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Ruparelia AA, Salavaty A, Barlow CK, Lu Y, Sonntag C, Hersey L, Eramo MJ, Krug J, Reuter H, Schittenhelm RB, Ramialison M, Cox A, Ryan MT, Creek DJ, Englert C, Currie PD. The African killifish: A short-lived vertebrate model to study the biology of sarcopenia and longevity. Aging Cell 2024; 23:e13862. [PMID: 37183563 PMCID: PMC10776123 DOI: 10.1111/acel.13862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023] Open
Abstract
Sarcopenia, the age-related decline in muscle function, places a considerable burden on health-care systems. While the stereotypic hallmarks of sarcopenia are well characterized, their contribution to muscle wasting remains elusive, which is partly due to the limited availability of animal models. Here, we have performed cellular and molecular characterization of skeletal muscle from the African killifish-an extremely short-lived vertebrate-revealing that while many characteristics deteriorate with increasing age, supporting the use of killifish as a model for sarcopenia research, some features surprisingly reverse to an "early-life" state in the extremely old stages. This suggests that in extremely old animals, there may be mechanisms that prevent further deterioration of skeletal muscle, contributing to an extension of life span. In line with this, we report a reduction in mortality rates in extremely old killifish. To identify mechanisms for this phenomenon, we used a systems metabolomics approach, which revealed that during aging there is a striking depletion of triglycerides, mimicking a state of calorie restriction. This results in the activation of mitohormesis, increasing Sirt1 levels, which improves lipid metabolism and maintains nutrient homeostasis in extremely old animals. Pharmacological induction of Sirt1 in aged animals was sufficient to induce a late life-like metabolic profile, supporting its role in life span extension in vertebrate populations that are naturally long-lived. Collectively, our results demonstrate that killifish are not only a novel model to study the biological processes that govern sarcopenia, but they also provide a unique vertebrate system to dissect the regulation of longevity.
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Affiliation(s)
- Avnika A. Ruparelia
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health SciencesUniversity of MelbourneMelbourneAustralia
- Centre for Muscle Research, Department of Anatomy and PhysiologyUniversity of MelbourneMelbourneAustralia
| | - Adrian Salavaty
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
- Systems Biology Institute Australia, Monash UniversityClaytonAustralia
| | - Christopher K. Barlow
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
- Monash Proteomics and Metabolomics FacilityMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Yansong Lu
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
| | - Carmen Sonntag
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
| | - Lucy Hersey
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
| | - Matthew J. Eramo
- Department of Biochemistry and Molecular BiologyMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Johannes Krug
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI)JenaGermany
| | - Hanna Reuter
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI)JenaGermany
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
- Monash Proteomics and Metabolomics FacilityMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
- Systems Biology Institute Australia, Monash UniversityClaytonAustralia
| | - Andrew Cox
- Peter MacCallum Cancer CentreMelbourneAustralia
- Department of Biochemistry and PharmacologyThe University of MelbourneMelbourneAustralia
| | - Michael T. Ryan
- Department of Biochemistry and Molecular BiologyMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
| | - Darren J. Creek
- Monash Proteomics and Metabolomics FacilityMonash Biomedicine Discovery Institute, Monash UniversityClaytonAustralia
- Drug Delivery, Disposition and DynamicsMonash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Christoph Englert
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI)JenaGermany
- Institute of Biochemistry and Biophysics, Friedrich‐Schiller‐University JenaJenaGermany
| | - Peter D. Currie
- Australian Regenerative Medicine Institute, Monash UniversityClaytonAustralia
- EMBL Australia, Victorian NodeMonash UniversityClaytonAustralia
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2
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Omondi C, Chou A, Fond KA, Morioka K, Joseph NR, Sacramento JA, Iorio E, Torres-Espin A, Radabaugh HL, Davis JA, Gumbel JH, Russell Huie J, Ferguson AR. Improving rigor and reproducibility in western blot experiments with the blotRig analysis software. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551674. [PMID: 37577570 PMCID: PMC10418285 DOI: 10.1101/2023.08.02.551674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Western blot is a popular biomolecular analysis method for measuring the relative quantities of independent proteins in complex biological samples. However, variability in quantitative western blot data analysis poses a challenge in designing reproducible experiments. The lack of rigorous quantitative approaches in current western blot statistical methodology may result in irreproducible inferences. Here we describe best practices for the design and analysis of western blot experiments, with examples and demonstrations of how different analytical approaches can lead to widely varying outcomes. To facilitate best practices, we have developed the blotRig tool for designing and analyzing western blot experiments to improve their rigor and reproducibility. The blotRig application includes functions for counterbalancing experimental design by lane position, batch management across gels, and analytics with covariates and random effects.
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Affiliation(s)
- Cleopa Omondi
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Austin Chou
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Kenneth A. Fond
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Kazuhito Morioka
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Nadine R. Joseph
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Jeffrey A. Sacramento
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Emma Iorio
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Abel Torres-Espin
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
- School of Public Health Sciences, Faculty of Health Sciences, University of Waterloo, ON, Canada
- Department of Physical Therapy, Faculty of Rehabilitation Medicine, University of Alberta, AB, Canada
| | - Hannah L. Radabaugh
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Jacob A. Davis
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Jason H. Gumbel
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - J. Russell Huie
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
- San Francisco Veterans Affairs Medical Center, San Francisco, San Francisco, CA USA
| | - Adam R. Ferguson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
- San Francisco Veterans Affairs Medical Center, San Francisco, San Francisco, CA USA
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3
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Primo C, Navarre C, Chaumont F, André B. Plasma membrane H +-ATPases promote TORC1 activation in plant suspension cells. iScience 2022; 25:104238. [PMID: 35494253 PMCID: PMC9046228 DOI: 10.1016/j.isci.2022.104238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022] Open
Abstract
The TORC1 (Target of Rapamycin Complex 1) kinase complex plays a pivotal role in controlling cell growth in probably all eukaryotic species. The signals and mechanisms regulating TORC1 have been intensely studied in mammals but those of fungi and plants are much less known. We have previously reported that the yeast plasma membrane H+-ATPase Pma1 promotes TORC1 activation when stimulated by cytosolic acidification or nutrient-uptake-coupled H+ influx. Furthermore, a homologous plant H+-ATPase can substitute for yeast Pma1 to promote this H+-elicited TORC1 activation. We here report that TORC1 activity in Nicotiana tabacum BY-2 cells is also strongly influenced by the activity of plasma membrane H+-ATPases. In particular, stimulation of H+-ATPases by fusicoccin activates TORC1, and this response is also observed in cells transferred to a nutrient-free and auxin-free medium. Our results suggest that plant H+-ATPases, known to be regulated by practically all factors controlling cell growth, contribute to TOR signaling. Isolation of a tobacco BY-2 cell line suitable for analyzing TOR signaling Activation of plasma membrane H+-ATPases in BY-2 suspension cells elicits TOR signaling TOR signaling upon H+-ATPase activation also occurs in the absence of nutrients and auxin
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Affiliation(s)
- Cecilia Primo
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), Biopark, B-6041 Gosselies, Belgium
| | - Catherine Navarre
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - François Chaumont
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - Bruno André
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), Biopark, B-6041 Gosselies, Belgium
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Schätzle H, Brouwer EM, Liebhart E, Stevanovic M, Schleiff E. Comparative Phenotypic Analysis of Anabaena sp. PCC 7120 Mutants of Porinlike Genes. J Microbiol Biotechnol 2021; 31:645-658. [PMID: 33879642 PMCID: PMC9705863 DOI: 10.4014/jmb.2103.03009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022]
Abstract
Porins are essential for the viability of Gram-negative bacteria. They ensure the uptake of nutrients, can be involved in the maintenance of outer membrane integrity and define the antibiotic or drug resistance of organisms. The function and structure of porins in proteobacteria is well described, while their function in photoautotrophic cyanobacteria has not been systematically explored. We compared the domain architecture of nine putative porins in the filamentous cyanobacterium Anabaena sp. PCC 7120 and analyzed the seven candidates with predicted OprB-domain. Single recombinant mutants of the seven genes were created and their growth capacity under different conditions was analyzed. Most of the putative porins seem to be involved in the transport of salt and copper, as respective mutants were resistant to elevated concentrations of these substances. In turn, only the mutant of alr2231 was less sensitive to elevated zinc concentrations, while mutants of alr0834, alr4741 and all4499 were resistant to high manganese concentrations. Notably the mutant of alr4550 shows a high sensitivity against harmful compounds, which is indicative for a function related to the maintenance of outer membrane integrity. Moreover, the mutant of all5191 exhibited a phenotype which suggests either a higher nitrate demand or an inefficient nitrogen fixation. The dependency of porin membrane insertion on Omp85 proteins was tested exemplarily for Alr4550, and an enhanced aggregation of Alr4550 was observed in two omp85 mutants. The comparative analysis of porin mutants suggests that the proteins in parts perform distinct functions related to envelope integrity and solute uptake.
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Affiliation(s)
- Hannah Schätzle
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,FIERCE, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
| | - Eva-Maria Brouwer
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Elisa Liebhart
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Mara Stevanovic
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany,FIERCE, Goethe University, Frankfurt am Main, Germany,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany,Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany,Corresponding author Phone: +49 69 798 29287 Fax: +49 69 798 29286 E-mail:
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5
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Ruparelia AA, McKaige EA, Williams C, Schulze KE, Fuchs M, Oorschot V, Lacene E, Meregalli M, Lee C, Serrano RJ, Baxter EC, Monro K, Torrente Y, Ramm G, Stojkovic T, Lavoie JN, Bryson-Richardson RJ. Metformin rescues muscle function in BAG3 myofibrillar myopathy models. Autophagy 2020; 17:2494-2510. [DOI: 10.1080/15548627.2020.1833500] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Emily A. McKaige
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Caitlin Williams
- School of Biological Sciences, Monash University, Melbourne, Australia
| | | | - Margit Fuchs
- Centre de Recherche Sur le Cancer de l’Université Laval, Ville de Québec, Canada
- Oncologie, Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Ville de Québec, Canada
| | - Viola Oorschot
- Monash Ramaciotti Centre for Structural Cryo-Electron Microscopy, Monash University, Melbourne, Australia
| | - Emmanuelle Lacene
- Institut de Myologie, Laboratoire de Pathologie Risler, APHP, Centre de Référence de Pathologie Neuromusculaire Nord/Est/Ile-de-France, Paris, France
| | - Mirella Meregalli
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università Degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Centro Dino Ferrari, Milan, Italy
| | - Clara Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Rita J. Serrano
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Emily C. Baxter
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Yvan Torrente
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università Degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Centro Dino Ferrari, Milan, Italy
| | - Georg Ramm
- Monash Ramaciotti Centre for Structural Cryo-Electron Microscopy, Monash University, Melbourne, Australia
- Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Tanya Stojkovic
- Institut de Myologie, Centre de Référence des Maladies Neuromusculaires, Hôpital Pitié-Salpétrière, Assistance-Publique Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Josée N. Lavoie
- Centre de Recherche Sur le Cancer de l’Université Laval, Ville de Québec, Canada
- Oncologie, Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Ville de Québec, Canada
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Ville de Québec, Canada
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Misleading Westerns: Common Quantification Mistakes in Western Blot Densitometry and Proposed Corrective Measures. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5214821. [PMID: 30800670 PMCID: PMC6360618 DOI: 10.1155/2019/5214821] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/12/2018] [Indexed: 02/07/2023]
Abstract
Densitometry data generated for Western blots are commonly used to compare protein abundance between samples. In the last decade, it has become apparent that assumptions underpinning these comparisons are often violated in studies reporting Western blot data in the literature. These violations can lead to erroneous interpretations of data and may contribute to poor reproducibility of research. We assessed the reliability of Western blot data obtained to study human myometrial tissue proteins. We ran dilution series of protein lysates to explore the linearity of densitometry data. Proteins analysed included αSMA, HSP27, ERK1/2, and GAPDH. While ideal densitometry data are directly proportional to protein abundance, our data confirm that densitometry data often deviate from this ideal, in which case they can fit nonproportional linear or hyperbolic mathematical models and can reach saturation. Nonlinear densitometry data were observed when Western blots were detected using infrared fluorescence or chemiluminescence, and under different SDS-PAGE conditions. We confirm that ghosting artefacts associated with overabundance of proteins of interest in Western blots can skew findings. We also confirm that when data to be normalised are not directly proportional to protein abundance, it is a mistake to use the normalisation technique of dividing densitometry data from the protein-of-interest with densitometry data from loading control protein(s), as this can cause the normalised data to be unusable for making comparisons. Using spiked proteins in a way that allowed us to control the total protein amount per lane, while only changing the amount of spiked proteins, we confirm that nonlinearity and saturation of densitometry data, and errors introduced from normalisation processes, can occur in routine assays that compare equal amounts of lysate. These findings apply to all Western blot studies, and we highlight quality control checks that should be performed to make Western blot data more quantitative.
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7
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Kirshner ZZ, Gibbs RB. Use of the REVERT ® total protein stain as a loading control demonstrates significant benefits over the use of housekeeping proteins when analyzing brain homogenates by Western blot: An analysis of samples representing different gonadal hormone states. Mol Cell Endocrinol 2018; 473:156-165. [PMID: 29396126 PMCID: PMC6045444 DOI: 10.1016/j.mce.2018.01.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/21/2018] [Accepted: 01/22/2018] [Indexed: 01/01/2023]
Abstract
Western blot is routinely used to quantify differences in the levels of target proteins in tissues. Standard methods typically use measurements of housekeeping proteins to control for variations in loading and protein transfer. This is problematic, however, when housekeeping proteins also are affected by experimental conditions such as injury, disease, and/or gonadal hormone manipulations. Our goal was to evaluate an alternative and perhaps superior method for conducting Western blot analysis of brain tissue homogenates from rats with distinct physiologically relevant gonadal hormone states. Tissues were collected from the hippocampus, frontal cortex, and striatum of young adult female rats that either were ovariectomized to model surgical menopause, or were treated with the ovatotoxin 4-vinylcyclohexene diepoxide (VCD) to model transitional menopause. Tissues also were collected from rats with a normal estrous cycle killed at proestrus when estradiol levels are high, and at diestrus when estradiol levels are low. Western blot detection of α-tubulin, β-actin, and GAPDH was performed and were compared for sensitivity and reliability with a fluorescent total protein stain (REVERT®). Results show that the total protein stain was much less variable across samples and had a greater linear range than α-tubulin, β-actin, or GAPDH. The stain was stable and easy to use, and did not interfere with the immunodetection or multiplexed detection of the housekeeping proteins. In addition, we show that normalization of our data to total protein, but not to GAPDH, revealed significant differences in α-tubulin expression in the hippocampus as a function of treatment, and that gel-to-gel consistency in measuring differences between paired samples run on multiple gels was significantly better when data were normalized to total protein than when normalized to GAPDH. These results demonstrate that the REVERT® total protein stain can be used in Western blot analysis of brain tissue homogenates to control for variations in loading and protein transfer, and provides significant advantages over the use of housekeeping proteins for quantifying changes in the levels of multiple target proteins.
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Affiliation(s)
- Z Z Kirshner
- University of Pittsburgh, Department of Pharmaceutical Sciences, 1004 Salk Hall, Pittsburgh, PA 15261, USA.
| | - R B Gibbs
- University of Pittsburgh, Department of Pharmaceutical Sciences, 1004 Salk Hall, Pittsburgh, PA 15261, USA.
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8
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A Multidisciplinary Approach Reveals an Age-Dependent Expression of a Novel Bioactive Peptide, Already Involved in Neurodegeneration, in the Postnatal Rat Forebrain. Brain Sci 2018; 8:brainsci8070132. [PMID: 29996490 PMCID: PMC6070872 DOI: 10.3390/brainsci8070132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 11/16/2022] Open
Abstract
The basal forebrain has received much attention due to its involvement in multiple cognitive functions, but little is known about the basic neuronal mechanisms underlying its development, nor those mediating its primary role in Alzheimer’s disease. We have previously suggested that a novel 14-mer peptide, ‘T14’, could play a pivotal role in Alzheimer’s disease, via reactivation of a developmental signaling pathway. In this study, we have characterized T14 in the context of post-natal rat brain development, using a combination of different techniques. Ex-vivo rat brain slices containing the basal forebrain, at different stages of development, were used to investigate large-scale neuronal network activity in real time with voltage-sensitive dye imaging. Subsequent Western blot analysis revealed the expression profile of endogenous T14, its target alpha7 nicotinic receptor and the familiar markers of Alzheimer’s: amyloid beta and phosphorylated Tau. Results indicated maximal neuronal activity at the earliest ages during development, reflected in a concomitant profile of T14 peptide levels and related proteins. In conclusion, these findings show that the peptide, already implicated in neurodegenerative events, has an age-dependent expression, suggesting a possible contribution to the physiological mechanisms underlying brain maturation.
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9
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Brai E, Simon F, Cogoni A, Greenfield SA. Modulatory Effects of a Novel Cyclized Peptide in Reducing the Expression of Markers Linked to Alzheimer's Disease. Front Neurosci 2018; 12:362. [PMID: 29950969 PMCID: PMC6008575 DOI: 10.3389/fnins.2018.00362] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/09/2018] [Indexed: 12/17/2022] Open
Abstract
Despite many studies attempt to identify the primary mechanisms underlying neurodegeneration in Alzheimer's disease (AD), the key events still remain elusive. We have previously shown that a peptide cleaved from the acetylcholinesterase (AChE) C-terminus (T14) can play a pivotal role as a signaling molecule in neurodegeneration, via its interaction with the α7 nicotinic acetylcholine receptor. The main goal of this study is to determine whether a cyclized variant (NBP14) of the toxic AChE-derived peptide can antagonize the effects of its linear counterpart, T14, in modulating well-known markers linked to neurodegeneration. We investigate this hypothesis applying NBP14 on ex-vivo rat brain slices containing the basal forebrain. Western blot analysis revealed an inhibitory action of NBP14 on naturally occurring T14 peptide, as well as on endogenous amyloid beta, whereas the expression of the nicotinic receptor and phosphorylated Tau was relatively unaffected. These results further confirm the neurotoxic properties of the AChE-peptide and show for the first time in an ex-vivo preparation the possible neuroprotective activity of NBP14, over a protracted period of hours, indicating that T14 pathway may offer a new prospect for therapeutic intervention in AD pathobiology.
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Affiliation(s)
- Emanuele Brai
- Culham Science Centre, Neuro-Bio Ltd., Oxfordshire, United Kingdom
| | - Florian Simon
- Culham Science Centre, Neuro-Bio Ltd., Oxfordshire, United Kingdom.,Department of Biotechnology, University of Nîmes, Nîmes, France
| | - Antonella Cogoni
- Culham Science Centre, Neuro-Bio Ltd., Oxfordshire, United Kingdom
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10
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Optimization of the cydex blue assay: A one-step colorimetric protein assay using cyclodextrins and compatible with detergents and reducers. PLoS One 2018; 13:e0195755. [PMID: 29641569 PMCID: PMC5895047 DOI: 10.1371/journal.pone.0195755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/28/2018] [Indexed: 01/21/2023] Open
Abstract
Sodium dodecyl sulfate electrophoresis (SDS) is a protein separation technique widely used, for example, prior to immunoblotting. Samples are usually prepared in a buffer containing both high concentrations of reducers and high concentrations of SDS. This conjunction renders the samples incompatible with common protein assays. By chelating the SDS, cyclodextrins make the use of simple, dye-based colorimetric assays possible. In this paper, we describe the optimization of the assay, focussing on the cyclodextrin/SDS ratio and the use of commercial assay reagents. The adaptation of the assay to a microplate format and using other detergent-containing conventional extraction buffers is also described.
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11
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Brai E, Stuart S, Badin AS, Greenfield SA. A Novel Ex Vivo Model to Investigate the Underlying Mechanisms in Alzheimer's Disease. Front Cell Neurosci 2017; 11:291. [PMID: 29033787 PMCID: PMC5627036 DOI: 10.3389/fncel.2017.00291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/04/2017] [Indexed: 01/09/2023] Open
Abstract
Currently there is no widely accepted animal model reproducing the full pathological profile of Alzheimer's disease (AD), since the basic mechanisms of neurodegeneration are still poorly understood. We have proposed that the interaction between the α7 nicotinic acetylcholine receptor (α7-nAChR) and a recently discovered toxic peptide, cleaved from the acetylcholinesterase (AChE) C-terminus, could account for the aberrant processes occurring in AD. In this article we describe a new application on ex vivo model procedure, which combines the advantages of both in vivo and in vitro preparations, to study the effects of the AChE-derived peptide on the rat basal forebrain (BF). Western blot analysis showed that the levels of α7-nAChR, p-Tau and Aβ are differentially expressed upon the AChE-peptide administration, in a selective site-dependent manner. In conclusion, this methodology demonstrates the action of a novel peptide in triggering an AD-like phenotype and proposes a new ex vivo approach for manipulating and monitoring neurochemical processes contributing to neurodegeneration, in a time-dependent and site-specific manner.
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Affiliation(s)
- Emanuele Brai
- Neuro-Bio Ltd., Culham Science CentreAbingdon, United Kingdom
| | - Skye Stuart
- Neuro-Bio Ltd., Culham Science CentreAbingdon, United Kingdom.,School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of BristolBristol, United Kingdom
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12
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Primo C, Ferri-Blázquez A, Loewith R, Yenush L. Reciprocal Regulation of Target of Rapamycin Complex 1 and Potassium Accumulation. J Biol Chem 2016; 292:563-574. [PMID: 27895122 DOI: 10.1074/jbc.m116.746982] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/16/2016] [Indexed: 12/19/2022] Open
Abstract
The proper maintenance of potassium homeostasis is crucial for cell viability. Among the major determinants of potassium uptake in the model organism Saccharomyces cerevisiae are the Trk1 high affinity potassium transporter and the functionally redundant Hal4 (Sat4) and Hal5 protein kinases. These kinases are required for the plasma membrane accumulation of not only Trk1 but also several nutrient permeases. Here, we show that overexpression of the target of rapamycin complex 1 (TORC1) effector NPR1 improves hal4 hal5 growth defects by stabilizing nutrient permeases at the plasma membrane. We subsequently found that internal potassium levels and TORC1 activity are linked. Specifically, growth under limiting potassium alters the activities of Npr1 and another TORC1 effector kinase, Sch9; hal4 hal5 and trk1 trk2 mutants display hypersensitivity to rapamycin, and reciprocally, TORC1 inhibition reduces potassium accumulation. Our results demonstrate that in addition to carbon and nitrogen, TORC1 also responds to and regulates potassium fluxes.
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Affiliation(s)
- Cecilia Primo
- From the Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia, Spain 46022 and
| | - Alba Ferri-Blázquez
- From the Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia, Spain 46022 and
| | - Robbie Loewith
- the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Swiss National Centre for Competence in Research in Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Lynne Yenush
- From the Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia, Spain 46022 and
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13
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Rabilloud T. A single step protein assay that is both detergent and reducer compatible: The cydex blue assay. Electrophoresis 2016; 37:2595-2601. [PMID: 27445231 DOI: 10.1002/elps.201600270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/06/2016] [Accepted: 07/10/2016] [Indexed: 11/06/2022]
Abstract
Determination of protein concentration is often an absolute prerequisite in preparing samples for biochemical and proteomic analyses. However, current protein assay methods are not compatible with both reducers and detergents, which are however present simultaneously in most denaturing extraction buffers used in proteomics and electrophoresis, and in particular in SDS electrophoresis. It was found that inclusion of cyclodextrins in a Coomassie blue-based assay made it compatible with detergents, as cyclodextrins complex detergents in a 1:1 molecular ratio. As this type of assay is intrinsically resistant to reducers, a single-step assay that is both detergent and reducer compatible was developed. Depending on the type and concentration of detergents present in the sample buffer, either beta-cyclodextrin or alpha-cyclodextrin can be used, the former being able to complex a wider range of detergents and the latter being able to complex higher amounts of detergents due to its greater solubility in water. Cyclodextrins are used at final concentrations of 2-10 mg/mL in the assay mix. This typically allows to measure samples containing as little as 0.1 mg/mL protein, in the presence of up to 2% detergent and reducers such as 5% mercaptoethanol or 50 mM DTT in a single step with a simple spectrophotometric assay.
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Affiliation(s)
- Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals, CNRS UMR 5249 Grenoble, France. .,Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, Grenoble, France. .,CEA Grenoble, BIG/CBM, Laboratory of Chemistry and Biology of Metals, CEA Grenoble, Grenoble, France.
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14
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Zeng L, Zeng B, Wang H, Li B, Huo R, Zheng P, Zhang X, Du X, Liu M, Fang Z, Xu X, Zhou C, Chen J, Li W, Guo J, Wei H, Xie P. Microbiota Modulates Behavior and Protein Kinase C mediated cAMP response element-binding protein Signaling. Sci Rep 2016; 6:29998. [PMID: 27444685 PMCID: PMC4956747 DOI: 10.1038/srep29998] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/27/2016] [Indexed: 12/19/2022] Open
Abstract
Evolutionary pressure drives gut microbiota–host coevolution and results in complex interactions between gut microbiota and neural development; however, the molecular mechanisms by which the microbiota governs host behavior remain obscure. Here, we report that colonization early in life is crucial for the microbiota to modulate brain development and behavior; later colonization or deletion of microbiota cannot completely reverse the behaviors. Microarray analysis revealed an association between absence of gut microbiota and expression in cAMP responding element-binding protein (CREB) regulated genes in the hippocampus. The absence of gut microbiota from birth was shown to be associated with decreased CREB expression, followed by decreases of protein kinase C beta (PRKCB) and AMPA receptors expression, and an increase of phosphorylation CREB (pCREB) expression. Microbiota colonization in adolescence restored CREB and pCREB expression, but did not alter PRKCB and AMPARs expression. The removal of the gut microbiota from SPF mice using antibiotics only reduced pCREB expression. These findings suggest that (i) colonization of the gut microbiota early in life might facilitate neurodevelopment via PKC–CREB signaling and (ii) although GF mice and ABX mice display reduced anxiety-related behaviors, the molecular mechanisms behind this might differ.
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Affiliation(s)
- Li Zeng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Benhua Zeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Haiyang Wang
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Bo Li
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China.,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Ran Huo
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China.,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Peng Zheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Xiaotong Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Xiangyu Du
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Meiling Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Zheng Fang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Xuejiao Xu
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Chanjuan Zhou
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Jianjun Chen
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Wenxia Li
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Jing Guo
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China.,Chongqing Cancer Hospital &Institute &Cancer Center, Chongqing, China
| | - Hong Wei
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Neurobiology, Chongqing, China.,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China.,Department of Neurology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China.,South Australian Health and Medical Research Institute, Mind and Brain Theme, and Flinders University, Adelaide, SA, Australia
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15
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Fortes MAS, Marzuca-Nassr GN, Vitzel KF, da Justa Pinheiro CH, Newsholme P, Curi R. Housekeeping proteins: How useful are they in skeletal muscle diabetes studies and muscle hypertrophy models? Anal Biochem 2016; 504:38-40. [PMID: 27060530 DOI: 10.1016/j.ab.2016.03.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 12/15/2022]
Abstract
The use of Western blot analysis is of great importance in research, and the measurement of housekeeping proteins is commonly used for loading controls. However, Ponceau S staining has been shown to be an alternative to analysis of housekeeping protein levels as loading controls in some conditions. In the current study, housekeeping protein levels were measured in skeletal muscle hypertrophy and streptozotocin-induced diabetes experimental models. The following housekeeping proteins were investigated: glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-actin, α-tubulin, γ-tubulin, and α-actinin. Evidence is presented that Ponceau S is more reliable than housekeeping protein levels for specific protein quantifications in Western blot analysis.
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Affiliation(s)
- Marco Aurélio Salomão Fortes
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Butantã, São Paulo 05508-900, Brazil.
| | - Gabriel Nasri Marzuca-Nassr
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Butantã, São Paulo 05508-900, Brazil
| | - Kaio Fernando Vitzel
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Butantã, São Paulo 05508-900, Brazil
| | - Carlos Hermano da Justa Pinheiro
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Butantã, São Paulo 05508-900, Brazil
| | - Philip Newsholme
- School of Biomedical Sciences, Curtin Health Innovation Research Institute (CHIRI) Biosciences, Curtin University, Bentley, Perth, Western Australia 6102, Australia
| | - Rui Curi
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Butantã, São Paulo 05508-900, Brazil
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16
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Collins MA, An J, Peller D, Bowser R. Total protein is an effective loading control for cerebrospinal fluid western blots. J Neurosci Methods 2015; 251:72-82. [PMID: 26004848 DOI: 10.1016/j.jneumeth.2015.05.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cerebrospinal fluid (CSF) has been used to identify biomarkers of neurological disease. CSF protein biomarkers identified by high-throughput methods, however, require further validation. While Western blotting (WB) is well-suited to this task, the lack of a validated loading control for CSF WB limits the method's accuracy. NEW METHOD We investigated the use of total protein (TP) as a CSF WB loading control. Using iodine-based reversible membrane staining, we determined the linear range and consistency of the CSF TP signal. We then spiked green fluorescent protein (GFP) into CSF to create defined sample-to-sample differences in GFP levels that were measured by WB before and after TP loading correction. Levels of CSF complement C3 and cystatin C measured by WB with TP loading correction and ELISA in amyotrophic lateral sclerosis and healthy control CSF samples were then compared. RESULTS CSF WB with the TP loading control accurately detected defined differences in GFP levels and corrected for simulated loading errors. Individual CSF sample Western blot and ELISA measurements of complement C3 and cystatin C were significantly correlated and the methods showed a comparable ability to detect between-groups differences. COMPARISON WITH EXISTING METHOD CSF TP staining has a greater linear dynamic range and sample-to-sample consistency than albumin, a commonly used CSF loading control. The method accurately corrects for simulated errors in loading and improves the sensitivity of CSF WB compared to using no loading control. CONCLUSIONS The TP staining loading control improves the sensitivity and accuracy of CSF WB results.
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Affiliation(s)
- Mahlon A Collins
- Department of Neurobiology, University of Pittsburgh, 200 South Lothrop Street, Pittsburgh, PA 15213, USA; Departments of Neurobiology and Neurology, St. Joseph's Hospital and Medical Center and Barrow Neurological Institute, 350 West Thomas Road, Phoenix, AZ 85013, USA.
| | - Jiyan An
- Departments of Neurobiology and Neurology, St. Joseph's Hospital and Medical Center and Barrow Neurological Institute, 350 West Thomas Road, Phoenix, AZ 85013, USA.
| | - Danielle Peller
- Departments of Neurobiology and Neurology, St. Joseph's Hospital and Medical Center and Barrow Neurological Institute, 350 West Thomas Road, Phoenix, AZ 85013, USA.
| | - Robert Bowser
- Departments of Neurobiology and Neurology, St. Joseph's Hospital and Medical Center and Barrow Neurological Institute, 350 West Thomas Road, Phoenix, AZ 85013, USA.
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17
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Steinberger B, Brem G, Mayrhofer C. Evaluation of SYPRO Ruby total protein stain for the normalization of two-dimensional Western blots. Anal Biochem 2015; 476:17-9. [PMID: 25640586 DOI: 10.1016/j.ab.2015.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 01/14/2015] [Accepted: 01/19/2015] [Indexed: 10/24/2022]
Abstract
Due to post-translational modifications such as phosphorylation, proteins exist as distinct charge variants. Two-dimensional (2D) gel electrophoresis followed by immunoblotting enables the detection of these isoforms. For their accurate relative quantitation in different samples, a loading control is necessary to compensate for technical errors such as imprecise sample loading or transfer. The study reveals that the combinatory approach of SYPRO Ruby and chemiluminescence-based 2D Western blot analysis exhibits high linearity and excellent reproducibility and is applicable for limited sample amounts.
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Affiliation(s)
- Birgit Steinberger
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, A-1210 Vienna, Austria; Institute of Biotechnology in Animal Production, Department of Agrobiotechnology (IFA Tulln), University of Natural Resources and Applied Life Sciences Vienna, A-3430 Tulln, Austria.
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Corina Mayrhofer
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, A-1210 Vienna, Austria; Institute of Biotechnology in Animal Production, Department of Agrobiotechnology (IFA Tulln), University of Natural Resources and Applied Life Sciences Vienna, A-3430 Tulln, Austria
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18
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Western blotting using in-gel protein labeling as a normalization control: stain-free technology. Methods Mol Biol 2015; 1295:381-91. [PMID: 25820735 DOI: 10.1007/978-1-4939-2550-6_27] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Western blotting is a commonly used laboratory technique for semi-quantifying protein amounts. It is important when quantifying protein expression to account for differences in the amount of total protein loaded onto the gel using a loading control. Common loading controls include housekeeping proteins, such as β-actin or GAPDH, quantified by Western blot, or total protein, quantified using a stain such as Coomassie Brilliant Blue or Ponceau S. A more recently developed method for total protein quantification utilizes stain-free technology, which has a linear dynamic detection range and allows for protein detection on both gels and membranes. Here, we describe the theory and use of stain-free gels for total protein quantification and normalization of Western blots.
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19
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Prokopec SD, Watson JD, Pohjanvirta R, Boutros PC. Identification of reference proteins for Western blot analyses in mouse model systems of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity. PLoS One 2014; 9:e110730. [PMID: 25329058 PMCID: PMC4201576 DOI: 10.1371/journal.pone.0110730] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 09/24/2014] [Indexed: 01/15/2023] Open
Abstract
Western blotting is a well-established, inexpensive and accurate way of measuring protein content. Because of technical variation between wells, normalization is required for valid interpretation of results across multiple samples. Typically this involves the use of one or more endogenous controls to adjust the measured levels of experimental molecules. Although some endogenous controls are widely used, validation is required for each experimental system. This is critical when studying transcriptional-modulators, such as toxicants like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).To address this issue, we examined hepatic tissue from 192 mice representing 47 unique combinations of strain, sex, Ahr-genotype, TCDD dose and treatment time. We examined 7 candidate reference proteins in each animal and assessed consistency of protein abundance through: 1) TCDD-induced fold-difference in protein content from basal levels, 2) inter- and intra- animal stability, and 3) the ability of each candidate to reduce instability of the other candidates. Univariate analyses identified HPRT as the most stable protein. Multivariate analysis indicated that stability generally increased with the number of proteins used, but gains from using >3 proteins were small. Lastly, by comparing these new data to our previous studies of mRNA controls on the same animals, we were able to show that the ideal mRNA and protein control-genes are distinct, and use of only 2–3 proteins provides strong stability, unlike in mRNA studies in the same cohort, where larger control-gene batteries were needed.
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Affiliation(s)
- Stephenie D. Prokopec
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John D. Watson
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Raimo Pohjanvirta
- Laboratory of Toxicology, National Institute for Health and Welfare, Kuopio, Finland
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Paul C. Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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20
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Ghosh R, Gilda JE, Gomes AV. The necessity of and strategies for improving confidence in the accuracy of western blots. Expert Rev Proteomics 2014; 11:549-60. [PMID: 25059473 DOI: 10.1586/14789450.2014.939635] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Western blotting is one of the most commonly used laboratory techniques for identifying proteins and semi-quantifying protein amounts; however, several recent findings suggest that western blots may not be as reliable as previously assumed. This is not surprising since many labs are unaware of the limitations of western blotting. In this manuscript, we review essential strategies for improving confidence in the accuracy of western blots. These strategies include selecting the best normalization standard, proper sample preparation, determining the linear range for antibodies and protein stains relevant to the sample of interest, confirming the quality of the primary antibody, preventing signal saturation and accurately quantifying the signal intensity of the target protein. Although western blotting is a powerful and indispensable scientific technique that can be used to accurately quantify relative protein levels, it is necessary that proper experimental techniques and strategies are employed.
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Affiliation(s)
- Rajeshwary Ghosh
- Department of Neurobiology, Physiology, and Behavior, University of California, Davis, 191 Briggs Hall, One Shields Avenue, CA 95616, USA
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Kovács T, Bánsági B, Kelemen O, Kéri S. Neuregulin 1-induced AKT and ERK phosphorylation in patients with fragile X syndrome (FXS) and intellectual disability associated with obstetric complications. J Mol Neurosci 2014; 54:119-24. [PMID: 24563264 DOI: 10.1007/s12031-014-0257-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 02/05/2014] [Indexed: 12/16/2022]
Abstract
Animal models of fragile X syndrome (FXS) suggest the impairment of the intracellular AKT messenger system, which is activated by neuregulin 1 (NRG1), a key regulator of neurodevelopment. We investigated NRG1-induced activation of the AKT and extracellular signal-regulated kinase (ERK) systems by the measurement of the phosphorylated AKT/ERK to total AKT/ERK ratio in peripheral B lymphoblasts of patients with FXS, IQ-matched controls with intellectual disability (obstetric complications, preterm birth, perinatal hypoxia, and low birth weight), and typically developed healthy participants. Results revealed that patients with FXS displayed decreased AKT but normal ERK activation after the administration of NRG1. IQ-matched controls with intellectual disability displayed intact AKT/ERK activation. In conclusion, FXS, but not intellectual disability associated with obstetric complications, is associated with decreased NRG1-induced AKT phosphorylation.
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Affiliation(s)
- Tamás Kovács
- Nyírő Gyula Hospital-National Institute of Psychiatry and Addictions, Budapest, Hungary
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