for organic acidemias and also measures amino acids. All states also perform enzymatic testing for carbohydrate disorders such as galactosemia. Because the results can be non-specific, follow-up testing of positive results is required using a more definitive method. The present report describes the "urease" method of sample preparation for inborn error screening. Crystalline urease enzyme is used to remove urea from body fluids which permits most other water-soluble metabolites to be dehydrated and derivatized for gas chromatography in a single procedure. Dehydration by evaporation in a nitrogen stream is facilitated by adding acetonitrile and methylene chloride. Then, trimethylsilylation takes place in the presence of a unique catalyst, triethylammonium trifluoroacetate. Automated injection and chromatography is followed by macro-driven custom quantification of 192 metabolites and semi-quantification of every major component using specialized libraries of mass spectra of TMS derivatized biological compounds. The analysis may be performed on the widely-used Chemstation platform using the macros and libraries available from the author. In our laboratory, over 16,000 patient samples have been analyzed using the method with a diagnostic yield of about 17%--that is, 17% of the samples results reveal findings that should be acted upon by the ordering physician. Included in these are over 180 confirmed inborn errors, of which about 38% could not have been diagnosed using previous methods.

Watch this Scientific Journal Video about One-step Metabolomics: Carbohydrates, Organic and Amino Acids Quantified in a Single Procedure at JoVE.com

One-step Metabolomics: Carbohydrates, Organic and Amino Acids Quantified in a Single Procedure

The urease method of sample preparation for GC/MS analysis of intermediary metabolites is presented by its inventor. The method allows one-step follow-up of newborn screening for inborn errors by tandem mass spectrometry by quantifying carbohydrates, organic and amino acids all in a single process.

Every infant born in the US is now screened for up to 42 rare genetic disorders called "inborn errors of metabolism". The screening method is based on ...

one-step-metabolomics-carbohydrates-organic-amino-acids-quantified

Research

JoVE Journal

Biology

13.0K Views.  Saint Louis University School of Medicine. The urease method of sample preparation for GC/MS analysis of intermediary metabolites is presented by its inventor. The method allows one-step follow-up of newborn screening for inborn errors by tandem mass spectrometry by quantifying carbohydrates, organic and amino acids all in a single process.

Video: One-step Metabolomics: Carbohydrates, Organic and Amino Acids Quantified in a Single Procedure

Murine Renal Transplantation Procedure

Renal orthotopic transplantation in mice is a technically challenging procedure. Although the first kidney transplants in mice were performed by Russell et al over 30 years ago (1) and refined by Zhang et al years later (2), few people in the world have mastered this procedure. In our laboratory we have successfully performed 1200 orthotopic kidney transplantations with &gt; 90% survival rate. The key points for success include stringent control of reperfusion injury, bleeding and thrombosis, both during the procedure and post-transplantation, and use of 10-0 instead of 11-0 suture for anastomoses.
Post-operative care and treatment of the recipient is extremely important to transplant success and evaluation. All renal graft recipients receive antibiotics in the form of an injection of penicillin immediately post-transplant and sulfatrim in the drinking water continually. Overall animal health is evaluated daily and whole blood creatinine analyses are performed routinely with a portable I-STAT machine to assess graft function.

Renal transplantation in mice is a technically challenging procedure that requires careful post-operative care and treatment for success.

Renal orthotopic transplantation in mice is a technically challenging procedure. Although the first kidney transplants in mice were performed by Russell ...

Mammary Epithelial Transplant Procedure

This article describes and compares the fat pad clearance procedure developed by DeOme KB et al.1 and the sparing procedure developed by Brill B et al.2, followed by the mammary epithelial transplant procedure. The mammary transplant procedure is widely used by mammary biologists because it takes advantage of the fact that significant development of the mammary epithelium doesn't occur until after puberty. At 3 weeks of age, growth of the mammary epithelial tree is confined to the vicinity of the nipple and the fat pad is largely devoid of mammary epithelium, but by 7 weeks of age the epithelial ductal tree extends throughout the entire fat pad. Therefore, if this small portion of the fat pad containing epithelium, the region between the nipple and the lymph node, is removed at 3 weeks of age, the endogenous epithelium will never populate the mammary fat pad and the fat pad is described as "cleared". At this time, mammary epithelium from another source can be transplanted in the cleared fat pad where it has the potential to extend mammary ductal trees through out the fat pad. This procedure has been utilized in many experimental models including the examination of tumor phenotype in transgenic mammary epithelial tissue without the confounding effects of genotype on the entire animal3, in the identification of mammary stem cells by transplanting cells in limited dilution4,5, determining if hyperplastic nodules proceed to mammary tumors6, and to assess the effect of prior hormone exposure on the behavior of the mammary epithelium7,8.
Three week old host mice are anesthetized, cleaned and restrained on a surgical stage. A mid-sagittal incision is made through the skin, but not the peritoneum, extending from the pubis to the sternum. Oblique cuts are made through the skin from the mid-sagittal incision across the pelvis toward each leg. The skin is pulled away from the peritoneum to expose the 4th inguinal mammary gland. The fat pad is cleared by removing the fat pad tissue anterior to the lymph node. Epithelium fragments or epithelial cells are transplanted into the remaining cleared fat pad and the mouse is closed.

This article demonstrates the procedure developed by DeOme KB et al. (1959) and the sparing procedure developed by Brill B et al. (2008) for clearing the 4th inguinal mammary fat pad of a pubescent mouse in preparation for transplantation of mammary fragments, mammary epithelial cells, or mammary tumor cells.

This article describes and compares the fat pad clearance procedure developed by DeOme KB et al.1 and the sparing procedure developed by Brill B et al.2, ...

Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids

Microbes have complex metabolic pathways that can be investigated using biochemistry and functional genomics methods. One important technique to examine cell central metabolism and discover new enzymes is 13C-assisted metabolism analysis 1. This technique is based on isotopic labeling, whereby microbes are fed with a 13C labeled substrates. By tracing the atom transition paths between metabolites in the biochemical network, we can determine functional pathways and discover new enzymes. 
As a complementary method to transcriptomics and proteomics, approaches for isotopomer-assisted analysis of metabolic pathways contain three major steps 2. First, we grow cells with 13C labeled substrates. In this step, the composition of the medium and the selection of labeled substrates are two key factors. To avoid measurement noises from non-labeled carbon in nutrient supplements, a minimal medium with a sole carbon source is required. Further, the choice of a labeled substrate is based on how effectively it will elucidate the pathway being analyzed. Because novel enzymes often involve different reaction stereochemistry or intermediate products, in general, singly labeled carbon substrates are more informative for detection of novel pathways than uniformly labeled ones for detection of novel pathways3, 4. Second, we analyze amino acid labeling patterns using GC-MS. Amino acids are abundant in protein and thus can be obtained from biomass hydrolysis. Amino acids can be derivatized by N-(tert-butyldimethylsilyl)-N-methyltrifluoroacetamide (TBDMS) before GC separation. TBDMS derivatized amino acids can be fragmented by MS and result in different arrays of fragments. Based on the mass to charge (m/z) ratio of fragmented and unfragmented amino acids, we can deduce the possible labeled patterns of the central metabolites that are precursors of the amino acids. Third, we trace 13C carbon transitions in the proposed pathways and, based on the isotopomer data, confirm whether these pathways are active 2. Measurement of amino acids provides isotopic labeling information about eight crucial precursor metabolites in the central metabolism. These metabolic key nodes can reflect the functions of associated central pathways.
13C-assisted metabolism analysis via proteinogenic amino acids can be widely used for functional characterization of poorly-characterized microbial metabolism1. In this protocol, we will use Cyanothece 51142 as the model strain to demonstrate the use of labeled carbon substrates for discovering new enzymatic functions.

Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids

13C-isotope labeling is a useful technique for determining the cell central metabolism for various types of microorganisms. After cells have been cultured with a specific labeled substrate, GC-MS measurement can reveal functional metabolic pathways based on unique labeling patterns in proteinogenic amino acids.

Microbes have complex metabolic pathways that can be investigated using biochemistry and functional genomics methods. One important technique to examine ...

Quantitative Measurement of Invadopodia-mediated Extracellular Matrix Proteolysis in Single and Multicellular Contexts

Cellular invasion into local tissues is a process important in development and homeostasis. Malregulated invasion and subsequent cell movement is characteristic of multiple pathological processes, including inflammation, cardiovascular disease and tumor cell metastasis1. Focalized proteolytic degradation of extracellular matrix (ECM) components in the epithelial or endothelial basement membrane is a critical step in initiating cellular invasion. In tumor cells, extensive in vitro analysis has determined that ECM degradation is accomplished by ventral actin-rich membrane protrusive structures termed invadopodia2,3. Invadopodia form in close apposition to the ECM, where they moderate ECM breakdown through the action of matrix metalloproteinases (MMPs). The ability of tumor cells to form invadopodia directly correlates with the ability to invade into local stroma and associated vascular components3. 
Visualization of invadopodia-mediated ECM degradation of cells by fluorescent microscopy using dye-labeled matrix proteins coated onto glass coverslips has emerged as the most prevalent technique for evaluating the degree of matrix proteolysis and cellular invasive potential4,5. Here we describe a version of the standard method for generating fluorescently-labeled glass coverslips utilizing a commercially available Oregon Green-488 gelatin conjugate. This method is easily scaled to rapidly produce large numbers of coated coverslips. We show some of the common microscopic artifacts that are often encountered during this procedure and how these can be avoided. Finally, we describe standardized methods using readily available computer software to allow quantification of labeled gelatin matrix degradation mediated by individual cells and by entire cellular populations. The described procedures provide the ability to accurately and reproducibly monitor invadopodia activity, and can also serve as a platform for evaluating the efficacy of modulating protein expression or testing of anti-invasive compounds on extracellular matrix degradation in single and multicellular settings.

We describe the prototypical method for producing microscope coverslips coated with fluorescent gelatin for visualizing invadopodia-mediated matrix degradation. Computational techniques using available software are presented for quantifying the resultant levels of matrix proteolysis by single cells within a mixed population and for multicellular groups encompassing entire microscopic fields.

Cellular invasion into local tissues is a process important in development and homeostasis.  Malregulated invasion and subsequent cell movement is ...

A Chemical Screening Procedure for Glucocorticoid Signaling with a Zebrafish Larva Luciferase Reporter System

Glucocorticoid stress hormones and their artificial derivatives are widely used drugs to treat inflammation, but long-term treatment with glucocorticoids can lead to severe side effects. Test systems are needed to search for novel compounds influencing glucocorticoid signaling in vivo or to determine unwanted effects of compounds on the glucocorticoid signaling pathway. We have established a transgenic zebrafish assay which allows the measurement of glucocorticoid signaling activity in vivo and in real-time, the GRIZLY assay (Glucocorticoid Responsive In vivo Zebrafish Luciferase activitY). The luciferase-based assay detects effects on glucocorticoid signaling with high sensitivity and specificity, including effects by compounds that require metabolization or affect endogenous glucocorticoid production. We present here a detailed protocol for conducting chemical screens with this assay. We describe data acquisition, normalization, and analysis, placing a focus on quality control and data visualization. The assay provides a simple, time-resolved, and quantitative readout. It can be operated as a stand-alone platform, but is also easily integrated into high-throughput screening workflows. It furthermore allows for many applications beyond chemical screening, such as environmental monitoring of endocrine disruptors or stress research.

We describe the procedure and data analysis of a chemical screening system for glucocorticoid stress hormone signaling using zebrafish larvae: the Glucocorticoid Responsive In vivo Zebrafish Luciferase activitY (GRIZLY) assay. The assay sensitively and specifically detects effects on glucocorticoid signaling by compounds that require metabolization or affect endogenous glucocorticoid production.

Glucocorticoid stress hormones and their artificial derivatives are widely used drugs to treat inflammation, but long-term treatment with glucocorticoids ...

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting factors, such as labor intensive sample preparations, low detection limits, slow scan speeds, intensive method optimization for each metabolite, and the inability to measure both positively and negatively charged ions in single experiments. Therefore, a novel metabolomics protocol could advance metabolomics studies. Amide-based hydrophilic chromatography enables polar metabolite analysis without any chemical derivatization. High resolution MS using the Q-Exactive (QE-MS) has improved ion optics, increased scan speeds (256 msec at resolution 70,000), and has the capability of carrying out positive/negative switching. Using a cold methanol extraction strategy, and coupling an amide column with QE-MS enables robust detection of 168 targeted polar metabolites and thousands of additional features simultaneously.&#160; Data processing is carried out with commercially available software in a highly efficient way, and unknown features extracted from the mass spectra can be queried in databases.

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. Utilizing normal-phased liquid chromatography coupled to high-resolution mass spectrometry with polarity switching and a rapid duty cycle, we describe a protocol to analyze the polar metabolic composition of biological material with high sensitivity, accuracy, and resolution.

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting ...

One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bis(sulfosuccinimidyl) Suberate (BS3)

Affinity purification of Strep-tagged fusion proteins on resins carrying an engineered streptavidin (Strep-Tactin) has become a widely used method for isolation of protein complexes under physiological conditions. Fusion proteins containing two copies of Strep-tag II, designated twin-Strep-tag or SIII-tag, have the advantage of higher affinity for Strep-Tactin compared to those containing only a single Strep-tag, thus allowing more efficient protein purification. However, this advantage is offset by the fact that elution of twin-Strep-tagged proteins with biotin may be incomplete, leading to low protein recovery. The recovery can be dramatically improved by using denaturing elution with sodium dodecyl sulfate (SDS), but this leads to sample contamination with Strep-Tactin released from the resin, making the assay incompatible with downstream proteomic analysis. To overcome this limitation, we have developed a method whereby resin-coupled tetramer of Strep-Tactin is first stabilized by covalent cross-linking with Bis(sulfosuccinimidyl) suberate (BS3) and the resulting cross-linked resin is then used to purify target protein complexes in a single batch purification step. Efficient elution with SDS ensures good protein recovery, while the absence of contaminating Strep-Tactin allows downstream protein analysis by mass spectrometry. As a proof of concept, we describe here a protocol for purification of SIII-tagged viral protein VPg-Pro from nuclei of virus-infected N. benthamiana plants using the Strep-Tactin polymethacrylate resin cross-linked with BS3. The same protocol can be used to purify any twin-Strep-tagged protein of interest and characterize its physiological binding partners.

One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bissulfosuccinimidyl Suberate BS3

A method is described for efficient purification of twin-Strep-tagged fusion proteins and their specific complexes on modified streptavidin (Strep-Tactin) resin covalently cross-linked with Bis(sulfosuccinimidyl) suberate (BS3). The method has the advantages of fast speed, good target protein recovery and high purity, and is compatible with subsequent analysis by mass spectrometry.

Affinity purification of Strep-tagged fusion proteins on resins carrying an engineered streptavidin (Strep-Tactin) has become a widely used method for ...

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

S-Adenosyl-l-methionine (AdoMet or SAM)-dependent methyltransferases (MTase) catalyze the transfer of the activated methyl group from AdoMet to specific positions in DNA, RNA, proteins and small biomolecules. This natural methylation reaction can be expanded to a wide variety of alkylation reactions using synthetic cofactor analogues. Replacement of the reactive sulfonium center of AdoMet with an aziridine ring leads to cofactors which can be coupled with DNA by various DNA MTases. These aziridine cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific Methyltransferase-Induced Labeling of DNA (SMILing DNA). As a typical example we give a protocol for biotinylation of pBR322 plasmid DNA at the 5&#8217;-ATCGAT-3&#8217; sequence with the DNA MTase M.BseCI and the aziridine cofactor 6BAz in one step. Extension of the activated methyl group with unsaturated alkyl groups results in another class of AdoMet analogues which are used for methyltransferase-directed Transfer of Activated Groups (mTAG). Since the extended side chains are activated by the sulfonium center and the unsaturated bond, these cofactors are called double-activated AdoMet analogues. These analogues not only function as cofactors for DNA MTases, like the aziridine cofactors, but also for RNA, protein and small molecule MTases. They are typically used for enzymatic modification of MTase substrates with unique functional groups which are labeled with reporter groups in a second chemical step. This is exemplified in a protocol for fluorescence labeling of histone H3 protein. A small propargyl group is transferred from the cofactor analogue SeAdoYn to the protein by the histone H3 lysine 4 (H3K4) MTase Set7/9 followed by click labeling of the alkynylated histone H3 with TAMRA azide. MTase-mediated labeling with cofactor analogues is an enabling technology for many exciting applications including identification and functional study of MTase substrates as well as DNA genotyping and methylation detection.

DNA and proteins are sequence-specifically labeled with affinity or fluorescent reporter groups using DNA or protein methyltransferases and synthetic cofactor analogues. Depending on the cofactor specificity of the enzymes, aziridine or double activated cofactor analogues are employed for one- or two-step labeling.

S-Adenosyl-l-methionine (AdoMet or SAM)-dependent methyltransferases (MTase) catalyze the transfer of the activated methyl group from AdoMet to specific ...

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

The canonical set of amino acids leads to an exceptionally wide range of protein functionality. Nevertheless, the set of residues still imposes limitations on potential protein applications. The incorporation of noncanonical amino acids can enlarge this scope. There are two complementary approaches for the incorporation of noncanonical amino acids. For site-specific incorporation, in addition to the endogenous canonical translational machineries, an orthogonal aminoacyl-tRNA-synthetase-tRNA pair must be provided that does not interact with the canonical ones. Consequently, a codon that is not assigned to a canonical amino acid, usually a stop codon, is also required. This genetic code expansion enables the incorporation of a noncanonical amino acid at a single, given site within the protein. The here presented work describes residue-specific incorporation where the genetic code is reassigned within the endogenous translational system. The translation machinery accepts the noncanonical amino acid as a surrogate to incorporate it at canonically prescribed locations, i.e., all occurrences of a canonical amino acid in the protein are replaced by the noncanonical one. The incorporation of noncanonical amino acids can change the protein structure, causing considerably modified physical and chemical properties. Noncanonical amino acid analogs often act as cell growth inhibitors for expression hosts since they modify endogenous proteins, limiting in vivo protein production. In vivo incorporation of toxic noncanonical amino acids into proteins remains particularly challenging. Here, a cell-free approach for a complete replacement of L-arginine by the noncanonical amino acid L-canavanine is presented. It circumvents the inherent difficulties of in vivo expression. Additionally, a protocol to prepare target proteins for mass spectral analysis is included. It is shown that L-lysine can be replaced by L-hydroxy-lysine, albeit with lower efficiency. In principle, any noncanonical amino acid analog can be incorporated using the presented method as long as the endogenous in vitro translation system recognizes it.

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

An easy-to-use, cell-free expression protocol for the residue-specific incorporation of noncanonical amino acid analogs into proteins, including downstream analysis, is presented for medical, pharmaceutic, structural and functional studies.

The canonical set of amino acids leads to an exceptionally wide range of protein functionality. Nevertheless, the set of residues still imposes ...

Filtration Isolation of Nucleic Acids:  A Simple and Rapid DNA Extraction Method

FINA, filtration isolation of nucleic acids, is a novel extraction method which utilizes vertical filtration via a separation membrane and absorbent pad to extract cellular DNA from whole blood in less than 2 min. The blood specimen is treated with detergent, mixed briefly and applied by pipet to the separation membrane. The lysate wicks into the blotting pad due to capillary action, capturing the genomic DNA on the surface of the separation membrane. The extracted DNA is retained on the membrane during a simple wash step wherein PCR inhibitors are wicked into the absorbent blotting pad. The membrane containing the entrapped DNA is then added to the PCR reaction without further purification. This simple method does not require laboratory equipment and can be easily implemented with inexpensive laboratory supplies. Here we describe a protocol for highly sensitive detection and quantitation of HIV-1 proviral DNA from 100 &#181;l whole blood as a model for early infant diagnosis of HIV that could readily be adapted to other genetic targets.

We describe here a simple and rapid paper-based DNA extraction method of HIV proviral DNA from whole blood detected by quantitative PCR. This protocol can be extended for use in detecting other genetic markers or using alternative amplification methods.

FINA, filtration isolation of nucleic acids, is a novel extraction method which utilizes vertical filtration via a separation membrane and absorbent pad ...