Degenerate Probe Research Articles

The 3237 cm−1 diamond defect: Ultrafast vibrational dynamics, concentration calibration, and relationship to the N3VH0 defect

The dynamics of the 3237 cm−1 local vibrational mode in diamond, associated with an unknown defect, was investigated using ultrafast infrared pump-probe spectroscopy. When pumped at 3237 cm−1, a degenerate probe was used to study the ground state's recovery, while a non-degenerate probe tracked excited state absorption at 3029 cm−1, corresponding to the 1 → 2 vibrational state transition. The similar population lifetimes for the ground state recovery and excited state absorption suggests a single population decay pathway, with a lifetime of T1=2.2±0.1ps. Perturbed free induction decay signals observed in negative time delays gave the dephasing time of the coherent state between the 0 and 1 vibrational states, and further predicted the 3029 cm−1 transition. Images from FTIR microscopy show that the 3237 cm−1 feature and the 3107 cm−1 absorption line from the N3VH0 defect are not correlated, and our pump-probe study shows the 3237 cm−1 feature does not share a common ground state with the N3VH0 defect, both of which suggest that this local vibrational mode does not originate from the N3VH0 defect. A calibration factor was obtained via a Morse potential model constrained by the observed transition energies, which relates the concentration of the defect producing the 3237 cm−1 feature to its absorption coefficient measured by FTIR spectroscopy. Based on FTIR absorption spectroscopy under uniaxial stress, we further assign a trigonal symmetry character to the defect that gives the 3237 cm−1 feature. The results presented are consistent with the theory that the 3237 cm−1 feature originates from the N4VH defect, the quantification of which allows better tracking of the nitrogen content in diamond.

A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern.

Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key ΔH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes.

Atomic memory based on recoil-induced resonances

In this work, we perform a detailed theoretical and experimental investigation of an atomic memory based on recoil-induced resonance in cold cesium atoms. We consider the interaction of nearly degenerate pump and probe beams with an ensemble of two-level atoms. A full theoretical density matrix calculation in the extended Hilbert space of the internal and external atomic degrees of freedom allows us to obtain, from first principles, the transient and stationary responses determining the probe transmission and the forward four-wave-mixing spectra. These two signals are generated together at the same order of perturbation with respect to the intensities of pump and probe beams. Moreover, we have investigated the storage of optical information on the spatial modes of light beams in the atomic external degrees of freedom, which provided a simple interpretation for the previously reported nonvolatile character of this memory. The retrieved signals after storage reveal the equivalent role of probe transmission and four-wave mixing, as the two signals have similar amplitudes. Probe transmission and forward four-wave-mixing spectra were then experimentally measured for both continuous excitation and after storage. The experimental observations are in good agreement with the developed theory, and they open another pathway for the reversible exchange of optical information with atomic systems.

Impedimetric genosensor based on graphene nanoribbons for detection and identification of oncogenic types of human papillomavirus

AbstractBACKGROUNDHuman papillomavirus (HPV) is a large group of viruses that infect skin and mucosa causing warts and epithelial tumors known as papillomas. Although HPV can be contracted during sexual intercourse including vaginal, anal and oral sex, skin‐to‐skin contact is sufficient to cause infection. Asymptomatic patients can have the virus and pass it on without knowing it. Due to the scarcity of rapid and inexpensive methods available to identify HPV serotypes, herein we report an electrochemical genosensor as an alternative to current molecular and serological HPV identification methods. Graphene nanoribbons were used as transducers to immobilize MY11 DNA probe, a degenerate probe generally employed in polymerase chain reaction amplification of a broad spectrum of HPV DNA types.RESULTSCyclic voltammetry, electrochemical impedance spectroscopy and atomic force microscopy were used to characterize the construction of the platform and the biodetection process. Our results suggest that oncogenic subtypes of HPV are quickly detected and identified in the picogram range. Impedimetric responses grouped for known genotypically related HPV 51, 53 and 66 subtypes related to anogenital lesions. Additionally, our genosensor was able to successfully detect HPV types 16 and 18 in cervical specimens (cDNA samples) at concentrations of 1 amol L−1, 100 amol L−1, 100 fmol L−1, 50 pmol L−1 and 100 pmol L−1 with a detection limit of 3.5 and 1.2 amol L−1 for HPV 16 and HPV 18, respectively.CONCLUSIONSThe proposed genosensor platform can be considered a new tool for detecting and identifying HPV genotypes. © 2021 Society of Chemical Industry (SCI).

All-optical switching of an epsilon-near-zero plasmon resonance in indium tin oxide

Nonlinear optical devices and their implementation into modern nanophotonic architectures are constrained by their usually moderate nonlinear response. Recently, epsilon-near-zero (ENZ) materials have been found to have a strong optical nonlinearity, which can be enhanced through the use of cavities or nano-structuring. Here, we study the pump dependent properties of the plasmon resonance in the ENZ region in a thin layer of indium tin oxide (ITO). Exciting this mode using the Kretschmann-Raether configuration, we study reflection switching properties of a 60 nm layer close to the resonant plasmon frequency. We demonstrate a thermal switching mechanism, which results in a shift in the plasmon resonance frequency of 20 THz for a TM pump intensity of 70 GW cm−2. For degenerate pump and probe frequencies, we highlight an additional two-beam coupling contribution, not previously isolated in ENZ nonlinear optics studies, which leads to an overall pump induced change in reflection from 1% to 45%.

Five-color fluorescence in situ hybridization system for karyotyping of Panax ginseng

Chromosomal mapping of repetitive elements is invaluable in understanding genome structure and evolution. Repetitive elements constitute ~ 80% of the allotetraploid ginseng (Panax ginseng) genome. Preparing sporophytic metaphase chromosomes of ginseng is laborious; therefore, it would be advantageous to maximize the information obtained from a single slide. Here, we investigated the suitability of simultaneous five-color fluorescence in situ hybridization using major ginseng repeats, namely PgDel1, PgDel2, PgTel, and Pg167TR. For Pg167TR, we generated two degenerate probe libraries (Pg167TRa and Pg167TRb) based on the chromosomal target coverage. We labeled the probes with dark-red, blue, red, orange, and green fluorochromes and used excitation/emission filter sets specific to each fluorochrome to detect fluorescence in situ hybridization signals. PgDel1 was distributed across all 24 chromosome pairs, except for the secondary constriction region of chromosome 16, whereas PgDel2 was distributed over 12 of the 24 pairs. PgTel was localized in the termini of chromosomes and in an intercalary region in chromosome 13. Pg167TRa and Pg167TRb were distributed among 22 chromosome pairs with loci polymorphisms. These results showed the utility of five-color fluorescence in situ hybridization for chromosomal mapping of five repeats to expedite karyotyping and facilitate genome evolution studies in ginseng and other plant species.

Controllable optical bistability and multistability in asymmetric quantum wells via Fano-type interference

We theoretically investigate the hybrid absorptive-dispersive optical bistability (OB) and optical multistability (OM) behaviors induced by Fano-type interference in a four-subband asymmetric semiconductor double quantum wells scheme driven by a degenerate probe field and a coherent coupling field. We show that the appearance or disappearance of OB can be controlled by modulating the strength of the Fano-type interference. We also present the threshold and hysteresis cycle of the OB can be controlled by adjusting the intensity of the coherent coupling field. Moreover, OB can be switched to OM by tuning the frequency detuning of the coherent coupling field or vice versa. This interesting scheme may provide guidance for technological applications in optoelectronics and solid-state quantum information science.

Dynamics of A-exciton and spin relaxation in WS<sub>2</sub> and WSe<sub>2</sub> monolayer

Two-dimensional transitional metal dichalcogenide (2D TMD) emerges as a good candidate material in optoelectronics and valleytronics due to its particular exciton effect and strong spin-valley locking. Owing to the enhancement of quantum confinement effect and the decline of dielectric shielding effect, the optical excitation of electron-hole pair is enhanced substantially, which makes large TMD exciton binding energy and makes excitons observed easily at room temperature or even higher temperature. Optical response of 2D TMD is dominated by excitons at room temperature, which provides an ideal medium for studying the generation, relaxation and interaction of excitons or trions. By employing ultrafast time resolved spectroscopy, we investigate experimentally the dynamic behaviors of A-exciton and spin relaxations for two types of TMDs, i.e. WS<sub>2</sub> and WSe<sub>2</sub> monolayers, respectively. By tuning the excitation wavelength of the degenerate pump and probe laser beam, the WS<sub>2</sub> monolayer and WSe<sub>2</sub> monolayer are excited at their A-exciton resonance transition position or near their A-exciton resonance transition position in order to compare the dynamical evolutions of band structure and exciton polarization of the two similar WS<sub>2</sub> and WSe<sub>2</sub> monolayer structures. Our experimental results reveal that the relaxation of A exciton in WS<sub>2</sub> shows biexponential decay, while that of WSe<sub>2</sub> shows triexponential decay, and the A-exciton life time in WSe<sub>2</sub> is much longer than that of WS<sub>2</sub> counterpart. The spin relaxation of A exciton in WS<sub>2</sub> shows a monoexponential feature with a lifetime of 0.35 ps, which is dominated by the electron-hole exchange interaction. For the case of WSe<sub>2</sub>, the spin relaxation can be well fitted with biexponential function, the fast component has a lifetime of 0.5 ps and the slow one has a lifetime of 28 ps. The fast relaxation is dominated by the electron-hole exchange interaction, and the slow one comes from the formation of dark exciton via spin-lattice coupling. By tuning the excitation wavelength around A-exciton transition, the formation of dark exciton in WSe<sub>2</sub> is demonstrated to be much more effective than that in WS<sub>2</sub> monolayer. Our experimental results provide qualitative physical images for an in-depth understanding of the relationship between exciton and TMD structure, and also provide reference for further designing and regulating the TMDs based optoelectronic devices.

Tuning emergent magnetism in a Hund's impurity.

The recently proposed concept of a Hund's metal--a metal in which electron correlations are driven by Hund's rule coupling-can be used to explain the exotic magnetic and electronic behaviour of strongly correlated electron systems of multi-orbital metallic materials. Tuning the abundance of parameters that determine these materials is, however, experimentally challenging. Here, we show that the basic constituent of a Hund's metal--a Hund's impurity--can be realized using a single iron atom adsorbed on a platinum surface, a system that comprises a magnetic moment in the presence of strong charge fluctuations. The magnetic properties can be controlled by using the tip of a scanning tunnelling microscope to change the binding site and degree of hydrogenation of the 3d transition-metal atom. We are able to experimentally explore a regime of four almost degenerate energy scales (Zeeman energy, temperature, Kondo temperature and magnetic anisotropy) and probe the magnetic excitations with the microscope tip. The regime of our Hund's impurity can be tuned from an emergent magnetic moment to a multi-orbital Kondo state, and the system could be used to test predictions of advanced many-body theories for non-Fermi liquids in quantum magnets or unconventional superconductors.

A Single Nucleotide Polymorphism at the TaqMan Probe-Binding Site Impedes Real-Time Reverse Transcription-PCR-Based Detection of Norovirus GII.4 Sydney.

A single nucleotide polymorphism (SNP) in the TaqMan probe-binding site resulted in decreased sensitivity of real-time reverse transcription-PCR (RT-rtPCR) for detection of norovirus genogroup II genotype 4 (GII.4) Sydney. A new degenerate probe was designed that improved the sensitivity of the detection while not interfering with the detection of other GII and GI strains.

Sequence-Based Optimization of a Quantitative Real-Time PCR Assay for Detection of Plasmodium ovale and Plasmodium malariae

Although microscopic examination of Giemsa-stained blood smears remains the gold standard for the diagnosis of malaria, molecular detection using PCR is becoming increasingly popular. Due to discrepant PCR and microscopy results, we aimed to optimize our detection assays for Plasmodium malariae and Plasmodium ovale by sequencing the 18S rRNA region and developing a new primer and probe set for real-time quantitative PCR (qPCR). Clinical specimens positive for P. malariae (n = 15) or P. ovale (n = 33) underwent amplification and sequencing of the 18S rRNA region. Based on sequence discrepancies between our current primer/probe and clinical isolates, degenerate P. ovale primer and probe were developed to determine if their performance characteristics improved. The reference (gold) standard was microscopy. No 18S sequence heterogeneity was observed among the P. malariae isolates, and the sensitivity and specificity of our current P. malariae qPCR assay were both 100%. Compared to microscopy, the sensitivity and specificity of our current P. ovale qPCR assay were 72.7% and 100%, respectively. Five single nucleotide polymorphisms (SNPs) were identified in P. ovale. The sensitivity of the new P. ovale assay increased to 100% with 100% specificity. We therefore improved the performance characteristics of our P. ovale molecular detection assay through the development of a degenerate primer and probe set which accommodates 18S SNPs among the 2 subspecies of P. ovale. Given the suboptimal sensitivity of rapid diagnostic tests for non-falciparum malaria and the typically low parasitemia of P. malariae and P. ovale, a well-performing confirmatory molecular assay is imperative for clinical laboratories.

Development of Primers and Probes for Genus and Species Specific Detection of 'Candidatus Liberibacter Species' by Real-Time PCR.

Huanglongbing (HLB), also known as citrus greening, is currently the most devastating disease impacting citrus production. The disease is associated with three different 'Candidatus Liberibacter species', 'Ca. Liberibacter asiaticus', 'Ca. Liberibacter americanus', and 'Ca. Liberibacter africanus', which induce similar and overlapping symptoms. When HLB-symptomatic trees are tested, one of the Candidatus Liberibacters is normally detected by conventional or real-time PCR (qPCR). The most widely used assays use primers and probes based on the 16S ribosomal RNA (rRNA) gene. The 16S rRNA-based assays to detect the three species are species-specific and must be performed sequentially. We describe a single assay that detected all species of 'Ca. Liberibacter' at the genus level, providing increased convenience. Recent molecular analyses of 'Ca. Liberibacter species' and other bacteria suggest that the rpoB gene (encoding the β-subunit of RNA polymerase) provides an alternative target for bacterial identification. We report here the design of a single pair of degenerate primers and a hybridization probe corresponding to the rpoB region and their application for the detection of all three citrus 'Ca. Liberibacter species', enabling detection of 'Ca. Liberibacter' at the genus level. In addition, species-specific primers and probes based on the rplJ/rplK genes were designed and used for detection at the species level in a multiplexed format. Both the genus- and species-specific assays were validated in both SYBR Green I and TaqMan formats, and with both plant and insect extracts that contained the pathogen. These one-step qPCR diagnostic methods are useful for the detection of all species of Liberibacter infecting citrus. In addition, the degenerate genus-specific primers and probe successfully detected 'Ca. Liberibacter solanacearum', a psyllid-transmitted pathogen associated with disease in tomato, carrot, and potato.

Enteric Coronavirus in Ferrets, the Netherlands

Enteric Coronavirus in Ferrets, the Netherlands

Plexciton Dynamics: Exciton−Plasmon Coupling in a J-Aggregate−Au Nanoshell Complex Provides a Mechanism for Nonlinearity

Coherently coupled plasmons and excitons give rise to new optical excitations--plexcitons--due to the strong coupling of these two oscillator systems. Time-resolved studies of J-aggregate-Au nanoshell complexes when the nanoshell plasmon and J-aggregate exciton energies are degenerate probe the dynamical behavior of this coupled system. Transient absorption of the interacting plasmon-exciton system is observed, in dramatic contrast to the photoinduced transmission of the pristine J-aggregate. An additional, transient Fano-shaped modulation within the Fano dip is also observable. The behavior of the J-aggregate-Au nanoshell complex is described by a combined one-exciton and two-exciton state model coupled to the nanoshell plasmon.

Effect of pump-probe detuning on the Faraday rotation and ellipticity signals of mode-locked spins in (In,Ga)As/GaAs quantum dots

We have studied the Faraday rotation and ellipticity signals in ensembles of singly charged (In,Ga)As/GaAs quantum dots by pump-probe spectroscopy. For degenerate pump and probe we observe that the Faraday rotation signal amplitude first grows with increasing the time separation between pump and probe before a decay is observed for large temporal separations. The temporal behavior of the ellipticity signal, on the other hand, is regular: its amplitude decays with the separation. By contrast, for detuned pump and probe the Faraday rotation and ellipticty signals both exhibit similar and conventional behavior. The experimental results are well described in the frame of a recently developed microscopic theory [I. A. Yugova, M. M. Glazov, E. L. Ivchenko, and Al. L. Efros, Phys. Rev. B 80, 104436 (2009)]. The comparison between calculations and experimental data allows us to provide insight into the spectral dependence of the electron spin precession frequencies and extract the electron $g$ factor dependence on energy.

A One-Step, Real-Time PCR Assay for Rapid Detection of Rhinovirus

One-step, real-time PCR assays for rhinovirus have been developed for a limited number of PCR amplification platforms and chemistries, and some exhibit cross-reactivity with genetically similar enteroviruses. We developed a one-step, real-time PCR assay for rhinovirus by using a sequence detection system (Applied Biosystems; Foster City, CA). The primers were designed to amplify a 120-base target in the noncoding region of picornavirus RNA, and a TaqMan (Applied Biosystems) degenerate probe was designed for the specific detection of rhinovirus amplicons. The PCR assay had no cross-reactivity with a panel of 76 nontarget nucleic acids, which included RNAs from 43 enterovirus strains. Excellent lower limits of detection relative to viral culture were observed for the PCR assay by using 38 of 40 rhinovirus reference strains representing different serotypes, which could reproducibly detect rhinovirus serotype 2 in viral transport medium containing 10 to 10,000 TCID(50) (50% tissue culture infectious dose endpoint) units/ml of the virus. However, for rhinovirus serotypes 59 and 69, the PCR assay was less sensitive than culture. Testing of 48 clinical specimens from children with cold-like illnesses for rhinovirus by the PCR and culture assays yielded detection rates of 16.7% and 6.3%, respectively. For a batch of 10 specimens, the entire assay was completed in 4.5 hours. This real-time PCR assay enables detection of many rhinovirus serotypes with the Applied Biosystems reagent-instrument platform.

Time-resolved pump-probe technology with phase object for measurements of optical nonlinearities

A new time-resolved pump-probe system with phase object, which is based on the PO Z-scan technique and the standard pump-probe system, is presented. This new method can simultaneously investigate the dynamic of nonlinear absorption and refraction conveniently. On the other hand, both degenerate and nondegenerate pump and probe beams in any polarization states can be used in this system. The nonlinear optical properties of tetrasulfonated copper phthalocyanine dissolved in dimethyl sulfoxide solution are investigated by using this system.

Sensitive Detection of Multiple Rotavirus Genotypes with a Single Reverse Transcription-Real-Time Quantitative PCR Assay

Rotaviruses are one of the major causes of diarrhea in infants and children under 5 years old, especially affecting developing countries. In natural disasters, fecal matter and potable waters can mix, allowing low, yet infective, concentrations of rotavirus to be present in water supplies, constituting a risk for the population. Any of the most commonly detected rotavirus genotypes could originate an outbreak. The development of a fast and sensitive method that could detect the broadest possible range of rotavirus genotypes would help with efficient diagnosis and prevention. We have designed a reverse transcription (RT)-real-time quantitative PCR approach targeted to the rotaviral VP2 gene, based on a multiple-sequence alignment of different human rotaviral strains. To overcome the high nucleotide sequence diversity, multiple forward and reverse primers were used, in addition to a degenerate probe. The performance of the assay was tested on isolates representing the most prevalent human genotypes: G1P[8], G2P[4], G3P[8], G4P[8], G9P[8], and G12P[8]. The developed method improved classical rotavirus detection by enzyme-linked immunosorbent assay and nested RT-PCR by 5 and at least 1 order of magnitude, respectively. A survey of 159 stool samples indicated that the method can efficiently detect a broad range of rotavirus strains, including different G-P genotype combinations of human, porcine, and bovine origin. No cross-reactivity was observed with other enteric viruses, such as astrovirus, sapovirus, and norovirus.

Time-resolved pump-probe system based on a nonlinear imaging technique with phase object

A nonlinear imaging technique with phase object, which can deduce nonlinear absorption and refraction coefficients by single laser-shot exposure, is expanded to a time-resolved pump-probe system by introducing a pump beam with a variable temporal delay. This new system, in which both degenerate and nondegenerate pump and probe beams in any polarization states can be used, can simultaneously measure dynamic nonlinear absorption and refraction conveniently. In addition, the sensitivity of this new pump-probe system is more than twice that of the Z-scan-based system. The semiconductor ZnSe is used to demonstrate this system.

Development of combined DNA-based piezoelectric biosensors for the simultaneous detection and genotyping of high risk Human Papilloma Virus strains

BackgroundHuman Papilloma Virus (HPV) is a DNA virus belonging to the Papovavirus family. Genital HPV types have been subdivided into medium-low risk, and high-risk (HPV 16 and 18), frequently associated with cervical cancer. Three DNA-based piezoelectric biosensors were here developed for a quick detection and genotyping of HPV. MethodsWe developed a method for the detection and genotyping of HPV in human cervical scraping samples based on coupling DNA piezoelectric sensors with Polymerase Chain Reaction (PCR). The novelty of this work was the design and immobilisation of a degenerate probe (chosen in a conserved region of the viral genome) for the simultaneous detection of 16 virus strains and of two specific probes (chosen in a less-conserved region of the viral genome) for genotyping. ResultsThe three biosensors were optimised with synthetic oligonucleotides with good reproducibility (HPVdeg CV% av 9%, HPV16 CV%av 9%; HPV18 CV%av 11%) with a detection limit of 50 nM. Cervical scraping samples after PCR amplification (in 40–200 nM range), were tested without the need of label with high selectivity and reproducibility. The results were in agreement with a reference method used in routinary analysis. ConclusionPiezoelectric biosensors have proven to be suitable for detection and genotyping of HPV.