Cryo-EM structures reveal two allosteric inhibition modes of PI3KαH1047R involving a re-shaping of the activation loop.

PI3Kα is a lipid kinase that phosphorylates PIP2 and generates PIP3. The hyperactive PI3Kα mutation, H1047R, accounts for about 14% of breast cancer, making it a highly attractive target for drug discovery. Here, we report the cryo-EM structures of PI3KαH1047R bound to two different allosteric inhibitors QR-7909 and QR-8557 at a global resolution of 2.7 Å and 3.0 Å, respectively. The structures reveal two distinct binding pockets on the opposite sides of the activation loop. Structural and MD simulation analyses show that the allosteric binding of QR-7909 and QR-8557 inhibit PI3KαH1047R hyper-activity by reducing the fluctuation and mobility of the activation loop. Our work provides a strong rational basis for a further optimization and development of highly selective drug candidates to treat PI3KαH1047R-driven cancers.

The Interplay Between Epilepsy and Parkinson's Disease: Gene Expression Profiling and Functional Analysis.

The results of many epidemiological studies suggest a bidirectional causality may exist between epilepsy and Parkinson's disease (PD). However, the underlying molecular landscape linking these two diseases remains largely unknown. This study aimed to explore this possible bidirectional causality by identifying differentially expressed genes (DEGs) in each disease as well as their intersection based on two respective disease-related datasets. We performed enrichment analyses and explored immune cell infiltration based on an intersection of the DEGs. Identifying a protein-protein interaction (PPI) network between epilepsy and PD, and this network was visualised using Cytoscape software to screen key modules and hub genes. Finally, exploring the diagnostic values of the identified hub genes. NetworkAnalyst 3.0 and Cytoscape software were also used to construct and visualise the transcription factor-micro-RNA regulatory and co-regulatory networks, the gene-microRNA interaction network, as well as gene-disease association. Based on the enrichment results, the intersection of the DEGs mainly revealed enrichment in immunity-, phosphorylation-, metabolism-, and inflammation-related pathways. The boxplots revealed similar trends in infiltration of many immune cells in epilepsy and Parkinson's disease, with greater infiltration in patients than in controls. A complex PPI network comprising 186 nodes and 512 edges were constructed. According to node connection degree, top 15 hub genes were considered the kernel targets of epilepsy and PD. The area under curve values of hub gene expression profiles confirmed their excellent diagnostic values. This study is the first to analyse the molecular landscape underlying the epidemiological link between epilepsy and Parkinson's disease. The two diseases are closely linked through immunity-, inflammation-, and metabolism-related pathways. This information was of great help in understanding the pathogenesis, diagnosis, and treatment of the diseases. The present results may provide guidance for further in-depth analysis about molecular mechanisms of epilepsy and PD and novel potential targets.

Prediction of fruit characteristics of grafted plants of Camellia oleifera by deep neural networks.

BACKGROUND: Camellia oleifera, an essential woody oil tree in China, propagates through grafting. However, in production, it has been found that the interaction between rootstocks and scions may affect fruit characteristics. Therefore, it is necessary to predict fruit characteristics after grafting to identify suitable rootstock types. METHODS: This study used Deep Neural Network (DNN) methods to analyze the impact of 106 6-year-old grafting combinations on the characteristics of C.oleifera, including fruit and seed characteristics, and fatty acids. The prediction of characteristics changes after grafting was explored to provide technical support for the cultivation and screening of specialized rootstocks. After determining the unsaturated fat acids, palmitoleic acid C16:1, cis-11 eicosenoic acid C20:1, oleic acid C18:1, linoleic acid C18:2, linolenic acid C18:3, kernel oil content, fruit height, fruit diameter, fresh fruit weight, pericarp thickness, fresh seed weight, and the number of fresh seeds, the DNN method was used to calculate and analyze the model. The model was screened using the comprehensive evaluation index of Mean Absolute Error (MAPE), determinate correlation R2 and and time consumption. RESULTS: When using 36 neurons in 3 hidden layers, the deep neural network model had a MAPE of less than or equal to 16.39% on the verification set and less than or equal to 13.40% on the test set. Compared with traditional machine learning methods such as support vector machines and random forests, the DNN method demonstrated more accurate predictions for fruit phenotypic characteristics, with MAPE improvement rates of 7.27 and 3.28 for the 12 characteristics on the test set and maximum R2 improvement values of 0.19 and 0.33. In conclusion, the DNN method developed in this study can effectively predict the oil content and fruit phenotypic characteristics of C. oleifera, providing a valuable tool for predicting the impact of grafting combinations on the fruit of C. oleifera.

Variation in pigments in pecan testa during kernel development and storage.

The pecan (Carya illinoinensis) is an important tree nut worldwide. Browning of the testa during storage considerably reduces its quality. However, the pigments that cause browning and their accumulation patterns are poorly understood. We analyzed the color changes in the testa during the five developmental stages of the kernel after storage at room temperature to compare differences in their color and identify the pigments. Samples exhibiting different colors along with their corresponding -80 °C storage samples were selected for metabolomic analysis. A total of 591 phenolic compounds were detected, 52 phenolics showed regulatory effects on testa discoloration, and 59 metabolites were identified as possible precursors of the pigments. This study revealed the most thorough phenolic composition of pecan to date. Further, the findings provide new insights into the mechanisms of testa browning, deepens our understanding of the bioactive value of pecans, and contributes to the breeding of less browning-susceptible varieties.

Transcriptomic Time-Course Sequencing: Insights into the Cell Wall Macromolecule-Mediated Fruit Dehiscence during Ripening in Camellia oleifera.

Camellia oleifera (C. oleifera), one of the world's four major edible woody oil crops, has been widely planted in southern China's subtropical region for the extremely high nutritional and health benefits of its seed oil. Timing and synchronization of fruit dehiscence are critical factors influencing the oil output and quality, as well as the efficiency and cost of harvesting C. oleifera, yet they extremely lack attention. To gain an understanding of the molecular basis underlying the dehiscence of C. oleifera fruit, we sampled pericarp-replum tissues containing dehiscence zones from fruits at different developmental stages and performed time-series transcriptomic sequencing and analysis for the first time. Statistical and GO enrichment analysis of differentially expressed genes revealed that drastic transcriptional changes occurred over the last short sampling interval (4 days, 18th-22nd October), which directed functional classifications link to cell wall and cell wall macromolecule activity. WGCNA further showed that factors controlling cell wall modification, including endo-1,3;1,4-beta-D-glucanase, WAT1-like protein 37, LRR receptor-like serine/threonine-protein kinase, and cellulose synthase A catalytic subunit, were identified as core members of the co-expression network of the last stage highly related modules. Furthermore, in these modules, we also noted genes that were annotated as coding for polygalacturonase and pectinesterase, two pectinases that were expected to be major players in cell separation during dehiscence. qRT-PCR further confirmed the expression profiles of these cell wall modification relating factors, which possessed a special high transcriptional abundance at the final stage. These results suggested the cell wall associated cell separation, one of the essential processes downstream of fruit dehiscence, happened in dehiscing fruit of C. oleifera during ripening. Hydrolases acting on cell wall components are good candidates for signal mediating dehiscence of C. oleifera fruit. In conclusion, our analysis provided insights into the cell wall macromolecule-mediated fruit dehiscence during ripening in C. oleifera.

Transcriptome Analysis of Resistant and Susceptible Pecan (Carya illinoinensis) Reveals the Mechanism of Resistance to Black Spot Disease (Colletotrichum fioriniae).

Pecan, Carya illinoinensis (Wangenh.) K. Koch, is an important dried fruit and woody oil tree species grown worldwide. With continuous expansion of pecan cultivation, the frequency and scope of diseases, especially black spot disease, are increasing, damaging trees and reducing yields. In this study, the key factors in resistance to black spot disease (Colletotrichum fioriniae) were investigated between the high-resistance pecan variety "Kanza" and the low-resistance variety "Mahan". Leaf anatomy and antioxidase activities confirmed much stronger resistance to black spot disease in "Kanza" than in "Mahan". Transcriptome analysis indicated that the increased expression of genes associated with defense response, oxidation-reduction, and catalytic activity was involved in disease resistance. A connection network identified a highly expressed hub gene CiFSD2 (CIL1242S0042), which might participate in redox reactions to affect disease resistance. Overexpression of CiFSD2 in tobacco inhibited enlargement of necrotic spots and increased disease resistance. Overall, the expression of differentially expressed genes differed in pecan varieties with different levels of resistance to C. fioriniae infection. In addition, the hub genes associated with black spot resistance were identified and the functions clarified. The in-depth understanding of resistance to black spot disease provides new insights for early screening of resistant varieties and molecular-assisted breeding in pecan.

Identification of a new QTL underlying seminal root number in a maize-teosinte population.

Seminal roots play an important role in acquisition of water and nutrients by maize seedlings. Compared with its teosinte ancestor, maize underwent a change in seminal root number (SRN). Although several key genes controlling SRN have been cloned, identification and utilization of new genes from teosinte would be useful for improving maize root architecture. In this study, a maize-teosinte BC2F6 population containing 206 individuals genotyped by resequencing was used to conduct high-resolution quantitative trait locus (QTL) mapping of SRN. A new major QTL on chromosome 7 (qSRN7) was identified. Differentially expressed genes (DEGs) based on RNA-Seq were identified between two inbred lines with no SRN and multiple SRN at two periods of seminal roots primordia formation. A total of 116 DEGs detected in at least one period were identified within the qSRN7 interval. Three DEGs (Zm00001d021572, Zm00001d021579 and Zm00001d021861) associated with SRN were identified through regional association mapping. When compared with reported domestication-related selective sweeps, Zm00001d021572 was selected during maize domestication. Our findings provide important insights into the genetic basis of SRN and identify a promising candidate gene for further studies on SRN.

Aidi injection enhances the anti-tumor impact of doxorubicin in H22 tumor-containing mice.

ETHNOPHARMACOLOGICAL RELEVANCE: Aidi injection (AD) is a traditional medical preparation that has a Chinese origin. It is extensively used particularly in combination with doxorubicin (DOX) for the management of hepatocellular carcinoma (HCC). However, the combination's synergistic mechanism has not yet been clarified. AIM OF THE STUDY: To investigate the anti-tumor impact of AD in combination with DOX and their synergistic mechanism in HCC. MATERIALS AND METHODS: An H22 mouse xenograft model was utilized to study the impact of AD, DOX, and their combination on HCC in vivo. Their effects on cell vitality, apoptosis, mitochondrial membrane potential, reactive oxygen species (ROS) production, caspase-3, and cleaved caspase-3 protein expression were also investigated in H22 cells in vitro. Subsequently, human umbilical vein endothelial cells (HUVECs) were utilized to investigate the impacts of AD, DOX, and their combination on cell viability, migration, invasion, tube formation, and vascular endothelial growth factor (VEGF) protein expression. RESULTS: The study established that the tumor inhibition rate of AD combined with DOX reached 79.51%, which was significantly higher than that of AD (25.14%) or DOX (49.48%) alone. Additionally, the Q-value characterizing the synergy between AD and DOX was 1.72, demonstrating a strong synergistic effect. Furthermore, compared to AD or DOX administration alone, the combined administration group significantly decreased the alpha-fetoprotein (AFP) level in the serum, increased the tumor necrosis area, increased the Bax/Bcl-2, Cyt-c, caspase-9, Fas, Fasl, caspase-8, and caspase-3 protein expression, and significantly increased the CD31 and Ki67 protein expression in tumor tissue. Compared to AD or DOX alone, AD combined with DOX treatment had a synergistic effect on H22 cells (combination index values < 0.9), which inhibited cell viability, reduced mitochondrial membrane potential (MMP), induced apoptosis, promoted MMP loss, and increased ROS generation, cleaved caspase-3/caspase-3 levels, and caspase-3 activity. Moreover, combined administration showed a more pronounced inhibition of cell viability, migration, invasion, tube formation, and VEGF protein expression in HUVECs. CONCLUSIONS: AD enhances the anti-tumor effect of DOX by promoting apoptosis and inhibiting angiogenesis and cell proliferation. The findings of this study lay experimental foundations for the clinical combination of AD and DOX.

The role of the orbitofrontal cortex and insula for prognosis of mesial temporal lobe epilepsy.

OBJECTIVE: We investigated the network between the medial temporal lobe (MTL) and extratemporal structures in patients with mesial temporal lobe epilepsy (MTLE) in order to explain the recurrence of MTLE after surgery. This study contributes to our current understanding of MTLE with stereotactic electroencephalography (SEEG). METHODS: We conducted a retrospective study of SEEG in 20 patients with MTLE in order to observe and analyze the intensity of interictal high-frequency oscillations (HFOs), as well as the dynamic course of coherence connectivity values of the MTL and extratemporal structures during the initial phase of the seizure. The results correlated with the patient prognosis. RESULTS: First, the presence of HFOs was observed during the interictal period in all 20 patients; these were localized to the MTL in 17 patients and the orbitofrontal cortex in seven patients and the insula in six patients. The better the prognosis, the greater the localization of the HFOs concentration in the MTL structures (p < 0.05). Second, significantly enhanced connectivity of MTL structures with the orbitofrontal cortex and insula was observed in most patients with MTLE, before and after the seizure onset (p < 0.05). Finally, the connectivity between extratemporal structures, such as the orbitofrontal cortex and insula, and MTL structures was significantly stronger in patients who had a worse prognosis than in other patients, before and after seizure onset (p < 0.05). INTERPRETATION: The epileptogenic network in recurrent MTLE is not limited to MTL structures but is also associated with the orbitofrontal cortex and insula. This can be used as a potential indicator for predicting the prognosis of patients after surgery, providing an important avenue for future clinical evaluation.

Untargeted metabolism approach reveals difference of varieties of bud and relation among characteristics of grafting seedlings in Camellia oleifera.

Camellia oleifera is one of the essential wood oil trees in the world. C.oleifera was propagated by nurse seedling grafting. Since the scion of C.oleifera had a significant regulated effect on the properties of rootstock after grafting and impacted on the growth of the grafted seedlings, it was necessary to understand the characteristics of buds among varieties to cultivate high-quality grafted seedlings. The metabolome was thought to be a powerful tool for understanding connecting phenotype-genotype interactions, which has an important impact on plant growth and development. In this study, UPLC-MS was used to determine the metabolites of the apical buds of CL3, CL4, CL40, and CL53 spring shoots after 30 days of sprout and to measure the growth characteristics of roots and stems after grafting. Metabolomics analysis revealed 554 kinds of metabolites were significant differences among four varieties, and 29 metabolic pathways were identified to have significant changes (p< 0.05), including carboxylic acids and derivatives, fatty Acyls, organooxygen compounds, and prenol lipids metabolites. The metabolites appeared in all varieties, including phenethyl rutinoside in glycosyl compounds and hovenidulcioside A1 in terpene glycosides. Metabolite-metabolite correlations in varieties revealed more complex patterns in relation to bud and enabled the recognition of key metabolites (e.g., Glutamate, (±)Catechin, GA52, ABA, and cs-Zeatin) affecting grafting and growth ability. Each variety has a unique metabolite type and correlation network relationship. Differentiated metabolites showed different growth trends for development after grafting. Many metabolites regulate the growth of scions in buds before grafting, which plays a crucial role in the growth of seedlings after grafting. It not only regulates the growth of roots but also affects the development of this stem. Finally, those results were associated with the genetic background of each cultivar, showing that metabolites could be potentially used as indicators for the genetic background, indicating that metabolites could potentially be used as indicators for seedling growth characteristics. Together, this study will enrich the theoretical basis of seedling growth and lay a foundation for further research on the molecular regulation mechanism interaction between rootstock and scion, rootstock growth, and the development of grafted seedlings after grafting.

Metabolomics and Transcriptomics Analyses Reveal Regulatory Networks Associated with Fatty Acid Accumulation in Pecan Kernels.

Pecans are a globally important tree nut crop. Pecan nuts are rich in fatty acids (FAs), proteins, and flavonoids in addition to thiamine and numerous micronutrients. Although several of these nutriments have been studied in this plant, the comprehensive metabolite variations and molecular mechanisms associated with them have not been fully elucidated. In this study, untargeted metabolomics and transcriptomics were integrated to reveal the metabolite accumulation patterns and their associated molecular mechanisms during pecan kernel development. In total, 4260 (under positive mode) and 2726 (under negative mode) high quality features were retained. Overall, 163 differentially accumulated metabolites were identified. Most components were classified into the categories "organic acids and derivatives" and "lipids and lipid-like molecules." The accumulation patterns of amino acids, FAs, carbohydrates, organic acids, vitamins, flavonoids, and phenylpropanoids alongside embryo development were determined. Furthermore, transcriptomes from four pecan kernel developmental stages were used to assess transcript expression levels. Coexpression analyses were performed between FAs and their related genes. This study provides a comprehensive overview of the metabolic changes and regulations during pecan kernel development. We believe that the identification of nutriment accumulation trends and hub genes associated with the biosynthesis of the components will be valuable for genetically improving this plant.

Mineral nutrient dynamics in pecans (Carya illinoensis) 'Mahan' grown in southern China.

It is of great significance to study the nutritional characteristics of plants. Further understanding of plant mineral nutrient dynamics can provide theoretical basis for scientific fertilization to improve fruit quality and yield. In this study, eight mineral elements (N, P, K, Ca, Mg, Mn, Zn, B) were measured at regular intervals in leaves and kernels of the pecan "Mahan" planted in southern China. The study discussed the characteristics of mineral nutrient dynamics of pecan through the indicators of concentration, accumulation and cumulative relative rate, a new first proposed indicator, and focused on critical time, intensity, amount of mineral nutrients required in pecan during the fruit developing period, as well as the transfer information of the elements in leaves and kernels. The results show that the mineral nutrient requirements of the leaves and kernels are not identical, with an upward trend in nutrient accumulation within the kernel. The most abundant mineral nutrients in the leaves and kernels were N, K and Ca with Ca being greater than N in leaves. In particular, the concentration of Mn in pecan 'Mahan' is higher than that of other plants, and its Mg content is also higher than that of P in kernels. The dynamic changes of mineral nutrients in walnut showed obvious stages, with a trend of "slow (before mid-July) - fast (mid-July to late August) - slow (late August to late September) - fast (late September to harvest)". The "critical period" of kernels was before mid-July, during which the cumulative relative rates increased rapidly, indicating that the kernels had a great potential to absorb mineral nutrients. Significant accumulation of mineral nutrients occurred from mid-July to late August and late September to the end.

Comparative Genomic Analysis Uncovers the Chloroplast Genome Variation and Phylogenetic Relationships of Camellia Species.

Camellia is the largest genus in the family Theaceae. Due to phenotypic diversity, frequent hybridization, and polyploidization, an understanding of the phylogenetic relationships between Camellia species remains challenging. Comparative chloroplast (cp) genomics provides an informative resource for phylogenetic analyses of Camellia. In this study, 12 chloroplast genome sequences from nine Camellia species were determined using Illumina sequencing technology via de novo assembly. The cp genome sizes ranged from 156,545 to 157,021 bp and were organized into quadripartite regions with the typical angiosperm cp genomes. Each genome harbored 87 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes in the same order and orientation. Differences in long and short sequence repeats, SNPs, and InDels were detected across the 12 cp genomes. Combining with the complete cp sequences of seven other species in the genus Camellia, a total of nine intergenic sequence divergent hotspots and 14 protein-coding genes with high sequence polymorphism were identified. These hotspots, especially the InDel (~400 bp) located in atpH-atpI region, had sufficient potential to be used as barcode markers for further phylogenetic analysis and species identification. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These cp genomes could facilitate the development of new molecular markers, accurate species identification, and investigations of the phylogenomic relationships of the genus Camellia.

Retrospective Multicenter Study on Outcome Measurement for Dyskinesia Improvement in Parkinson's Disease Patients with Pallidal and Subthalamic Nucleus Deep Brain Stimulation.

Deep brain stimulation (DBS) is an effective treatment for dyskinesia in patients with Parkinson's disease (PD), among which the therapeutic targets commonly used include the subthalamic nucleus (STN) and the globus pallidus internus (GPi). Levodopa-induced dyskinesia (LID) is one of the common motor complications arising in PD patients on chronic treatment with levodopa. In this article, we retrospectively evaluated the outcomes of LID with the Unified Dyskinesia Rating Scale (UDysRS) in patients who underwent DBS in multiple centers with a GPi or an STN target. Meanwhile, the Med off MDS-Unified Parkinson's Disease Rating Scale (MDS-UPDRS-Ⅲ) and the levodopa equivalent daily dose (LEDD) were also observed as secondary indicators. PD patients with a GPi target showed a more significant improvement in the UDysRS compared with an STN target (92.9 ± 16.7% vs. 66.0 ± 33.6%, p < 0.0001). Both the GPi and the STN showed similar improvement in Med off UPDRS-III scores (49.8 ± 22.6% vs. 52.3 ± 29.5%, p = 0.5458). However, the LEDD was obviously reduced with the STN target compared with the GPi target (44.6 ± 28.1% vs. 12.2 ± 45.8%, p = 0.006).

Cell metabolomics study on synergistic anti-hepatocellular carcinoma effect of Aidi injection combined with doxorubicin.

Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and the second most common cause of cancer deaths. This study aimed to explore the inhibitory effect and mechanism of Aidi injection (ADI) combined with doxorubicin (DOX) in HCC treatment. The drug concentrations in the combined therapy was determined by investigating the effect of various concentrations of ADI and DOX on the viability of H22 cells. The combination index was also calculated. A metabolomic strategy based on a ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) platform was established to analyze the metabolites. As a result, the combination index values were less than 1, indicating that the combination of ADI and DOX exerted a synergistic effect on HCC treatment. The combination of 40‰ ADI and 1 µmol/l DOX had the strongest inhibitory effect and was used for subsequent metabolomic analysis. A total of 19 metabolic markers were obtained in metabolomic analysis, including amino acids (l-glutamic acid, l-arginine and l-tyrosine), organic acids (succinic acid and citric acid), adenosine and hypoxanthine. Compared with the treatment using DOX or ADI alone, the combined therapy further regulated the levels of metabolic markers in HCC, which may be the reason for the synergistic effect. Seven metabolic pathways were significantly enriched, including phenylalanine, tyrosine and tryptophan biosynthesis, d-glutamine and d-glutamate metabolism, alanine, aspartate and glutamate metabolism, phenylalanine metabolism, arginine biosynthesis, the tricarboxylic acid cycle and purine metabolism. These findings demonstrated that ADI combined with DOX can effectively inhibit the viability of H22 cells, which may exert a synergistic antitumor effect by balancing the metabolism of amino acids and energy-related substances.