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1.
Int J Mol Sci ; 23(10)2022 May 22.
Article in English | MEDLINE | ID: covidwho-1875645

ABSTRACT

Actinidia latifolia is one of the very few kiwifruit genotypes with extremely high ascorbic acid (AsA) content. However, a transcriptome atlas of this species is lacking. The accumulation of AsA during fruit development and ripening and the associated molecular mechanisms are still poorly understood. Herein, dynamic changes in AsA content at six different stages of A. latifolia fruit development and ripening were determined. AsA content of A. latifolia fruit reached 1108.76 ± 35.26 mg 100 g-1 FW at full maturity. A high-quality, full-length (FL) transcriptome of A. latifolia was successfully constructed for the first time using third-generation sequencing technology. The transcriptome comprises 326,926 FL non-chimeric reads, 15,505 coding sequences, 2882 transcription factors, 18,797 simple sequence repeats, 3328 long noncoding RNAs, and 231 alternative splicing events. The genes involved in AsA biosynthesis and recycling pathways were identified and compared with those in different kiwifruit genotypes. The correlation between the AsA content and expression levels of key genes in AsA biosynthesis and recycling pathways was revealed. LncRNAs that participate in AsA-related gene expression regulation were also identified. Gene expression patterns in AsA biosynthesis and metabolism exhibited a trend similar to that of AsA accumulation. Overall, this study paves the way for genetic engineering to develop kiwifruits with super-high AsA content.


Subject(s)
Actinidia , Actinidia/genetics , Actinidia/metabolism , Ascorbic Acid/metabolism , Fruit/metabolism , Gene Expression Regulation, Plant , Transcriptome
2.
Nutrients ; 14(5)2022 Mar 05.
Article in English | MEDLINE | ID: covidwho-1732145

ABSTRACT

BACKGROUND: Pulmonary fibrosis (PF) is a chronic, progressive, and, ultimately, terminal interstitial disease caused by a variety of factors, ranging from genetics, bacterial, and viral infections, to drugs and other influences. Varying degrees of PF and its rapid progress have been widely reported in post-COVID-19 patients and there is consequently an urgent need to develop an appropriate, cost-effective approach for the prevention and management of PF. AIM: The potential "therapeutic" effect of the tocotrienol-rich fraction (TRF) and carotene against bleomycin (BLM)-induced lung fibrosis was investigated in rats via the modulation of TGF-ß/Smad, PI3K/Akt/mTOR, and NF-κB signaling pathways. DESIGN/METHODS: Lung fibrosis was induced in Sprague-Dawley rats by a single intratracheal BLM (5 mg/kg) injection. These rats were subsequently treated with TRF (50, 100, and 200 mg/kg body wt/day), carotene (10 mg/kg body wt/day), or a combination of TRF (200 mg/kg body wt/day) and carotene (10 mg/kg body wt/day) for 28 days by gavage administration. A group of normal rats was provided with saline as a substitute for BLM as the control. Lung function and biochemical, histopathological, and molecular alterations were studied in the lung tissues. RESULTS: Both the TRF and carotene treatments were found to significantly restore the BLM-induced alterations in anti-inflammatory and antioxidant functions. The treatments appeared to show pneumoprotective effects through the upregulation of antioxidant status, downregulation of MMP-7 and inflammatory cytokine expressions, and reduction in collagen accumulation (hydroxyproline). We demonstrated that TRF and carotene ameliorate BLM-induced lung injuries through the inhibition of apoptosis, the induction of TGF-ß1/Smad, PI3K/Akt/mTOR, and NF-κB signaling pathways. Furthermore, the increased expression levels were shown to be significantly and dose-dependently downregulated by TRF (50, 100, and 200 mg/kg body wt/day) treatment in high probability. The histopathological findings further confirmed that the TRF and carotene treatments had significantly attenuated the BLM-induced lung injury in rats. CONCLUSION: The results of this study clearly indicate the ability of TRF and carotene to restore the antioxidant system and to inhibit proinflammatory cytokines. These findings, thus, revealed the potential of TRF and carotene as preventive candidates for the treatment of PF in the future.


Subject(s)
COVID-19 , Pulmonary Fibrosis , Tocotrienols , Animals , Bleomycin/toxicity , Carotenoids/adverse effects , Humans , NF-kappa B/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Proto-Oncogene Proteins c-akt/metabolism , Pulmonary Fibrosis/chemically induced , Pulmonary Fibrosis/drug therapy , Pulmonary Fibrosis/prevention & control , Rats , Rats, Sprague-Dawley , SARS-CoV-2 , Signal Transduction , TOR Serine-Threonine Kinases/metabolism , Tocotrienols/adverse effects , Transforming Growth Factor beta/metabolism
3.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-323695

ABSTRACT

Knowing the residual and future effect of SARS-CoV-2 on recovered COVID-19 patients is critical for optimized long-term patient management. Recent studies focus on the symptoms and clinical indices of recovered patients, but the pathophysiological change is still unclear. To address this question, we examined the metabolomic profiles of recovered asymptomatic (RA), moderate (RM) and severe and critical (RC) patients without previous underlying diseases discharged from the hospital for 3 months, along with laboratory and CT findings. We found that the serum metabolic profiles in recovered COVID-19 patients still conspicuously differed from that in healthy control (HC), especially in the RM, and RC patients. Additionally, these changes bore close relationship with the function of pulmonary, renal, hepatic, microbial and energetic metabolism and inflammation. These findings suggested that RM and RC patients sustained multi-organ and multi-system damage and these patients should be followed up on regular basis for possible organ and system damage.

4.
PLoS One ; 17(2): e0263794, 2022.
Article in English | MEDLINE | ID: covidwho-1674022

ABSTRACT

Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-based SARS-CoV-2 detection tests, which use anterior nasal swabs for SARS-CoV-2 antigen detection. Despite this shift in testing methods, the need for whole-genome sequence surveillance remains. Thus, we developed a workflow for whole-genome sequencing with antigen test-derived swabs as an input rather than nasopharyngeal swabs. In this study, we use excess clinical specimens processed using the BinaxNOW™ COVID-19 Ag Card. We demonstrate that whole-genome sequencing from antigen tests is feasible and yields similar results from RT-PCR-based assays utilizing a swab in viral transport media.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Culture Media/analysis , High-Throughput Nucleotide Sequencing/methods , SARS-CoV-2/genetics , Specimen Handling/methods , Whole Genome Sequencing/methods , COVID-19/genetics , COVID-19/virology , Culture Media/metabolism , Humans , SARS-CoV-2/isolation & purification
6.
J Inflamm Res ; 14: 4485-4501, 2021.
Article in English | MEDLINE | ID: covidwho-1410010

ABSTRACT

BACKGROUND: It remains unclear whether discharged COVID-19 patients have fully recovered from severe complications, including the differences in the post-infection metabolomic profiles of patients with different disease severities. METHODS: COVID-19-recovered patients, who had no previous underlying diseases and were discharged from Wuhan Union Hospital for 3 months, and matched healthy controls (HCs) were recruited in this prospective cohort study. We examined the blood biochemical indicators, cytokines, lung computed tomography scans, including 39 HCs, 18 recovered asymptomatic (RAs), 34 recovered moderate (RMs), and 44 recovered severe/ critical patients (RCs). A liquid chromatography-mass spectrometry-based metabolomics approach was employed to profile the global metabolites of fasting plasma of these participants. RESULTS: Clinical data and metabolomic profiles suggested that RAs recovered well, but some clinical indicators and plasma metabolites in RMs and RCs were still abnormal as compared with HCs, such as decreased taurine, succinic acid, hippuric acid, some indoles, and lipid species. The disturbed metabolic pathway mainly involved the tricarboxylic cycle, purine, and glycerophospholipid metabolism. Moreover, metabolite alterations differ between RMs and RCs when compared with HCs. Correlation analysis revealed that many differential metabolites were closely associated with inflammation and the renal, pulmonary, heart, hepatic, and coagulation system functions. CONCLUSION: We uncovered metabolite clusters pathologically relevant to the recovery state in discharged COVID-19 patients which may provide new insights into the pathogenesis of potential organ damage in recovered patients.

7.
Cell Death Dis ; 12(6): 541, 2021 05 25.
Article in English | MEDLINE | ID: covidwho-1243286

ABSTRACT

More and more patients suffered from Coronavirus disease 2019 (COVID-19) have got recovery gradually due to suitable intervention. Increasing data mainly studies the clinical characteristics of recovered COVID-19 patients, and their molecular changes especially proteome changes also play the same important role in understanding of biological characteristics of recovered COVID-19 patients as clinical characteristics do. In our study, we reported the whole lung-ground glass-CT value-average of mild/severe recovered patients 3 months after discharge without underlying diseases was significantly lower than that of healthy subjects. Then we isolated the extracellular vesicles (EVs) of plasma from 19 healthy subjects and 67 recovered COVID-19 patients. Mass Spectrometry was used to catalogue the proteins of these EVs compared to a defined group of controls. Identified 174 proteins were differentially expressed in the EVs of COVID-19 patients compared with healthy subjects, which involved in lipid metabolic process, response to cellular, and response to stress oxygen-containing compound. Besides, we identified several protein of plasma EVs in recovered patients associated with coagulation activity, inflammatory reaction, immune response, and low organ function. In addition, proteins correlating with clinical index such as alkaline phosphatase (ALP) and alanine aminotransferase (ALT) were also detected. Moreover, we also identified many unique or characteristic associations found in the recovered COVID-19 patients, which especially involved the kidney, serum electrolyte levels, and inflammation functions. This finding suggests that monitoring the situation of recovered patients might be useful, especially the indexes of coagulation, inflammation, immunity, and organ function, which can prevent bleeding, reinfection and organ dysfunction.


Subject(s)
COVID-19/metabolism , Convalescence , Extracellular Vesicles/metabolism , Adult , COVID-19/blood , COVID-19/pathology , COVID-19/physiopathology , Extracellular Vesicles/pathology , Female , Humans , Lipids/blood , Male , Middle Aged , Prospective Studies , Proteins/metabolism , Proteomics , SARS-CoV-2 , Severity of Illness Index
8.
Mathematical Problems in Engineering ; 2021, 2021.
Article in English | ProQuest Central | ID: covidwho-1241061

ABSTRACT

In current large-scale supply chain networks, unexpected disruptions degrade the supply availability and network connectivity for modern enterprises. How to improve the robustness of supply chain networks is very important for modern enterprises. In this paper, we explore how to improve the robustness of supply chain networks from a topological perspective. Firstly, through the empirical data-driven study, we show that the directed betweenness metric is more suitable than the other topological metrics in evaluating the robustness of supply chain networks. Then, we propose a rewiring algorithm based on directed betweenness to improve network robustness under the impact of disruptions. The experimental results in the large-scale supply chain network show that the rewiring algorithm based on directed betweenness effectively improves the network robustness.

9.
Mil Med ; 187(1-2): e130-e137, 2022 01 04.
Article in English | MEDLINE | ID: covidwho-1091235

ABSTRACT

INTRODUCTION: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a global pandemic resulting in over 1 million deaths worldwide. In the Department of Defense (DoD), over 129,000 personnel (civilians, dependents, and active duty) have been infected with the virus to date. Rapid estimations of transmission and mutational patterns of virus outbreaks can be accomplished using whole-genome viral sequencing. Deriving interpretable and actionable results from pathogen sequence data is accomplished by the construction of phylogenetic trees (from local and global virus sequences) and by the creation of protein maps, to visualize and predict the effects of structural protein amino acid mutations. MATERIALS AND METHODS: We developed a sequencing and bioinformatics workflow for molecular epidemiological SARS-CoV-2 surveillance using excess clinical specimens collected under an institutional review board exempt protocol at Joint Base San Antonio, Lackland AFB. This workflow includes viral RNA isolation, viral load quantification, tiling-based next-generation sequencing, sequencing and bioinformatics analysis, and data visualization via phylogenetic trees and protein mapping. RESULTS: Sequencing of 37 clinical specimens collected at JBSA/Lackland revealed that by June 2020, SAR-CoV-2 strains carrying the 614G mutation were the predominant cause of local coronavirus disease 2019 infections. We identified 109 nucleotide changes in the coding region of the SARS-CoV-2 genome (which lead to 63 unique, non-synonymous amino acid mutations), one mutation in the 5'-untranslated region (UTR), and two mutations in the 3'UTR. Furthermore, we identified and mapped six additional spike protein amino acid changes-information which could potentially aid vaccine design. CONCLUSION: The workflow presented here is designed to enable DoD public health officials to track viral evolution and conduct near real-time evaluation of future outbreaks. The generation of molecular epidemiological sequence data is critical for the development of disease intervention strategies-most notably, vaccine design. Overall, we present a streamlined sequencing and bioinformatics methodology aimed at improving long-term readiness efforts in the DoD.


Subject(s)
COVID-19 , SARS-CoV-2 , Genome, Viral , Humans , Phylogeny , Spike Glycoprotein, Coronavirus/genetics , United States
10.
Aging (Albany NY) ; 13(1): 16-26, 2020 12 11.
Article in English | MEDLINE | ID: covidwho-979244

ABSTRACT

We aimed to compare the age-related clinical characteristics between younger and elderly deceased COVID-19 patients. This single-center retrospective study included 163 adult deceased COVID-19 patients who were admitted to Wuhan Union Hospital West Campus from January 12, 2020, to March 30, 2020. Demographic and clinical features were collected by reviewing the medical records. The median age of the 163 deceased patients was 69 (interquartile range [IQR], 62-78) years. They were classified as younger (age 18-69 years; 86/163, 52.8%) and elderly (≥70 years; 77/163, 47.2%) subjects. Younger deceased patients were more likely to develop fever (72/86 vs 54/77, P=0.039) than elderly deceased patients were while anorexia was (29/77 vs 19/86, P=0.029) more common in elderly deceased patients than in younger deceased patients. In multivariate analyses, age was a protective factor for acute cardiac injury of deceased COVID-19 patients (odds ratio [OR] 0.968, [95% confidence interval (CI), 0.940-0.997]; P=0.033) while chronic cardiac disease was a risk factor for acute cardiac injury of deceased COVID-19 patients (OR 2.660 [95%CI, 1.034-6.843]; P=0.042). Our study described the clinical characteristics of younger and elderly deceased COVID-19 patients and demonstrated that younger deceased patients were more likely to develop an acute cardiac injury.


Subject(s)
COVID-19/mortality , COVID-19/pathology , SARS-CoV-2 , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , Aging , Female , Humans , Male , Middle Aged , Multivariate Analysis , Retrospective Studies , Risk Factors , Young Adult
11.
Bioorg Chem ; 104: 104257, 2020 11.
Article in English | MEDLINE | ID: covidwho-739774

ABSTRACT

BACKGROUND: Oseltamivir is a first-line antiviral drug, especially in primary hospitals. During the ongoing outbreak of coronavirus disease 2019 (COVID-19), most patients with COVID-19 who are symptomatic have used oseltamivir. Considering its popular and important role as an antiviral drug, it is necessary to evaluate oseltamivir in the treatment of COVID-19. OBJECTIVE: To evaluate the effect of oseltamivir against COVID-19. METHODS: Swiss-model was used to construct the structure of the N-terminal RNA-binding domain (NRBD) of the nucleoprotein (NC), papain-like protease (PLpro), and RNA-directed RNA polymerase (RdRp) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). TM-align program was performed to compare the structure of the viral proteins with the structure of the neuraminidase of influenza A. Molecular docking was used to analyze the theoretical possibility of effective binding of oseltamivir with the active centers of the viral proteins. In vitro study was used to evaluate the antiviral efficiency of oseltamivir against SARS-CoV-2. By clinical case analysis, we statistically evaluated whether the history of oseltamivir use influenced the progression of the disease. RESULTS: The structures of NRBD, PLpro, and RdRp were built successfully. The results from TM-align suggested that the S protein, NRBD, 3C-like protease (3CLpro), PLPrO, and RdRp were structurally similar to the influenza A neuraminidase, with TM-scores of 0.30077, 0.19254, 0.28766, 0.30666, and 0.34047, respectively. Interestingly, the active center of 3CL pro was found to be similar to the active center from the neuraminidase of influenza A. Through an analysis of molecular docking, we discovered that oseltamivir carboxylic acid was more favorable to bind to the active site of 3CLpro effectively, but its inhibitory effect was not strong compared with the positive group. Finally, we used in vitro study and retrospective case analysis to verify our speculations. We found that oseltamivir is ineffective against SARS-CoV-2 in vitro study and the clinical use of oseltamivir did not improve the patients' symptoms and signs and did not slow the disease progression. CONCLUSIONS: We consider that oseltamivir isn't suitable for the treatment of COVID-19. During the outbreak of novel coronavirus, when oseltamivir is not effective for the patients after they take it, health workers should be highly vigilant about the possibility of COVID-19.


Subject(s)
Antiviral Agents/therapeutic use , COVID-19/drug therapy , Oseltamivir/therapeutic use , SARS-CoV-2/drug effects , Adult , Aged , Animals , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Catalytic Domain , Chlorocebus aethiops , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/metabolism , Coronavirus Nucleocapsid Proteins/chemistry , Coronavirus Nucleocapsid Proteins/metabolism , Cysteine Proteinase Inhibitors/metabolism , Cysteine Proteinase Inhibitors/therapeutic use , Female , Humans , Male , Middle Aged , Molecular Docking Simulation , Oseltamivir/chemistry , Oseltamivir/metabolism , Phosphoproteins/chemistry , Phosphoproteins/metabolism , Protein Binding , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/metabolism , Retrospective Studies , Vero Cells
12.
Acad. J. Second Mil. Med. Univ. ; 6(41): 616-620, 2020.
Article in Chinese | WHO COVID, ELSEVIER | ID: covidwho-727546

ABSTRACT

Objective To summarize the clinical features and imaging findings of six coronavirus disease 2019 (COVID-19) patients, so as to provide evidences for early diagnosis and clinical intervention. Methods Six COVID-19 patients with positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were enrolled from the Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine from Jan. 1 to Feb. 22, 2020. The epidemiological history, clinical manifestations, imaging data and laboratory indicators were retrospectively analyzed. Results All six patients had a clear travel or residence history in Wuhan. Four patients had fever, three had cough, two had upper respiratory tract symptoms such as runny nose and sore throat, and two had systemic symptoms such as headache and muscle ache. Chest computed tomography (CT) showed that all the six patients had abnormal manifestations in bilateral lungs, and the lower lung lesions were more common than the upper lung lesions. The main manifestations were multiple ground-glass opacities, consolidation shadows, crazy paving sign and different degrees of fibrosis in lateral field of bilateral lungs. Chest CT examination later after onset showed lung consolidation and severe fibrosis. Conclusion The imaging of COVID-19 has special characteristics. Combined with the epidemiological history, clinical manifestations and the detection of SARS-CoV-2 nucleic acid, COVID-19 can be effectively diagnosed in the early stage.

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