The laboratory of GSCh is supported in part by grant IN201222 from Programa de Apoyo a Proyectos de Investigaci&#243;n e Innovaci&#243;n Tecnol&#243;gica (PAPIIT), Direcci&#243;n General de Asuntos del Personal Acad&#233;mico -UNAM.

This procedure is schematized in Supplementary Figure 1. The reagents and equipment used for the study are listed in the Table of Materials.
1. Detection of mRL and dRL in culture supernatants of P. aeruginosa using TLC
<ol>
	<li>Start with the centrifuged broth of the P. aeruginosa strain of interest, cultivated in liquid medium for 24 h (to reach the stationary phase of growth where RL is produced). Typically, these cultures contain 1 x 109 bacteria per mL.</li>
	<li>Adjust the pH of the culture to 2 using concentrated HCl.</li>
	<li>Put 5 mL of the acidified culture supernatant in a 50 mL polypropylene tube and add 5 mL of a 2:1 chloroform: methanol mixture.</li>
	<li>Agitate the tube by inversion three times, each time for 10 s, and leave the tube without inversion for 2 min between each agitation.</li>
	<li>Leave the tube without agitation for approximately 3 h until the two phases are separated, or centrifuge the tube for 10 min at 3,000 x g at 4 &#176;C.</li>
	<li>Transfer the organic phase (bottom layer) to a clean tube and leave the tube in an extraction hood until dryness occurs.</li>
	<li>Repeat the process starting from step 1.3, putting the organic phase from the second chloroform: methanol extraction, into the tube that was used in the first extraction.</li>
	<li>Evaporate the organic phase until 1 mL or 1.5 mL are left. Transfer this volume to a 1.5 mL centrifuge tube and evaporate the solvent to dryness overnight.</li>
	<li>Add 50 &#181;L of methanol to the dried tube to resuspend RL.</li>
	<li>Perform thin-layer chromatography on silica gel plates. 
	NOTE: The size of the TLC plate should be cut according to the number of samples that will be analyzed. Each sample should be applied at 1.5 cm, and the point of application should be 1 cm from the edge of the plate (draw a horizontal line with a pencil).</li>
	<li>Apply 5 &#181;L of each sample using a 10 &#181;L micropipette.</li>
	<li>The TLC liquid phase consists of a 65:15:2 mixture of chloroform: methanol: acetic acid. To prepare 35 mL of this mixture, mix 26 mL of chloroform, 6 mL of methanol, and 0.8 mL of a 20% stock solution of acetic acid. Mix these solvents and place them in the closed TLC chamber for at least 10 min before beginning the chromatography, so the atmosphere is saturated with the volatile solvents.</li>
	<li>Place the TLC plate into the chamber, avoiding contact with the point where the samples were applied.</li>
	<li>Close the chamber and leave the TLC until the solvent reaches 1 cm before the edge of the plate. At this point, remove the plate and let it dry (a flow of air can be applied to accelerate the process).</li>
	<li>Prepare a solution of &#945;-naphthol by dissolving 5 g of this compound in 33 mL of ethanol. Once dissolved, add 127.5 mL of ethanol, 12.6 mL of water, and 20.5 mL of cold H2SO4.</li>
	<li>To detect the presence of mRL and dRL, spray the &#945;-naphthol solution onto the plate in the extraction hood and place the sprayed plate in an oven at 85 &#176;C for several minutes until the pinkish mark of RL is apparent.</li>
	<li>Use a picture of the TLC to calculate the proportion of mono- and di-RL present in each sample using software that detects the density of each spot.</li>
</ol>
2. Quantification of the total amount of RL measuring the rhamnose equivalents present in the biosurfactant
<ol>
	<li>Place 1.2 mL of a stationary phase culture (grown for 24 h) in a 1.5 mL centrifuge tube and centrifuge for 3 min at 3,000 x g at 4 &#176;C. Collect the supernatant in a clean tube.</li>
	<li>Transfer 333 &#181;L to a clean tube (perform this step in triplicate) and add 1 mL of ether.</li>
	<li>Vigorously mix in a vortex for 30 s. Repeat this procedure with one tube at a time.</li>
	<li>Centrifuge for 2 min at 3,000 x g at 4 &#176;C. Collect the organic phase (upper phase), transfer it to a clean tube, and leave it open in the extraction hood until dryness occurs.</li>
	<li>Repeat the extraction with ether as described in step 2.2. Repeat steps 2.3 and 2.4.</li>
	<li>Once completely dried, add 1 mL of water to each tube. Leave the tubes for 12 h to allow the RL to hydrate, then agitate vigorously in the vortex.</li>
	<li>Place a clean flask in ice for 5 min (as it is an exothermic reaction). Prepare a solution of 60% H2SO4 (protect the flask from light).</li>
	<li>In a clean tube, prepare a 1.6% orcinol solution in distilled water. To prepare the orcinol reagent, mix 4.4 mL of the 60% H2SO4 solution with 0.6 mL of the 1.6% orcinol solution.</li>
	<li>Calculate the final volume of the orcinol reagent needed. Add 900 &#181;L of this reagent to each sample and to each concentration of the calibration curve, using different rhamnose concentrations (typically, 9 concentrations of rhamnose are used in the range of 1 &#181;g/mL to 9 &#181;g/mL), and one with 100 &#181;L of water, ensuring that all are performed in triplicate.</li>
	<li>Add 100 &#181;L of each RL sample to 900 &#181;L of the orcinol reagent in a glass tube and mix the two solutions.</li>
	<li>Incubate for 30 min in a water bath preheated to 80 &#176;C.</li>
	<li>Allow the tubes to cool to room temperature.</li>
	<li>Read the absorbance of the samples and calibration curve at 421 nm using a quartz cell.</li>
	<li>Calculate the concentration of rhamnose in each sample by interpolating the absorbance on the calibration curve and considering the volume used for the determination.</li>
	<li>To calculate the &#181;M concentration, divide the concentration obtained in &#181;g/mL by 182.2 (the molecular weight of rhamnose) and multiply by 1000.</li>
</ol>

Comparative Analysis of Rhamnolipid Production in Pseudomonas aeruginosa Strains

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P., Serv&#237;n-Gonz&#225;lez, L., Sober&#243;n-Ch&#225;vez, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overproduction+of+rhamnolipids+in+Pseudomonas+aeruginosa+PA14+by+redirection+of+the+carbon+flux+from+polyhydroxyalcanoate+synthesis+and+overexpression+of+the+rhlAB-R+operon.">Overproduction of rhamnolipids in Pseudomonas aeruginosa PA14 by redirection of the carbon flux from polyhydroxyalcanoate synthesis and overexpression of the rhlAB-R operon.</a> Biotechnology Letters. 40 (11), 1561-1566 (2018).</li><li>Zibek, S., Sober&#243;n-Ch&#225;vez, G., Hausmann, R., Henkel, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overview+on+glycosylated+lipids+produced+by+bacteria+and+fungi:+Rhamno-,+Sophoro-,+Mannosylerythritol+and+Cellobiose+Lipids.">Overview on glycosylated lipids produced by bacteria and fungi: Rhamno-, Sophoro-, Mannosylerythritol and Cellobiose Lipids.</a> Biosurfactants for a Biobased. 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The authors have no conflict of interest to disclose.

The most accurate method for detecting and quantifying RL is HPLC coupled with mass spectrometry (MS)7,8,27; however, it requires specialized and expensive equipment that may not be accessible to many researchers. The methods described here can be routinely performed with basic laboratory materials and equipment to detect and estimate RL concentrations, but they have some limitations, particularly their inaccuracy in determining...

Pseudomonas aeruginosa is an environmental bacterium and an opportunistic pathogen of great concern due to its production of virulence-associated traits and its high antibiotic resistance1,2. A characteristic secondary metabolite produced by this bacterium is the biosurfactant RL, which is produced in a coordinated manner with several virulence-associated traits such as the phenazine pyocyanin, an antibiotic with redox activity, and the protease elastase3. The tensio-active and emulsification properties of RL have been exploited in different industrial applications and are currently commercialized4.
Most P. aeruginosa strains, belonging to phylogroups 1 and 2, produce two types of RL: mRL, which consists of one rhamnose moiety linked to a fatty acid dimer mainly of 10 carbons, and dRL, which contains an additional rhamnose moiety linked to the first rhamnose4 (see Figure 1). However, it has been reported that two minor P. aeruginosa phylogroups (groups 3 and 5) only produce mRL5,6. The two types of RL contain a mixture of fatty acid dimers, which, as mentioned, are mainly C10-C10, but smaller proportions of molecules containing C12-C10, C12-C12, and C10-C12:1 dimers are also produced. The characterization of the RL congeners produced by different strains using HPLC MS/MS has been reported7,8. The methods described in this work can only differentiate between mRL and dRL but cannot be used for the characterization of the RL congeners.
P. aeruginosa and some Burkholderia species are natural producers of RL9, but the former bacterium is the most efficient producer. However, commercially used RL is currently produced in Pseudomonas putida KT2440 derivatives expressing P. aeruginosa genes to avoid the use of this opportunistic pathogen10,11. The detection and quantification of RL produced by P. aeruginosa are of great importance for studying the molecular mechanisms involved in the expression of virulence-related traits12, in the characterization of strains belonging to clades 3 or 513, and for constructing P. aeruginosa derivatives that overproduce these biosurfactants while having reduced virulence14. The production of biosurfactants by different microorganisms has been detected based on some general characteristics of these compounds, such as the collapse drop method or emulsification index15, but these methods are neither accurate nor specific16.
Here, we describe the protocol to detect mRL and dRL using the liquid extraction of total RL from the culture supernatants of different P. aeruginosa-type strains and the separation of both types of RL using TLC. In this method, the RL extracted from the culture supernatant is separated by their differential solubility in the solvents used for TLC, causing differential migration on the silica gel plate. Thus, mRL have a more rapid migration than dRL, and they can be detected as separate spots when the plates are dried and stained with &#945;-naphthol.
The method described here for detecting mRL and dRL by TLC is based on a previously published article17, which is easy to perform and does not require expensive equipment. This method has been useful for detecting RL in various P. aeruginosa isolates13 using appropriate controls, such as a P. aeruginosa-derived mutant unable to produce RL. However, it is not the preferred method for characterizing novel biosurfactants produced by bacteria other than Pseudomonas aeruginosa due to its lack of specificity.
Additionally, a method for quantifying the rhamnose equivalents of total RL extracted from a P. aeruginosa culture supernatant is presented. This method quantifies these biosurfactants based on the reaction of orcinol with reductive sugars, resulting in a product that can be measured spectrophotometrically at 421 nm, as previously described18. Since the reaction with orcinol is not specific to rhamnose, it is important to perform this method with RL extracted from the culture supernatant that does not contain significant amounts of other sugar-containing molecules, such as lipopolysaccharides (LPS). An acidified chloroform/methanol mixture is used here for liquid extraction of RL18, but ethyl acetate can also be used, and solid-phase extraction (SPE) yields very good results19. The orcinol method described here does not require sophisticated equipment and can provide reliable results if performed with special care in preparing the analyzed samples, as discussed. To ensure proper sample preparation, it is important to include a Pseudomonas aeruginosa rhlA mutant unable to produce RL20 and to perform three biological and three technical replicates for each determination.
There has been significant controversy in the literature16,21regarding RL determination by the orcinol method, with some studies suggesting that RL production is overestimated and that the assay lacks specificity for rhamnose, potentially detecting other sugars. However, we demonstrate here that the methods described can be accurate and specific under the appropriate conditions. Furthermore, for comparison with the procedures outlined in this article, we utilize UPLC-MS/MS detection of a dRL standard and demonstrate that similar results are obtained with the orcinol method. The detailed protocol for quantifying RL using this method is included in Supplementary File 1.
These protocols are exemplified using the type strains PAO1 (phylogroup 1), PA14 (phylogroup 2), and PA7 (phylogroup 3). These strains were chosen because they are well-characterized and produce different RL profiles.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1-NAPHTHOL</td>
			<td>SIGMA-ALDRICH</td>
			<td>70442</td>
			<td></td>
		</tr>
		<tr>
			<td>ACETIC ACID</td>
			<td>J.T. BAKER</td>
			<td>9508-02</td>
			<td></td>
		</tr>
		<tr>
			<td>CENTRIFUGE</td>
			<td></td>
			<td></td>
			<td>For centrifuging tubes 1.5 mL and&#160; 50 mL</td>
		</tr>
		<tr>
			<td>CHLOROFORM</td>
			<td>J.T. BAKER</td>
			<td>9180-02</td>
			<td></td>
		</tr>
		<tr>
			<td>DRYING OVEN</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>ETHER</td>
			<td>J.T. BAKER</td>
			<td>9244-02</td>
			<td></td>
		</tr>
		<tr>
			<td>GLASS PIPETTE</td>
			<td>SIGMA-ALDRICH</td>
			<td>CLS706510</td>
			<td></td>
		</tr>
		<tr>
			<td>HYDROCHLORIC ACID</td>
			<td>J.T. BAKER</td>
			<td>5622-02</td>
			<td></td>
		</tr>
		<tr>
			<td>LB</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>L-RHAMNOSE MONOHYDRATE</td>
			<td>SIGMA-ALDRICH</td>
			<td>R-3875</td>
			<td></td>
		</tr>
		<tr>
			<td>METHANOL</td>
			<td>J.T. BAKER</td>
			<td>9049-02</td>
			<td></td>
		</tr>
		<tr>
			<td>ORCINOL MONOHYDRATE</td>
			<td>SIGMA-ALDRICH</td>
			<td>O1875</td>
			<td></td>
		</tr>
		<tr>
			<td>PPGAS Broth</td>
			<td></td>
			<td></td>
			<td>Tris HCL (0.12M), Potassium Chloride ( 0.02M) Ammonium Chloride (0.02M),&#160; Peptone (1%), pH 7.4&#160;&#160; Autoclaved. Add&#160; Glucose (5%) and Magnesium Sulfate (0.0016M)</td>
		</tr>
		<tr>
			<td>QUARTZ CELL (CUVETTE)</td>
			<td>SIGMA-ALDRICH</td>
			<td>Z276669</td>
			<td></td>
		</tr>
		<tr>
			<td>RECTANGULAR TLC DEVELOPING TANK</td>
			<td>FISHER SCIENTIFIC</td>
			<td>K4161801020</td>
			<td></td>
		</tr>
		<tr>
			<td>RHAMNOLIPIDS&#160;</td>
			<td>SIGMA-ALDRICH</td>
			<td>R-90</td>
			<td></td>
		</tr>
		<tr>
			<td>SPECTROPHOTOMETER</td>
			<td></td>
			<td></td>
			<td>VIS</td>
		</tr>
		<tr>
			<td>SPRAYER</td>
			<td>SIGMA-ALDRICH</td>
			<td>Z529710-1EA</td>
			<td></td>
		</tr>
		<tr>
			<td>SULFURIC ACID</td>
			<td>J.T. BAKER</td>
			<td>9681-02</td>
			<td></td>
		</tr>
		<tr>
			<td>TES TUBES 5mL</td>
			<td>CORNING</td>
			<td>352002</td>
			<td></td>
		</tr>
		<tr>
			<td>TLC SILICA GEL 60 F254</td>
			<td>MERCK</td>
			<td>1.05554.0001</td>
			<td></td>
		</tr>
		<tr>
			<td>WATER BATH</td>
			<td></td>
			<td></td>
			<td>&#62; 80 &#176;C</td>
		</tr>
	</tbody>
</table>

detection and quantification of mono-rhamnolipids and di-rhamnolipids produced by pseudomonas aeruginosa

The environmental bacterium Pseudomonas aeruginosa is an opportunistic pathogen with high antibiotic resistance that represents a health hazard. This bacterium produces high levels of biosurfactants known as rhamnolipids (RL), which are molecules with significant biotechnological value but are also associated with virulence traits. In this respect, the detection and quantification of RL may be useful for both biotechnology applications and biomedical research projects. In this article, we demonstrate step-by-step the technique to detect the production of the two forms of RL produced by P. aeruginosa using thin-layer chromatography (TLC): mono-rhamnolipids (mRL), molecules constituted by a dimer of fatty acids (mainly C10-C10) linked to one rhamnose moiety, and di-rhamnolipids (dRL), molecules constituted by a similar fatty acid dimer linked to two rhamnose moieties. Additionally, we present a method to measure the total amount of RL based on the acid hydrolysis of these biosurfactants extracted from a P. aeruginosa culture supernatant and the subsequent detection of the concentration of rhamnose that reacts with orcinol. The combination of both techniques can be used to estimate the approximate concentration of mRL and dRL produced by a specific strain, as exemplified here with the type strains PAO1 (phylogroup 1), PA14 (phylogroup 2), and PA7 (phylogroup 3).

In this article, three different P. aeruginosa type strains were utilized to represent three phylogroups, each with varying RL production levels and proportions of mRL and dRL. These strains include PAO1 (a wound isolate from Australia, 195522), PA14 (a plant isolate from the USA, 197723), and PA7 (a clinical isolate from Argentina, 201024). As a negative control, the PAO1 rhlA mutant was employed, which is incapable of RL production. All st...

Read this Scientific Article Protocol about Author Spotlight: Understanding Rhamnolipid Regulation in Pseudomonas aeruginosa at JoVE.com

Author Spotlight: Understanding Rhamnolipid Regulation in Pseudomonas aeruginosa

Pseudomonas aeruginosa&#160;produces the rhamnolipid biosurfactants. Thin-layer chromatography detects and determines the proportion of mono- and di-rhamnolipids produced by each strain. Quantification of total rhamnolipids involves assessing rhamnose equivalents present in these biosurfactants extracted from the culture supernatants using the orcinol method.

Detection and Quantification of Mono-Rhamnolipids and Di-Rhamnolipids Produced by Pseudomonas aeruginosa

The environmental bacterium Pseudomonas aeruginosa is an opportunistic pathogen with high antibiotic resistance that represents a health hazard. This ...

detection-quantification-mono-rhamnolipids-di-rhamnolipids-produced

Research

JoVE Journal

Biochemistry

1.0K Views.  Universidad Nacional Autónoma de México. Pseudomonas aeruginosa produces the rhamnolipid biosurfactants. Thin-layer chromatography detects and determines the proportion of mono- and di-rhamnolipids produced by each strain. Quantification of total rhamnolipids involves assessing rhamnose equivalents present in these biosurfactants extracted from the culture supernatants using the orcinol method.

Video: Author Spotlight: Understanding Rhamnolipid Regulation in Pseudomonas aeruginosa

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep-proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an extensive LC/LC-MS/MS platform, and post-MS computational interference correction to accurately quantitate whole proteomes. This protocol includes the following main steps: protein extraction and digestion, TMT labeling, 2-dimensional (2D) LC, high-resolution mass spectrometry, and computational data processing. Quality control steps are included for troubleshooting and evaluating experimental variation. More than 10,000 proteins in mammalian samples can be confidently quantitated with this protocol. This protocol can also be applied to the quantitation of post translational modifications with minor changes. This multiplexed, robust method provides a powerful tool for proteomic analysis in a variety of complex samples, including cell culture, animal tissues, and human clinical specimens.

We present a protocol to accurately quantitate proteins with isobaric labelling, extensive fractionation, bioinformatics tools, and quality control steps in combination with liquid chromatography interfaced to a high-resolution mass spectrometer.

Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) ...

Rab10 Phosphorylation Detection by LRRK2 Activity Using SDS-PAGE with a Phosphate-binding Tag

Mutations in leucine-rich repeat kinase 2 (LRRK2) have been shown to be linked with familial Parkinson&#39;s disease (FPD). Since abnormal activation of the kinase activity of LRRK2 has been implicated in the pathogenesis of PD, it is essential to establish a method to evaluate the physiological levels of the kinase activity of LRRK2. Recent studies revealed that LRRK2 phosphorylates members of the Rab GTPase family, including Rab10, under physiological conditions. Although the phosphorylation of endogenous Rab10 by LRRK2 in cultured cells could be detected by mass spectrometry, it has been difficult to detect it by immunoblotting due to the poor sensitivity of currently available phosphorylation-specific antibodies for Rab10. Here, we describe a simple method of detecting the endogenous levels of Rab10 phosphorylation by LRRK2 based on immunoblotting utilizing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) combined with a phosphate-binding tag (P-tag), which is N-(5-(2-aminoethylcarbamoyl)pyridin-2-ylmetyl)-N,N&#39;,N&#39;-tris(pyridin-2-yl-methyl)-1,3-diaminopropan-2-ol. The present protocol not only provides an example of the methodology utilizing the P-tag but also enables the assessment of how mutations as well as inhibitor treatment/administration or any other factors alter the downstream signaling of LRRK2 in cells and tissues.

The present study describes a simple method of detecting endogenous levels of Rab10 phosphorylation by leucine-rich repeat kinase 2.

Mutations in leucine-rich repeat kinase 2 (LRRK2) have been shown to be linked with familial Parkinson&#39;s disease (FPD). Since abnormal activation of ...

Highly Sensitive and Quantitative Detection of Proteins and Their Isoforms by Capillary Isoelectric Focusing Method

Immunoblotting has become a routine technique in many laboratories for protein characterization from biological samples. The following protocol provides an alternative strategy, capillary isoelectric focusing (cIEF), with many advantages compared to conventional immunoblotting. This is an antibody-based, automated, rapid, and quantitative method in which a complete western blotting procedure takes place inside an ultrathin capillary. This technique does not require a gel to transfer to a membrane, stripping of blots, or x-ray films, which are typically required for conventional immunoblotting. Here, proteins are separated according to their charge (isoelectric point; pI), using less than a microliter (400 nL) of total protein lysate. After electrophoresis, proteins are immobilized onto the capillary walls by ultraviolet light treatment, followed by primary and secondary (horseradish peroxidase (HRP) conjugated) antibody incubation, whose binding is detected through enhanced chemiluminescence (ECL), generating a light signal that can be captured and recorded by a charge-coupled device (CCD) camera. The digital image can be analyzed and quantified (peak area) using software. This high throughput procedure can handle 96 samples at a time; is highly sensitive, with protein detection in the picogram range; and produces highly reproducible results because of automation. All of these aspects are extremely valuable when the quantity of samples (e.g., tissue samples and biopsies) is a limiting factor. The technique has wider applications as well, including screening of drugs or antibodies, biomarker discovery, and diagnostic purposes.

Capillary isoelectric focusing is an antibody-based, ultrasensitive, high throughput technique, enabling detailed characterization of proteins and their isoforms from extremely small biological samples. The following describes a protocol for detection and quantification of specific proteins and their isoforms in an automated and robotized manner.

Immunoblotting has become a routine technique in many laboratories for protein characterization from biological samples. The following protocol provides ...

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

Translation of mRNA into proteins is a complex process involving several layers of regulation. It is often assumed that changes in mRNA transcription reflect changes in protein synthesis, but many exceptions have been observed. Recently, a technique called ribosome profiling (or Ribo-Seq) has emerged as a powerful method that allows identification, with high accuracy, which regions of mRNA are translated into proteins and quantification of translation at the genome-wide level. Here, we present a generalized protocol for genome-wide quantification of translation using Ribo-Seq in budding yeast. In addition, combining Ribo-Seq data with mRNA abundance measurements allows us to simultaneously quantify translation efficiency of thousands of mRNA transcripts in the same sample and compare changes in these parameters in response to experimental manipulations or in different physiological states. We describe a detailed protocol for generation of ribosome footprints using nuclease digestion, isolation of intact ribosome-footprint complexes via sucrose gradient fractionation, and preparation of DNA libraries for deep sequencing along with appropriate quality controls necessary to ensure accurate analysis of in vivo translation.

Translational regulation plays an important role in the control of protein abundance. Here, we describe a high-throughput method for quantitative analysis of translation in the budding yeast Saccharomyces cerevisiae.

Translation of mRNA into proteins is a complex process involving several layers of regulation. It is often assumed that changes in mRNA transcription ...

Quantification of Hypopigmentation Activity In Vitro

This study presents laboratory methods for the quantification of hypopigmentation activity in vitro. Melanin, the major pigment in melanocytes, is synthesized in response to multiple cellular and environmental factors. Melanin protects skin cells from ultraviolet damage, but also has biophysical and biochemical functions. Excessive production or accumulation of melanin in melanocytes can cause dermatological problems, such as freckles, dark spots, melasma, and moles. Therefore, the control of melanogenesis with hypopigmentation agents is important in individuals with clinical or cosmetic needs. Melanin is primarily synthesized in the melanosomes of melanocytes in a complex biochemical process called melanogenesis, which is influenced by extrinsic and intrinsic factors, such as hormones, inflammation, age, and ultraviolet light exposure. We describe three methods to determine the hypopigmentation activity of chemicals or natural substances in melanocytes: measurement of the 1) cellular tyrosinase activity and 2) melanin content, and 3) staining and quantifying cellular melanin with image analysis.
In melanogenesis, tyrosinase catalyzes the rate-limiting step that converts L-tyrosine into 3,4-dihydroxyphenylalanine (L-DOPA) and then into dopaquinone. Therefore, the inhibition of tyrosinase is a primary hypopigmentation mechanism. In cultured melanocytes, tyrosinase activity can be quantified by adding L-DOPA as a substrate and measuring dopaquinone production by spectrophotometry. Melanogenesis can also be measured by quantifying the melanin content. The melanin-containing cellular fraction is extracted with NaOH and melanin is quantified spectrophotometrically. Finally, the melanin content can be quantified by image analysis following Fontana-Masson staining of melanin. Although the results of these in vitro assays may not always be reproduced in human skin, these methods are widely used in melanogenesis research, especially as the initial step to identify potential hypopigmentation activity. These methods can also be used to assess melanocyte activity, growth, and differentiation. Consistent results with the three different methods ensure the validity of the effects.

We describe three experimental methods for evaluating the hypopigmentation activity of chemicals in vitro: quantification of 1) cellular tyrosinase activity and 2) melanin content, and 3) measurement of melanin by cellular melanin staining and image analysis.

This study presents laboratory methods for the quantification of hypopigmentation activity in vitro. Melanin, the major pigment in melanocytes, is ...

Detection and Isolation of Apoptotic Bodies to High Purity

Apoptotic bodies (ApoBDs), microvesicles and exosomes are the key members of the extracellular vesicle family, with ApoBDs being one of the largest type. It has been proposed that ApoBDs can aid cell clearance as well as intercellular communication through trafficking biomolecules. Conventional approaches used for the identification and isolation of ApoBDs are often limited by the lack of accurate quantification and low sample purity. Here, we describe a workflow to confirm the induction of apoptosis, validate ApoBD formation, and isolate ApoBDs to high purity. We will also outline and compare fluorescence-activated cell sorting (FACS) and differential centrifugation based approaches to isolate ApoBDs. Furthermore, the purity of isolated ApoBDs will be confirmed using a previously establish flow cytometry-based staining and analytical method. Taken together, using the described approach, THP-1 monocyte apoptosis and apoptotic cell disassembly was induced and validated, and ApoBD generated from THP-1 monocytes were isolated to a purity of 97-99%.

A workflow using flow cytometry or differential centrifugation is developed to detect, quantify and isolate apoptotic bodies from an apoptotic sample to high purity.

Apoptotic bodies (ApoBDs), microvesicles and exosomes are the key members of the extracellular vesicle family, with ApoBDs being one of the largest type. ...

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

The posttranslational modification of proteins by the small protein ubiquitin is involved in many cellular events. After tryptic digestion of ubiquitinated proteins, peptides with a diglycine remnant conjugated to the epsilon amino group of lysine (&#39;K-&#949;-diglycine&#39; or simply &#39;diGly&#39;) can be used to track back the original modification site. Efficient immunopurification of diGly peptides combined with sensitive detection by mass spectrometry has resulted in a huge increase in the number of ubiquitination sites identified up to date. We have made several improvements to this workflow, including offline high pH reverse-phase fractionation of peptides prior to the enrichment procedure, and the inclusion of more advanced peptide fragmentation settings in the ion routing multipole. Also, more efficient cleanup of the sample using a filter-based plug in order to retain the antibody beads results in a greater specificity for diGly peptides. These improvements result in the routine detection of more than 23,000 diGly peptides from human cervical cancer cells (HeLa) cell lysates upon proteasome inhibition in the cell. We show the efficacy of this strategy for in-depth analysis of the ubiquitinome profiles of several different cell types and of in vivo samples, such as brain tissue. This study presents an original addition to the toolbox for protein ubiquitination analysis to uncover the deep cellular ubiquitinome.

We present a method for the purification, detection, and identification of diGly peptides that originate from ubiquitinated proteins from complex biological samples. The presented method is reproducible, robust, and outperforms published methods with respect to the level of depth of the ubiquitinome analysis.

The posttranslational modification of proteins by the small protein ubiquitin is involved in many cellular events. After tryptic digestion of ...

Study on the Metabolism of Six Systemic Insecticides in a Newly Established Cell Suspension Culture Derived from Tea (Camellia Sinensis L.) Leaves

A platform for studying insecticide metabolism using in vitro tissues of tea plant was developed. Leaves from sterile tea plantlets were induced to form loose callus on Murashige and Skoog (MS) basal media with the plant hormones 2,4-dichlorophenoxyacetic acid (2,4-D, 1.0 mg L-1) and kinetin (KT, 0.1 mg L-1). Callus formed after 3 or 4 rounds of subculturing, each lasting 28 days. Loose callus (about 3 g) was then inoculated into B5 liquid media containing the same plant hormones and was cultured in a shaking incubator (120 rpm) in the dark at 25 &#177; 1 &#176;C. After 3&#8722;4 subcultures, a cell suspension derived from tea leaf was established at a subculture ratio ranging between 1:1 and 1:2 (suspension mother liquid: fresh medium). Using this platform, six insecticides (5 &#181;g mL-1 each thiamethoxam, imidacloprid, acetamiprid, imidaclothiz, dimethoate, and omethoate) were added into the tea leaf-derived cell suspension culture. The metabolism of the insecticides was tracked using liquid chromatography and gas chromatography. To validate the usefulness of the tea cell suspension culture, the metabolites of thiamethoxan and dimethoate present in treated cell cultures and intact plants were compared using mass spectrometry. In treated tea cell cultures, seven metabolites of thiamethoxan and two metabolites of dimethoate were found, while in treated intact plants, only two metabolites of thiamethoxam and one of dimethoate were found. The use of a cell suspension simplified the metabolic analysis compared to the use of intact tea plants, especially for a difficult matrix such as tea.

Study on the Metabolism of Six Systemic Insecticides in a Newly Established Cell Suspension Culture Derived from Tea Camellia Sinensis L. Leaves

This work presents a protocol for establishing a cell suspension culture derived from tea (Camellia sinensis L.) leaves that can be used to study the metabolism of external compounds that can be taken up by the whole plant, such as insecticides.

A platform for studying insecticide metabolism using in vitro tissues of tea plant was developed. Leaves from sterile tea plantlets were induced to form ...

Quantification of Coenzyme A in Cells and Tissues

Emerging research has revealed that the cellular coenzyme A (CoA) supply can become limiting with a detrimental impact on growth, metabolism and survival. Measurement of cellular CoA is a challenge due to its relatively low abundance and the dynamic conversion of free CoA to CoA thioesters that, in turn, participate in numerous metabolic reactions. A method is described that navigates through potential pitfalls during sample preparation to yield an assay with a broad linear range of detection that is suitable for use in many biomedical laboratories.

This method describes sample preparation from cultured cells and animal tissues, extraction and derivatization of coenzyme A in the samples, followed by high pressure liquid chromatography for purification and quantification of the derivatized coenzyme A by absorbance or fluorescence detection.

Emerging research has revealed that the cellular coenzyme A (CoA) supply can become limiting with a detrimental impact on growth, metabolism and survival. ...

Absolute Quantification of Cell-Free Protein Synthesis Metabolism by Reversed-Phase Liquid Chromatography-Mass Spectrometry

Cell-free protein synthesis (CFPS) is an emerging technology in systems and synthetic biology for the in vitro production of proteins. However, if CFPS is going to move beyond the laboratory and become a widespread and standard just in time manufacturing technology, we must understand the performance limits of these systems. Toward this question, we developed a robust protocol to quantify 40 compounds involved in glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, energy metabolism and cofactor regeneration in CFPS reactions. The method uses internal standards tagged with 13C-aniline, while compounds in the sample are derivatized with 12C-aniline. The internal standards and sample were mixed and analyzed by reversed-phase liquid chromatography-mass spectrometry (LC/MS). The co-elution of compounds eliminated ion suppression, allowing the accurate quantification of metabolite concentrations over 2-3 orders of magnitude where the average correlation coefficient was 0.988. Five of the forty compounds were untagged with aniline, however, they were still detected in the CFPS sample and quantified with a standard curve method. The chromatographic run takes approximately 10 min to complete. Taken together, we developed a fast, robust method to separate and accurately quantify 40 compounds involved in CFPS in a single LC/MS run. The method is a comprehensive and accurate approach to characterize cell-free metabolism, so that ultimately, we can understand and improve the yield, productivity and energy efficiency of cell-free systems.

Here, we present a robust protocol to quantify 40 compounds involved in central carbon and energy metabolism in cell-free protein synthesis reactions. The cell-free synthesis mixture is derivatized with aniline for effective separation using reversed-phase liquid chromatography and then quantified by mass spectrometry using isotopically labelled internal standards.

Cell-free protein synthesis (CFPS) is an emerging technology in systems and synthetic biology for the in vitro production of proteins. However, if CFPS is ...