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Search Results (586)

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10 pages, 325 KiB  
Communication
High Prevalence of aCL-IgA and aβ2GPI-IgA in Drug-Free Schizophrenia Patients: Evidence of a Potential Autoimmune Link
by Samar Samoud, Imen Zamali, Fatma Korbi, Ahlem Mtiraoui, Ahlem Ben Hmid, Neila Hannachi, Yousr Galai, Hechmi Louzir and Yousri El Kissi
Antibodies 2024, 13(4), 92; https://doi.org/10.3390/antib13040092 - 15 Nov 2024
Viewed by 268
Abstract
Background/Objectives: Schizophrenia (SZ) is a complex psychiatric disorder with increasing evidence pointing to an autoimmune component, including the presence of antiphospholipid antibodies (aPLs). This study aims to assess the prevalence of anticardiolipin (aCL) and anti-beta-2 glycoprotein I (aβ2GPI) antibodies, particularly the IgG, IgA, [...] Read more.
Background/Objectives: Schizophrenia (SZ) is a complex psychiatric disorder with increasing evidence pointing to an autoimmune component, including the presence of antiphospholipid antibodies (aPLs). This study aims to assess the prevalence of anticardiolipin (aCL) and anti-beta-2 glycoprotein I (aβ2GPI) antibodies, particularly the IgG, IgA, and IgM isotypes, in drug-free SZ patients compared to healthy controls, and explore their possible involvement in the disease’s pathophysiology. Methods: Eighty SZ patients meeting DSM-IV criteria were recruited, along with 80 matched healthy controls. Serum samples were analyzed using enzyme-linked immunosorbent assays (ELISA) to quantify IgG, IgA, and IgM isotypes of aCL and aβ2GPI. Results: SZ patients exhibited significantly higher levels of aCL-IgM and aCL-IgA (p < 0.05), as well as elevated aβ2GPI-IgA (22.5%, p < 0.001), compared to controls. No significant differences were observed in the aCL-IgG isotype. Interestingly, 72% of aPL-positive SZ patients were positive for aβ2GPI-IgA, with some also co-expressing multiple isotypes, suggesting a potential link between SZ and antiphospholipid syndrome (APS). Conclusions: This study is the first to report a high prevalence of aCL-IgA and aβ2GPI-IgA in SZ patients, highlighting a possible autoimmune involvement in the disease. The presence of multiple aPL isotypes, particularly IgA, suggests a need for further investigation into their role in SZ pathogenesis and their potential association with APS. Full article
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<p>Distribution of aCL (IgG, IgA, and IgM) and aβ2GPI (IgG, IgA, and IgM) in patients and controls.</p>
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10 pages, 842 KiB  
Article
Detection of Elementary White Mucosal Lesions by an AI System: A Pilot Study
by Gaetano La Mantia, Federico Kiswarday, Giuseppe Pizzo, Giovanna Giuliana, Giacomo Oteri, Mario G. C. A. Cimino, Olga Di Fede and Giuseppina Campisi
Oral 2024, 4(4), 557-566; https://doi.org/10.3390/oral4040043 - 14 Nov 2024
Viewed by 265
Abstract
Aim: Accurately identifying primary lesions in oral medicine, particularly elementary white lesions, is a significant challenge, especially for trainee dentists. This study aimed to develop and evaluate a deep learning (DL) model for the detection and classification of elementary white mucosal lesions (EWMLs) [...] Read more.
Aim: Accurately identifying primary lesions in oral medicine, particularly elementary white lesions, is a significant challenge, especially for trainee dentists. This study aimed to develop and evaluate a deep learning (DL) model for the detection and classification of elementary white mucosal lesions (EWMLs) using clinical images. Materials and Methods: A dataset was created by collecting photographs of various oral lesions, including oral leukoplakia, OLP plaque-like and reticular forms, OLL, oral candidiasis, and hyperkeratotic lesions from the Unit of Oral Medicine. The SentiSight.AI (Neurotechnology Co.®, Vilnius, Lithuania) AI platform was used for image labeling and model training. The dataset comprised 221 photos, divided into training (n = 179) and validation (n = 42) sets. Results: The model achieved an overall precision of 77.2%, sensitivity of 76.0%, F1 score of 74.4%, and mAP of 82.3%. Specific classes, such as condyloma and papilloma, demonstrated high performance, while others like leucoplakia showed room for improvement. Conclusions: The DL model showed promising results in detecting and classifying EWMLs, with significant potential for educational tools and clinical applications. Expanding the dataset and incorporating diverse image sources are essential for improving model accuracy and generalizability. Full article
(This article belongs to the Special Issue Current Issues in Oral Health)
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<p>The graph shows the mAP during the training of the Faster R-CNN model with ResNet-101. Initially, the validation mAP is low, but it rises as the model learns. The mAP fluctuates due to the complexity of the data but peaks at 47 min and 22 s, indicating the best model performance. This peak is marked by a dashed red line. After this point, the mAP stabilizes or slightly declines, suggesting that further training may lead to overfitting. In summary, the graph highlights the optimal model performance at 47 min and 22 s, balancing accuracy and generalization.</p>
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<p>Normalized confusion matrix for multiclass performance. The values on the diagonal represent the <span class="html-italic">TP</span>, indicating the proportion of correct classifications for each class. The proportions of misclassifications for each class are shown in the far-right column, labeled as “NC”, which represents <span class="html-italic">FN</span>. These are cases where the model failed to classify an image into any of the specified classes. The other cells outside the diagonal represent <span class="html-italic">FP</span>, where the model incorrectly classified an image as belonging to a particular class when it did not. Abbreviations: STR/RET, striate-reticular lesions; MB, morsicatio buccarum; LA, linea alba; LEU, leukoplakia; CON/PAP, condyloma–papilloma; CAN, oral candidiasis; NC, not classified.</p>
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11 pages, 1647 KiB  
Article
Effect of SARS-CoV-2 Infection on Selected Parameters of the Apelinergic System in Repeat Blood Donors
by Marta Stanek, Anna Leśków and Dorota Diakowska
Biomedicines 2024, 12(11), 2583; https://doi.org/10.3390/biomedicines12112583 - 12 Nov 2024
Viewed by 573
Abstract
Background: SARS-CoV-2 enters cells primarily by binding to the angiotensin-converting enzyme 2 (ACE2) receptor, thereby blocking its physiological functions, affecting the apelinergic system, and inhibiting the cleavage of its peptides. The appropriate concentration of peptides in the apelinergic system influences the maintenance [...] Read more.
Background: SARS-CoV-2 enters cells primarily by binding to the angiotensin-converting enzyme 2 (ACE2) receptor, thereby blocking its physiological functions, affecting the apelinergic system, and inhibiting the cleavage of its peptides. The appropriate concentration of peptides in the apelinergic system influences the maintenance of homeostasis and protects against cardiovascular diseases. In our research, we determined the level of selected parameters of the apelinergic system—apelin (AP), elabela (ELA), and the apelin receptor (APJ)—in repeat blood donors. Methods: We analyzed 120 serum samples obtained from 30 repeat donors (study group) within four time periods after a SARS-CoV-2 infection: <60 days, 61–90 days, 91–120 days, and >120 days. We compared the results from the study groups with those of the control group, which consisted of 30 serum samples collected from donors donating blood in the years 2018–2019. Results: We observed that the AP, ELA, and APJ concentrations in the control group are higher than in any period in the study group. In the study group, the concentrations of AP and ELA increased in subsequent study periods. AP and ELA concentrations were lower shortly after SARS-CoV-2 transfection and then slowly increased in subsequent periods. APJ concentrations, on the other hand, were lowest at 61–90 days after the infection, but the decrease, relative to their level in healthy subjects, was significant in every period studied. Conclusions: The results suggest that infection with SARS-CoV-2 causes changes in the parameters of the apelinergic system, both after a short period of time has passed since the onset of the SARS-CoV-2 infection, and even up to 4 months after the infection. Full article
(This article belongs to the Section Endocrinology and Metabolism Research)
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<p>Selection of the study group.</p>
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<p>The concentration of AP in the serum of repeat blood donors in 4 time periods after SARS-CoV-2 infection. Horizontal dashed line indicates the average concentration of the tested parameter determined in the control group. *: Period 1 vs. Period 4, <span class="html-italic">p</span> = 0.004; **: Period 2 vs. Period 3, <span class="html-italic">p</span> = 0.006; ***: Period 2 vs. Period 4, <span class="html-italic">p</span> &lt; 0.001; #: Period 3 vs. Period 4, <span class="html-italic">p</span> &lt; 0.001.</p>
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<p>The concentration of ELA in the serum of repeat blood donors in 4 time periods after SARS-CoV-2 infection. Horizontal dashed line indicates the average concentration of the tested parameter determined in the control group. *: Period 1 vs. Period 2, <span class="html-italic">p</span> = 0.002; **: Period 1 vs. Period 3, <span class="html-italic">p</span> &lt; 0.001; ***: Period 1 vs. Period 4, <span class="html-italic">p</span> &lt; 0.001; #: Period 2 vs. Period 3, <span class="html-italic">p</span> = 0.017; ##: Period 2 vs. Period 4, <span class="html-italic">p</span> = 0.002; ###: Period 3 vs. Period 4, <span class="html-italic">p</span> = 0.002.</p>
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<p>The concentration of APJ in the serum of repeat blood donors in 4 time periods after SARS-CoV-2 infection. Horizontal dashed line indicates the average concentration of the tested parameter determined in the control group. *: Period 1 vs. Period 2, <span class="html-italic">p</span> = 0.002; **: Period 1 vs. Period 3, <span class="html-italic">p</span> = 0.002; ***: Period 2 vs. Period 4, <span class="html-italic">p</span> = 0.044; #: Period 3 vs. Period 4, <span class="html-italic">p</span> = 0.002.</p>
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<p>Heatmap for correlation coefficients of selected variables. Red color indicates a statistically significant correlation between AP and APJ (R = 0.566, <span class="html-italic">p</span> = 0.001).</p>
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20 pages, 7608 KiB  
Article
Anti-Sintering Behavior of GYYSZ, Thermophysical Properties, and Thermal Shock Behavior of Thermal Barrier Coating with YSZ/Composite/GYYSZ System by Atmospheric Plasma Spraying
by Chunxia Jiang, Rongbin Li, Feng He, Zhijun Cheng, Wenge Li and Yuantao Zhao
Nanomaterials 2024, 14(22), 1787; https://doi.org/10.3390/nano14221787 - 7 Nov 2024
Viewed by 488
Abstract
In this study, Gd2O3 and Yb2O3 co-doped YSZ (GYYSZ) ceramic coatings were prepared via atmospheric plasma spraying (APS). The GYYSZ ceramic coatings were subjected to heat treatment at different temperatures for 5 h to analyze their high-temperature [...] Read more.
In this study, Gd2O3 and Yb2O3 co-doped YSZ (GYYSZ) ceramic coatings were prepared via atmospheric plasma spraying (APS). The GYYSZ ceramic coatings were subjected to heat treatment at different temperatures for 5 h to analyze their high-temperature phase stability and sintering resistance. The thermophysical properties of GYYSZ, YSZ, and composite coatings were compared. Three types of thermal barrier coatings (TBCs) were designed: GYYSZ (TBC-1), YSZ/GYYSZ (TBC-2), and YSZ/Composite/GYYSZ (TBC-3). The failure mechanisms of these three TBCs were investigated. The results indicate that both the powder and the sprayed GYYSZ primarily maintain a homogeneous cubic phase c-ZrO2, remaining stable at 1500 °C after annealing. The sintering and densification of the coatings are influenced by the annealing temperature; higher temperatures lead to faster sintering rates. At 1500 °C, the grain size and porosity of GYYSZ are 4.66 μm and 9.9%, respectively. At 1000 °C, the thermal conductivity of GYYSZ is 1.35 W·m−1 K−1, which is 44% lower than that of YSZ. The thermal conductivity of the composite material remains between 1.79 W·m−1 K−1 and 1.99 W·m−1 K−1 from room temperature to 1000 °C, positioned between GYYSZ and YSZ. In the TBC thermal shock water quenching experiment, TBC-3 demonstrated an exceptionally long thermal shock lifetime of 246.3 cycles, which is 5.8 times that of TBC-1 and 1.8 times that of TBC-2. The gradient coating structure effectively reduces the thermal mismatch stress between layers, while the dense surface microcracks provide a certain toughening effect. Failure analysis of the TBC reveals that TBC-3 exhibits a mixed failure mode characterized by both spallation and localized peeling. The ultimate failure was attributed to the propagation of transverse cracks during the final stage of water quenching, which led to the eventual spallation of the ceramic blocks. Full article
(This article belongs to the Special Issue Design and Applications of Heterogeneous Nanostructured Materials)
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<p>The schematic diagrams of the TBC structures: (<b>a</b>) bilayer; (<b>b</b>) bilayer ceramic; (<b>c</b>) functionally graded ceramic.</p>
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<p>(<b>a</b>) The GYYSZ ceramic coating macroscopic photograph; (<b>b</b>,<b>c</b>) the surface morphology; and the EDS mapping.</p>
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<p>(<b>a</b>) The XRD patterns of the YSZ powder and coating; (<b>a1</b>) the XRD patterns of the YSZ ceramic coating after heat treatment for 5 h at different temperatures; (<b>a2</b>) the XRD patterns and fitting curves in the 2θ = 72.5°–75° range of the YSZ coating after heat treatment at 1300 °C; (<b>b</b>) the XRD patterns of GYYSZ in the sprayed state and powder state; (<b>b1</b>) the XRD patterns of the GYYSZ ceramic coating after heat treatment for 5 h at different temperatures.</p>
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<p>The surface morphology images of GYYSZ coatings after heat treatment for 5 h: (<b>a</b>) as-sprayed; (<b>b</b>) 1100 °C; (<b>c</b>) 1200 °C; (<b>d</b>) 1300 °C; (<b>e</b>) 1400 °C; and (<b>f</b>) 1500 °C.</p>
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<p>The grain distributions of GYYSZ coatings after heat treatment for 5 h: (<b>a</b>) as-sprayed; (<b>b</b>) 1100 °C; (<b>c</b>) 1200 °C; (<b>d</b>) 1300 °C; (<b>e</b>) 1400 °C; (<b>f</b>) 1500 °C.</p>
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<p>The cross-sectional morphology of GYYSZ coatings after heat treatment at different temperatures: (<b>a</b>) as-sprayed; (<b>b</b>) 1100 °C; (<b>c</b>) 1200 °C; (<b>d</b>) 1300 °C; (<b>e</b>) 1400 °C; (<b>f</b>) 1500 °C.</p>
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<p>(<b>a</b>) The thermal conductivity; (<b>b</b>) the thermal expansion coefficient for YSZ [<a href="#B38-nanomaterials-14-01787" class="html-bibr">38</a>], GYYSZ, and the composite material.</p>
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<p>The cross-sectional SEM images and EDS element distribution maps for (<b>a</b>) TBC-1; (<b>b</b>) TBC-2; and (<b>c</b>) TBC-3.</p>
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<p>Average thermal shock times of three different structural TBCs.</p>
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<p>Macro photographs of three TBCs after varying times of thermal cycles: (<b>a1</b>–<b>a4</b>) TBC-1; (<b>b1</b>–<b>b5</b>) TBC-2; (<b>c1</b>–<b>c6</b>) TBC-3.</p>
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<p>(<b>a</b>) The failure surface morphology of TBC-1; (<b>a1</b>) BSE diffraction image; (<b>b</b>) failure photographs of TBC-1; (<b>b1</b>) surface morphology of the failure location; (<b>b2</b>) EDS results and elemental distribution; and (<b>c</b>,<b>c1</b>) the cross-sectional microstructure of two locations of TBC-1 after thermal shock failure.</p>
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<p>(<b>a</b>) Failure surface morphology of TBC-2; (<b>a1</b>) BSE image; (<b>b</b>) failure image of TBC-1; (<b>b1</b>) surface morphology of failure area; (<b>b2</b>) EDS mapping; (<b>c</b>,<b>c1</b>) cross-sectional microstructure of TBC-1 at two locations after thermal shock failure.</p>
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<p>(<b>a</b>) The surface morphology of the failed TBC-3 coating; (<b>a1</b>) a BSE image of the non-spalled area; (<b>b</b>,<b>b1</b>) the surface morphology and EDS spectra at positions S2, and at (<b>c</b>,<b>c1</b>) S3.</p>
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<p>(<b>a</b>) The spalled area of TBC-3 after thermal cycling failure; (<b>b</b>) a local magnified view; (<b>c</b>) the cross-sections of the spall center; the (<b>d</b>) edge spall area.</p>
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22 pages, 8176 KiB  
Article
Genome-Wide Analysis of HECT E3 Ligases Members in Phyllostachys edulis Provides Insights into the Role of PeHECT1 in Plant Abiotic Stress Response
by Xinru Xie, Songping Hu, Linxiu Liu, Huanhuan Pan, Hu Huang, Xun Cao, Guirong Qiao, Xiaojiao Han, Wenmin Qiu, Zhuchou Lu, Renying Zhuo and Jing Xu
Int. J. Mol. Sci. 2024, 25(22), 11896; https://doi.org/10.3390/ijms252211896 - 5 Nov 2024
Viewed by 382
Abstract
Homology to E6-AP Carboxy Terminus (HECT) E3 ubiquitin ligases play pivotal roles in plant growth, development, and responses to abiotic stresses. However, the function of HECT genes in Phyllostachys edulis (P. edulis) remains largely uninvestigated. In this study, a comprehensive genome-wide [...] Read more.
Homology to E6-AP Carboxy Terminus (HECT) E3 ubiquitin ligases play pivotal roles in plant growth, development, and responses to abiotic stresses. However, the function of HECT genes in Phyllostachys edulis (P. edulis) remains largely uninvestigated. In this study, a comprehensive genome-wide analysis of the HECT E3 ubiquitin ligases gene family in P. edulis was conducted, aiming to elucidate its evolutionary relationships and gene expansion. Analysis of gene structure, conserved motifs and domains, and synteny genome regions were performed. Furthermore, cis-elements in HECT gene promoters that respond to plant hormones and environmental stresses were identified and corroborated by expression data from diverse abiotic stress conditions and hormone treatments. Based on the co-expression network of PeHECTs under cold and dehydration stresses, PeHECT1 was identified as a key candidate gene associated with abiotic stress tolerance. Overexpression of PeHECT1 in tobacco leaves significantly upregulated genes related to reactive oxygen species (ROS) detoxification and polyamine biosynthesis. Yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), and dual-luciferase (dual-LUC) assays suggested that the transcription factor ETHYLENE RESPONSE FACTOR 3 (PeERF3) bound to the dehydration-responsive element (DRE) of the promoter of PeHECT1 and activated its transcription activity. Phylogenetic analysis indicated that PeHECT1 in P. edulis exhibited a close association with the diploid herbaceous bamboo Olyra latifolia, followed by the divergence of rice and bamboo. In summary, this study enhances our comprehensive understanding of the HECT E3 ubiquitin ligases gene family in P. edulis and highlights the potential role of PeHECT1 in plant abiotic stress response. Full article
(This article belongs to the Special Issue Plant Resistance to Biotic and Abiotic Stresses)
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<p>Alignment of the HECT domain surrounding the active-site cysteine residue in PeHECT E3 ligases. The red box indicates the conserved cysteine residue.</p>
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<p>Phylogenetic tree of HECT E3 ligases in plants. A total of 90 HECT proteins were identified from <span class="html-italic">Phyllostachys edulis</span> (<span class="html-italic">Pe</span>), <span class="html-italic">Zea mays</span> (<span class="html-italic">Zm</span>), <span class="html-italic">Oryza sativa</span> (<span class="html-italic">Os</span>), <span class="html-italic">Glycine max</span> (<span class="html-italic">Gm</span>), <span class="html-italic">Malus domestica</span> (<span class="html-italic">Md</span>), <span class="html-italic">Sorghum bicolor</span> (<span class="html-italic">Sb</span>), <span class="html-italic">Solanum lycopersicum</span> (<span class="html-italic">Sl</span>), and <span class="html-italic">Arabidopsis thaliana</span> (<span class="html-italic">At</span>). The tree was divided into six groups, each indicated by a different color representing the background and labeled with individual HECT family names. Different colors in circles represent different species. Blue stars indicate dicotyledonous plants, while red stars indicate monocots.</p>
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<p>Gene structures, conserved motifs, and conserved domains of <span class="html-italic">P. edulis</span> HECT members. (<b>A</b>) Phylogenetic tree generated using MEGA11. (<b>B</b>) Exon/intron structure of putative <span class="html-italic">PeHECT</span> genes. Blue boxes indicate exons, while orange boxes represent 3′ or 5′ UTRs (untranslated regions). (<b>C</b>) Domain architectures of <span class="html-italic">P. edulis</span> HECT E3 ligases based on phylogenetic relationships, with each domain represented by a colored box. (<b>D</b>) Motif compositions of PeHECT E3 ligases, with differently colored boxes representing different motifs. (<b>E</b>) Sequence logo of conserved motifs one to five in the HECT domain.</p>
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<p>Scaffolds distribution of PeHECTs in <span class="html-italic">P. edulis</span>. The scale denotes the length of the <span class="html-italic">P. edulis</span> scaffolds.</p>
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<p>Synteny relationships and <span class="html-italic">Ka/Ks</span> ratios of gene pairs in the synteny regions of <span class="html-italic">PeHECTs</span> and <span class="html-italic">OsHECTs</span>. (<b>A</b>) Duplicated genes between <span class="html-italic">PeHECTs</span> and <span class="html-italic">OsHECTs</span> are indicated with red lines, while duplicated genes within <span class="html-italic">PeHECTs</span> are indicated with blue lines. (<b>B</b>) Analysis of <span class="html-italic">Ka/Ks</span> ratios for gene pairs of <span class="html-italic">PeHECTs-PeHECTs</span> and <span class="html-italic">PeHECTs-OsHECTs</span>.</p>
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<p><span class="html-italic">Cis</span>-elements analysis associated with phytohormone and abiotic stress responsiveness in the promoter regions of PeHECTs. The heatmap demonstrates the number of cis-elements, with the higher number shown in red and the lower number shown in white.</p>
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<p>The expression patterns of PeHECTs in various tissues at developmental stages. The expression patterns were analyzed based on the RNA-seq data of <span class="html-italic">P. edulis</span>. The hierarchical clustering heatmap was plotted according to the FPKM values. The red color indicates high expression levels, and the blue color indicates low levels.</p>
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<p>Expression patterns of PeHECT genes in response to different hormones. The relative expression levels of PeHECT genes were analyzed using RNA-seq data from <span class="html-italic">P. edulis</span> seedlings treated with CK, GA, NAA, SA, ABA. The expression of PeHECTs in seedlings treated with tap water was used as the reference. Data are presented as mean ± standard deviation. Student’s <span class="html-italic">t</span>-test was used to generate the <span class="html-italic">p</span> value; * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01.</p>
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<p>Expression levels of PeHECTs in response to dehydration and cold stress. The relative expression levels of PeHECT genes were analyzed using RNA-seq data from <span class="html-italic">P. edulis</span> seedlings treated with dehydration (dehy) stress and cold stress for 0 h, 2 h, and 8 h. Data are presented as mean ± standard deviation. Student’s <span class="html-italic">t</span>-test was used to generate the <span class="html-italic">p</span> value; * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01.</p>
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<p>Co-expression network analysis of the PeHECT genes. (<b>A</b>) Gene enrichment analysis in the blue modules. (<b>B</b>) Hub genes co-expressed with PeHECTs in the blue modules.</p>
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<p>Subcellular localization of <span class="html-italic">PeHECT1</span> and its potential functional validation in tobacco. (<b>A</b>) Subcellular localization of <span class="html-italic">PeHECT1</span>. Scale bar = 20 μm. (<b>B</b>) Overexpression of <span class="html-italic">PeHECT1</span> in tobacco leaves. (<b>C</b>) Analysis of relative expression of stress-related genes in tobacco. Data are presented as mean ± standard deviation. Student’s <span class="html-italic">t</span>-test was used to generate the <span class="html-italic">p</span> value; ** <span class="html-italic">p</span> &lt; 0.01.</p>
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<p>PeERF3 binds to the promoter of <span class="html-italic">PeHECT1</span> and activates its transcription activity. (<b>A</b>) Y1H assay of PeERF3 binding the promoter of <span class="html-italic">PeHECT1</span>. (<b>B</b>) EMSA assay of PeERF3 binding DNA probes. (<b>C</b>) Schematic diagrams of the effector (PeERF3) and reporter (proPeHECT1) constructs used in the dual-luciferase reporter assay. (<b>D</b>) Transcriptional activities of PeERF3 on <span class="html-italic">PeHECT1</span> promoter in tobacco epidermal cells. (<b>E</b>) Relative luciferase activity of PeERF3 on <span class="html-italic">PeHECT1</span> promoter. Data are presented as mean ± standard deviation. Student’s <span class="html-italic">t</span>-test was used to generate the <span class="html-italic">p</span> value; * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01.</p>
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<p>Evolutionary relationship of PeHECT1 among different bamboo species and rice. As shown in the figure: <span class="html-italic">Phyllostachys edulis</span> (<span class="html-italic">P</span>. <span class="html-italic">edulis</span>), <span class="html-italic">Oryza sativa</span> (<span class="html-italic">O</span>. <span class="html-italic">sativa</span>), <span class="html-italic">Raddia guianensis</span> (<span class="html-italic">Ra</span>. <span class="html-italic">guianensis</span>), <span class="html-italic">Dendrocalamus sinicus</span> (<span class="html-italic">D</span>. <span class="html-italic">sinicus</span>), <span class="html-italic">Bonia amplexicaulis</span> (<span class="html-italic">B</span>. <span class="html-italic">amplexicaulis</span>), <span class="html-italic">Hsuehochloa calcarea</span> (<span class="html-italic">H</span>. <span class="html-italic">calcarea</span>), <span class="html-italic">Ampelocalamus luodianensis</span> (<span class="html-italic">A</span>. <span class="html-italic">luodianensis</span>), <span class="html-italic">Melocanna baccifera</span> (<span class="html-italic">M</span>. <span class="html-italic">baccifera</span>), <span class="html-italic">Rhipidocladum racemiflorum</span> (<span class="html-italic">Rh</span>. <span class="html-italic">racemiflorum</span>), <span class="html-italic">Guadua angustifolia</span> (<span class="html-italic">G</span>. <span class="html-italic">angustifolia</span>), <span class="html-italic">Otatea glauca</span> (<span class="html-italic">Ot</span>. <span class="html-italic">glauca</span>), and <span class="html-italic">Olyra latifolia</span> (<span class="html-italic">Ol</span>. <span class="html-italic">latifolia</span>). Red circle indicates the paleotropical woody bamboo, green circle indicates neotropical woody bamboo, yellow circle indicates temperate woody bamboo, blue circle indicates herbaceous bamboo, and red star indicates rice.</p>
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12 pages, 739 KiB  
Article
Prevalence of Babesia microti Co-Infection with Other Tick-Borne Pathogens in Pennsylvania
by Lovepreet S. Nijjar, Sarah Schwartz, Destiny Sample Koon Koon, Samantha M. Marin, Mollie E. Jimenez, Trevor Williams and Nicole Chinnici
Microorganisms 2024, 12(11), 2220; https://doi.org/10.3390/microorganisms12112220 - 1 Nov 2024
Viewed by 733
Abstract
Babesia microti is a protozoan that infects red blood cells, causing hemolytic anemia and flu-like symptoms in humans. Understanding co-infections is crucial for the better diagnosis, treatment, and management of tick-borne diseases. This study examined the prevalence of Babesia microti co-infection with other [...] Read more.
Babesia microti is a protozoan that infects red blood cells, causing hemolytic anemia and flu-like symptoms in humans. Understanding co-infections is crucial for the better diagnosis, treatment, and management of tick-borne diseases. This study examined the prevalence of Babesia microti co-infection with other prevalent tick-borne pathogens in Pennsylvania. The dataset acquired from the Dr. Jane Huffman Wildlife Genetics Institute included passive surveillance data from Ixodes spp. from 2021 to 2023. Submitted ticks were screened for tick-borne pathogens using species-specific TaqMan qPCR. Of the 793 B. microti-positive ticks pulled for analysis, 65.0% were co-infected with other pathogens (n = 516). Notably, 60.9% of the B. microti-positive ticks were co-infected with Borrelia burgdorferi, 10.2% with Anaplasma phagocytophilum Ap-ha, and 7.5% carried a triple co-infection with B. burgdorferi and A. phagocytophilum Ap-ha. The rates of B. microti infection and its co-infections are on the rise, with patterns observed in Pennsylvania and other regions of the USA. While other studies have collected both nymphal and adult ticks to screen for co-infections in Pennsylvania, our study stood out as a unique contribution to the field by focusing exclusively on B. microti-positive ticks. The continued monitoring of tick-borne co-infections is vital to prevent misdiagnosis and ensure effective treatment regimens. Full article
(This article belongs to the Special Issue Ticks and Tick-Borne Pathogens—from Understanding to Control)
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<p>Locations of all 793 <span class="html-italic">B. microti</span>-positive ticks obtained from passive surveillance data collected between 2021 and 2023.</p>
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<p>Individual counts of other pathogens observed with the 793 <span class="html-italic">B. microti</span>-positive ticks.</p>
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<p>Counts of individual cases of co-infection among tick-borne pathogens. Abbreviations for pathogens: <span class="html-italic">B. microti</span> (BMI), <span class="html-italic">B. burgdorferi</span> (BBU), <span class="html-italic">B. miyamotoi</span> (BMY), deer tick virus (DTV), <span class="html-italic">A. phagocytophilum</span> Human-Active (Ap-ha), and <span class="html-italic">A. phagocytophilum</span> Variant 1 (Ap-v1).</p>
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<p>Counts of individual cases of co-infection among tick-borne pathogens by tick life stage.</p>
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<p>Association rules analysis of the co-infection with <span class="html-italic">B. microti.</span> A support threshold of 0.01 captured co-infections in at least 1.0% of interactions while a confidence of 1 produced strong associations with <span class="html-italic">B. microti.</span> A total of 60.9% of ticks positive for <span class="html-italic">B. microti</span> were co-infected with <span class="html-italic">B. burgdorferi.</span> The likelihood of co-infection with Ap-ha was 10.2% while the chance of harboring a triple infection with <span class="html-italic">B. burgdorferi</span> and Ap-ha alongside <span class="html-italic">B. microti</span> was 7.5%. Additionally, the presence of <span class="html-italic">B. microti</span> suggested a 1.6% chance of co-infection with <span class="html-italic">B. miyamotoi</span> and a 1.1% chance of co-infection with Ap-v1.</p>
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17 pages, 2109 KiB  
Article
Integrated Climate Change Mitigation and Public Health Protection Strategies: The Case of the City of Bologna, Italy
by Isabella Nuvolari-Duodo, Michele Dolcini, Maddalena Buffoli, Andrea Rebecchi, Giuliano Dall’Ò, Carol Monticelli, Camilla Vertua, Andrea Brambilla and Stefano Capolongo
Int. J. Environ. Res. Public Health 2024, 21(11), 1457; https://doi.org/10.3390/ijerph21111457 - 31 Oct 2024
Viewed by 494
Abstract
Introduction: The ongoing process of global warming, driven by the escalating concentration of greenhouse gases generated by human activities, especially in urban areas, significantly impacts public health. Local authorities play an important role in health promotion and disease prevention, and some aim to [...] Read more.
Introduction: The ongoing process of global warming, driven by the escalating concentration of greenhouse gases generated by human activities, especially in urban areas, significantly impacts public health. Local authorities play an important role in health promotion and disease prevention, and some aim to achieve net-zero greenhouse gas emissions. There is a consistent action underway to reach this goal, hence the need for mapping and implementing effective strategies and regulations. Materials and Methods: This study includes the analysis of policy guidelines adopted by the city of Bologna, consulted in March and April 2024. Bologna is one of the 100 cities committed to achieving climate neutrality by 2030, 20 years ahead of the EU target. To identify the strategies adopted to mitigate climate change, the following methodology was used: (i) the systematic mapping of sources and spatial planning documents; (ii) the extrapolation of goals, measures, and target indicators; and (iii) the development of an overall matrix. Results: The main findings of the study and their connection to public health pertain to the identification of key macro-areas contributing to the reduction of greenhouse gas emissions, while reducing the impact of climate change on health: (1) built environment and renewable energy sources, (2) transport and mobility, (3) energy, (4) green areas and land use, and (5) citizen support. Within these five macro-areas, 14 goals have been identified, to which a total of 36 measures correspond, and, finally, a target indicator is determined, mainly with respect to the reduction of tons of CO2 equivalent per year. Conclusions: In order to protect public health, it is evident that buildings and urban activities should not produce carbon emissions throughout their lifecycle. This paper presents a method to evaluate municipal policies regarding dual-impact solutions that address both environmental protection through sustainability strategies and public health, in compliance with the Health in All Policies (HiAP) approach. Full article
(This article belongs to the Special Issue The Impact of Health-Promoting Built Environments on Public Health)
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<p>Analysis of the climate scenarios in the city of Bologna (elaborated), ARPAE.</p>
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<p>Methodological steps.</p>
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<p>List of goals associated with the respective sources, divided by type.</p>
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18 pages, 3306 KiB  
Article
Deciphering Nitrogen Stress Responses in Maize Rhizospheres: Comparative Transcriptomics of Monocropping and Intercropping Systems
by Bing Zhang, Jamal Nasar, Siqi Dong, Guozhong Feng, Xue Zhou and Qiang Gao
Agronomy 2024, 14(11), 2554; https://doi.org/10.3390/agronomy14112554 - 31 Oct 2024
Viewed by 421
Abstract
A well-developed rhizospheric system is crucial for maize to adapt to environmental stresses, thereby enhancing yield and quality. However, nitrogen (N) stress significantly impedes rhizospheric development and growth in maize. The genetic responses of maize’s rhizosphere to N stress under monocropping systems with [...] Read more.
A well-developed rhizospheric system is crucial for maize to adapt to environmental stresses, thereby enhancing yield and quality. However, nitrogen (N) stress significantly impedes rhizospheric development and growth in maize. The genetic responses of maize’s rhizosphere to N stress under monocropping systems with exogenous inorganic N fertilization and intercropping systems reliant on biological N fixation are not well understood, especially regarding common and specific response genes. Therefore, through transcriptomic analysis, this study systematically investigated the gene expression and molecular responses of maize’s rhizosphere under two N supply regimes to N stress. The results showed that N stress generated 196 common and 3350 specific differentially expressed genes across the two systems, with the intercropping system exhibiting a stronger specific response. KEGG analysis revealed that the common genes, though few, are involved in key pathways essential for crop growth. Maize monocropping specific differentially expressed genes (MM) were enriched in pathways related to membrane lipids, cell wall formation, and intracellular signaling, while maize/alfalfa intercropping specific differentially expressed genes (MA) were linked to stress resistance through the glutathione metabolic pathway. WGCNA analysis identified five co-expression modules (CM). MA significantly increased the transcription factor families and structural domains directly targeting rhizospheric growth and development genes, including AP2, GRAS, Cys2His2 Zinc Finger, and LBD in CM blue. Conversely, MM significantly increased the transcription factor families and NAC structural domain targeting the promoters of N transporter protein genes in CM pink. This study emphasizes the importance of both common and specific genes in maintaining maize growth under suboptimal N supply in monocropping and intercropping systems. Full article
(This article belongs to the Section Innovative Cropping Systems)
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<p>Experimental design and layout plot map.</p>
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<p>Gene expression profiles and differential analysis between monocropping and intercropping systems under N stress. (<b>a</b>) Gene expression profiles under different treatments, including maize monocropping without N (N0MM), maize monocropping with N (N1MM), maize/alfalfa intercropping without N (N0MA), and maize/alfalfa intercropping with N (N1MA). The expression levels represent the overall transcriptional response across all treatments. (<b>b</b>) FC-FC scatter plot that illustrates the distribution of differentially expressed genes (DEGs) between the two cropping systems under N stress (N1MM vs. N0MM and N1MA vs. N0MA). Each point in the scatter plot represents DEG. Red points indicate genes upregulated in both MM and MA (common upregulated genes), blue points indicate genes downregulated in both systems (common downregulated genes), pink points indicate genes upregulated specifically in either MM or MA (system-specific upregulated genes), and light blue points indicate genes downregulated specifically in MM or MA (system-specific downregulated genes). Genes were identified as DEGs with |log2FC| ≥ 1 and FDR &lt; 0.05. CG: genes showing significant differential expression in both maize monocropping and maize/alfalfa intercropping. MM: genes differentially expressed only in maize monocropping. MA: genes differentially expressed only in maize/alfalfa intercropping.</p>
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<p>KEGG-enriched pathway maps for three comparisons (CG, MM, MA). The treatments include maize monocropping without N (N0MM), maize monocropping with N (N1MM), maize/alfalfa intercropping without N (N0MA), and maize/alfalfa intercropping with N (N1MA). In both comparisons, N0MM vs. N1MM and N0MA vs. N1MA, differentially expressed genes (DEGs) to N stress were identified. CG: maize monocropping and maize/alfalfa intercropping common DEGs, MM: maize monocropping specific DEGs, MA: maize/alfalfa intercropping specific DEGs. Each treatment included three replicates.</p>
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<p>Co-expression module identification, gene distribution, and KEGG pathway enrichment analysis via WGCNA. (<b>a</b>) WGCNA method was used to assign significantly differentially expressed genes into distinct co-expression modules (CMs). (<b>b</b>) Number of genes annotated that were contained in each module. (<b>c</b>) KEGG enrichment pathways associated with the different modules. (<b>d</b>) Gene expression profiles across different modules in MM and MA. The treatments include maize monocropping without N (N0MM), maize monocropping with N (N1MM), maize/alfalfa intercropping without N (N0MA), and maize/alfalfa intercropping with N (N1MA). In both comparisons, N0MM vs. N1MM and N0MA vs. N1MA, differentially expressed genes (DEGs) to N stress were identified. CG: maize monocropping and maize/alfalfa intercropping common DEGs, MM: maize monocropping specific DEGs, MA: maize/alfalfa intercropping specific DEGs. Each treatment included three replicates.</p>
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<p>Network analysis of CM blue. (<b>a</b>) Network derived from CM blue with a weight value greater than 0.5. Internal connections within the network reflect associations between genes, while the outer rings and links represent connections between genes and TFs. (<b>b</b>) Heatmap of the TFs in overall DEGs across MM and MA. Asterisks in the heatmap indicate TFs with significant differences in N0MM vs. N1MM and N0MA vs. N1MA (FDR ≤ 0.05). (<b>c</b>) The most significant biological process of GO terms for the genes that appeared in the network (<span class="html-italic">p</span> ≤ 0.001)<b>.</b> The treatments include maize monocropping without N (N0MM), maize monocropping with N (N1MM), maize/alfalfa intercropping without N (N0MA), and maize/alfalfa intercropping with N (N1MA). In both comparisons, N0MM vs. N1MM and N0MA vs. N1MA, differentially expressed genes (DEGs) to N stress were identified. CG: maize monocropping and maize/alfalfa intercropping common DEGs, MM: maize monocropping specific DEGs, MA: maize/alfalfa intercropping specific DEGs. Each treatment included three replicates. Asterisks denote for significant probability levels (*, <span class="html-italic">p</span> &lt; 0.05).</p>
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<p>Network analysis of CM pink. (<b>a</b>) Network derived from CM pink with a weight value greater than 0.5. Internal connections within the network reflect associations between genes, while the outer rings and links represent connections between genes and transcription factor (TF) families. (<b>b</b>) Heatmap shows the TFs in overall DEGs across MM and MA. Asterisks in the heatmap indicate TFs with significant differences in N0MM vs. N1MM and N0MA vs. N1MA (FDR ≤ 0.05). (<b>c</b>) The most significant biological process of GO terms for the genes that appeared in the network (<span class="html-italic">p</span> ≤ 0.001). The treatments include maize monocropping without N (N0MM), maize monocropping with N (N1MM), maize/alfalfa intercropping without N (N0MA), and maize/alfalfa intercropping with N (N1MA). In both comparisons, N0MM vs. N1MM and N0MA vs. N1MA, differentially expressed genes (DEGs) to N stress were identified. CG: maize monocropping and maize/alfalfa intercrop-ping common DEGs, MM: maize monocropping specific DEGs, MA: maize/alfalfa intercropping specific DEGs. Each treatment included three replicates. Asterisks denote for significant probability levels (* <span class="html-italic">p</span> &lt; 0.05; ** <span class="html-italic">p</span> &lt; 0.01).</p>
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22 pages, 3760 KiB  
Article
Synthesis and Docking Studies of Novel Spiro[5,8-methanoquinazoline-2,3′-indoline]-2′,4-dione Derivatives
by Tünde Faragó, Rebeka Mészáros, Edit Wéber and Márta Palkó
Molecules 2024, 29(21), 5112; https://doi.org/10.3390/molecules29215112 - 29 Oct 2024
Viewed by 503
Abstract
In this study, a set of spiro[5,8-methanoquinazoline-2,3′-indoline]-2′,4-dione derivatives 3ap were synthesized starting from unsubstituted and N-methyl-substituted diendo- and diexo-2-aminonorbornene carboxamides, as well as various substituted isatins. The typical method involves a condensation reaction of alicyclic aminocarboxamide and isatin [...] Read more.
In this study, a set of spiro[5,8-methanoquinazoline-2,3′-indoline]-2′,4-dione derivatives 3ap were synthesized starting from unsubstituted and N-methyl-substituted diendo- and diexo-2-aminonorbornene carboxamides, as well as various substituted isatins. The typical method involves a condensation reaction of alicyclic aminocarboxamide and isatin in the presence of a catalyst, using a solvent and an acceptable temperature. We developed a cost-effective and ecologically benign high-speed ball milling (HSBM), microwave irradiation (MW), and continuous flow (CF) technique to synthesize spiroquinazolinone molecule 3a. The structures of the synthesized compounds 3ap were determined using 1D and 2D NMR spectroscopies. Furthermore, docking studies and absorption, distribution, metabolism, and toxicity (ADMET) predictions were used in this work. In agreement with the corresponding features found in the case of both the SARS-CoV-2 main protease (RCSB Protein Data Bank: 6LU7) and human mast cell tryptase (RCSB Protein Data Bank: 2ZA5) based on the estimated total energy and binding affinity, H bonds, and hydrophobicity in silico, compound 3d among our 3ag, 3ik, and 3m derivatives was found to be our top-rated compound. Full article
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<p>Structure of novel spiro[5,8-methanoquinazoline-2,3′-indoline]-2′,4-dione derivatives <b>3a</b>–<b>p</b>.</p>
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<p>NOE interactions proving the relative configuration of <b>3a</b> and <b>3e</b>. Red arrows show the detected NOESY cross-peaks; black crossed arrows represent missing NOE contacts.</p>
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<p>(<b>a</b>) Molecular interactions and binding pose of compound <b>3d</b> at the interface of SARS-CoV-2 main protease (PDB: 6LU7); H bonds between the macromolecule and compound <b>3d</b> are shown as yellow dashes and distances are in Å units; (<b>b</b>) Connelly surface of docking pose of 6LU7 with <b>3d</b> shown as stick model; (<b>c</b>) receptor surface: H-bond donor vs. acceptor ability of surrounding amino acids; (<b>d</b>) 2D interaction map between 6LU7 and <b>3d</b>.</p>
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<p>(<b>a</b>) Molecular interactions and binding pose of compound <b>3e</b> at the interface of SARS-CoV-2 main protease (PDB: 6LU7); H bonds between the macromolecule and compound <b>3e</b> are shown as yellow dashes and distances are in Å units; (<b>b</b>) Connelly surface of docking pose of 6LU7 with <b>3e</b> shown as stick model; (<b>c</b>) receptor surface: H-bond donor vs. acceptor ability of surrounding amino acids; (<b>d</b>) 2D interaction map between 6LU7 and <b>3e</b>.</p>
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<p>(<b>a</b>) Molecular interactions and binding pose of compound <b>3d</b> at the interface of human tryptase with potent non-peptide inhibitor (PDB: 2ZA5); H bonds between the macromolecule and compound <b>3d</b> are shown as yellow dashes and distances are in Å units; (<b>b</b>) Connelly surface of docking pose of 2ZA5 with <b>3d</b> shown as stick model; (<b>c</b>) receptor surface: H-bond donor vs. acceptor ability of surrounding amino acids; (<b>d</b>) 2D interaction map between 2ZA5 and <b>3d</b>.</p>
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<p>Spirocondensation reaction of <span class="html-italic">diexo</span>- and <span class="html-italic">diendo</span>-2-aminonorbornene carboxamides <b>1a</b>–<b>d</b> with unsubstituted, 5-methyl, 5-iodo- and 7-chloro-substituted isatins <b>2a</b>–<b>d</b>.</p>
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<p>The spirocondensation reaction pathway.</p>
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17 pages, 3119 KiB  
Article
Transcription Factors Are Involved in Wizened Bud Occurrence During the Growing Season in the Pyrus pyrifolia Cultivar ‘Sucui 1’
by Hui Li, Jialiang Kan, Chunxiao Liu, Qingsong Yang, Jing Lin and Xiaogang Li
Epigenomes 2024, 8(4), 40; https://doi.org/10.3390/epigenomes8040040 - 25 Oct 2024
Viewed by 414
Abstract
Background: Flowers are important plant organs, and their development is correlated with yield in woody fruit trees. For Pyrus pyrifolia cultivar ‘Sucui 1’, the research on how DNA methylation accurately regulates the expression of TFs and affects the specific regulatory mechanism of flower [...] Read more.
Background: Flowers are important plant organs, and their development is correlated with yield in woody fruit trees. For Pyrus pyrifolia cultivar ‘Sucui 1’, the research on how DNA methylation accurately regulates the expression of TFs and affects the specific regulatory mechanism of flower bud wizening will help reduce wizened buds. Methods: Here, the DNA methylomes and transcriptomes of two types of flower buds from the Pyrus pyrifolia cultivar ‘Sucui 1’ were compared. Results: 320 differentially expressed transcription factors (TFs), in 43 families, were obtained from the wizened bud transcriptome versus the normal bud transcriptome. Most were members of the AP2/ERF, bHLH, C2H2, CO-like, MADS, MYB, and WRKY families, which are involved in flower development. As a whole, the methylation level of TFs in the ‘Sucui 1’ genome increased once flower bud wizening occurred. A cytosine methylation analysis revealed that the methylation levels of the same gene regions in TFs from two kinds of buds were similar. However, differentially methylated regions were found in gene promoter sequences. The combined whole-genome bisulfite sequencing and RNA-Seq analyses revealed 162 TF genes (including 164 differentially methylated regions) with both differential expression and methylation differences between the two flower bud types. Among them, 126 were classified as mCHH-type methylation genes. Furthermore, the transcriptional down regulation of PpbHLH40, PpERF4, PpERF061, PpLHW, PpMADS6, PpZF-HD11, and PpZFP90 was accompanied by increased DNA methylation. However, PpbHLH130, PpERF011, and PpMYB308 displayed the opposite trend. The expression changes for these TFs were negatively correlated with their methylation states. Conclusions: Overall, our results offer initial experimental evidence of a correlation between DNA methylation and TF transcription in P. pyrifolia in response to bud wizening. This enriched our understanding of epigenetic modulations in woody trees during flower development. Full article
(This article belongs to the Collection Epigenetic Control in Plants)
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<p>Numbers of differentially expressed genes (DEGs) (<b>A</b>) and types and proportions of differentially expressed transcription factors (<b>B</b>) in normal flower buds versus wizened flower buds of <span class="html-italic">Pyrus pyrifolia</span> cultivar ‘Sucui 1’, as determined by a transcriptome analysis. The number indicates the number of differentially expressed transcription factor genes and the percentage represents the proportion of the family members of the total differentially expressed transcription factors. A list of abbreviations is given in <a href="#app1-epigenomes-08-00040" class="html-app">Supplementary Materials, Table S3</a>.</p>
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<p>The heat maps of transcription factor expression in different flower buds of <span class="html-italic">Pyrus pyrifolia</span> cultivar ‘Sucui 1’ based on transcriptome sequencing results. CKM, normal flower buds; SM, wizened flower buds. A list of abbreviations is given in <a href="#app1-epigenomes-08-00040" class="html-app">Supplementary Materials, Table S3</a>.</p>
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<p>Distribution of methylation levels in different gene regions of transcription factors in flower buds of <span class="html-italic">Pyrus pyrifolia</span> cultivar ‘Sucui 1’ based on the whole-genome bisulfite sequencing result. CKM, normal flower buds; SM, wizened flower buds; 2K, 2 kilobase; TSS, transcription initiation site; TTS, transcription termination site.</p>
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<p>The numbers of differentially methylated regions (DMRs) in two flower buds of the <span class="html-italic">Pyrus pyrifolia</span> cultivar ‘Sucui 1’ based on the whole-genome bisulfite sequencing results. TFs, transcription factors.</p>
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<p>The number of differentially methylated transcription factors (TFs, (<b>A</b>)), their family distribution (<sup>m</sup>CHH type, (<b>B</b>)) and the heat maps of DMRs in DMGs from TFs (<b>C</b>) in different buds of the <span class="html-italic">Pyrus pyrifolia</span> cultivar ‘Sucui 1’ based on the whole-genome bisulfite sequencing results. CKM, normal flower buds; SM, wizened flower buds. A list of abbreviations is given in <a href="#app1-epigenomes-08-00040" class="html-app">Supplementary Materials, Table S3</a>.</p>
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<p>The fragments per kilo-base per million read values (FPKM valued, blue points) and DNA methylation levels of <sup>m</sup>CHH-type differentially methylated regions (red points) in transcription factor genes in different buds of <span class="html-italic">Pyrus pyrifolia</span> cultivar ‘Sucui 1’ based on transcriptome sequencing and whole-genome bisulfite sequencing results, respectively. CKM, normal flower buds; SM, wizened flower buds.</p>
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<p>IGV software depiction of the methylation states of differentially methylated regions of the 10 genes in wizened flower buds (SM) versus normal flower buds (CKM) of the <span class="html-italic">Pyrus pyrifolia</span> cultivar ‘Sucui 1’ as assessed by whole-genome bisulfite sequencing. DMRs are marked with green boxes; [0–1.00] indicates the methylation level range of <sup>m</sup>CHH sites.</p>
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<p>qPCR analysis of the transcription levels of differentially methylated region-associated transcription factor genes in different buds of the <span class="html-italic">Pyrus pyrifolia</span> cultivar ‘Sucui 1’. <span class="html-italic">PbEF-1α</span> was selected as an internal control gene for normalization. The experimental data were tested via SPSS 26 (IBM, Armonk, NY, USA), and values are shown as the means ± standard deviations (SDs). SDs of the means of three biological replicates are displayed as vertical bars. The significant differences (** <span class="html-italic">p</span> &lt; 0.01) in gene expression data between normal flower buds (CKM) and wizened flower buds (SM) were analyzed using Student’s <span class="html-italic">t</span>-tests.</p>
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21 pages, 10239 KiB  
Article
Accurate Estimation of Gross Primary Production of Paddy Rice Cropland with UAV Imagery-Driven Leaf Biochemical Model
by Xiaolong Hu, Liangsheng Shi, Lin Lin, Shenji Li, Xianzhi Deng, Jinmin Li, Jiang Bian, Chenye Su, Shuai Du, Tinghan Wang, Yujie Wang and Zhitao Zhang
Remote Sens. 2024, 16(20), 3906; https://doi.org/10.3390/rs16203906 - 21 Oct 2024
Viewed by 750
Abstract
Accurate estimation of gross primary production (GPP) of paddy rice fields is essential for understanding cropland carbon cycles, yet remains challenging due to spatial heterogeneity. In this study, we integrated high-resolution unmanned aerial vehicle (UAV) imagery into a leaf biochemical properties-based model for [...] Read more.
Accurate estimation of gross primary production (GPP) of paddy rice fields is essential for understanding cropland carbon cycles, yet remains challenging due to spatial heterogeneity. In this study, we integrated high-resolution unmanned aerial vehicle (UAV) imagery into a leaf biochemical properties-based model for improving GPP estimation. The key parameter, maximum carboxylation rate at the top of the canopy (Vcmax,025), was quantified using various spatial information representation methods, including mean (μref) and standard deviation (σref) of reflectance, gray-level co-occurrence matrix (GLCM)-based features, local binary pattern histogram (LBPH), and convolutional neural networks (CNNs). Our models were evaluated using a two-year eddy covariance (EC) system and UAV measurements. The result shows that incorporating spatial information can vastly improve the accuracy of Vcmax,025 and GPP estimation. CNN methods achieved the best Vcmax,025 estimation, with an R of 0.94, an RMSE of 19.44 μmol m−2 s−1, and an MdAPE of 11%, and further produced highly accurate GPP estimates, with an R of 0.92, an RMSE of 6.5 μmol m−2 s−1, and an MdAPE of 23%. The μref-GLCM texture features and μref-LBPH joint-driven models also gave promising results. However, σref contributed less to Vcmax,025 estimation. The Shapley value analysis revealed that the contribution of input features varied considerably across different models. The CNN model focused on nir and red-edge bands and paid much attention to the subregion with high spatial heterogeneity. The μref-LBPH joint-driven model mainly prioritized reflectance information. The μref-GLCM-based features joint-driven model emphasized the role of GLCM texture indices. As the first study to leverage the spatial information from high-resolution UAV imagery for GPP estimation, our work underscores the critical role of spatial information and provides new insight into monitoring the carbon cycle. Full article
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<p>Flowchart of the study (<span class="html-italic">μ<sub>ref</sub></span>: the mean value of UAV reflectance; <span class="html-italic">σ<sub>ref</sub></span>: the standard deviation value of UAV reflectance; GLCM: gray-level co-occurrence matrix-based texture features; LBPH: local binary pattern histogram texture feature; <span class="html-italic">GPP</span>: gross primary production; <span class="html-italic">SW<sub>IN</sub></span>: incoming shortwave radiation; <span class="html-italic">C<sub>a</sub></span>: ambient CO<sub>2</sub> concentration; <span class="html-italic">T<sub>a</sub></span>: air temperature; <span class="html-italic">RH</span>: relative humidity; <span class="html-italic">u</span>: wind speed).</p>
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<p>The location of the experiment site. The red five-pointed star represents the EC system. The contour lines of the footprint during the growing period in (3) are shown in steps of 10% from 10 to 90%. The background maps in (<b>a</b>,<b>b</b>) are RGB images from Google Earth. The background map in (<b>c</b>) is the RGB image from the UAV platform.</p>
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<p>Seasonal variation in daily carbon fluxes, environmental elements and biophysical indicators. (<b>a</b>) Carbon fluxes, including net ecosystem exchange, gross primary production, and ecosystem respiration; (<b>b</b>) incoming shortwave radiation; (<b>c</b>) air temperature; (<b>d</b>) humidity; (<b>e</b>) wind speed; (<b>f</b>) ambient CO<sub>2</sub> concentration; (<b>g</b>) precipitation; (<b>h</b>) soil moisture; (<b>i</b>) plant area index; (<b>j</b>) leaf area index; (<b>k</b>) clumping index; (<b>l</b>) canopy height. The term ‘Doy’ means day of the year.</p>
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<p>Seasonal variation in field-scale <math display="inline"><semantics> <msubsup> <mi>V</mi> <mrow> <mi>c</mi> <mi>m</mi> <mi>a</mi> <mi>x</mi> <mo>,</mo> <mn>0</mn> </mrow> <mn>25</mn> </msubsup> </semantics></math>.</p>
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<p>The accuracy of 8 field-scale <math display="inline"><semantics> <msubsup> <mi>V</mi> <mrow> <mi>c</mi> <mi>m</mi> <mi>a</mi> <mi>x</mi> <mo>,</mo> <mn>0</mn> </mrow> <mn>25</mn> </msubsup> </semantics></math> models. The blue points represent the training samples, and the orange points represent the validation samples. The sample numbers of the training and validation dataset are 224 and 57, respectively.</p>
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<p>The accuracy of <span class="html-italic">GPP</span> estimation based on the 8 field-scale <math display="inline"><semantics> <msubsup> <mi>V</mi> <mrow> <mi>c</mi> <mi>m</mi> <mi>a</mi> <mi>x</mi> <mo>,</mo> <mn>0</mn> </mrow> <mn>25</mn> </msubsup> </semantics></math> models. The blue bar represents the accuracy metrics on the training dataset, and the orange bar represents the accuracy metrics on the testing dataset.</p>
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<p>SHAP-based feature importance analysis for the DNN <math display="inline"><semantics> <msubsup> <mi>V</mi> <mrow> <mi>c</mi> <mi>m</mi> <mi>a</mi> <mi>x</mi> <mo>,</mo> <mn>0</mn> </mrow> <mn>25</mn> </msubsup> </semantics></math> model. The feature importance is defined as the mean of the absolute value of the SHAP for each feature (mean(|SHAP|)). Only the top 5 most important features are displayed.</p>
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<p>The spatial distribution of the AlexNet-model-based SHAP.</p>
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11 pages, 253 KiB  
Article
Genetic Variability in the CPA1 Gene and Its Impact on Acute Pancreatitis Risk: New Insights from a Large-Scale Study
by Stanisław Głuszek, Wioletta Adamus-Białek, Magdalena Chrapek, Anna Dziuba, Julia Dulębska, Dorota Kozieł, Jarosław Matykiewicz and Monika Wawszczak-Kasza
Int. J. Mol. Sci. 2024, 25(20), 11301; https://doi.org/10.3390/ijms252011301 - 21 Oct 2024
Viewed by 623
Abstract
Acute pancreatitis (AP) is a common and potentially lethal disease. Over the last 10 years, AP has become one of the most important healthcare problems. On a global scale, the incidence has increased by 63% over the last 20 years. AP is usually [...] Read more.
Acute pancreatitis (AP) is a common and potentially lethal disease. Over the last 10 years, AP has become one of the most important healthcare problems. On a global scale, the incidence has increased by 63% over the last 20 years. AP is usually caused by gallstones and excessive alcohol consumption and genetic factors play an important role in the development of inflammation. Recent studies involving the CPA1 mutations are ambiguous and dependent on the population studied. In this study, the variability of the CPA1 gene in patients with AP was analyzed. Genetic material was isolated from the blood of 301 patients with AP and 184 healthy individuals. Identification of the variants in exons 5, 6, 8, and 9 with introns was performed using molecular biology methods. Mutations were identified by comparison to the reference sequence (NM_001868.4). Statistical analysis included the identification of mutations correlating with the risk of AP, the etiology of inflammation, and family history. Several novel mutations in the CPA1 gene have been identified, along with a high degree of variability within the coding region of the carboxypeptidase gene. A correlation between mutations CPA1:c.1072 + 84del; c.987 + 57G>A and increased risk of developing AP was found. Two protective mutations, CPA1:c.625A>T, c.1072 + 94del, were identified. The CPA1 gene is characterized by high sequence variability and regions in which mutations lead to an increased risk of developing AP. Single or co-occurring mutations of the CPA1 gene can significantly affect the risk of developing AP. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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25 pages, 35874 KiB  
Article
Implementation of Smart Farm Systems Based on Fog Computing in Artificial Intelligence of Things Environments
by Sukjun Hong, Seongchan Park, Heejun Youn, Jongyong Lee and Soonchul Kwon
Sensors 2024, 24(20), 6689; https://doi.org/10.3390/s24206689 - 17 Oct 2024
Viewed by 752
Abstract
Cloud computing has recently gained widespread attention owing to its use in applications involving the Internet of Things (IoT). However, the transmission of massive volumes of data to a cloud server often results in overhead. Fog computing has emerged as a viable solution [...] Read more.
Cloud computing has recently gained widespread attention owing to its use in applications involving the Internet of Things (IoT). However, the transmission of massive volumes of data to a cloud server often results in overhead. Fog computing has emerged as a viable solution to address this issue. This study implements an Artificial Intelligence of Things (AIoT) system based on fog computing on a smart farm. Three experiments are conducted to evaluate the performance of the AIoT system. First, network traffic volumes between systems employing and not employing fog computing are compared. Second, the performance of the communication protocols—hypertext transport protocol (HTTP), message queuing telemetry transport protocol (MQTT), and constrained application protocol (CoAP)—commonly used in IoT applications is assessed. Finally, a convolutional neural network-based algorithm is introduced to determine the maturity level of coffee tree images. Experimental data are collected over ten days from a coffee tree farm in the Republic of Korea. Notably, the fog computing system demonstrates a 26% reduction in the cumulative data volume compared with a non-fog system. MQTT exhibits stable results in terms of the data volume and loss rate. Additionally, the maturity level determination algorithm performed on coffee fruits provides reliable results. Full article
(This article belongs to the Section Sensor Networks)
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<p>Fog computing architecture.</p>
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<p>Technical framework of the application of AIoT.</p>
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<p>System architecture: smart farm system integrating fog computing.</p>
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<p>WMN in fog computing: optimizing IoT communication.</p>
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<p>Fog computing-based smart farm environment at a hydroponic coffee farm.</p>
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<p>User interface of the web service page for the smart farm system.</p>
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<p>Fog computing/cloud computing data volume measurement results. (<b>a</b>) Data volume of fog computing. (<b>b</b>) Data volume of cloud computing. (<b>c</b>) Data volume of cumulative data transmission and forecast results.</p>
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<p>AI learning results. (<b>a</b>) Results for precision. (<b>b</b>) Results for recall. (<b>c</b>) Results for mAP50. (<b>d</b>) Results for mAP50-95.</p>
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<p>AI learning results. (<b>a</b>) Confusion matrix. (<b>b</b>) Precision–recall curve.</p>
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<p>Coffee fruit AI inference results.</p>
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<p>Fruit AI inference results.</p>
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19 pages, 15466 KiB  
Article
Transcriptomic Analysis Reveals the Mechanism of Color Formation in the Peel of an Evergreen Pomegranate Cultivar ‘Danruo No.1’ During Fruit Development
by Xiaowen Wang, Chengkun Yang, Wencan Zhu, Zhongrui Weng, Feili Li, Yuanwen Teng, Kaibing Zhou, Minjie Qian and Qin Deng
Plants 2024, 13(20), 2903; https://doi.org/10.3390/plants13202903 - 17 Oct 2024
Viewed by 562
Abstract
Pomegranate (Punica granatum L.) is an ancient fruit crop that has been cultivated worldwide and is known for its attractive appearance and functional metabolites. Fruit color is an important index of fruit quality, but the color formation pattern in the peel of [...] Read more.
Pomegranate (Punica granatum L.) is an ancient fruit crop that has been cultivated worldwide and is known for its attractive appearance and functional metabolites. Fruit color is an important index of fruit quality, but the color formation pattern in the peel of evergreen pomegranate and the relevant molecular mechanism is still unknown. In this study, the contents of pigments including anthocyanins, carotenoids, and chlorophyll in the peel of ‘Danruo No. 1’ pomegranate fruit during three developmental stages were measured, and RNA-seq was conducted to screen key genes regulating fruit color formation. The results show that pomegranate fruit turned from green to red during development, with a dramatic increase in a* value, indicating redness and anthocyanins concentration, and a decrease of chlorophyll content. Moreover, carotenoids exhibited a decrease–increase accumulation pattern. Through RNA-seq, totals of 30, 18, and 17 structural genes related to anthocyanin biosynthesis, carotenoid biosynthesis and chlorophyll metabolism were identified from differentially expressed genes (DEGs), respectively. Transcription factors (TFs) such as MYB, bHLH, WRKY and AP2/ERF were identified as key candidates regulating pigment metabolism by K-means analysis and weighted gene co-expression network analysis (WGCNA). The results provide an insight into the theory of peel color formation in evergreen pomegranate fruit. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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<p>Coloration and pigment contents in ‘Danruo No.1’ pomegranate peel during fruit development. (<b>A</b>) Representative images of fruits at developmental stage 1 (S1), stage 2 (S2), and stage 3 (S3). (<b>B</b>) Fruit peel lightness (<span class="html-italic">L*</span> value). (<b>C</b>) Fruit peel <span class="html-italic">a*</span> value (higher value means redness and lower value means greenness). (<b>D</b>) Fruit peel <span class="html-italic">b*</span> value (higher value means yellowness and lower value means blueness). (<b>E</b>) Chlorophyll a content. (<b>F</b>) Chlorophyll b content. (<b>G</b>) Total chlorophyll content. (<b>H</b>) Anthocyanin content. (<b>I</b>) Carotenoid content. Each value represents the mean ± standard deviation of three biological replicates. Different letters above the bars indicate significant differences (<span class="html-italic">p</span> &lt; 0.05) according to one-way analysis of variance (ANOVA) followed by Tukey test.</p>
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<p>Differentially expressed genes (DEGs) identification and KEGG analysis. Volcano plots of DEGs from S2 vs. S1 (<b>A</b>), S3 vs. S1 (<b>B</b>), and S3 vs. S2 (<b>C</b>). Horizontal coordinates indicate the fold change of gene expression between different groups, and vertical coordinates indicate the significance level of gene expression difference in the two groups. Red dots indicate upregulated genes, green dots indicate downregulated genes, and grey dots indicate insignificant genes. Top 20 metabolic pathways analyzed by KEGG enrichment for DEGs from S2 vs. S1 (<b>D</b>), S3 vs. S1 (<b>E</b>), and S3 vs. S2 (<b>F</b>). The pathways associated with pigments metabolism are highlighted in red color.</p>
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<p>Expression patterns of the DEGs involved in anthocyanins synthesis in pomegranate peel at developmental stage 1 (S1), stage 2 (S2), and stage 3 (S3). The color scale from green to red represents the fragments per kilobase of transcript per million of fragments mapped (FPKM) values, from low to high.</p>
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<p>Expression pattern of the DEGs involved in carotenoids synthesis in pomegranate peel at developmental stage 1 (S1), stage 2 (S2), and stage 3 (S3). The color scale from blue to red represents the fragments per kilobase of transcript per million of fragments mapped (FPKM) values from low to high.</p>
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<p>Expression pattern of the DEGs involved in chlorophyll biosynthesis and degradation in pomegranate peel at developmental stage 1 (S1), stage 2 (S2), and stage 3 (S3). The color scale from green to red represents the fragments per kilobase of transcript per million of fragments mapped (FPKM) values from low to high.</p>
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<p>Identification of transcription factors (TFs) regulating pigments metabolism in pomegranate peel during fruit development. (<b>A</b>) K-means analysis of DEGs identified from transcriptome sequencing. The expression profiles of genes in each cluster are represented in different colors, and the average expression levels of all genes in developmental stage 1 (S1), S2, and S3 are represented in black. (<b>B</b>) Weighted gene co-expression network analysis (WGCNA) of DEGs identified from transcriptome sequencing. Module-trait correlations and corresponding <span class="html-italic">p</span>-values in parentheses. The left panel shows the six modules with gene numbers. The color scale on the right shows the module-trait correlations from −1 (blue) to 1 (red). ‘Anthocyanin’, ‘Chlorophyll a’, ‘Chlorophyll b’, ‘Total chlorophyll’ and ‘Carotenoid’ represent the changes in corresponding substances’ concentrations. (<b>C</b>) Heatmap presenting the expression patterns of regulatory genes regulating pomegranate peel pigments metabolism during fruit development. (<b>D</b>) Correlation network between TFs’ expression and pigments’ contents; pink and blue circles represent positive and negative correlations, respectively. Purple, orange, and green lines representing the relation between TFs and anthocyanin, carotenoid, and chlorophyll, respectively.</p>
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<p>The expressions of seven genes in pomegranate peel at developmental stage 1 (S1), S2, and S3 from transcriptome data were examined by quantitative polymerase chain reaction (q-PCR). The expression levels obtained by RNA-seq and q-PCR are shown with a line chart and histogram, respectively. Data are presented as the mean ± standard deviation of three biological replicates. Different letters above the bars indicate significant differences (<span class="html-italic">p</span> &lt; 0.05) according to one-way analysis of variance (ANOVA) followed by Tukey test. Data analyzed by qPCR (marked with gray letters) or RNA-seq (marked with red letters) were tested separately.</p>
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22 pages, 7040 KiB  
Article
Integrated Transcriptional and Metabolomic Analysis of Factors Influencing Root Tuber Enlargement during Early Sweet Potato Development
by Yaqin Wu, Xiaojie Jin, Lianjun Wang, Jian Lei, Shasha Chai, Chong Wang, Wenying Zhang and Xinsun Yang
Genes 2024, 15(10), 1319; https://doi.org/10.3390/genes15101319 - 14 Oct 2024
Viewed by 792
Abstract
Background: Sweet potato (Ipomoea batatas (L.) Lam.) is widely cultivated as an important food crop. However, the molecular regulatory mechanisms affecting root tuber development are not well understood. Methods: The aim of this study was to systematically reveal the regulatory network of [...] Read more.
Background: Sweet potato (Ipomoea batatas (L.) Lam.) is widely cultivated as an important food crop. However, the molecular regulatory mechanisms affecting root tuber development are not well understood. Methods: The aim of this study was to systematically reveal the regulatory network of sweet potato root enlargement through transcriptomic and metabolomic analysis in different early stages of sweet potato root development, combined with phenotypic and anatomical observations. Results: Using RNA-seq, we found that the differential genes of the S1 vs. S2, S3 vs. S4, and S4 vs. S5 comparison groups were enriched in the phenylpropane biosynthesis pathway during five developmental stages and identified 67 differentially expressed transcription factors, including AP2, NAC, bHLH, MYB, and C2H2 families. Based on the metabolome, K-means cluster analysis showed that lipids, organic acids, organic oxides, and other substances accumulated differentially in different growth stages. Transcriptome, metabolome, and prophetypic data indicate that the S3-S4 stage is the key stage of root development of sweet potato. Weighted gene co-expression network analysis (WGCNA) showed that transcriptome differential genes were mainly enriched in fructose and mannose metabolism, pentose phosphate, selenium compound metabolism, glycolysis/gluconogenesis, carbon metabolism, and other pathways. The metabolites of different metabolites are mainly concentrated in amino sugar and nucleotide sugar metabolism, flavonoid biosynthesis, alkaloid biosynthesis, pantothenic acid, and coenzyme A biosynthesis. Based on WGCNA analysis of gene-metabolite correlation, 44 differential genes and 31 differential metabolites with high correlation were identified. Conclusions: This study revealed key gene and metabolite changes in early development of sweet potato root tuber and pointed out potential regulatory networks, providing new insights into sweet potato root tuber development and valuable reference for future genetic improvement. Full article
(This article belongs to the Special Issue Plant Genetic Diversity and Omics Research)
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<p>Phenotypic indicators measured at five different developmental stages. (<b>a</b>) Root length and stem length, (<b>b</b>) Diameter of main root and stem diameter, (<b>c</b>) Weight of blade, stem weight, weight above ground, and fresh weight of root system, (<b>d</b>) Number of roots. * stands for significance, the more ‘*’ indicates the higher significance.</p>
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<p>S1–S5 showed the morphologic maps of differentiated roots on days 7, 14, 21, 28, and 35 of growth, respectively. (<b>a</b>–<b>d</b>) were the cross-sectional structure of differentiated root of sweet potato S1–S4, respectively. Ep: epidermis, Co: cortex, Cpc: cortical parenchyma cells, Px: primary xylem, Sx: secondary xylem, PPh: primary phloem.</p>
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<p>Changes of sucrose, soluble sugar, and starch at different developmental stages. * stands for significance, the more ‘*’ indicates the higher significance.</p>
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<p>(<b>a</b>) The number of differentially expressed genes (DEGs) in comparison groups S1 vs. S2, S2 vs. S3, S3 vs. S4, S4 vs. S5, (<b>b</b>) Venn diagram of different developmental stages.</p>
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<p>Heat map of correlation between sweet potato root development and differential gene expression patterns at different periods. The heat map shows the expression patterns of eight modules, with color bars representing the expression levels from high (red) to low (blue).</p>
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<p>Statistics of types and quantities of transcription factors.</p>
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<p>Comparison of metabolites at different developmental stages in sweet potato roots. (<b>a</b>) Principal Component Analysis (PCA) score map of all metabolites in the sample, (<b>b</b>) differential accumulation of metabolites in the five periods, (<b>c</b>) compare the number of DAMs in groups S1 vs. S2, S2 vs. S3, S3 vs. S4, and S4 vs. S5, (<b>d</b>) DAMs diagram of different developmental stages.</p>
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<p>Cluster analysis of differential metabolites. (<b>a</b>) K-means cluster analysis of differential metabolites. The gray line represents the intergroup trend of differential metabolite content in each k-means cluster, and the red line represents the average trend, (<b>b</b>) The number of metabolites in each category. Nodes represent the number of metabolites from small to large and from shallow to deep, (<b>c</b>) class1 metabolite accumulation model, (<b>d</b>) class3 metabolite accumulation model, (<b>e</b>) class4 metabolite accumulation model.</p>
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<p>Heat map of correlation between sweet potato root development and metabolite expression patterns at different periods. The heat map shows the expression patterns of eight modules, with color bars representing the expression levels from high (red) to low (blue).</p>
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<p>Gene-metabolite correlation analysis heat map. The color bar represents the level of correlation from high (red) to low (green). * represents the degree of correlation. * represents correlation, ** represents significant correlation, and *** represents extremely significant correlation.</p>
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