Detection Of Specific Proteins Research Articles

Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions.

Antibodies have long served as vital tools in biological and clinical laboratories for the specific detection of proteins. Conventional methods employ fluorophore or horseradish peroxidase-conjugated antibodies to detect signals. More recently, DNA-conjugated antibodies have emerged as a promising technology, capitalizing on the programmability and amplification capabilities of DNA to enable highly multiplexed and ultrasensitive protein detection. However, the nonspecific binding of DNA-conjugated antibodies has impeded the widespread adoption of this approach. Here, we present a novel DNA-conjugated antibody staining protocol that addresses these challenges and demonstrates superior performance in suppressing nonspecific signals compared to previously published protocols. We further extend the utility of DNA-conjugated antibodies for signal-amplified in situ protein imaging through the hybridization chain reaction (HCR) and design a novel HCR DNA pair to expand the HCR hairpin pool from the previously published 5 pairs to 13, allowing for flexible hairpin selection and higher multiplexing. Finally, we demonstrate highly multiplexed in situ protein imaging using these techniques in both cultured cells and tissue sections.

Shedding Light on Intracellular Proteins using Flow Cytometry.

Intracellular protein abundance is routinely measured in mammalian cells using population-based techniques such as western blotting which fail to capture single cell protein levels or using fluorescence microscopy which is although suitable for single cell protein detection but not for rapid analysis of large no. of cells. Flow cytometry offers rapid, high-throughput, multiparameter-based analysis of intracellular protein expression in statistically significant no. of cells at single cell resolution. In past few decades, customized assays have been developed for flow cytometric detection of specific intracellular proteins. This review discusses the scope of flow cytometry for intracellular protein detection in mammalian cells along with specific applications. Technological advancements to overcome the limitations of traditional flow cytometry for the same are also discussed.

High performance THz metasurface sensor based on modified-SWCNTs film for femtomolar protein detection

Terahertz (THz) metasurface sensor plays an important role in environmental monitoring, biomedical diagnostics, and materials science. However, most traditional THz metasurfaces for trace biological substance detection either suffer from high ohmic loss, or cannot achieve ultra-low concentration detection at the femtomolar level, which limits the application range of THz metasurfaces. Here, we propose a novel metasurface based on modified single-walled carbon nanotubes (SWCNTs) film for specific detection of SAA protein in femtomolar concentration. By modifying the SWCNTs film with concentrated sulfuric acid and introducing functionalized gold nanoparticles (Au-NPs), not only the non-resonant loss of the SWCNTs film was greatly reduced, but also the specific selection of trace SAA proteins was achieved. We experimentally demonstrated that the sensitivity of this THz metasurface sensor for SAA protein detection is 37.5 GHz/fM. In contrast to conventional metal or dielectric metasurfaces, because the unique mesh-like structure of the SWCNTs film can greatly increase the interaction between trace substances and the sensor, this new modifiable metasurface can achieve the lowest detection limit of 0.1 fM, which has increased by an order of magnitude. Our results provide a new and promising method for THz metasurfaces to realize high-performance biosensors.

Peptide-Based Turn-On Fluorescent Probes for Highly Specific Detection of Survivin Protein in the Cancer Cells

Peptide-Based Turn-On Fluorescent Probes for Highly Specific Detection of Survivin Protein in the Cancer Cells

Investigating the impact of empagliflozin on the retina of diabetic mice.

Diabetic retinopathy (DR) frequently results in compromised visual function, with hyperglycemia-induced disruption of the blood-retinal barrier (BRB) through various pathways as a critical mechanism. Existing DR treatments fail to address early and potentially reversible microvascular alterations. This study examined the effects of empagliflozin (EMPA), a selective Sodium-glucose transporter 2 (SGLT2) inhibitor, on the retina of db/db mice. The objective of this study is to investigate the potential role of EMPA in the prevention and delay of DR. db/db mice were randomly assigned to either the EMPA treatment group (db/db + Emp) or the model group (db/db), while C57 mice served as the normal control group (C57). Mice in the db/db + Emp group received EMPA for eight weeks. Body weight, fasting blood glucose (FBG), and blood VEGF were subsequently measured in all mice, along with the detection of specific inflammatory factors and BRB proteins in the retina. Retinal SGLT2 protein expression was compared using immunohistochemical analysis, and BRB structural changes were observed via electron microscopy. EMPA reduced FBG, blood VEGF, and retinal inflammatory factors TNF-α, IL-6, and VEGF levels in the eye tissues of db/db mice. EMPA also increased Claudin-1, Occludin-1, and ZO-1 levels while decreasing ICAM-1 and Fibronectin, thereby preserving BRB function in db/db mice. Immunohistochemistry revealed that EMPA reduced SGLT2 expression in the retina of diabetic mice, and electron microscopy demonstrated that EMPA diminished tight junction damage between retinal vascular endothelial cells and prevented retinal vascular basement membrane thickening in diabetic mice. EMPA mitigates inflammation and preserves BRB structure and function, suggesting that it may prevent DR or serve as an effective early treatment for DR.

Gold structured nanourchin as anesthetic biosensor for determining neuroprotective effect

Research has proven that confusion, delirium, and cognitive dysfunction are the common symptoms caused by anesthesia. In general, neuroproteins fluctuation is common during the process of anesthetic treatment. Among others, tau protein was found to the higher fluctuations after the anesthetic process, and it is highly associated with various neuro-related diseases. Monitoring the level of tau protein helps to identify the neuro-related problems during and after the anesthetic processes. This research was focused on developing a tau electrochemical impedance biosensor on aptamer and antibody-modified electrodes. Aptamer and antibody were immobilized on the gold nanourchin with a chemical linker. Gold nanourchin enhances the probe of aptamer and antibody attachment on the electrode and improves the tau protein detection as low as 1 fM [y = 1.5604x − 1.5643; R2 = 0.9681], determined on a linear range from 1 fM to 1 nM. Further, control performances with complementary aptamer and non-immune antibodies fail to change the response of the current, indicating the specific detection of tau protein. This tau sensor detects the tau protein in its lower level and helps to identify the neuro-related problem caused by anesthetics.

Multimetal-Based Metal-Organic Framework System for the Sensitive Detection of Heart-Type Fatty Acid Binding Protein in Electrochemiluminescence Immunoassay.

In this work, an electrochemiluminescence (ECL) quenching system using multimetal-organic frameworks (MMOFs) was proposed for the sensitive and specific detection of heart-type fatty acid-binding protein (H-FABP), a marker of acute myocardial infarction (AMI). Bimetallic MOFs containing Ru and Mn as metal centers were synthesized via a one-step hydrothermal method, yielding RuMn MOFs as the ECL emitter. The RuMn MOFs not only possessed the strong ECL performance of Ru(bpy)32+ but also maintained high porosity and original metal active sites characteristic of MOFs. Moreover, under the synergistic effect of MOFs and Ru(bpy)32+, RuMn MOFs have more efficient and stable ECL emission. The trimetal-based MOF (FePtRh MOF) was used as the ECL quencher because of the electron transfer between FePtRh MOFs and RuMn MOFs. In addition, active intramolecular electron transfer from Pt to Fe or Rh atoms also occurred in FePtRh MOFs, which could promote intermolecular electron transfer and improve electron transfer efficiency to enhance the quenching efficiency. The proposed ECL immunosensor demonstrated a wide dynamic range and a low detection limit of 0.01-100 ng mL-1 and 6.8 pg mL-1, respectively, under optimal conditions. The ECL quenching system also presented good specificity, stability, and reproducibility. Therefore, an alternative method for H-FABP detection in clinical diagnosis was provided by this study, highlighting the potential of MMOFs in advancing ECL technology.

Pathogen perception and signaling in plant immunity.

Plant diseases are a constant and serious threat to agriculture and ecological biodiversity. Plants possess a sophisticated innate immunity system capable of detecting and responding to pathogen infection to prevent disease. Our understanding of this system has grown enormously over the past century. Early genetic descriptions of plant disease resistance and pathogen virulence were embodied in the gene-for-gene hypothesis, while physiological studies identified pathogen-derived elicitors that could trigger defense responses in plant cells and tissues. Molecular studies of these phenomena have now coalesced into an integrated model of plant immunity involving cell surface and intracellular detection of specific pathogen-derived molecules and proteins culminating in the induction of various cellular responses. Extracellular and intracellular receptors engage distinct signaling processes but converge on many similar outputs with substantial evidence now for integration of these pathways into interdependent networks controlling disease outcomes. Many of the molecular details of pathogen recognition and signaling processes are now known, providing opportunities for bioengineering to enhance plant protection from disease. Here we provide an overview of the current understanding of the main principles of plant immunity, with an emphasis on the key scientific milestones leading to these insights.

Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for Cypridina Luciferin.

Enzymatic reactions that involve a luminescent substrate (luciferin) and enzyme (luciferase) from luminous organisms enable a luminescence detection of target proteins and cells with high specificity, albeit that conventional assay design requires a prelabeling of target molecules with luciferase. Here, we report a luciferase-independent luminescence assay in which the target protein directly catalyzes the oxidative luminescence reaction of luciferin. The SARS-CoV-2 antigen (spike) protein catalyzes the light emission of Cypridina luciferin, whereas no such catalytic function was observed for salivary proteins. This selective luminescence reaction is due to the enzymatic recognition of the 3-(1-guanidino)propyl group in luciferin at the interfaces between the units of the spike protein, allowing a specific detection of the spike protein in human saliva without sample pretreatment. This method offers a novel platform to detect virus antigens simply and rapidly without genetic manipulation or antibodies.

Antibody Design for the Quantification of Photosynthetic Proteins and Their Isoforms.

Antibodies are a valuable research tool, with uses including detection and quantification of specific proteins. By using peptide fragments to raise antibodies, they can be designed to differentiate between structurally similar proteins, or to bind conserved motifs in divergent proteins. Peptide sequence selection and antibody validation are crucial to ensure reliable results from antibody-based experiments. This chapter describes the steps for the identification of peptide sequences to produce protein- or isoform-specific antibodies using recombinant technologies as well as the subsequent validation of such antibodies. The photosynthetic protein Rubisco activase is used as a case study to explain the various steps involved and key aspects to take into consideration.

Proximity Ligation Assay to Detect the Proximity Between Host Proteins and Viral Proteins of HIV-1.

The study of host-pathogen interaction often requires interrogating the protein-protein interactions and examining post-translational modifications of the proteins. Traditional protein detection strategies are limited in their sensitivity, specificity, and multiplexing capabilities. The Proximity Ligation Assay (PLA), a versatile and powerful molecular technique, can overcome these limitations. PLA blends the specificity of antibodies, two antibodies detecting two different epitopes on the same or two different proteins, with the amplification efficiency of a polymerase to allow highly specific and sensitive detection of low-abundant proteins, protein-protein interactions, or protein modifications. In this protocol, we describe the application of PLA to detect the proximity between HIV-1 Tat with one of its cellular partners, p65, in an infected host cell. The protocol could be applied to any other context with slight modifications. Of note, PLA can only confirm the physical proximity between two epitopes or proteins; however, the proximity need not necessarily allude to the functional interaction between the two proteins.

Metallic nanostructure-based aptasensors for robust detection of proteins.

There is a significant need for fast, cost-effective, and highly sensitive protein target detection, particularly in the fields of food, environmental monitoring, and healthcare. The integration of high-affinity aptamers with metal-based nanomaterials has played a crucial role in advancing the development of innovative aptasensors tailored for the precise detection of specific proteins. Aptamers offer several advantages over commonly used molecular recognition methods, such as antibodies. Recently, a variety of metal-based aptasensors have been established. These metallic nanomaterials encompass noble metal nanoparticles, metal oxides, metal-carbon nanotubes, carbon quantum dots, graphene-conjugated metallic nanostructures, as well as their nanocomposites, metal-organic frameworks (MOFs), and MXenes. In general, these materials provide enhanced sensitivity through signal amplification and transduction mechanisms. This review primarily focuses on the advancement of aptasensors based on metallic materials for the highly sensitive detection of protein targets, including enzymes and growth factors. Additionally, it sheds light on the challenges encountered in this field and outlines future prospects. We firmly believe that this review will offer a comprehensive overview and fresh insights into metallic nanomaterials-based aptasensors and their capabilities, paving the way for the development of innovative point-of-care (POC) diagnostic devices.

B-083 Novel High Affinity Monoclonal Antibodies for Specific Detection of Neurofilament Light Protein in Serum and Cerebrospinal Fluid

Abstract Background Neurofilaments are very important protein components of axons, and they maintain the function of nervous system. Cerebrospinal fluid (CSF) and serum neurofilament levels elevate due to damages in nervous system making neurofilaments promising biomarkers for neural diseases and injuries, such as Alzheimer’s disease, traumatic brain injury and Multiple sclerosis. Based on their size, neurofilaments are divided in groups: Neurofilament light (NfL), neurofilament medium (NfM), neurofilament heavy (NfH), α-internexin, and peripherin. Of these, NfL is considered to be the most promising biomarker since it is the most abundant form of neurofilaments. Methods We have developed four mouse monoclonal antibodies against human NfL. These antibodies, designated as Anti-h NfL 12601, 12603, 12604 or 12605, were tested as pairs in sandwich fluorescence-based immunoassay (FIA) with NfL spiked serum and buffer to determine linear measuring ranges and the matrix effect. Furthermore, the ability of the antibodies to measure NfL in clinical samples was tested in sandwich FIA by testing 10 CSF samples in the range of 0 to 5 083 pg/mL. The antibodies were also compared against commercially available reference antibodies in FIA. Kinetic parameters were determined with bio-layer interferometry (BLI). Results In sandwich FIA, the widest linear measuring range of 10 to 40 960 pg/mL of recombinant human NfL spiked in normal serum was achieved with antibody pair 12603 and 12604. In contrast, the commercial reference antibody pair achieved a linear measuring range of 2560 to 40 960 pg/mL. Matrix effect caused by serum was negligible. With clinical samples, the best correlation with the reference method (NF-light CSF ELISA from Uman Diagnostics) with a coefficient of correlation of 0.986 was achieved with antibody pair 12604 and 12601. This pair also showed a good correlation with the commercial reference pair with a coefficient of correlation of 0.984. In kinetics measurements, none of four antibodies showed dissociation indicating very high affinity. The fastest association of 4.0 × 105 1/Ms was achieved with antibody 12605. Conclusion These results demonstrate that the newly developed mouse monoclonal NfL antibodies are promising tools for development of diagnostic immunoassays measuring NfL levels in human serum and CSF samples. Comparison against commercial reference antibodies indicates that higher NfL detection sensitivity and wider detection ranges can be achieved with antibody pairs developed in this study. Additionally, the kinetic measurement results forecast these antibodies to be suitable for fast reaction kinetic assay formats, such as lateral flow assays, which might become a key resolution in acute neural injury diagnostics.

Gold-coated tilted fiber Bragg gratings for lead ion sensing.

Surface plasmon resonance sensor based on gold-coated tilted fiber Bragg gratings (SPR-TFBGs) are perfectly suited for fine refractometry. Thanks to the functionalization of the gold layer, they can be used for label-free biosensing. They have been largely used for the specific detection of proteins and cells. In this work, we experimentally demonstrate that they are enough sensitive to detect a very small entity like an environmental pollutant. In this context, we report here a bio-functionalization of the SPR-TFBG with thrombin aptamers for lead ion detection. We used aqueous solutions of lead ions with increasing concentrations from 0.001 ppb to 10 ppb. Based on the affinity bending of Pb2+ ions to the thrombin aptamer, we experimentally demonstrated low detection level of lead ion concentration (0.001 ppb) while the saturation limit is meanly fixed by the physical dimension of the sensor and the binding efficiency.

A polydopamine nanospheres modified fiber optic SPR biosensor for specific detection of C-reactive protein

C-reactive protein (CRP) is a vital inflammatory marker in humans and a key single marker of cardiovascular diseases. In this paper, the concentration of CRP was specifically detected by a polydopamine nanospheres (PDA-NPs) developed surface plasmon resonance (SPR) sensor with high accuracy. PDA-NPs is a self-polymerizing material that can be obtained from dopamine through the mussel adhesion effect. The PDA-NPs (diameter ≈ 100 nm) modified SPR sensor exhibits enhanced refractive index (RI) sensitivity and bio-sensitivity attributed to the large specific surface area and high surface reactivity of the PDA-NPs. The developed sensor demonstrates a RI sensitivity of 2427.68 nm/RIU, presenting a 55.7% increase compared to the raw sensor (RI sensitivity was 1559.08 nm/RIU). Moreover, the developed biosensor is used to detect CRP specifically. The bio-sensitivity reaches 0.09 nm/(µg/mL), while the limit of detection (LOD) reaches 0.22 µg/mL. These findings indicate that the developed biosensor can specifically detect CRP with a low LOD. Therefore, this PDA-NPs modified biosensor has great potential in clinical detection and other bio-detection filed.

Western Blotting with Fast SDS-PAGE and Semi-Dry Protein Transfer.

Western blotting is a method widely used in cell and molecular biology for the specific detection of proteins in biological samples. It is time-consuming and normally takes up to 2 days to complete. This protocol introduces a more time-efficient method to complete western blots, covering the preparation of protein extracts (including strategies for solubilization), electrophoretic separation of proteins, transfer of proteins to the membrane, and probing with antibodies. We describe an SDS-PAGE protocol that achieves a gradient-like separation of proteins (10-400 kDa) on a single-percentage polyacrylamide gel in only 45 min. Additionally, we present a rapid (10-14 min) semi-dry transfer of proteins from standard Tris/glycine polyacrylamide gels onto a membrane using homemade Tris/HEPES- or Tris/EPPS-based buffers. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) Support Protocol 1: Cell lysis and protein extraction Support Protocol 2: Protein quantification with BCA assay and sample preparation for loading on gel Basic Protocol 2: Protein transfer with a fast semi-dry transfer (FSDT) buffer Basic Protocol 3: Immunoprobing, chemiluminescent visualization, stripping, and reuse of membranes.

Polymerase-Driven Logic Signal Amplification for the Detection of Small Extracellular Vesicle Surface Proteins and the Identification of Breast Cancer.

Small extracellular vesicles (sEVs) derived from tumors contain a vast amount of cellular information and are regarded as a potential diagnostic biomarker for noninvasive cancer diagnosis. Nevertheless, it remains challenging to accurately measure sEVs from clinical samples due to the low abundance of these vesicles as well as their phenotypic heterogeneity. Herein, a polymerase-driven logic signal amplification system (PLSAS) was developed for the high-sensitivity detection of sEV surface proteins and breast cancer (BC) identification. Aptamers were introduced to serve as sensing modules to specifically recognize target proteins. By changing the input DNA sequences, two polymerase-driven primer exchange reaction systems were rationally designed for DNA logic computing. This allows for autonomous targeting of a limited number of targets using "OR" and "AND" logic, leading to a significant increase in fluorescence signals and enabling the specific and ultrasensitive detection of sEV surface proteins. In this work, we investigated surface proteins of mucin 1 (MUC1) and the epithelial cell adhesion molecule (EpCAM) as model proteins. When MUC1 or EpCAM proteins were used as single signal input in the "OR" DNA logic system, the detection limit of sEVs was 24 or 58 particles/μL, respectively. And MUC1 and EpCAM proteins of sEVs can be simultaneously detected in the AND logic method, which can significantly reduce the effect of phenotypic heterogeneity of sEVs to distinguish the source of sEVs derived from various mammary cell lines, such as MCF-7, MDA MB 231, SKBR3, and MCF-10A. The approach has achieved high discrimination in serologically tested positive BC samples (AUC 98.1%) and holds significant potential in advancing the early diagnosis and prognostic assessments of BC.

Development and Application of an iELISA for the Detection of Antibody against Salmonella Abortusequi

Equine abortus salmonellosis is a bacterial disease that causes high abortion rates in susceptible equids and therefore significant economic losses. Although the tube agglutination test (TAT) is a commonly used serological test for S. Abortusequi, it is not highly specific or sensitive, and the development of more sensitive, specific and rapid assays is therefore urgently required. In this study, an indirect enzyme-linked immunosorbent assay (iELISA) was developed for the specific detection of flagellum protein (FljB) antibodies against S. Abortusequi. Negative sera from horses in China (n = 1030) were used to establish the baseline for a negative population, and reference antisera positive against other viruses or bacteria were used to test the cross reactivity of the technique. The performance of the FljB iELISA was evaluated against that of the standard TAT, and was tested using field serum samples. The FljB iELISA assay was 8–16 times more sensitive than TAT. ROC analysis showed that the FljB iELISA was accurate, with an area under the curve (AUC) = 0.9943 (95% CI, 0.9815–1.000). The diagnostic sensitivity (DSe) of the FljB iELISA was 98.9% (95% Cl, 93.84%–100.00%), which was higher than that of TAT (DSe 38.6; 95% CI, 29.14%–49.08%). The diagnostic specificity (DSp) of the iELISA was 100.0% (95% CI, 95.82%–100.0%). When the 508 clinical samples were tested, the FljB iELISA had a positive detection rate of 51.38% (261/508, 95% CI, 51.24%–51.51%), which was higher than that of TAT (44/508). We also performed a serological survey for S. Abortusequi infection, using a series of samples collected from across eighteen provinces of China in 2021. The results showed that all provinces except Jiangsu had a certain number of cases, and the positive rates ranged from 0% to 96.9%, indicating the wide spread of S. Abortusequi in China. The abovementioned results suggest that the FljB iELISA developed in this study is rapid, sensitive, specific, and repeatable and is likely to be a suitable test for large-scale serological surveys for the detection and control of S. Abortusequi infection.

Specific, sensitive and quantitative protein detection by in-gel fluorescence

Recombinant proteins in complex solutions are typically detected with tag-specific antibodies in Western blots. Here we describe an antibody-free alternative in which tagged proteins are detected directly in polyacrylamide gels. For this, the highly specific protein ligase Connectase is used to selectively fuse fluorophores to target proteins carrying a recognition sequence, the CnTag. Compared to Western blots, this procedure is faster, more sensitive, offers a better signal-to-noise ratio, requires no optimization for different samples, allows more reproducible and accurate quantifications, and uses freely available reagents. With these advantages, this method represents a promising alternative to the state of the art and may facilitate studies on recombinant proteins.

Specific Detection of Proteins by a Nanobody-Functionalized Nanopore Sensor

Nanopores are label-free single-molecule analytical tools that show great potential for stochastic sensing of proteins. Here, we described a ClyA nanopore functionalized with different nanobodies through a 5-6 nm DNA linker at its periphery. Ty1, 2Rs15d, 2Rb17c, and nb22 nanobodies were employed to specifically recognize the large protein SARS-CoV-2 Spike, a medium-sized HER2 receptor, and the small protein murine urokinase-type plasminogen activator (muPA), respectively. The pores modified with Ty1, 2Rs15d, and 2Rb17c were capable of stochastic sensing of Spike protein and HER2 receptor, respectively, following a model where unbound nanobodies, facilitated by a DNA linker, move inside the nanopore and provoke reversible blockade events, whereas engagement with the large- and medium-sized proteins outside of the pore leads to a reduced dynamic movement of the nanobodies and an increased current through the open pore. Exploiting the multivalent interaction between trimeric Spike protein and multimerized Ty1 nanobodies enabled the detection of picomolar concentrations of Spike protein. In comparison, detection of the smaller muPA proteins follows a different model where muPA, complexing with the nb22, moves into the pore, generating larger blockage signals. Importantly, the components in blood did not affect the sensing performance of the nanobody-functionalized nanopore, which endows the pore with great potential for clinical detection of protein biomarkers.