External Environmental Signals Research Articles

Relevance and regulation of alternative splicing in plant secondary metabolism: current understanding and future directions.

The secondary metabolism of plants is an essential life process enabling organisms to navigate various stages of plant development and cope with ever-changing environmental stresses. Secondary metabolites, abundantly found in nature, possess significant medicinal value. Among the regulatory mechanisms governing these metabolic processes, alternative splicing stands out as a widely observed post-transcriptional mechanism present in multicellular organisms. It facilitates the generation of multiple mRNA transcripts from a single gene by selecting different splicing sites. Selective splicing events in plants are widely induced by various signals, including external environmental stress and hormone signals. These events ultimately regulate the secondary metabolic processes and the accumulation of essential secondary metabolites in plants by influencing the synthesis of primary metabolites, hormone metabolism, biomass accumulation, and capillary density. Simultaneously, alternative splicing plays a crucial role in enhancing protein diversity and the abundance of the transcriptome. This paper provides a summary of the factors inducing alternative splicing events in plants and systematically describes the progress in regulating alternative splicing with respect to different secondary metabolites, including terpenoid, phenolic compounds, and nitrogen-containing compounds. Such elucidation offers critical foundational insights for understanding the role of alternative splicing in regulating plant metabolism and presents novel avenues and perspectives for bioengineering.

Computer-aided discovery of novel aryl hydrocarbon receptor ligands to regulate CYP1A1 expression in inflammatory macrophages.

The environmental factor aryl hydrocarbon receptor (AhR), a key protein connecting the external environmental signals (e.g., environmental endocrine disruptor TCDD) to internal cellular processes, is involved in the activation of peripheral macrophages and inflammatory response in human body. Thus, there is widespread interest in finding compounds to anti-inflammatory response in macrophages by targeting human AhR. Here, ensemble docking based-virtual screening was first used to screen a library (~200,000 compounds) against human AhR ligand binding domain (LBD) and 25 compounds were identified as potential inhibitors. Then, 9 out of the 25 ligands were found to down-regulate the mRNA expression of CYP1A1 (a downstream gene of AhR signaling) in AhR overexpressing macrophages. The most potent compound AE-411/41415610 was selected for further study and found to reduce both mRNA and protein expressions level of CYP1A1 in mouse peritoneal macrophage. Moreover, protein chip signal pathway analysis indicated that AE-411/41415610 play a role in regulating JAK-STAT and AKT-mTOR pathways. In sum, the discovered hits with novel scaffolds provided a starting point for future design of more effective AhR-targeted lead compounds to regulate CYP1A1 expression of inflammatory peritoneal macrophages.

Carbon nanotube/nonwoven fabric-based electronic skins for smart clothing and electronic glove

In recent years, flexible, easy-to-fabricate, and low-cost electronic skins (E-skins) have attracted considerable attention, due to their enormous demand in wearable device applications. Based on a carbon nanotube (CNT)/nonwoven fabric, three types of E-skins were fabricated using a low-cost and scalable approach, and detected various signals, like pressure, stretch, flexion, temperature, and humidity. Due to the wrinkled and porous microstructure of CNT/nonwoven fabric, the pressure-sensitive E-skin demonstrates a high gauge factor (GF) value of 19.12 kPa-1 and 5.38 kPa-1 with a pressure range of 15–6125 Pa and 6125–12005 Pa, respectively. Unlike traditional paper-based E-skins, the stretch/flexion/temperature-sensitive E-skin could detect the stretch strain, and its GF values were 3.81, 0.51 rad-1, and 1.4×10-3 ℃-1 for the detection of stretch, flexion and temperature. For the humidity-sensitive E-skin, its GF value was calculated to be 2.8×10-2 and 0.20 with the relative humidity range of 55–75% and 75–95%. The favorable performance of the E-skins allows their integration into smart clothing, where they successfully monitored human motion, physiological and external environmental signals in real time. Furthermore, the prepared E-skins have also been integrated into an electronic glove, where they simultaneously detected the bending and pressure signals of human fingers, demonstrating application potential in the field of telediagnosis.

Photoperiod and temperature synergistically regulate heading date and regional adaptation in rice.

Plants must accurately integrate external environmental signals with their own development to initiate flowering at the appropriate time for reproductive success. Photoperiod and temperature are key external signals that determine flowering time; both are cyclical and periodic, and they are closely related. In this review, we describe photoperiod-sensitive genes that simultaneously respond to temperature signals in rice (Oryza sativa). We introduce the mechanisms by which photoperiod and temperature synergistically regulate heading date and regional adaptation in rice. We also discuss the prospects for designing different combinations of heading date genes and other cold tolerance or thermo-tolerance genes to help rice better adapt to changes in light and temperature via molecular breeding to enhance yield in the future.

AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis

Roots are essential to terrestrial plants, as their growth and morphology are crucial for plant development. The growth of the roots is affected and regulated by several internal and external environmental signals and metabolic pathways. Among them, chromatin modification plays an important regulatory role. In this study, we explore the potential roles of the histone deacetylase AtHD2D in root development and lay the foundation for further research on the biological processes and molecular mechanisms of AtHD2D in the future. Our study indicates that AtHD2D affects the root tip microenvironment homeostasis by affecting the gene transcription levels required to maintain the root tip microenvironment. In addition, we confirmed that AtHD2D is involved in regulating Arabidopsis lateral root development and further explained the possible role of AtHD2D in auxin-mediated lateral root development. AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. We believe that AtHD2D is involved in coping with abiotic stress by promoting the development of lateral roots. Overexpression of AtHD2D promotes the accumulation of reactive oxygen species (ROS) in roots, indicating that AtHD2D is also involved in developing lateral roots mediated by ROS. Previous studies have shown that the overexpression of AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. Based on our data, we believe that AtHD2D participates in the response to abiotic stress by promoting the development of lateral roots. AtHD2D-mediated lateral root development provides new ideas for studying the mechanism of HDAC protein in regulating root development.

A Neural Decision Signal during Internal Sampling from Working Memory in Humans.

How humans transform sensory information into decisions that steer purposeful behavior is a central question in psychology and neuroscience that is traditionally investigated during the sampling of external environmental signals. The decision-making framework of gradual information sampling toward a decision has also been proposed to apply when sampling internal sensory evidence from working memory. However, neural evidence for this proposal remains scarce. Here we show (using scalp EEG in male and female human volunteers) that sampling internal visual representations from working memory elicits a scalp EEG potential associated with gradual evidence accumulation-the central parietal positivity. Consistent with an evolving decision process, we show how this signal (1) scales with the time participants require to reach a decision about the cued memory content and (2) is amplified when having to decide among multiple contents in working memory. These results bring the electrophysiology of decision-making into the domain of working memory and suggest that variability in memory-guided behavior may be driven (at least in part) by variations in the sampling of our inner mental contents.

The degradation and detection of environmental signals in sediment transport systems.

Autogenic processes contribute noise to sediment transport systems that can degrade or mask externally derived environmental signals and hinder our ability to reconstruct past environmental signals from landscapes and strata. To explore this further, we measure efflux from a physical rice pile to ascertain the temporal structure of autogenic noise, and how this influences the degradation and detection of environmental signals. Our results reveal a tripartite temporal spectral structure segmented at two key autogenic time scales. The shorter autogenic time scale set limits on environmental signal degradation, while the longer autogenic time scale sets limits on environmental signal detection. This work establishes a framework that can be used to explore how autogenic processes interact with external environmental signals in field-scale systems to influence their detectability. We anticipate that the temporal structure and associated time scales identified will arise from autogenic processes in numerous sediment transport systems.

GDU-952, a novel AhR agonist ameliorates skin barrier abnormalities and immune dysfunction in DNFB-induced atopic dermatitis in mice

The aryl hydrocarbon receptor (AhR) is widely expressed in the skin. It controls immune-mediated skin responses to various external environmental signals, promote terminal differentiation of epidermal keratinocytes and participates the maintenance of the skin barrier function. As a therapeutic target, AhR activation modulates many diseases progression driven by immune/inflammatory processes such as atopic dermatitis (AD) and psoriasis. In this study, we revealed that GDU-952 is a novel AhR agonist, which is able to decreases IgE serum levels, to inhibit pro-inflammatory cytokines such as IL-6 and TNF-α and to induce immunoregulatory effects through restoring Th1/Th2 immune balance and promoting CD4+FOXP3+regulatory T (Treg) populations in AD skin lesions. Furthermore, GDU-952 can strengthen the skin barrier function through upregulating epidermal differentiation-related and tight junction proteins. This may alleviate AD symptoms, such as dermatitis scores, epidermal hyperplasia and mast cell infiltration. These results offer a rationale for further preclinical/clinical studies to evaluate the possible use of GDU-952 in the management of AD.

The SOD7/DPA4-GIF1 module coordinates organ growth and iron uptake in Arabidopsis.

Organ growth is controlled by both intrinsic genetic factors and external environmental signals. However, the molecular mechanisms that coordinate plant organ growth and nutrient supply remain largely unknown. We have previously reported that the B3 domain transcriptional repressor SOD7 (NGAL2) and its closest homologue DPA4 (NGAL3) act redundantly to limit organ and seed growth in Arabidopsis. Here we report that SOD7 represses the interaction between the transcriptional coactivator GRF-INTERACTING FACTOR 1 (GIF1) and growth-regulating factors (GRFs) by competitively interacting with GIF1, thereby limiting organ and seed growth. We further reveal that GIF1 physically interacts with FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), which acts as a central regulator of iron uptake and homeostasis. SOD7 can competitively repress the interaction of GIF1 with FIT to influence iron uptake and responses. The sod7-2 dpa4-3 mutant enhances the expression of genes involved in iron uptake and displays high iron accumulation. Genetic analyses support that GIF1 functions downstream of SOD7 to regulate organ and seed growth as well as iron uptake and responses. Thus, our findings define a previously unrecognized mechanism that the SOD7/DPA4-GIF1 module coordinates organ growth and iron uptake by targeting key regulators of growth and iron uptake.

The two-component system expression patterns and immune regulatory mechanism of Vibrio parahaemolyticus with different genotypes at the early stage of infection in THP-1 cells.

Vibrio parahaemolyticus must endure various challenging circumstances while being swallowed by phagocytes of the innate immune system. Moreover, bacteria should recognize and react to environmental signals quickly in host cells. Two-component system (TCS) is an important way for bacteria to perceive external environmental signals and transmit them to the interior to trigger the associated regulatory mechanism. However, the regulatory function of V. parahaemolyticus TCS in innate immune cells is unclear. Here, the expression patterns of TCS in V. parahaemolyticus-infected THP-1 cell-derived macrophages at the early stage were studied for the first time. Based on protein-protein interaction network analysis, we mined and analyzed seven critical TCS genes with excellent research value in the V. parahaemolyticus regulating macrophages, as shown below. VP1503, VP1502, VPA0021, and VPA0182 could regulate the ATP-binding-cassette (ABC) transport system. VP1735, uvrY, and peuR might interact with thermostable hemolysin proteins, DNA cleavage-related proteins, and TonB-dependent siderophore enterobactin receptor, respectively, which may assist V. parahaemolyticus in infected macrophages. Subsequently, the potential immune escape pathways of V. parahaemolyticus regulating macrophages were explored by RNA-seq. The results showed that V. parahaemolyticus might infect macrophages by controlling apoptosis, actin cytoskeleton, and cytokines. In addition, we found that the TCS (peuS/R) could enhance the toxicity of V. parahaemolyticus to macrophages and might contribute to the activation of macrophage apoptosis. IMPORTANCE This study could offer crucial new insights into the pathogenicity of V. parahaemolyticus without tdh and trh genes. In addition, we also provided a novel direction of inquiry into the pathogenic mechanism of V. parahaemolyticus and suggested several TCS key genes that may assist V. parahaemolyticus in innate immune regulation and interaction.

FAR-RED ELONGATED HYPOCOTYL3 increases leaf longevity by delaying senescence in arabidopsis.

Senescence is the final stage of leaf development, limits and dictates the longevity of leaf. This stage is strictly controlled by internal developmental age signals and external environmental signals. However, the underlying mechanisms by which various signals integrating together to regulate leaf senescence remain largely unknown. Here, we show that the light signalling protein FAR-RED ELONGATED HYPOCOTYL3 (FHY3) directly represses the transcription of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and NON-YELLOWING1/STAY-GREEN1 (NYE1/SGR1), two key regulators of senescence, thus preventing chlorophyll degradation and extending the leaf longevity in Arabidopsis thaliana. Disrupting either PIF4 or NYE1 function completely rescued the early leaf senescence of fhy3-4 mutant. Interestingly, we found that FHY3 competes with PIF4 to bind to the G-box cis-element in NYE1 promoter, subsequently preventing the transcriptional activation of this gene by PIF4. Moreover, FHY3 transcript levels gradually increased in senescent leaves, which consist with disrupting FHY3 function accelerated chlorophyll degradation and shorted the leaf longevity. All these findings reveal that FHY3 is a master regulator that participates in multiple signalling pathways to increase leaf longevity. In addition, our study shed light on the dynamic regulatory mechanisms by which plants integrate light signalling and internal developmental cues to control leaf senescence and longevity.

Disassembly of fascin bundled actin by MICAL.

Actin is an abundant cytoskeleton protein that constantly transitions between its monomeric (G-actin) and filamentous (F-actin) forms. F-actin further assembles into higher-order structures, such as bundles. Fascin facilitates that step by crosslinking F-actin into parallel and dense bundles. Fascin-actin bundles are the main constituents of filopodia in humans and Drosophila's bristles, and they play a vital role in cell motility and the sensing of external environmental signals. The mechanism of actin bundles formation is understood better than that of their disassembly. Recently, the MICAL family of oxidation-reduction (redox) enzymes has emerged as a new class of actin filaments disassembly proteins. Mical's oxidizes F-actin via direct interactions in response to different growth factors and repulsive guidance cues. Using biochemical, imaging, and in vivo studies, we unraveled the mechanism by which Mical mediates the disassembly of bundled actin. Mical-oxidized actin shows impaired bundles formation, resulting in loose bundles that become an easy target for other known severing proteins. Overall, our results shed new light on the mechanism of actin bundles disassembly and its impact on cellular remodeling.

Low-Dimensional-Materials-Based Flexible Artificial Synapse: Materials, Devices, and Systems.

With the rapid development of artificial intelligence and the Internet of Things, there is an explosion of available data for processing and analysis in any domain. However, signal processing efficiency is limited by the Von Neumann structure for the conventional computing system. Therefore, the design and construction of artificial synapse, which is the basic unit for the hardware-based neural network, by mimicking the structure and working mechanisms of biological synapses, have attracted a great amount of attention to overcome this limitation. In addition, a revolution in healthcare monitoring, neuro-prosthetics, and human-machine interfaces can be further realized with a flexible device integrating sensing, memory, and processing functions by emulating the bionic sensory and perceptual functions of neural systems. Until now, flexible artificial synapses and related neuromorphic systems, which are capable of responding to external environmental stimuli and processing signals efficiently, have been extensively studied from material-selection, structure-design, and system-integration perspectives. Moreover, low-dimensional materials, which show distinct electrical properties and excellent mechanical properties, have been extensively employed in the fabrication of flexible electronics. In this review, recent progress in flexible artificial synapses and neuromorphic systems based on low-dimensional materials is discussed. The potential and the challenges of the devices and systems in the application of neuromorphic computing and sensory systems are also explored.

Achieving Single-Molecule Tracking of Subcellular Regulation in Bacteria during Real-Time Environmental Perturbations.

Bacteria rely on protein systems for regulation in response to external environmental signals. Single-molecule fluorescence imaging and tracking has elucidated the complex mechanism of these protein systems in a variety of bacteria. We recently investigated Vibrio cholerae, the Gram-negative bacterium responsible for the human cholera disease, and its regulation of the production of toxins and virulence factors through the membrane-localized transcription factors TcpP and ToxR. These experiments determined that TcpP and ToxR work cooperatively under steady-state conditions, but measurements of how these dynamical interactions change over the course of environmental perturbations were precluded by the traditional preparation of bacterial cells confined on agarose pads. Here, we address this gap in technology and access single-molecule dynamics during real-time changes by implementing two alternative sample preparations: microfluidic devices and chitosan-coated coverslips. We report the first demonstration of single-molecule tracking within live bacterial cells in a microfluidic device. Additionally, using the chitosan-coated coverslips, we show that real-time environmental changes impact TcpP-PAmCherry dynamics, activating a virulence condition in the bacteria about 45 min after dropping to pH 6 and about 20 min after inducing ToxR expression. These new technology advances open our ability for new experiments studying a variety of bacteria with single-molecule imaging and tracking during real-time environmental perturbations.

Leaf senescence of Christella hispidula (Decne.) Holttum throughout climatic seasons in an urban park with a remnant of the Atlantic Forest

The term senescence is used mainly for plants to define genetically programmed degenerative physiological changes. Leaf senescence is the result of internal and external environmental signals as well as information on leaf age. Christella hispidula (Decne.) Holttum is a species of fern characterized by its adaptation ease and consequent broad occupation of different environments. The aim of the present study was to investigate the phenology of C. hispidula in a remnant of the Atlantic Forest to gain knowledge on abiotic and biotic factors associated with leaf senescence throughout the seasons. Multiple regression analysis was used to estimate correlations between leaf senescence and both the occurrence of herbivory and presence of sori in the population studied. Positive correlations were found with these two variables. Senescence increased significantly with each new sign of herbivory on the plant (p = 0.46) and with the emergence of sori on the plant (p = 0.02). The multiple coefficients of determination (R2= 0.47) explained approximately 47% of the dependence of senescence on herbivory and sori. The findings reveal that the seasons exert an influence on leaf senescence in C. hispidula.

DNA Methylation Inhibitor 5-Azacytidine Promotes Leaf Senescence in Pak Choi (Brassica rapa subsp. chinensis) by Regulating Senescence-Related Genes

Leaf senescence is strictly regulated by multiple internal factors and external environmental signals, with the epigenetic modification being an important element among them. However, the epigenetic mechanism of leaf senescence is largely unknown in horticultural crops, especially the leaf vegetable pak choi, which easily senesces, and becomes yellow post-harvest. In this study, we found that the expression of DNA methyltransferases (BcMET1, BcSUVH4, BcDRM2, BcRDR2, and BcCMT3) of pak choi decreased during storage. The preliminary results showed that its senescence process was accompanied by DNA methylation changes. Moreover, treatment with 500 μM 5-Azacytidine (5-Aza) (DNA methylation inhibitor) can promote the senescence of pak choi leaves by (1) increasing the degradation of chlorophyll (Chl) and its derivatives, (2) increasing the activities of Mg-dechelatase (MDCase), pheophytinase (PPH) and pheophorbide a oxygenase (PAO), and (3) inducing the expression of senescence-related genes (BcSAG12, BcNYC1, BcSGR1, BcSGR2, BcPPH1, BcPPH2, BcPAO, and BcRCCR), thereby accelerating the senescence of the pak choi leaves. Further studies showed that DNA demethylation occurred in the promoter regions of BcSGR2 and BcSAG12 during storage, with the bisulfite sequencing detection showing that their degrees of methylation decreased. Therefore, our findings help us understand how epigenetic modifications affect the storage tolerance of leafy vegetables, which is highly significant for cultivating anti-senescent vegetable varieties.

Temporal variation in DNA methylation during gonadal development in a reptile with temperature-dependent sex determination†.

DNA methylation plays a significant role in transducing external environmental signals to a cellular response in reptiles; however, whether the methylation patterns are conserved across species remains unclear. Here, we examined the genome-wide DNA methylation differentiation between male and female hatchling gonads of the temperature-dependent sex determination (TSD) Mauremys mutica (M. mutica) using methylation-dependent restriction-site associated DNA sequencing (MethylRAD-seq) to test differentially methylated genes underlying sexual development. Several categories, including heat-shock genes (HSP90A, HSP30C), histone- (KDM8) and ubiquitin-related genes (TRIM39), kinases (WNK3), and gonad differentiation or gonadal-development-related genes (HSD17B8, HSD17B12), were identified as candidates for future study. Additionally, we identified several regulatory pathways potentially mediating TSD thermosensitivity such as the GnRH signaling pathway and calcium signaling pathway. These findings provide evidence that sexually dimorphic DNA methylation may be associated with sex determination or sex differentiation in TSD M. mutica.

BBX24 Interacts with DELLA to Regulate UV-B-Induced Photomorphogenesis in Arabidopsis thaliana.

UV-B radiation, sensed by the photoreceptor UVR8, induces signal transduction for plant photomorphogenesis. UV-B radiation affects the concentration of the endogenous plant hormone gibberellin (GA), which in turn triggers DELLA protein degradation through the 26S proteasome pathway. DELLA is a negative regulator in GA signaling, partially relieving the inhibition of hypocotyl growth induced by UV-B in Arabidopsis thaliana. However, GAs do usually not work independently but integrate in complex networks linking to other plant hormones and responses to external environmental signals. Until now, our understanding of the regulatory network underlying GA-involved UV-B photomorphogenesis had remained elusive. In the present research, we investigate the crosstalk between the GA and UV-B signaling pathways in UV-B-induced photomorphogenesis of Arabidopsis thaliana. Compared with wild type Landsberg erecta (Ler), the abundance of HY5, CHS, FLS, and UF3GT were found to be down-regulated in rga-24 and gai-t6 mutants under UV-B radiation, indicating that DELLA is a positive regulator in UV-B-induced photomorphogenesis. Our results indicate that BBX24 interacts with RGA (one of the functional DELLA family members). Furthermore, we also found that RGA interacts with HY5 (the master regulator in plant photomorphogenesis). Collectively, our findings suggest that the HY5–BBX24–DELLA module serves as an important signal regulating network, in which GA is involved in UV-B signaling to regulate hypocotyl inhibition.

Agricultural Management Drive Bacterial Community Assembly in Different Compartments of Soybean Soil-Plant Continuum.

Flowering stage of soybean is an important agronomic trait, which is important for soybean yield, quality and adaptability, and is the external expression of integrating external environmental factors and endogenous signals of the plant itself. Cropping system can change soil properties and fertility, which in turn determine plant growth and yield. The microbial community is the key regulator of plant health and production performance. Currently, there is limited understanding of the effects of cropping systems on microbial community composition, ecological processes controlling community assembly in different soil-plant continuum compartments of soybean. Here, we hope to clarify the structure and assembly process of different soybean compartments bacterial community at flowering stage through our work. The results showed that intercropping decreased the species diversity of rhizosphere and phyllosphere, and phylloaphere microbes mainly came from rhizosphere. FAPROTAX function prediction showed that indicator species sensitive to intercropping and crop rotation were involved in nitrogen/phosphorus cycle and degradation process, respectively. In addition, compared to the continuous cropping, intercropping increased the stochastic assembly processes of bacterial communities in plant-associated compartments, while crop rotation increased the complexity and stability of the rhizosphere network and the deterministic assembly process. Our study highlights the importance of intercropping and crop rotation, as well as rhizosphere and phyllosphere compartments for future crop management and sustainable agricultural regulation of crop microbial communities.

Mechanisms of Weight Control by Primary Cilia.

A primary cilium, a hair-like protrusion of the plasma membrane, is a pivotal organelle for sensing external environmental signals and transducing intracellular signaling. An interesting linkage between cilia and obesity has been revealed by studies of the human genetic ciliopathies Bardet-Biedl syndrome and Alström syndrome, in which obesity is a principal manifestation. Mouse models of cell type-specific cilia dysgenesis have subsequently demonstrated that ciliary defects restricted to specific hypothalamic neurons are sufficient to induce obesity and hyperphagia. A potential mechanism underlying hypothalamic neuron cilia-related obesity is impaired ciliary localization of G protein-coupled receptors involved in the regulation of appetite and energy metabolism. A well-studied example of this is melanocortin 4 receptor (MC4R), mutations in which are the most common cause of human monogenic obesity. In the paraventricular hypothalamus neurons, a blockade of ciliary trafficking of MC4R as well as its downstream ciliary signaling leads to hyperphagia and weight gain. Another potential mechanism is reduced leptin signaling in hypothalamic neurons with defective cilia. Leptin receptors traffic to the periciliary area upon leptin stimulation. Moreover, defects in cilia formation hamper leptin signaling and actions in both developing and differentiated hypothalamic neurons. The list of obesity-linked ciliary proteins is expending and this supports a tight association between cilia and obesity. This article provides a brief review on the mechanism of how ciliary defects in hypothalamic neurons facilitate obesity.