Publications by authors named "Li-Jun Ma"

148 Publications

Obesity rather than Metabolic Syndrome is a Risk Factor for Subclinical Hypothyroidism and Thyroid Autoimmunity.

Biomed Environ Sci 2021 Oct;34(10):819-823

Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, Heilongjiang, China.

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http://dx.doi.org/10.3967/bes2021.111DOI Listing
October 2021

Rational Design of the Lotus-Like N-Co VO -Co Heterostructures with Well-Defined Interfaces in Suppressing the Shuttle Effect and Dendrite Growth in Lithium-Sulfur Batteries.

Small 2021 Oct 27:e2104109. Epub 2021 Oct 27.

New Energy Research Institute, School of Environment and Energy, South China University of Technology, Higher Education Mega Center, 382 East Waihuan Road, Guangzhou, 510006, China.

The shuttle effect caused by soluble lithium polysulfides (LiPSs) and intrinsic slow electrochemical transformation from LiPSs to Li S/Li S will induce undesirable cycling performance, which is the primary obstruct limiting the practical applications of lithium-sulfur (Li-S) batteries. Here a convenient method is designed to fabricate the 2D louts-like N-Co VO -Co heterostructures with well-abundant interfaces and oxygen vacancies (V ), endowing the materials with both "sulfiphilic" and "lithiophilic" features. When employed as the modification layer coated on commercial Celgard 2400 separator, the as-prepared N-Co VO -Co/PP with synergistic adsorption-electrocatalysis effects achieves desirable sulfur electrochemistry, thus showing a high initial discharge capacity of 1466.4 mAh g at 0.1 C and stable cycle life with a fade rate of 0.03% per cycle over 1000 cycle at 3.0 C. Moreover, a superior areal capacity of 12.84 mAh cm is preserved under high sulfur loading of 14.3 mg cm .
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http://dx.doi.org/10.1002/smll.202104109DOI Listing
October 2021

High-Throughput Screening Assays to Identify Plant Natural Products with Antifungal Properties Against Fusarium oxysporum.

Methods Mol Biol 2022 ;2391:171-184

Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA.

Fusarium oxysporum is a cross-kingdom fungal pathogen that not only causes devastating plant vascular diseases but can also opportunistically infect humans. Here we describe two high-throughput screening assays, a resazurin cell viability assay and an optical density assay, to screen natural products from cultured plant cells with antifungal properties against a clinical isolate of F. oxysporum. After elicitation by applying methyl jasmonate or by co-culture with F. oxysporum, as an abiotic elicitor and a biotic elicitor, respectively, we identified three cell lines that produce materials that inhibit fungal growth. Our procedure validates the powerful potential of combining high-throughput methods for the discovery of novel anti-pathogenic leads.
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http://dx.doi.org/10.1007/978-1-0716-1795-3_14DOI Listing
January 2022

Understanding of supramolecular emulsion interfacial polymerization in silico.

J Chem Phys 2021 May;154(18):184903

State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China.

The composition and structure of a membrane determine its functionality and practical application. We study the supramolecular polymeric membrane prepared by supramolecular emulsion interfacial polymerization (SEIP) on the oil-in-water droplet via the computer simulation method. The factors that may influence its structure and properties are investigated, such as the degree of polymerization and molecular weight distribution (MWD) of products in the polymeric membranes. We find that the SEIP can lead to a higher total degree of polymerization as compared to the supramolecular interfacial polymerization (SIP). However, the average chain length of products in the SEIP is lower than that of the SIP due to its obvious interface curvature. The stoichiometric ratio of reactants in two phases will affect the MWD of the products, which further affects the performance of the membranes in practical applications, such as drug release rate and permeability. Besides, the MWD of the product by SEIP obviously deviates from the Flory distribution as a consequence of the curvature of reaction interface. In addition, we obtain the MWD for the emulsions whose size distribution conforms to the Gaussian distribution so that the MWD may be predicted according to the corresponding emulsion size distribution. This study helps us to better understand the controlling factors that may affect the structure and properties of supramolecular polymeric membranes by SEIP.
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http://dx.doi.org/10.1063/5.0047824DOI Listing
May 2021

Metatranscriptomic Comparison of Endophytic and Pathogenic -Arabidopsis Interactions Reveals Plant Transcriptional Plasticity.

Mol Plant Microbe Interact 2021 Sep 11;34(9):1071-1083. Epub 2021 Oct 11.

Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A.

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of independently challenged with a endophyte Fo47 versus a pathogen Fo5176. These two strains share a core genome of about 46 Mb, in addition to 1,229 and 5,415 unique accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (about 80%) in responding to both fungal inoculums at all timepoints from 12 to 96 h postinoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses functions related to plant growth and development, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest timepoint sampled, and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the and interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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http://dx.doi.org/10.1094/MPMI-03-21-0063-RDOI Listing
September 2021

TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.

Genes (Basel) 2021 02 4;12(2). Epub 2021 Feb 4.

Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA.

Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs has resulted in a growing number of bioinformatics software to identify insertion events. However, the application of existing tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we reported a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software and input file dependencies. The external software requirements are BEDTools, SAMtools, and Picard. Necessary input files include the reference genome sequence in FASTA format, an alignment file from paired-end reads, existing TEs in GTF format, and a text file of TE names. We tested TEfinder among several evolving populations of generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis.
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http://dx.doi.org/10.3390/genes12020224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7914406PMC
February 2021

Erratum.

New Phytol 2020 Dec 9;228(6):2004. Epub 2020 Jul 9.

Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong Province, China.

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http://dx.doi.org/10.1111/nph.16718DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097616PMC
December 2020

Molecular Profiling Reveals a Common Metabolic Signature of Tissue Fibrosis.

Cell Rep Med 2020 Jul 21;1(4):100056. Epub 2020 Jul 21.

Department of Chemistry, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.

Fibrosis, or the accumulation of extracellular matrix, is a common feature of many chronic diseases. To interrogate core molecular pathways underlying fibrosis, we cross-examine human primary cells from various tissues treated with TGF-β, as well as kidney and liver fibrosis models. Transcriptome analyses reveal that genes involved in fatty acid oxidation are significantly perturbed. Furthermore, mitochondrial dysfunction and acylcarnitine accumulation are found in fibrotic tissues. Substantial downregulation of the PGC1α gene is evident in both and fibrosis models, suggesting a common node of metabolic signature for tissue fibrosis. In order to identify suppressors of fibrosis, we carry out a compound library phenotypic screen and identify AMPK and PPAR as highly enriched targets. We further show that pharmacological treatment of MK-8722 (AMPK activator) and MK-4074 (ACC inhibitor) reduce fibrosis . Altogether, our work demonstrate that metabolic defect is integral to TGF-β signaling and fibrosis.
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http://dx.doi.org/10.1016/j.xcrm.2020.100056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7659620PMC
July 2020

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic that Includes the Species Complex.

Phytopathology 2021 07 9;111(7):1064-1079. Epub 2021 Sep 9.

Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain.

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the community voiced near unanimous support for a concept of that represented a clade comprising all agriculturally and clinically important species, including the species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus into seven genera, including the FSSC described as members of the genus , with subsequent justification in 2018 based on claims that the 2013 concept of is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of including the FSSC. We reassert the practical and scientific argument in support of a genus that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus were recombined in genus , and nine others were renamed Here the global community voices strong support for the inclusion of the FSSC in , as it remains the best scientific, nomenclatural, and practical taxonomic option available.
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http://dx.doi.org/10.1094/PHYTO-08-20-0330-LEDOI Listing
July 2021

Accessory Chromosomes in .

Phytopathology 2020 Sep 6;110(9):1488-1496. Epub 2020 Aug 6.

University of Massachusetts, Biochemistry and Molecular Biology, Amherst, MA 01003.

Most genomes within the species complex of are organized into two compartments: the core chromosomes (CCs) and accessory chromosomes (ACs). As opposed to CCs, which are conserved and vertically transmitted to carry out essential housekeeping functions, lineage- or strain-specific ACs are believed to be initially horizontally acquired through unclear mechanisms. These two genomic compartments are different in terms of gene density, the distribution of transposable elements, and epigenetic markers. Although common in eukaryotes, the functional importance of ACs is uniquely emphasized among fungal species, specifically in relationship to fungal pathogenicity and their adaptation to diverse hosts. With a focus on the cross-kingdom fungal pathogen , this review provides a summary of the differences between CCs and ACs based on current knowledge of gene functions, genome structures, and epigenetic signatures, and explores the transcriptional crosstalk between the core and accessory genomes.
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http://dx.doi.org/10.1094/PHYTO-03-20-0069-IADOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8086798PMC
September 2020

Circular RNAs in gastric cancer: Biomarkers for early diagnosis.

Oncol Lett 2020 Jul 14;20(1):465-473. Epub 2020 May 14.

Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, P.R. China.

Circular RNAs (circRNAs) are highly conserved and stable closed-loop non-coding RNAs. They are involved in numerous biological functions, including regulating gene transcription or protein translation by interacting with proteins and regulating expression of microRNAs. The aberrant expression of circRNAs has been reported in many cancers, including gastric cancer. By regulating gene expression, circRNAs are able to affect the proliferation, invasion and metastasis of gastric cancer. The current review focused on the characteristics and biological functions of circRNAs, the carcinogenic potential and the possible implications of circRNAs on the diagnosis and treatment of gastric cancer. In conclusion, circRNAs may serve as potential biomarkers for diagnosis, as well as therapeutic targets.
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http://dx.doi.org/10.3892/ol.2020.11623DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285985PMC
July 2020

Hsa_circ_0003998 promotes epithelial to mesenchymal transition of hepatocellular carcinoma by sponging miR-143-3p and PCBP1.

J Exp Clin Cancer Res 2020 Jun 17;39(1):114. Epub 2020 Jun 17.

Department of Laboratory Diagnosis and Reproductive Medical Center, Changhai Hospital, Naval military Medical University, 168, Changhai Road, Shanghai, 200433, China.

Background: Circular RNAs (circRNAs) play a critical regulatory role in cancer progression. However, the underlying mechanisms of circRNAs in hepatocellular carcinoma (HCC) metastasis remain mostly unknown.

Methods: Has_circ_0003998 (circ0003998) was identified by RNAs sequencing in HCC patients with /without portal vein tumor thrombus (PVTT) metastasis. The expression level of circ0003998 was further detected by in situ hybridization on tissues microarray (ISH-TMA) and qRT-PCR in 25 HCC patients with PVTT metastasis. Moreover, the 25 HCC patients with PVTT metastasis and 50 HCC patients without PVTT metastasis were recruited together to analyze the correlation between circ0003998 expression and HCC clinical characteristics. Transwell, migration and CCK8 assays, as well as nude mice model of lung or liver metastasis were used to evaluate the role of circ0003998 in epithelial to mesenchymal transition (EMT) in HCC. The regulatory mechanisms of circ0003998 in miR-143-3p and PCBP1 were determined by dual-luciferase reporter assay, nuclear-cytoplasmic fractionation, fluorescent in situ hybridization, RNA pull- down, microRNA sequence, western blot and RNA immunoprecipitation.

Results: Compared with adjacent normal liver tissues (ANL), circ0003998 expression was significantly upregulated in PVTT tissues and HCC tissues, and its expression correlates with the aggressive characteristics of HCC patients. Further assays suggested that circ0003998 promoted EMT of HCC both in vitro and in vivo. Mechanistically, our data indicated that circ0003998 may act as a ceRNA (competing endogenous RNA) of microRNA-143-3p to relieve the repressive effect on EMT-related stimulator, FOSL2; meanwhile, circ0003998 could bind with PCBP1-poly(rC) binding protein 1 (PCBP1) to increase the expression level of EMT-related genes, CD44v6.

Conclusion: Circ0003998 promotes EMT of HCC by circ0003998/miR-143-3p/FOSL2 axis and circ0003998 /PCBP1/CD44v6 axis.
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http://dx.doi.org/10.1186/s13046-020-01576-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7302140PMC
June 2020

Chromosome-Scale Genome Assembly of Strain Fo47, a Fungal Endophyte and Biocontrol Agent.

Mol Plant Microbe Interact 2020 Sep 28;33(9):1108-1111. Epub 2020 Jul 28.

MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.

Here, we report a chromosome-level genome assembly of Fo47 (12 pseudomolecules; contig N: 4.52 Mb), generated using a combination of PacBio long-read, Illumina paired end, and high-throughput chromosome conformation capture sequencing data. Although causes vascular wilt to over 100 plant species, the strain Fo47 is classified as an endophyte and is widely used as a biocontrol agent for plant disease control. The Fo47 genome carries a single accessory chromosome of 4.23 Mb, compared with the reference genome of f. sp. Fol4287. The high-quality assembly and annotation of the Fo47 genome will be a valuable resource for studying the mechanisms underlying the endophytic interactions between and plants as well as for deciphering the genome evolution of the species complex.
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http://dx.doi.org/10.1094/MPMI-05-20-0116-ADOI Listing
September 2020

Application of the respiratory "critical care-sub-critical care-rehabilitation integrated management model" in severe stroke associated pneumonia.

BMC Pulm Med 2020 Mar 5;20(1):61. Epub 2020 Mar 5.

Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, No. 7 of Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China.

Background: This study aimed to explore the feasibility of applying the respiratory "critical care-sub-critical care-rehabilitation integrated management model" in severe stroke-associated pneumonia and evaluate its effect.

Methods: From January to September 2018, 24 patients with severe stroke-associated pneumonia, who were admitted to the Respiratory Intensive Care Unit of the Respiratory and Critical Care Medicine Department of Henan Provincial People's Hospital, were randomly divided into two groups: integrated management group and control group. According to the admission criteria of the respiratory "critical care-sub-critical care-rehabilitation integrated model" prescribed by the above-mentioned hospital, patients were grouped. The professional respiratory therapy team participated in the whole treatment. The acute physiology and chronic health evaluation II (APACHE II) score, clinical pulmonary infection score (CPIS) and oxygenation index of these two groups were dynamically observed, and the average hospital stay, 28-day mortality and patient satisfaction were investigated.

Results: Patients in the integrated management group and control group were similar before treatment (P > 0.05). After treatment, the main indicators, the APACHE II score, CPIS score and oxygenation index, were significantly different between the integration group and control group (P < 0.05). The secondary indicators, the average hospitalization days and patient/family member satisfaction scores, were also significantly different between the integration group and control group (P < 0.05). However, the 28-day mortality wasn't significantly different (P > 0.05).

Conclusions: For patients with severe stroke-associated pneumonia, it was feasible to implement the respiratory "critical care-sub-critical care-rehabilitation integrated management model", which could significantly improve the treatment effect, shorten average hospitalization days and improve patient/family satisfaction.
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http://dx.doi.org/10.1186/s12890-020-1100-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059713PMC
March 2020

The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes.

Commun Biol 2020 01 31;3(1):50. Epub 2020 Jan 31.

Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA.

Fusarium oxysporum is a cross-kingdom fungal pathogen that infects plants and humans. Horizontally transferred lineage-specific (LS) chromosomes were reported to determine host-specific pathogenicity among phytopathogenic F. oxysporum. However, the existence and functional importance of LS chromosomes among human pathogenic isolates are unknown. Here we report four unique LS chromosomes in a human pathogenic strain NRRL 32931, isolated from a leukemia patient. These LS chromosomes were devoid of housekeeping genes, but were significantly enriched in genes encoding metal ion transporters and cation transporters. Homologs of NRRL 32931 LS genes, including a homolog of ceruloplasmin and the genes that contribute to the expansion of the alkaline pH-responsive transcription factor PacC/Rim1p, were also present in the genome of NRRL 47514, a strain associated with Fusarium keratitis outbreak. This study provides the first evidence, to our knowledge, for genomic compartmentalization in two human pathogenic fungal genomes and suggests an important role of LS chromosomes in niche adaptation.
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http://dx.doi.org/10.1038/s42003-020-0770-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6994591PMC
January 2020

Genome Sequence of f. sp. , a Brassicaceae Pathogen.

Mol Plant Microbe Interact 2020 Apr 3;33(4):569-572. Epub 2020 Mar 3.

Plant Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A.

The filamentous fungus is a soilborne pathogen of many cultivated species and an opportunistic pathogen of humans. f. sp. is one of three formae speciales that are pathogenic to crucifers, including , a premier model for plant molecular biology and genetics. Here, we report a genome assembly of f. sp. strain PHW726, generated using a combination of PacBio and Illumina sequencing technologies. The genome assembly presented here should facilitate in-depth investigation of - interactions and shed light on the genetics of fungal pathogenesis and plant immunity.
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http://dx.doi.org/10.1094/MPMI-11-19-0324-ADOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233306PMC
April 2020

A sensitive pH fluorescent probe based on triethylenetetramine bearing double dansyl groups in aqueous solutions and its application in cells.

Spectrochim Acta A Mol Biomol Spectrosc 2020 Mar 2;229:117881. Epub 2019 Dec 2.

School of Chemistry, South China Normal University, Guangzhou 510006, PR China; School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou 510006, PR China; Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510631, PR China. Electronic address:

pH fluorescent probes possess many advantages, including intracellular detection, rapid response time and nondestructive testing. In this paper, a highly selective and sensitive fluorescent pH probe based on triethylenetetramine bearing double dansyl groups (1) was synthesized. This probe offers fluorescent measurement of pH value in the range of 5.81-7.21 in aqueous solution, with an 8.64-fold enhancement of fluorescent emission intensity over the unmodified probe. Probe 1 shows a fluorescent color change from a pale yellow to bright green when the pH is increased from 5.81 to 7.21. In addition, probe 1 shows good potential as a fluorescent visualizing sensor for pH values in living GS cells of epinepheluscoioides. The mechanism of the fluorescent response of probe 1 to solution pHs was further clarified by NMR, fluorescent spectra, and UV-vis absorption spectra. The results indicate that the fluorescent emission will shift with an increase in solution pHs, due to increasing deprotonation of the nitrogen atom on the sulfonamides. Deprotonation of the sulfonamide group will inhibits the intramolecular charge transfer process between the imino group and the naphthalene ring, resulting in the recognition phenomenon of blue shift and enhancement of fluorescent emission intensity.
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http://dx.doi.org/10.1016/j.saa.2019.117881DOI Listing
March 2020

Clinical Outcomes Of Using Nebulized Budesonide As The Initial Treatment For Acute Exacerbations Of Chronic Obstructive Pulmonary Disease: A Post-Hoc Analysis.

Int J Chron Obstruct Pulmon Dis 2019 29;14:2725-2731. Epub 2019 Nov 29.

Department of Respiratory Medicine, Peking University Third Hospital, Beijing, People's Republic of China.

Purpose: The current guidelines recommend the use of systemic corticosteroids (SCS) as the optimal treatment for acute exacerbations of chronic obstructive pulmonary disease (AECOPD). The aim of this real-world study was to evaluate whether nebulized budesonide (NBS) could also be used as an initial treatment for AECOPD.

Patients And Methods: AECOPD patients initially treated with NBS or SCS (oral/intravenous) were enrolled. A large-scale, long-term multicenter cohort study of AECOPD patients was performed to analyze outcomes for each treatment (NCT02051166).

Results: Initial NBS and SCS treatment resulted in similar outcomes in terms of improvements in FEV, PaO, SaO, and PaCO. Disease severity affected outcome similarly in both groups. When the groups were stratified according to whether the initial treatment was subsequently intensified or reduced, more intubation was seen in the groups in which initial treatment was intensified. NBS escalation and SCS reduction groups spent more days in the hospital. The NBS escalation group was associated with the highest medical expenditure and a relatively higher rate of new-onset pneumonia. The NBS maintenance/reduction group showed the lowest mortality rate between groups. Stratification according to initial PaCO level showed more intubation in the groups with high initial PaCO concentrations.

Conclusion: These results indicate that NBS may be used as an initial treatment in certain AECOPD patients, and further studies are needed to better define those most likely to benefit.
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http://dx.doi.org/10.2147/COPD.S196615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889964PMC
April 2020

N, S-codoped CNTs supported CoS nanoparticles prepared by using CdS nanorods as sulfur sources and hard templates: An efficient catalyst for reversible oxygen electrocatalysis.

J Colloid Interface Sci 2020 Feb 18;560:186-197. Epub 2019 Oct 18.

Guangzhou Key Laboratory for Surface Chemistry of Energy Materials, New Energy Research Institute, School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming 525000, China; State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou 510641, China. Electronic address:

Non-precious efficient bifunctional catalysts towards oxygen reduction/evolution reactions (ORR/OER) are highly desired to enable the widespread application of rechargeable Zn-air batteries (r-ZABs). Herein, Prussian blue analogues (PBA) anchored on CdS nanorods (CdS NRs) pre-coated with polydopamine (PDA) are utilized as precursors to prepare ultrafine CoS nanoparticles supported on N, S-codoped CNTs ([email protected],S-CNT), where CdS NRs are served as sulfur sources and hard templates. After pyrolysis, the resulting [email protected],S-CNT-800 shows a high specific surface area of 142.4 m g, together with merely 0.780 V difference between the OER potential at 10 mA cm and the ORR potential at 3 mA cm. The [email protected],S-CNT-800 based air cathode displays a higher discharge capacity of 787 mAh g at 10 mA cm, a higher output power density of 154 mW cm, better working stability, as well as a lower charge-discharge voltage gap than the Pt/C + RuO based air electrode at various working current density. The remarkable oxygen reversible catalytic activities are mainly attributed to the presence of a thin layer of mesoporous carbon on partial sections of the open-end N,S-CNTs, which not only shortens the mass diffusion length but also prevents N,S-CNTs from excessively bundling to maximize the exposure of CoS nanocrystallites and graphitized carbon skeletons with N or S heteroatoms.
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http://dx.doi.org/10.1016/j.jcis.2019.10.069DOI Listing
February 2020

Shuffling effector genes through mini-chromosomes.

PLoS Genet 2019 Sep 12;15(9):e1008345. Epub 2019 Sep 12.

Department of Pathology, Purdue University, West Lafayette, Indiana, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742211PMC
September 2019

Fusaric acid instigates the invasion of banana by Fusarium oxysporum f. sp. cubense TR4.

New Phytol 2020 01 24;225(2):913-929. Epub 2019 Oct 24.

Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.

Fusaric acid (FSA) is a phytotoxin produced by several Fusarium species and has been associated with plant disease development, although its role is still not well understood. Mutation of key genes in the FSA biosynthetic gene (FUB) cluster in Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) reduced the FSA production, and resulted in decreased disease symptoms and reduced fungal biomass in the host banana plants. When pretreated with FSA, both banana leaves and pseudostems exhibited increased sensitivity to Foc TR4 invasion. Banana embryogenic cell suspensions (ECSs) treated with FSA exhibited a lower rate of O uptake, loss of mitochondrial membrane potential, increased reactive oxygen species (ROS) accumulation, and greater nuclear condensation and cell death. Consistently, transcriptomic analysis of FSA-treated ECSs showed that FSA may induce plant cell death through regulating the expression of genes involved in mitochondrial functions. The results herein demonstrated that the FSA from Foc TR4 functions as a positive virulence factor and acts at the early stage of the disease development before the appearance of the fungal hyphae in the infected tissues.
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http://dx.doi.org/10.1111/nph.16193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6973005PMC
January 2020

Hsa_circ_0003998 may be used as a new biomarker for the diagnosis and prognosis of hepatocellular carcinoma.

Onco Targets Ther 2019 19;12:5849-5860. Epub 2019 Jul 19.

Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.

Background: Circular RNAs (circRNAs) play important roles in the progression of cancers, but the precise role of circRNAs in the diagnosis and prognosis of hepatocellular carcinoma (HCC) remains to be clarified. The aim of the current study was to explore the diagnostic and prognostic values of hsa_circ_0003998 in HCC.

Methods: CircRNAs expression was measured using RNA-seq analysis from HCC tissues (n=6) (three cases with or without portal vein invasion). Hsa_circ_0003998 in 200 pairs of HCC and adjacent noncancerous tissues and HCC cell lines was examined using qRT-PCR and the clinicopathologic significance was determined. We also detected the plasma levels of hsa_circ_0003998 in HCC, hepatitis B patients and healthy controls. The clinical diagnosis and prognostic values were further determined using receiver operating characteristic (ROC) curve, Kaplan-Meier curve and Cox regression.

Results: Hsa_circ_0003998 was upregulated in HCC tissues (<0.001) and HCC cell lines (HepG2, HuH7, MHCC97H) (<0.001). In addition, upregulation of hsa_circ_0003998 level was associated with higher serum alpha-fetoprotien (AFP) level (=0.003), larger tumor diameter (=0.009), lower differentiation level (=0.023) and microvascular invasion (=0.028). The plasma level of hsa_circ_0003998 in HCC patients was significantly higher than those in hepatitis B patients (<0.001) and healthy controls (<0.001). Its level was significantly reduced after the operation (<0.001). The area under the ROC curve (AUC) for distinguishing HCC from adjacent noncancerous tissues was 0.894 (95% CI=0.86-0.922, <0.001), the sensitivity and specificity were 0.84 and 0.8, respectively. Comparing with hepatitis B patients and healthy controls, hsa_circ_0003998, respectively, had an AUC value of 0.833 (95% CI=0.763-0.889, <0.001) and 0.892 (95% CI=0.831-0.937, <0.001). Their sensitivity and specificity were 0.83, 0.7 and 0.8, 0.84, respectively. Moreover, the combination of hsa_circ_0003998 and AFP showed the highest AUC value of 0.947, the sensitivity and specificity were 0.88 and 0.92, respectively. The hsa_circ_0003998 (=0.003) and AFP (=0.008) levels were independent prognostic factors for HCC. The overall survival of HCC patients with high level of hsa_circ_0003998 was significantly poorer than those with low level (0.005).

Conclusion: Our findings suggest that hsa_circ_0003998 may be used as a novel potential biomarker for the diagnosis and prognosis of HCC patients.
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http://dx.doi.org/10.2147/OTT.S210363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650091PMC
July 2019

The response to the DNA damaging agent methyl methanesulfonate in a fungal plant pathogen.

Fungal Biol 2019 05 6;123(5):408-422. Epub 2019 Apr 6.

Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel. Electronic address:

DNA damage can cause mutations that in fungal plant pathogens lead to hypervirulence and resistance to pesticides. Almost nothing is known about the response of these fungi to DNA damage. We performed transcriptomic and phosphoproteomic analyses of Fusarium oxysporum exposed to methyl methanesulfonate (MMS). At the RNA level we observe massive induction of DNA repair pathways including the global genome nucleotide excision. Cul3, Cul4, several Ubiquitin-like ligases and components of the proteasome are significantly induced. In agreement, we observed drug synergism between a proteasome inhibitor and MMS. While our data suggest that Yap1 and Xbp1 networks are similarly activated in response to damage in yeast and F. oxysporum we were able to observe modules that were MMS-responsive in F. oxysporum and not in yeast. These include transcription/splicing modules that are upregulated and respiration that is down-regulated. In agreement, MMS treated cells are much more sensitive to a respiration inhibitor. At the phosphoproteomic level, Adenylate cyclase, which generates cAMP, is phosphorylated in response to MMS and forms a network of phosphorylated proteins that include cell cycle regulators and several MAPKs. Our analysis provides a starting point in understanding how genomic changes in response to DNA damage occur in Fusarium species.
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http://dx.doi.org/10.1016/j.funbio.2019.03.007DOI Listing
May 2019

Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism.

Fungal Genet Biol 2019 07 3;128:60-73. Epub 2019 Apr 3.

USDA, ARS, US National Poultry Research Center, Toxicology & Mycotoxin Research Unit, Athens, GA, USA. Electronic address:

Horizontal gene transfer (HGT) is believed to shape genomes by facilitating the rapid acquisition of adaptive traits. We hypothesized that the economically important fungus Fusarium verticillioides is an excellent candidate for investigating the potential impact of HGT on the expansion of metabolic activities given its soilborne nature and versatile lifestyle as both a symptomless endophyte as well as a maize pathogen. To test this hypothesis, we used a phylogenomic pipeline followed by manual curation to perform a genome-wide identification of inter-kingdom derived HGT events. We found strong support for 36 genes in F. verticillioides putatively acquired from bacteria. Functional enrichment assessment of these 36 candidates suggested HGT potentially influenced several biochemical activities, including lysine, glycine and nitrogen metabolism. The expression of 25 candidate HGT genes was detected among RNA-Seq datasets from normal and various stress-related growth conditions, thus indicating potential functionality. FVEG_10494, one of the HGT candidates with homologs in only a few Fusarium species, was highly and specifically up-regulated under nitric oxide (NO) challenge. Functional analysis of FVEG_10494 suggests the gene moderately enhanced NO-triggered protective responses and suppressed expression of the F. verticillioides secondary metabolism gene cluster responsible for production of fusarin C. Overall, our global analysis of HGT events in F. verticillioides identified a well-supported set of transferred genes, providing further evidence that HGT offers a mechanism by which fungi can expand their metabolic capabilities, which in turn may enhance their adaptive strategies.
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http://dx.doi.org/10.1016/j.fgb.2019.04.002DOI Listing
July 2019

How Does Sense and Respond to Nicotinaldehyde, an Inhibitor of the NAD Salvage Biosynthesis Pathway?

Front Microbiol 2019 27;10:329. Epub 2019 Feb 27.

Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.

Plant pathogenic fungi are a major threat to food security and impose a severe economic burden, thus there is a continuous need to develop new strategies to manage them. NAD is a co-factor in numerous enzymatic activities and determines the metabolic fate of the cell. Therefore, maintenance of NAD concentration is important for cellular viability. Consequently, the NAD biosynthetic pathway and redox homeostasis was suggested as a target for antifungal development. We aimed to study how senses and responds to nicotinaldehyde (NA), an inhibitor of Pnc1, a key enzyme in the salvage pathway of NAD biosynthesis. We were able to show that NA was inhibitory in high concentrations to several fungal plant pathogens, with much milder effects on tomato growth. Under low nutrient conditions NA reduced the total amounts of NAD in the fungal cell, a trend that was also observed in rich media, although without statistical significance. In low and high nutrient availability NA dramatically reduced the NAD/NADH ratio. After exposure to NA, NADH levels were increased and NAD levels and the biomass were greatly reduced. Cells responded to NA by up-regulation of oxidoreductases, with hardly any up-regulation of the classic response to oxidative stress. Direct measurement of oxidative stress response showed that unlike formaldehyde and hydrogen peroxide, NA caused reductive rather than oxidative stress. Surprisingly, alcohol dehydrogenases were significantly up-regulated more than any other dehydrogenases, including aldehyde dehydrogenases. We propose that conidia of efficiently detoxified the aldehyde group of NA by reducing NAD to NADH; the high concentrations of the latter provoked the expression of alcohol dehydrogenases that in yeast can act to reduce NADH and increase NAD amounts, respectively. Overall, the results suggest that targeting NAD biosynthesis pathway and redox homeostasis can be a potential approach to manage fungal plant pathogens. Many of the natural antifungal compounds produced by bio-control agents or even the natural biome are aldehydes, and thus the results presented here predict the possible response of to wide sources of toxicity in the environment.
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http://dx.doi.org/10.3389/fmicb.2019.00329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400851PMC
February 2019

Improved Assembly of Reference Genome Fusarium oxysporum f. sp. lycopersici Strain Fol4287.

Microbiol Resour Announc 2018 Sep 13;7(10). Epub 2018 Sep 13.

Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA.

Fusarium oxysporum is a pathogenic fungus that infects hundreds of plant species. This paper reports the improved genome assembly of a reference strain, F. oxysporum f. sp. lycopersici Fol4287, a tomato pathogen.
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http://dx.doi.org/10.1128/MRA.00910-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256600PMC
September 2018

Identifying TF Binding Motifs from a Partial Set of Target Genes and its Application to Regulatory Network Inference.

IEEE/ACM Trans Comput Biol Bioinform 2020 Jul-Aug;17(4):1211-1221. Epub 2018 Nov 21.

Motif identification has been one of the most widely studied problems in bioinformatics. Many methods have been developed to discover binding motifs from a large set of genes. But when the given genes are only a partial set of target genes, the statistical significance usually contains a bias towards the input. If we can identify the TF binding motif from a partial set of target genes, we can save the labor costs and resources for doing many experiments. In this paper, we propose a method MISA (Motif Identification through Segments Assembly) to identify binding motifs from a subset of target genes. By ranking and assembling the segments, MISA discovers a set of binding motifs with the best length to fit our proposed objective function. We also predict the additional target genes as an application of regulatory network inference. We compare our approach with two widely used methods MEME and AlignACE by analyzing both the quality of the binding motif and network inference. Using two model organisms S. cerevisiae and E. coli, we show that with 20 percent of the target genes (minimum sample size of 20), we can achieve a motif similarity of 82 percent with the known motifs. Our results also show that 73 percent of target genes on average can be correctly predicted without introducing many false target genes.
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http://dx.doi.org/10.1109/TCBB.2018.2882377DOI Listing
April 2021

Prognostic value of CD44v6 expression in breast cancer: a meta-analysis.

Onco Targets Ther 2018 4;11:5451-5457. Epub 2018 Sep 4.

Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,

Purpose: The prognostic value and clinical significance of CD44 variant isoform v6 (CD44v6) in breast cancer remains controversial. Our study aimed to generalize the correlation between CD44v6 expression and clinicopathological features and prognosis in breast cancer by using a meta-analysis.

Methods: We performed a comprehensive search of relevant literature from PubMed, Cochrane Database, and EMBASE database that were published before January 2018. The pooled ORs and HRs with 95% CIs were used to estimate the effects.

Results: Thirteen articles comprising 1,458 patients were included for analysis. The results revealed that CD44v6 expression was associated with histological grade (overall: OR=1.56, 95% CI [1.06, 2.29], =0.023; Asian: OR=1.78, 95% CI [1.12, 2.85], =0.016) and lymph node metastasis (overall: OR=1.96, 95% CI [1.01, 3.78], =0.046; Asian: OR=2.11, 95% CI [1.00, 4.44], =0.049). CD44v6 expression was significantly associated with poor prognosis in patients with breast cancer (overall survival: overall: HR=1.55, 95% CI [1.09, 2.22], =0.015; Asian: HR=2.22, 95% CI [1.34, 3.68], =0.002).

Conclusion: Our meta-analysis demonstrates that CD44v6 is significantly associated with poor prognosis, histological grade, and lymph node metastasis in breast cancer patients, especially among Asian patients.
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http://dx.doi.org/10.2147/OTT.S156101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129017PMC
September 2018

A Computational Protocol to Analyze Metatranscriptomic Data Capturing Fungal-Host Interactions.

Methods Mol Biol 2018 ;1848:207-233

Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA.

Plant diseases cause significant losses to agricultural production and pose serious threats to food security worldwide. Understanding the mechanism of host-pathogen interaction is essential for the development of novel diagnostic methods and disease management strategies. RNA sequencing (or RNA-Seq) technology enables a global characterization and quantification of all transcripts of organisms from which RNA can be obtained, and it is particularly useful in identifying pathogen virulence factors involved in disease development and host immunity involved in the development of resistance. This chapter describes a computational protocol to manage, analyze and interpret RNA-Seq data. We have included two transcriptome analysis approaches, one reference-guided and the other de novo assembly-based, and discuss pros and cons for each method. We have also presented visualization methods to generate high quality figures as well as data mining strategies for identifying candidate genes/pathways involved in host immunity and pathogen virulence. In summary, this protocol captures the fungal-plant interactions at the transcriptional level and facilitates rapid gene discovery and expression analysis using next-generation sequencing data of mixed host and pathogen transcripts (i.e., metatranscriptomics). All bioinformatic tools used to build this protocol are publically available, and we strove to make them accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-fungal interactions.
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http://dx.doi.org/10.1007/978-1-4939-8724-5_15DOI Listing
May 2019

Kinome Expansion in the Fusarium oxysporum Species Complex Driven by Accessory Chromosomes.

mSphere 2018 06 13;3(3). Epub 2018 Jun 13.

Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA

The species complex (FOSC) is a group of soilborne pathogens causing severe disease in more than 100 plant hosts, while individual strains exhibit strong host specificity. Both chromosome transfer and comparative genomics experiments have demonstrated that lineage-specific (LS) chromosomes contribute to the host-specific pathogenicity. However, little is known about the functional importance of genes encoded in these LS chromosomes. Focusing on signaling transduction, this study compared the kinomes of 12 isolates, including both plant and human pathogens and 1 nonpathogenic biocontrol strain, with 7 additional publicly available ascomycete genomes. Overall, kinomes are the largest, facilitated in part by the acquisitions of the LS chromosomes. The comparative study identified 99 kinases that are present in almost all examined fungal genomes, forming the core signaling network of ascomycete fungi. Compared to the conserved ascomycete kinome, the expansion of the kinome occurs in several kinase families such as histidine kinases that are involved in environmental signal sensing and target of rapamycin (TOR) kinase that mediates cellular responses. Comparative kinome analysis suggests a convergent evolution that shapes individual isolates with an enhanced and unique capacity for environmental perception and associated downstream responses. Isolates of are adapted to survive a wide range of host and nonhost conditions. In addition, was recently recognized as the top emerging opportunistic fungal pathogen infecting immunocompromised humans. The sensory and response networks of these fungi undoubtedly play a fundamental role in establishing the adaptability of this group. We have examined the kinomes of 12 isolates and highlighted kinase families that distinguish from other fungi, as well as different isolates from one another. The amplification of kinases involved in environmental signal relay and regulating downstream cellular responses clearly sets apart from other Although the functions of many of these kinases are still unclear, their specific proliferation highlights them as a result of the evolutionary forces that have shaped this species complex and clearly marks them as targets for exploitation in order to combat disease.
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http://dx.doi.org/10.1128/mSphere.00231-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001611PMC
June 2018
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