Straightforward Readout Research Articles

Electrical Signal Reporter, Pore-Forming Protein, for Rapid, Miniaturized, and Universal Identification of Microorganisms.

Despite recent advances in signal reporter-based assays for bacteria detection and profiling, the low-cost, ultrasensitive, accurate, and fast diagnosis remains a challenge for better patient care. Herein, we present a novel bacteria identification method based on α-hemolysin-labeled sandwich assay (HLSA). A pore-forming protein, α-hemolysin, is used as an electrical signal reporter. The assay takes advantage of the specific binding of target nucleic acid with two hybridization probes: capture probe decorated magnetic microparticles and oligonucleotides detecting probe and α-hemolysin modified gold nanoparticles. α-Hemolysin was then released by competitive gold binding peptide incubation into an electric cell with a lipid bilayer between the electrodes. The nanopores formed by α-hemolysin on the lipid layer allowed target nucleic acid concentration-dependent currents for quantification. Sandwich probes against 16S rRNAs of 10 common bacteria pathogens were designed and single cell level nucleic acid concentration detection was achieved. Compared with nanopore technique-based DNA sequencing, HLSA gives a quantitive and straightforward readout that is not dependent on an ultrasensitive and expensive instrument (Axopatch 200B amplifier), thus, is faster and requires no large-scale instruments. Also, since α-hemolysin-modified nanoparticles will be washed out before the α-hemolysin releasing step without the target nucleic acid, no current will be detected, and thus, the assay is more specific. The current strategy based on the electrical signal reporter offers a new insight for pathogen and virus diagnostics.

Assaying Mechanonociceptive Behavior in Drosophila Larvae.

Drosophila melanogaster larvae have been extensively used as a model to study the molecular and cellular basis of nociception. The larval nociceptors, class IV dendritic arborization (C4da) neurons, line the body wall of the animal and respond to various stimuli including noxious heat and touch. Activation of C4da neurons results in a stereotyped escape behavior, characterized by a 360° rolling response along the body axis followed by locomotion speedup. The genetic accessibility of Drosophila has allowed the identification of mechanosensory channels and circuit elements required for nociceptive responses, making it a useful and straightforward readout to understand the cellular and molecular basis of nociceptive function and behavior. We have optimized the protocol to assay mechanonociceptive behavior in Drosophila larvae.

Square Wave Bipolar Electrochemistry for the Detection of Proteins

Rapid and specific quantitation of proteins is desirable for assays used at the point-of-care, as well as in clinical and research laboratories. The advantages of such devices include short turnaround times for acquiring critical data, low cost, and improved patient compliance with diagnosis and therapeutic regimens. Electrochemical detection is currently employed in a wide range of biosensors because of its inherent signal stability, high sensitivity, and ease of calibration. Our laboratories have developed the electrochemical proximity assay (ECPA) for protein detection, a sensitive and selective assay based on the electrochemical detection of surface-confined affinity complexes. ECPA demonstrates extremely high sensitivity (e.g., 10 fM for insulin). Bipolar electrodes (BPEs) have been used for decades in industrial applications ranging from organic electrosynthesis to catalysis. Recently, sensor platforms have been reported in which electrochemiluminescence (ECL) is used to readout the state of a bipolar sensor operating under steady state conditions. In these measurements ECL intensity is directly proportional to the analyte concentration. In contrast to these conventional amperometric sensors, the ECPA signal is based on a surface limited reaction, and therefore does not lend itself to such a straightforward readout strategy. In this paper, we describe the development of an ECPA based on a bipolar platform in which a square wave voltage program is employed both to interrogate and reset the redox state of the surface confined affinity complex. Signal averaging over multiple cycles allows us to detect proteins at low concentration levels.

Chimeric Autofluorescent Proteins as Photophysical Model System for Multicolor Bimolecular Fluorescence Complementation.

The yellow fluorescent protein (YFP) is frequently used in a protein complementation assay called bimolecular fluorescence complementation (BiFC), and is employed to visualize protein-protein interactions. In this analysis, two different, nonfluorescent fragments of YFP are genetically attached to proteins of interest. Upon interaction of these proteins, the YFP fragments are brought into proximity close enough to reconstitute their original structure, enabling fluorescence. BiFC allows for a straightforward readout of protein-protein interactions and furthermore facilitates their functional investigation by in vivo imaging. Furthermore, it has been observed that the available color range in BiFC can be extended upon complementing fragments of different proteins that are, like YFP, derived from the Aequorea victoria green fluorescent protein, thereby allowing for a multiplexed investigation of protein-protein interactions. Some spectral characteristics of "multicolor" BiFC (mcBiFC) complexes have been reported before; however, no in-depth analysis has been performed yet. Therefore, little is known about the photophysical characteristics of these mcBiFC complexes because a proper characterization essentially relies on in vitro data. This is particularly difficult for fragments of autofluorescent proteins (AFPs) because they show a very strong tendency to form supramolecular aggregates which precipitate ex vivo. In this study, this intrinsic difficulty is overcome by directly fusing the coding DNA of different AFP fragments. Translation of the genetic sequence in Escherichia coli leads to fully functional, highly soluble fluorescent proteins with distinct properties. On the basis of their construction, they are designated chimeric AFPs, or BiFC chimeras, here. Comparison of their spectral characteristics with experimental in vivo BiFC data confirmed the utility of the chimeric proteins as a BiFC model system. In this study, nine different chimeras were thoroughly analyzed at both the ensemble and the single-molecular level. The data indicates that mutations believed to be photophysically silent significantly alter the properties of AFPs.

Enhanced Fluorescence ELISA Based on HAT Triggering Fluorescence "Turn-on" with Enzyme-Antibody Dual Labeled AuNP Probes for Ultrasensitive Detection of AFP and HBsAg.

At present, enzyme-linked immunosorbent assay (ELISA) is considered to be the most appropriate approach in clinical biomarker detection, with good specificity, low cost, and straightforward readout. However, unsatisfactory sensitivity severely hampers its wide application in clinical diagnosis. Herein, we designed a new kind of enhanced fluorescence enzyme-linked immunosorbent assay (FELISA) based on the human alpha-thrombin (HAT) triggering fluorescence "turn-on" signals. In this system, detection antibodies (Ab2) and HAT were labeled on the gold nanoparticles (AuNPs) to form the detection probes, and a bisamide derivative of Rhodamine110 with fluorescence quenched served as the substrate of HAT. After the sandwich immunoreaction, HAT on the sandwich structure could catalyze the cleavage of the fluorescence-quenched substrate, leading to a strong fluorescence signal for sensing ultralow levels of alpha fetoprotein (AFP) and hepatitis B virus surface antigen (HBsAg). Under the optimized reaction conditions, AFP and HBsAg were detected at the ultralow concentrations of 10-8 ng mL-1 and 5 × 10-4 IU mL-1, respectively, which were at least 104 times lower than those of the conventional fluorescence assay and 106 times lower than those of the conventional ELISA. In addition, we further discussed the efficiency of the sensitive FELISA in clinical serum samples, showing great potential in practical applications.

Click Chemistry-Mediated Nanosensors for Biochemical Assays.

Click chemistry combined with functional nanoparticles have drawn increasing attention in biochemical assays because they are promising in developing biosensors with effective signal transformation/amplification and straightforward signal readout for clinical diagnostic assays. In this review, we focus on the latest advances of biochemical assays based on Cu (I)-catalyzed 1, 3-dipolar cycloaddition of azides and alkynes (CuAAC)-mediated nanosensors, as well as the functionalization of nanoprobes based on click chemistry. Nanoprobes including gold nanoparticles, quantum dots, magnetic nanoparticles and carbon nanomaterials are covered. We discuss the advantages of click chemistry-mediated nanosensors for biochemical assays, and give perspectives on the development of click chemistry-mediated approaches for clinical diagnosis and other biomedical applications.

Peripheral effects induced in BALB/c mice infected with DENV by the intracerebral route

The lack of an immunocompetent animal model for dengue mimicking the disease in humans is a limitation for advances in this field. Inoculation by intracerebral route of neuroadapted dengue strains in mice is normally lethal and provides a straightforward readout parameter for vaccine testing. However, systemic effects of infection and the immune response elicited in this model remain poorly described. In the present work, BALB/c mice infected by the intracerebral route with neuroadapted DENV2 exhibited several evidences of systemic involvement. DENV-inoculated mice presented virus infective particles in the brain followed by viremia, especially in late stages of infection. Infection induced cellular and humoral responses, with presence of activated T cells in spleen and blood, lymphocyte infiltration and tissue damages in brain and liver, and an increase in serum levels of some pro-inflammatory cytokines. Data highlighted an interplay between the central nervous system commitment and peripheral effects under this experimental condition.

Abstract 5386: Disrupting p53:Mdm2 and p53:Mdm4 - Comparative cell-based assays for drug screening

Abstract The important interconnected protein-protein interactions between the tumor suppressor p53 and its regulatory binding partners Mdm2 and Mdm4 (= MdmX/ HdmX) are implicated in pathogenesis of various cancers. However, until now there is a lack of reversible cell-based assays for concurrent analysis for both PPIs: p53/Mdm2 and p53/Mdm4. Our aim was to develop two comparative assays based on the Fluorescent 2-Hybrid (F2H) assay principle, which enable side-by-side analysis of antagonistic compounds. The F2H assay is a fully reversible microscopy-assisted assay for the direct intracellular analysis of PPIs. It offers a fast and straight-forward readout: an interaction-dependent co-localization of two fluorescent signals at a defined spot in the nucleus of mammalian cells. With these assays we analyzed a set of newly developed stapled peptides as potent p53:Mdm2 and/ or p53:Mdm4 inhibitors. Live cell data generated by the F2H assays enabled us to discriminate and describe the peptides according to their ability to penetrate into the cells, their efficacy on the PPIs and their cytotoxic side effects in one single assay. In parallel we performed a pilot F2H screen with a sub-set or 20 small molecule compounds (including Nutlin-3) that exhibited activity against one or both interactions at various potencies in ELISAs before. We could identify 5 potent compounds, which were dramatically reducing the number of p53:Mdm2 interactions. However, none of the small molecules, but only the stapled peptides exhibited an intracellular activity on p53:Mdm4. Furthermore, we were able to expand these assays and to identify mutants of Mdm2 resistant to Nutlin inhibition. In summary, we show that the p53:Mdm2 and p53:Mdm4 F2H assays described here, - enable side-by-side analysis of substances' dual Mdm2-Mdm4 activity - are suitable for screening and testing various types of compounds, such as peptidic inhibitors or small molecules - concurrently provide initial data on compound cell-permeability and cytotoxicity - allow real-time visualization of PPI dynamics in living cells. Citation Format: Larisa Yurlova, Christopher J. Brown, Maarten Derks, Farid John Ghadessy, Ian Hickson, David P. Lane, Eberhard Krausz, Kourosh Zolghadr. Disrupting p53:Mdm2 and p53:Mdm4 - Comparative cell-based assays for drug screening. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5386. doi:10.1158/1538-7445.AM2014-5386

Abstract 3236: Development of a novel cross-linking strategy to identify distinct proteasome subtypes

Abstract Introduction: This research was conducted to develop a practical method to identify distinct proteasome subtypes. Approval of the proteasome inhibitors bortezomib and carfilzomib for clinical use has validated the proteasome as an anticancer target. These inhibitors target two well-recognized proteasome subtypes, the constitutive proteasome and the immunoproteasome, which comprise distinct sets of catalytic subunits. Additional proteasome subtypes containing mixtures of constitutive and immunoproteasome catalytic subunits have more recently been identified. These intermediate proteasome subtypes display unique proteolytic activity profiles and play important roles in the production of certain tumor antigens. However, much regarding their regulation, functions, and relevance as drug targets remains unknown, largely due to limitations in current experimental methods used to differentiate between proteasome subtypes. We have therefore developed bifunctional activity-based probes capable of cross-linking different catalytic subunit pairs within individual proteasome complexes. These probes allow a straightforward readout of proteasome catalytic subunit composition and facilitate functional studies of distinct proteasome subtypes. Experimental Procedures: Bifunctional proteasome probes were synthesized by coupling pairs of proteasome inhibitors via linkers of varying lengths and compositions. Positions for inhibitor derivatization were selected based on computational modeling, and linkers were chosen based on distances between the active sites of each targeted subunit pair. The ability of these compounds to cross-link distinct catalytic subunit pairs in both purified proteasomes and in cancer cell lysates was visualized by western blotting analysis. Competition assays with subunit-selective proteasome inhibitors were employed to confirm the identities of the cross-linked subunit pairs. Data Summary: The structures of the bifunctional proteasome probes were confirmed by mass spectrometry and nuclear magnetic resonance spectroscopy. Western blotting results demonstrated the ability of these compounds to cross-link multiple pairs of proteasome catalytic subunits, allowing the composition of distinct proteasome subtypes present within cancer cells to be evaluated. Conclusions: We have successfully developed a set of bifunctional proteasome probes for analysis of proteasome catalytic subunit composition. These probes will be used to elucidate the unique functions of distinct proteasome subtypes present within cancer cells. Citation Format: Kimberly C. Carmony, Do-Min Lee, Lalit Kumar Sharma, Jieun Park, Kyung-Bo Kim, Wooin Lee. Development of a novel cross-linking strategy to identify distinct proteasome subtypes. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3236. doi:10.1158/1538-7445.AM2014-3236

Multi-colored immunochromatography using nanobeads for rapid and sensitive typing of seasonal influenza viruses

Immunochromatography (IC) is an antigen-detection assay that plays an important role in the rapid diagnosis of influenza viruses because of its rapid turnaround and ease of use. Despite the usefulness of IC, the limit of detection of common IC kits is as high as 103–104 plaque forming units (pfu) per reaction, resulting in their limited sensitivities. Early diagnosis within 24h would provide more appropriate timing of treatment.In this study, a multi-colored NanoAct™ bead IC was established to detect seasonal influenza viruses. This method has approximately 10-fold higher sensitivity than that of colloidal gold or colored latex bead IC assays, and does not require specific instruments. More notably, NanoAct™ bead IC can distinguish influenza A and B viruses from clinical samples with a straightforward readout composed of colored lines. Our results will provide new strategies for the diagnosis, treatment, and a chance to survey of influenza viruses in developing countries and in the field research.

Colorimetric logic gates through molecular recognition and plasmonic nanoparticles.

A colorimetric logic system capable of AND, OR, INHIBIT and AND + OR logic operations is constructed. The principle is modulation of the distance between arginine (lysine)-modified gold nanoparticles via metal ions. A lab-on-chip format for the assembly of versatile logic gates is demonstrated as a proof of concept. These logic gates allow a straightforward readout by the naked eye.

The Fluorescent Two-Hybrid Assay to Screen for Protein–Protein Interaction Inhibitors in Live Cells: Targeting the Interaction of p53 with Mdm2 and Mdm4

Protein–protein interactions (PPIs) are attractive but challenging targets for drug discovery. To overcome numerous limitations of the currently available cell-based PPI assays, we have recently established a fully reversible microscopy-assisted fluorescent two-hybrid (F2H) assay. The F2H assay offers a fast and straightforward readout: an interaction-dependent co-localization of two distinguishable fluorescent signals at a defined spot in the nucleus of mammalian cells.We developed two reversible F2H assays for the interactions between the tumor suppressor p53 and its negative regulators, Mdm2 and Mdm4. We then performed a pilot F2H screen with a subset of compounds, including small molecules (such as Nutlin-3) and stapled peptides. We identified five cell-penetrating compounds as potent p53–Mdm2 inhibitors. However, none exhibited intracellular activity on p53–Mdm4. Live cell data generated by the F2H assays enable the characterization of stapled peptides based on their ability to penetrate cells and disrupt p53–Mdm2 interaction as well as p53–Mdm4 interaction.Here, we show that the F2H assays enable side-by-side analysis of substances’ dual Mdm2–Mdm4 activity. In addition, they are suitable for testing various types of compounds (e.g., small molecules and peptidic inhibitors) and concurrently provide initial data on cellular toxicity. Furthermore, F2H assays readily allow real-time visualization of PPI dynamics in living cells.

Protective Vaccination against Papillomavirus-Induced Skin Tumors under Immunocompetent and Immunosuppressive Conditions: A Preclinical Study Using a Natural Outbred Animal Model

Certain cutaneous human papillomaviruses (HPVs), which are ubiquitous and acquired early during childhood, can cause a variety of skin tumors and are likely involved in the development of non-melanoma skin cancer, especially in immunosuppressed patients. Hence, the burden of these clinical manifestations demands for a prophylactic approach. To evaluate whether protective efficacy of a vaccine is potentially translatable to patients, we used the rodent Mastomys coucha that is naturally infected with Mastomys natalensis papillomavirus (MnPV). This skin type papillomavirus induces not only benign skin tumours, such as papillomas and keratoacanthomas, but also squamous cell carcinomas, thereby allowing a straightforward read-out for successful vaccination in a small immunocompetent laboratory animal. Here, we examined the efficacy of a virus-like particle (VLP)-based vaccine on either previously or newly established infections. VLPs raise a strong and long-lasting neutralizing antibody response that confers protection even under systemic long-term cyclosporine A treatment. Remarkably, the vaccine completely prevents the appearance of benign as well as malignant skin tumors. Protection involves the maintenance of a low viral load in the skin by an antibody-dependent prevention of virus spread. Our results provide first evidence that VLPs elicit an effective immune response in the skin under immunocompetent and immunosuppressed conditions in an outbred animal model, irrespective of the infection status at the time of vaccination. These findings provide the basis for the clinical development of potent vaccination strategies against cutaneous HPV infections and HPV-induced tumors, especially in patients awaiting organ transplantation.

Biomolecular patterning of glass surfaces via strain-promoted cycloaddition of azides and cyclooctynes

Metal-free, strain-promoted alkyne–azide cycloaddition (SPAAC) is employed as a versatile technology for the modification of glass with biomolecules. Patterning is executed by stamping of a fluorogenic azidocoumarin or a cyclooctyne to the glass surface, to obtain a unique anchor point for subsequent functionalization by SPAAC. The azidocoumarin at the same time enables straightforward fluorescent read-out of surface reactions. A strong increase in fluorescence is indeed observed upon metal-free reaction with two readily available cyclooctynes, BCN or DIBAC. In addition, functionalized BCN derivatives are employed for glass surface patterning with biotin or even a 27 kDa protein (green fluorescent protein), upon simple incubation.

Quantum dynamics of an atom orbiting around an optical nanofiber

We propose a novel platform for the investigation of quantum wave packet dynamics, offering a complementary approach to existing theoretical models and experimental systems. It relies on laser-cooled neutral atoms which orbit around an optical nanofiber in an optical potential produced by a red-detuned guided light field. We show that the atomic center-of-mass motion exhibits genuine quantum effects like collapse and revival of the atomic wave packet. As distinctive advantages, our approach features a tunable dispersion relation as well as straightforward readout for the wave packet dynamics and can be implemented using existing quantum optics techniques.

SelEXSIDE: Fast and Easy Measurement of Multiple-Bond 1H,13C Coupling Constants for Stereochemical Analysis

Long-range (1)H,(13)C coupling constants ((n)J(CH)) are underutilized parameters for stereochemical structure determination, primarily because they are not easy to measure. This report describes a rapid and easily interpreted method for the measurement of one or more (n)J(CH) values based on a (13)C band-selective EXSIDE (SelEXSIDE), which reduces experiment times from many hours down to a few minutes while allowing a simple and straightforward readout of (n)J(CH) values from the resulting in-phase doublet signal.

Stability Screening of Arrays of Major Histocompatibility Complexes on Combinatorially Encoded Flow Cytometry Beads

The binding and stabilization capacity of potential T cell epitopes to class I MHC molecules form the basis for their immunogenicity and provide fundamental insight into factors that dictate cellular immune responses. We have developed a versatile high throughput cell-free method to measure MHC stability by capturing a variety of MHC products on the surface of streptavidin-coated particles followed by flow cytometry analysis. Arrays of peptide-MHC combinations, generated by exchanging conditional ligand-loaded MHC, could be probed in a single experiment, thus combining the molecular precision of biochemically purified MHCs with high content multiparametric flow cytometry-based assays. Semiquantitative determination of the peptide affinity for the restriction element could also be accomplished through competition experiments using this bead-based assay. Furthermore, the generated peptide-MHC reagents could directly be applied to antigen-specific CD8(+) T lymphocyte analysis. The combinatorial labeling of beads allowed straightforward identification by their unique fluorescent signatures and provided a convenient means for extended assay multiplexing.

First come, first served revisited: Factors affecting the same alternative splicing event have different effects on the relative rates of intron removal

Alternative splicing accounts for much of the complexity in higher eukaryotes. Thus, its regulation must allow for flexibility without hampering either its specificity or its fidelity. The mechanisms involved in alternative splicing regulation, especially those acting through coupling with transcription, have not been deeply studied in in vivo models. Much of our knowledge comes from in vitro approaches, where conditions can be precisely controlled at the expense of losing several levels of regulation present in intact cells. Here we studied the relative order of removal of the introns flanking a model alternative cassette exon. We show that there is a preferential removal of the intron downstream from the cassette exon before the upstream intron has been removed. Most importantly, both cis-acting mutations and trans-acting factors that regulate the model alternative splicing event differentially affect the relative order of removal. However, reduction of transcriptional elongation causing higher inclusion of the cassette exon does not change the order of intron removal, suggesting that the assumption, according to the "first come, first served" model, that slow elongation promotes preferential excision of the upstream intron has to be revised. We propose instead that slow elongation favors commitment to exon inclusion during spliceosome assembly. Our results reveal that measuring the order of intron removal may be a straightforward read-out to discriminate among different mechanisms of alternative splice site selection.

High Levels of Human Antigen-Specific CD4+ T Cells in Peripheral Blood Revealed by Stimulated Coexpression of CD25 and CD134 (OX40)

Ag-specific human CD4(+) memory T lymphocytes have mostly been studied using assays of proliferation in vitro. Intracellular cytokine and ELISPOT assays quantify effector cell populations but barely detect responses to certain recall Ags that elicit strong proliferative responses, e.g., tetanus toxoid, that comprise non-Th1 CD4(+) cells. We have found that culturing whole blood with Ag for 40-48 h induces specific CD4(+) T cells to simultaneously express CD25 and CD134. This new technique readily detects responses to well-described CD4(+) T cell recall Ags, including preparations of mycobacteria, CMV, HSV-1, influenza, tetanus toxoid, Candida albicans, and streptokinase, as well as HIV-1 peptides, with high specificity. The assay detects much higher levels of Ag-specific cells than intracellular cytokine assays, plus the cells retain viability and can be sorted for in vitro expansion. Furthermore, current in vitro assays for human CD4(+) memory T lymphocytes are too labor-intensive and difficult to standardize for routine diagnostic laboratories, whereas the whole-blood CD25(+)CD134(+) assay combines simplicity of setup with a straightforward cell surface flow cytometry readout. In addition to revealing the true extent of Ag-specific human CD4(+) memory T lymphocytes, its greatest use will be as a simple in vitro monitor of CD4(+) T cell responses to Ags such as tuberculosis infection or vaccines.

Multiple Andreev reflections in a quantum dot coupled to superconducting leads: Effect of spin-orbit coupling

We study the out of equilibrium current through a multilevel quantum dot contacted to two superconducting leads and in the presence of Rashba and Dresselhaus spin-orbit couplings, in the regime of strong dot-lead coupling. The multiple Andreev reflection (MAR) subgap peaks in the current-voltage characteristics are found to be modified (but not suppressed) by the spin-orbit interaction in a way that it strongly depends on the shape of the dot confining potential. In a perfectly isotropic dot the MAR peaks are enhanced when the strength ${\ensuremath{\alpha}}_{R}$ and ${\ensuremath{\alpha}}_{D}$ of Rashba and Dresselhaus terms are equal. When the anisotropy of the dot confining potential increases, the dependence of the subgap structure on the spin-orbit angle $\ensuremath{\theta}=\text{arctan}({\ensuremath{\alpha}}_{D}/{\ensuremath{\alpha}}_{R})$ decreases. Furthermore, when an in-plane magnetic field is applied to a strongly anisotropic dot, the peaks of the nonlinear conductance oscillate as a function of the magnetic-field angle and the location of the maxima and minima allows for a straightforward read-out of the spin-orbit angle $\ensuremath{\theta}$.