MolPhase, an advanced prediction algorithm for protein phase separation.

We introduce MolPhase, an advanced algorithm for predicting protein phase separation (PS) behavior that improves accuracy and reliability by utilizing diverse physicochemical features and extensive experimental datasets. MolPhase applies a user-friendly interface to compare distinct biophysical features side-by-side along protein sequences. By additional comparison with structural predictions, MolPhase enables efficient predictions of new phase-separating proteins and guides hypothesis generation and experimental design. Key contributing factors underlying MolPhase include electrostatic pi-interactions, disorder, and prion-like domains. As an example, MolPhase finds that phytobacterial type III effectors (T3Es) are highly prone to homotypic PS, which was experimentally validated in vitro biochemically and in vivo in plants, mimicking their injection and accumulation in the host during microbial infection. The physicochemical characteristics of T3Es dictate their patterns of association for multivalent interactions, influencing the material properties of phase-separating droplets based on the surrounding microenvironment in vivo or in vitro. Robust integration of MolPhase's effective prediction and experimental validation exhibit the potential to evaluate and explore how biomolecule PS functions in biological systems.

Molecular Mechanism Analysis of STIM1 Thermal Sensation.

STIM1 has been identified as a new warm sensor, but the exact molecular mechanism remains unclear. In this study, a variety of mutants of STIM1, Orai1 and Orai3 were generated. The single-cell calcium imaging and confocal analysis were used to evaluate the thermal sensitivity of the resulting STIM mutants and the interaction between STIM1 and Orai mutants in response to temperature. Our results suggested that the CC1-SOAR of STIM1 was a direct activation domain of temperature, leading to subsequent STIM1 activation, and the transmembrane (TM) region and K domain but not EF-SAM were needed for this process. Furthermore, both the TM and SOAR domains exhibited similarities and differences between STIM1-mediated thermal sensation and store-operated calcium entry (SOCE), and the key sites of Orai1 showed similar roles in these two responses. Additionally, the TM23 (comprising TM2, loop2, and TM3) region of Orai1 was identified as the key domain determining the STIM1/Orai1 thermal response pattern, while the temperature reactive mode of STIM1/Orai3 seemed to result from a combined effect of Orai3. These findings provide important support for the specific molecular mechanism of STIM1-induced thermal response, as well as the interaction mechanism of STIM1 with Orai1 and Orai3 after being activated by temperature.

A ratiometric luminescence probe for selective detection of Ag+ based on thiolactic acid-capped gold nanoclusters with near-infrared emission and employing bovine serum albumin as a signal amplifier.

When thiolactic acid-capped gold nanoclusters (AuNCs@TLA) with strong near-infrared (NIR, 800 nm) emission were applied to detect metal ions, only Ag+ induced the generation of two new emission peaks at 610 and 670 nm in sequence and quenching the original NIR emission. The new peak at 670 nm generated after the 800-nm emission disappeared utterly. The ratiometric and turn-on responses showed different linear concentration ranges (0.10-4.0 µmol·L-1 and 10-50 µmol·L-1) toward Ag+, and the limit of detection (LOD) was 40 nmol·L-1. Especially, the probe exhibited extremely high selectivity and strong anti-interference from other metal ions. Mechanism studies showed that the novel responses were attributed to the anti-galvanic reaction of AuNCs to Ag+ and formation of bimetallic nanoclusters. The two new emission peaks were due to the composition change and size growth of the metal core. Besides, bovine serum albumin (BSA) has been employed as a signal amplifier based on the assembly-induced emission enhancement properties of AuNCs, which improved the LOD to 10 nmol·L-1. Moreover, the ratiometric method is feasible for Ag+ detection in diluted serum with high recovery rates, showing large application potential in the biological system. The present study supplies a novel ratiometric probe for Ag+ with a two-stage response and provides a novel signal amplifier of BSA, which will facilitate and promote the application of NIR-emitted metal nanoclusters in biological system.

Time-Course Comparative Metabolome Analysis of Different Barley Varieties during Malting.

Malt production is one of the important uses of barley, and its quality differs greatly depending on the barley varieties used. In this study, ultraperformance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry technology was used to investigate the temporal changes of metabolites during malting in two barley varieties: Franklin (malt barley) and Yerong (non-malt barley). Also, differences in metabolite profiles were compared in the kilned malt between two other malt barley varieties (Copeland and Planet) and two non-malt varieties (ZD10 and Hua30). Results showed that degradation of trisaccharide and accumulation of UDP-glucose and mannose-1-phosphate are the key metabolic events during steeping, with Franklin showing earlier and greater changes. Earlier increase of sugars and amino acids in Franklin is associated with its faster germination rate. Comparative metabolome analysis of kilned malt from the different barley varieties indicated that malt barley accumulated more sugars, hordatine-glucoside, and oxoproline, and non-malt barley accumulated more polyphenols and monogalactosylmonoacylglycerol. These results improved the understanding of the genotypic difference in the formation of malt quality at the metabolomic level.

Observation of three-photon bound states in a quantum nonlinear medium.

Bound states of massive particles, such as nuclei, atoms, or molecules, constitute the bulk of the visible world around us. By contrast, photons typically only interact weakly. We report the observation of traveling three-photon bound states in a quantum nonlinear medium where the interactions between photons are mediated by atomic Rydberg states. Photon correlation and conditional phase measurements reveal the distinct bunching and phase features associated with three-photon and two-photon bound states. Such photonic trimers and dimers possess shape-preserving wave functions that depend on the constituent photon number. The observed bunching and strongly nonlinear optical phase are described by an effective field theory of Rydberg-induced photon-photon interactions. These observations demonstrate the ability to realize and control strongly interacting quantum many-body states of light.

Symmetry-protected collisions between strongly interacting photons.

Realizing robust quantum phenomena in strongly interacting systems is one of the central challenges in modern physical science. Approaches ranging from topological protection to quantum error correction are currently being explored across many different experimental platforms, including electrons in condensed-matter systems, trapped atoms and photons. Although photon-photon interactions are typically negligible in conventional optical media, strong interactions between individual photons have recently been engineered in several systems. Here, using coherent coupling between light and Rydberg excitations in an ultracold atomic gas, we demonstrate a controlled and coherent exchange collision between two photons that is accompanied by a π/2 phase shift. The effect is robust in that the value of the phase shift is determined by the interaction symmetry rather than the precise experimental parameters, and in that it occurs under conditions where photon absorption is minimal. The measured phase shift of 0.48(3)π is in excellent agreement with a theoretical model. These observations open a route to realizing robust single-photon switches and all-optical quantum logic gates, and to exploring novel quantum many-body phenomena with strongly interacting photons.

Effects of parallelogram-shaped pavement markings on vehicle speed and safety of pedestrian crosswalks on urban roads in China.

The primary objective of this study was to evaluate the effects of parallelogram-shaped pavement markings on vehicle speed and crashes in the vicinity of urban pedestrian crosswalks. The research team measured speed data at twelve sites, and crash data at eleven sites. Observational cross-sectional studies were conducted to identify if the effects of parallelogram-shaped pavement markings on vehicle speeds and speed violations were statistically significant. The results showed that parallelogram-shaped pavement markings significantly reduced vehicle speeds and speed violations in the vicinity of pedestrian crosswalks. More specifically, the speed reduction effects varied from 1.89km/h to 4.41km/h with an average of 3.79km/h. The reduction in the 85th percentile speed varied from 0.81km/h to 5.34km/h with an average of 4.19km/h. Odds ratios (OR) showed that the parallelogram-shaped pavement markings had effects of a 7.1% reduction in the mean speed and a 6.9% reduction in the 85th percentile speed at the pedestrian crosswalks. The reduction of proportion of drivers exceeding the speed limit varied from 8.64% to 14.15% with an average of 11.03%. The results of the crash data analysis suggested that the use of parallelogram-shaped pavement markings reduced both the frequency and severity of crashes at pedestrian crosswalks. The parallelogram-shaped pavement markings had a significant effect on reducing the vehicle-pedestrian crashes. Two crash prediction models were developed for vehicle-pedestrian crashes and rear-end crashes. According to the crash models, the presence of parallelogram-shaped pavement markings reduced vehicle-pedestrian crashes at pedestrian crosswalks by 24.87% with a 95% confidence interval of [10.06-30.78%]. However, the model results also showed that the presence of parallelogram-shaped pavement markings increased rear-end crashes at pedestrian crosswalks by 5.4% with a 95% confidence interval of [0-11.2%].

Attractive photons in a quantum nonlinear medium.

The fundamental properties of light derive from its constituent particles--massless quanta (photons) that do not interact with one another. However, it has long been known that the realization of coherent interactions between individual photons, akin to those associated with conventional massive particles, could enable a wide variety of novel scientific and engineering applications. Here we demonstrate a quantum nonlinear medium inside which individual photons travel as massive particles with strong mutual attraction, such that the propagation of photon pairs is dominated by a two-photon bound state. We achieve this through dispersive coupling of light to strongly interacting atoms in highly excited Rydberg states. We measure the dynamical evolution of the two-photon wavefunction using time-resolved quantum state tomography, and demonstrate a conditional phase shift exceeding one radian, resulting in polarization-entangled photon pairs. Particular applications of this technique include all-optical switching, deterministic photonic quantum logic and the generation of strongly correlated states of light.

Quantum nonlinear optics with single photons enabled by strongly interacting atoms.

The realization of strong nonlinear interactions between individual light quanta (photons) is a long-standing goal in optical science and engineering, being of both fundamental and technological significance. In conventional optical materials, the nonlinearity at light powers corresponding to single photons is negligibly weak. Here we demonstrate a medium that is nonlinear at the level of individual quanta, exhibiting strong absorption of photon pairs while remaining transparent to single photons. The quantum nonlinearity is obtained by coherently coupling slowly propagating photons to strongly interacting atomic Rydberg states in a cold, dense atomic gas. Our approach paves the way for quantum-by-quantum control of light fields, including single-photon switching, all-optical deterministic quantum logic and the realization of strongly correlated many-body states of light.