bluuebunny/crossref_metadata_2025 huggingface dataset:
Case Report: Therapeutic Drug Monitoring of Polymyxin B During Continuous Renal Replacement Therapy in Two Pediatric Patients: Do Not Underestimate Extracorporeal Clearance
Authors: Xu Caifang , Liu Xiaofen , Cui Yun , Huang Xiaolan , Wang Yu , Fan Yaxin , Wu Hailan , Li Xin , Guo Beining , Zhang Jing , Zhang Yucai
Published: March 2022

Background: Polymyxin B has become the last choice for patient with carbapenem-resistant bacterial infection. However, the optimal dosing of polymyxin B in critically ill children receiving continuous renal replacement therapy (CRRT) remains unclear.

Case Presentation: Two cases of critically ill pediatric patients (7 years old) with acute kidney injury requiring continuous renal replacement (CRRT) received polymyxin B treatment due to carbapenem-resistant organism bloodstream infections. Therapeutic drug monitoring (TDM) of polymyxin B was carried out by liquid chromatography tandem mass spectrometry (LC-MS/MS). The average steady-state plasma concentration (Css,avg) of 2–4 mg/L was set as the target level. Initial polymyxin B dose was 1 mg/kg every 12 h, and the Css,avg at 4–5th dosing were 1.76 and 1.06 mg/L for patient 1 and patient 2, respectively. TDM-guided polymyxin B dose was escalated to 2 mg/kg every 12 h for both patients, resulting in the Css,avg of 2.60 and 1.73 mg/L, and the infection was controlled subsequently. Css,avg of polymyxin B with the same dosing regimens and infusion length were different during CRRT and after termination of CRRT for both patients (2.60 mg/L vs. 4.94 mg/L with 2 mg/kg every 12 h in 2 h infusion for patient 1; and 1.73 mg/L vs. 3.53 mg/L with 2 mg/kg every 12 h in 2 h infusion for patient 2). The estimation of drug exposure (estimated by AUCss,12h at the same dose) during CRRT and cessation of CRRT showed that 45% and 51% of polymyxin B was cleared during CRRT.

Conclusion: Our study showed high clearance of polymyxin B through CRRT, and supplanted dosing of polymyxin B is necessary in pediatric patients undergoing CRRT.
Optimization of SARS-CoV-2 Pseudovirion Production in Lentivirus Backbone With a Novel Liposomal System
Authors: Mahalingam Gokulnath , Rachamalla Hari Krishnareddy , Arjunan Porkizhi , Periyasami Yogapriya , M Salma , Thangavel Saravanabhavan , Mohankumar Kumarasamypet M. , Moorthy Mahesh , Velayudhan Shaji R. , Srivastava Alok , Marepally Srujan
Published: March 2022

Due to the fast mutating nature of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the development of novel therapeutics, vaccines, and evaluating the efficacies of existing one’s against the mutated strains is critical for containing the virus. Pseudotyped SARS-CoV-2 viruses are proven to be instrumental in evaluating the efficiencies of therapeutics, owing to their ease in application and safety when compared to handling the live virus. However, a comprehensive protocol that includes selecting transfection reagents, validating different packaging systems for high-throughput screening of neutralizing antibodies, is still a requisite. To this end, we designed and synthesized amide linker-based cationic lipids with varying hydrophilic head groups from dimethyl (Lipo-DME) to methyl, ethylhydroxyl (Lipo-MeOH), and diethylhydroxyl (Lipo-DOH) keeping the hydrophobic tail, stearic acid, as constant. Among the liposomal formulations of these lipids, Lipo-DOH was found to be superior in delivering plasmids and demonstrated comparable transfection efficiencies with commercial standard Lipofectamine 3000. We further used Lipo-DOH for lentivirus and SARS-CoV-2 pseudovirion preparation. For comparing different lentivirus packaging systems, we optimized conditions using Addgene and BEI systems and found that the BEI lenti plasmid system was found to be efficient in making lentiviruses using Lipo-DOH. Using the optimized transfection reagent and the lentivirus system, we developed a robust protocol for the generation of SARS-CoV-2 pseudovirions and characterized their infectivity in human ACE2 expressing HEK-293T cells and neutralizing properties in IgG against spike protein of SARS-CoV-2 positive human sera from individuals recovered from COVID-19.
Potential Target Analysis of Triptolide Based on Transcriptome-Wide m6A Methylome in Rheumatoid Arthritis
Authors: Fan Danping , Liu Bin , Gu Xiaofeng , Zhang Qian , Ye Qinbin , Xi Xiaoyu , Xia Ya , Wang Qiong , Wang Zheng , Wang Bailiang , Xu Yuan , Xiao Cheng
Published: March 2022

Triptolide (TP), a major active component of the herb Tripterygium wilfordii Hook F (TwHF), has been shown to exert therapeutic potential against rheumatoid arthritis (RA). However, its molecular mechanism of action has not been fully elucidated. This study aimed to analyze the potential target of TP based on the discovery of differentially methylated and expressed genes (DMEGs) in RA using methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq). Five RA samples and ten control samples were obtained from China-Japan Friendship Hospital. The various levels of m6A methylation and genes expressed in the RA and control groups were compared by MeRIP-seq and RNA-seq. Bioinformatics explorations were also performed to explore the enriched biological roles and paths of the differentially expressed m6A methylation and genes. Molecular networks between TP target proteins and DMEGs were performed using Ingenuity Pathway Analysis (IPA) software. Potential target of TP was determined with Gene Expression Omnibus (GEO) database mining, molecular docking, and in vitro experiment validation. In total, 583 dysregulated m6A peaks, of which 295 were greatly upregulated and 288 were greatly downregulated, were identified. Similarly, 1,570 differentially expressed genes were identified by RNA-seq, including 539 upregulated and 1,031 downregulated genes. According to the deeper joint exploration, the m6A methylation and mRNA expression degrees of 35 genes varied greatly. Molecular networks between TP target proteins and DMEGs were constructed, and the results revealed that tubulin beta-2A chain (TUBB2A), insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), cytoplasmic dynein 1 intermediate chain 1 (DYNC1I1), and FOS-like 1 (FOSL1) were the most relevant genes that correlated with the target proteins of TP. The results of the GEO database showed that the gene expression of IGF2BP3 was increased in RA synovial tissue and consistent with the trend of our sequencing results of RA PBMCs. Molecular docking and in vitro experiment suggested that TP and IGF2BP3 had a high binding affinity and TP could decrease the mRNA expression of IGF2BP3 in PBMCs and MH7A.This research established a transcriptional map of m6A in RA PBMCs and displayed the hidden association between RNA methylation alterations and associated genes in RA. IGF2BP3 might be a potential therapeutic target of TP during RA treatment.
Extracellular Vesicles: Emerging Roles in Developing Therapeutic Approach and Delivery Tool of Chinese Herbal Medicine for the Treatment of Depressive Disorder
Authors: Wu Qian , Duan Wen-Zhen , Chen Jian-Bei , Zhao Xiao-Peng , Li Xiao-Juan , Liu Yue-Yun , Ma Qing-Yu , Xue Zhe , Chen Jia-Xu
Published: March 2022

Extracellular vesicles (EVs) are lipid bilayer-delimited particles released by cells, which play an essential role in intercellular communication by delivering cellular components including DNA, RNA, lipids, metabolites, cytoplasm, and cell surface proteins into recipient cells. EVs play a vital role in the pathogenesis of depression by transporting miRNA and effector molecules such as BDNF, IL34. Considering that some herbal therapies exhibit antidepressant effects, EVs might be a practical delivery approach for herbal medicine. Since EVs can cross the blood-brain barrier (BBB), one of the advantages of EV-mediated herbal drug delivery for treating depression with Chinese herbal medicine (CHM) is that EVs can transfer herbal medicine into the brain cells. This review focuses on discussing the roles of EVs in the pathophysiology of depression and outlines the emerging application of EVs in delivering CHM for the treatment of depression.
Inhibitory Mechanism of Combined Hydroxychavicol With Epigallocatechin-3-Gallate Against Glioma Cancer Cell Lines: A Transcriptomic Analysis
Authors: Abdul Rahman Amirah , Wan Ngah Wan Zurinah , Jamal Rahman , Makpol Suzana , Harun Roslan , Mokhtar Norfilza
Published: March 2022

Emerging reports have shown therapeutic potential of hydroxychavicol (HC) and epigallocatechin-3-gallate (EGCG) against cancer cells, however high concentrations are required to achieve the anticancer activity. We reported the synergy of low combination doses of EGCG+HC in glioma cell lines 1321N1, SW1783, and LN18 by assessing the effects of EGCG+HC through functional assays. Using high throughput RNA sequencing, the molecular mechanisms of EGCG+HC against glioma cell lines were revealed. EGCG/HC alone inhibited the proliferation of glioma cell lines, with IC50 values ranging from 82 to 302 µg/ml and 75 to 119 µg/ml, respectively. Sub-effective concentrations of combined EGCG+HC enhanced the suppression of glioma cell growth, with SW1783 showing strong synergism with a combination index (CI) of 0.55 and LN18 showing a CI of 0.51. A moderate synergistic interaction of EGCG+HC was detected in 1321N1 cells, with a CI value of 0.88. Exposure of 1321N1, SW1783, and LN18 cells to EGCG+HC for 24 h induces cell death, with caspase-3 activation rates of 52%, 57%, and 9.4%, respectively. However, the dose for SW1783 is cytotoxic to normal cells, thus this dose was excluded from other tests. EGCG+HC induced cell cycle arrest at S phase and reduced 1321N1 and LN18 cell migration and invasion. Combined EGCG+HC amplified its anticancer effect by downregulating the axon guidance process and metabolic pathways, while simultaneously interfering with endoplasmic reticulum unfolded protein response pathway. Furthermore, EGCG+HC exerted its apoptotic effect through the alteration of mitochondrial genes such as MT-CO3 and MT-RNR2 in 1321N1 and LN18 cells respectively. EGCG+HC dynamically altered DYNLL1 alternative splicing expression in 1321N1 and DLD splicing expression in LN18 cell lines. Our work indicated the pleiotropic effects of EGCG+HC treatment, as well as particular target genes that might be investigated for future glioma cancer therapeutic development.
The Anti-Inflammatory Effect of Cabbage Leaves Explained by the Influence of bol-miRNA172a on FAN Expression
Authors: Kasarello Kaja , Köhling Iwona , Kosowska Anna , Pucia Katarzyna , Lukasik Anna , Cudnoch-Jedrzejewska Agnieszka , Paczek Leszek , Zielenkiewicz Urszula , Zielenkiewicz Piotr
Published: March 2022

Recently, the possibility of cross-kingdom gene expression regulation by miRNAs from other species (“xenomiRs”), specifically from plants, has acquired scientific meaning. Based on the one of oldest methods for dealing with inflammation via the use of cabbage leaf compresses, we investigated the effects of Brassica oleracea derived miR172a on the potential human target gene encoding FAN (Factor Associated with Neutral Sphingomyelinase Activation) protein. In vitro experiments showed a decrease in FAN protein levels in both human and mouse cells transfected with bol-miRNA172a. As the FAN protein mediates inflammatory responses, the potential of miR172a to mitigate the inflammatory process was tested in a mouse model of rheumatoid arthritis. Animal studies showed the decreased oedema of inflamed paws in mouse with rheumatoid arthritis model induced after treatment with miR172a.
Adverse Event Profiles of PARP Inhibitors: Analysis of Spontaneous Reports Submitted to FAERS
Authors: Tian Xiaojiang , Chen Lin , Gai Di , He Sijie , Jiang Xuan , Zhang Ni
Published: March 2022

Background: Several poly ADP ribose polymerase inhibitors (PARPis) are currently approved for the treatment of a variety of cancers. The safety profile of PARPis has not yet been systemically analyzed in the real world. We conducted this pharmacovigilance analysis using the US FDA’s Adverse Event Reporting System (FAERS) database to explore the difference in adverse events (AEs) among PARPis.

Methods: FAERS data (December 2014 to October 2021) were searched for reports of all FDA-approved PARPis across all indications. We used the standardized MedDRA query (SMQ) generalized search AEs on the preferred term (PT) level based on case reports. After filtering duplicate reports, disproportionality analysis was used to detect safety signals by calculating reporting odds ratios (ROR). Reports were considered statistically significant if the 95% confidence interval did not contain the null value.

Results: Within the standardized MedDRA queries, significant safety signals were found, including those for olaparib [blood premalignant disorders (ROR = 17.06)], rucaparib [taste and smell disorders (ROR = 9.17)], niraparib [hematopoietic throbocytopenia (ROR = 28.2)], and talazoparib [hematopoietic erythropenia (ROR = 9.38)]. For AEs on the PT level, we found several significant signals, including platelet count decreased with niraparib (ROR = 52.78); red blood cell count decreased with niraparib (ROR = 70.47) and rucaparib (ROR = 15.09); myelodysplastic syndrome with olaparib (ROR = 35.47); acute myeloid leukaemia with olaparib (ROR = 25.14); blood pressure fluctuation with niraparib (ROR = 20.54); lymphangioleiomyomatosis with niraparib (ROR = 471.20); photosensitivity reaction with niraparib (ROR = 21.77) and rucaparib (ROR = 18.92); renal impairment with rucaparib (ROR = 33.32); and interstitial lung disease with Olaparib (ROR = 11.31). All the detected safety signals were confirmed using signals of disproportionality reporting methods.

Conclusion: PARPis differed in their safety profile reports. The analysis of the FAERS database revealed significant safety signals that matched previously published case reports, including serious gastrointestinal, blood and lymphatic system, cardiovascular and respiratory complications, which require individualized drug administration according to patients’ conditions.
Inhibition of STAT3 Signaling Pathway by Terphenyllin Suppresses Growth and Metastasis of Gastric Cancer
Authors: Yu Dehua , Qi Simin , Guan Xiaoqing , Yu Wenkai , Yu Xuefei , Cai Maohua , Li Qinglin , Wang Weiyi , Zhang Weidong , Qin Jiang-Jiang
Published: March 2022

Gastric cancer is a common type of malignant tumor with a relatively poor prognosis and presents a serious threat to global health. Signal Transducer and Activator of Transcription-3 (STAT3) has been strongly implicated in many cancers, and its constitutive activation promotes growth, angiogenesis, inflammation, and immune evasion. Therefore, considerable efforts have been put into developing effective and safe STAT3 inhibitors. In this study, we performed a virtual screening by molecular docking and found that terphenyllin, a marine-derived natural product, directly interacted with STAT3. We further found that terphenyllin inhibited the phosphorylation and activation of STAT3 and decreased the protein levels of STAT3-dependent target genes, including c-Myc and Cyclin D1. Subsequently, we demonstrated that terphenyllin exerted its potent anticancer efficacy against gastric cancer in vitro and in vivo. Terphenyllin concentration-dependently inhibited growth, proliferation, and colony formation and induced cell cycle arrest and apoptosis of gastric cancer cells in vitro. Moreover, terphenyllin treatment suppressed the tumor growth and metastasis in a gastric cancer orthotopic mouse model without notable toxicity in vivo. Taken together, our results indicated that terphenyllin exerts its anticancer activity by inhibiting the STAT3 signaling pathway and may serve as a potent STAT3 inhibitor for gastric cancer treatment.
Electron-Ion Temperature Relaxation in Warm Dense Hydrogen Observed With Picosecond Resolved X-Ray Scattering
Authors: Fletcher L. B. , Vorberger J. , Schumaker W. , Ruyer C. , Goede S. , Galtier E. , Zastrau U. , Alves E. P. , Baalrud S. D. , Baggott R. A. , Barbrel B. , Chen Z. , Döppner T. , Gauthier M. , Granados E. , Kim J. B. , Kraus D. , Lee H. J. , MacDonald M. J. , Mishra R. , Pelka A. , Ravasio A. , Roedel C. , Fry A. R. , Redmer R. , Fiuza F. , Gericke D. O. , Glenzer S. H.
Published: March 2022

Angularly resolved X-ray scattering measurements from fs-laser heated hydrogen have been used to determine the equilibration of electron and ion temperatures in the warm dense matter regime. The relaxation of rapidly heated cryogenic hydrogen is visualized using 5.5 keV X-ray pulses from the Linac Coherent Light (LCLS) source in a 1 Hz repetition rate pump-probe setting. We demonstrate that the electron-ion energy transfer is faster than quasi-classical Landau-Spitzer models that use ad hoc cutoffs in the Coulomb logarithm.
Correlated Insulating Behavior in Infinite-Layer Nickelates
Authors: Hsu Y.-T. , Osada M. , Wang B. Y. , Berben M. , Duffy C. , Harvey S. P. , Lee K. , Li D. , Wiedmann S. , Hwang H. Y. , Hussey N. E.
Published: March 2022

Unlike their cuprate counterparts, the undoped nickelates are weak insulators without long-range antiferromagnetic order. Identifying the origin of this insulating behavior, found on both sides of the superconducting dome, is potentially a crucial step in the development of a coherent understanding of nickelate superconductivity. In this work, we study the normal-state resistivity of infinite-layer nickelates using high magnetic fields to suppress the superconductivity and examine the impact of disorder and doping on its overall temperature (T) dependence. In superconducting samples, the resistivity of Nd- and La-based nickelates continues to exhibit weakly insulating behavior with a magnitude and functional form similar to that found in underdoped electron-doped cuprates. We find a systematic evolution of the insulating behavior as a function of nominal hole doping across different rare-earth families, suggesting a pivotal role for strong electron interactions, and uncover a correlation between the suppression of the resistivity upturn and the robustness of the superconductivity. By contrast, we find very little correlation between the level of disorder and the magnitude and onset temperature of the resistivity upturn. Combining these experimental observations with previous Hall effect measurements on these two nickelate families, we consider various possible origins for this correlated insulator behavior and its evolution across their respective phase diagrams.
Diffuse Imaging Approach for Universal Noninvasive Blood Glucose Measurements
Authors: Liu Ming , Xu Ge , Zhao Yuejin , Kong Lingqin , Dong Liquan , Li Fen , Hui Mei
Published: March 2022

We proposed a diffuse imaging approach for universal noninvasive blood glucose measurements based on visible light, which can predict the blood glucose concentration without personal calibration. The proposed approach used a CCD to obtain diffuse images from human index finger pulp. The denoising autoencoder algorithm adopted effectively extracted the scattering information highly related to blood glucose concentration from the diffuse images, and the gradient boosting regression algorithm enabled an accurate calculation of blood glucose concentration without prior personalized calibration.In vivoexperimental results showed that the proposed approach had a mean absolute error of 19.44 mg/dl, with all the predicted results observed within the clinically acceptable region (Region A: 78.9%) in the Clarke error grid analysis. Compared to other blood glucose concentration measurement methods of scattering coefficient, this new method does not require individual calibration, therefore it is easier to implement and popularize, which is critical for the noninvasive monitoring of blood glucose concentration.
Fundamentals and Applications of Topological Polarization Singularities
Authors: Wang Feifan , Yin Xuefan , Zhang Zixuan , Chen Zihao , Wang Haoran , Li Peishen , Hu Yuefeng , Zhou Xinyi , Peng Chao
Published: March 2022

Radiations towards the continuum not only brings non-Hermicity to photonic systems but also provides observable channels for understanding their intrinsic physics underneath. In this article, we review the fundamental physics and applications of topological polarization singularities, which are defined upon the far-field radiation of photonic systems and characterized by topological charges as the winding numbers of polarization orientation around a given center. A brief summarizing of topological charge theory is presented. A series of applications related to topological polarization singularities are then discussed.
Simulations and Experiments Toward Continuous Wave 167 nm Laser Generation for ARPES With High Energy Resolution
Authors: Zhang Ziyue , Han Hainian , Zhao Guodong , Liu Guodong , Zhou Xingjiang , Wei Zhiyi
Published: March 2022

Continuous wave (CW) laser at a vacuum ultraviolet (VUV) range with the narrow-linewidth is an ideal optical source in angle-resolved photoemission spectroscopy (ARPES) for the research of superconductors with a narrow band gap. In this study, we present an eighth-harmonic-generation (EHG) laser scheme for CW laser generation at the VUV range, in particular at 167.75 nm, based on the cascaded power enhancement cavities. An intracavity second-harmonic generation (ICSHG) 671 nm laser with the narrow-linewidth and active frequency stabilization is built as the first stage, delivering the 2.55 W output power. A resonant cavity for fourth-harmonic-generation (FHG) constitutes the second stage, which generates the 335.5 nm laser with the output power of up to 1.25 W. The third stage is designed for the EHG of 167.75 nm based on the KBBF crystal. To realize the efficient CW laser generation at 167.75 nm, a theoretical analysis concerning the enhancement factor and the conversion efficiency of the KBBF-based EHG is carried out. The results show that it is possible for mW-level 167.75 nm generation if the transmittance of the KBBF prism-coupled device is increased to 97%. A 59 W circular intracavity power is observed in the 335.5 nm enhanced cavity experiments, corresponding to the peak power density of up to 20.86 MW/cm2. This work paves a solid way for CW VUV laser generation with the narrow-linewidth, which would be an ideal tool for the extremely high resolution ARPES.
Comparing the Respiratory Compensation Point With Muscle Oxygen Saturation in Locomotor and Non-locomotor Muscles Using Wearable NIRS Spectroscopy During Whole-Body Exercise
Authors: Yogev Assaf , Arnold Jem , Clarke Dave , Guenette Jordan A. , Sporer Ben C. , Koehle Michael S.
Published: March 2022

The relationship between the muscle deoxygenation breakpoint (Deoxy-BP) measured with near-infrared spectroscopy (NIRS), and the respiratory compensation point (RCP) has been well established. This relationship has also been reported using wearable NIRS, however not in locomotor and non-locomotor muscles simultaneously during whole-body cycling exercise. Our aim was to measure muscle oxygen saturation (SmO2) using wearable NIRS sensors, and to compare the Deoxy-BPs at each muscle with RCP during a ramp cycling exercise test. Twenty-two trained female and male cyclists completed a ramp exercise test to task intolerance on a cycling ergometer, at a ramp rate of 1 W every 2 s (30 W/min). SmO2 was recorded at the subjects’ right vastus lateralis (VL) and right lateral deltoid. SmO2 and the Deoxy-BPs were assessed using a piecewise double-linear regression model. Ventilation (V̇E) and gas exchange were recorded, and RCP was determined from V̇E and gas exchange using a V-slope method and confirmed by two physiologists. The SmO2 profiles of both muscles and gas exchange responses are reported as V̇O2, power output (W), and time of occurrence (TO). SmO2 profiles at both muscles displayed a near-plateau or breakpoint response near the RCP. No differences were detected between the mean RCP and mean Deoxy-BP from either the locomotor or non-locomotor muscles; however, a high degree of individual variability was observed in the timing and order of occurrence of the specific breakpoints. These findings add insight into the relationships between ventilatory, locomotor, and non-locomotor muscle physiological breakpoints. While identifying a similar relationship between these breakpoints, individual variability was high; hence, caution is advised when using wearable NIRS to estimate RCP in an incremental ramp test.
Generalizable Beat-by-Beat Arrhythmia Detection by Using Weakly Supervised Deep Learning
Authors: Liu Yang , Li Qince , He Runnan , Wang Kuanquan , Liu Jun , Yuan Yongfeng , Xia Yong , Zhang Henggui
Published: March 2022

Beat-by-beat arrhythmia detection in ambulatory electrocardiogram (ECG) monitoring is critical for the evaluation and prognosis of cardiac arrhythmias, however, it is a highly professional demanding and time-consuming task. Current methods for automatic beat-by-beat arrhythmia detection suffer from poor generalization ability due to the lack of large-sample and finely-annotated (labels are given to each beat) ECG data for model training. In this work, we propose a weakly supervised deep learning framework for arrhythmia detection (WSDL-AD), which permits training a fine-grained (beat-by-beat) arrhythmia detector with the use of large amounts of coarsely annotated ECG data (labels are given to each recording) to improve the generalization ability. In this framework, heartbeat classification and recording classification are integrated into a deep neural network for end-to-end training with only recording labels. Several techniques, including knowledge-based features, masked aggregation, and supervised pre-training, are proposed to improve the accuracy and stability of the heartbeat classification under weak supervision. The developed WSDL-AD model is trained for the detection of ventricular ectopic beats (VEB) and supraventricular ectopic beats (SVEB) on five large-sample and coarsely-annotated datasets and the model performance is evaluated on three independent benchmarks according to the recommendations from the Association for the Advancement of Medical Instrumentation (AAMI). The experimental results show that our method improves the F1 score of supraventricular ectopic beats detection by 8%–290% and the F1 of ventricular ectopic beats detection by 4%–11% on the benchmarks compared with the state-of-the-art methods of supervised learning. It demonstrates that the WSDL-AD framework can leverage the abundant coarsely-labeled data to achieve a better generalization ability than previous methods while retaining fine detection granularity. Therefore, this framework has a great potential to be used in clinical and telehealth applications. The source code is available at https://github.com/sdnjly/WSDL-AD.
A Secondary Metabolism Pathway Involved in the Production of a Putative Toxin Is Expressed at Early Stage of Monilinia laxa Infection
Authors: Villarino Maria , Rodríguez-Pires Silvia , Requena Elena , Melgarejo Paloma , De Cal Antonieta , Espeso Eduardo A.
Published: March 2022

The necrotrophic pathogenic fungus Monilinia laxa causes brown rot disease on stone fruit generating significant yield losses. So far, a limited number of pathogenesis-related virulence factors, such as cell wall degrading enzymes and potential phytotoxins, have been described in Monilinia spp. Using RNA-sequencing data from highly virulent M. laxa ML8L strain at early stages of the infection process (6, 14, 24, and 48 h post-inoculation, hpi) on nectarine and the Pathogen-Host-Interactions (PHI) database, we selected a number of genes for further study and ranked them according to their transcription levels. We identified a class of genes highly expressed at 6 hpi and that their expression decreased to almost undetectable levels at 14 to 48 hpi. Among these genes we found Monilinia__061040 encoding a non-ribosomal peptide synthase (NRPS). Monilinia__061040 together with other five co-regulated genes, forms a secondary metabolism cluster potentially involved in the production of epipolythiodioxopiperazine (ETP) toxin. Quantitative-PCR data confirmed previous RNA sequencing results from the virulent ML8L strain. Interestingly, in a less virulent M. laxa ML5L strain the expression levels of this pathway were reduced compared to the ML8L strain during nectarine infection. In vitro experiments showed that liquid medium containing peach extract mimicked the results observed using nectarines. In fact, upregulation of the NRPS coding gene was also observed in minimal medium suggesting the existence of a fruit-independent mechanism of regulation for this putative toxin biosynthetic pathway that is also downregulated in the less virulent strain. These results emphasize the role of this secondary metabolism pathway during the early stage of brown rot disease development and show alternative models to study the induction of virulence genes in this fungus.
Overexpression of CsSAMT in Citrus sinensis Induces Defense Response and Increases Resistance to Xanthomonas citri subsp. citri
Authors: Nascimento Cesar Augusto , Teixeira-Silva Natalia Sousa , Caserta Raquel , Marques Marcia Ortiz Mayo , Takita Marco Aurelio , de Souza Alessandra A.
Published: March 2022

Citrus canker is a destructive disease caused by Xanthomonas citri subsp. citri, which affects all commercial sweet orange (Citrus sinensis [L.] Osbeck) cultivars. Salicylic acid (SA) and systemic-acquired resistance (SAR) have been demonstrated to have a crucial role in mediating plant defense responses against this phytopathogen. To induce SAR, SA is converted to methyl salicylate (MeSA) by an SA-dependent methyltransferase (SAMT) and translocated systemically to prime noninfected distal tissues. Here, we generated sweet orange transgenic plants (based on cvs. Hamlin and Valencia) overexpressing the SAMT gene from Citrus (CsSAMT) and evaluated their resistance to citrus canker. We obtained four independent transgenic lines and confirmed their significantly higher MeSA volatilization compared to wild-type controls. Plants overexpressing CsSAMT showed reduced symptoms of citrus canker and bacterial populations in all transgenic lines without compromising plant development. One representative transgenic line (V44SAMT) was used to evaluate resistance response in primary and secondary sites. Without inoculation, V44SAMT modulated CsSAMT, CsNPR1, CsNPR3, and CsWRKY22 expression, indicating that this plant is in a primed defense status. The results demonstrate that MeSA signaling prompts the plant to respond more efficiently to pathogen attacks and induces immune responses in transgenic plants at both primary and secondary infection sites.
Association Mapping of Lathyrus sativus Disease Response to Uromyces pisi Reveals Novel Loci Underlying Partial Resistance
Authors: Martins Davide Coelho , Rubiales Diego , Vaz Patto Maria Carlota
Published: March 2022

Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding.
Physiological and Proteomic Analyses Indicate Delayed Sowing Improves Photosynthetic Capacity in Wheat Flag Leaves Under Heat Stress
Authors: Fei Liwei , Chu Jinpeng , Zhang Xiu , Dong Shuxin , Dai Xinglong , He Mingrong
Published: March 2022

Background and Aims

Climate warming has become an indisputable fact, and wheat is among the most heat-sensitive cereal crops. Heat stress during grain filling threatens global wheat production and food security. Here, we analyzed the physiological and proteomic changes by delayed sowing on the photosynthetic capacity of winter wheat leaves under heat stress. Our aim is to provide a new cultivation way for the heat stress resistance in wheat.

Methods

Through 2 years field experiment and an open warming simulation system, we compared the changes in wheat grain weight, yield, photosynthetic rate, and chlorophyll fluorescence parameters under heat stress at late grain–filling stage during normal sowing and delayed sowing. At the same time, based on the iTRAQ proteomics, we compared the changes of differentially expressed proteins (DEPs) during the two sowing periods under high temperature stress.

Key Results

In our study, compared with normal sowing, delayed sowing resulted in a significantly higher photosynthetic rate during the grain-filling stage under heat stress, as well as significantly increased grain weight and yield at maturity. The chlorophyll a fluorescence transient (OJIP) analysis showed that delayed sowing significantly reduced the J-step and I-step. Moreover, OJIP parameters, including RC/CSm, TRo/CSm, ETo/CSm, DIo/CSm and ΦPo, ψo, ΦEo, were significantly increased; DIo/CSm and ΦDo, were significantly reduced. GO biological process and KEGG pathway enrichment analyses showed that, among DEPs, proteins involved in photosynthetic electron transport were significantly increased and among photosynthetic metabolic pathways, we have observed upregulated proteins, such as PsbH, PsbR, and PetB.

Conclusion

Physiological and proteomic analyses indicate delaying the sowing date of winter wheat reduced heat dissipation by enhancing the scavenging capacity of reactive oxygen species (ROS) in flag leaves, and ensuring energy transmission along the photosynthetic electron transport chain; this increased the distribution ratio of available energy in photochemical reactions and maintained a high photosynthetic system assimilation capacity, which supported a high photosynthetic rate. Hence, delayed sowing may represent a new cultivation strategy for promoting heat stress tolerance in winter wheat.
Agrobacterium-Mediated High-Efficiency Genetic Transformation and Genome Editing of Chaling Common Wild Rice (Oryza rufipogon Griff.) Using Scutellum Tissue of Embryos in Mature Seeds
Authors: Xiang Zhipan , Chen Yi , Chen Yan , Zhang Lin , Liu Min , Mao Dandan , Chen Liangbi
Published: March 2022

Genetic transformation is an important strategy for revealing gene function, and it is used extensively in both functional genomics study and molecular breeding of rice. Demand for its application in wild Oryza species is rising for their extensive genetic diversity. However, genetic transformation of wild Oryza accessions with AA genome using calli induced from scutellum tissue of embryos in mature seeds has not been successfully established. In the present study, we used Chaling common wild rice (CLCWR) (Oryza rufipogon Griff.) with AA genome to successfully establish an Agrobacterium-mediated genetic transformation system based on scutellum tissue of embryos in mature seeds. The calli from embryos in mature seeds of CLCWR were easy to be induced and regenerated. The callus induction rate and texture were optimum under 2.5 mg/L 2,4-D. The optimal hormone combination used for regeneration was 2 mg/L ZT + 0.1 mg/L NAA. Studies on genetic transformation and genome editing showed that the transformation efficiency was 87–94%, the efficiency of single genome editing and multiplex genome editing were about 60–70% and 20–40%, respectively. Compared with Nipponbare (Nip), CLCWR had higher Hygromycin-resistant callus frequency and transformation efficiency. Taken together, our study establishes a highly efficient transformation system for common wild rice with AA genome and provides a good rice material for de novo domestication by genome editing in the future.
Integrative Analysis of Elicitor-Induced Camptothecin Biosynthesis in Camptotheca acuminata Plantlets Through a Combined Omics Approach
Authors: Pu Xiang , Gao Hu-Chuan , Wang Min-Ji , Zhang Jia-Hua , Shan Jia-Heng , Chen Meng-Han , Zhang Li , Wang Han-Guang , Wen An-Xiang , Luo Ying-Gang , Huang Qian-Ming
Published: March 2022

Treatments with abiotic elicitors can efficiently induce the accumulation of specialized metabolites in plants. We used a combined omics approach to analyze the elicitation effects of MeJa, AgNO3, and PEG on camptothecin (CPT) biosynthesis in Camptotheca acuminata plantlets. Untargeted analyses revealed that treatments with MeJa, AgNO3, and PEG significantly inhibited the photosynthetic pathway and promoted carbon metabolism and secondary metabolic pathways. The CPT levels increased by 78.6, 73.3, and 50.0% in the MeJa, AgNO3, and PEG treatment groups, respectively. Using C. acuminata plantlets after elicitation treatment, we mined and characterized 15 new alkaloids, 25 known CPT analogs and precursors, 9 iridoid biosynthetic precursors, and 15 tryptamine biosynthetic precursors based on their MS/MS fragmentation spectra. Using 32 characterized genes involved in CPT biosynthesis as bait, we mined 12 prioritized CYP450 genes from the 416 CYP450 candidates that had been identified based on co-expression analysis, conserved domain analysis, and their elicitation-associated upregulation patterns. This study provides a comprehensive perspective on CPT biosynthesis in C. acuminata plantlets after abiotic elicitation. The findings enable us to elucidate the previously unexplored CYP450-mediated oxidation steps for CPT biosynthesis.
Effects of Different Nitrogen Forms and Competitive Treatments on the Growth and Antioxidant System of Wedelia trilobata and Wedelia chinensis Under High Nitrogen Concentrations
Authors: Huang Ping , Shen Fangyuan , Abbas Adeel , Wang Hao , Du Yizhou , Du Daolin , Hussain Sadam , Javed Talha , Alamri Saud
Published: March 2022

Nitrogen (N) is one of the essential nutrients for plant growth. Appropriate application of N can improve the N use efficiency (NUE) and significantly promote plants’ growth. However, under N toxic conditions, the relationship between the growth and antioxidant system of invasive plants under different N forms and competitive treatments is not fully understood. Therefore, in this study, the performance of invasive species Wedelia trilobata and its native species Wedelia chinensis was evaluated under two sets of N forms and ratios, namely, NH4+-N(AN)/NO3–-N(NN) = 2:1 and NH4+-N(AN)/NO3–-N(NN) = 1:2 along with two intraspecific and interspecific competitions under without N and high N level of 15 g N⋅m–2 year–1, respectively. Data regarding the growth indices, antioxidant enzyme activities, including peroxidase (POD) and catalase (CAT), malondialdehyde (MDA), and proline contents were determined. Results showed that for competitive treatments, growth status was better for interspecific competition than intraspecific competition. The plant biomass of W. trilobata was significantly higher than that of W. chinensis. N significantly promoted the plants’ growth in terms of leaf area and biomass yield, and the antioxidant enzyme activities were significantly increased under a high N treatment than that of the control. Among N forms/ratios, ammonium N (AN)/nitrate N (NN) = 2:1 significantly enhanced the enzyme activity, particularly in W. trilobata. Furthermore, for intraspecific competition, MDA contents of W. trilobata were significantly decreased compared to that of W. chinensis. In conclusion, our results showed that W. trilobata adapted well under competitive conditions through better growth and antioxidant defense system.
Integrated Metabolomic and Transcriptomic Analysis and Identification of Dammarenediol-II Synthase Involved in Saponin Biosynthesis in Gynostemma longipes
Authors: Ye Shuang , Feng Lei , Zhang Shiyu , Lu Yingchun , Xiang Guisheng , Nian Bo , Wang Qian , Zhang Shuangyan , Song Wanling , Yang Ling , Liu Xiangyu , Feng Baowen , Zhang Guanghui , Hao Bing , Yang Shengchao
Published: March 2022

Gynostemma longipes contains an abundance of dammarane-type ginsenosides and gypenosides that exhibit extensive pharmacological activities. Increasing attention has been paid to the elucidation of cytochrome P450 monooxygenases (CYPs) and UDP-dependent glycosyltransferases (UGTs) that participate downstream of ginsenoside biosynthesis in the Panax genus. However, information on oxidosqualene cyclases (OSCs), the upstream genes responsible for the biosynthesis of different skeletons of ginsenoside and gypenosides, is rarely reported. Here, an integrative study of the metabolome and the transcriptome in the leaf, stolon, and rattan was conducted and the function of GlOSC1 was demonstrated. In total, 46 triterpenes were detected and found to be highly abundant in the stolon, whereas gene expression analysis indicated that the upstream OSC genes responsible for saponin skeleton biosynthesis were highly expressed in the leaf. These findings indicated that the saponin skeletons were mainly biosynthesized in the leaf by OSCs, and subsequently transferred to the stolon via CYPs and UGTs biosynthesis to form various ginsenoside and gypenosides. Additionally, a new dammarane-II synthase (DDS), GlOSC1, was identified by bioinformatics analysis, yeast expression assay, and enzyme assays. The results of the liquid chromatography–mass spectrometry (LC–MS) analysis proved that GlOSC1 could catalyze 2,3-oxidosqualene to form dammarenediol-II via cyclization. This work uncovered the biosynthetic mechanism of dammarenediol-II, an important starting substrate for ginsenoside and gypenosides biosynthesis, and may achieve the increased yield of valuable ginsenosides and gypenosides produced under excess substrate in a yeast cell factory through synthetic biology strategy.
The Hierarchical Contribution of Organic vs. Conventional Farming, Cultivar, and Terroir on Untargeted Metabolomics Phytochemical Profile and Functional Traits of Tomato Fruits
Authors: Rocchetti Gabriele , Senizza Biancamaria , Zengin Gokhan , Bonini Paolo , Bontempo Luana , Camin Federica , Trevisan Marco , Lucini Luigi
Published: March 2022

In this work, the impact of terroir, cultivar, seasonality, and farming systems on functional traits of tomato was hierarchically investigated. Untargeted metabolomics, antioxidant capacity, colorimetric assays, and enzyme inhibition were determined. The total phenolic and carotenoid contents significantly varied between growing years, whereas an interaction between the farming system and growing year (p < 0.01) was observed for total phenolics, carotenoids, and flavonoids, and for acetylcholinesterase inhibition. Hierarchical clustering showed that geographical origin and growing year were the major contributors to the differences in phytochemical profiles. Nonetheless, supervised modeling allowed highlighting the effect of the farming system. Several antioxidants (L-ascorbic acid, α-tocopherol, and 7,3′,4′-trihydroxyflavone) decreased, whereas the alkaloid emetine and phytoalexin phenolics increased under organic farming. Taken together, our findings indicate that cultivar and pedo-climatic conditions are the main determinants for the functional quality of tomato, whereas the farming system plays a detectable but hierarchically lower.
Regulation of Phytohormones on the Growth and Development of Plant Root Hair
Authors: Li Mengxia , Zhu Yanchun , Li Susu , Zhang Wei , Yin Changxi , Lin Yongjun
Published: March 2022

The tubular-shaped unicellular extensions of plant epidermal cells known as root hairs are important components of plant roots and play crucial roles in absorbing nutrients and water and in responding to stress. The growth and development of root hair include, mainly, fate determination of root hair cells, root hair initiation, and root hair elongation. Phytohormones play important regulatory roles as signal molecules in the growth and development of root hair. In this review, we describe the regulatory roles of auxin, ethylene (ETH), jasmonate (JA), abscisic acid (ABA), gibberellin (GA), strigolactone (SL), cytokinin (CK), and brassinosteroid (BR) in the growth and development of plant root hairs. Auxin, ETH, and CK play positive regulation while BR plays negative regulation in the fate determination of root hair cells; Auxin, ETH, JA, CK, and ABA play positive regulation while BR plays negative regulation in the root hair initiation; Auxin, ETH, CK, and JA play positive regulation while BR, GA, and ABA play negative regulation in the root hair elongation. Phytohormones regulate root hair growth and development mainly by regulating transcription of root hair associated genes, including WEREWOLF (WER), GLABRA2 (GL2), CAPRICE (CPC), and HAIR DEFECTIVE 6 (RHD6). Auxin and ETH play vital roles in this regulation, with JA, ABA, SL, and BR interacting with auxin and ETH to regulate further the growth and development of root hairs.