Signal Coordination Research Articles

Cross-regulation of cytoskeleton and calcium signaling at plant-pathogen interface

During plant-pathogen interactions, cytoskeleton and calcium signaling work independently as well as in coordination with each other for developing preformed and induced defense responses. A cell wall (CW) – plasma membrane (PM) – cytoskeleton (CS) continuum is maintained by coordination of cytoskeleton and calcium signaling. The current review is focused on the current knowledge of cytoskeleton‑calcium cross-regulation during plant-pathogen interactions. Implications of recent technological developments in the existing toolkit that can address the outstanding questions of cytoskeleton‑calcium coordination plant immunity are also discussed.

CPK28 is a modulator of purinergic signaling in plant growth and defense.

Extracellular ATP (eATP) is a key signaling molecule that plays a pivotal role in plant growth and defense responses. The receptor P2K1 is responsible for perceiving eATP and initiating its signaling cascade. However, the signal transduction mechanisms downstream of P2K1 activation remain incompletely understood. We conducted a comprehensive analysis of the P2K1 interactome using co-immunoprecipitation-coupled tandem mass spectrometry, leading to the identification of 121 candidate proteins interacting with P2K1. In silico analysis narrowed down the candidates to 47 proteins, including Ca2+-binding proteins, ion transport-related proteins, and receptor kinases. To investigate their involvement in eATP signaling, we employed a screening strategy based on changes in gene expression in response to eATP in mutants of the identified interactors. This screening revealed several Ca2+-dependent protein kinases (CPKs) that significantly affected the expression of eATP-responsive genes, suggesting their potential roles in eATP signaling. Notably, CPK28 and CPK6 showed physical interactions with P2K1 both in yeast and plant systems. Calcium influx and gene expression studies demonstrated that CPK28 perturbed eATP-induced Ca2+ mobilization and some early transcriptional responses. Overexpression of CPK28 resulted in an antagonistic physiological response to P2K1-mediated eATP signaling during both plant growth and defense responses to the necrotrophic pathogen Botrytis cinerea. Our findings highlight CPK28, among other CPKs, as a modulator of P2K1-mediated eATP signaling, providing valuable insights into the coordination of eATP signaling in plant growth and immunity.

A Comprehensive Review on Real-Time Traffic Signal Coordination Using Machine Learning: Optimizing Urban Traffic Flow for Efficiency and Sustainability

Abstract: Cities globally grapple with escalating traffic congestion stemming from urban expansion, aginginfrastructure, suboptimal traffic signal coordination, and a deficiency in real-time data. INRIX quantified the resulting toll at $305 billion for U.S. commuters in 2020, underscoring the pressing need for cities to adopt innovative strategies within the constraints of building new roads. This challenge is further complicated by disparate data collection times at various junctions, creating a mosaic of information from different periods. Some junctions provide limited or sporadic data, necessitating careful consideration for future projections. To address these challenges, cities must embrace cutting-edge approaches that integrate real-time data, efficient traffic management systems, and forward-thinking projections, enabling them to navigate the intricacies of contemporary urban mobility and pioneer sustainable solutions for the future.

EMARLIN$+$: Addressing Partial Observability to Promote Traffic Signal Coordination by Leveraging Historical Information

eMARLIN$+$: Addressing Partial Observability to Promote Traffic Signal Coordination by Leveraging Historical Information

Research on coordinated control optimization of adjacent intersections based on numerical solution

In order to improve the efficiency of traffic flow and reduce the delay of arterial intersections, a coordinated signal control method based on numerical solution is proposed. Firstly, considering the factors such as the shortest green time and saturation of a single intersection, the intersection delay model is established. Secondly, the traffic capacity of the trunk line is improved by optimizing the public cycle and the green ratio of each intersection. Finally, an optimization model with minimum delay as the optimization objective is constructed, and the signal coordination of arterial intersections is realized by taking Yancheng City as an example. The results show that the coordinated control model of adjacent intersections based on the numerical method can reduce the average vehicle delay of two-way vehicles, achieve the purpose of green wave coordinated control of road sections, and improve the road traffic capacity.

Histone Trimethylations and HDAC5 Regulate Spheroid Subpopulation and Differentiation Signaling of Human Adipose-Derived Stem Cells.

Human adipose-derived stem cells (ASCs) have shown immense potential for regenerative medicine. Our previous work demonstrated that chitosan nano-deposited surfaces induce spheroid formation and differentiation of ASCs for treating sciatic nerve injuries. However, the underlying cell fate and differentiation mechanisms of ASC-derived spheroids remain unknown. Here, we investigate the epigenetic regulation and signaling coordination of these therapeutic spheroids. During spheroid formation, we observed significant increases in histone 3 trimethylation at lysine 4 (H3K4me3), lysine 9 (H3K9me3), and lysine 27 (H3K27me3), accompanied by increased histone deacetylase (HDAC) activities and decreased histone acetyltransferase activities. Additionally, HDAC5 translocated from the cytoplasm to the nucleus, along with increased nuclear HDAC5 activities. Utilizing single-cell RNA sequencing (scRNA-seq), we analyzed the chitosan-induced ASC spheroids and discovered distinct cluster subpopulations, cell fate trajectories, differentiation traits, and signaling networks using the 10x Genomics platform, R studio/language, and the Ingenuity Pathway Analysis (IPA) tool. Specific subpopulations were identified within the spheroids that corresponded to a transient reprogramming state (Cluster 6) and the endpoint cell state (Cluster 3). H3K4me3 and H3K9me3 were discovered as key epigenetic regulators by IPA to initiate stem cell differentiation in Cluster 6 cells, and confirmed by qPCR and their respective histone methyltransferase inhibitors: SNDX-5613 (a KMT2A inhibitor for H3K4me3) and SUVi (an SUV39H1 inhibitor for H3K9me3). Moreover, H3K9me3 and HDAC5 were involved in regulating downstream signaling and neuronal markers during differentiation in Cluster 3 cells. These findings emphasize the critical role of epigenetic regulation, particularly H3K4me3, H3K9me3, and HDAC5, in shaping stem cell fate and directing lineage-specific differentiation.

Stochastic-priority-integrated signal coordination considering connected bus operation uncertainties

Multimodal arterial signal coordination for buses and passenger vehicles can improve arterial travel smoothness and efficiency. However, uncertainty in bus operations requires signal priority at intersections, which impacts coordination and increases stop times for other traffic types. Therefore, this study proposes a stochastic priority-integrated signal coordination (SPIC) method. It includes an offline stochastic programme to determine the arterial signal coordination, i.e. cycle length and offsets, considering the stochastic signal priority, and an online mixed-integer nonlinear programme to determine the signal priority together with the bus arrival and departure times at and from stops and intersections in a connected vehicle environment. A scenario-based heuristic algorithm is proposed to solve the SPIC efficiently. Numerical studies have validated that SPIC can improve the efficiency of buses and passenger vehicles. Sensitivity analyses show that the SPIC effectively reduces delays with fluctuations in the bus travel time, dwell time, and passenger vehicle demands.

Extracellular matrix stiffness activates mechanosensitive signals but limits breast cancer cell spheroid proliferation and invasion.

Breast cancer is characterized by physical changes that occur in the tumor microenvironment throughout growth and metastasis of tumors. Extracellular matrix stiffness increases as tumors develop and spread, with stiffer environments thought to correlate with poorer disease prognosis. Changes in extracellular stiffness and other physical characteristics are sensed by integrins which integrate these extracellular cues to intracellular signaling, resulting in modulation of proliferation and invasion. However, the co-ordination of mechano-sensitive signaling with functional changes to groups of tumor cells within 3-dimensional environments remains poorly understood. Here we provide evidence that increasing the stiffness of collagen scaffolds results in increased activation of ERK1/2 and YAP in human breast cancer cell spheroids. We also show that ERK1/2 acts upstream of YAP activation in this context. We further demonstrate that YAP, matrix metalloproteinases and actomyosin contractility are required for collagen remodeling, proliferation and invasion in lower stiffness scaffolds. However, the increased activation of these proteins in higher stiffness 3-dimensional collagen gels is correlated with reduced proliferation and reduced invasion of cancer cell spheroids. Our data collectively provide evidence that higher stiffness 3-dimensional environments induce mechano-signaling but contrary to evidence from 2-dimensional studies, this is not sufficient to promote pro-tumorigenic effects in breast cancer cell spheroids.

Therapeutic Study of Cinnamic Acid Derivative for Oxidative Stress Ablation: The Computational and Experimental Answers.

This study aimed to examine the therapeutic activity of the cinnamic acid derivative KAD-7 (N'-(2,4-dichlorobenzylidene)-3-(4-methoxyphenyl) acrylohydrazide) on Fe2+-induced oxidative hepatic injury via experimental and computational models. In addition, the role of ATPase and ectonucleoside triphosphate diphosphohydrolase (ENTPDase) in the coordination of cellular signals is speculated upon to proffer suitable therapeutics for metabolic stress disorder upon their inhibition. While we know little about therapeutics with flexible dual inhibitors for these protein targets, this study was designed to screen KAD-7's (N'-(2,4-dichlorobenzylidene)-3-(4-methoxyphenyl) acrylohydrazide) inhibitory potential for both protein targets. We induced oxidative hepatic damage via the incubation of hepatic tissue supernatant with 0.1 mM FeSO4 for 30 min at 37 °C. We achieved the treatment by incubating the hepatic tissues with KAD-7 under the same conditions. The catalase (CAT), glutathione (GSH), malondialdehyde (MDA), ATPase, and ENTPDase activity were all measured in the tissues. We predicted how the drug candidate would work against ATPase and ENTPDase targets using molecular methods. When hepatic injury was induced, there was a significant decrease in the levels of the GSH, CAT, and ENTPDase (p < 0.05) activities. In contrast, we found a noticeable rise in the MDA levels and ATPase activity. KAD-7 therapy resulted in lower levels of these activities overall (p < 0.05), as compared to the control levels. We found the compound to have a strong affinity for ATPase (-7.1 kcal/mol) and ENTPDase (-7.4 kcal/mol), and a better chemical reactivity than quercetin. It also met all drug-likeness parameters. Our study shows that KAD-7 can protect the liver from damage caused by FeSO4 by reducing oxidative stress and purinergic actions. Our studies indicate that KAD-7 could be developed as a therapeutic option since it can flexibly inhibit both ATPase and ENTPDase.

Cdc42 activity in the trailing edge is required for persistent directional migration of keratinocytes.

Fibroblasts migrate discontinuously by generating transient leading-edge protrusions and irregular, abrupt retractions of a narrow trailing edge. In contrast, keratinocytes migrate persistently and directionally via a single, stable, broad protrusion paired with a stable trailing-edge. The Rho GTPases Rac1, Cdc42 and RhoA are key regulators of cell protrusions and retractions. However, how these molecules mediate cell-type specific migration modes is still poorly understood. In fibroblasts, all three Rho proteins are active at the leading edge, suggesting short-range coordination of protrusive Rac1 and Cdc42 signals with RhoA retraction signals. Here, we show that Cdc42 was surprisingly active in the trailing-edge of migrating keratinocytes. Elevated Cdc42 activity colocalized with the effectors MRCK and N-WASP suggesting that Cdc42 controls both myosin activation and actin polymerization in the back. Indeed, Cdc42 was required to maintain the highly dynamic contractile acto-myosin retrograde flow at the trailing edge of keratinocytes, and its depletion induced ectopic protrusions in the back, leading to decreased migration directionality. These findings suggest that Cdc42 is required to stabilize the dynamic cytoskeletal polarization in keratinocytes, to enable persistent, directional migration.

ASF1 regulates asexual and sexual reproduction in Stemphylium eturmiunum by DJ-1 stimulation of the PI3K/AKT signaling pathway

Most fungi display a mixed mating system with both asexual and sexual reproduction. The timing of the two modes of reproduction must be carefully coordinated through signal perception and coordination in the cell along with chromatin modification. Here, we investigated coordination of reproductive output by investigating the function of the histone chaperone anti-silencing factor 1 (ASF1) in a fungal species amenable to characterization of both asexual and sexual reproduction. We used knockout approach to show that SeASF1 influenced asexual and sexual reproduction in Stemphylium eturmiunum. SeASF1-deleted strains failed to produce pseudothecia, but produce abnormal conidia and showed an irregular distribution of nuclei in mycelium. Transcriptome sequencing was then used to identify genes with altered expression in the SeASF1-deleted strains. The transcriptional expression of the identified SeDJ-1 was strongly regulated by SeASF1. The interaction of SeDJ-1 and SeASF1 was confirmed using Y2H, Co-IP, and pull-down. Due to some components of phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway were known to interact with DJ-1 in mammals, we verified SePI3K, an element of PI3K/AKT signaling pathway in S. eturmiunum, was directly linked to SeDJ-1 and then these two proteins were defined as a coordinator of reproduction. However, knockout of SeDJ-1 or SePI3K altered the asexual and sexual reproduction, but SePI3K recovered the asexual and sexual development of ∆Sedj-1. The SeDJ-1-M6 segment of SeDJ-1 was essential for its interaction with SePI3K and played a critical role in restoring sexual reproduction in the ∆Sepi3k, providing a deep understanding of the regulatory mechanism of SeDJ-1 in S. eturmiunum development. Summarily, SeASF1 is able to trigger SeDJ-1 and SeDJ-1can also activate SePI3K, which is orchestrally involved in asexual and sexual reproduction in S. eturmiunum. All these results reveal that SeASF1 manipulates asexual and sexual reproduction in S. eturmiunum by SeDJ-1 perception of PI3K/AKT signaling pathway. These data highlight the deep similarities in coordinating asexual and sexual processes in both fungi and eukaryotes in general.

Evaluating the Impacts of Different Exit Strategies of Emergency Vehicle Preemption on Arterial Signal Coordination: A Case Study in Reno, Nevada

Evaluating the Impacts of Different Exit Strategies of Emergency Vehicle Preemption on Arterial Signal Coordination: A Case Study in Reno, Nevada

Adaptive signal light timing for regional traffic optimization based on graph convolutional network empowered traffic forecasting

With the acceleration of urbanization, urban traffic congestion is becoming more and more serious, in which the timing of signal lights for regional traffic optimization is particularly important. Since existing signal lights-based traffic optimization technologies, especially green wave, do not take the regional traffic follow into consideration, therefore not being efficient. Therefore, we propose Adaptive Signal Light Timing for Regional Traffic Optimization based on Graph Convolutional Network Empowered Traffic Forecasting. First, we propose a multi-intersection traffic flow prediction model, namely, A-GCN+ with an improved prediction accuracy of 6.3%, which utilizes the attention-aggregated graph convolutional neural networks (A-GCN) and temporal convolutional networks (TCN) to extract spatial and temporal features of the traffic flow. Second, we propose a dynamic regional traffic signal coordination optimization control method, which utilizes the predicted intersection approach traffic flow from A-GCN+ and combines it with the improved whale optimization algorithm (IWOA) to obtain the optimal solution for the regional average vehicle delay model. Finally, we propose a bidirectional green wave automatic control method for the main line, which utilizes the optimized results of dynamic regional traffic signal timing and employs a multi-strategy fusion graphical method to obtain the dynamic main line bidirectional green wave. Experimental results show that compared to the traditional graphical method, the multi-strategy fusion graphical method increases the green wave bandwidth by 20%. The mainline bidirectional green wave adaptive coordinated control method improves main line traffic efficiency by 32.3% and regional network traffic efficiency by 8.7%.

A Signal Coordination Model for Long Arterials Considering Link Traffic Flow Characteristics

In order to improve the travel efficiency on a long arterial with massive signals, this paper proposed a mixed integer linear programming model, MaxBandLAM, to simultaneously optimize the arterial partition scheme and signal coordination schemes with the consideration of link traffic flow characteristics. The weighted sum of the two-way green bandwidths on links across the arterial was taken as its objective. The link volume to capacity rations were taken as the weights. The number of sub-zones, the allocation of signals and links, signal cycle, offset and phase sequence, the coordination speed, as well as the two-way green bandwidths of sub-zones and of links are the decision variables. A numerical test was carried out on a virtual arterial with twenty signals. The results indicate the scheme generated by the MaxBandLAM model can provide a more reasonable partition scheme and coordination schemes compared to those generated by Synchro and the models with no traffic flow characteristics of links consideration. For the scenario of dominating the main road through flows, the average delay, average stop number, and average travel speed at intersections for all-turning flows and main road through flows in the MaxBandLAM scheme, all performed well.

Arterial Signal Coordination Considering the Impacts of Left-Turn Waiting Areas

Arterial Signal Coordination Considering the Impacts of Left-Turn Waiting Areas

A Two-Stage Real-Time Optimization Model of Arterial Signal Coordination Based on Reverse Causal-Effect Modeling Approach

The arterial signal coordination is an effective method to improve traffic operational efficiency and reduce vehicle delay. In this paper, a two-stage arterial signal coordination model under dynamic traffic demands is established, and the signal timing and offset are adjusted according to the dynamic traffic demands. The objective is to minimize the expected intersection delay and the overflow of the coordinated direction. In the first stage, a calculation model for intersection signal timing based on phase clearing reliability is proposed by the reverse causal-effect modeling approach, which can calculate the signal timing of each intersection in real time. In the second stage, an offset calculation model is established to achieve the goal of minimizing delay in the coordinated direction, which can calculate the offset of trunk coordination in real time. The concept of phase clearance reliability is introduced in the model, which can dynamically adjust the balance between the coordinated phase and the non-coordinated phase, thus taking the overall control efficiency of intersections into account. We then develop an algorithm to solve the problem and then apply the model and the solution algorithm to an arterial road with three intersections to investigate and compare its performance with the Allsop’s method and the Webster’s method. A comparison between the proposed coordinated two-stage logic and a coordinated actuated logic is also conducted in the case study to show the advantages and disadvantages.

Potential role of tocopherol in protecting crop plants against abiotic stresses.

The changing global climate have given rise to abiotic stresses that adversely affect the metabolic activities of plants, limit their growth, and agricultural output posing a serious threat to food production. The abiotic stresses commonly lead to production of reactive oxygen species (ROS) that results in cellular oxidation. Over the course of evolution, plants have devised efficient enzymatic and non-enzymatic anti-oxidative strategies to counteract harmful effects of ROS. Among the emerging non-enzymatic anti-oxidative technologies, the chloroplast lipophilic antioxidant vitamin A (Tocopherol) shows great promise. Working in coordination with the other cellular antioxidant machinery, it scavenges ROS, prevents lipid peroxidation, regulates stable cellular redox conditions, simulates signal cascades, improves membrane stability, confers photoprotection and enhances resistance against abiotic stresses. The amount of tocopherol production varies based on the severity of stress and its proposed mechanism of action involves arresting lipid peroxidation while quenching singlet oxygen species and lipid peroxyl radicals. Additionally, studies have demonstrated its coordination with other cellular antioxidants and phytohormones. Despite its significance, the precise mechanism of tocopherol action and signaling coordination are not yet fully understood. To bridge this knowledge gap, the present review aims to explore and understand the biosynthesis and antioxidant functions of Vitamin E, along with its signal transduction and stress regulation capacities and responses. Furthermore, the review delves into the light harvesting and photoprotection capabilities of tocopherol. By providing insights into these domains, this review offers new opportunities and avenues for using tocopherol in the management of abiotic stresses in agriculture.

The role of Class II KNOX family in controlling compound leaf patterning in Medicago truncatula.

Compound leaf development requires the coordination of genetic factors, hormones, and other signals. In this study, we explored the functions of Class Ⅱ KNOTTED-like homeobox (KNOXⅡ) genes in the model leguminous plant Medicago truncatula. Phenotypic and genetic analyses suggest that MtKNOX4, 5 are able to repress the leaflet formation, while MtKNOX3, 9, 10 are not involved in this developmental process. Further investigations show that MtKNOX4 represses the CK signal transduction, which is downstream of MtKNOXI-mediated CK biosynthesis. Additionally, two boundary genes, FUSED COMPOUND LEAF1 (ortholog of Arabidopsis class M KNOX) and NO APICAL MERISTEM (ortholog of Arabidopsis CUP-SHAPED COTYLEDON), are necessary for the MtKNOX4-mediated compound leaf formation. These findings suggest that among the members of MtKNOXII, MtKNOX4 plays a crucial role in integrating the CK pathway and boundary regulators, providing new insights into the roles of MtKNOXⅡ in regulating the elaboration of compound leaves in M. truncatula. This article is protected by copyright. All rights reserved.

Setting the Intermittent Bus Approach of Intersections: A Novel Lane Multiplexing-Based Method with an Intersection Signal Coordination Model

Intermittent bus lanes (IBLs) can alleviate the contradiction between bus priority and the urgent demand of general vehicles for road resources. However, existing IBL strategies seldom pay attention to the setting method of the dynamic bus lanes at intersections, which leads to the still serious delay of buses at intersections in the traffic congestion environment. To tackle this issue, this research explores a novel method of setting the intermittent bus approach (IBA) of intersections for lane sharing and bus priority at intersections. In particular, a time slice division strategy with an intersection signal coordination model is developed to fully and reasonably allocate the idle time of bus lanes at intersections. Besides, considering the lane-changing demands of general vehicles at intersections, the parameters of the IBA lane system are modeled and optimized. For testing and verifying the feasibility of the proposed method, comparative experiments are conducted through microscopic traffic simulation. Results show that the proposed IBA setting method can effectively solve the problem of bus priority failure at intersections. It can maintain the continuity of vehicle running on intersection sections, which better exerts the operational benefits of dynamic bus lanes.

Impact Analysis of Traffic Factors on Urban Bus Bunching

Due to the mixed right-of-way and varying traffic conditions, urban bus operations are often subject to random delays and eventually bus bunching, undermining the schedule reliability. The existing studies have proposed different models to emulate bus bunching and control strategies to mitigate bus bunching, yet few of them considered the effect of the three important traffic factors: intersections with signal coordination, varying traffic volume, and passenger demand. To fill in the research gap, we first define the stop-level frequency of bus bunching events for a bus route in this study. We proceed to present a simulation-based approach to quantify the impact of the three traffic factors on bus bunching. Numerical experiments based on different scenarios are carried out to reveal the cause–effect relationship between these factors and bus bunching events. Contributors to bus bunching are evaluated, and the effect of control delays is examined through statistical measurements. Finally, a real-world case study based on bus route 51 in Singapore is performed, and some insights are provided to alleviate the bus bunching phenomenon.