Phase-sensitive Mode Research Articles

Naphthopyran-based photoswitching for simpler chemical sensing and imaging using phase-sensitive mode

Naphthopyran-based photoswitching for simpler chemical sensing and imaging using phase-sensitive mode

Phase-resolved visualization of radio-frequency standing waves in superconducting spiral resonator for metamaterial applications

Superconducting microcircuits and metamaterials are promising candidates for use in new generation cryogenic electronics. Their functionality is largely justified by the macroscopic distribution of electromagnetic fields in arranged unit cells, rather than by the microscopic properties of composite materials. We present a new method for visualizing the spatial structure of penetrating microwaves with microscopic resolution in planar superconducting macroscopic resonators as the most important circuit-forming elements of modern microelectronics. This method uses a low-temperature laser scanning microscope that examines the phase (i.e., direction) and amplitude of local radio-frequency currents versus the two-dimensional coordinates of the superconducting resonant structure under test. Phase-sensitive contrast is achieved by synchronizing the intensity-modulated laser radiation with the resonant harmonics of the microwave signal passing through the sample. In this case, the laser-beam-induced loss in the illuminated area will strongly depend on the local phase difference between the RF carrier signal and the spatially temporal structure of the focused laser oscillation. This approach eliminates the hardware limitations of the existing technique of radio-frequency microscopy and brings the phase-sensitive demodulation mode to the level necessary for studying the physics of superconducting metamaterials. The advantage of the presented method over the previous method of RF laser scanning micros-copy is demonstrated by the example of the formation of standing waves in a spiral superconducting Archimedean resonator up to the 38th eigenmode resonance.

Digital ocular swept source optical coherence aberrometry.

Ocular aberrometry is an essential technique in vision science and ophthalmology. We demonstrate how a phase-sensitive single mode fiber-based swept source optical coherence tomography (SS-OCT) setup can be employed for quantitative ocular aberrometry with digital adaptive optics (DAO). The system records the volumetric point spread function at the retina in a de-scanning geometry using a guide star pencil beam. Succeeding test-retest repeatability assessment with defocus and astigmatism analysis on a model eye within ± 3 D dynamic range, the feasibility of technique is demonstrated in-vivo at a B-scan rate of >1 kHz in comparison with a commercially available aberrometer.

Cavity-induced coherence phenomena in a Josephson parametric amplifier

By adjusting the frequency of the cavity, we perform a microwave reflection measurement and directly probe the coherence and interference effects in a phase-sensitive Josephson parametric amplifier. We demonstrate the shift in the peak and the dip in the reflection spectra of the amplifier, which operates in the phase-sensitive mode. The behavior of the shift can be precisely controlled by tuning the pump power, the frequency of the cavity, and the relative phase between the incident signal and pump field. Theoretical simulations are in good agreement with the experimental results. These results provide an alternative way of controlling the parametric process by adjusting the frequency of the cavity.

Scheme features of radio pulse gating for radar measurements

The model of a radio pulse stroboscopic converter consisting of a mixer and a narrowband filter tuned to the difference frequency of the carrier signals is considered. We demonstrate that the measurement of the phase structure of the input signals can be made at low frequency by amplitude methods by changing the phase both in the channel of the gating radio pulses and in the low frequency channel. The radio-pulse gating scheme goes into a phase-sensitive mode when the system clock frequency is synchronized with the second harmonic of the difference frequency, however, in this case, a parasitic phase modulation occurs in the converted signal, which does not depend on the transformation coefficient of the spectrum and is determined only by the duty cycle of the input signal. To eliminate parasitic modulation, which distorts the envelope of the output signal of the converter in a phase-sensitive mode, it is proposed to use an auto-shift circuit with a falling “slow” sawtooth voltage when generating gating radio pulses.

Demonstration of Ultra Wideband Phase-Sensitive Fiber Optical Parametric Amplifier

This letter demonstrates the capability of fiber optical parametric amplifiers, in phase-sensitive mode, to provide low-noise amplification over a bandwidth in excess of 170 nm, with the cutoff set as minimum gain of 10 dB. We have measured both gain and noise figure for two different lengths of the gain medium offering diverse gain profiles. Noise figure measurements confirm ultra-low noise operation along the four telecom bands— namely $S$ -, $C$ -, $L$ -, and U-band. Electrical noise figures for a limited wavelength range were also measured to confirm the measured optical noise figures.

A Bifunctional Glycosyltransferase from Agrobacterium tumefaciens Synthesizes Monoglucosyl and Glucuronosyl Diacylglycerol under Phosphate Deprivation

Glycolipids are mainly found in phototrophic organisms (like plants and cyanobacteria), in Gram-positive bacteria, and a few other bacterial phyla. Besides the function as bulk membrane lipids, they often play a role under phosphate deprivation as surrogates for phospholipids. The Gram-negative Agrobacterium tumefaciens accumulates four different glycolipids under phosphate deficiency, including digalactosyl diacylglycerol and glucosylgalactosyl diacylglycerol synthesized by a processive glycosyltransferase. The other two glycolipids have now been identified by mass spectrometry and nuclear magnetic resonance spectroscopy as monoglucosyl diacylglycerol and glucuronosyl diacylglycerol. These two lipids are synthesized by a single promiscuous glycosyltransferase encoded by the ORF atu2297, with UDP-glucose or UDP-glucuronic acid as sugar donors. The transfer of sugars differing in their chemistry is a novel feature not observed before for lipid glycosyltransferases. Furthermore, this enzyme is the first glucuronosyl diacylglycerol synthase isolated. Deletion mutants of Agrobacterium lacking monoglucosyl diacylglycerol and glucuronosyl diacylglycerol or all glycolipids are not impaired in growth or virulence during infection of tobacco leaf discs. Our data suggest that the four glycolipids and the nonphospholipid diacylglyceryl trimethylhomoserine can mutually replace each other during phosphate deprivation. This redundancy of different nonphospholipids may represent an adaptation mechanism to enhance the competitiveness in nature.

Generation of propagating backward volume spin waves by phase-sensitive mode conversion in two-dimensional microstructures

We present the generation of propagating backward volume (BV) spin waves in a T shaped Ni81Fe19 microstructure. These waves are created from counterpropagating Damon Eshbach spin waves, which are excited using microstrip antennas. By employing Brillouin light scattering microscopy, we show how the phase relation between the counterpropagating waves determines the mode generated in the center of the structure, and prove its propagation inside the longitudinally magnetized part of the T shaped microstructure. This gives access to the effective generation of backward volume spin waves with full control over the generated transverse mode.

Noise figure of hybrid optical parametric amplifiers

Following a fiber optical parametric amplifier, used as a wavelength converter or in the phase-sensitive mode, by a phase-insensitive amplifier (PIA) can significantly reduce four-wave mixing between signals in broadband systems. We derive the quantum mechanical noise figures (NF) for these two hybrid configurations, and show that adding the PIA only leads to a moderate increase in NF.

Discrete mode tuning in terahertz quantum cascade lasers

A holographically designed, aperiodic distributed feedback grating is used as a multi-resonance filter and embedded within an existing Fabry-Pérot (FP) terahertz (THz) quantum cascade laser (QCL) cavity. Balancing the feedback strengths of the filter resonances and the FP cavity creates a system capable of a high degree of single-mode selectivity, which is sensitive to changes in driving current. Multi-moded QCLs operating around 2.9 THz are thus modified to achieve purely electronic discrete tuning spanning over 160 GHz with an average tuning resolution of 30 GHz. Applying the same multi-resonance filter to QCLs with gain peaks around 2.65 and 2.9 THz leads to dual-mode lasing with an electrically controlled frequency separation of between 190 and 267 GHz. A phase sensitive mode selection mechanism is experimentally confirmed by the observation of divergent fine-tuning of the lasing modes.

Reprint of “Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurements of 1H–1H spin–spin coupling constants in proteins”

Two-dimensional correlated spectroscopy (COSY) is used for measurements of proton-proton spin-spin coupling constants in protein 1H NMR spectra. High digital resolution along the frequency axis ω2 is achieved by placing the carrier frequency in the center of the spectrum, using quadrature detection in both dimensions and presenting the spectrum in the phase sensitive mode. Compared to other techniques for studies of spin-spin coupling constants, COSY provides greatly improved spectral resolution. This is illustrated by experiments with H2O solutions of the small globular protein BUSI IIA (bull seminal inhibitor IIA).

The Use of Coupled HSQC Spectra to Aid in Stereochemical Assignments of Molecules with Severe Proton Spectral Overlap

A simple glycoside with only 13 carbons exhibited extensive overlapping of four of the glycosidic protons, causing extreme difficulty in the determination of the stereochemistry of the pyranose unit. However, acquisition of a high-resolution coupled heteronuclear single-quantum coherence (HSQC) spectrum overcame this problem. This spectrum provides a useful method for determining vicinal proton coupling constants between strongly coupled protons. To show the potential of high-resolution coupled HSQC spectra in overcoming spectral overlap. The sample was obtained by methanol extraction, followed by fractionation and column chromatography of the dried leaves of Montrichardia arborescens (Araceae). NMR spectra were obtained on 1.5 mg of sample dissolved in 120 μL of CD₃OD containing 0.1% trimethylsilyl (TMS) as internal standard. A gradient-selected HSQC spectrum was obtained using standard Varian library pulse sequences in phase sensitive mode. The high-resolution coupled HSQC spectrum focused on the saccharide region with a 1025 Hz ¹H spectral window, a 6300 Hz ¹³C spectral window, 1024 data points, a 0.3 Hz relaxation delay, 384 time increments (linear predicted to 4096), and 80 scans per time increment. The use of a high-resolution coupled HSQC spectrum allowed determination of the coupling patterns of the various pyranose protons with sufficient accuracy. This enabled completion of the assignments and identification of the pyranose unit as glucose. The study has shown the effectiveness of the use of a high-resolution coupled HSQC spectrum in the assignment of molecules with severe spectral overlap.

Hard-X-Ray Phase-Difference Microscopy Using a Fresnel Zone Plate and a Transmission Grating

Novel hard x-ray phase imaging microscopy that simply uses an objective and a transmission grating is described. The microscope generated an image that exhibited twin features of a sample with an opposite phase contrast having a separation of a specific distance. Furthermore, the twin features were processed to generate an image mapping the x-ray phase shift through a simple algorithm. The presence of the grating did not degrade the spatial resolution of the microscope. The sensitivity of our microscope to light elements was about 2 orders of magnitude higher than that of the absorption contrast microscope that was attained by simply removing the grating. Our method is attractive for easily appending a quantitative phase-sensitive mode to normal x-ray microscopies, and it has potentially broad applications in biology and material sciences.

Role of Conserved Salt Bridges in Homeodomain Stability and DNA Binding

The sequence information available for homeodomains reveals that salt bridges connecting pairs 19/30, 31/42, and 17/52 are frequent, whereas aliphatic residues at these sites are rare and mainly restricted to proteins from homeotherms. We have analyzed the influence of salt and hydrophobic bridges at these sites on the stability and DNA binding properties of human Hesx-1 homeodomain. Regarding the protein stability, our analysis shows that hydrophobic side chains are clearly preferred at positions 19/30 and 31/42. This stabilizing influence results from the more favorable packing of the aliphatic side chains with the protein core, as illustrated by the three-dimensional solution structure of a thermostable variant, herein reported. In contrast only polar side chains seem to be tolerated at positions 17/52. Interestingly, despite the significant influence of pairs 19/30 and 31/42 on the stability of the homeodomain, their effect on DNA binding ranges from modest to negligible. The observed lack of correlation between binding strength and conformational stability in the analyzed variants suggests that salt/hydrophobic bridges at these specific positions might have been employed by evolution to independently modulate both properties.

Numerical studies of multimodal phase-sensitive parametric amplification

In the presence of a nonzero idler beam or, equivalently, in the collinear degenerate configuration, optical parametric amplification (OPA) can be phase sensitive. When the photon deamplification mode is selected in the OPA process, amplification of the optical phase occurs instead of the usual amplification of photon number. We demonstrate for the first time, to the best of our knowledge, that the operation of a spatially multimodal optical parametric amplifier in the phase-sensitive mode can result in a significant redistribution of spatial frequencies and near-ideal beam angle amplification. A numerical model is presented for phase-sensitive parametric amplification via three-wave mixing. The model is applied to monochromatic beams and finite beam apertures. The sensitivity of gain to the incident phase, noncollinear angle, and aperture size is studied in particular. Simple conditions are derived for the operation of the optical parametric amplifier in the phase-sensitive mode. Potential applications of the concept are discussed.

Inhibition of Neuronal Nicotinic Acetylcholine Receptor Subtypes by α-Conotoxin GID and Analogues

alpha-Conotoxins are small disulfide-rich peptides from the venom of the Conus species that target the nicotinic acetylcholine receptor (nAChR). They are valuable pharmacological tools and also have potential therapeutic applications particularly for the treatment of chronic pain. alpha-Conotoxin GID is isolated from the venom of Conus geographus and has an unusual N-terminal tail sequence that has been shown to be important for binding to the alpha4beta2 subtype of the nAChR. To date, only four conotoxins that inhibit the alpha4beta2 subtype have been characterized, but they are of considerable interest as it is the most abundant nAChR subtype in the mammalian brain and has been implicated in a range of diseases. In this study, analysis of alanine-scan and truncation mutants of GID reveals that a conserved proline in alpha-conotoxins is important for activity at the alpha7, alpha3beta2, and alpha4beta2 subtypes. Although the proline residue was the most critical residue for activity at the alpha3beta2 subtype, Asp(3), Arg(12), and Asn(14) are also critical at the alpha7 subtype. Interestingly, very few of the mutations tested retained activity at the alpha4beta2 subtype indicating a tightly defined binding site. This lack of tolerance to sequence variation may explain the lack of selective ligands discovered for the alpha4beta2 subtype to date. Overall, our findings contribute to the understanding of the structure-activity relationships of alpha-conotoxins and may be beneficial for the ongoing attempts to exploit modulators of the neuronal nAChRs as therapeutic agents.

The Identification and Location of Succinyl Residues and the Characterization of the Interior Arabinan Region Allow for a Model of the Complete Primary Structure of Mycobacterium tuberculosis Mycolyl Arabinogalactan

The complex cell wall of Mycobacterium tuberculosis is the hallmark of acid fast bacteria and is responsible for much of its physiological characteristics. Hence, much effort has been made to determine its primary structure. Such studies have been hampered by its extreme complexity. Also, its insolubility leads to difficulties determining the presence or absence of base labile groups. We have used an endogenous arabinase to solubilize the arabinan region of the cell wall and have shown using mass spectrometry and NMR that succinyl esters are present on O2 of the inner-branched 1,3,5-alpha-d-arabinofuranosyl residues. In addition, an inner arabinan region of 14 linear alpha-1,5 arabinofuranosyl residues has been identified. These and earlier results now allow the presentation of a model of the entire primary structure of the mycobacterial mycolyl arabinogalactan highlighted by three arabinan chains of 31 residues each.

Conopressin-T from Conus tulipa Reveals an Antagonist Switch in Vasopressin-like Peptides

We report the discovery of conopressin-T, a novel bioactive peptide isolated from Conus tulipa venom. Conopressin-T belongs to the vasopressin-like peptide family and displays high sequence homology to the mammalian hormone oxytocin (OT) and to vasotocin, the endogenous vasopressin analogue found in teleost fish, the cone snail's prey. Conopressin-T was found to act as a selective antagonist at the human V 1a receptor. All peptides in this family contain two conserved amino acids within the exocyclic tripeptide (Pro7 and Gly9), which are replaced with Leu7 and Val9 in conopressin-T. Whereas conopressin-T binds only to OT and V 1a receptors, an L7P analogue had increased affinity for the V 1a receptor and weak V2 receptor binding. Surprisingly, replacing Gly9 with Val9 in OT and vasopressin revealed that this position can function as an agonist/antagonist switch at the V 1a receptor. NMR structures of both conopressin-T and L7P analogue revealed a marked difference in the orientation of the exocyclic tripeptide that may serve as templates for the design of novel ligands with enhanced affinity for the V 1a receptor.

Engineered Sarafotoxins as Tissue Inhibitor of Metalloproteinases-like Matrix Metalloproteinase Inhibitors

The sarafotoxins and endothelins are approximately 25-residue peptides that spontaneously fold into a defined tertiary structure with specific pairing of four cysteines into two disulfide bonds. Their structures show an interesting topological similarity to the core of the metalloproteinase interaction sites of the tissue inhibitors of metalloproteinases. Previous work indicates that sarafotoxins and endothelins can be engineered to eliminate or greatly reduce their vasopressive action and that their structural framework can withstand multiple sequence changes. When sarafotoxin 6b, which possesses modest matrix metalloproteinase inhibitory activity, was C-terminally truncated to remove its toxic vasopressive activity, the metalloproteinase inhibitory activity was essentially abolished. However, further changes, based on the sequences of peptides selected from libraries of sarafotoxin variants or suggested by analogy with tissue inhibitors of metalloproteinases, progressively enhanced the matrix metalloproteinase inhibitory activity. Peptide variants with multiple substitutions folded correctly and formed native disulfide bonds. Improvements in matrix metalloproteinase affinity have generated a peptide with micromolar K(i) values for matrix metalloproteinase-1 and -9 that are selective inhibitors of different metalloproteinases. Characterization of its solution structure indicates a close similarity to sarafotoxin but with a more extended C-terminal helix. The effects of N-acetylation and other changes, as well as docking studies, support the hypothesis that the engineered sarafotoxins bind to matrix metalloproteinases in a manner analogous to the tissue inhibitors of metalloproteinases.

Comparison of Lipoteichoic Acid from Different Serotypes of Streptococcus pneumoniae

Pneumococcal lipoteichoic acid (LTA) is known to have a completely different chemical structure compared with that of Staphylococcus aureus: the polyglycerophosphate in the backbone is replaced in the pneumococcal LTA by a pentamer repeating unit consisting of one ribitol and a tetrasaccharide carrying the unusual substituents phosphocholine and N-acetyl-D-galactosamine. Neither D-alanine nor N-acetyl-D-glucosamine, which play central roles in the biological activity of the staphylococcal LTA, has been reported. The extraction using butanol is more gentle compared with the previously reported chloroform-methanol extraction and results in a higher yield of LTA. We characterized the LTA of two different strains of Streptococcus pneumoniae:R6 (serotype 2) and Fp23 (serotype 4). NMR analysis confirmed the structure of LTA from R6 but showed that its ribitol carries an N-acetyl-D-galactosamine substituent. The NMR data for the LTA from Fp23 indicate that this LTA additionally contains ribitol-bound D-alanine. Dose-response curves of the two pneumococcal LTAs in human whole blood revealed that LTA from Fp23 was significantly more potent than LTA from R6 with regard to the induction of all cytokines measured (tumor necrosis factor, interleukin-1 (IL-1), IL-8, IL-10, granulocyte colony-stimulating factor, and interferon gamma). However, other characteristics, such as lack of inhibition by endotoxin-specific LAL-F, Toll-like receptor 2 and not 4 dependence, and lack of stimulation of neutrophilic granulocytes, were shared by both LTAs. This is the first report of a difference in the structure of LTA between two pneumococcal serotypes resulting in different immunostimulatory potencies.