Alginate oligosaccharide assimilation by gut microorganisms and the potential role in gut inflammation alleviation.

Dietary fiber metabolism by gut microorganisms plays important roles in host physiology and health. Alginate, the major dietary fiber of daily diet seaweeds, is drawing more attention because of multiple biological activities. To advance the understanding of alginate assimilation mechanism in the gut, we show the presence of unsaturated alginate oligosaccharides (uAOS)-specific alginate utilization loci (AUL) in human gut microbiome. As a representative example, a working model of the AUL from the gut microorganism Bacteroides clarus was reconstructed from biochemistry and transcriptome data. The fermentation of resulting monosaccharides through Entner-Doudoroff pathway tunes the metabolism of short-chain fatty acids and amino acids. Furthermore, we show that uAOS feeding protects the mice against dextran sulfate sodium-induced acute colitis probably by remodeling gut microbiota and metabolome. IMPORTANCE: Alginate has been included in traditional Chinese medicine and daily diet for centuries. Recently discovered biological activities suggested that alginate-derived alginate oligosaccharides (AOS) might be an active ingredient in traditional Chinese medicine, but how these AOS are metabolized in the gut and how it affects health need more information. The study on the working mechanism of alginate utilization loci (AUL) by the gut microorganism uncovers the role of unsaturated alginate oligosaccharides (uAOS) assimilation in tuning short-chain fatty acids and amino acids metabolism and demonstrates that uAOS metabolism by gut microorganisms results in a variation of cell metabolites, which potentially contributes to the physiology and health of gut.

Tailoring nondiffracting fields with a non-Markovian phase imprint.

We experimentally generate nondiffracting speckles that carry non-Markovian properties by encoding the wavefront of a monochromatic laser beam with ring-shaped non-Markovian phases. The resulting non-Markovian nondiffracting fields present a ring-shaped pattern and central dark notches, which are analyzed with an expression of the orbital angular momentum spectra of the wavefront possessing ring-shaped non-Markovian phases. Furthermore, we demonstrate that the intensity profiles of these non-Markovian nondiffracting fields exhibit stability over multiple Rayleigh ranges, and their statistical properties could be controlled with the non-Markovianity of the input phase masks. This work presents an approach for simultaneously tailoring the diffracting property and non-Markovianity of optical fields and provides a deeper understanding of non-Markovian processes.

Magnon-Skyrmion Hybrid Quantum Systems: Tailoring Interactions via Magnons.

Coherent and dissipative interactions between different quantum systems are essential for the construction of hybrid quantum systems and the investigation of novel quantum phenomena. Here, we propose and analyze a magnon-skyrmion hybrid quantum system, consisting of a micromagnet and nearby magnetic skyrmions. We predict a strong-coupling mechanism between the magnonic mode of the micromagnet and the quantized helicity degree of freedom of the skyrmion. We show that with this hybrid setup it is possible to induce magnon-mediated nonreciprocal interactions and responses between distant skyrmion qubits or between skyrmion qubits and other quantum systems like superconducting qubits. This work provides a quantum platform for the investigation of diverse quantum effects and quantum information processing with magnetic microstructures.

Screening of astaxanthin-overproducing Xanthophyllomyces dendrorhous strains via iterative ARTP mutagenesis and cell sorting by flow cytometry.

AIMS: The astaxanthin-producing yeast Xanthophyllomyces dendrorhous is widely used in aquaculture. Due to the production of carotenoid, this yeast shows visible color; however, high-throughput approaches for identification of astaxanthin-overproducing strains remain rare. METHODS AND RESULTS: This study verified an effective approach to identify astaxanthin-overproducing mutants of X. dendrorhous by flow cytometry (FCM) and cell sorting. First, the mutant libraries were generated by atmospheric and room-temperature plasma (ARTP) mutagenesis. Second, a highly direct correlation between the concentrations of intracellular astaxanthin and the levels of emitting fluorescence was constructed by testing a variety of astaxanthin-contained populations via FCM and cell sorting. Third, iterative cell sorting efficiently improves the identification of astaxanthin-overproducing strains. Finally, two mutants producing 4.96 mg astaxanthin g-1 DCW (dry cell weight) and 5.30 mg astaxanthin g-1 DCW were obtained, which were 25.3% and 33.8% higher than that of the original strain, respectively. CONCLUSIONS: This study demonstrated that iterative ARTP mutagenesis along with cell sorting by FCM is effective for identifying astaxanthin-overproduction strains.

The horizontal gene transfer of perchlorate reduction genomic island in three bacteria from an ecological niche.

Three new strains of dissimilatory perchlorate-reducing bacteria (DPRB), QD19-16, QD1-5, and P3-1, were isolated from an active sludge. Phylogenetic trees based on 16S rRNA genes indicated that QD19-16, QD1-5, and P3-1 belonged to Brucella, Acidovorax, and Citrobacter, respectively, expanding the distribution of DPRB in the Proteobacteria. The three strains were gram-negative and facultative anaerobes with rod-shaped cells without flagella, which were 1.0-1.6 µm long and 0.5-0.6 µm wide. The three DPRB strains utilized similar broad spectrum of electron donors and acceptors and demonstrated a similar capability to reduce perchlorate within 6 days. The enzyme activity of perchlorate reductase in QD19-16 toward chlorate was higher than that toward perchlorate. The high sequence similarity of the perchlorate reductase operon and chlorite dismutase genes in the perchlorate reduction genomic islands (PRI) of the three strains implied that they were monophyletic origin from a common ancestral PRI. Two transposase genes (tnp1 and tnp2) were found in the PRIs of strain QD19-16 and QD1-5, but were absent in the strain P3-1 PRI. The presence of fragments of IR sequences in the P3-1 PRI suggested that P3-1 PRI had previously contained these two tnp genes. Therefore, it is plausible to suggest that a common ancestral PRI transferred across the strains Brucella sp. QD19-16, Acidovorax sp. QD1-5, and Citrobacter sp. P3-1 through horizontal gene transfer, facilitated by transposases. These results provided a direct evidence of horizontal gene transfer of PRI that could jump across phylogenetically unrelated bacteria through transposase. KEY POINTS: • Three new DPRB strains can effectively remove high concentration of perchlorate. • The PRIs of three DPRB strains are acquired from a single ancestral PRI. • PRIs are incorporated into different bacteria genome through HGT by transposase.

Spin Defects in hBN assisted by Metallic Nanotrenches for Quantum Sensing.

The omnipresence of hexagonal boron nitride (hBN) in devices embedding two-dimensional materials has prompted it as the most sought after platform to implement quantum sensing due to its testing while operating capability. The negatively charged boron vacancy (VB-) in hBN plays a prominent role, as it can be easily generated while its spin population can be initialized and read out by optical means at room-temperature. But the lower quantum yield hinders its widespread use as an integrated quantum sensor. Here, we demonstrate an emission enhancement amounting to 400 by nanotrench arrays compatible with coplanar waveguide (CPW) electrodes employed for spin-state detection. By monitoring the reflectance spectrum of the resonators as additional layers of hBN are transferred, we have optimized the overall hBN/nanotrench optical response, maximizing thereby the luminescence enhancement. Based on these finely tuned heterostructures, we achieved an enhanced DC magnetic field sensitivity as high as 6 × 10-5 T/Hz1/2.

Multi-target object scattering imaging with intensity correlation of structured illumination.

Imaging through scattering layers based on the optical memory effect (OME) concept has been widely investigated in recent years. Among many scattering scenarios, it is very important to recover hidden targets with proper spatial distribution in the scene where multiple targets out of the OME range exist. In this Letter, we put forward a method for multi-target object scattering imaging. With the help of intensity correlation between the structured illumination patterns and recorded speckle images, the relative position of all hidden targets can be obtained and the movement of the targets within the OME range can be tracked. We experimentally implement scattering imaging with 16 targets and the motion tracking of them. Our results present a significant advance in a large field of view scattering imaging with multiple targets.

Simultaneously improving the efficiencies of photo- and thermal isomerization of an oxindole-based light-driven molecular rotary motor by a structural redesign.

We designed a novel highly efficient light-driven molecular rotary motor theoretically by using electronic structure calculations and nonadiabatic dynamics simulations, and it showed excellent performance for both photo- and thermal isomerization processes simultaneously. By the small structural modification based on 3-(2,7-dimethyl-2,3-dihydro-1H-inden-1-ylidene)-1-methylindolin-2-one (DDIYM) synthesized by Feringa et al. recently, an oxindole-based light-driven molecular rotary motor, 3-(1,5-dimethyl-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene)-1-methylindolin-2-one (DDPYM), is proposed, which displays a significant electronic push-pull character and weak steric hindrance for double-bond isomerization. The newly designed motor DDPYM shows a remarkable improvement of the quantum yield for both EP → ZM and ZP → EM photoisomerization processes, compared to the original motor DDIYM. Furthermore, the rotary motion in photoisomerization processes of DDPYM behaves more like a pure axial rotational motion approximately, while that of DDIYM is an obvious precessional motion. The weakness of the steric hindrance reduces the energy barriers of the thermal helix EM → EP and ZM → ZP inversion steps, and would accelerate two ground-state isomerization steps significantly. Our results confirm the feasibility of simultaneously improving the efficiencies of photo- and thermal isomerization of oxindole-based light-driven molecular rotary motors and this design idea sheds light on the future development of more efficient molecular motors.

Distinct roles of carbohydrate-binding modules in multidomain ß-1,3-1,4-glucanase on polysaccharide degradation.

Lam16A is a novel GH16 ß-1,3-1,4-lichenase isolated from the genus Caldicellulosiruptor which can utilize untreated carbohydrate components of plant cell walls. Its catalytic module has been characterized that the six carbohydrate-binding modules (CBMs) were queued in the C-terminus, but their roles were still unclear. Here, full-length and CBM-truncated mutants of Lam16A were purified and characterized through heterologous expression in Escherichia coli. The profiles of these proteins, including the enzyme activity, degrading efficiency, substrate-binding affinity, and thermostability, were explored. Full-length Lam16A with six CBMs showed excellent thermostability and the highest activity against barley ß-glucan and laminarin with optimum pH of 6.5. The CBMs stimulated degrading ability of the catalytic module, especially against ß-1,3(4)-glucan-based polysaccharides. The released products from ß-1,3-1,4-glucan by Lam16A or its truncated mutants revealed an endo-type glycoside hydrolase. Lam16As exhibited strong binding affinities to the insoluble polysaccharides, especially Lam16A-1CBM. The degradation of yeast cell walls by Lam16A enzyme solution relative to the control reduced the absorbance values at OD800 by ~ 85% ± 1.2, enabling the release of up to ~ 0.057 ± 0.0039 µg/mL of the cytoplasmic protein into the supernatant, lowering the viability of the cells by ~ 70.3% ± 6.9, thus causing significant damage in the cell wall structure. Taken together, CBMs could influence the substrate specificity, thermal stability, and binding affinity of ß-1,3-1,4-glucanase. These results demonstrate the great potential of these enzymes to promote the bioavailability of ß-1,3-glucan oligosaccharides for health benefits. KEY POINTS: • Carbohydrate-binding modules strongly influenced the enzyme activity and binding affinity, and further impacted glycoside hydrolase activity. • Lam16A enzymes have sufficient ability to hydrolyze ß-1,3-1,4-glucan-based polysaccharides. • Lam16As provide a powerful tool to promote the bioavailability of ß-1,3-glucan oligosaccharides.

Quantum Interference of Resonance Fluorescence from Germanium-Vacancy Color Centers in Diamond.

Resonance fluorescence from a quantum emitter is an ideal source to extract indistinguishable photons. By using the cross-polarization to suppress the laser scattering, we observed resonance fluorescence from GeV color centers in diamond at cryogenic temperature. The Fourier-transform-limited line width emission with T2/2T1 ∼ 0.86 allows for two-photon interference based on single GeV color center. Under pulsed excitation, the separated photons exhibit a Hong-Ou-Mandel quantum interference above classical limit, whereas the continuous-wave excitation leads to a coalescence time window of 1.05 radiative lifetime. In addition, we demonstrated a single-shot readout of spin states with a fidelity of 74%. Our experiments lay down the foundation for building a quantum network with GeV color centers in diamond.

Towards fine recognition of orbital angular momentum modes through smoke.

Light beams carrying orbital angular momentum (OAM) have been constantly developing in free-space optical (FSO) communications. However, perturbations in the free space link, such as rain, fog, and atmospheric turbulence, may affect the transmission efficiency of this technique. If the FSO communications procedure takes place in a smoke condition with low visibility, the communication efficiency also will be worse. Here, we use deep learning methods to recognize OAM eigenstates and superposition states in a thick smoke condition. In a smoke transmission link with visibility about 5 m to 6 m, the experimental recognition accuracy reaches 99.73% and 99.21% for OAM eigenstates and superposition states whose Bures distance is 0.05. Two 6 bit/pixel pictures were also successfully transmitted in the extreme smoke conditions. This work offers a robust and generalized proposal for FSO communications based on OAM modes and allows an increase of the communication capacity under the low visibility smoke conditions.

Retrieving High-Dimensional Quantum Steering from a Noisy Environment with N Measurement Settings.

One of the most often implied benefits of high-dimensional (HD) quantum systems is to lead to stronger forms of correlations, featuring increased robustness to noise. Here, we experimentally demonstrate the n-setting linear HD quantum steering criterion. We verify the large violation of the steering inequalities without full-state tomography. The lower bound of the violation is 2.24±0.01 in 11 dimensions, exceeding the bound (V<2) of two-setting criteria. Hence, a higher strength of steering has been revealed. Moreover, we demonstrate the method for enhancing the noise robustness without increasing dimension, alternatively, by increasing measurement settings. Using the entanglement in 11 dimensions, we experimentally retrieve steering nonlocality with 63.4±1.4% isotropic noise fraction, surpassing the 50% limitation of two-setting criteria. Our Letter offers the potential for practical one-sided device-independent quantum information processing that tolerates the noisy environment, lossy detection, and transcends the present transmission distance limitation.

Design and Nonadiabatic Photoisomerization Dynamics Study of a Three-Stroke Light-Driven Molecular Rotary Motor.

Working cycle of conventional light-driven molecular rotary motors (LDMRMs), especially Feringa-type motors, usually have four steps, two photoisomerization steps, and two thermal helix inversion (THI) steps. THI steps hinder the ability of the motor to operate at lower temperatures and limit the rotation speed of LDMRMs. A three-stroke LDMRM, 2-(2,7-dimethyl-2,3-dihydro-1H-inden-1-ylidene)-1,2-dihydro-3H-pyrrol-3-one (DDIY), is proposed, which is capable of completing an unidirectional rotation by two photoisomerization steps and one thermal helix inversion step at room temperature. On the basis of trajectory surface-hopping simulation at the semi-empirical OM2/MRCI level, the EP→ZP and ZP→EM nonadiabatic photoisomerization dynamics of DDIY were systematically analyzed. Quantum yields of EP→ZP and ZP→EM photoisomerization of DDIY are ca. 34% and 18%, respectively. Both EP→ZP and ZP→EM photoisomerization processes occur on an ultrafast time scale (ca. 100-300 fs). This three-stroke LDMRM may stimulate further research for the development of new families of more efficient LDMRMs.

Effect of Temperature on Photoisomerization Dynamics of a Newly Designed Two-Stroke Light-Driven Molecular Rotary Motor.

The working mechanism of conventional light-driven molecular rotary motors, especially Feringa-type motors, contains two photoisomerization steps and two thermal helix inversion steps. Due to the existence of a thermal helix inversion step, both the ability to work at lower temperatures and the rotation speed are limited. In this work, a two-stroke light-driven molecular rotary motor, 2-(1,5-dimethyl-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene)-1,2-dihydro-3H-pyrrol-3-one (DDPY), is proposed, which is capable of performing unidirectional and repetitive rotation by only two photoisomerization (EP→ZP and ZP→EP) steps. With trajectory surface-hopping simulation at the semi-empirical OM2/MRCI level, the EP→ZP and ZP→EP nonadiabatic dynamics of DDPY were systematically studied at different temperatures. Both EP→ZP and ZP→EP photoisomerizations are on an ultrafast timescale (ca. 200-300 fs). The decay mode of EP→ZP photoisomerization is approximately bi-exponential, while that of ZP→EP photoisomerization is found to be periodic. For EP and ZP isomers of DDPY, after the S0→S1 excitation, the dynamical processes of nonadiabatic decay are both followed by twisting about the central C=C double bond and the pyramidalization of the C atom at the stator-axle linkage. The effect of temperature on the nonadiabatic dynamics of EP→ZP and ZP→EP photoisomerizations of DDPY has been systematically investigated. The average lifetimes of the S1 excited state and quantum yields for both EP→ZP and ZP→EP photoisomerization are almost temperature-independent, while the corresponding unidirectionality of rotation is significantly increased (e.g., 74% for EP→ZP and 72% for ZP→EP at 300 K vs 100% for EP→ZP and 94% for ZP→EP at 50 K) with lowering the temperature.

Structural basis for the exolytic activity of polysaccharide lyase family 6 alginate lyase BcAlyPL6 from human gut microbe Bacteroides clarus.

Alginate is the structural polysaccharide of the cell wall of brown algae, which is an important carbon source for marine life. The depolymerization of alginate is dependent on alginate lyases. Recent studies showed that the alginate utilization ability had been obtained by human gut microbes. In contrast to the great number of studies on alginate lyases from marine/soil organisms, studies on alginate lyases from gut microbes are still limited. Here, the structure of a polysaccharide lyase family 6 (PL6) alginate lyase from human gut microbe Bacteroides clarus was solved by X-ray crystallography, which represents the cluster of two-domain PL6 alginate lyases from Bacteroidetes. Similar with the two-domain alginate lyase AlyGC originated from marine bacterium, both the N terminal domain (NTD) and C terminal domain (CTD) of BcAlyPL6 show right-handed parallel ß-helix fold. However, unlike AlyGC, which forms a homodimer, BcAlyPL6 functions as a monomer. Biochemical analysis indicates that the substrate binding affinity is mainly contributed by the NTD while the CTD of BcAlyPL6 is involved in the formation of -1 subsite, which is essential for substrate turnover rate. Furthermore, CTD is involved in shaping a closed catalytic pocket, and deletion of it leads to increased activity towards highly polymerized substrate. Structure comparison of PL6 family alginate lyases implies that the linkers of two-domain alginate lyases might have evolutionary relationship with the N/C terminal extension of single-domain lyases.

Observing two-photon subwavelength interference of broadband chaotic light in a polarization-selective Michelson interferometer.

We demonstrated a method to achieve the two-photon subwavelength effect of true broadband chaotic light in polarization-selective Michelson interferometer based on two-photon absorption detection. To our knowledge, it is the first time that this effect has been observed with broadband chaotic light. In theory, the two-photon polarization coherence matrix and probability amplitudes matrix are combined to develop polarized two-photon interference terms, which explains the experimental results well. To make better use of this interferometer to produce the subwavelength effect, we also make a series of error analyses to find out the relationship between the visibility and the degree of polarization error. Our experimental and theoretical results contribute to the understanding of the two-photon subwavelength interference, which shed light on the development of the two-photon interference theory of vector light field based on quantum mechanics. The characteristic of the two-photon subwavelength effect have significant applications in temporal ghost imaging, such as it helps to improve the resolution of temporal objects.

Phase gradient protection of stored spatially multimode perfect optical vortex beams in a diffused rubidium vapor.

We experimentally investigate the optical storage of perfect optical vortex (POV) and spatially multimode perfect optical vortex (MPOV) beams via electromagnetically induced transparency (EIT) in a hot vapor cell. In particular, we study the role that phase gradients and phase singularities play in reducing the blurring of the retrieved images due to atomic diffusion. Three kinds of manifestations are enumerated to demonstrate such effect. Firstly, the suppression of the ring width broadening is more prominent for POVs with larger orbital angular momentum (OAM). Secondly, the retrieved double-ring MPOV beams' profiles present regular dark singularity distributions that are related to their vortex charge difference. Thirdly, the storage fidelities of the triple-ring MPOVs are substantially improved by designing line phase singularities between multi-ring MPOVs with the same OAM number but π offset phases between adjacent rings. Our experimental demonstration of MPOV storage opens new opportunities for increasing data capacity in quantum memories by spatial multiplexing, as well as the generation and manipulation of complex optical vortex arrays.

Experimentally measuring the mode indices of Laguerre-Gaussian beams by weak measurement.

As a special experimental technique, weak measurements extract very little information from the measured system and does not cause the measured state to collapse. When coupling the Laguerre-Gaussian (LG) state with a well-defined pre- and post-selected system of a weak measurement process, there will be an indirect interconnection between the expected value of coordinate operators of the final state and the mode indices of the measured LG state. The mode of the light is impacted very slightly after the weak measurement. Based on this we propose an experiment scheme and have managed to experimentally measure the mode indices of LG beams spanning from l = -6 to l = +6, p = 0 to p = +8 accurately with the final intensity distributions approximatly at their origin.

Optical storage of Ince-Gaussian modes in warm atomic vapor.

We report on the optical storage of Ince-Gaussian modes in a warm rubidium vapor cell based on electromagnetically induced transparency protocol, and we also qualitatively analyze how atomic diffusion affects the retrieved beams after storage. Ince-Gaussian modes possess very complex and abundant spatial structures and form a complete infinite-dimensional Hilbert space. Successfully storing such modes could open up possibilities for fundamental high-dimensional optical communication experiments.

Trans-spectral vector beam nonlinear conversion via parametric four-wave mixing in alkali vapor.

Coherent frequency conversion of vector beams (VBs) without distorting their intensity profile or spatial polarization distribution is important for novel applications in quantum and classical regimes. Here, we experimentally and theoretically investigate VB transfer from near-infrared to blue light using a Sagnac interferometer, combining the parametric four-wave mixing process in atomic vapor. The vector probe beam is converted into a completely different wavelength, and the vector mode of the generated blue beam is highly similar to the incident probe beam. These results may provide a feasible solution for communication interfaces in classical and quantum science fields based on atomic ensembles.