Complementary Probes Research Articles

JoXSZ: Joint X-SZ fitting code for galaxy clusters

The thermal Sunyaev-Zeldovich (SZ) effect and the X-ray emission offer separate and highly complementary probes of the thermodynamics of the intracluster medium. We presentJoXSZ, the first publicly available code designed to jointly fit SZ and X-ray data coming from various instruments to derive the thermodynamic profiles of galaxy clusters.JoXSZfollows a fully Bayesian forward-modelling approach, accounts for the SZ calibration uncertainty, and for the X-ray background level systematic. It improves upon most current and not publicly available analyses because it adopts the correct Poisson-Gauss expression for the joint likelihood, makes full use of the information contained in the observations, even in the case of missing values within the datasets, has a more inclusive error budget, and adopts a consistent temperature in the various parts of the code, allowing for differences between X-ray and SZ gas-mass weighted temperatures when required by the user.JoXSZaccounts for beam smearing and data analysis transfer function, accounts for the temperature and metallicity dependencies of the SZ and X-ray conversion factors, adopts flexible parametrisation for the thermodynamic profiles, and on user request, allows either adopting or relaxing the assumption of hydrostatic equilibrium (HE). When HE holds,JoXSZuses a physical (positive) prior on the radial derivative of the enclosed mass and derives the mass profile and overdensity radiirΔ. For these reasons,JoXSZgoes beyond simple SZ and electron density fits. We illustrate the use ofJoXSZby combining Chandra and NIKA data of the high-redshift cluster CL J1226.9+3332. The code is written in Python, it is fully documented, and the users are free to customise their analysis in accordance with their needs and requirements.JoXSZis publicly available on GitHub.

Multiplexed detection of tumor biomarkers utilizing immunohybridization Chain reaction integrated photonic barcodes

Multiplexed detection of cancer markers is of great value in clinical diagnosis. Herein, we present a new immunoassay method for simultaneous quantification of multiple tumor biomarkers. Our approach integrates photonic crystals (PhC) barcodes with DNA hybridization chain reaction (HCR) to amplify signal. Target biomarkers are captured by primary antibodies which are immobilized onto the PhC barcodes, forming sandwich immunocomplex with the assistance of second antibodies that are conjugated with DNA initiator. Subsequently, a chain reaction of hybridization events is propagated in attendance of a pair of complementary FAM-decorated H1 and H2 hairpin probes. As a result, the PhC barcodes exhibit multiplex encoding ability for different markers. By utilizing PhC barcodes with HCR for immunoassay, low-abundance cancer biomarkers (CEA, AFP and PSA) can be screened with high detection sensitivity and specificity. Our results showed a wide range from 0.001 to 1000 ng/mL; and the detection limit as low as 0.50 pg/mL. Our approach was also evaluated for analyzing human serum sample with considerable accuracy, which implies its potential as a new platform for simultaneous multiplex immunoassay.

Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis

Chemical tools to monitor drug-target engagement of endogenously expressed protein kinases are highly desirable for preclinical target validation in drug discovery. Here, we describe a chemical genetics strategy to selectively study target engagement of endogenous kinases. By substituting a serine residue into cysteine at the DFG-1 position in the ATP-binding pocket, we sensitize the non-receptor tyrosine kinase FES towards covalent labeling by a complementary fluorescent chemical probe. This mutation is introduced in the endogenous FES gene of HL-60 cells using CRISPR/Cas9 gene editing. Leveraging the temporal and acute control offered by our strategy, we show that FES activity is dispensable for differentiation of HL-60 cells towards macrophages. Instead, FES plays a key role in neutrophil phagocytosis via SYK kinase activation. This chemical genetics strategy holds promise as a target validation method for kinases.

Functionalized, Complementary Live-Charge Quantum Surface-Enhanced Raman Scattering Probes for Biomolecular Detection

The detection of molecules that cannot access the hot spots of plasmonic nanostructures with surface-enhanced Raman scattering (SERS) is challenging. This can result in weak SERS as well as low rep...

Systematic investigation of synthetic polyelectrolyte bottlebrush solutions by neutron and dynamic light scattering, osmometry, and molecular dynamics simulation.

There is a great interest in the synthesis and characterization of polyelectrolytes that mimic naturally occurring bottlebrush polyelectrolytes to capitalize on the unique properties of this class of macromolecules. Charged bottlebrush polymers form the protective mucus layer in the lungs, stomach, and orifices of animals and provide osmotic stabilization and lubrication to joints. In the present work, we systematically investigate bottlebrush poly(sodium acrylates) through a combination of measurements of solution properties (osmometry, small-angle neutron scattering, and dynamic light scattering) and molecular dynamics simulations, where the bottlebrush properties are compared in each case to their linear polymer counterparts. These complementary experimental and computational methods probe vastly different length- and timescales, allowing for a comprehensive characterization of the supermolecular structure and dynamics of synthetic polyelectrolyte bottlebrush molecules in solution.

CP -violating dark photon interaction

We introduce a scenario for CP-violating (CPV) dark photon interactions in the context of non-abelian kinetic mixing. Assuming an effective field theory that extends the Standard Model (SM) field content with an additional $U(1)$ gauge boson ($X$) and a $SU(2)_L$ triplet scalar, we show that there exist both CP-conserving and CPV dimension five operators involving these new degrees of freedom and the SM $SU(2)_L$ gauge bosons. The former yields kinetic mixing between the $X$ and the neutral $SU(2)_L$ gauge boson (yielding the dark photon), while the latter induces CPV interactions of the dark photon with the SM particles. We discuss experimental probes of these interactions using searches for permanent electric dipole moments (EDMs) and di-jet correlations in high-energy $pp$ collisions. It is found that the experimental limit on the electron EDM currently gives the strongest restriction on the CPV interaction. In principle, high energy $pp$ collisions provide a complementary probe through azimuthal angular correlations of the two forward tagging jets in vector boson fusion. In practice, observation of the associated CPV asymmetry is likely to be challenging.

SLAM-MS: Mutation scanning of stem-loop amplicons with TaqMan probes by quantitative DNA melting analysis

DNA Melting Analysis (DMA) with a TaqMan probe covering the mutation “hot spot” is a simple, sensitive, and “closed tube” method of mutation detection. However, DMA requires asymmetric PCR to produce single-stranded amplicons capable of interacting with TaqMan probes. This makes quantitative analysis impossible owing to low amplification efficiency. Moreover, bi-strand mutation detection necessitates two independent PCRs. The SLAM-MS (Stem-Loop AMplicon Mutation Scanning) assay, in which symmetric PCR is performed using primers with 5'-universal primer sequence (UPS), has been developed to detect KRAS mutations. Some of the resulting amplicons, sense and antisense, adopt single-stranded stem-loop conformation and become unable to renature, but able to hybridize with TaqMan probes. Hybrids of stem-loops and complementary TaqMan probes are suitable for melting analysis and simultaneous bi-strand mutation scanning. In addition, the areas under the melting peaks are determined by the PeakFit software, a non-linear iterative curve fitting program, to evaluate the wild-type/mutant allele ratio. Thus, the SLAM-MS assay permits quantification of both the number of copies of the target sequence and the percentage of mutant alleles. For mutant enrichment, the SLAM-MS assay uses TaqMan probes as PCR blocking agents allowing an ~10 times higher mutation detection sensitivity than High Resolution Melting (HRM) assay.

Multi-cycle signal-amplified colorimetric detection of tobramycin based on dual-strand displacement and three-way DNA junction

A colorimetric aptasensor for tobramycin was developed using a multi-cycle signal amplification strategy which combines the application of dual-strand displacement and DNA three-way junction structure with the catalysis of G-quadruplex/hemin DNAzyme. The assay starts with a partially complementary double-stranded probe template1/template2 (T1/T2). The aptamer of tobramycin is included in T1. Tobramycin can bind with the aptamer region of T1 and expose the 3′-terminal of T2. In the presence of a pair of primers, Bsm DNA polymerase and Nt.BstNBI endonuclease-assisted isothermal amplification generates a single-stranded DNA reporter probe. The later can hybridize with a specially designed DNA three-way junction and further trigger Lambda exonuclease-assisted loop amplification, which regenerates the reporter probe and produces a large number of signal probe (containing G-quadruplex-forming sequence). Finally, the G-quadruplex/hemin DNAzyme catalyzes ABTS2−/H2O2 reaction system to generate a colorimetric signal. The assay exhibits high selectivity and sensitivity to tobramycin, with a detection limit of 12.24 nM and a linear response range of 20–800 nM. Moreover, the assay was successfully used to detect tobramycin in milk and water samples, indicating its potential application in both food safety control and environmental monitoring.

Amperometric Bioplatforms To Detect Regional DNA Methylation with Single-Base Sensitivity.

This work reports the first bioplatform able to determine electrochemically 5-hydroxymethylcytosine (5-hmC) methylation events at localized sites and single-base sensitivity. The described bioplatform relies on a specific antibody (anti-5-hmC), further conjugated with commercial bioreagents loaded with multiple horseradish peroxidase (HRP) molecules, recognizing the epimark in a target DNA, captured through hybridization onto streptavidin-magnetic microbeads (Strep-MBs) modified with a complementary DNA capture probe. The electrochemical detection is performed by amperometry (-0.20 V vs Ag pseudoreference electrode) at disposable screen-printed carbon electrodes (SPCEs) in the presence of H2O2/hydroquinone (HQ) upon magnetic capture of the modified MBs onto the SPCE. The use of the commercial bioreagents ProtA-polyHRP80 and Histostar, very scarcely explored so far in electrochemical biosensors, provides high sensitivities for a synthetic target DNA sequence with a unique 5-hmC in the promoter region of MGMT tumor suppressor gene. Amplification factors of 43.6 and 55.2 were achieved using ProtA-polyHRP80 or Histostar, respectively, compared to the conventional secondary antibody labeling. This amplification was crucial to detect methylation events at single-nucleotide resolution achieving limits of detection (LODs) of 23.0 and 13.2 pM, respectively, without any target DNA amplification. The ProtA-polyHRP80-based bioplatform, selected as a compromise between sensitivity and cost per determination, exhibited full discrimination toward the target 5-hmC against the closely related 5-mC. In addition, the bioplatform detected 5-hmC at the regional level (MGMT promoter region) in just 10 ng of genomic DNA (gDNA, ∼2700 genomes) extracted from cancer cells and tissues from colorectal cancer (CRC) patients within 60 min.

Nanopore Resistive Pulse Sensing with Multiple Alpha-Hemolysin Pores Improves the Detection Limit of Microrna

The concentration profile of microRNAs in body fluids has been related to a variety of diseases, including specific cancers. By conjugation with a complementary DNA probe, specific miRNA species can be enumerated by nanopore resistive pulsing. This is possible because a miRNA-DNA probe duplex temporarily blocks a nanopore of ∼1.5 nm diameter, causing a decrease in the electrical current by displacing electrolyte ions. Under the influence of the electrophoretic driving force, the duplex dissociates after ∼10-1000 ms, and both the miRNA and the DNA molecules transit through the pore. The pore is now open again and can capture another duplex, with the frequency of the duplex pore translocations corresponding to the miRNA concentration in the solution. Biological porins are attractive because of their reproducible self-assembly, but the lipid bilayer matrix prevents the application of voltages >120 mV. It has previously been shown that the electrophoretic driving force can also be enhanced by an electrolyte concentration gradient of 0.5 / 4 M KCl, but few pulses were observed below 1 nM duplex concentration. Here, we demonstrate that the frequency can be further increased by incorporating multiple pores in the same bilayer. With an electrolyte gradient of 0.2 / 1 M KCl, it was possible to perform resistive pulse sensing with up to 100 alpha-hemolysin pores in an aperture-suspended DPhPC bilayer. We characterize the effect of electrolyte salt gradients on the stability of bilayer-incorporated alpha-hemolysin and quantify the resistive pulses for duplex concentrations in the range 0.01-100 nM. The achieved ∼10-fold increase in frequency, with respect to single-pore sensing with a 0.5 / 4 M KCl gradient, demonstrates the potential of multi-pore sensing to achieve miRNA detection at clinically relevant concentrations.

The synergy between CMB spectral distortions and anisotropies

Spectral distortions and anisotropies of the CMB provide independent and complementary probes to study energy injection processes in the early universe. Here we discuss the synergy between these observables, and show the promising future of spectral distortion missions to constrain both exotic and non-exotic energy injections. We show that conventional probes such as Big Bang Nucleosynthesis and CMB anisotropies can benefit from and even be surpassed by future spectral distortion experiments. For this, we have implemented a unified framework within the Boltzmann code CLASS to consistently treat the thermal evolution of photons and baryons. Furthermore, we give an extensive and pedagogical introduction into the topic of spectral distortions and energy injections throughout the thermal history of the universe, highlighting some of their unique features and potential as a novel probe for cosmology and particle physics.

Evolution of the Deterministic Collapse Barrier of the Field Clusters as a Probe of Cosmology

The collapse barrier, $\delta_{c}$, of the field clusters located in the low-density environment is deterministic rather than diffusive, unlike that of the wall counterparts located in the superclusters. Analyzing the data from the Mira-Titan simulations for eleven different cosmologies including the standard $\Lambda$CDM cosmology at various redshifts, we investigate the evolution of the deterministic collapse barrier of the field clusters and explore its dependence on the background cosmology. Regardless of the background cosmology, the deterministic $\delta_{c}$ exhibits a universal behavior of having a higher value than the Einstein-de Sitter spherical collapse barrier height of $\delta_{sc}=1.686$, at $z=0$ but gradually converging down to $\delta_{sc}$ as the dominance of dark energy diminishes with the increment of $z$. A significant difference among different cosmologies, however, is found in its convergence rate as well as in the critical redshift $z_{c}$ at which $\delta_{c}=\delta_{sc}$. Showing that the convergence rate and critical redshifts can distinguish even between the degenerate cosmologies which yield almost identical linear growth factor and cluster mass functions, we suggest that the evolution of the deterministic collapse barrier of the field clusters should be a powerful complementary probe of cosmology.

Ray tracing the integrated Sachs-Wolfe effect through the light cones of the dark energy universe simulation-full universe runs

The late integrated Sachs-Wolfe (ISW) effect correlates the Cosmic Microwave Background (CMB) temperature anisotropies with foreground cosmic large-scale structures. As the correlation depends crucially on the growth history in the era of dark energy, it is a key observational probe for constraining the cosmological model. Here we present a detailed study based on full-sky and deep light cones generated from very large volume numerical N-body simulations, which allow us to avoid the use of standard replica techniques, while capturing the entirety of the late ISW effect on the large scales. We post-process the light cones using an accurate ray-tracing method and construct full-sky maps of the ISW temperature anisotropy for three different dark energy models. We quantify in detail the extent to which the ISW effect can be used to discriminate between different dark energy scenarios when cross-correlated with the matter distribution or the CMB lensing potential. We also investigate the onset of non-linearities, the so-called Rees-Sciama effect which provides a complementary probe of the dark sector. We find the signal of the lensing-lensing and ISW-lensing correlation of the three dark energy models to be consistent with measurements from the Planck satellite. Future surveys of the large-scale structures may provide cross-correlation measurements that are sufficiently precise to distinguish the signal of these models. Our methodology is very general and can be applied to any dark energy or modified gravity scenario as long as the metric seen by photons can still be characterized by a Weyl potential.

TiO2 nanotubes loaded with CdS nanocrystals as enhanced emitters of electrochemiluminescence: application to an assay for prostate-specific antigen.

An enhanced cathodic electrochemiluminescence (ECL) assay for prostate-specific antigen (PSA) is developed based on the in situ activation of a semiconductor nanomaterial. An excellent ECL emitter (CdS/TiO2 nanotubes) was fabricated by the combination of TiO2 nanotubes (NTs) and thioglycolic acid-capped CdS nanocrystals (NCs). After the activation of the hydrogen peroxide-citric acid solution, the ECL signal was enhanced 265 times compared with that of the original TiO2 NT with H2O2 as co-reactant. For the ECL assay, activated CdS/TiO2 NTs were assembled with complementary DNA, PSA aptamer and probe DNA-functionalized SiO2@Pt nanoparticles (NPs) via DNA hybridization to form the detection platform. The SiO2@Pt NPs acted as ECL quencher of CdS/TiO2 NTs. In the presence of PSA, ECL increased after the release of pDNA-SiO2@Pt NPs because of the binding of PSA to the aptamer. An "off-on" ECL phenomenon appeared. The enhanced ECL signals were used for sensitive determination of PSA. The dynamic range was 0.001 to 50ngmL-1 with a detection limit of 0.4pgmL-1 (S/N = 3). This new approach conceivably paves the way for fabricating various other enhanced ECL emitter systems, with good application prospects in clinical practice. Graphical abstract The activated CdS/TiO2 nanotubes and SiO2@Pt nanoparticles were synthesized and used to develop an energy-transfer electrochemiluminescence analysis method with high sensitivity and anti-interference performance.

Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures.

One of the most commonly used bonds between two biomolecules is the bond between biotin and streptavidin (SA) or streptavidin homologues (SAHs). A high dissociation constant and the consequent high-temperature stability even allows for its use in nucleic acid detection under polymerase chain reaction (PCR) conditions. There are a number of SAHs available, and for assay design, it is of great interest to determine as to which SAH will perform the best under assay conditions. Although there are numerous single studies on the characterization of SAHs in solution or selected solid phases, there is no systematic study comparing different SAHs for biomolecule-binding, hybridization, and PCR assays on solid phases. We compared streptavidin, core streptavidin, traptavidin, core traptavidin, neutravidin, and monomeric streptavidin on the surface of microbeads (10-15 μm in diameter) and designed multiplex microbead-based experiments and analyzed simultaneously the binding of biotinylated oligonucleotides and the hybridization of oligonucleotides to complementary capture probes. We also bound comparably large DNA origamis to capture probes on the microbead surface. We used a real-time fluorescence microscopy imaging platform, with which it is possible to subject samples to a programmable time and temperature profile and to record binding processes on the microbead surface depending on the time and temperature. With the exception of core traptavidin and monomeric streptavidin, all other SA/SAHs were suitable for our investigations. We found hybridization efficiencies close to 100% for streptavidin, core streptavidin, traptavidin, and neutravidin. These could all be considered equally suitable for hybridization, PCR applications, and melting point analysis. The SA/SAH-biotin bond was temperature-sensitive when the oligonucleotide was mono-biotinylated, with traptavidin being the most stable followed by streptavidin and neutravidin. Mono-biotinylated oligonucleotides can be used in experiments with temperatures up to 70 °C. When oligonucleotides were bis-biotinylated, all SA/SAH-biotin bonds had similar temperature stability under PCR conditions, even if they comprised a streptavidin variant with slower biotin dissociation and increased mechanostability.

Going deep with Minkowski functionals of convergence maps

Aims. Stage IV lensing surveys promise to make an unprecedented amount of excellent data available. This will represent a huge leap in terms of quantity and quality and will open the way for the use of novel tools that surpass the standard second-order statistics for probing the high-order properties of the convergence field. Motivated by these considerations, some of us have started a long-term project aiming at using Minkowski functionals (MFs) as complementary and supplementary probes to increase the lensing figure of merit (FoM). Methods. As a second step on this path, we discuss the use of MFs for a survey consisting of a wide total area Atot that is imaged at a limiting magnitude magW and contains a subset of area Adeep, where observations are pushed to a deeper limiting magnitude magD. We present an updated procedure to match the theoretically predicted MFs to the measured MFs, and take the effect of map reconstruction from noisy shear data into account. We validate this renewed method against simulated datasets with different source redshift distributions and total number density, setting these quantities in accordance with the depth of the survey. We can then rely on a Fisher matrix analysis to forecast the improvement in the FoM that is due to the joint use of shear tomography and MFs under different assumptions on (Atot, Adeep, and magD), and the prior on the MFs nuisance parameters. Results. We find that MFs can provide valuable help in increasing the FoM of the lensing survey when the nuisance parameters are known with non-negligible precision. The possibility of compensating for the loss of FoM through a cut in the multipole range that is probed by shear tomography is even more interesting. This makes the results more robust against uncertainties in the modeling of nonlinearities. This makes MFs a promising tool for increasing the FoM and also protects the constraints on the cosmological parameters mainly from theoretical systematic effects.

Multimodal spectroscopic investigation of the conformation and local environment of biomolecules at an electrified interface.

The complex and dynamic interfacial regions between biological samples and electronic components pose many challenges for characterization, including their evolution over multiple temporal and spatial scales. Spectroscopic probes of buried interfaces employing mid-infrared plasmon resonances and time-resolved fluorescence detection in the visible range are used to study the properties of polypeptides adsorbed at the surface of a working electrode. Information from these complementary spectroscopic probes reveals the interplay of solvation, electric fields, and ion concentration on their resulting macromolecular conformations.

Axion-like relics: new constraints from old comagnetometer data

The noble-alkali comagnetometer, developed in recent years, has been shown to be a very accurate measuring device of anomalous magnetic-like fields. An ultra-light relic axion-like particle can source an anomalous field that permeates space, allowing for its detection by comagnetometers. Here we derive new constraints on relic axion-like particles interaction with neutrons and electrons from old comagnetometer data. We show that the decade-old experimental data place the most stringent terrestrial constraints to date on ultra-light axion-like particles coupled to neutrons. The constraints are comparable to those from stellar cooling, providing a complementary probe. Future planned improvements of comagnetometer measurements through altered geometry, constituent content and data analysis techniques could enhance the sensitivity to axion-like relics coupled to nucleons or electrons by many orders of magnitude.

Magnetic and silver nanoparticle functionalized calcium carbonate particles—Dual functionality of versatile, movable delivery carriers which can surface-enhance Raman signals

Multifunctional probes play an increasing role even beyond applications in biomedicine. Multifunctionality introduced by the dual types of complementary probes is always attractive because, in this case, functionalized objects inherit the function of both materials. Porous calcium carbonate microparticles are becoming popular carriers of biomolecules and biosensors, as well as imaging enhancers. We demonstrate here a dual function of these carriers by incorporating both magnetic and silver nanoparticles. Magnetic nanoparticles enable movements and displacements by a magnetic field, while silver nanoparticles provide surface-enhanced Raman signal amplification necessary for the detection of biomolecules. Application of such dual-functional carriers is foreseen beyond the applications of biomedicine and theranostics.

A novel zinc finger protein-based amperometric biosensor for miRNA determination.

This paper reports a simple electrochemical strategy for the determination of microRNAs (miRNAs) using a commercial His-Tag-Zinc finger protein (His-Tag-ZFP) that binds preferably (but non-sequence specifically) RNA hybrids over ssRNAs, ssDNAs, and dsDNAs. The strategy involves the use of magnetic beads (His-Tag-Isolation-MBs) as solid support to capture the conjugate formed in homogenous solution between His-Tag-ZFP and the dsRNA homohybrid formed between the target miRNA (miR-21 selected as a model) and a biotinylated synthetic complementary RNA detector probe (b-RNA-Dp) further conjugated with a streptavidin-horseradish peroxidase (Strep-HRP) conjugate. The electrochemical detection is carried out by amperometry at disposable screen-printed carbon electrodes (SPCEs) (- 0.20 V vs Ag pseudo-reference electrode) upon magnetic capture of the resultant magnetic bioconjugates and H2O2 addition in the presence of hydroquinone (HQ). The as-prepared biosensor exhibits a dynamic concentration range from 3.0 to 100 nM and a detection limit (LOD) of 0.91 nM for miR-21 in just ~ 2 h. An acceptable discrimination was achieved between the target miRNA and other non-target nucleic acids (ssDNA, dsDNA, ssRNA, DNA-RNA, miR-122, miR-205, and single central- or terminal-base mismatched sequences). The biosensor was applied to the analysis of miR-21 from total RNA (RNAt) extracted from epithelial non-tumorigenic and adenocarcinoma breast cells without target amplification, pre-concentration, or reverse transcription steps. The versatility of the methodology due to the ZFP's non-sequence-specific binding behavior makes it easily extendable to determine any target RNA only by modifying the biotinylated detector probe.