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Western blot normalization

western blot normalization, western blot total protein normalization
Normalization of Western blot data is an analytical step that is performed to compare the relative abundance of a specific protein across the lanes of a blot or gel under diverse experimental treatments, or across tissues or developmental stages The overall goal of normalization is to minimize effects arising from variations in experimental errors, such as inconsistent sample preparation, unequal sample loading across gel lanes, or uneven protein transfer, which can compromise the conclusions that can be obtained from Western blot data Currently, there are two methods for normalizing Western blot data: i housekeeping protein normalization and ii total protein normalization

Contents

  • 1 Procedure
  • 2 Normalization Controls
    • 21 Housekeeping protein controls
      • 211 Fluorescent Antibodies
      • 212 Membrane Stripping
    • 22 Exogenous spike-in controls
  • 3 Normalization with Total Protein
  • 4 Imaging Techniques
    • 41 Pre-antibody stains
    • 42 Post antibody stains
  • 5 Stain-free technology
  • 6 References
  • 7 External links

Procedure

Normalization occurs directly on either the gel or the blotting membrane First, the stained gel or blot is imaged, a rectangle is drawn around the target protein in each lane, and the signal intensity inside the rectangle is measured The signal intensity obtained can then be normalized with respect to the signal intensity of the loading internal control detected on the same gel or blot When using protein stains, the membrane may be incubated with the chosen stain before or after immunodetection, depending on the type of stain

Normalization Controls

Housekeeping protein controls

Housekeeping genes and proteins, including ß-Actin, GAPDH, HPRT1, and RPLP1, are often used as internal controls in western blots because they are thought to be expressed constitutively, at the same levels, across experiments However, recent studies have shown that expression of housekeeping proteins HKPs can change across different cell types and biological conditions Therefore, scientific publishers and funding agencies now require that normalization controls be previously validated for each experiment to ensure reproducibility and accuracy of the results

Fluorescent Antibodies

When using fluorescent antibodies to image proteins in western blots, normalization requires that the user define the upper and lower limits of quantitation and characterize the linear relationship between signal intensity and the sample mass volume for each antigen Both the target protein and the normalization control need to fluoresce within the dynamic range of detection Many HKPs are expressed at high levels and are preferred for use with highly-expressed target proteins Lower expressing proteins are difficult to detect on the same blot

Fluorescent antibodies are commercially available, and fully characterized antibodies are recommended to ensure consistency of results

When fluorescent detection is not utilized, the loading control protein and the protein of interest must differ considerably in molecular weight so they are adequately separated by gel electrophoresis for accurate analysis

Membrane Stripping

Membranes need to be stripped and re-probed using a new set of detection antibodies when detecting multiple protein targets on the same blot Ineffective stripping could result in a weak signal from the target protein To prevent loss of the antigen, only three stripping incubations are recommended per membrane It could be difficult to completely eliminate signal from highly-abundant proteins, so it is recommended that one detects lowly-expressed proteins first

Exogenous spike-in controls

Since HKP levels can be inconsistent between tissues, scientists can control for the protein of interest by spiking in a pure, exogenous protein of a known concentration within the linear range of the antibody Compared to HKP, a wider variety of proteins are available for spike-in controls

Normalization with Total Protein

In total protein normalization TPN, the abundance of the target protein is normalized to the total amount of protein in each lane Because TPN is not dependent on a single loading control, validation of controls and stripping/reprobing of blots for detection of HKPs is not necessary This can improve precision down to 01 µg of total protein per lane, cost-effectiveness, and data reliability

Fluorescent stains and stain-free gels require special equipment to visualize the proteins on the gel/blot Stains may not cover the blot evenly; more stain might collect towards the edges of the blot than in the center Non-uniformity in the image can result in inaccurate normalization

Imaging Techniques

Pre-antibody stains

Anionic dyes such as Ponceau S and Coomassie Brilliant Blue, and fluorescent dyes like Sypro Ruby and Deep Purple, are used before antibodies are added because they do not affect downstream imumunodetection

Ponceau S is a negatively charged reversible dye that stains proteins a reddish pink color and is removed easily by washing in water The intensity of Ponceau S staining decreases quickly over time, so documentation should be conducted rapidly A linear range of up to 140 µg is reported for Ponceau S with poor reproducibility due to its highly time-dependent staining intensity and low signal-to-noise ratio

Fluorescent dyes like Sypro Ruby have a broad linear range and are more sensitive than anionic dyes They are permanent, photostable stains that can be visualized with a standard UV or blue-light transilluminator or a laser scan Membranes can then be documented either on film or digitally using a CCD camera Sypro Ruby blot staining is time-intensive and tends to saturate above 50 μg of protein per lane

Post antibody stains

Amido black is a commonly used permanent post-antibody anionic stain that is more sensitive than Ponceau S This stain is applied after imumunodetection

Stain-free technology

Stain-free technology employs an in-gel chemistry for imaging This chemical reaction does not affect protein transfer or downstream antibody binding Also, it does not involve staining/destaining steps, and the intensity of the bands remain constant over time

Stain-free technology cannot detect proteins that do not contain tryptophan residues A minimum of two tryptophans is needed to enable detection The linear range for stain-free normalization is up to 80 µg of protein per lane for 18-well and up to 100 µg per lane for 12-well Criterion mid-sized gels This range is compatible with typical protein loads in quantitative western blots and enables loading control calculations over a wide protein-loading range A more efficient stain-free method has also recently become available When using high protein loads, stain-free technology has demonstrated greater success than stains

References

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  2. ^ a b c Thellin, O; Zorzi, W; Lakaye, B; De Borman, B; Coumans, B; Hennen, G; Grisar, T; Igout, A; Heinen, E 1999-10-08 "Housekeeping genes as internal standards: use and limits" Journal of Biotechnology 75 2–3: 291–295 doi:101016/s0168-16569900163-7 ISSN 0168-1656 PMID 10617337 
  3. ^ a b Aldridge, Georgina M; Podrebarac, David M; Greenough, William T; Weiler, Ivan Jeanne 2008-07-30 "The use of total protein stains as loading controls: An alternative to high-abundance single-protein controls in semi-quantitative immunoblotting" Journal of Neuroscience Methods 172 2: 250–254 doi:101016/jjneumeth200805003 PMC 2567873  
  4. ^ a b c Collins, Mahlon A; An, Jiyan; Peller, Danielle; Bowser, Robert 2015-08-15 "Total protein is an effective loading control for cerebrospinal fluid western blots" Journal of Neuroscience Methods 251: 72–82 doi:101016/jjneumeth201505011 
  5. ^ a b c d "Total Protein Normalization for Western Blots - Advansta Inc" 2014-11-05 Retrieved 2016-10-01 
  6. ^ a b c d e f Bass, J J; Wilkinson, D J; Rankin, D; Phillips, B E; Szewczyk, N J; Smith, K; Atherton, P J 2016-06-05 "An overview of technical considerations for Western blotting applications to physiological research" Scandinavian Journal of Medicine & Science in Sports doi:101111/sms12702 ISSN 1600-0838 PMID 27263489 
  7. ^ Li, Rena; Shen, Yong 2013-04-19 "An old method facing a new challenge: re-visiting housekeeping proteins as internal reference control for neuroscience research" Life Sciences 92 13: 747–751 doi:101016/jlfs201302014 ISSN 1879-0631 PMC 3614345  PMID 23454168 
  8. ^ a b c Zhu, Jiang; He, Fuhong; Song, Shuhui; Wang, Jing; Yu, Jun 2008-01-01 "How many human genes can be defined as housekeeping with current expression data" BMC Genomics 9: 172 doi:101186/1471-2164-9-172 ISSN 1471-2164 
  9. ^ a b c Barber, Robert D; Harmer, Dan W; Coleman, Robert A; Clark, Brian J 2005-05-11 "GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues" Physiological Genomics 21 3: 389–395 doi:101152/physiolgenomics000252005 ISSN 1094-8341 PMID 15769908 
  10. ^ a b c Lee, Peter D; Sladek, Robert; Greenwood, Celia M T; Hudson, Thomas J 2002-02-01 "Control Genes and Variability: Absence of Ubiquitous Reference Transcripts in Diverse Mammalian Expression Studies" Genome Research 12 2: 292–297 doi:101101/gr217802 ISSN 1088-9051 PMC 155273  PMID 11827948 
  11. ^ Couchman, John R 2016-10-01 "Commercial Antibodies: The Good, Bad, and Really Ugly" Journal of Histochemistry and Cytochemistry 57 1: 7–8 doi:101369/jhc2008952820 ISSN 0022-1554 PMC 2605718  PMID 18854593 
  12. ^ Gilda, Jennifer E; Ghosh, Rajeshwary; Cheah, Jenice X; West, Toni M; Bodine, Sue C; Gomes, Aldrin V 2015-08-19 "Western Blotting Inaccuracies with Unverified Antibodies: Need for a Western Blotting Minimal Reporting Standard WBMRS" PLoS ONE 10 8: e0135392 doi:101371/journalpone0135392 ISSN 1932-6203 PMC 4545415  PMID 26287535 
  13. ^ "Validating Antibodies: An Urgent Need | The Scientist Magazine®" The Scientist Retrieved 2016-10-01 
  14. ^ "6 Changes That'll Make a Big Difference With Your RNA-seq; Part 3 - Cofactor Genomics" cofactorgenomicscom Retrieved 2016-10-01 
  15. ^ Fosang, Amanda J; Colbran, Roger J 2015-12-11 "Transparency Is the Key to Quality" The Journal of Biological Chemistry 290 50: 29692–29694 doi:101074/jbcE115000002 ISSN 0021-9258 PMC 4705984  PMID 26657753 
  16. ^ Moritz, CP 2017-09-20 "Tubulin or not tubulin: Heading toward total protein staining as loading control in Western blots" Proteomics doi:101002/pmic201600189 PMID 28941183 
  17. ^ Welinder, Charlotte; Ekblad, Lars 2011-03-04 "Coomassie Staining as Loading Control in Western Blot Analysis" Journal of Proteome Research 10 3: 1416–1419 doi:101021/pr1011476 ISSN 1535-3893 
  18. ^ Ranganathan, Velvizhi; De, Prabir K 1996-02-01 "Western Blot of Proteins from Coomassie-Stained Polyacrylamide Gels" Analytical Biochemistry 234 1: 102–104 doi:101006/abio19960057 PMID 8742090 
  19. ^ Steinberger, B 2015-05-01 "Evaluation of SYPRO Ruby total protein stain for the normalization of two-dimensional Western blots" Analytical Biochemistry 476 1: 17–19 doi:101016/jab201501015 PMID 25640586 
  20. ^ "Total Protein Normalization for Western Blots - Advansta Inc" Retrieved 2016-10-01 
  21. ^ a b Rivero-Gutiérrez, B; Anzola, A; Martínez-Augustin, O; de Medina, F Sánchez 2014-12-15 "Stain-free detection as loading control alternative to Ponceau and housekeeping protein immunodetection in Western blotting" Analytical Biochemistry 467: 1–3 doi:101016/jab201408027 ISSN 1096-0309 PMID 25193447 
  22. ^ a b c d e f Gürtler, Anne; Kunz, Nancy; Gomolka, Maria; Hornhardt, Sabine; Friedl, Anna A; McDonald, Kevin; Kohn, Jonathan E; Posch, Anton 2013-02-15 "Stain-Free technology as a normalization tool in Western blot analysis" Analytical Biochemistry 433 2: 105–111 doi:101016/jab201210010 
  23. ^ "Fluorescence Imaging: Principles and Methods" PDF Retrieved 10 January 2018 
  24. ^ a b Goldman, A; Harper, S; Speicher, DW 2016-11-01 "Detection of Proteins on Blot Membranes" Current Protocols in Protein Science 86: 1081–10811 doi:101002/cpps15 
  25. ^ Zeitler, Anna F; Gerrer, Katrin H; Haas, Rainer; Jiménez-Soto, Luisa F 2016-07-01 "Optimized semi-quantitative blot analysis in infection assays using the Stain-Free technology" Journal of Microbiological Methods 126: 38–41 doi:101016/jmimet201604016 
  26. ^ "Stain-Free Technology | Applications & Technologies | Bio-Rad" wwwbio-radcom Retrieved 2016-10-01 
  27. ^ Colella, Alex D; Chegenii, Nusha; Tea, Melinda N; Gibbins, Ian L; Williams, Keryn A; Chataway, Tim K 15 November 2012 "Comparison of Stain-Free gels with traditional immunoblot loading control methodology" Analytical Biochemistry 430 2: 108–110 doi:101016/jab201208015 PMID 22929699 
  28. ^ Gilda, Jennifer E; Gomes, Aldrin V 2013-09-15 "Stain-Free total protein staining is a superior loading control to β-actin for Western blots" Analytical Biochemistry 440 2: 186–188 doi:101016/jab201305027 PMC 3809032  PMID 23747530 
  29. ^ a b Simonyi, K & Yadav, G 7 August 2016 "Trends in Quantitative Western Blotting – the Emergence of Total Protein Normalization" Bioscience Technology Advantage Media 
  30. ^ "Stain-Free Approach for Western Blotting | GEN Magazine Articles | GEN" GEN Retrieved 2016-10-01 
  31. ^ Gilda, JenniferE; Gomes, AldrinV 2015-01-01 Posch, Anton, ed Proteomic Profiling Methods in Molecular Biology Springer New York pp 381–391 doi:101007/978-1-4939-2550-6_27 ISBN 9781493925490 

External links

  • V3 Stain-free Workflow for a Practical, Convenient, and Reliable Total Protein Loading Control in Western Blotting

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Western blot normalization


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    Western blot normalization beatiful post thanks!

    29.10.2014


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