GCNFORMER: graph convolutional network and transformer for predicting lncRNA-disease associations.

BACKGROUND: A growing body of researches indicate that the disrupted expression of long non-coding RNA (lncRNA) is linked to a range of human disorders. Therefore, the effective prediction of lncRNA-disease association (LDA) can not only suggest solutions to diagnose a condition but also save significant time and labor costs. METHOD: In this work, we proposed a novel LDA predicting algorithm based on graph convolutional network and transformer, named GCNFORMER. Firstly, we integrated the intraclass similarity and interclass connections between miRNAs, lncRNAs and diseases, and built a graph adjacency matrix. Secondly, to completely obtain the features between various nodes, we employed a graph convolutional network for feature extraction. Finally, to obtain the global dependencies between inputs and outputs, we used a transformer encoder with a multiheaded attention mechanism to forecast lncRNA-disease associations. RESULTS: The results of fivefold cross-validation experiment on the public dataset revealed that the AUC and AUPR of GCNFORMER achieved 0.9739 and 0.9812, respectively. We compared GCNFORMER with six advanced LDA prediction models, and the results indicated its superiority over the other six models. Furthermore, GCNFORMER's effectiveness in predicting potential LDAs is underscored by case studies on breast cancer, colon cancer and lung cancer. CONCLUSIONS: The combination of graph convolutional network and transformer can effectively improve the performance of LDA prediction model and promote the in-depth development of this research filed.

Three stilbenes from pigeon pea with promising anti-methicillin-resistant Staphylococcus aureus biofilm formation activity.

Cajaninstilbene acid (CSA), longistylin A (LLA), and longistylin C (LLC) are three characteristic stilbenes isolated from pigeon pea. The objective of this study was to evaluate the antibacterial activity of these stilbenes against Staphylococcus aureus and even methicillin-resistant Staphylococcus aureus (MRSA) and test the possibility of inhibiting biofilm formation. The minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of these stilbenes were evaluated. And the results showed that LLA was most effective against tested strains with MIC and MBC values of 1.56 µg/mL followed by LLC with MIC and MBC values of 3.12 µg/mL and 6.25 µg/mL as well as CSA with MIC and MBC values of 6.25 µg/mL and 6.25-12.5 µg/mL. Through growth curve and cytotoxicity analysis, the concentrations of these stilbenes were determined to be set at their respective 1/4 MIC in the follow-up research. In an anti-biofilm formation assay, these stilbenes were found to be effectively inhibited bacterial proliferation, biofilm formation, and key gene expressions related to the adhesion and virulence of MRSA. It is the first time that the anti-S. aureus and MRSA activities of the three stilbenes have been systematically reported. Conclusively, these findings provide insight into the anti-MRSA mechanism of stilbenes from pigeon pea, indicating these compounds may be used as antimicrobial agents or additives for food with health functions, and contribute to the development as well as application of pigeon pea in food science.

Genetic basis of resistance to southern corn leaf blight in the maize multi-parent population and diversity panel.

Southern corn leaf blight (SLB), caused by the necrotrophic pathogen Cochliobolus heterostrophus, is one of the maize foliar diseases and poses a great threat to corn production around the world. Identification of genetic variations underlying resistance to SLB is of paramount importance to maize yield and quality. Here, we used a random-open-parent association mapping population containing eight recombinant inbred line populations and one association mapping panel consisting of 513 diversity maize inbred lines with high-density genetic markers to dissect the genetic basis of SLB resistance. Overall, 109 quantitative trait loci (QTLs) with predominantly small or moderate additive effects, and little epistatic effects were identified. We found 35 (32.1%) novel loci in comparison with the reported QTLs. We revealed that resistant alleles were significantly enriched in tropical accessions and the frequency of about half of resistant alleles decreased during the adaptation process owing to the selection of agronomic traits. A large number of annotated genes located in the SLB-resistant QTLs were shown to be involved in plant defence pathways. Integrating genome-wide association study, transcriptomic profiling, resequencing and gene editing, we identified ZmFUT1 and MYBR92 as the putative genes responsible for the major QTLs for resistance to C. heterostrophus. Our results present a comprehensive insight into the genetic basis of SLB resistance and provide resistant loci or genes as direct targets for crop genetic improvement.

The Maize Hairy Sheath Frayed1 (Hsf1) Mutation Alters Leaf Patterning through Increased Cytokinin Signaling.

Leaf morphogenesis requires growth polarized along three axes-proximal-distal (P-D) axis, medial-lateral axis, and abaxial-adaxial axis. Grass leaves display a prominent P-D polarity consisting of a proximal sheath separated from the distal blade by the auricle and ligule. Although proper specification of the four segments is essential for normal morphology, our knowledge is incomplete regarding the mechanisms that influence P-D specification in monocots such as maize (Zea mays). Here, we report the identification of the gene underlying the semidominant, leaf patterning maize mutant Hairy Sheath Frayed1 (Hsf1). Hsf1 plants produce leaves with outgrowths consisting of proximal segments-sheath, auricle, and ligule-emanating from the distal blade margin. Analysis of three independent Hsf1 alleles revealed gain-of-function missense mutations in the ligand binding domain of the maize cytokinin (CK) receptor Z. mays Histidine Kinase1 (ZmHK1) gene. Biochemical analysis and structural modeling suggest the mutated residues near the CK binding pocket affect CK binding affinity. Treatment of the wild-type seedlings with exogenous CK phenocopied the Hsf1 leaf phenotypes. Results from expression and epistatic analyses indicated the Hsf1 mutant receptor appears to be hypersignaling. Our results demonstrate that hypersignaling of CK in incipient leaf primordia can reprogram developmental patterns in maize.

Euryachincoside, a Novel Phenolic Glycoside with Anti-Hepatic Fibrosis Activity from Eurya chinensis.

Eurya chinensis has been recorded as a folk medicine traditionally used for treatment of a variety of symptoms. However, the phytochemical and pharmacological investigations of this plant are still scarce. A novel phenolic glycoside named Euryachincoside (ECS) was isolated by chromatographic separation from E. chinensis, and its chemical structure was identified by analysis of HRMS and NMR data. Its anti-hepatic fibrosis effects were evaluated in both HSC-T6 (rat hepatic stellate cells) and carbon tetrachloride (CCl4)-induced mice with Silybin (SLB) as the positive control. In an in vitro study, ECS showed little cytotoxicity and inhibited transforming growth factor-beta (TGF-ß)-induced Collagen I (Col1) along with alpha-smooth muscle actin (α-SMA) expressions in HSC-T6. An in vivo study suggested ECS significantly ameliorated hepatic injury, secretions of inflammatory cytokines, and collagen depositions. Moreover, ECS markedly mediated Smad2/3, nuclear factor kappa B (NF-κB) and nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathways both in vitro and vivo. These present findings confirmed that ECS is a novel phenolic glycoside from E. chinensis with promising curative effects on hepatic fibrosis, and its mechanisms may include decreasing extracellular matrix accumulation, reducing inflammation and attenuating free radicals via Smad2/3, NF-κB and Nrf2 signaling pathways, which may shed light on the exploration of more effective phenolic glycoside-based anti-fibrotic agents.

The Rare Marine Bioactive Compounds in Neurological Disorders and Diseases: Is the Blood-Brain Barrier an Obstacle or a Target?

The blood-brain barrier (BBB) is a dynamic barrier separating neurocytes and brain tissues from blood that is extremely sealed and strictly regulated by transporters such as aquaporin-4 (AQP-4), glucose transporter (GLUT), and specialized tight junctional complexes (TJCs) including tight junctions (TJs), adherens junctions (AJs), and Zonulae occludens (ZOs). With specifically selective transcellular and paracellular permeability, the BBB maintains a homeostatic microenvironment to protect the central nervous system (CNS). In recent years, increasing attention has been paied to the importance of BBB disruption and dysfunction in the pathology of neurological disorders and diseases, such as Alzheimer's diseases (AD), Parkinson diseases (PD), stroke and cerebral edema. However, the further research on how the integral structure and function of BBB are altered under the physiological or pathological conditions is still needed. Focusing on the ultrastructural features of the BBB and combining the latest research on associated proteins and transporters, physiological regulation and pathological change of the BBB were elucidated. By summarizing the protective effects of known bioactive compounds derived from marine life on the BBB, this review aims to highlight the BBB as a key to the treatment of several major neurological diseases instead of a normally described obstacle to drug absorption and transport. Overall, the BBB's morphological characteristics and physiological function and their regulation provide the theoretical basis for the study on the BBB and inspire the diagnosis of and therapy for neurological diseases.

Two new withanolides from the whole plants of Physalis peruviana.

Two new withaphysalin-type withanolides (18-O-ethylwithaphysalin R and 5-O-ethylphysaminimin C, 1 and 2), along with twelve known withanolides (3-14), were purified and identified from Physalis peruviana L. The chemical structures of these new isolates were elucidated through analyzing spectroscopic and HRESIMS data. All the obtained metabolites were appraised for their potential antiproliferative activity against the human breast cancer cell line MCF-7. Compound 7 was discovered to exhibit potent activity with an IC50 value of 3.51 µM and compounds 2, 6 and 14 showed weak cytotoxic effect.

A Review on the Phytochemical and Pharmacological Properties of Rosa laevigata: A Medicinal and Edible Plant.

Rosa laevigata Michx., a medicinal and edible plant in China, has exerted a variety of medicinal values and health benefits. This present review aims to achieve a comprehensive and up-to-date investigation in the phytochemistry and pharmacology of R. laevigata. According to these findings in the literature, approximately 123 chemical ingredients covering triterpenoids, flavonoids, tannis, lignans and polysaccharides, have been characterized from various parts of this species. Among these isolates, 77 triterpenoids have been isolated and thus regarded as the primary and characteristic substance. Based on the chemical structures, most of the obtained triterpenoids can be classified into polyhydroxy triterpenoids and readily divided into four categories: ursane-type, oleanane-type, lupinane-type, as well as seco-triterpenoids. The crude extracts and the purified compounds have demonstrated various pharmacological effects in vitro and in vivo, such as antioxidant activity, immunomodulatory effect, anti-inflammatory effect, liver protection, kidney protection, cardiovascular protection, neuroprotective effect and improvement of diabetic cataract. Noticeably, these pharmacological results of R. laevigata provide evidences for its traditional uses. In addition, these different chemical ingredients existing in the title plant may have synergistic effects. In conclusion, the chemical profiles, including ingredients and structures, together with the modern pharmacological properties have been adequately summarized. These evidences have revealed this plant to be a valuable source for therapeutic foodstuff and more attention should be paid to a better utilization of this plant.

In Vitro Study of the Fibrinolytic Activity via Single Chain Urokinase-Type Plasminogen Activator and Molecular Docking of FGFC1.

Fungi fibrinolytic compound 1 (FGFC1) is a rare marine-derived compound that can enhance fibrinolysis both in vitro and in vivo. The fibrinolytic activity characterization of FGFC1 mediated by plasminogen (Glu-/Lys-) and a single-chain urokinase-type plasminogen activator (pro-uPA) was further evaluated. The binding sites and mode of binding between FGFC1 and plasminogen were investigated by means of a combination of in vitro experiments and molecular docking. A 2.2-fold enhancement of fibrinolytic activity was achieved at 0.096 mM FGFC1, whereas the inhibition of fibrinolytic activity occurred when the FGFC1 concentration was above 0.24 mM. The inhibition of fibrinolytic activity of FGFC1 by 6-aminohexanoic acid (EACA) and tranexamic acid (TXA) together with the docking results revealed that the lysine-binding sites (LBSs) play a crucial role in the process of FGFC1 binding to plasminogen. The action mechanism of FGFC1 binding to plasminogen was inferred, and FGFC1 was able to induce plasminogen to exhibit an open conformation by binding through the LBSs. The molecular docking results showed that docking of ligands (EACA, FGFC1) with receptors (KR1-KR5) mainly occurred through hydrophilic and hydrophobic interactions. In addition, the binding affinity values of EACA to KR1-KR5 were -5.2, -4.3, -3.7, -4.5, and -4.3 kcal/moL, respectively, and those of FGFC1 to KR1-KR5 were -7.4, -9.0, -6.3, -8.3, and -6.7 kcal/moL, respectively. The findings demonstrate that both EACA and FGFC1 bound to KR1-KR5 with moderately high affinity. This study could provide a theoretical basis for the clinical pharmacology of FGFC1 and establish a foundation for practical applications of FGFC1.

Intelligent Fault Identification for Rolling Bearings Fusing Average Refined Composite Multiscale Dispersion Entropy-Assisted Feature Extraction and SVM with Multi-Strategy Enhanced Swarm Optimization.

Rolling bearings act as key parts in many items of mechanical equipment and any abnormality will affect the normal operation of the entire apparatus. To diagnose the faults of rolling bearings effectively, a novel fault identification method is proposed by merging variational mode decomposition (VMD), average refined composite multiscale dispersion entropy (ARCMDE) and support vector machine (SVM) optimized by multistrategy enhanced swarm optimization in this paper. Firstly, the vibration signals are decomposed into different series of intrinsic mode functions (IMFs) based on VMD with the center frequency observation method. Subsequently, the proposed ARCMDE, fusing the superiorities of DE and average refined composite multiscale procedure, is employed to enhance the ability of the multiscale fault-feature extraction from the IMFs. Afterwards, grey wolf optimization (GWO), enhanced by multistrategy including levy flight, cosine factor and polynomial mutation strategies (LCPGWO), is proposed to optimize the penalty factor C and kernel parameter g of SVM. Then, the optimized SVM model is trained to identify the fault type of samples based on features extracted by ARCMDE. Finally, the application experiment and contrastive analysis verify the effectiveness of the proposed VMD-ARCMDE-LCPGWO-SVM method.

Identification and Fine Mapping of qSCR4.01, a Novel Major QTL for Resistance to Puccinia polysora in Maize.

Southern corn rust (SCR) is a prevalent foliar disease that can lead to severe yield losses in maize. Growing SCR-resistant varieties is the most effective way to control the disease. To identify major quantitative trait loci (QTLs) for SCR resistance, a recombinant inbred line population derived from a cross between CIMBL83 (resistant) and Lx9801 (susceptible) was analyzed. The resistance to SCR had high heritability within the population, and a major QTL on chromosome 4 (qSCR4.01), which can explain 48 to 65% of the total phenotypic variation, was consistently detected across multiple environments. Using a progeny-based fine-mapping strategy, we delimited qSCR4.01 to an interval of ∼770 kb. In contrast to other major QTLs for SCR resistance previously reported on the short arm of chromosome 10, qSCR4.01 is a novel QTL and, therefore, a desirable source of SCR resistance in maize breeding programs.

Identification and characterization of a novel stay-green QTL that increases yield in maize.

Functional stay-green is a valuable trait that extends the photosynthetic period, increases source capacity and biomass and ultimately translates to higher grain yield. Selection for higher yields has increased stay-green in modern maize hybrids. Here, we report a novel QTL controlling functional stay-green that was discovered in a mapping population derived from the Illinois High Protein 1 (IHP1) and Illinois Low Protein 1 (ILP1) lines, which show very different rates of leaf senescence. This QTL was mapped to a single gene containing a NAC-domain transcription factor that we named nac7. Transgenic maize lines where nac7 was down-regulated by RNAi showed delayed senescence and increased both biomass and nitrogen accumulation in vegetative tissues, demonstrating NAC7 functions as a negative regulator of the stay-green trait. More importantly, crosses between nac7 RNAi parents and two different elite inbred testers produced hybrids with prolonged stay-green and increased grain yield by an average 0.29 megagram/hectare (4.6 bushel/acre), in 2 years of multi-environment field trials. Subsequent RNAseq experiments, one employing nac7 RNAi leaves and the other using leaf protoplasts overexpressing Nac7, revealed an important role for NAC7 in regulating genes in photosynthesis, chlorophyll degradation and protein turnover pathways that each contribute to the functional stay-green phenotype. We further determined the putative target of NAC7 and provided a logical extension for the role of NAC7 in regulating resource allocation from vegetative source to reproductive sink tissues. Collectively, our findings make a compelling case for NAC7 as a target for improving functional stay-green and yields in maize and other crops.

Callistemonols A and B, Potent Antimicrobial Acylphloroglucinol Derivatives with Unusual Carbon Skeletons from Callistemon viminalis.

A phytochemical investigation on the leaves of Callistemon viminalis resulted in the isolation of two unusual compounds, callistemonols A (1) and B (2). Callistemonol A (1) possesses a novel skeleton of a furan ring fusing both an α,ß-triketone and a phloroglucinol unit, while callistemonol B (2) is an acylphloroglucinol derivative featuring two methyl substituents on a five-membered ring and an isovaleryl side chain. Their structures were fully characterized on the basis of extensive spectroscopic analysis, including 1D and 2D NMR parameters, as well as the IR and HRESIMS data. Callistemonol A (1) represents an example of a natural dibenzofuran with two phenyl moieties, and a plausible biogenetic pathway to generate this novel dibenzofuran through a C-C bond-forming radical SAM enzyme is proposed. Moreover, antimicrobial assays, in conjunction with time-killing and biophysical studies, revealed that 1 and 2 exert potent bactericidal activities against a panel of methicillin-resistant pathogenic microbes.

Rosanortriterpene C, a 3,24-Dinor-2,4-seco-ursane Triterpene from the Fruits of Rosa laevigata var. leiocapus.

One new 3,24-dinor-2,4-seco-ursane triterpene, rosanortriterpene C (1), together with four known compounds including 24-norursane-type nortriterpenes (2-3), 24-noroleanane-type nortriterpene (4), ursane-type triterpene (5), was isolated from the fruits of Rosa laevigata var. leiocapus. The new structure was elucidated through comprehensive spectroscopic analysis, including one dimensional (1D) and 2D NMR data, as well as electrospray ionization high resolution (HR-ESI) MS and IR spectrometry. Compounds 1-5 showed moderate anti-inflammatory activities against the production of nitric oxide (NO) in RAW264.7 cells stimulated by lipopolysaccharide (LPS) with IC50 values of 10.35 ± 0.92, 14.28 ± 1.20, 5.04 ± 1.43, 29.29 ± 3.64, and 14.37 ± 0.59 µM, respectively.

Simulation-Based Design and Optimization of Accelerometers Subject to High-Temperature and High-Impact Loads.

Due to multi-factor coupling behavior, the performance evaluation of an accelerometer subject to high-temperature and high-impact loads poses a significant challenge during its design phase. In this paper, the simulation-based method is applied to optimize the design of the accelerometer. The proposed method can reduce the uncertainties and improve the fidelity of the simulation in the sense that (i) the preloading conditions of fasteners are taken into consideration and modeled in static analysis; (ii) all types of loadings, including bolt preloads, thermal loads, and impact loads, are defined in virtual dynamic prototype of the accelerometer. It is our finding that from static and dynamic analysis, an accelerometer is exposed to the risk of malfunction and even a complete failure if the temperature rises to a certain limit; it has been proved that the thermal properties of sensing components are the most critical factors for an accelerometer to achieve its desired performance. Accordingly, we use a simulation-based method to optimize the thermal expansion coefficient of the sensing element and get the expected design objectives.

Three new kavalactone dimers from Piper methysticum (kava).

Three new dimeric kavalactones, designated as diyangonins A-C (1-3), along with two known analogs were isolated from the roots of Piper methysticum. Their structures were elucidated by means of extensive analysis of their 1D, 2D NMR, and mass spectroscopic data. All these dimers possess a skeleton featuring a cyclobutane ring connecting two kavalactone units in head-to-tail or head-to-head mode. Compounds 1-5 were evaluated for their cytotoxic activities against human tumor cell lines.

Two new ent-kaurane diterpenes from the stems of Eurya chinensis.

Two new ent-kaurane diterpenes (1-2), together with five known analogs, were isolated from the stems of Eurya chinensis. The structures of new compounds were established by extensive analysis of mass spectrometric and 1D and 2D NMR spectroscopic data. Compound 3 exhibited noticeable anti-inflammatory activity as denoted by inhibiting LPS-induced nitric oxide (NO) production in RAW264.7 cells with an IC50 value of 7.82 µM. Compound 4 showed potent cytotoxic activity against human cancer cell lines NCI-H46, HepG2 and SW480 with IC50 values ranging from 7.45 to 8.54 µM.

A single point mutation in Ms44 results in dominant male sterility and improves nitrogen use efficiency in maize.

Application of nitrogen fertilizer in the past 50 years has resulted in significant increases in crop yields. However, loss of nitrogen from crop fields has been associated with negative impacts on the environment. Developing maize hybrids with improved nitrogen use efficiency is a cost-effective strategy for increasing yield sustainably. We report that a dominant male-sterile mutant Ms44 encodes a lipid transfer protein which is expressed specifically in the tapetum. A single amino acid change from alanine to threonine at the signal peptide cleavage site of the Ms44 protein abolished protein processing and impeded the secretion of protein from tapetal cells into the locule, resulting in dominant male sterility. While the total nitrogen (N) content in plants was not changed, Ms44 male-sterile plants reduced tassel growth and improved ear growth by partitioning more nitrogen to the ear, resulting in a 9.6% increase in kernel number. Hybrids carrying the Ms44 allele demonstrated a 4%-8.5% yield advantage when N is limiting, 1.7% yield advantage under drought and 0.9% yield advantage under optimal growth conditions relative to the yield of wild type. Furthermore, we have developed an Ms44 maintainer line for fertility restoration, male-sterile inbred seed increase and hybrid seed production. This study reveals that protein secretion from the tapetum into the locule is critical for pollen development and demonstrates that a reduction in competition between tassel and ear by male sterility improves grain yield under low-nitrogen conditions in maize.

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize.

Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.

Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation.

Alternative splicing enhances transcriptome diversity in all eukaryotes and plays a role in plant tissue identity and stress adaptation. To catalog new maize (Zea mays) transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 RNA-seq libraries from maize inbred lines B73 and Mo17, as well as Syn10 doubled haploid lines (progenies from B73 × Mo17). Transcript discovery was augmented with publicly available data from 14 maize tissues, expanding the maize transcriptome by more than 30,000 and increasing the percentage of intron-containing genes that undergo alternative splicing to 40%. These newly identified transcripts greatly increase the diversity of the maize proteome, sometimes coding for entirely different proteins compared with their most similar annotated isoform. In addition to increasing proteome diversity, many genes encoding novel transcripts gained an additional layer of regulation by microRNAs, often in a tissue-specific manner. We also demonstrate that the majority of genotype-specific alternative splicing can be genetically mapped, with cis-acting quantitative trait loci (QTLs) predominating. A large number of trans-acting QTLs were also apparent, with nearly half located in regions not shown to contain genes associated with splicing. Taken together, these results highlight the currently underappreciated role that alternative splicing plays in tissue identity and genotypic variation in maize.