Mechanism of transcriptional bursting in bacteria.

Transcription of highly expressed genes has been shown to occur in stochastic bursts. But the origin of such ubiquitous phenomenon has not been understood. Here, we present the mechanism in bacteria. We developed a high-throughput, in vitro, single-molecule assay to follow transcription on individual DNA templates in real time. We showed that positive supercoiling buildup on a DNA segment by transcription slows down transcription elongation and eventually stops transcription initiation. Transcription can be resumed upon gyrase binding to the DNA segment. Furthermore, using single-cell mRNA counting fluorescence in situ hybridization (FISH), we found that duty cycles of transcriptional bursting depend on the intracellular gyrase concentration. Together, these findings prove that transcriptional bursting of highly expressed genes in bacteria is primarily caused by reversible gyrase dissociation from and rebinding to a DNA segment, changing the supercoiling level of the segment.

Application of LAMP coupled with NALF for precise detection of mycoplasma pneumoniae.

Mycoplasma pneumoniae (MP),as the most commonly infected respiratory pathogen in community-acquired pneumonia in preschool children,has becoming a prominent factor affecting children's respiratory health.Currently, there is a lack of easy, rapid, and accurate laboratory testing program for MP infection, which causes comparatively difficulty for clinical diagnostic.Here,we utilize loop-mediated isothermal amplification (LAMP) to amplify and characterize the P1 gene of MP, combined with nucleic acid lateral flow (NALF) for fast and visuallized detection of MP.Furthermore, we evaluated and analyzed the sensitivity, specificity and methodological consistency of the method.The results showed that the limit of detection(LoD) of MP-LAMP-NALF assay was down to 100 copys per reaction and there was no cross-reactivity with other pathogens infected the respiratory system. The concordance rate between MP-LAMP-NALF assay with quantitative real-time PCR was 94.3 %,which exhibiting excellent testing performance.We make superior the turnaround time of the MP-LAMP-NALF assay, which takes only about 50 min. In addition, there is no need for precision instruments and no restriction on the laboratory site.Collectively, LAMP-NALF assay targeting the P1 gene for Mycoplasma pneumoniae detection was a easy, precise and visual test which could be widely applied in outpatient and emergency departments or primary hospitals.When further optimized, it could be used as "point-of-care testing" of pathogens or multiple testing for pathogens.

Enhanced Efflux Activity Facilitates Drug Tolerance in Dormant Bacterial Cells.

Natural variations in gene expression provide a mechanism for multiple phenotypes to arise in an isogenic bacterial population. In particular, a sub-group termed persisters show high tolerance to antibiotics. Previously, their formation has been attributed to cell dormancy. Here we demonstrate that bacterial persisters, under ß-lactam antibiotic treatment, show less cytoplasmic drug accumulation as a result of enhanced efflux activity. Consistently, a number of multi-drug efflux genes, particularly the central component TolC, show higher expression in persisters. Time-lapse imaging and mutagenesis studies further establish a positive correlation between tolC expression and bacterial persistence. The key role of efflux systems, among multiple biological pathways involved in persister formation, indicates that persisters implement a positive defense against antibiotics prior to a passive defense via dormancy. Finally, efflux inhibitors and antibiotics together effectively attenuate persister formation, suggesting a combination strategy to target drug tolerance.

Spatiotemporal Acoustic Vortex Beams with Transverse Orbital Angular Momentum.

Recently, the discovery of optical spatiotemporal (ST) vortex beams with transverse orbital angular momentum (OAM) has attracted increasing attention and is expected to extend the research scope and open new opportunities for practical applications of OAM states. The ST vortex beams are also applicable to other physical fields that involve wave phenomena, and here we develop the ST vortex concept in the field of acoustics and report the generation of Bessel-type ST acoustic vortex beams. The ST vortex beams are fully characterized using the scalar approach for the pressure field and the vector approach for the velocity field. We further investigate the transverse spreading effect and construct ST vortex beams with an ellipse-shaped spectrum to reduce the spreading effect. We also experimentally demonstrated the orthogonality relations between ST vortex beams with different charges. Our study successfully demonstrates the versatility of the acoustic system for exploring and discovering spatiotemporally structured waves, inspiring further investigation of exotic wave physics.

Comparison of joint awareness after total knee arthroplasty, medial unicompartmental knee arthroplasty, and high tibial osteotomy: a retrospective study.

INTRODUCTION: This study aimed to compare the Forgotten Joint Score-12(FJS) outcomes and the minimum clinically important difference (MCID) of the FJS after high tibial osteotomy (HTO), unicompartmental knee arthroplasty (UKA), and total knee arthroplasty (TKA) with short-term follow-up (at least 2 years). Another objective of the study is to investigate the factors influencing FJS. It is hypothesized that there are differences in FJS outcomes among the three procedures. METHODS: Patients who underwent HTO, UKA, and TKA from January 2016 to December 2020 and were followed up for a minimum of 2 years were included in the study. The FJS were analyses from a cohort of people who submitted data to two years. The preoperative and postoperative clinical outcomes were compared and evaluated the patient-related factor. The FJS scores were predicted using multiple linear regression analysis. Additionally, Patient's Joint Perception (PJP) questions were used as anchors to determine the achievement of the forgotten joint, and FJS MCID were calculated using the receiver operating characteristic curve (ROC). RESULTS: Three hundred eighty-nine patients were included in the final study, and there were 111 patients in HTO groups,128patients in UKA groups, and 150 patients in TKA groups. The mean follow-up was 47.0 months. There was a significant difference in the total FJS, between the HTO, UKA, and TKA groups (FJS:59.38 ± 7.25, 66.69 ± 7.44 and 56.90 ± 6.85, p < 0.001. We found the MCID of the FJS of HTO, UKA, and TKA were 63.54, 69.79, and 61.45, respectively. In multiple linear regression, younger age, and higher FS were significant predictors of better FJS. CONCLUSION: Medial UKA demonstrated lower patient awareness in comparison to HTO and TKA, as assessed by the FJS. Younger age and higher FS were identified as significant predictors of improved FJS, providing valuable guidance for surgical decision-making.

Finite element analysis of the mechanical strength of a new hip Spacer.

BACKGROUND AND OBJECTIVE: At present, the influence of the internal metallic endoskeleton of Spacer on the biomechanical strength of Spacer remains unclear. The aim of this study was to analyze the mechanical stability of a novel Spacer applying a annular skeleton that mimics the structure of trabecular bone using finite element methods. METHEDS: The femur models of three healthy individuals and skeletonless Spacer, K-Spacer, and AD-Spacer were assembled to create 15 3D models. Finite element analysis was performed in an Ansys Bench2022R1. Biomechanical parameters such as stress and strain of the Spacer, internal skeleton and femur were evaluated under three loads, which were applied with the maximum force borne by the hip joint (2100 N), standing on one leg (700 N), and standing on two legs (350 N). The mechanical properties of the new hip Spacer were evaluated. RESULT: The stresses on the medial and lateral surfaces of the AD-Spacer and K-Spacer were smaller than the stresses in the state without skeletal support. The maximum stresses on the medial and lateral surfaces of the AD-Spacer were smaller than those of the inserted K-Spacer, and the difference gradually increased with the increase of force intensity. When the skeleton diameter was increased from 3 to 4 mm, the stresses in the medial and lateral sides of the AD-Spacer and K-Spacer necks decreased. The stress of both skeletons was concentrated at the neck, but the stress of the annular skeleton was evenly distributed on the medial and lateral sides of the skeleton. The mean stress in the proximal femur was higher in femurs with K-Spacer than in femurs with AD-Spacer. CONCLUSIONS: AD-Spacer has lower stress and higher load-bearing capacity than K-Spacer, and the advantages of AD-Spacer are more obvious under the maximum load state of hip joint.

Improved A* Algorithm for Path Planning of Spherical Robot Considering Energy Consumption.

Spherical robots have fully wrapped shells, which enables them to walk well on complex terrains, such as swamps, grasslands and deserts. At present, path planning algorithms for spherical robots mainly focus on finding the shortest path between the initial position and the target position. In this paper, an improved A* algorithm considering energy consumption is proposed for the path planning of spherical robots. The optimization objective of this algorithm is to minimize both the energy consumption and path length of a spherical robot. A heuristic function constructed with the energy consumption estimation model (ECEM) and the distance estimation model (DEM) is used to determine the path cost of the A* algorithm. ECEM and DCM are established based on the force analysis of the spherical robot and the improved Euclidean distance of the grid map, respectively. The effectiveness of the proposed algorithm is verified by simulation analysis based on a 3D grid map and a spherical robot moving with uniform velocity. The results show that compared with traditional path planning algorithms, the proposed algorithm can minimize the energy consumption and path length of the spherical robot as much as possible.

Investigation of the Temperature Actions of Bridge Cables Based on Long-Term Measurement and the Gradient Boosted Regression Trees Method.

Cable-stayed bridges have been commonly used on high-speed railways. The design, construction, and maintenance of cable-stayed bridges necessitate an accurate assessment of the cable temperature field. However, the temperature fields of cables have not been well established. Therefore, this research aims to investigate the distribution of the temperature field, the time variability of temperatures, and the representative value of temperature actions in stayed cables. A cable segment experiment, spanning over one year, is conducted near the bridge site. Based on the monitoring temperatures and meteorological data, the distribution of the temperature field is studied, and the time variability of cable temperatures is investigated. The findings show that the temperature distribution is generally uniform along the cross-section without a significant temperature gradient, while the amplitudes of the annual cycle variation and daily cycle variation in temperatures are significant. To accurately determine the temperature deformation of a cable, it is necessary to consider both the daily temperature fluctuations and the annual cycle of uniform temperatures. Then, using the gradient boosted regression trees method, the relationship between the cable temperature and multiple environmental variables is explored, and representative cable uniform temperatures for design are obtained by the extreme value analysis. The presented data and results provide a good basis for the operation and maintenance of in-service long-span cable-stayed bridges.

Single cell transcriptomic landscapes of pattern formation, proliferation and growth in Drosophila wing imaginal discs.

Organ formation relies on the orchestration of pattern formation, proliferation and growth during development. How these processes are integrated at the individual cell level remains unclear. In the past decades, studies using Drosophila wing imaginal discs as a model system have provided valuable insights into pattern formation, growth control and regeneration. Here, we provide single cell transcriptomic landscapes of pattern formation, proliferation and growth of wing imaginal discs. We found that patterning information is robustly maintained in the single cell transcriptomic data and can provide reference matrices for computationally mapping single cells into discrete spatial domains. Assignment of wing disc single cells to spatial subregions facilitates examination of patterning refinement processes. We also clustered single cells into different proliferation and growth states and evaluated the correlation between cell proliferation/growth states and spatial patterning. Furthermore, single cell transcriptomic analyses allowed us to quantitatively examine disturbances of differentiation, proliferation and growth in a well-established tumor model. We provide a database to explore these datasets at http://drosophilayanlab-virtual-wingdisc.ust.hk:3838/v2/This article has an associated 'The people behind the papers' interview.

Transcriptomic and metabolomic profiling of flavonoid biosynthesis provides novel insights into petals coloration in Asian cotton (Gossypium arboreum L.).

BACKGROUND: Asian cotton (Gossypium arboreum L.), as a precious germplasm resource of cotton with insect resistance and stress tolerance, possesses a broad spectrum of phenotypic variation related to pigmentation. Flower color affects insect pollination and the ornamental value of plants. Studying flower color of Asian cotton varieties improves the rate of hybridization and thus enriches the diversity of germplasm resources. Meanwhile, it also impacts the development of the horticultural industry. Unfortunately, there is a clear lack of studies concerning intricate mechanisms of cotton flower-color differentiation. Hereby, we report an integrative approach utilizing transcriptome and metabolome concerning flower color variation in three Gossypium arboreum cultivars. RESULTS: A total of 215 differentially accumulated metabolites (DAMs) were identified, including 83 differentially accumulated flavonoids (DAFs). Colorless kaempferol was more abundant in white flowers, while gossypetin-fer showed specificity in white flowers. Quercetin and gossypetin were the main contributors to yellow petal formation. Pelargonidin 3-O-beta-D-glucoside and cyanidin-3-O-(6''-Malonylglucoside) showed high accumulation levels in purple petals. Quercetin and gossypetin pigments also promoted purple flower coloration. Moreover, 8178 differentially expressed genes (DEGs) were identified by RNA sequencing. The correlation results between total anthocyanins and DEGs were explored, indicating that 10 key structural genes and 29 transcription factors promoted anthocyanin biosynthesis and could be candidates for anthocyanin accumulation. Ultimately, we constructed co-expression networks of key DAFs and DEGs and demonstrated the interactions between specific metabolites and transcripts in different color flowers. CONCLUSION: This study provides new insights into elucidating the regulatory mechanisms of cotton flower color and lays a potential foundation for generate cotton varieties with highly attractive flowers for pollinators.

TET-mediated DNA demethylation controls gastrulation by regulating Lefty-Nodal signalling.

Mammalian genomes undergo epigenetic modifications, including cytosine methylation by DNA methyltransferases (DNMTs). Oxidation of 5-methylcytosine by the Ten-eleven translocation (TET) family of dioxygenases can lead to demethylation. Although cytosine methylation has key roles in several processes such as genomic imprinting and X-chromosome inactivation, the functional significance of cytosine methylation and demethylation in mouse embryogenesis remains to be fully determined. Here we show that inactivation of all three Tet genes in mice leads to gastrulation phenotypes, including primitive streak patterning defects in association with impaired maturation of axial mesoderm and failed specification of paraxial mesoderm, mimicking phenotypes in embryos with gain-of-function Nodal signalling. Introduction of a single mutant allele of Nodal in the Tet mutant background partially restored patterning, suggesting that hyperactive Nodal signalling contributes to the gastrulation failure of Tet mutants. Increased Nodal signalling is probably due to diminished expression of the Lefty1 and Lefty2 genes, which encode inhibitors of Nodal signalling. Moreover, reduction in Lefty gene expression is linked to elevated DNA methylation, as both Lefty-Nodal signalling and normal morphogenesis are largely restored in Tet-deficient embryos when the Dnmt3a and Dnmt3b genes are disrupted. Additionally, a point mutation in Tet that specifically abolishes the dioxygenase activity causes similar morphological and molecular abnormalities as the null mutation. Taken together, our results show that TET-mediated oxidation of 5-methylcytosine modulates Lefty-Nodal signalling by promoting demethylation in opposition to methylation by DNMT3A and DNMT3B. These findings reveal a fundamental epigenetic mechanism featuring dynamic DNA methylation and demethylation crucial to regulation of key signalling pathways in early body plan formation.

Photocatalytic Dissolution of Precious Metals by TiO2 through Photogenerated Free Radicals.

Exploring the pathways for photocatalytic dissolution of precious metals (PMs) is crucial for optimizing recovery. In this work, we systematically investigated the selectivity and solvation effects observed for dissolution by focusing on photocatalysis, precious metals and solvents. By combining transient characterization, reaction kinetics, and density functional theory, we determined that the radicals generated in photocatalysis were the key active species in the entire reaction. The cyano functional group in the solvent was the driving factor for dissolution of gold, and the importance of chlorine radicals for dissolution of platinum group precious metals was further confirmed. In addition, the catalytic properties of different precious metals can promote different transformations of functional groups, leading to selective dissolution. The structures of photocatalytic precious metal leaches also precisely explains the special coordination forms of precious metals and functional group ligands.

Observation of Acoustic Skyrmions.

Despite a long history of studies, acoustic waves are generally regarded as spinless scalar waves, until recent research revealed their rich structures. Here, we report the experimental observation of skyrmion configurations in acoustic waves. We find that surface acoustic waves trapped by a designed hexagonal acoustic metasurface give rise to skyrmion lattice patterns in the dynamic acoustic velocity fields (i.e., the oscillating acoustic air flows). Using an acoustic velocity sensing technique, we directly visualize a Néel-type skyrmion configuration of the acoustic velocity fields. We further demonstrate, respectively, the controllability and robustness of the acoustic skyrmion lattices by tuning the phase differences between the acoustic sources and by introducing local perturbations in our setup. Our study unveils a fundamental acoustic phenomenon that may enable unprecedented manipulation of acoustic waves and may inspire future technologies including advanced acoustic tweezers for the control of small particles.

Fluctuating-rate model with multiple gene states.

Multiple phenotypic states of single cells often co-exist in the presence of positive feedbacks. Stochastic gene-state switchings and low copy numbers of proteins in single cells cause considerable fluctuations. The chemical master equation (CME) is a powerful tool that describes the dynamics of single cells, but it may be overly complicated. Among many simplified models, a fluctuating-rate (FR) model has been proposed recently to approximate the full CME model in the realistic intermediate region of gene-state switchings. However, only the scenario with two gene states has been carefully analysed. In this paper, we generalise the FR model to the case with multiple gene states, in which the mathematical derivation becomes more complicated. The leading order of fluctuations around each phenotypic state, as well as the transition rates between phenotypic states, in the intermediate gene-state switching region is characterized by the rate function of the stationary distribution of the FR model in the Freidlin-Wentzell-type large deviation principle (LDP). Under certain reasonable assumptions, we show that the derivative of the rate function is equal to the unique nontrivial solution of a dominant generalised eigenvalue problem, leading to a new numerical algorithm for obtaining the LDP rate function directly. Furthermore, we prove the Lyapunov property of the rate function for the corresponding deterministic mean-field dynamics. Finally, through a tristable example, we show that the local fluctuations (the asymptotic variance of the stationary distribution at each phenotypic state) in the intermediate and rapid regions of gene-state switchings are different. Finally, a tri-stable example is constructed to illustrate the validity of our theory.

Hybrid Acoustic Topological Insulator in Three Dimensions.

Topological insulators (TIs), featured by a symmetry-protected gapless surface Dirac cone(s) in their complete energy band gaps, have been extended from condensed-matter physics to classical bosonic systems in the last decade. However, acoustic TIs in three dimensions remain elusive because of a lack of a spin or polarization degree of freedom for longitudinal airborne sound. Here, we experimentally demonstrate a feasible way to hybridize an acoustic TI in three dimensions based on band inversion through a three-dimensional (3D) hybrid Dirac point (HDP). Such a 3D HDP, with linear dispersion in the layer plane while quadratic out of the layer, is distinct from a general point with linear dispersion in all directions. Interestingly, a single nearly gapless conical-like dispersion for acoustic surface states can be achieved at both zigzag and armchair interfaces, supporting robust sound transport. Our findings can serve as a tabletop platform for exploring unique acoustic applications based on the two-dimensional topological interfaces.

Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state.

Within an isogenic population, even in the same extracellular environment, individual cells can exhibit various phenotypic states. The exact role of stochastic gene-state switching regulating the transition among these phenotypic states in a single cell is not fully understood, especially in the presence of positive feedback. Recent high-precision single-cell measurements showed that, at least in bacteria, switching in gene states is slow relative to the typical rates of active transcription and translation. Hence using the lac operon as an archetype, in such a region of operon-state switching, we present a fluctuating-rate model for this classical gene regulation module, incorporating the more realistic operon-state switching mechanism that was recently elucidated. We found that the positive feedback mechanism induces bistability (referred to as deterministic bistability), and that the parameter range for its occurrence is significantly broadened by stochastic operon-state switching. We further show that in the absence of positive feedback, operon-state switching must be extremely slow to trigger bistability by itself. However, in the presence of positive feedback, which stabilizes the induced state, the relatively slow operon-state switching kinetics within the physiological region are sufficient to stabilize the uninduced state, together generating a broadened parameter region of bistability (referred to as stochastic bistability). We illustrate the opposite phenotype-transition rate dependence upon the operon-state switching rates in the two types of bistability, with the aid of a recently proposed rate formula for fluctuating-rate models. The rate formula also predicts a maximal transition rate in the intermediate region of operon-state switching, which is validated by numerical simulations in our model. Overall, our findings suggest a biological function of transcriptional "variations" among genetically identical cells, for the emergence of bistability and transition between phenotypic states.

Enhanced Photocatalytic Degradation Performance by Fluid-Induced Piezoelectric Field.

The introduction of a piezoelectric field has been proven a promising method to enhance photocatalytic activity by preventing photoelectron-hole recombination. However, the formation of a piezoelectric field requires additional mechanical force or high-frequency ultrasonic baths, which limits its potential application on industrial scale. Therefore, it is of great practical significance to design the catalyst that can harvest the discrete energy such as the fluid mechanical energy to form the electric field. Herein, PZT/TiO2 catalyst with a core-shell configuration was prepared by a simple coating method. By collecting the mechanical energy of water, an internal piezoelectric field was induced. Under 800 rpm stirring, transient photocurrent measured on PZT/TiO2 electrode is about 1.7 times higher than that of 400 rpm. Correspondingly, the photocatalytic degradation rate and mineralization efficiency of RhB, BPA, phenol, p-chlorophenol much improved, showing the promoting effect of piezoelectric field generated directly from harvesting the discrete fluid mechanical energy.

Integrated tempering enhanced sampling method as the infinite switching limit of simulated tempering.

A fast and accurate sampling method is in high demand, in order to bridge the large gaps between molecular dynamic simulations and experimental observations. Recently, an integrated tempering enhanced sampling (ITS) method has been proposed and successfully applied to various biophysical examples, significantly accelerating conformational sampling. The mathematical validation for its effectiveness has not been elucidated yet. Here we show that the integrated tempering enhanced sampling method can be viewed as a reformulation of the infinite switching limit of the simulated tempering method over a mixed potential. Moreover, we demonstrate that the efficiency of simulated tempering molecular dynamics improves as the frequency of switching between the temperatures is increased, based on the large deviation principle of empirical distributions. Our theory provides the theoretical justification of the advantage of ITS. Finally, we illustrate the utility of the infinite switching simulated tempering method through several numerical examples.

An efficient and assumption-free method to approximate protein level distribution in the two-states gene expression model.

Stochastic fluctuations at each step of gene expression might influence protein levels distributions across cell populations. However, current methods to model protein distribution of intrinsic gene expression dynamics are either computationally inefficient or rely on ad hoc assumptions, e.g., that the gene is always active. Taking advantage of the simple form of lower-order moments of distribution, we developed an efficient and assumption-free protein distribution approximation method (EFPD), for the two state gene expression model to accurately approximate the distribution. By EFPD, we computed nearly identical intensity of gene expression regulation at mRNA and protein level, implying a profound link between transcription and translation. Finally, by extending EFPD to approximate the distribution of protein level at any arbitrary temporal state, we proposed an explanation for the role of stochastic noise in gene expression in the context of a continuously changing environment. EFPD can be a powerful tool for modeling the particular molecular mechanisms of targeted gene expression pattern.

Coordinated photomorphogenic UV-B signaling network captured by mathematical modeling.

Long-wavelength and low-fluence UV-B light is an informational signal known to induce photomorphogenic development in plants. Using the model plant Arabidopsis thaliana, a variety of factors involved in UV-B-specific signaling have been experimentally characterized over the past decade, including the UV-B light receptor UV resistance locus 8; the positive regulators constitutive photomorphogenesis 1 and elongated hypocotyl 5; and the negative regulators cullin4, repressor of UV-B photomorphogenesis 1 (RUP1), and RUP2. Individual genetic and molecular studies have revealed that these proteins function in either positive or negative regulatory capacities for the sufficient and balanced transduction of photomorphogenic UV-B signal. Less is known, however, regarding how these signaling events are systematically linked. In our study, we use a systems biology approach to investigate the dynamic behaviors and correlations of multiple signaling components involved in Arabidopsis UV-B-induced photomorphogenesis. We define a mathematical representation of photomorphogenic UV-B signaling at a temporal scale. Supplemented with experimental validation, our computational modeling demonstrates the functional interaction that occurs among different protein complexes in early and prolonged response to photomorphogenic UV-B.