Identification of key genes and molecular mechanisms of chronic urticaria based on bioinformatics.

Chronic urticaria (CU) is characterized by persistent skin hives, redness, and itching, enhanced by immune dysregulation and inflammation. Our main objective is identifying key genes and molecular mechanisms of chronic urticaria based on bioinformatics. We used the Gene Expression Omnibus (GEO) database and retrieved two GEO datasets, GSE57178 and GSE72540. The raw data were extracted, pre-processed, and analyzed using the GEO2R tool to identify the differentially expressed genes (DEGs). The samples were divided into two groups: healthy samples and CU samples. We defined cut-off values of log2 fold change ≥1 and p < .05. Analyses were performed in the Kyoto Encyclopaedia of Genes and Genomes (KEGG), the Database for Annotation, Visualization and Integrated Discovery (DAVID), Metascape, Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and CIBERSOFT databases. We obtained 1613 differentially expressed genes. There were 114 overlapping genes in both datasets, out of which 102 genes were up-regulated while 12 were down-regulated. The biological processes included activation of myeloid leukocytes, response to inflammations, and response to organic substances. Moreover, the KEGG pathways of CU were enriched in the Nuclear Factor-Kappa B (NF-kB) signaling pathway, Tumor Necrosis Factor (TNF) signaling pathway, and Janus kinase/signal transducers and activators of transcription (JAK-STAT) signaling pathway. We identified 27 hub genes that were implicated in the pathogenesis of CU, such as interleukin-6 (IL-6), Prostaglandin-endoperoxide synthase 2 (PTGS2), and intercellular adhesion molecule-1 (ICAM1). The complex interplay between immune responses, inflammatory pathways, cytokine networks, and specific genes enhances CU. Understanding these mechanisms paves the way for potential interventions to mitigate symptoms and improve the quality of life of CU patients.

Comprehensive analysis revealed that titanium dioxide nanoparticles could strengthen the resistance of apple rootstock B9 to saline-alkali stress.

Apple growth and development can be adversely affected by saline-alkali stress, which has become a significant factor restricting the high yield of the apple industry. In recent years, nanomaterials have become a potential source for plant growth and development. Titanium dioxide nanoparticles (TiO2 NPs) play an important role in multiple plant development processes, including mitigating environmental stress. In this study, one-year-old apple rootstock B9 stem cuttings were used as research objects. Different concentrations of TiO2 NPs were applied to the roots before saline-alkali treatment. Principal component analysis showed that 1gkg-1 TiO2 NPs treatment had the best effect in alleviating the stress for B9. It significantly reduced the damage to B9 under salt-alkali stress, increased the content of photosynthetic pigment, enhanced the performance of Photosystem II, and promoted photosynthesis. At the same time, the content of K+ was increased, and the ion toxicity was alleviated. In addition, TiO2 NPs have also been shown to reduce B9 cell damage and lipid peroxidation, increase antioxidant enzyme activity, and regulate the accumulation of solutes. Overall, this study provides a theoretical basis for TiO2 NPs to mitigate the adverse effects of plants under saline-alkali stress and provides useful insights for managing other plants affected by global salinity and alkalinity.

Acupuncture combined with pricking and cupping therapy is effective in patients with chronic spontaneous urticaria.

OBJECTIVE: To determine the effects of acupuncture combined with pricking and cupping therapy on the balance of Th1/Th2 cytokines in patients with chronic spontaneous urticaria (CSU). METHODS: The medical records of 75 patients with CSU treated in The First Affiliated Hospital of Hebei College of Traditional Chinese Medicine from January 10, 2021 to January 10, 2022 were collected and analyzed retrospectively. Among them, 35 patients treated with traditional therapy were assigned to a control group, and 40 patients treated with acupuncture combined with pricking and cupping therapy to an observation group. The clinical efficacy and adverse reactions in the two groups were compared after therapy. The two groups were also compared in terms of the levels of immunoglobulin (Ig)-E, interleukin (IL)-4 and interferon-γ (INF-γ) before and after therapy. In addition, the visual analogue scale (VAS) for pruritus was adopted for recording the pruritus degree of patients before and after therapy. The Dermatology Quality of Life Index (DLQI) was adopted to compare the quality of life between the two groups before and after therapy. The Hamilton anxiety scale (HAMA) and Hamilton depression rating scale (HAMD) were adopted for comparison of the anxiety and depression between the two groups before and after therapy. Moreover, the Pittsburgh sleep quality index (PSQI) was used to compare sleep quality between the two groups before and after therapy. RESULTS: The control group showed a significantly lower total response rate than the observation group (P<0.05). Compared with the control group, the observation group showed significantly lower levels of IgE and IL-4, and a higher IFN-γ level and had significantly lower pruritus-VAS, DLQI, HAMA, HAMD and PSQI scores (P<0.05). Additionally, the two groups were not greatly different in adverse reactions (nausea, sleepiness, ecchymosis and dizziness) (P>0.05). CONCLUSION: Acupuncture combined with pricking and cupping therapy is highly effective in CSU, because it can significantly alleviate the symptoms as well as negative emotions, and improve the quality of life, sleep quality and the balance of Th1/Th2 cytokine in patients.

Interactions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.).

The response of plant growth and development to nutrient and water availability is an important adaptation for abiotic stress tolerance. Roots need to intercept both passing nutrients and water while foraging into new soil layers for further resources. Substantial amounts of nitrate can be lost in the field when leaching into groundwater, yet very little is known about how deep rooting affects this process. Here, we phenotyped root system traits and deep 15N nitrate capture across 1.5 m vertical profiles of solid media using tall mesocosms in switchgrass (Panicum virgatum L.), a promising cellulosic bioenergy feedstock. Root and shoot biomass traits, photosynthesis and respiration measures, and nutrient uptake and accumulation traits were quantified in response to a water and nitrate stress factorial experiment for switchgrass upland (VS16) and lowland (AP13) ecotypes. The two switchgrass ecotypes shared common plastic abiotic responses to nitrogen (N) and water availability, and yet had substantial genotypic variation for root and shoot traits. A significant interaction between N and water stress combination treatments for axial and lateral root traits represents a complex and shared root development strategy for stress mitigation. Deep root growth and 15N capture were found to be closely linked to aboveground growth. Together, these results represent the wide genetic pool of switchgrass and show that deep rooting promotes nitrate capture, plant productivity, and sustainability.

RhizoVision Explorer: open-source software for root image analysis and measurement standardization.

Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo™, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo™. The two software showed general agreement, except that WinRhizo™ substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.

A multiple ion-uptake phenotyping platform reveals shared mechanisms affecting nutrient uptake by roots.

Nutrient uptake is critical for crop growth and is determined by root foraging in soil. Growth and branching of roots lead to effective root placement to acquire nutrients, but relatively little is known about absorption of nutrients at the root surface from the soil solution. This knowledge gap could be alleviated by understanding sources of genetic variation for short-term nutrient uptake on a root length basis. A modular platform called RhizoFlux was developed for high-throughput phenotyping of multiple ion-uptake rates in maize (Zea mays L.). Using this system, uptake rates were characterized for the crop macronutrients nitrate, ammonium, potassium, phosphate, and sulfate among the Nested Association Mapping (NAM) population founder lines. The data revealed substantial genetic variation for multiple ion-uptake rates in maize. Interestingly, specific nutrient uptake rates (nutrient uptake rate per length of root) were found to be both heritable and distinct from total uptake and plant size. The specific uptake rates of each nutrient were positively correlated with one another and with specific root respiration (root respiration rate per length of root), indicating that uptake is governed by shared mechanisms. We selected maize lines with high and low specific uptake rates and performed an RNA-seq analysis, which identified key regulatory components involved in nutrient uptake. The high-throughput multiple ion-uptake kinetics pipeline will help further our understanding of nutrient uptake, parameterize holistic plant models, and identify breeding targets for crops with more efficient nutrient acquisition.

Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture.

The root economics space is a useful framework for plant ecology but is rarely considered for crop ecophysiology. In order to understand root trait integration in winter wheat, we combined functional phenomics with trait economic theory, utilizing genetic variation, high-throughput phenotyping, and multivariate analyses. We phenotyped a diversity panel of 276 genotypes for root respiration and architectural traits using a novel high-throughput method for CO2 flux and the open-source software RhizoVision Explorer to analyze scanned images. We uncovered substantial variation in specific root respiration (SRR) and specific root length (SRL), which were primary indicators of root metabolic and structural costs. Multiple linear regression analysis indicated that lateral root tips had the greatest SRR, and the residuals from this model were used as a new trait. Specific root respiration was negatively correlated with plant mass. Network analysis, using a Gaussian graphical model, identified root weight, SRL, diameter, and SRR as hub traits. Univariate and multivariate genetic analyses identified genetic regions associated with SRR, SRL, and root branching frequency, and proposed gene candidates. Combining functional phenomics and root economics is a promising approach to improving our understanding of crop ecophysiology. We identified root traits and genomic regions that could be harnessed to breed more efficient crops for sustainable agroecosystems.

RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping.

Root crown phenotyping measures the top portion of crop root systems and can be used for marker-assisted breeding, genetic mapping, and understanding how roots influence soil resource acquisition. Several imaging protocols and image analysis programs exist, but they are not optimized for high-throughput, repeatable, and robust root crown phenotyping. The RhizoVision Crown platform integrates an imaging unit, image capture software, and image analysis software that are optimized for reliable extraction of measurements from large numbers of root crowns. The hardware platform utilizes a backlight and a monochrome machine vision camera to capture root crown silhouettes. The RhizoVision Imager and RhizoVision Analyzer are free, open-source software that streamline image capture and image analysis with intuitive graphical user interfaces. The RhizoVision Analyzer was physically validated using copper wire, and features were extensively validated using 10,464 ground-truth simulated images of dicot and monocot root systems. This platform was then used to phenotype soybean and wheat root crowns. A total of 2,799 soybean (Glycine max) root crowns of 187 lines and 1,753 wheat (Triticum aestivum) root crowns of 186 lines were phenotyped. Principal component analysis indicated similar correlations among features in both species. The maximum heritability was 0.74 in soybean and 0.22 in wheat, indicating that differences in species and populations need to be considered. The integrated RhizoVision Crown platform facilitates high-throughput phenotyping of crop root crowns and sets a standard by which open plant phenotyping platforms can be benchmarked.

Maize with fewer nodal roots allocates mass to more lateral and deep roots that improve nitrogen uptake and shoot growth.

Simulations indicated that reduced nodal root (NR) number (NRN) was promising for maize breeding, and were partially confirmed by relying on variation in NRN among inbreds. Using maize inbred line B73, experiments were conducted in hydroponics and tall mesocosms containing solid media with treatments involving no NR excision (0% NRE) or excising either 33% or 67% of the NRs as they emerged under high or low levels of nitrogen (N). Reduced NRN was hypothesized to increase elongation of all remaining root classes, N acquisition under low N, and shoot mass. Plants with 67% NRE had 12% and 19% less root mass fraction, 61% and 91% greater lateral to axial root length ratio regardless of N levels, and 61% and 182% greater biomass of embryonic roots under low N, compared with 0% NRE for hydroponics and mesocosms studies, respectively. Under low N in mesocosms, plants with 67% NRE had 52% greater shoot biomass, 450% greater root length at depth, and 232% greater deep-injected 15N content in the shoot relative to 0% NRE. These results reveal the mechanism by which plants with fewer NRs increase N capture and shoot mass by reallocation of biomass to lateral roots, embryonic roots, and first whorl NRs that increases foraging efficiency in solid media.

Photonic RF vector signal generation with enhanced spectral efficiency using precoded double single-sideband modulation.

In this study, a novel photonic vector signal at frequency (RF) bands generation scheme based on the beating of double single sidebands (SSBs) is proposed and experimentally demonstrated. The double SSBs carry separate constant- or multi-amplitude quadrature-amplitude-modulation vector signals are generated from a single I/Q modulator. By adopting phase and amplitude precoding, different constellations can be generated, such as 3-ary phase-shift keying (PSK), 4-PSK, 7-PSK, 8-PSK, and so on. In this work, 10-Gbaud 7-PSK vector signal generation at 20 GHz enabled by two precoded 4-PSK SSB signals via a single I/Q modulator is theoretically and experimentally investigated. Compared to a single-drive Mach-Zehnder modulator or conventional I/Q modulator-based photonic vector signal generation scheme, the spectrum efficiency can be doubled. Differential coding is also implemented at the transmitter side for accurate demodulation of 7-PSK into two 4-PSK signals. The bit-error ratio for 10-Gbaud 7-PSK vector signals can be under hard-decision forward-error-correction threshold of 3.8×10-3 after 10 km standard single-mode fiber transmission.

Phosphorus status and microbial community of paddy soil with the growth of annual ryegrass (Lolium multiflorum Lam.) under different phosphorus fertilizer treatments.

Annual ryegrass (Lolium multiflorum Lam.) was grown in paddy soil in pots under different phosphorus (P) fertilizer treatments to investigate changes of P fractions and microbial community of the soil. The treatments included Kunyang phosphate rock (KPR) applications at 50 mg P/kg (KPR(50)) and 250 mg P/kg (KPR(250)), mono-calcium phosphate (MCP) application at 50 mg P/kg (MCP(50)), and the control without P application. The results showed that KPR(50), KPR(250), and MCP(50) applications significantly increased the dry weight of the ryegrass by 13%, 38%, and 55%, and increased P uptake by 19%, 135%, and 324%, respectively. Compared with MCP(50), the relative effectiveness of KPR(50) and KPR(250) treatments in ryegrass production was about 23% and 68%, respectively. After one season of ryegrass growth, the KPR(50), KPR(250), and MCP(50) applications increased soil-available P by 13.4%, 26.8%, and 55.2%, respectively. More than 80% of the applied KPR-P remained as HCl-P fraction in the soil. Phospholipid fatty acid (PLFA) analysis showed that the total and bacterial PLFAs were significantly higher in the soils with KPR(250) and MCP(50) treatments compared with KPR(50) and control. The latter had no significant difference in the total or bacterial PLFAs. The KPR(50), KPR(250), and MCP(50) treatments increased fungal PLFA by 69%, 103%, and 69%, respectively. Both the principal component analysis and the cluster analysis of the PLFA data suggest that P treatments altered the microbial community composition of the soils, and that P availability might be an important contributor to the changes in the microbial community structure during the ryegrass growth in the paddy soils.

Microbial community structure changes during Aroclor 1242 degradation in the rhizosphere of ryegrass (Lolium multiflorum L.).

Polychlorinated biphenyls in a commercial mixture (Aroclor 1242) were added to soil at 8.0 mg kg(-1) with and without ryegrass (Lolium multiflorum L.) planted in a specially designed rhizobox. At the end of 90 days, the presence of plants significantly increased Aroclor 1242 degradation compared with soils without ryegrass. Phospholipid fatty acids (PLFAs) profiles were affected by the distance from the rhizosphere, indicating a distance-dependent selective enrichment of competent species that may be responsible for efficient Aroclor 1242 degradation. The highest concentration of total PLFAs also occurred at 3 mm from the root zone in planted soils. The numbers of bacteria (cy17:0, 16:0), gram-positive bacteria (a15:0, i16:1, a17:0) and actinomycete (18:2 omega 6,9c) were significantly higher in planted soils than in unplanted soils. Furthermore, individual PLFAs [i16:0, 16:0 N alcohol, 18:0(10Me), i16:1, a15:0, i14:1, 14:0 2OH, 18:1 omega 9c, a17:0, 14:0 3OH, i14:0, a16:0, 16:1 omega 5c] were strongly correlated with the Aroclor 1242 degradation rates (%) (P<0.05) in planted treatments, whereas individual PLFAs of i16:1, 12:0 3OH, 15:0, a15:0 had significant correlations with the Aroclor 1242 degradation rates (%) (P<0.05) in unplanted soils. In particular, individual PLFAs i16:1 had strong correlations with Aroclor 1242 degradation in treatments both with and without ryegrass.

Effects of nitrogen fertilization strategies on nitrogen use efficiency in physiology, recovery, and agronomy and redistribution of dry matter accumulation and nitrogen accumulation in two typical rice cultivars in Zhejiang, China.

Field experiments were conducted in farmers' rice fields in 2001 and 2002 to study the effects of nitrogen (N) management strategies on N use efficiency in recovery (RE), agronomy (AE) and physiology (PE) and redistribution of dry matter accumulation (DMA) and nitrogen accumulation (NA) in two typical rice cultivars in Jinhua, Zhejiang Province. This study aimed mainly at identifying the possible causes of poor fertilizer N use efficiency (NUE) of rice in Zhejiang by comparing farmers' fertilizer practice (FFP) with advanced site-specific nutrient management (SSNM) and real-time N management (RTNM). The results showed that compared to FFP, SSNM and RTNM reduced DMA and NA before panicle initiation and increased DMA and NA at post-flowering. There is no significant difference between SSNM and FFP in post-flowering dry matter redistribution (post-DMR) and post-flowering nitrogen redistribution (post-NR). These results suggest that high input rate of fertilizer N and improper fertilizer N timing are the main factors causing low NUE of irrigated rice in the farmer's routine practice of Zhejiang. With SSNM, about 15% of the current total N input in direct-seeding early rice and 45% in single rice could be reduced without yield loss in Zhejiang, China.