scholarly journals MS Western, a Method of Multiplexed Absolute Protein Quantification is a Practical Alternative to Western Blotting

2017 ◽  
Author(s):  
Mukesh Kumar ◽  
Shai R. Joseph ◽  
Martina Augsburg ◽  
Aliona Bogdanova ◽  
David Drechsel ◽  
...  
Keyword(s):  
Western Blotting ◽  
Dynamic Range ◽  
Protein Detection ◽  
Absolute Quantification ◽  
Protein Quantification ◽  
Linear Dynamic Range ◽  
Reference Protein ◽  
Core Histones ◽  
Accurate Quantification

Absolute quantification of proteins elucidates the molecular composition, regulation and dynamics of multiprotein assemblies and networks. Here we report on a method termed MS Western that accurately determines the molar abundance of dozens of user-selected proteins at the sub-femtomole level in whole cell or tissue lysates without metabolic or chemical labelling and without using specific antibodies. MS Western relies upon GeLC-MS/MS and quantifies proteins by in-gel co-digestion with an isotopically labelled QconCAT protein chimera composed of concatenated proteotypic peptides. It requires no purification of the chimera and relates the molar abundance of all proteotypic peptides to a single reference protein. In comparative experiments, MS Western outperformed immunofluorescence Western blotting by the protein detection specificity, linear dynamic range and sensitivity of protein quantification. To validate MS Western in an in vivo experiment, we quantified the molar content of zebrafish core histones H2A, H2B, H3 and H4 during ten stages of early embryogenesis. Accurate quantification (CV<10%) corroborated the anticipated histones equimolar stoichiometry and revealed an unexpected trend in their total abundance.

scholarly journals Circ-SFMBT2 drives the malignant phenotypes of esophageal cancer by the miR-107-dependent regulation of SLC1A5

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhiwei Chang ◽  
Yang Fu ◽  
Yongxu Jia ◽  
Ming Gao ◽  
Lijie Song ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Esophageal Cancer ◽  
Protein Detection ◽  
Protein Quantification ◽  
Glutamine Metabolism ◽  
Luciferase Reporter ◽  
Morphological Observation ◽  
Circular Rnas ◽  
Ec Cells

Abstract Background Increasing studies focused on the regulatory roles of circular RNAs (circRNAs) in diverse cancers. This study was to evaluate the function and mechanism of circRNA Scm-like with four malignant brain tumor domains 2 (circ-SFMBT2) in esophageal cancer (EC). Methods The circ-SFMBT2, microRNA-107 (miR-107) and solute-linked carrier family A1 member 5 (SLC1A5) levels were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation was evaluated by 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT) assay, colony formation assay and EdU assay. Cell apoptosis and invasion were detected by flow cytometry and transwell assay. Glutamine metabolism was assessed by the corresponding kits for glutamine consumption, α-ketoglutarate production and glutamate production. Western blot was used for protein quantification. The binding analysis was performed using dual-luciferase reporter assay, RNA immunoprecipitation (RIP) and pull-down assays. The functional research of circ-SFMBT2 in vivo was performed by xenograft tumor assay. Exosomes were identified by morphological observation and protein detection. Results Circ-SFMBT2 was overexpressed in EC samples and cells. Circ-SFMBT2 downregulation inhibited EC cell proliferation, invasion and glutamine metabolism. Circ-SFMBT2 targeted miR-107 and the regulation of circ-SFMBT2 was achieved by sponging miR-107. SLC1A5 was a target of miR-107, and it worked as an oncogene in EC cells. MiR-107 retarded the EC progression by downregulating SLC1A5. Circ-SFMBT2 could affect the SLC1A5 expression by targeting miR-107. Circ-SFMBT2 regulated EC progression in vivo by miR-107/SLC1A5 axis. Circ-SFMBT2 was transferred by exosomes in EC cells. Conclusion These results suggested that circ-SFMBT2 upregulated the SLC1A5 expression to promote the malignant development of EC by serving as a miR-107 sponge.

scholarly journals HILIC-Enabled 13C Metabolomics Strategies: Comparing Quantitative Precision and Spectral Accuracy of QTOF High- and QQQ Low-Resolution Mass Spectrometry

Metabolites ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 63 ◽  
Author(s):  
André Feith ◽  
Attila Teleki ◽  
Michaela Graf ◽  
Lorenzo Favilli ◽  
Ralf Takors
Keyword(s):  
Mass Spectrometry ◽  
Isotope Dilution Mass Spectrometry ◽  
Absolute Quantification ◽  
Spectral Accuracy ◽  
Time Resolved ◽  
13C Tracer ◽  
Accurate Quantification ◽  
Tracer Experiments

Dynamic 13C-tracer-based flux analyses of in vivo reaction networks still require a continuous development of advanced quantification methods applying state-of-the-art mass spectrometry platforms. Utilizing alkaline HILIC chromatography, we adapt strategies for a systematic quantification study in non- and 13C-labeled multicomponent endogenous Corynebacterium glutamicum extracts by LC-QTOF high resolution (HRMS) and LC-QQQ tandem mass spectrometry (MS/MS). Without prior derivatization, a representative cross-section of 17 central carbon and anabolic key intermediates were analyzed with high selectivity and sensitivity under optimized ESI-MS settings. In column detection limits for the absolute quantification range were between 6.8–304.7 (QQQ) and 28.7–881.5 fmol (QTOF) with comparable linearities (3–5 orders of magnitude) and enhanced precision using QQQ-MRM detection. Tailor-made preparations of uniformly (U)13C-labeled cultivation extracts for isotope dilution mass spectrometry enabled the accurate quantification in complex sample matrices and extended linearities without effect on method parameters. Furthermore, evaluation of metabolite-specific m+1-to-m+0 ratios (ISR1:0) in non-labeled extracts exhibited sufficient methodical spectral accuracies with mean deviations of 3.89 ± 3.54% (QTOF) and 4.01 ± 3.01% (QQQ). Based on the excellent HILIC performance, conformity analysis of time-resolved isotopic enrichments in 13C-tracer experiments revealed sufficient spectral accuracy for QQQ-SIM detection. However, only QTOF-HRMS ensures determination of the full isotopologue space in complex matrices without mass interferences.

scholarly journals Increased sensitivity using real-time dPCR for detection of SARS-CoV-2

BioTechniques ◽  
2020 ◽  
Author(s):  
Kyra Duong ◽  
Jiajia Ou ◽  
Zhaoliang Li ◽  
Zhaoqing Lv ◽  
Hao Dong ◽  
...  
Keyword(s):  
Real Time ◽  
Dynamic Range ◽  
Limit Of Detection ◽  
Absolute Quantification ◽  
Linear Dynamic Range ◽  
End Point ◽  
Increased Sensitivity ◽  
Quantification Accuracy ◽  
Sensitivity Specificity ◽  
Real Time Qpcr

A real-time dPCR system was developed to improve the sensitivity, specificity and quantification accuracy of end point dPCR. We compared three technologies – real-time qPCR, end point dPCR and real-time dPCR – in the context of SARS-CoV-2. Some improvement in limit of detection was obtained with end point dPCR compared with real-time qPCR, and the limit of detection was further improved with the newly developed real-time dPCR technology through removal of false-positive signals. Real-time dPCR showed increased linear dynamic range compared with end point dPCR based on quantitation from amplification curves. Real-time dPCR can improve the performance of TaqMan assays beyond real-time qPCR and end point dPCR with better sensitivity and specificity, absolute quantification and a wider linear range of detection.

Single Particle Inductively Coupled Plasma Mass Spectrometry: Investigating Nonlinear Response Observed in Pulse Counting Mode and Extending the Linear Dynamic Range by Compensating for Dead Time Related Count Losses on a Microsecond Timescale

2019 ◽  
Author(s):  
Ingo Strenge ◽  
Carsten Engelhard
Keyword(s):  
Mass Spectrometry ◽  
Inductively Coupled Plasma ◽  
Nonlinear Response ◽  
Dynamic Range ◽  
Dead Time ◽  
Inorganic Nanoparticles ◽  
Linear Dynamic Range ◽  
Inductively Coupled ◽  
Icp Ms ◽  
Plasma Mass Spectrometry

<p>The article demonstrates the importance of using a suitable approach to compensate for dead time relate count losses (a certain measurement artefact) whenever short, but potentially strong transient signals are to be analysed using inductively coupled plasma mass spectrometry (ICP-MS). Findings strongly support the theory that inadequate time resolution, and therefore insufficient compensation for these count losses, is one of the main reasons for size underestimation observed when analysing inorganic nanoparticles using ICP-MS, a topic still controversially discussed.</p>

Quantification of Biological Resistance: Introducing a Unifying Unit and Scale of Resistance

2018 ◽  
Author(s):  
Rudolf Fullybright
Keyword(s):  
Drug Resistance ◽  
Living Organism ◽  
Pathogen Resistance ◽  
Absolute Quantification ◽  
Biological Resistance ◽  
The Third ◽  
Exact Measurement ◽  
Unit Function ◽  
Third Law ◽  
Accurate Quantification

Accurate quantification of biological resistance has been impossible so far. Among the various forms of biological resistance which exist in nature, pathogen resistance to drugs is a familiar one. However, as in the case of other forms of resistance, accurately quantifying drug resistance in pathogens has been impossible up to now. Here, we introduce a mathematically-defined and uniform procedure for the absolute quantification of biological resistance deployed by any living organism in the biological realm, including and beyond drug resistance in medicine. The scheme introduced makes possible the exact measurement or computation of the extent to which resistance is deployed by any living organism regardless of kingdom and regardless of the mechanism of resistance involved. Furthermore, the Second Law of Resistance indicating that resistance has the potential to increase to infinite levels, and the Third Law of Resistance indicating that resistance comes to an end once interaction stops, the resistance unit function introduced here is fully compatible with both the Second and Third Laws of Resistance.

scholarly journals Honeysuckle Aqueous Extracts Induced let-7a Suppress EV71 Replication and Pathogenesis In Vitro and In Vivo and Is Predicted to Inhibit SARS-CoV-2

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 308
Author(s):  
Ying-Ray Lee ◽  
Chia-Ming Chang ◽  
Yuan-Chieh Yeh ◽  
Chi-Ying F. Huang ◽  
Feng-Mao Lin ◽  
...  
Keyword(s):  
Protein Expression ◽  
Western Blotting ◽  
Expression Profiles ◽  
Plaque Assay ◽  
Virus Titer ◽  
Enterovirus 71 ◽  
Luciferase Reporter ◽  
Pathogen Invasion

Honeysuckle (Lonicera japonica Thunb) is a traditional Chinese medicine (TCM) with an antipathogenic activity. MicroRNAs (miRNAs) are small non-coding RNA molecules that are ubiquitously expressed in cells. Endogenous miRNA may function as an innate response to block pathogen invasion. The miRNA expression profiles of both mice and humans after the ingestion of honeysuckle were obtained. Fifteen overexpressed miRNAs overlapped and were predicted to be capable of targeting three viruses: dengue virus (DENV), enterovirus 71 (EV71) and SARS-CoV-2. Among them, let-7a was examined to be capable of targeting the EV71 RNA genome by reporter assay and Western blotting. Moreover, honeysuckle-induced let-7a suppression of EV71 RNA and protein expression as well as viral replication were investigated both in vitro and in vivo. We demonstrated that let-7a targeted EV71 at the predicted sequences using luciferase reporter plasmids as well as two infectious replicons (pMP4-y-5 and pTOPO-4643). The suppression of EV71 replication and viral load was demonstrated in two cell lines by luciferase activity, RT-PCR, real-time PCR, Western blotting and plaque assay. Furthermore, EV71-infected suckling mice fed honeysuckle extract or inoculated with let-7a showed decreased clinical scores and a prolonged survival time accompanied with decreased viral RNA, protein expression and virus titer. The ingestion of honeysuckle attenuates EV71 replication and related pathogenesis partially through the upregulation of let-7a expression both in vitro and in vivo. Our previous report and the current findings imply that both honeysuckle and upregulated let-7a can execute a suppressive function against the replication of DENV and EV71. Taken together, this evidence indicates that honeysuckle can induce the expression of let-7a and that this miRNA as well as 11 other miRNAs have great potential to prevent and suppress EV71 replication.

scholarly journals A Novel Mouse Monoclonal Antibody C42 against C-Terminal Peptide of Alpha-1-Antitrypsin

2021 ◽  
Vol 22 (4) ◽  
pp. 2141
Author(s):  
Srinu Tumpara ◽  
Elena Korenbaum ◽  
Mark Kühnel ◽  
Danny Jonigk ◽  
Beata Olejnicka ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Flow Cytometry ◽  
Western Blotting ◽  
Complex Mixture ◽  
Immunoglobulin M ◽  
Confocal Laser ◽  
Enzyme Linked Immunosorbent Assay ◽  
Dot Blot

The C-terminal-fragments of alpha1-antitrypsin (AAT) have been identified and their diverse biological roles have been reported in vitro and in vivo. These findings prompted us to develop a monoclonal antibody that specifically recognizes C-36 peptide (corresponding to residues 359–394) resulting from the protease-associated cleavage of AAT. The C-36-targeting mouse monoclonal Immunoglobulin M (IgM) antibody (containing κ light chains, clone C42) was generated and enzyme-linked immunosorbent assay (ELISA)-tested by Davids Biotechnologie GmbH, Germany. Here, we addressed the effectiveness of the novel C42 antibody in different immunoassay formats, such as dot- and Western blotting, confocal laser microscopy, and flow cytometry. According to the dot-blot results, our novel C42 antibody detects the C-36 peptide at a range of 0.1–0.05 µg and shows no cross-reactivity with native, polymerized, or oxidized forms of full-length AAT, the AAT-elastase complex mixture, as well as with shorter C-terminal fragments of AAT. However, the C42 antibody does not detect denatured peptide in SDS-PAGE/Western blotting assays. On the other hand, our C42 antibody, unconjugated as well as conjugated to DyLight488 fluorophore, when applied for immunofluorescence microscopy and flow cytometry assays, specifically detected the C-36 peptide in human blood cells. Altogether, we demonstrate that our novel C42 antibody successfully recognizes the C-36 peptide of AAT in a number of immunoassays and has potential to become an important tool in AAT-related studies.

Extracellular signal-regulated kinase inhibition prevents venous adaptive remodeling via regulation of Eph-B4

Vascular ◽  
2021 ◽  
pp. 170853812199985
Author(s):  
Yuanyuan Guo ◽  
Fan Zhu ◽  
Xiong Zhang ◽  
Guangmin Wu ◽  
Pinting Fu ◽  
...  
Keyword(s):  
Western Blotting ◽  
Vein Graft ◽  
Artery Bypass ◽  
Bypass Graft ◽  
Graft Loss ◽  
Elastic Fibers ◽  
Sprague Dawley ◽  
Vein Grafts ◽  
Graft Stenosis

Objectives Vein graft adaptation (VGA) is a process that vein as a vascular graft conduits in arterial reconstructive surgery; VGA can lead to postoperative vein graft stenosis (VGS) and complications after coronary artery bypass graft and other peripheral artery bypass surgeries. VGA is characterized by vein graft loss the venous features without exhibiting arterial features; furthermore, the activation of ERK inhibited the maintenance of venous properties of the vein graft. We hypothesized that ERK inhibition can affect vein VGS through regulating the expression of EphB4. Methods Rat vein transplantation model was established using wild-type and EphB4+/− Sprague-Dawley rats. Hematoxylin-eosin, Masson, Verhoeff, actin staining, and immunohistochemistry were applied to observe the structure of the vein grafts. Vascular smooth muscle cells (VSMCs) were isolated from the vein and vein grafts. Western blotting was used to determine the expression of p-ERK1/2 and EphB4, and immunofluorescence was applied to detect the expression and location of EphB4. Cell wound scratch assay and CCK8 assay were used to determine the migration and proliferation of VSMCs. Real-time polymerase chain reaction was used to determine the mRNA expression of EphB4. Results Western blotting in vein sample and vein graft sample detected p-ERK1/2 and ERK1/2 expression in both EphB4+/+ and EphB4+/− rats. The expression of p-ERK was increased in vein graft compared to vein. Immunofluorescence in VSMCs form EphB4+/+ and EphB4+/− rats detected EphB4 expression in both cells, and the expression of EphB4 was increased in VSMCs form EphB4+/+ rats. SCH772984 reduces the proliferation and migration of VSMCs. Inhibition of ERK suppressed the increase of vein graft wall thickness, and the expression of collagen fibers, elastic fibers, and α-actin was decreased. Vein graft from EphB4+/− rats reduces the expression of EphB4, and SCH772984 suppressed the decrease of EphB4 in vivo. Vein graft from EphB4+/− rats increased the expression of EphB4, and SCH772984 suppressed the increase of EphB4 in vivo. Conclusions The inhibition of ERK1/2 suppressed the process of VGS by decreasing the proliferation of VSMCs. The ERK-inhibitor SCH772984 suppressed the level of VGS by extending the time of EphB4 expression during the process of VGA, thus maintaining the venousization of vein graft. The mechanism may be that the inhibitor SCH772984 suppresses the level of VGS by extending the time of EphB4 expression during the process of VGA. Therefore, our research provides a new target of VGS treatment by inhibiting the expression of ERK1/2 through the process of VGA.

scholarly journals POS1388 ULTRASOUND FOR PANNICULITIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 977.1-977
Author(s):  
A. Potapova ◽  
O. Egorova ◽  
O. Alekseeva ◽  
A. Volkov ◽  
S. Radenska-Lopovok
Keyword(s):  
Dynamic Range ◽  
Subcutaneous Fat ◽  
Diagnostic Value ◽  
High Energy ◽  
Contralateral Side ◽  
Imaging Method ◽  
Non Invasive ◽  
M 12

Background:Ultrasound (US) is a non-invasive and safe imaging method that allows in vivo differentiation of the morphological structures of subcutaneous fat (SCF) tissue in in normal and pathology.Objectives:Reveal features of ultrasound changes in SCF in panniculitis (Pn).Methods:57 patients (f – 45, m - 12) aged 18 - 67 years with an initial diagnosis of erythema nodosum and a disease duration of 3.6 ± 1.4 years were examined. In addition to the general clinical examination, a computed tomography of the chest organs and a pathomorphological examination of a skin biopsy from the site of the node were performed. Ultrasound was performed on a MyLabTwice apparatus (ESAOTE, Italy) using a multi-frequency linear transducer (10-18 MHz) with the PD technique, the parameters of which were adapted for recording low-speed flows (PRF 300-600 Hz, low filter, dynamic range - 20-40 dB), the presence of vascularization was assessed not only in the affected area, but also on the contralateral side using high-energy Doppler.Results:33 patients were diagnosed with septal Pn (SPn), 24 - lobular Pn (LPn). In all cases, the diagnosis was verified by histological examination. Ultrasound made it possible to assess the thickness, echoicity and vascularization of the SCF. In 35 patients, significant thickening of the SCF was revealed (as compared to the contralateral side), of which in 14 cases with SPn, in 21 - with LPn. Significant diffuse thickening of the SCF with the contralateral side was observed in 18 patients, incl. in 12 (66%) patients with LPn. Limited thickening was more typical for SPn (73%). A significant increase in the echoicity of the SCF was noted in all forms of Pn. A “lobular” echo pattern with an anechogenic environment was observed in 25 patients, of which 18 (72%) had LPn. An increase in vascularization compared to the contralateral side was recorded in 30 cases (SPn-17, LPn-13).Conclusion:The obtained preliminary results indicate the important role of ultrasound in assessing the depth and prevalence of the inflammatory process at Pn. To clarify the diagnostic value of this method, further studies are needed on a larger sample of patients.Disclosure of Interests:None declared

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