This work was financially supported by the Fundamental Research Funds for the Central Universities (KJQN202060), the National Natural Science Foundation of China (31900907), the Natural Science Foundation of Jiangsu Province (BK20190528), the International Centre for Genetic Engineering and Biotechnology (CRP/CHN20-04_EC) to M.C., and the Fundamental Research Funds for the Central Universities (LGZD202004) to X.L.

1 Plant growth and materials collection
<ol>
	<li>Ensure that Arabidopsis seeds are sterilized in 70% ethanol for 10 min and sowed on the agar plates, which were prepared with one-half-strength Murashige and Skoog nutrients.</li>
	<li>Incubate the plates containing Arabidopsis seeds under dark at 4 &#176;C for 48 h, and then transfer them into a controlled growth chamber under 16 h light of 55 &#181;mol m-2 s-1 at 22 &#176;C and 8 h dark at 20 &#176;C.</li>
	<li>Harvest 100 mg of 2-week seedlings (fresh weight) and freeze in liquid nitrogen for metabolites extraction. 
	&#8203;CAUTION: Researchers should appropriately wear gloves, protective glasses, and a lab coat to avoid the human-tissue contamination during the materials collection.</li>
</ol>
2 Nucleosides/Nucleotides extraction
<ol>
	<li>Ground 100 mg of frozen plant tissues with 7-8 steel beads in a pre-cold mixer mill for 5 min at a frequency of 60 Hz.</li>
	<li>Prepare the extraction solution, which contains methanol, acetonitrile, and water in a ratio of 2:2:1.</li>
	<li>Resuspend the homogenized materials (including most metabolites but not proteins) with 1 mL of extraction solution.</li>
	<li>Centrifuge the resulting solution at 12,000 x g for 15 min at 4 &#176;C.</li>
	<li>Transfer 0.5 mL of the suspension to a new 1.5 mL tube and freeze in the liquid nitrogen.</li>
	<li>Evaporate the frozen sample in a freeze dyer and resuspend in 0.1 mL of 5% acetonitrile and 95% water.</li>
	<li>Centrifuge the resulting solution (0.1 mL) at 40,000 x g for 10 min at 4 &#176;C. Load the supernatant in a vial for LC-MS/MS measurement.</li>
</ol>
3 LC-MS/MS measurement
<ol>
	<li>Prepare a 10 mM ammonium acetate buffer by dissolving 1.1 g of ammonium acetate in 2 L of double deionized water (Mobile phase A). Adjust the pH to 9.5 by 10% ammonium and acetate acid.</li>
	<li>Prepare 2 L of ultrapure 100% methanol (Mobile phase B1) for nucleosides measurement. Also, prepare 2 L of ultrapure 100% acetonitrile (Mobile phase B2) for nucleotides measurement.</li>
	<li>Inject 0.02 mL of pre-treated metabolites extraction of each sample from step 2.7 into a HPLC system with binary pumps (LC) coupled with a triple quadrupole mass spectrometer (MS). 
	CAUTION: HPLC system employs a C18 column (50 x 4.6 mm, particle size 5 &#181;m; working at 25 &#176;C) buffering with mobile phase A and B1 (Figure 1A) for the nucleosides separation and use a porous graphitic carbon (PGC) column (50 x 4.6 mm, particle size 5 &#181;m; working at 25 &#176;C) with mobile phase A and B2 (Figure 1B) for the nucleotides separation. Each sample was injected three times for the technical replication.</li>
	<li>Program the method as shown in Table 1 for the C18 column, and the method as shown in Table 2 for the PGC column. Set a flow rate of 0.65 mL min-1. 
	NOTE: The mass transitions (Table 3) were monitored by mass spectrometer. The mass spectrum analysis conditions of eight nucleosides and five nucleotides containing canonical ones and modified ones are listed in Table 3.</li>
	<li>Record the peak areas of every target compound (Figure 1).</li>
</ol>
4 Generation of the standard calibration curves
<ol>
	<li>Pool six sample extractions together, which were produced following the description in section 2, and vortex it. Then, aliquot it to six extractions (same volume) again to get each background.</li>
	<li>Add six different concentrations of each standard to these six extractions, respectively, and inject them one by one following step 3.3.</li>
	<li>Record the peak areas of each standard at different concentrations via the mass transitions as described in steps 3.4 and 3.5.</li>
	<li>Plot the peak area against the nominal concentration of each standard to generate a six-point curve. 
	NOTE: The peak areas of nucleosides/nucleotides recorded in the step 3.5 should fall in the range of standard calibration curves.</li>
	<li>Calculate the equation of a straight line for each standard compound: Y = aX + b</li>
</ol>
5 Metabolites&#39; quantification
<ol>
	<li>Calculate the metabolites&#39; contents using the peak area recorded in step 3.5 and the equation from step 4.5.</li>
</ol>

<ol>
	<li>Liu, B., Winkler, F., Herde, M., Witte, C. -. P., Gro&#223;hans, 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+link+between+deoxyribonucleotide+metabolites+and+embryonic+cell-cycle+control.">A link between deoxyribonucleotide metabolites and embryonic cell-cycle control.</a> Current Biology. 29 (7), 1187-1192 (2019).</li><li>Zrenner, R., Stitt, M., Sonnewald, U., Boldt, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pyrimidine+and+purine+biosynthesis+and+degradation+in+plants.">Pyrimidine and purine biosynthesis and degradation in plants.</a> Annual Review of Plant Biology. 57, 805-836 (2006).</li><li>Witte, C. -. P., Herde, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nucleotide+metabolism+in+plants.">Nucleotide metabolism in plants.</a> Plant Physiology. 182 (1), 63-78 (2020).</li><li>Chen, M., Herde, M., Witte, C. -. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Of+the+nine+cytidine+deaminase-like+genes+in+Arabidopsis,+eight+are+pseudogenes+and+only+one+is+required+to+maintain+pyrimidine+homeostasis+in+vivo.">Of the nine cytidine deaminase-like genes in Arabidopsis, eight are pseudogenes and only one is required to maintain pyrimidine homeostasis in vivo.</a> Plant Physiology. 171 (2), 799-809 (2016).</li><li>Chen, 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=m6A+RNA+degradation+products+are+catabolized+by+an+evolutionarily+conserved+N6-methyl-AMP+deaminase+in+plant+and+mammalian+cells.">m6A RNA degradation products are catabolized by an evolutionarily conserved N6-methyl-AMP deaminase in plant and mammalian cells.</a> The Plant Cell. 30 (7), 1511-1522 (2018).</li><li>Chen, M., Witte, C. -. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+kinase+and+a+glycosylase+catabolize+pseudouridine+in+the+peroxisome+to+prevent+toxic+pseudouridine+monophosphate+accumulation.">A kinase and a glycosylase catabolize pseudouridine in the peroxisome to prevent toxic pseudouridine monophosphate accumulation.</a> The Plant Cell. 32 (3), 722-739 (2020).</li><li>Dahncke, K., Witte, C. -. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plant+purine+nucleoside+catabolism+employs+a+guanosine+deaminase+required+for+the+generation+of+xanthosine+in+Arabidopsis.">Plant purine nucleoside catabolism employs a guanosine deaminase required for the generation of xanthosine in Arabidopsis.</a> The Plant Cell. 25 (10), (2013).</li><li>Jung, B., 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=Uridine-ribohydrolase+is+a+key+regulator+in+the+uridine+degradation+pathway+of+Arabidopsis.">Uridine-ribohydrolase is a key regulator in the uridine degradation pathway of Arabidopsis.</a> The Plant Cell. 21 (3), 876-891 (2009).</li><li>Jung, B., Hoffmann, C., Moehlmann, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arabidopsis+nucleoside+hydrolases+involved+in+intracellular+and+extracellular+degradation+of+purines.">Arabidopsis nucleoside hydrolases involved in intracellular and extracellular degradation of purines.</a> Plant Journal. 65 (5), 703-711 (2011).</li><li>Riegler, H., Geserick, C., Zrenner, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arabidopsis+thaliana+nucleosidase+mutants+provide+new+insights+into+nucleoside+degradation.">Arabidopsis thaliana nucleosidase mutants provide new insights into nucleoside degradation.</a> New Phytologist. 191 (2), 349-359 (2011).</li><li>Zrenner, R., 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+functional+analysis+of+the+pyrimidine+catabolic+pathway+in+Arabidopsis.">A functional analysis of the pyrimidine catabolic pathway in Arabidopsis.</a> New Phytologist. 183 (1), 117-132 (2009).</li><li>Hauck, O. K., 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=Uric+acid+accumulation+in+an+Arabidopsis+urate+oxidase+mutant+impairs+seedling+establishment+by+blocking+peroxisome+maintenance.">Uric acid accumulation in an Arabidopsis urate oxidase mutant impairs seedling establishment by blocking peroxisome maintenance.</a> The Plant Cell. 26 (7), 3090-3100 (2014).</li><li>Qu, C., 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=Comparative+analysis+of+nucleosides,+nucleobases,+and+amino+acids+in+different+parts+of+Angelicae+Sinensis+Radix+by+ultra+high+performance+liquid+chromatography+coupled+to+triple+quadrupole+tandem+mass+spectrometry.">Comparative analysis of nucleosides, nucleobases, and amino acids in different parts of Angelicae Sinensis Radix by ultra high performance liquid chromatography coupled to triple quadrupole tandem mass spectrometry.</a> Journal of Separation Science. 42 (6), 1122-1132 (2019).</li><li>Zong, S. -. 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=Fast+simultaneous+determination+of+13+nucleosides+and+nucleobases+in+Cordyceps+sinensis+by+UHPLC-ESI-MS/MS.">Fast simultaneous determination of 13 nucleosides and nucleobases in Cordyceps sinensis by UHPLC-ESI-MS/MS.</a> Molecules. 20 (12), 21816-21825 (2015).</li><li>Moravcov&#225;, D., 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=Separation+of+nucleobases,+nucleosides,+and+nucleotides+using+two+zwitterionic+silica-based+monolithic+capillary+columns+coupled+with+tandem+mass+spectrometry.">Separation of nucleobases, nucleosides, and nucleotides using two zwitterionic silica-based monolithic capillary columns coupled with tandem mass spectrometry.</a> Journal of Chromatography. A. 1373, 90-96 (2014).</li><li>Guo, 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=Hydrophilic+interaction+ultra-high+performance+liquid+chromatography+coupled+with+triple+quadrupole+mass+spectrometry+for+determination+of+nucleotides,+nucleosides+and+nucleobases+in+Ziziphus+plants.">Hydrophilic interaction ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry for determination of nucleotides, nucleosides and nucleobases in Ziziphus plants.</a> Journal of Chromatography. A. 1301, 147-155 (2013).</li><li>Seifar, R. 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=Simultaneous+quantification+of+free+nucleotides+in+complex+biological+samples+using+ion+pair+reversed+phase+liquid+chromatography+isotope+dilution+tandem+mass+spectrometry.">Simultaneous quantification of free nucleotides in complex biological samples using ion pair reversed phase liquid chromatography isotope dilution tandem mass spectrometry.</a> Analytical Biochemistry. 388 (2), 213-219 (2009).</li><li>Baccolini, C., Witte, C. -. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AMP+and+GMP+catabolism+in+Arabidopsis+converge+on+xanthosine,+which+is+degraded+by+a+nucleoside+hydrolase+heterocomplex.">AMP and GMP catabolism in Arabidopsis converge on xanthosine, which is degraded by a nucleoside hydrolase heterocomplex.</a> The Plant Cell. 31 (3), 734-751 (2019).</li></ol>

The authors have no conflict of interest to disclose.

Organisms contain various nucleosides/nucleotides, including canonical and aberrant ones. However, the origin and metabolic endpoints of them, especially modified nucleosides, are still obscure. Furthermore, the current understanding of the function and homeostasis of nucleosides/nucleotides metabolism remain to be explored and expanded. To investigate them, a precise and gold-standard method for these metabolites identification and quantification needs to be employed. Here, we described a protocol using the mass spectru...

Nucleosides/Nucleotides are central metabolic components in all living organisms, which are the precursors for nucleic acids and many coenzymes, such as nicotinamide adenine dinucleotide (NAD), and important in the synthesis of macromolecules such as phospholipids, glycolipids, and polysaccharides. Structurally, nucleoside contains a nucleobase, which can be an adenine, guanine, uracil, cytosine, or thymine, and a sugar moiety, which can be a ribose or a deoxyribose1,2. Nucleotides have up to three phosphate groups binding to the 5-carbon position of the sugar moiety of the nucleosides3. The metabolism of nucleotides in plants is essential for seed germination and leaf growth4,5,6. To better understand their physiological roles in plant development, the methods for the absolute quantification of different nucleosides/nucleotides in vivo should be established.
One of the most commonly used approaches to measure nucleosides/nucleotides employs a high-performance liquid chromatography (HPLC) coupled with an ultraviolet-visible (UV-VIS) detector4,7,8,9,10,11. In 2013, using HPLC, Dahncke and Witte quantified several types of the nucleosides in Arabidopsis thaliana7. They identified an enhanced guanosine content in a T-DNA insertion mutant targeting in the guanosine deaminase gene compared to the wild-type plant. Another pyrimidine nucleoside, cytidine, was also quantitatively detected in plants employing this method, which resulted in the identification of a bona fide cytidine deaminase gene4. Based on the UV detector, this method, however, cannot easily distinguish the nucleosides which have similar spectrums and retention times, e.g., guanosine or xanthosine. The detection limit of HPLC method is relatively high, therefore, it is frequently used for the measurement of high content of nucleosides in vivo, such as cytidine, uridine, and guanosine.
In addition, gas chromatography coupled to mass spectrometry (GC-MS) can also be used in nucleoside measurement. Benefiting from it, Hauck et. al. successfully detected uridine and uric acid, which is a downstream metabolite of nucleoside catabolic pathway, in the seeds of A. thaliana12. However, GC is normally used to separate volatile compounds but not suitable for the thermally labile substances. Therefore, a liquid chromatography coupled to mass spectrometry (LC-MS/MS) is probably a more suitable and accurate analytical technique for the&#160;in vivo identification, separation, and quantification of the nucleosides/nucleotides13,14. Several previous studies reported that a HILIC column can be used for nucleosides and nucleotides separation15,16 and isotopically labeled internal standards were employed for the compound quantification17. However, both components are relatively expensive, especially the commercial isotope-labeled standards. Here, we report an economically applicable LC-MS/MS approach for nucleosides/nucleotides measurement. This method has been already successfully used for the quantitation of diverse nucleosides/nucleotides, including ATP, N6-methyl-AMP, AMP, GMP, uridine, cytidine, and pseudouridine1,5,6,18, in plants and Drosophila. Moreover, the method we report here can be used in other organisms as well.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>acetonitrile</td>
			<td>Sigma-Aldrich</td>
			<td>1000291000</td>
			<td></td>
		</tr>
		<tr>
			<td>adenosine</td>
			<td>Sigma-Aldrich</td>
			<td>A9251-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>ammonium acetate</td>
			<td>Sigma-Aldrich</td>
			<td>73594-100G-F</td>
			<td></td>
		</tr>
		<tr>
			<td>AMP</td>
			<td>Sigma-Aldrich</td>
			<td>01930-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>CMP</td>
			<td>Sigma-Aldrich</td>
			<td>C1006-500MG</td>
			<td></td>
		</tr>
		<tr>
			<td>cytidine</td>
			<td>Sigma-Aldrich</td>
			<td>C122106-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>GMP</td>
			<td>Sigma-Aldrich</td>
			<td>G8377-500MG</td>
			<td></td>
		</tr>
		<tr>
			<td>guanosine</td>
			<td>Sigma-Aldrich</td>
			<td>G6752-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>Hypercarb column</td>
			<td>Thermo Fisher Scientific GmbH</td>
			<td>35005-054630</td>
			<td></td>
		</tr>
		<tr>
			<td>IMP</td>
			<td>Sigma-Aldrich</td>
			<td>57510-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>inosine</td>
			<td>Sigma-Aldrich</td>
			<td>I4125-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>methanol</td>
			<td>Sigma-Aldrich</td>
			<td>34860-1L-R</td>
			<td></td>
		</tr>
		<tr>
			<td>N1-methyladenosine</td>
			<td>Carbosynth</td>
			<td>NM03697</td>
			<td></td>
		</tr>
		<tr>
			<td>O6-methylguanosine</td>
			<td>Carbosynth</td>
			<td>NM02922</td>
			<td></td>
		</tr>
		<tr>
			<td>Murashige and Skoog Medium</td>
			<td>Duchefa Biochemie</td>
			<td>M0255.005</td>
			<td></td>
		</tr>
		<tr>
			<td>Polaris 5 C18A column</td>
			<td>Agilent Technologies</td>
			<td>A2000050X046</td>
			<td></td>
		</tr>
		<tr>
			<td>pseudouridine</td>
			<td>Carbosynth</td>
			<td>NP11297</td>
			<td></td>
		</tr>
		<tr>
			<td>UMP</td>
			<td>Sigma-Aldrich</td>
			<td>U6375-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>uridine</td>
			<td>Sigma-Aldrich</td>
			<td>U3750-1G</td>
			<td></td>
		</tr>
	</tbody>
</table>

plant sample preparation for nucleoside/nucleotide content measurement with an hplc-ms/ms

Nucleosides/nucleotides are building blocks of nucleic acids, parts of cosubstrates and coenzymes, cell signaling molecules, and energy carriers, which are involved in many cell activities. Here, we describe a rapid and reliable method for the absolute qualification of nucleoside/nucleotide contents in plants. Briefly, 100 mg of homogenized plant material was extracted with 1 mL of extraction buffer (methanol, acetonitrile, and water at a ratio of 2:2:1). Later, the sample was concentrated five times in a freeze dryer and then injected into an HPLC-MS/MS. Nucleotides were separated on a porous graphitic carbon (PGC) column and nucleosides were separated on a C18 column. The mass transitions of each nucleoside and nucleotide were monitored by mass spectrometry. The contents of the nucleosides and nucleotides were quantified against their external standards (ESTDs). Using this method, therefore, researchers can easily quantify nucleosides/nucleotides in different plants.

Here, we show the identification and quantification of N1-methyladenosine, a known modified nucleoside, in 2-week-old Arabidopsis wild type (Col-0) seedlings as an example. Mass spectrometry profile indicates that the product ions generated from the N1-methyladenosine standard are 150 m/z and 133 m/z (Figure 2A), and the same profile is also observed in Col-0 extraction (Figure 2B). Due to high abun...

Watch this Scientific Journal Video about Plant Sample Preparation for Nucleoside/Nucleotide Content Measurement with An HPLC-MS/MS at JoVE.com

Plant Sample Preparation for Nucleoside/Nucleotide Content Measurement with An HPLC-MS/MS

A precise and reproducible method for in vivo nucleosides/nucleotides quantification in plants is described here. This method employs an HPLC-MS/MS.

Nucleosides/nucleotides are building blocks of nucleic acids, parts of cosubstrates and coenzymes, cell signaling molecules, and energy carriers, which ...

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5.1K Views.  Nanjing Agricultural University. A precise and reproducible method for in vivo nucleosides/nucleotides quantification in plants is described here. This method employs an HPLC-MS/MS.

Video: Plant Sample Preparation for Nucleoside/Nucleotide Content Measurement with An HPLC-MS/MS

Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development

Genes with important roles in development frequently have spatially and/or temporally restricted expression patterns. Often these gene transcripts are not detected or are not identified as differentially expressed (DE) in transcriptomic analyses of whole plant organs. Laser Microdissection RNA-Seq (LM RNA-Seq) is a powerful tool to identify genes that are DE in specific developmental domains. However, the choice of cellular domains to microdissect and compare, and the accuracy of the microdissections are crucial to the success of the experiments. Here, two examples illustrate design considerations for transcriptomics experiments; a LM RNA-seq analysis to identify genes that are DE along the maize leaf proximal-distal axis, and a second experiment to identify genes that are DE in liguleless1-R (lg1-R) mutants compared to wild-type. Key elements that contributed to the success of these experiments were detailed histological and in situ hybridization analyses of the region to be analyzed, selection of leaf primordia at equivalent developmental stages, the use of morphological landmarks to select regions for microdissection, and microdissection of precisely measured domains. This paper provides a detailed protocol for the analysis of developmental domains by LM RNA-Seq. The data presented here illustrate how the region selected for microdissection will affect the results obtained.

Many developmentally important genes have cell- or tissue-specific expression patterns. This paper describes LM RNA-seq experiments to identify genes that are differentially expressed at the maize leaf blade-sheath boundary and in lg1-R mutants compared to wild-type. The experimental considerations discussed here apply to transcriptomic analyses of other developmental phenomena.

Genes with important roles in development frequently have spatially and/or temporally restricted expression patterns. Often these gene transcripts are not ...

Determination of the Glycogen Content in Cyanobacteria

Cyanobacteria accumulate glycogen as a major intracellular carbon and energy storage&#160;during photosynthesis. Recent developments in research have highlighted complex mechanisms of glycogen metabolism, including the diel cycle of biosynthesis and catabolism, redox regulation, and the involvement of non-coding RNA. At the same time, efforts are being made to redirect carbon from glycogen to desirable products in genetically engineered cyanobacteria to enhance product yields. Several methods are used to determine the glycogen contents in cyanobacteria, with variable accuracies and technical complexities. Here, we provide a detailed protocol for the reliable determination of the glycogen content in cyanobacteria that can be performed in a standard life science laboratory. The protocol entails the selective precipitation of glycogen from the cell lysate and the enzymatic depolymerization of glycogen to generate glucose monomers, which are detected by a glucose oxidase-peroxidase (GOD-POD) enzyme coupled assay. The method has been applied to Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002, two model cyanobacterial species that are widely used in metabolic engineering. Moreover, the method successfully showed differences in the glycogen contents between the wildtype and mutants defective in regulatory elements or glycogen biosynthetic genes.

Here, we present a reliable and easy assay to measure the glycogen content in cyanobacterial cells. The procedure entails precipitation, selectable depolymerization, and the detection of glucose residues. This method is suitable for both wildtype and genetically engineered strains and can facilitate the metabolic engineering of cyanobacteria.

Cyanobacteria accumulate glycogen as a major intracellular carbon and energy storage&#160;during photosynthesis. Recent developments in research have ...

Spectrophotometric Determination of Phycobiliprotein Content in Cyanobacterium Synechocystis

This is a simple protocol for the quantitative determination of phycobiliprotein content in the model cyanobacterium Synechocystis. Phycobiliproteins are the most important components of phycobilisomes, the major light-harvesting antennae in cyanobacteria and several algae taxa. The phycobilisomes of Synechocystis contain two phycobiliproteins: phycocyanin and allophycocyanin. This protocol describes a simple, efficient, and reliable method for the quantitative determination of both phycocyanin and allophycocyanin in this model cyanobacterium. We compared several methods of phycobiliprotein extraction and spectrophotometric quantification. The extraction procedure as described in this protocol was also successfully applied to other cyanobacteria strains such as Cyanothece sp., Synechococcuselongatus, Spirulina sp., Arthrospira sp., and Nostoc sp., as well as to red algae Porphyridium cruentum. However, the extinction coefficients of specific phycobiliproteins from various taxa can differ and it is, therefore, recommended to validate the spectrophotometric quantification method for every single strain individually. The protocol requires little time and can be performed in any standard life science laboratory since it requires only standard equipment.

Spectrophotometric Determination of Phycobiliprotein Content in Cyanobacterium Synechocystis

Here, we present a protocol to quantitatively determine phycobiliprotein content in the cyanobacterium Synechocystis using a spectrophotometric method. The extraction procedure was also successfully applied to other cyanobacteria and algae strains; however, due to variations in pigment absorption spectra, it is necessary to test the spectrophotometric equations for each strain individually.

This is a simple protocol for the quantitative determination of phycobiliprotein content in the model cyanobacterium Synechocystis. Phycobiliproteins are ...

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. A prerequisite for the method is that highly ordered crystalline specimen need to be grown from the macromolecule to be studied, which then need to be prepared for the diffraction experiment. This preparation procedure typically involves removal of the crystal from the solution, in which it was grown, soaking of the crystal in ligand solution or cryo-protectant solution and then immobilizing the crystal on a mount suitable for the experiment. A serious problem for this procedure is that macromolecular crystals are often mechanically unstable and rather fragile. Consequently, the handling of such fragile crystals can easily become a bottleneck in a structure determination attempt. Any mechanical force applied to such delicate crystals may disturb the regular packing of the molecules and may lead to a loss of diffraction power of the crystals. Here, we present a novel all-in-one sample holder, which has been developed in order to minimize the handling steps of crystals and hence to maximize the success rate of the structure determination experiment. The sample holder supports the setup of crystal drops by replacing the commonly used microscope cover slips. Further, it allows in-place crystal manipulation such as ligand soaking, cryo-protection and complex formation without any opening of the crystallization cavity and without crystal handling. Finally, the sample holder has been designed in order to enable the collection of in situ X-ray diffraction data at both, ambient and cryogenic temperature. By using this sample holder, the chances to damage the crystal on its way from crystallization to diffraction data collection are considerably reduced since direct crystal handling is no longer required.

A novel sample holder for macromolecular X-ray crystallography along with a suitable handling protocol is presented. The system allows crystal growth, crystal soaking and in situ diffraction data collection at both, ambient and cryogenic temperature without the need of any crystal manipulation or mounting.

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. ...

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation

Sample preparation for mass spectrometry analysis in proteomics requires enzymatic cleavage of proteins into a peptide mixture. This process involves numerous incubation and liquid transfer steps in order to achieve denaturation, reduction, alkylation, and cleavage. Adapting this workflow onto an automated workstation can increase efficiency and reduce coefficients of variance, thereby providing more reliable data for statistical comparisons between sample types. We previously described an automated proteomic sample preparation workflow1. Here, we report the development of a more efficient and better controlled workflow with the following advantages: 1) The number of liquid transfer steps is reduced from nine to six by combining reagents; 2) Pipetting time is reduced by selective tip pipetting using a 96-position pipetting head with multiple channels; 3) Potential throughput is increased by the availability of up to 45 deck positions; 4) Complete enclosure of the system provides improved temperature and environmental control and reduces the potential for contamination of samples or reagents; and 5) The addition of stable isotope labeled peptides, as well as &#946;-galactosidase protein, to each sample makes monitoring and quality control possible throughout the entire process. These hardware and process improvements provide good reproducibility and improve intra-assay and inter-assay precision (CV of less than 20%) for LC-MS based protein and peptide quantification. The entire workflow for digesting 96 samples in a 96-well plate can be completed in approximately 5 hours.

Here, we present an automated plasma protein digestion method for mass spectrometry-based quantitative proteomic analysis. In this protocol, the liquid transferring and incubation steps for protein denaturation, reduction, alkylation, and trypsin digestion reactions are streamlined and automated. It takes approximately five hours to prepare a 96-well plate with desired precision.

Sample preparation for mass spectrometry analysis in proteomics requires enzymatic cleavage of proteins into a peptide mixture. This process involves ...

Sample Preparation for Probe Electrospray Ionization Mass Spectrometry

Mass spectrometry (MS) is a powerful tool in analytical chemistry because it provides very accurate information about molecules, such as mass-to-charge ratios (m/z), which are useful to deduce molecular weights and structures. While it is essentially a destructive analytical method, recent advancements in the ambient ionization technique have enabled us to acquire data while leaving tissue in a relatively intact state in terms of integrity. Probe electrospray ionization (PESI) is a so-called direct method because it does not require complex and time-consuming pretreatment of samples. A fine needle serves as a sample picker, as well as an ionization emitter. Based on the very sharp and fine property of the probe tip, destruction of the samples is minimal, allowing us to acquire the real-time molecular information from living things in situ. Herein, we introduce three applications of PESI-MS technique that will be useful for biomedical research and development. One involves the application to solid tissue, which is the basic application of this technique for the medical diagnosis. As this technique requires only 10 mg of the sample, it may be very useful in the routine clinical settings. The second application is for in vitro medical diagnostics where human blood serum is measured. The ability to measure fluid samples is also valuable in various biological experiments where a sufficient volume of sample for conventional analytical techniques cannot be provided. The third application leans toward the direct application of probe needles in living animals, where we can obtain real-time dynamics of metabolites or drugs in specific organs. In each application, we can infer the molecules that have been detected by MS or use artificial intelligence to obtain a medical diagnosis.

This article introduces sample preparation methods for a unique real-time analytical method based on the ambient mass spectrometry. This method lets us perform real-time analysis of the biological molecules in vivo without any special pretreatments.

Mass spectrometry (MS) is a powerful tool in analytical chemistry because it provides very accurate information about molecules, such as mass-to-charge ...

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Proteomic technologies are powerful methodologies that can aid our understanding of mechanisms of action in biological systems by providing a global view of the impact of a disease, treatment, or other condition on the proteome as a whole. This report provides a detailed protocol for the extraction, quantification, precipitation, digestion, labeling, and subsequent data analysis of protein samples. Our optimized TMT labeling protocol requires a lower tag-label concentration and achieves consistently reliable data. We have used this protocol to evaluate protein expression profiles in a variety of mouse tissues (i.e., heart, skeletal muscle, and brain) as well as cells cultured in vitro. In addition, we demonstrate how to evaluate thousands of proteins from the resulting dataset.

We present an optimized tandem mass tag (TMT) labeling protocol that includes detailed information for each of the following steps: protein extraction, quantification, precipitation, digestion, labeling, submission to a proteomics facility, and data analyses.

Proteomic technologies are powerful methodologies that can aid our understanding of mechanisms of action in biological systems by providing a global view ...

Estimation of Plant Biomass Lignin Content using Thioglycolic Acid (TGA)

Lignin is a natural polymer that is the second most abundant polymer on Earth after cellulose. Lignin is mainly deposited in plant secondary cell walls and is an aromatic heteropolymer primarily composed of three monolignols with significant industrial importance. Lignin plays an important role in plant growth and development, protects&#160;from biotic and abiotic stresses, and in the quality of animal fodder, the wood, and industrial lignin products. Accurate estimation of lignin content is essential for both fundamental understanding of the lignin biosynthesis and industrial applications of biomass. The thioglycolic acid (TGA) method is a highly reliable method of estimating the total lignin content in the plant biomass. This method estimates the lignin content by forming thioethers with the benzyl alcohol groups of lignin, which are soluble in alkaline conditions and insoluble in acidic conditions. The total lignin content is estimated using a standard curve generated from commercial bamboo lignin.

Estimation of Plant Biomass Lignin Content using Thioglycolic Acid TGA

Here, we present a modified TGA method for estimation of lignin content in herbaceous plant biomass. This method estimates the lignin content by forming specific thioether bonds with lignin and presents an advantage over the Klason method, as it requires a relatively small sample for lignin content estimation.

Lignin is a natural polymer that is the second most abundant polymer on Earth after cellulose. Lignin is mainly deposited in plant secondary cell walls ...

A Sample Preparation Pipeline for Microcrystals at the VMXm Beamline

The mounting of microcrystals (&#60;10 &#181;m) for single crystal cryo-crystallography presents a non-trivial challenge. Improvements in data quality have been seen for microcrystals with the development of beamline optics, beam stability and variable beam size focusing from submicron to microns, such as at the VMXm beamline at Diamond Light Source1. Further improvements in data quality will be gained through improvements in sample environment and sample preparation. Microcrystals inherently generate weaker diffraction, therefore improving the signal-to-noise is key to collecting quality X-ray diffraction data and will predominantly come from reductions in background noise. Major sources of X-ray background noise in a diffraction experiment are from their interaction with the air path before and after the sample, excess crystallization solution surrounding the sample, the presence of crystalline ice and scatter from any other beamline instrumentation or X-ray windows. The VMXm beamline comprises instrumentation and a sample preparation protocol to reduce all these sources of noise.
Firstly, an in-vacuum sample environment at VMXm removes the air path between X-ray source and sample. Next, sample preparation protocols for macromolecular crystallography at VMXm utilize a number of processes and tools adapted from cryoTEM. These include copper grids with holey carbon support films, automated blotting and plunge cooling robotics making use of liquid ethane. These tools enable the preparation of hundreds of microcrystals on a single cryoTEM grid with minimal surrounding liquid on a low-noise support. They also minimize the formation of crystalline ice from any remaining liquid surrounding the crystals. 
We present the process for preparing and assessing the quality of soluble protein microcrystals using visible light and scanning electron microscopy before mounting the samples on the VMXm beamline for X-ray diffraction experiments. We will also provide examples of good quality samples as well as those which require further optimization and strategies to do so.

The signal-to-noise ratio of data is one of the most important considerations in performing X-ray diffraction measurements from microcrystals. The VMXm beamline provides a low-noise environment and microbeam for such experiments. Here, we describe sample preparation methods for mounting and cooling microcrystals for VMXm and other microfocus macromolecular crystallography beamlines.

The mounting of microcrystals (&#60;10 &#181;m) for single crystal cryo-crystallography presents a non-trivial challenge. Improvements in data quality ...

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization

Both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) are widely used metabolomics approaches to detect and quantify hundreds of thousands of metabolite features. However, the application of these techniques to a large number of samples is subject to more complex interactions, particularly for genome-wide association studies (GWAS). This protocol describes an optimized metabolic workflow, which combines an efficient and fast sample preparation with the analysis of a large number of samples for legume crop species. This slightly modified extraction method was initially developed for the analysis of plant and animal tissues and is based on extraction in methyl tert-butyl ether: methanol solvent to allow the capture of polar and lipid metabolites. In addition, we provide a step-by-step guide for reducing analytical variations, which are essential for the high-throughput evaluation of metabolic variance in GWAS.

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization

In this protocol, we present an optimized workflow, which combines an efficient and fast sample preparation of many samples. In addition, we provide a step-by-step guide to reduce analytical variations for high-throughput evaluation of metabolic GWAS studies.

Both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) are widely used metabolomics approaches to detect ...