Publications by authors named "Di Liu"

857 Publications

Cyto-friendly polymerization at cell surfaces modulates cell fate by clustering cell-surface receptors.

Chem Sci 2020 Mar 25;11(16):4221-4225. Epub 2020 Mar 25.

Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital of Zhejiang University Lishui 323000 China

Lots of strategies, using multivalent synthetic polymers, have been developed to control the spatial distribution of cell-surface receptors, thus modulating the cell function and fate in a custom-tailored manner. However, clustering cell-surface receptors multivalent synthetic polymers is highly dependent on the structure as well as the ligand-density of the polymers, which may impose difficulties on the synthesis of polymers with a high density of ligands. Here, we pioneered the utilization of a cyto-friendly polymerization at the cell surface to cluster cell-surface receptors. As a proof of concept, an anti-CD20 aptamer conjugated macromer was initially synthesized, which was then efficiently and stably introduced onto the Raji cell surface ligand-receptor interaction. With the assistance of an initiator, ammonium peroxysulfate (APS), the macromer bound onto the Raji cell surface polymerized, inducing the clustering of CD20 receptors, and thereby triggering cell apoptosis. This cell-surface polymerization induced cell-surface receptor crosslinking could alternatively be applied in modulating the fates and functions of other cells, especially those mediated by the spatial distribution of cell-surface receptors, such as T cell activation. Our work opens new possibilities in the area of chemical biology to some extent.
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http://dx.doi.org/10.1039/c9sc06385dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8152676PMC
March 2020

METTL14 Acts as a Potential Regulator of Tumor Immune and Progression in Clear Cell Renal Cell Carcinoma.

Front Genet 2021 28;12:609174. Epub 2021 May 28.

Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Clear cell renal cell carcinoma (ccRCC) is characterized by its insensitivity to chemoradiotherapy and lacks effective diagnostic and prognostic biomarkers. In this study, we focused on the role of m6A RNA methylation regulators for tumor immunity. Based on the expression of 20 m6A regulators, consensus clustering was performed to divide patients into cluster1/cluster2 and showed that there was a survival difference between the two clusters. Through cox regression analysis, five hub m6A regulators were screened to construct a risk model. Further analysis showed that the risk score was an independent prognostic factor. GSEA, GSVA, and KEGG analysis revealed that immune cell pathways played a critical role between the high risk group and low risk group. Combined with CIBERSORT and survival analysis, five hub tumor-infiltrating immune cells (TIICs) were identified for further study. Meanwhile, correlation analysis indicated that IGF2BP2 was positively associated with activated memory CD4 T cell and METTL14 was negatively correlated to the regulatory T cell. Therefore, IGF2BP2 and METTL14 were regarded as key genes. Further study verified that only METTL14 possessed good diagnostic and prognostic value. Then, GSEA exhibited that METTL14 was mainly enriched in chemokine related pathways. We also found that CCL5 was negatively correlated to METTL14 and might serve as a potential target of METTL14. In conclusion, these findings suggest that the METTL14/CCL5/Tregs axis is a potential signaling pathway for regulating tumor immunity, and might become novel therapeutic targets for ccRCC.
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http://dx.doi.org/10.3389/fgene.2021.609174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8194313PMC
May 2021

An inactivated recombinant rabies virus displaying the Zika virus prM-E induces protective immunity against both pathogens.

PLoS Negl Trop Dis 2021 Jun 4;15(6):e0009484. Epub 2021 Jun 4.

Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.

The global spread of Zika virus (ZIKV), which caused a pandemic associated with Congenital Zika Syndrome and neuropathology in newborns and adults, prompted the pursuit of a safe and effective vaccine. Here, three kinds of recombinant rabies virus (RABV) encoding the prM-E protein of ZIKV were constructed: ZI-D (prM-E), ZI-E (transmembrane domain (TM) of prM-E replaced with RABV G) and ZI-F (signal peptide and TM domain of prM-E replaced with the region of RABV G). When the TM of prM-E was replaced with the region of RABV G (termed ZI-E), it promoted ZIKV E protein localization on the cell membrane and assembly on recombinant viruses. In addition, the change in the signal peptide with RABV G (termed ZI-F) was not conducive to foreign protein expression. The immunogenicity of recombinant viruses mixed with a complex adjuvant of ISA 201 VG and poly(I:C) was tested in BALB/c mice. After immunization with ZI-E, the anti-ZIKV IgG antibody lasted for at least 10 weeks. The titers of neutralizing antibodies (NAbs) against ZIKV and RABV at week 6 were all greater than the protective titers. Moreover, ZI-E stimulated the proliferation of splenic lymphocytes and promoted the secretion of cytokines. It also promoted the production of central memory T cells (TCMs) among CD4+/CD8+ T cells and stimulated B cell activation and maturation. These results indicate that ZI-E could induce ZIKV-specific humoral and cellular immune responses, which have the potential to be developed into a promising vaccine for protection against both ZIKV and RABV infections.
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http://dx.doi.org/10.1371/journal.pntd.0009484DOI Listing
June 2021

Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids.

Nat Commun 2021 06 2;12(1):3276. Epub 2021 Jun 2.

Hubei Institute for Drug Control, Wuhan, China.

Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.
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http://dx.doi.org/10.1038/s41467-021-23611-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8172641PMC
June 2021

Pollution by Antibiotics and Antimicrobial Resistance in LiveStock and Poultry Manure in China, and Countermeasures.

Antibiotics (Basel) 2021 May 6;10(5). Epub 2021 May 6.

NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, NO-1431 Ås, Norway.

The demand for animal protein has increased considerably worldwide, especially in China, where large numbers of livestock and poultry are produced. Antibiotics have been widely applied to promote growth and prevent diseases. However, the overuse of antibiotics in animal feed has caused serious environmental and health risks, especially the wide spread of antimicrobial resistance (AMR), which seriously affects animal and human health, food safety, ecosystems, and the sustainable future development of animal protein production. Unfortunately, AMR has already become a worldwide challenge, so international cooperation is becoming more important for combatting it. China's efforts and determination to restrict antibiotic usage through law enforcement and effective management are of significance. In this review, we address the pollution problems of antibiotics; in particular, the AMR in water, soil, and plants caused by livestock and poultry manure in China. The negative impact of widespread and intensive use of antibiotics in livestock production is discussed. To reduce and mitigate AMR problems, we emphasize in this review the development of antibiotic substitutes for the era of antibiotic prohibition.
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http://dx.doi.org/10.3390/antibiotics10050539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8148549PMC
May 2021

Image-Based Polygonal Lattices for Mechanical Modeling of Biological Materials: 2D Demonstrations.

ACS Biomater Sci Eng 2021 Jun 1. Epub 2021 Jun 1.

Department of Mechanical and Aerospace Engineering, Syracuse University, Syracuse, New York 13244, United States.

Understanding the structure-property relationship of biological materials, such as bones, teeth, cells, and biofilms, is critical for diagnosing diseases and developing bioinspired materials and structures. The intrinsic multiphase heterogeneity with interfaces places great challenges for mechanical modeling. Here, we develop an image-based polygonal lattice model for simulating the mechanical deformation of biological materials with complicated shapes and interfaces. The proposed lattice model maintains the uniform meshes inside the homogeneous phases and restricts the irregular polygonal meshes near the boundaries or interfaces. This approach significantly simplifies the mesh generation from images of biological structures with complicated geometries. The conventional finite element simulations validate this polygonal lattice model. We further demonstrate that the image-based polygonal lattices generate meshes from images of composite structures with multiple inclusions and capture the nonlinear mechanical deformation. We conclude the paper by highlighting a few future research directions that will benefit from the functionalities of polygonal lattice modeling.
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http://dx.doi.org/10.1021/acsbiomaterials.0c01772DOI Listing
June 2021

One-step self-assembly of magnetic supramolecular metal-organic coordination functionalized MoS complex as nanoenzyme-reactor.

Colloids Surf B Biointerfaces 2021 May 26;205:111879. Epub 2021 May 26.

State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China. Electronic address:

In the present study, a kind of magnetic supramolecular metal-organic coordination complex (SMOCC) functionalized MoS was prepared with one-step in aqueous solution for enzyme immobilization. As possessing a protective nanocoating of PDA/PEI/Cu (polydopamine: PDA, polyethyleneimine: PEI), the proposed material can provide biocompatible microenvironment and flexible adhesion force on particle interface, which is conductive to loading laccase (170.0 ± 1.8 mg/g) with high activity (93.0 ± 1.1 %). Compared with the free laccase, the immobilized laccase has higher stability in a broader range of pH (3-10), temperature (20-80 °C), storage time (1-18 days) and reusability (1-16 cycles). The removal of carcinogenic persistent organic pollutant malachite green in the water with the immobilized laccase shows a higher efficiency (89.4 ± 1.2 %) than free laccase (16.2 ± 0.2 %). The [email protected]@(PDA/PEI/Cu) nanocomposites can also be used successfully to immobilize trypsin, lipase and catalase respectively, showing a satisfactory enzyme loading (157.0 ± 0.1 mg/g, 151.6 ± 1.4 mg/g, 162.6 ± 1.6 mg/g, respectively) and activity (95.0 ± 0.5 %, 90.0 ± 0.8 %, 91.0 ± 0.9 %, respectively). The MoS can be replaced by carbon material and similar results can be obtained.
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http://dx.doi.org/10.1016/j.colsurfb.2021.111879DOI Listing
May 2021

Low-voltage and fast-response SnOnanotubes/perovskite heterostructure photodetector.

Nanotechnology 2021 Jun 21;32(37). Epub 2021 Jun 21.

College of Physics and State Key Laboratory of Bio Fibers and Eco Textiles, Qingdao University, Qingdao 266071, People's Republic of China.

One-dimensional metal-oxides (1D-MO) nanostructure has been regarded as one of the most promising candidates for high-performance photodetectors due to their outstanding electronic properties, low-cost and environmental stability. However, the current bottlenecks are high energy consumption and relatively low sensitivity. Here, Schottky junctions between nanotubes (NTs) and FTO were fabricated by electrospinning SnONTs on FTO glass substrate, and the bias voltage of SnONTs photodetectors was as low as ∼1.76 V, which can effectively reduce energy consumption. Additionally, for improving the response and recovery speed of SnONTs photodetectors, the NTs were covered with organic/inorganic hybrid perovskite. SnONTs/perovskite heterostructure photodetectors exhibit fast response/recovery speed (∼0.075/0.04 s), and a wide optical response range (∼220-800 nm). At the same time, the bias voltage of heterostructure photodetectors was further reduced to 0.42 V. The outstanding performance is mainly attributed to the formation of type-II heterojunctions between SnONTs and perovskite, which can facilitate the separation of photogenerated carriers, as well as Schottky junction between SnONTs and FTO, which reduce the bias voltage. All the results indicate that the rational design of 1D-MO/perovskite heterostructure is a facile and efficient way to achieve high-performance photodetectors.
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http://dx.doi.org/10.1088/1361-6528/ac05e7DOI Listing
June 2021

An anionic potassium-organic framework for selective removal of uranyl ions.

Dalton Trans 2021 May 25. Epub 2021 May 25.

Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing 100083, China.

Effective and selective removal of radioactive metal ions from aqueous solutions is of great importance due to their harmful effects on humans and other living species. However, it is a big challenge for researchers to develop effective adsorbents with high selectivity and a wide pH application range even if some progress has been achieved. Herein, we report an anionic potassium organic framework (UPC-K1) with protonated dimethylamine (Me2NH2+) residing inside the rhomboid channels. The unique 3D firm structure of UPC-K1 is constructed by the cross-linking of the 2D arrangement using weak K-O bonds (2.9270 Å) and strong hydrogen bonds (1.6498 Å), which endows it with excellent chemical stability in organic solvents, boiling water, and aqueous solution in the pH range 3-10. Based on the cation exchange, depending on pore size selectivity, UPC-K1 shows excellent adsorption performance towards UO22+ in aqueous solutions at 298 K with the following characteristics: (1) effective removal in the pH range 3-10; (2) high selectivity over other metal cations; (3) a high adsorption capacity of 551.4 mg g-1; (4) a rapid adsorption equilibrium within 3 hours under stirring; and (5) effective adsorption at low concentrations, with a residual concentration of 0.69 ppm even at an initial concentration of 10.3 ppm after stirring for 24 hours. These results indicate the great potential of UPC-K1 in the treatment of uranium-containing nuclear wastewater.
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http://dx.doi.org/10.1039/d1dt00822fDOI Listing
May 2021

Mixed elastohydrodynamic lubrication model of rotary lip seal with non-Gaussian surfaces: experimentation verification and numerical analysis on effects of sealed pressure.

Sci Prog 2021 Apr-Jun;104(2):368504211017010

School of Automation Science and Electrical Engineering, Beihang University, Beijing, China.

Many published models can be used to analyse the sealing performance of rotary lip seal. The surfaces are normally assumed to be periodic variation. However, the quasi-randomness of surface height distribution should be considered, especially the non-Gaussian distribution. Hence, a mixed elastohydrodynamic lubrication model with non-Gaussian surfaces is proposed and used to analyse the effects of sealed fluid pressure on the seal performance in this paper. Based on digital filter and Johnson's translator system, a rough surface simulation method is introduced to simulate non-Gaussian rough surface. Based on this method the mixed lubrication model with non-Gaussian surfaces is built. The proposed model is verified by comparing the simulation results to experimental observations. Furthermore, it is hardly to find the research focused on the effects of sealed pressure. Hence, the effects of sealed fluid pressure on the seal performance is focused.
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http://dx.doi.org/10.1177/00368504211017010DOI Listing
May 2021

Parathyroid hormone-related protein inhibits nitrogen-containing bisphosphonate-induced apoptosis of human periodontal ligament fibroblasts by activating MKP1 phosphatase.

Bioengineered 2021 Dec;12(1):1997-2006

Department of Bone Metabolism, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan China.

Massive production of reactive oxygen species (ROS) in human periodontal ligament fibroblasts (HPdLFs) by nitrogen-containing bisphosphonates (BPs) is the main factor causing BP-related osteonecrosis of the jaw. Further, oxidative stress and apoptosis of fibroblasts induced by ROS are closely associated with the activation of MAPK. Parathyroid hormone-related protein (PTHrP) can block the activity of MAPK by regulating the levels of MAPK phosphatase 1 (MKP1). Therefore, it is speculated that PTHrP can inhibit the apoptosis of HPdLFs caused by nitrogen-containing BP via regulating the expression levels of MKP1. Herein, alendronate sodium salt trihydrate (nitrogen-containing BP, FOS) and HPdLFs were co-cultured for 24 h, 48 h, and 72 h, and the levels of ROS and apoptosis were determined, respectively. After 48 h co-culture, FOS significantly increased the levels of ROS and apoptosis, and high phosphorylation levels of p38, ERK1/2 and p66 were found in this study. However, the inhibitors of p38 and ERK1/2 significantly reduced the apoptosis of HPdLFs. Interestingly, PTHrP pre-treatment significantly reduced the phosphorylation levels of p38, ERK1/2, and p66. More importantly, MKP1 inhibitor sanguinarine inhibited the dephosphorylation levels of p38, ERK1/2, and p66 caused by PTHrP. Altogether, PTHrP can inhibit nitrogen-containing BP-induced apoptosis of HPdLFs by activating MKP1 phosphatase.
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http://dx.doi.org/10.1080/21655979.2021.1928930DOI Listing
December 2021

Sensing of joint and spinal bending or stretching via a retractable and wearable badge reel.

Nat Commun 2021 05 19;12(1):2950. Epub 2021 May 19.

CAS Center for Excellence in Nanoscience, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, China.

Human motions, such as joint/spinal bending or stretching, often contain information that is useful for orthopedic/neural disease diagnosis, rehabilitation, and prevention. Here, we show a badge-reel-like stretch sensing device with a grating-structured triboelectric nanogenerator exhibiting a stretching sensitivity of 8 V mm, a minimum resolution of 0.6 mm, a low hysteresis, and a high durability (over 120 thousand cycles). Experimental and theoretical investigations are performed to define the key features of the device. Studies from human natural daily activities and exercise demonstrate the functionality of the sensor for real-time recording of knee/arm bending, neck/waist twisting, and so on. We also used the device in a spinal laboratory, monitoring human subjects' spine motions, and validated the measurements using the commercial inclinometer and hunchback instrument. We anticipate that the lightweight, precise and durable stretch sensor applied to spinal monitoring could help mitigate the risk of long-term abnormal postural habits induced diseases.
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http://dx.doi.org/10.1038/s41467-021-23207-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136475PMC
May 2021

Transcriptome Analyses Implicate Endogenous Retroviruses Involved in the Host Antiviral Immune System through the Interferon Pathway.

Virol Sin 2021 May 19. Epub 2021 May 19.

CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.

Human endogenous retroviruses (HERVs) are the remains of ancient retroviruses that invaded our ancestors' germline cell and were integrated into the genome. The expression of HERVs has always been a cause for concern because of its association with various cancers and diseases. However, few previous studies have focused on specific activation of HERVs by viral infections. Our previous study has shown that dengue virus type 2 (DENV-2) infection induces the transcription of a large number of abnormal HERVs loci; therefore, the purpose of this study was to explore the relationship between exogenous viral infection and HERV activation further. In this study, we retrieved and reanalyzed published data on 21 transcriptomes of human cells infected with various viruses. We found that infection with different viruses could induce transcriptional activation of HERV loci. Through the comparative analysis of all viral datasets, we identified 43 key HERV loci that were up-regulated by DENV-2, influenza A virus, influenza B virus, Zika virus, measles virus, and West Nile virus infections. Furthermore, the neighboring genes of these HERVs were simultaneously up-regulated, and almost all such neighboring genes were interferon-stimulated genes (ISGs), which are enriched in the host's antiviral immune response pathways. Our data supported the hypothesis that activation of HERVs, probably via an interferon-mediated mechanism, plays an important role in innate immunity against viral infections.
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http://dx.doi.org/10.1007/s12250-021-00370-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131884PMC
May 2021

Rapid Recovery in COVID-19 Patients with Chronic Hepatitis B Virus Infection Treated with Tenofovir Disoproxil Fumarate.

J Clin Transl Hepatol 2021 Apr 9;9(2):269-273. Epub 2021 Apr 9.

Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.

The coronavirus disease 2019 (COVID-19) pandemic continues worldwide. We report here two cases of chronic hepatitis B patients with acute respiratory syndrome coronavirus 2 infection treated with tenofovir disoproxil fumarate who demonstrated a favorable outcome. This report adds some evidence that concurrent HBV infection may not worsen COVID-19 infection and tenofovir disoproxil fumarate treatment may have partial positive effect on COVID-19 rapid recovery.
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http://dx.doi.org/10.14218/JCTH.2020.00129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111112PMC
April 2021

Ginseng polysaccharides alter the gut microbiota and kynurenine/tryptophan ratio, potentiating the antitumour effect of antiprogrammed cell death 1/programmed cell death ligand 1 (anti-PD-1/PD-L1) immunotherapy.

Gut 2021 May 18. Epub 2021 May 18.

Dr Neher's Biophysics Laboratory for Innovative Drug Discovery/State Key laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China.

Objective: Programmed death 1 and its ligand 1 (PD-1/PD-L1) immunotherapy is promising for late-stage lung cancer treatment, however, the response rate needs to be improved. Gut microbiota plays a crucial role in immunotherapy sensitisation and has been shown to possess immunomodulatory potential. In this study, we aimed to investigate whether the combination treatment of ginseng polysaccharides (GPs) and αPD-1 monoclonal antibody (mAb) could sensitise the response by modulating gut microbiota.

Design: Syngeneic mouse models were administered GPs and αPD-1 mAb, the sensitising antitumour effects of the combination therapy on gut microbiota were assessed by faecal microbiota transplantation (FMT) and 16S PacBio single-molecule real-time (SMRT) sequencing. To assess the immune-related metabolites, metabolomics analysis of the plasma samples was performed.

Results: We found GPs increased the antitumour response to αPD-1 mAb by increasing the microbial metabolites valeric acid and decreasing L-kynurenine, as well as the ratio of Kyn/Trp, which contributed to the suppression of regulatory T cells and induction of T cells after combination treatment. Besides, the microbial analysis indicated that the abundance of and was higher in responders to anti-PD-1 blockade than non-responders in the clinic. Furthermore, the combination therapy sensitised the response to PD-1 inhibitor in the mice receiving microbes by FMT from six non-responders by reshaping the gut microbiota from non-responders towards that of responders.

Conclusion: Our results demonstrate that GPs combined with αPD-1 mAb may be a new strategy to sensitise non-small cell lung cancer patients to anti-PD-1 immunotherapy. The gut microbiota can be used as a novel biomarker to predict the response to anti-PD-1 immunotherapy.
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http://dx.doi.org/10.1136/gutjnl-2020-321031DOI Listing
May 2021

Speckled 100 kDa gene in pigs: Alternative splicing, subcellular localization, and response to interferon-α stimulation.

Gene 2021 Jul 11;791:145710. Epub 2021 May 11.

Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China. Electronic address:

Speckled 100 kDa (Sp100) plays an important role in the antiviral immune response, however, little is known about porcine Sp100. In this study, porcine Sp100 was cloned and its response to interferon (IFN) α was identified. We obtained the cDNA (V1) of the gene, SP100, and seven alternative splicing variants (V2-8). Isoform V1 encoded a 386 amino acid protein and contained a homogeneously-staining region (HSR) domain. Isoforms V3, 4, 6 and 7 were deletion/insertion variants and contained HSR domain as V1. The splicing of porcine SP100 was very complicated and many transcripts existed as revealed by cloning and minigene analyses. Using GFP-fusion constructs isoforms V1, 3, 4, 6 and 7 were localized to nucleus and the nuclear localization signal was identified as PSNRKRR at positions 331-337 of V1. Porcine SP100 was unevenly distributed in all tissues studied and differentially expressed between pigs with different disease-resistance/susceptibilities. Porcine SP100 was strongly increased by IFNα due to the existence of an IFN-stimulated response element in the promoter. A single nucleotide - 70A > C polymorphism enhanced promoter activity. The results provided the basis for determining the role of Sp100 in antiviral responses and may assist in breeding pigs with high disease-resistance.
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http://dx.doi.org/10.1016/j.gene.2021.145710DOI Listing
July 2021

Discovery of genes involved in anthocyanin biosynthesis from the rind and pith of three sugarcane varieties using integrated metabolic profiling and RNA-seq analysis.

BMC Plant Biol 2021 May 12;21(1):214. Epub 2021 May 12.

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, 100193, Beijing, P. R. China.

Background: Sugarcane (Saccharum officinarum) is one of the most valuable feedstocks for sugar production. In addition to the production of industrial raw materials such as alcohol, papermaking, the fiber of livestock feed, respectively, sugarcane can produce bioactive compounds such as anthocyanins. Elucidation of the anthocyanin biosynthesis pathway is critical for the molecular breeding of sugarcane varieties with favorable traits. We aimed to identify candidate genes involved in anthocyanin biosynthesis by transcriptomic and metabolomic analyses.

Results: Three varieties of sugarcane displaying different colors were used in this study: FN15 (greed rind), ROC22 (red rind), and Badila (purple rind). Sample materials were subjected to metabolomic analysis using UPLC-Q-TOF/MS and RNA-seq analysis. The metabolomic profiling results showed Cyanidin, Cyanidin (6'-malonylglucoside), Cyanidin O-glucoside, and Peonidin O-glucoside were the main components responsible for the rind color. Then, through RNA-seq analysis, we identified a total of 3137, 3302, 3014 differentially expressed genes (DEGs) between the rind and pith tissues for the corresponding varieties Badila rind, ROC22, and FN15. We then compared the expression levels of genes among the rind tissues from the three varieties. We identified 2901, 2821, and 3071 DEGs between Badila rind vs. ROC22 rind, Badila rind vs. FN15 rind, ROC22 rind vs. FN15 rind, respectively. We identified two enriched pathways, including phenylpropanoid biosynthesis and flavonoid biosynthesis. Sequencing similarity search identified a total of 50 unigenes belonging to 15 enzyme families as putative genes involved in anthocyanin biosynthesis in sugarcane rind. Seven of them were identified as candidate genes related to anthocyanin biosynthesis in the rind of sugarcane through co-localization analysis with the anthocyanin content in sugarcane. In total, 25 unigenes were selected and subjected to RT-qPCR analysis, and qRT-PCR results were consistent with those obtained with the RNA-Seq experiments.

Conclusions: We proposed a pathway for anthocyanin biosynthesis in sugarcane rind. This is the first report on the biosynthesis of anthocyanin in sugarcane using the combined transcriptomic and metabolomic methods. The results obtained from this study will lay the foundation for breeding purple pith sugarcane varieties with high anthocyanin contents.
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http://dx.doi.org/10.1186/s12870-021-02986-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8117289PMC
May 2021

Nonblinking carbon dots for imaging and tracking receptors on a live cell membrane.

Chem Commun (Camb) 2021 Jun 10;57(45):5554-5557. Epub 2021 May 10.

State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China.

Blinking occurs with nearly all fluorophores including organic dyes, fluorescent proteins, semiconductor quantum dots and carbon dots (CDs). We developed non-blinking and photoresistant fluorescent CDs by introducing multiple aromatic domains onto a single carbon dot and demonstrated their great potential for imaging and tracking of receptors on a live cell membrane.
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http://dx.doi.org/10.1039/d1cc01120kDOI Listing
June 2021

Morphing pasta and beyond.

Sci Adv 2021 May 5;7(19). Epub 2021 May 5.

Human-Computer Interaction Institute, Carnegie Mellon University, Pittsburgh, PA, USA.

Morphing structures are often engineered with stresses introduced into a flat sheet by leveraging structural anisotropy or compositional heterogeneity. Here, we identify a simple and universal diffusion-based mechanism to enable a transient morphing effect in structures with parametric surface grooves, which can be realized with a single material and fabricated using low-cost manufacturing methods (e.g., stamping, molding, and casting). We demonstrate from quantitative experiments and multiphysics simulations that parametric surface grooving can induce temporary asynchronous swelling or deswelling and can transform flat objects into designed, three-dimensional shapes. By tuning the grooving pattern, we can achieve both zero (e.g., helices) and nonzero (e.g., saddles) Gaussian curvature geometries. This mechanism allows us to demonstrate approaches that could improve the efficiency of certain food manufacturing processes and facilitate the sustainable packaging of food, for instance, by creating morphing pasta that can be flat-packed to reduce the air space in the packaging.
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http://dx.doi.org/10.1126/sciadv.abf4098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099191PMC
May 2021

Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification.

BMC Biol 2021 May 5;19(1):93. Epub 2021 May 5.

National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China.

Background: Brassica oleracea includes several morphologically diverse, economically important vegetable crops, such as the cauliflower and cabbage. However, genetic variants, especially large structural variants (SVs), that underlie the extreme morphological diversity of B. oleracea remain largely unexplored.

Results: Here we present high-quality chromosome-scale genome assemblies for two B. oleracea morphotypes, cauliflower and cabbage. Direct comparison of these two assemblies identifies ~ 120 K high-confidence SVs. Population analysis of 271 B. oleracea accessions using these SVs clearly separates different morphotypes, suggesting the association of SVs with B. oleracea intraspecific divergence. Genes affected by SVs selected between cauliflower and cabbage are enriched with functions related to response to stress and stimulus and meristem and flower development. Furthermore, genes affected by selected SVs and involved in the switch from vegetative to generative growth that defines curd initiation, inflorescence meristem proliferation for curd formation, maintenance and enlargement, are identified, providing insights into the regulatory network of curd development.

Conclusions: This study reveals the important roles of SVs in diversification of different morphotypes of B. oleracea, and the newly assembled genomes and the SVs provide rich resources for future research and breeding.
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http://dx.doi.org/10.1186/s12915-021-01031-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097969PMC
May 2021

Porphyran-derived oligosaccharides alleviate NAFLD and related cecal microbiota dysbiosis in mice.

FASEB J 2021 Jun;35(6):e21458

Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.

Porphyran and its derivatives possess a variety of biological activities, such as ameliorations of oxidative stress, inflammation, hyperlipemia, and immune deficiencies. In this study, we evaluated the potential efficacy of porphyran-derived oligosaccharides from Porphyra yezoensis (PYOs) in alleviating nonalcoholic fatty liver disease (NAFLD) and preliminarily clarified the underlying mechanism. NAFLD was induced by a high-fat diet for six months in C57BL/6J mice, followed by treatment with PYOs (100 or 300 mg/kg/d) for another six weeks. We found that PYOs reduced hepatic oxidative stress in mice with NAFLD, which plays a critical role in the occurrence and development of NAFLD. In addition, PYOs could markedly decrease lipid accumulation in liver by activating the IRS-1/AKT/GSK-3β signaling pathway and the AMPK signaling pathway in mice with NAFLD. PYOs also apparently relieved the hepatic fibrosis induced by oxidative stress via downregulation of TGF-β and its related proteins, so that liver injury was markedly alleviated. Furthermore, PYOs treatment relieved cecal microbiota dysbiosis (such as increasing the relative abundance of Akkermansia, while decreasing the Helicobacter abundance), which could alleviate oxidative stress, inflammation, and lipid metabolism, and protect the liver to a certain degree. In summary, PYOs treatment remarkably improved NAFLD via a specific molecular mechanism and reshaped the cecal microbiota.
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http://dx.doi.org/10.1096/fj.202000763RRRDOI Listing
June 2021

Evaluation of lignin inhibition in anaerobic digestion from the perspective of reducing the hydrolysis rate of holocellulose.

Bioresour Technol 2021 Aug 24;333:125204. Epub 2021 Apr 24.

Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin 150086, PR China; Rural Energy & Environmental Protection Institute of Heilongjiang Academy of Agricultural Sciences, Key Laboratory Combining Farming & Animal Husbandry, Key Laboratory of Straw Energy Utilization, Harbin 150086, PR China. Electronic address:

In this study, Anaerobic Digestion Model No. 1 (ADM1) were modified to simulate anaerobic digestion (AD) process of microcrystalline cellulose (MCC) and five lignocellulosic substrates, with the goal of predicting the hydrolysis rates of holocellulose fractions in environments with and without lignin inhibition. After model verification, the hydrolysis rate constant of MCC, i.e., the hydrolyzability of cellulose without lignin inhibition, was 3.227 d, while those of the holocellulose fractions of five lignocellulosic substrates (I_k) were in the range of 1.270 d to 3.364 d (average of 2.242 d), which demonstrated remarkable suppression of holocellulose hydrolysis by lignin. Lignin inhibition index (LII) was proposed as an indicator to intuitively quantify and characterize the lignin inhibitory strength in a specific substrate. A series of factors with the potential to affect the LII were analyzed sequentially. This study provides an advanced understanding of the participation and behavior of lignin in the AD process.
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http://dx.doi.org/10.1016/j.biortech.2021.125204DOI Listing
August 2021

KCNQ Channels in the Mesolimbic Reward Circuit Regulate Nociception in Chronic Pain in Mice.

Neurosci Bull 2021 May 26;37(5):597-610. Epub 2021 Apr 26.

Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, 221004, China.

Mesocorticolimbic dopaminergic (DA) neurons have been implicated in regulating nociception in chronic pain, yet the mechanisms are barely understood. Here, we found that chronic constructive injury (CCI) in mice increased the firing activity and decreased the KCNQ channel-mediated M-currents in ventral tegmental area (VTA) DA neurons projecting to the nucleus accumbens (NAc). Chemogenetic inhibition of the VTA-to-NAc DA neurons alleviated CCI-induced thermal nociception. Opposite changes in the firing activity and M-currents were recorded in VTA DA neurons projecting to the medial prefrontal cortex (mPFC) but did not affect nociception. In addition, intra-VTA injection of retigabine, a KCNQ opener, while reversing the changes of the VTA-to-NAc DA neurons, alleviated CCI-induced nociception, and this was abolished by injecting exogenous BDNF into the NAc. Taken together, these findings highlight a vital role of KCNQ channel-mediated modulation of mesolimbic DA activity in regulating thermal nociception in the chronic pain state.
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http://dx.doi.org/10.1007/s12264-021-00668-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099961PMC
May 2021

Cellular FADD-like IL-1β-converting enzyme-inhibitory protein attenuates myocardial ischemia/reperfusion injury via suppressing apoptosis and autophagy simultaneously.

Nutr Metab Cardiovasc Dis 2021 06 2;31(6):1916-1928. Epub 2021 Mar 2.

Institute of Cardiovascular Disease, China Three Gorges University, Yichang, 443003, China.

Background And Aims: Myocardial ischemia/reperfusion injury (MI/RI) is a result of coronary revascularization, and often increases cell apoptosis and autophagy. Downregulated cellular FADD-like-IL-1β-converting enzyme-inhibitory protein (cFLIP) was associated with development of several myocardial diseases, whether overexpression of cFLIP can attenuate MI/RI remains unclear. This study aimed to determine the effects of cFLIP on apoptosis and autophagy in MI/RI.

Methods And Results: Ischemia/reperfusion (I/R) rat model and hypoxia/reoxygenation (H/R) cardiomyocytes model were established. Both I/R injury and H/R injury down-regulated expression of two cFLIP isoforms (cFLIPL and cFLIPS), and instigated apoptosis and autophagy simultaneously. Overexpression of cFLIPL and/or cFLIPS led to a significant increase in cardiomyocytes viability in vitro, and also reduced the myocardial infarct volume in vivo, these changes were associated with suppressed apoptosis and autophagy. Mechanistically, overexpression of cFLIP significantly downregulated pro-apoptotic molecules (Caspase-3, -8, -9), and pro-autophagic molecules (Beclin-1 and LC3-II). Moreover, cFLIP significantly suppressed activity of NF-κB pathway to upregulate the expression of Bcl-2, which is the molecular of interplay of apoptosis and autophagy.

Conclusion: Overexpression of cFLIP significantly attenuated MI/RI both in vivo and vitro via suppression of apoptosis and lethal autophagy. cFLIP can suppress activity of NF-κB pathway, and further upregulated expression of Bcl-2.
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http://dx.doi.org/10.1016/j.numecd.2021.02.026DOI Listing
June 2021

Biochar and compost enhance soil quality and growth of roselle (Hibiscus sabdariffa L.) under saline conditions.

Sci Rep 2021 Apr 22;11(1):8739. Epub 2021 Apr 22.

Department of Ornamental Plants and Landscape Gardening, Faculty of Agriculture, Assuit University, Assiut, Egypt.

Soil amendments may increase the slate tolerance of plants consequently; it may increase the opportunity of using saline water in agricultural production. In the present pot trial, the effects of biochar (BIC) and compost (COM) on roselle (Hibiscus sabdariffa L.) irrigated with saline water (EC = 7.50 dS m) was studied. Roselle plants were amended with biochar (BIC and BIC) or compost (COM and COM) at rates of 1 and 2% (w/w), as well as by a mixture of the two amendments (BIC+). The experiment included a control soil without any amendments. Biochar and compost significantly enhanced the soil quality and nutrients availability under saline irrigation. Compost and biochar improved the degree of soil aggregation, total soil porosity and soil microbial biomass. BIC + COM increased the soil microbial biomass carbon and nitrogen over the individual application of each amendments and control soil. BIC + COM increased the activity of dehydrogenase and phosphatase enzymes. Growth of roselle plants including: plant height, shoot fresh and dry weight, and chlorophyll were significantly responded to the added amendments. The maximum sepal's yield was achieved from the combined application of compost and biochar. All the investigated treatments caused remarkable increases in the total flavonol and anthocyanin. BIC + COM increased the total anthocyanin and flavonol by 29 and 17% above the control. Despite the notable improvement in soil and roselle quality as a result of the single addition of compost or biochar, there is a clear superiority due to mixing the two amendments. It can be concluded that mixing of biochar and compost is recommended for roselle plants irrigated with saline water.
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http://dx.doi.org/10.1038/s41598-021-88293-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8062538PMC
April 2021

Potentilla anserine L. polysaccharide inhibits cadmium-induced neurotoxicity by attenuating autophagy.

Neurochem Int 2021 Jul 20;147:105045. Epub 2021 Apr 20.

Institute of Integrated Traditional Chinese and Western Medicine, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China.

Cadmium (Cd), a heavy metal with cytotoxicity, can activate autophagy. This study aimed to explore the effects and mechanisms of Potentilla anserine L. polysaccharide (PAP) on autophagy in N2a cells, primary neurons, and the brain of BALB/c mice exposed to Cd. The CCK-8 assay results showed that the cell viability decreased and the number of acidic vesicular organelles, autophagic vacuoles, lysosomes, and dysfunctional mitochondria increased in the cytoplasm of Cd-exposed N2a cells and primary neurons, as revealed by acridine orange staining, monodansylcadaverine staining, and transmission electron microscopy. PAP mitigated Cd-induced neuronal death and characteristic changes in autophagy. The expression of LC3 IILC3 II, Bcl-2, p62, Beclin-1, and PI3K class III was examined by Western blot analysis. Furthermore, the PI3K inhibitor (LY294002 or 3-MA) and/or PAP reversed the Cd-induced upregulated expression of LC3 II, Beclin-1, and PI3K class III, with a synergy between PI3K inhibitor and PAP against Cd-induced autophagy. The findings suggested that PAP partially prevented Cd-induced autophagic cell death in neurons by inhibiting the PI3K class III/Beclin-1 signaling pathway in vitro and in vivo.
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http://dx.doi.org/10.1016/j.neuint.2021.105045DOI Listing
July 2021

Sacraoxides A-G, Bioactive Cembranoids from Gum Resin of .

Front Chem 2021 30;9:649287. Epub 2021 Mar 30.

School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China.

Seven undescribed cembranoids, sacraoxides A-G (-) were isolated from the gum resin of . Their structures were elucidated by extensive physicochemical and spectroscopic analysis, as well as ECD calculation, modified Mosher's method and X-ray diffraction crystallography. Compounds and exhibited inhibitory activities on nitric oxide (NO) production induced by lipopolysaccharide in RAW264.7 cells with IC values of 24.9 ± 1.7 and 36.4 ± 2.9 M.
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http://dx.doi.org/10.3389/fchem.2021.649287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044883PMC
March 2021

Mendelian randomization integrating GWAS and eQTL data revealed genes pleiotropically associated with major depressive disorder.

Transl Psychiatry 2021 Apr 17;11(1):225. Epub 2021 Apr 17.

Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.

Previous genome-wide association studies (GWAS) have identified potential genetic variants associated with the risk of major depressive disorder (MDD), but the underlying biological interpretation remains largely unknown. We aimed to prioritize genes that were pleiotropically or potentially causally associated with MDD. We applied the summary data-based Mendelian randomization (SMR) method integrating GWAS and gene expression quantitative trait loci (eQTL) data in 13 brain regions to identify genes that were pleiotropically associated with MDD. In addition, we repeated the analysis by using the meta-analyzed version of the eQTL summary data in the brain (brain-eMeta). We identified multiple significant genes across different brain regions that may be involved in the pathogenesis of MDD. The prime-specific gene BTN3A2 (corresponding probe: ENSG00000186470.9) was the top hit showing pleiotropic association with MDD in 9 of the 13 brain regions and in brain-eMeta, after correction for multiple testing. Many of the identified genes are located in the human major histocompatibility complex (MHC) region on chromosome 6 and are mainly involved in the immune response. Our SMR analysis indicated that multiple genes showed pleiotropic association with MDD across the brain regions. These findings provided important leads to a better understanding of the mechanism of MDD and revealed potential therapeutic targets for the prevention and effective treatment of MDD.
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http://dx.doi.org/10.1038/s41398-021-01348-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8053199PMC
April 2021

Avian influenza A (H7N9) virus: from low pathogenic to highly pathogenic.

Front Med 2021 Apr 16. Epub 2021 Apr 16.

Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518114, China.

The avian influenza A (H7N9) virus is a zoonotic virus that is closely associated with live poultry markets. It has caused infections in humans in China since 2013. Five waves of the H7N9 influenza epidemic occurred in China between March 2013 and September 2017. H7N9 with low-pathogenicity dominated in the first four waves, whereas highly pathogenic H7N9 influenza emerged in poultry and spread to humans during the fifth wave, causing wide concern. Specialists and officials from China and other countries responded quickly, controlled the epidemic well thus far, and characterized the virus by using new technologies and surveillance tools that were made possible by their preparedness efforts. Here, we review the characteristics of the H7N9 viruses that were identified while controlling the spread of the disease. It was summarized and discussed from the perspectives of molecular epidemiology, clinical features, virulence and pathogenesis, receptor binding, T-cell responses, monoclonal antibody development, vaccine development, and disease burden. These data provide tools for minimizing the future threat of H7N9 and other emerging and re-emerging viruses, such as SARS-CoV-2.
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http://dx.doi.org/10.1007/s11684-020-0814-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190734PMC
April 2021

Rapid Acquisition of High-Quality SARS-CoV-2 Genome via Amplicon-Oxford Nanopore Sequencing.

Virol Sin 2021 Apr 13. Epub 2021 Apr 13.

CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.

Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic such as pathogen identification and virus preliminary tracing. While the rapid acquisition of SARS-CoV-2 genome from clinical specimens is limited by their low nucleic acid load and the complexity of the nucleic acid background. To address this issue, we modified and evaluated an approach by utilizing SARS-CoV-2-specific amplicon amplification and Oxford Nanopore PromethION platform. This workflow started with the throat swab of the COVID-19 patient, combined reverse transcript PCR, and multi-amplification in one-step to shorten the experiment time, then can quickly and steadily obtain high-quality SARS-CoV-2 genome within 24 h. A comprehensive evaluation of the method was conducted in 42 samples: the sequencing quality of the method was correlated well with the viral load of the samples; high-quality SARS-CoV-2 genome could be obtained stably in the samples with Ct value up to 39.14; data yielding for different Ct values were assessed and the recommended sequencing time was 8 h for samples with Ct value of less than 20; variation analysis indicated that the method can detect the existing and emerging genomic mutations as well; Illumina sequencing verified that ultra-deep sequencing can greatly improve the single read error rate of Nanopore sequencing, making it as low as 0.4/10,000 bp. In summary, high-quality SARS-CoV-2 genome can be acquired by utilizing the amplicon amplification and it is an effective method in accelerating the acquisition of genetic resources and tracking the genome diversity of SARS-CoV-2.
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http://dx.doi.org/10.1007/s12250-021-00378-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043101PMC
April 2021