Name: isolation and analysis of plasma lipoproteins by ultracentrifugation
Uploaded: 2021-01-28T15:00:00
Description: Watch this Scientific Journal Video about Isolation and Analysis of Plasma Lipoproteins by Ultracentrifugation at JoVE.com

This work was supported in part by a research grants from JSPS KAKENHI Grant Number JP 20K08858, the National Natural Science Foundation of China (No. 81941001 and 81770457), JSPS-CAS under the Japan-China Research Cooperative Program.

All procedures for rabbit studies were performed with approval of University of Yamanashi Institutional Animal Care and Use Committee (Approved number: A28-39).
1. Plasma separation from rabbit blood
<ol>
	<li>Prepare 1.5 mL microtubes containing 15 &#181;L of 0.5 M EDTA (pH 8.0) for blood collection.</li>
	<li>Put a rabbit in a restrainer and puncture an auricular intermediate artery using a 22 gauge needle and collect blood into a tube. Mix the blood with EDTA gently and put them on ice.</...

<ol>
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J., Lee, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lipoprotein+Lipase+Inhibitor,+Nordihydroguaiaretic+Acid,+Aggravates+Metabolic+Phenotypes+and+Alters+HDL+Particle+Size+in+the+Western+Diet-Fed+db/db+Mice.">Lipoprotein Lipase Inhibitor, Nordihydroguaiaretic Acid, Aggravates Metabolic Phenotypes and Alters HDL Particle Size in the Western Diet-Fed db/db Mice.</a> International Journal of Molecular Sciences. 20 (12), 3057 (2019).</li><li>De Silva, H. 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Hyperlipidemia is one of the most important risk factors of atherosclerotic disease. Thus, analysis of plasma lipoproteins is not only essential for diagnosis of dyslipidemia patients but also important for investigation of molecular mechanisms of lipoprotein metabolism and atherosclerosis. In this study, we described the protocol of isolation and analysis of plasma lipoproteins which can be applied in the laboratories where ultracentrifugation is available. Information obtained by this method is comprehensive and straig...

Dyslipidemia is the major risk factor of atherosclerotic disease in the world. High levels of low-density lipoproteins (LDLs) and low levels of high-density lipoproteins (HDLs) are closely associated with a high risk of coronary heart disease (CHD)1,2. In the clinical setting, both LDL-cholesterol (LDL-C) and HDL-cholesterol (HDL-C) are routinely measured using an automated analyzer in a clinical laboratory3,4. Despite this, it is essential to analyze lipoprotein profiles in details for the diagnosis of dyslipidemia and the study of lipid metabolism and atherosclerosis in human and experimental animals. Several methods have been reported to analyze plasma lipoproteins such as ultracentrifugation, size exclusion chromatography [fast protein liquid chromatography (FPLC) and high performance liquid chromatography (HPLC)], electrophoresis by agarose and polyacrylamide gels, nuclear magnetic resonance, and selective chemical precipitation using polyanions and divalent cations or other chemicals. In 1950s, Havel&#8217;s group first proposed the concept of lipoproteins defined by densities using ultracentrifugation and classified them into chylomicrons (CM), very-low-density lipoproteins (VLDL), intermediate-density lipoproteins (IDL), LDL, and HDL5 and later on, the method was further modified by other groups6,7. Until now, ultracentrifugation is the most popular and reliable method while the practical protocol is still not available. In this paper, we attempted to describe an easy-to-use protocol for isolating a small scale of plasma using sequential density floating ultracentrifugation originally described previously8. Isolation of seven plasma lipoprotein fractions [VLDL (d&#60;1.006 g/mL), IDL (d=1.02 g/mL), LDLs (d=1.04 and 1.06 g/mL), HDLs (d=1.08, 1.10, and 1.21 g/mL)] enables researchers to make an extensive analysis of both lipoproteins and their compositional apolipoproteins9,10,11. The intact seven consecutive density lipoproteins can be used for analyzing lipoprotein functions and also serving to&#160;cell-based in vitro strategies. This protocol should be useful for both clinical diagnosis and basic research. Here we used&#160;rabbit plasma as an example to demonstrate this technique while plasma from other species can be applied in the same way.

<table>
	<tbody>
		<tr>
			<td>22-gauge needle</td>
			<td>Terumo</td>
			<td>NN-2232S</td>
			<td>For blood collection</td>
		</tr>
		<tr>
			<td>96-well microplate</td>
			<td>greiner bio-one</td>
			<td>655101</td>
			<td>For lipids measurment</td>
		</tr>
		<tr>
			<td>Anti-apolipoprotein A-I antibody</td>
			<td>LifeSpan BioSciences</td>
			<td>LS-C314186</td>
			<td>For Western blottng, use 1:1,000</td>
		</tr>
		<tr>
			<td>Anti-apolipoprotein B antibody</td>
			<td>ROCKLAND</td>
			<td>600-101-111</td>
			<td>For Western blottng, use 1:1,000</td>
		</tr>
		<tr>
			<td>Anti-apolipoprotein E antibody</td>
			<td>Merck Millipore</td>
			<td>AB947</td>
			<td>For Western blottng, use 1:1,000</td>
		</tr>
		<tr>
			<td>CBB staining kit</td>
			<td>FUJIFILM Wako Pure Chemical</td>
			<td>299-50101</td>
			<td>For apolipoprotein analysis</td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>HITACHI</td>
			<td></td>
			<td>himac CF15RN</td>
		</tr>
		<tr>
			<td>Closure</td>
			<td>Spectrum</td>
			<td>132736</td>
			<td>For lipoprotein dialysis</td>
		</tr>
		<tr>
			<td>Dialysis tubing</td>
			<td>FUJIFILM Wako Pure Chemical</td>
			<td>043-30921</td>
			<td>For lipoprotein dialysis, MWCO 14,000</td>
		</tr>
		<tr>
			<td>Dry heat block</td>
			<td>Major Science</td>
			<td>MD-01N</td>
			<td>For SDS-PAGE sample preparation</td>
		</tr>
		<tr>
			<td>ECL Western blotting detection reagents</td>
			<td>GE Healthcare</td>
			<td>RPN2209</td>
			<td>For Western blotting</td>
		</tr>
		<tr>
			<td>Electrophoresis Chamber</td>
			<td>BIO-RAD</td>
			<td></td>
			<td>Mini-PROTEAN Tetra Cell</td>
		</tr>
		<tr>
			<td>Ethylenediamine-N,N,N&#39;,N&#39;-tetraacetic acid (EDTA) disodium salt dihydrate</td>
			<td>FUJIFILM Wako Pure Chemical</td>
			<td>345-01865</td>
			<td>For anticoagulant (0.5 M), for dialysis (1 mM)</td>
		</tr>
		<tr>
			<td>Filter paper</td>
			<td>ADVANTEC</td>
			<td>590</td>
			<td>For Western blotting</td>
		</tr>
		<tr>
			<td>Fixed angle ultracentrifuge rotor</td>
			<td>BECKMAN COULTER</td>
			<td>357656</td>
			<td>TLA-120.2</td>
		</tr>
		<tr>
			<td>Fixing solution</td>
			<td></td>
			<td></td>
			<td>For SDS-PAGE (50% Methanol/ 10% Acetic acid)</td>
		</tr>
		<tr>
			<td>Immun-Blot PVDF menbrane</td>
			<td>BIO-RAD</td>
			<td>1620177</td>
			<td>For Western blotting</td>
		</tr>
		<tr>
			<td>Lumino image analyzer</td>
			<td>GE Healthcare</td>
			<td></td>
			<td>For Western blotting, ImageQuant LAS 4000</td>
		</tr>
		<tr>
			<td>Magnetic stirrer</td>
			<td>ADVANTEC</td>
			<td>SR-304</td>
			<td>For lipoprotein dialysis</td>
		</tr>
		<tr>
			<td>Microplate reader iMARK</td>
			<td>BIO-RAD</td>
			<td></td>
			<td>For lipids measurment</td>
		</tr>
		<tr>
			<td>Microtube</td>
			<td>INA-OPTIKA</td>
			<td>SC-0150</td>
			<td></td>
		</tr>
		<tr>
			<td>Orbital agitator USBDbo</td>
			<td>Stovall Life Science</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Peroxidase congugated anti goat IgG antibody</td>
			<td>Jackson ImmunoResearch</td>
			<td>705-035-003</td>
			<td>For Western blotting, use 1:2,000</td>
		</tr>
		<tr>
			<td>Peroxidase congugated anti mouse IgG antibody</td>
			<td>Jackson ImmunoResearch</td>
			<td>715-035-150</td>
			<td>For Western blotting, use 1:2,000</td>
		</tr>
		<tr>
			<td>Phospholipids assay kit</td>
			<td>FUJIFILM Wako Pure Chemical</td>
			<td>433-36201</td>
			<td>For lipids measurment</td>
		</tr>
		<tr>
			<td>Polycarbonate ultracentrifuge Tubes</td>
			<td>BECKMAN COULTER</td>
			<td>343778</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Bromide</td>
			<td>FUJIFILM Wako Pure Chemical</td>
			<td>168-03475</td>
			<td>For density solution</td>
		</tr>
		<tr>
			<td>Power Supply</td>
			<td>BIO-RAD</td>
			<td></td>
			<td>For SDD-PAGE and Western blotting, PowerPac 300, PowerPac HC</td>
		</tr>
		<tr>
			<td>Protein standards Precidion Plus Protein Dual Xtra</td>
			<td>BIO-RAD</td>
			<td>161-0377</td>
			<td>For SDS-PAGE and Western blotting</td>
		</tr>
		<tr>
			<td>Rabbit restrainer</td>
			<td>Natsume Seisakusho</td>
			<td>KN-318</td>
			<td>For blood collection</td>
		</tr>
		<tr>
			<td>Rotor</td>
			<td>HITACHI</td>
			<td></td>
			<td>T15A43</td>
		</tr>
		<tr>
			<td>SDS-PAGE running buffer</td>
			<td></td>
			<td></td>
			<td>25 mM Tris/ 192 mM Glycine/ 0.1% SDS</td>
		</tr>
		<tr>
			<td>SDS-PAGE sample buffer (2x)</td>
			<td></td>
			<td></td>
			<td>0.1M Tris-HCl (pH 6.8)/ 4% SDS/ 20% glycerol/ 0.01% BPB/12% 2-merpaptoethanol</td>
		</tr>
		<tr>
			<td>SDS-polyacrylamide gel</td>
			<td></td>
			<td></td>
			<td>4-20% gradient polyacrylamide gel</td>
		</tr>
		<tr>
			<td>Skim milk powder</td>
			<td>FUJIFILM Wako Pure Chemical</td>
			<td>190-12865</td>
			<td>For Western blotting blocking buffer (5% skim milk/ 0.1% Tween 20/ PBS)</td>
		</tr>
		<tr>
			<td>Total cholesterol assay kit</td>
			<td>FUJIFILM Wako Pure Chemical</td>
			<td>439-17501</td>
			<td>For lipids measurment</td>
		</tr>
		<tr>
			<td>Triglyicerides assay kit</td>
			<td>FUJIFILM Wako Pure Chemical</td>
			<td>432-40201</td>
			<td>For lipids measurment</td>
		</tr>
		<tr>
			<td>Tube slicer for thick-walled tube</td>
			<td>BECKMAN COULTER</td>
			<td>347960</td>
			<td>For lipoprotein isolation</td>
		</tr>
		<tr>
			<td>Tween 20</td>
			<td>SIGMA-ALDRICH</td>
			<td>P1379</td>
			<td>For Western blotting washing buffer (0.1% Tween 20/ PBS)</td>
		</tr>
		<tr>
			<td>Ultracentrifuge</td>
			<td>BECKMAN COULTER</td>
			<td>A95761</td>
			<td>Optima MAX-TL</td>
		</tr>
		<tr>
			<td>Western blotting wet transfer system</td>
			<td>BIO-RAD</td>
			<td></td>
			<td>Mini Trans-Blot Cell</td>
		</tr>
	</tbody>
</table>

isolation and analysis of plasma lipoproteins by ultracentrifugation

Analysis of plasma lipoproteins and apolipoproteins is an essential part for the diagnosis of dyslipidemia and studies of lipid metabolism and atherosclerosis. Although there are several methods for analyzing plasma lipoproteins, ultracentrifugation is still one of the most popular and reliable methods. Because of its intact separation procedure, the lipoprotein fractions isolated by this method can be used for analysis of lipoproteins, apolipoproteins, proteomes, and functional study of lipoproteins with cultured cells in vitro. Here, we provide a detailed protocol to isolate seven lipoprotein fractions including VLDL (d&#60;1.006 g/mL), IDL (d=1.02 g/mL), LDLs (d=1.04 and 1.06 g/mL), HDLs (d=1.08, 1.10, and 1.21 g/mL) from rabbit plasma using sequential floating ultracentrifugation. In addition, we introduce the readers how to analyze apolipoproteins such as apoA-I, apoB, and apoE by SDS-PAGE and Western blotting and show representative results of lipoprotein and apolipoprotein profiles using hyperlipidemic rabbit models. This method can become a standard protocol for both clinicians and basic scientists to analyze lipoprotein functions.

Using this protocol, we isolated rabbit lipoproteins using 1 mL of plasma and obtained seven density fractions. Isolated density fractions are enough for measuring lipids and apolipoproteins as described above for most research purposes. The same procedure can also be used for isolating plasma lipoproteins from human and other species. For small-sized animals such as mice, pooled plasma is required. Figure 3 shows lipoprotein profiles of wild-type (WT) rabbits fed either a normal standard (N...

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Isolation and Analysis of Plasma Lipoproteins by Ultracentrifugation

Several methods have been used for analyzing plasma lipoproteins; however, ultracentrifugation is still one of the most popular and reliable methods. Here, we describe a method regarding how to isolate lipoproteins from plasma using sequential density ultracentrifugation and how to analyze the apolipoproteins for both diagnostic and research purposes.

Analysis of plasma lipoproteins and apolipoproteins is an essential part for the diagnosis of dyslipidemia and studies of lipid metabolism and ...

Analysis of plasma lipoproteins is very important for the diagnosis of hyperlipidemia and the investigation of atherosclerosis. In is this protocol, we'll introduce the basic method using ultracentrifugation to isolate plasma lipoproteins. This method allows the researchers to use one milliliter of plasma to isolate seven lipoprotein fractions.These fractions can be used for the of lipids, apolipoproteins, as well as well-functional studies This method can be applied for both human and animal samples for the diagnosis of dyslipidemia and the related disease. Begin by transferring one milliliter of plasma into each polycarbonate ultracentrifuge tube. Then load the tubes in a fixed angle rotor and centrifuge the plasma at 356, 000 times G for 2.5 hours at four degrees Celsius.Adjust the position of the blade in the tube slicer to a level between the top fraction and the bottom fraction. Cut the tubes using a slicer and collect the top fraction, approximately 200 microliters, into a new micro tube. Collect the remaining bottom fraction into a new polycarbonate ultracentrifuge tube for the next separation.Adjust the total volume to 800 microliters by adding the same density solution. Adjust the bottom fraction to a density of 1.02 grams per milliliter by adding 58.9 microliters of 1.21 grams per milliliter solution, and 141.1 microliters of 1.02 grams per milliliter solution for a total volume of one milliliter. Load these tubes in the fixed angle rotor and centrifuge at 356, 000 times G for 2.5 hours at four degrees Celsius.Continue collecting top fractions, adjusting the density of bottom fractions, and centrifuging for fraction densities of 1.02, 1.04, 1.06, 1.08, 1.1, and 1.21 grams per milliliter. For the final ultracentrifugation, centrifuge at 513, 000 times G for four hours at four degrees Celsius. Lipoprotein profiles of rabbits fed either a normal standard diet or a high cholesterol diet are shown here.Rabbits are herbivores, so their plasma TC, TG, and PL levels are generally lower than those of humans and mice. In normal standard diet-fed rabbits, TC is mainly distributed in HDL3 and LDL. In wild type rabbits on a normal standard diet, 39%of plasma TG are distributed in VLDLs, whereas 57%of plasma PL is contained in HDL3.When rabbits were challenged with a high-cholesterol diet, they rapidly developed hypercholesterolemia. Their lipoprotein profiles were characterized by marked elevation of VLDLs. Seven lipoprotein fractions from wild type rabbits fed either a normal standard or a high-cholesterol diet were run on an SDS polyacrylamide gel and visualized with CBB staining.On a high-cholesterol diet, both ApoB-100 and ApoE contents in VLDLs, IDLs, and LDLs were markedly elevated. Western blotting was used to compare apolipoproteins and lipoprotein profiles of three different hyperlipidemic rabbits:high-cholesterol diet-fed wild type rabbits, ApoE knockout rabbits, and Watanabe Heritable Hyperlipidemic rabbits with LDL receptor deficiency. The ApoB containing particles of high-cholesterol diet-fed wild type rabbits are characterized by increased ApoB-100 and ApoE contents, whereas ApoE knockout rabbits showed an increase of ApoB-48 along with the appearance of ApoA-1.Watanabe Heritable Hyperlipidemic rabbits are genetically deficient in LDL receptor functions, so a marked increase of ApoB-100 in LDLs accompanied by reduced ApoA-1 in HDLs was observed, similar to human familial hypercholesterolemia patients. Sample recovery is the most critical in this procedure. To minimize sample loss, one should it be careful to collect fraction and completely dissolve viscous precipitation in the bottom fraction.After the collection of seven lipoprotein fractions, dialysis is require for the sorting. Once dialysis is complete, the lipoproteins samples for analysis using SDS page, western blotting, and cell-based study. In the clinical setting, ultracentrifugation usually separates lipoproteins into four fractions.The current method can isolate seven lipoproteins fractions, which provides more detail of lipoproteins for investigation of hyperlipidemia.

isolation-and-analysis-of-plasma-lipoproteins-by-ultracentrifugation

Research

JoVE Journal

Biochemistry

Isolation of High-density Lipoproteins for Non-coding Small RNA Quantification

The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most interestingly, sRNAs are also found outside of cells and are stably present in all biological fluids. As such, extracellular sRNAs represent a novel class of disease biomarkers and are likely involved in cell signaling and intercellular communication networks. To assess their potential as biomarkers, sRNAs can be quantified in plasma, urine, and other fluids. Nevertheless, to fully understand the impact of extracellular sRNAs as endocrine signals, it is important to determine which carriers are transporting and protecting them in biological fluids (e.g., plasma), which cells and tissues contribute to extracellular sRNA pools, and cells and tissues capable of accepting and utilizing extracellular sRNA. To accomplish these goals, it is critical to isolate highly pure populations of extracellular carriers for sRNA profiling and quantification. We have previously demonstrated that lipoproteins, particularly high-density lipoproteins (HDL), transport functional microRNAs (miRNA) between cells and HDL-miRNAs are significantly altered in disease. Here, we detail a new protocol that utilizes tandem HDL isolation with density-gradient ultracentrifugation (DGUC) and fast-protein-liquid chromatography (FPLC) to obtain highly pure HDL for downstream profiling and quantification of all sRNAs, including miRNAs, using both high-throughput sequencing and real-time PCR approaches. This protocol will be a valuable resource for the investigation of sRNAs on HDL.

This protocol describes the isolation and quantification of high-density lipoprotein small RNAs.

The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most ...

Protein Digestion, Ultrafiltration, and Size Exclusion Chromatography to Optimize the Isolation of Exosomes from Human Blood Plasma and Serum

Exosomes, a type of nanovesicle released from all cell types, can be isolated from any bodily fluid. The contents of exosomes, including proteins and RNAs, are unique to the cells from which they are derived and can be used as indicators of disease. Several common enrichment protocols, including ultracentrifugation, yield exosomes laden with soluble protein contaminants. Specifically, we have found that the most abundant proteins within blood often co-purify with exosomes and can confound downstream proteomic studies, thwarting the identification of low abundance biomarker candidates. Of additional concern is irreproducibility of exosome protein quantification due to inconsistent representation of non-exosomal protein levels. The protocol detailed here was developed to remove non-exosomal proteins that co-purify along with exosomes, adding rigor to the exosome purification process. Five methods were compared using paired blood plasma and serum from five donors. Analysis using nanoparticle tracking analysis and micro bicinchoninic acid protein assay revealed that a combined protocol utilizing ultrafiltration and size exclusion chromatography yielded the optimal vesicle enrichment and soluble protein removal. Western blotting was used to verify that the expected abundant blood proteins, including albumin and apolipoproteins, were depleted.

Here, we present a protocol to purify exosomes from both plasma and serum with reduced co-purification of non-exosomal blood proteins. The optimized protocol includes ultrafiltration, protease treatment, and size exclusion chromatography. Enhanced purification of exosomes benefits downstream analyses, including more accurate quantification of vesicles and proteomic characterization.

Exosomes, a type of nanovesicle released from all cell types, can be isolated from any bodily fluid. The contents of exosomes, including proteins and ...

Measuring Trans-Plasma Membrane Electron Transport by C2C12 Myotubes

Trans-plasma membrane electron transport (tPMET) plays a role in protection of cells from intracellular reductive stress as well as protection from damage by extracellular oxidants. This process of transporting electrons from intracellular reductants to extracellular oxidants is not well defined. Here we present spectrophotometric assays by C2C12 myotubes to monitor tPMET utilizing the extracellular electron acceptors: water-soluble tetrazolium salt-1 (WST-1) and 2,6-dichlorophenolindophenol (DPIP or DCIP). Through reduction of these electron acceptors, we are able to monitor this process in a real-time analysis. With the addition of enzymes such as ascorbate oxidase (AO) and superoxide dismutase (SOD) to the assays, we can determine which portion of tPMET is due to ascorbate export or superoxide production, respectively. While WST-1 was shown to produce stable results with low background, DPIP was able to be re-oxidized after the addition of AO and SOD, which was demonstrated with spectrophotometric analysis. This method demonstrates a real-time, multi-well, quick spectrophotometric assay with advantages over other methods used to monitor tPMET, such as ferricyanide (FeCN) and ferricytochrome c reduction.

The goal of this protocol is to spectrophotometrically monitor trans-plasma membrane electron transport utilizing extracellular electron acceptors and to analyze enzymatic interactions that may occur with these extracellular electron acceptors.

Trans-plasma membrane electron transport (tPMET) plays a role in protection of cells from intracellular reductive stress as well as protection from damage ...

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and the degradation of target proteins in live cells. By using short (pulse) radiolabeling times (&lt;30 min) and tightly controlled chase times, it is possible to label only a small fraction of the total protein pool and follow its folding. When combined with nonreducing/reducing SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoprecipitation with (conformation-specific) antibodies, folding processes can be examined in great detail. This system has been used to analyze the folding of proteins with a huge variation in properties such as soluble proteins, single and multi-pass transmembrane proteins, heavily N- and O-glycosylated proteins, and proteins with and without extensive disulfide bonding. Pulse-chase methods are the basis of kinetic studies into a range of additional features, including co- and posttranslational modifications, oligomerization, and polymerization, essentially allowing the analysis of a protein from birth to death. Pulse-chase studies on protein folding are complementary with other biochemical and biophysical methods for studying proteins in vitro by providing increased temporal resolution and physiological information. The methods as described within this paper are adapted easily to study the folding of almost any protein that can be expressed in mammalian or insect-cell systems.

Here we describe a protocol for a general pulse-chase method that allows the kinetic analysis of folding, transport, and degradation of proteins to be followed in live cells.

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and ...

High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

Proteins generally exert biological functions through interactions with other proteins, either in dynamic protein assemblies or as a part of stably formed complexes. The latter can be elegantly resolved according to molecular size using native polyacrylamide gel electrophoresis (BN-PAGE). Coupling of such separations to sensitive mass spectrometry (BN-MS) has been well-established and theoretically allows for exhaustive assessment of the extractable complexome in biological samples. However, this approach is rather laborious and provides limited complex size resolution and sensitivity. Also, its application has remained restricted to abundant mitochondrial and plastid proteins. Thus, for a majority of proteins, information regarding integration into stable protein complexes is still lacking. Presented here is an optimized approach for complexome profiling comprising preparative-scale BN-PAGE separation, sub-millimeter sampling of broad gel lanes by cryomicrotome slicing, and mass spectrometric analysis with label-free protein quantification. The procedures and tools for critical steps are described in detail. As an application, the report describes complexome analysis of a solubilized endosome-enriched membrane fraction from mouse kidneys, with 2,545 proteins profiled in total. The results demonstrate identification of uniform, low-abundance membrane proteins such as intracellular ion channels as well as high resolution, complex protein assembly patterns, including glycosylation isoforms. The results are in agreement with independent biochemical analyses. In summary, this methodology allows for comprehensive and unbiased identification of protein (super)complexes and their subunit composition, providing a basis for investigating stoichiometry, assembly, and interaction dynamics of protein complexes in any biological system.

A versatile cryoslicing BN-MS protocol using a microtome is presented for high-resolution complexome profiling.

Proteins generally exert biological functions through interactions with other proteins, either in dynamic protein assemblies or as a part of stably formed ...

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Gene transcription is an essential process in cell biology, and allows cells to interpret and respond to internal and external cues. Traditional bulk population methods (Northern blot, PCR, and RNAseq) that measure mRNA levels lack the ability to provide information on cell-to-cell variation in responses. Precise single cell and allelic visualization and quantification is possible via single molecule RNA fluorescence in situ hybridization (smFISH). RNA-FISH is performed by hybridizing target RNAs with labeled oligonucleotide probes. These can be imaged in medium/high throughput modalities, and, through image analysis pipelines, provide quantitative data on both mature and nascent RNAs, all at the single cell level. The fixation, permeabilization, hybridization and imaging steps have been optimized in the lab over many years using the model system described herein, which results in successful and robust single cell analysis of smFISH labeling. The main goal with sample preparation and processing is to produce high quality images characterized by a high signal-to-noise ratio to reduce false positives and provide data that are more accurate. Here, we present a protocol describing the pipeline from sample preparation to data analysis in conjunction with suggestions and optimization steps to tailor to specific samples.&#160;

Single molecule RNA fluorescence in situ hybridization (smFISH) is a method to accurately quantify levels and localization of specific RNAs at the single cell level. Here, we report our validated lab protocols for wet-bench processing, imaging and image analysis for single cell quantification of specific RNAs.

Gene transcription is an essential process in cell biology, and allows cells to interpret and respond to internal and external cues. Traditional bulk ...

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Peptidoglycan is an important component of bacterial cell walls and a common cellular target for antimicrobials. Although aspects of peptidoglycan structure are fairly conserved across all bacteria, there is also considerable variation between Gram-positives/negatives and between species. In addition, there are numerous known variations, modifications, or adaptations to the peptidoglycan that can occur within a bacterial species in response to growth phase and/or environmental stimuli. These variations produce a highly dynamic structure that is known to participate in many cellular functions, including growth/division, antibiotic resistance, and host defense avoidance. To understand the variation within peptidoglycan, the overall structure must be broken down into its constitutive parts (known as muropeptides) and assessed for overall cellular composition. Peptidoglycomics uses advanced mass spectrometry combined with high-powered bioinformatic data analysis to examine peptidoglycan composition in fine detail. The following protocol describes the purification of peptidoglycan from bacterial cultures, the acquisition of muropeptide intensity data through a liquid chromatograph&#8212;mass spectrometer, and the differential analysis of peptidoglycan composition using bioinformatics.

This protocol covers a detailed analysis of peptidoglycan composition using liquid chromatography mass spectrometry coupled with advanced feature extraction and bioinformatic analysis software.

Peptidoglycan is an important component of bacterial cell walls and a common cellular target for antimicrobials. Although aspects of peptidoglycan ...

Spot Variation Fluorescence Correlation Spectroscopy for Analysis of Molecular Diffusion at the Plasma Membrane of Living Cells

Dynamic biological processes in living cells, including those associated with plasma membrane organization, occur on various spatial and temporal scales, ranging from nanometers to micrometers and microseconds to minutes, respectively. Such a broad range of biological processes challenges conventional microscopy approaches. Here, we detail the procedure for implementing spot variation Fluorescence Correlation Spectroscopy (svFCS) measurements using a classical fluorescence microscope that has been customized. The protocol includes a specific performance check of the svFCS setup and the guidelines for molecular diffusion measurements by svFCS on the plasma membrane of living cells under physiological conditions. Additionally, we provide a procedure for disrupting plasma membrane raft nanodomains by cholesterol oxidase treatment and demonstrate how these changes in the lateral organization of the plasma membrane might be revealed by svFCS analysis. In conclusion, this fluorescence-based method can provide unprecedented details on the lateral organization of the plasma membrane with the appropriate spatial and temporal resolution.

This article aims to present a protocol on how to build a spot variation Fluorescence Correlation Spectroscopy (svFCS) microscope to measure molecular diffusion at the plasma membrane of living cells.

Dynamic biological processes in living cells, including those associated with plasma membrane organization, occur on various spatial and temporal scales, ...

Density Gradient Ultracentrifugation for Investigating Endocytic Recycling in Mammalian Cells

Endosomal trafficking is an essential cellular process that regulates a broad range of biological events. Proteins are internalized from the plasma membrane and then transported to the early endosomes. The internalized proteins could be transited to the lysosome for degradation or recycled back to the plasma membrane. A robust endocytic recycling pathway is required to balance the removal of membrane materials from endocytosis. Various proteins are reported to regulate the pathway, including ADP-ribosylation factor 6 (ARF6). Density gradient ultracentrifugation is a classical method for cell fractionation. After the centrifugation, organelles are sedimented at their isopycnic surface. The fractions are collected and used for other downstream applications. Described here is a protocol to obtain a recycling endosome-containing fraction from transfected mammalian cells using density gradient ultracentrifugation. The isolated fractions were subjected to standard Western blotting for analyzing their protein contents. By employing this method, we identified that the plasma membrane targeting of engulfment and cell motility 1 (ELMO1), a Ras-related C3 botulinum toxin substrate 1 (Rac1) guanine nucleotide exchange factor, is through ARF6-mediated endocytic recycling.

This paper aims to present a protocol for preparing recycling endosomes from mammalian cells using sucrose density gradient ultracentrifugation.

Endosomal trafficking is an essential cellular process that regulates a broad range of biological events. Proteins are internalized from the plasma ...

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Immunopeptidomics is an emerging field that fuels and guides the development of vaccines and immunotherapies. More specifically, it refers to the science of investigating the composition of peptides presented by major histocompatibility complex (MHC) class I and class II molecules using mass spectrometry (MS) technology platforms. Among all the steps in an MS-based immunopeptidomics workflow, sample preparation is critically important for capturing high-quality data of therapeutic relevance. Here, step-by-step instructions are described to isolate MHC class I and II-associated peptides by immunoaffinity purification from quality control samples, from mouse (EL4 and A20), and human (JY) cell lines more specifically. The various reagents and specific antibodies are thoroughly described to isolate MHC-associated peptides from these cell lines, including the steps to verify the beads-binding efficiency of the antibody and the elution efficiency of the MHC-peptide complexes from the beads. The protocol can be used to establish and standardize an immunopeptidomics workflow, as well as to benchmark new protocols. Moreover, the protocol represents a great starting point for any non-experts in addition to foster the intra- and inter-laboratory reproducibility of the sample preparation procedure in immunopeptidomics.

Here, we present a protocol for the purification of MHC class I and class II peptide complexes from mouse and human cell lines providing high-quality immunopeptidomics data. The protocol focuses on sample preparation using commercially available antibodies.

Immunopeptidomics is an emerging field that fuels and guides the development of vaccines and immunotherapies. More specifically, it refers to the science ...