Publications by authors named "Ming Sun"

642 Publications

Choroidal and Retinal Thickness and Axial Eye Elongation in Chinese Junior Students.

Invest Ophthalmol Vis Sci 2021 Jul;62(9):26

School of Public Health, Capital Medical University, Beijing, China.

Purpose: To explore the associations between macular choroidal and retinal thickness and axial elongation in non-myopic and myopic junior students.

Methods: In this school-based longitudinal observational study, axial length was measured by optical low-coherence reflectometry, and choroidal thickness and retinal thickness were measured by spectral-domain optical coherence tomography. Myopia was defined as non-cycloplegic objective spherical equivalent refraction ≤ -0.50 diopters. Structural equation modeling and multiple linear regression models were used to analyze the associations between baseline choroidal and retinal thickness with axial elongation.

Results: Out of 1307 students examined at baseline in 2017, 1197 (91.58%) returned for follow-up examination in 2018, with a median age of 12.00 years (interquartile range [IQR], 1.00) and included 667 boys (55.72%). Within a 1-year period, the median axial elongation of right eyes was 230 µm (IQR, 180) in boys and 200 µm (IQR, 160) in girls (P = 0.032). The thinner temporal choroidal thickness was associated with greater 1-year axial elongation only in myopic students (β, -0.20; 95% confidence interval [CI], -0.37, -0.03), the thinner temporal retinal thickness was associated with greater 1-year axial elongation in both non-myopic (β, -2.67; 95% CI, -4.52, -0.82) and myopic (β, -0.99; 95% CI, -1.68, -0.30) students, after adjustment for sex, age, and height. Subfoveal and nasal choroidal and retinal thickness were not significantly associated with axial elongation in either non-myopic or myopic students.

Conclusions: A thinner temporal choroid at age 12 years may predict greater 1-year axial elongation in myopic students, and a thinner temporal retina may predict greater 1-year axial elongation in both non-myopic and myopic students. This finding may help to identify children at risk and control axial elongation with potential preventive strategies.
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http://dx.doi.org/10.1167/iovs.62.9.26DOI Listing
July 2021

BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis.

Bioinformatics 2021 Jul 9. Epub 2021 Jul 9.

State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.

Summary: Bacillus thuringiensis (Bt) has been used as the most successful microbial pesticide for decades. Its toxin genes are used for the development of GM crops against pests. We previously developed a web-based insecticidal gene mining tool BtToxin_scanner. It has been frequently used by many researchers worldwide. However, it can only handle the genome one by one online. To facilitate efficiently mining toxin genes from large-scale sequence data, we re-designed this tool with a new workflow and the novel bacterial pesticidal protein database. Here we present BtToxin_Digger, a comprehensive and high-throughput Bt toxin mining tool. It can be used to predict Bt toxin genes from thousands of raw genome and metagenome data, and provides accurate results for downstream analysis and experiment testing. Moreover, it can also be used to mine other targeting genes from large-scale genome and metagenome data with the replacement of the database.

Availability And Implementation: The BtToxin_Digger codes and web services are freely available at https://github.com/BMBGenomics/BtToxin_Digger and https://bcam.hzau.edu.cn/BtToxin_Digger, respectively.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btab506DOI Listing
July 2021

CAR T cells targeting tumor-associated exons of glypican 2 regress neuroblastoma in mice.

Cell Rep Med 2021 Jun 1;2(6):100297. Epub 2021 Jun 1.

Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Targeting solid tumors must overcome several major obstacles, in particular, the identification of elusive tumor-specific antigens. Here, we devise a strategy to help identify tumor-specific epitopes. Glypican 2 (GPC2) is overexpressed in neuroblastoma. Using RNA sequencing (RNA-seq) analysis, we show that exon 3 and exons 7-10 of GPC2 are expressed in cancer but are minimally expressed in normal tissues. Accordingly, we discover a monoclonal antibody (CT3) that binds exons 3 and 10 and visualize the complex structure of CT3 and GPC2 by electron microscopy. The potential of this approach is exemplified by designing CT3-derived chimeric antigen receptor (CAR) T cells that regress neuroblastoma in mice. Genomic sequencing of T cells recovered from mice reveals the CAR integration sites that may contribute to CAR T cell proliferation and persistence. These studies demonstrate how RNA-seq data can be exploited to help identify tumor-associated exons that can be targeted by CAR T cell therapies.
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http://dx.doi.org/10.1016/j.xcrm.2021.100297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8233664PMC
June 2021

Circ_0008956 contributes to IL-1β-induced osteoarthritis progression via miR-149-5p/NAMPT axis.

Int Immunopharmacol 2021 Jun 18;98:107857. Epub 2021 Jun 18.

Center For Traumatology, Ninth People's Hospital of Chongqing, Chongqing City, China. Electronic address:

Circular RNAs (circRNAs) have been identified to involve in the pathophysiology of osteoarthritis (OA). Herein, this study aimed to investigate the role and mechanisms underlying circ_0008956 in the process of OA. The expression of circ_0008956 and microRNA (miR)-149-5p and Nicotinamide phosphoribosyl transferase 1 (NAMPT) was detected using quantitative real-time polymerase chain reaction and Western blot assays. Cell viability, apoptosis, cell cycle and extracellular matrix (ECM) degradation were analyzed using cell counting kit-8, flow cytometry, and Western blot assays, respectively. The binding interaction between miR-149-5p and circ_0008956 or NAMPT was confirmed using dual-luciferase reporter assay. Circ_0008956 was highly expressed in OA cartilage tissues and interleukin (IL)-1β mediated chondrocytes. Knockdown of circ_0008956 promoted cell viability, cell cycle, suppressed cell apoptosis, and increased type II collagen and aggracan expression in IL-1β-treated chondrocytes. MiR-149-5p was verified to be a target of circ_0008956, inhibition of miR-149-5p reversed the protective effects of circ_0008956 knockdown on IL-1β-stimulated chondrocytes. NAMPT was a target of miR-149-5p, miR-149-5p attenuated IL-1β-induced growth arrest and ECM degradation in chondrocytes, which was abolished by NAMPT overexpression. Importantly, circ_0008956 served as a sponge for miR-149-5p to up-regulate NAMPT expression in chondrocytes. Circ_0008956 contributed to IL-1β-induced growth arrest and ECM degradation in chondrocytes via miR-149-5p/NAMPT axis, suggesting a new insight into the pathogenesis of OA and a promising therapeutic target for OA treatment.
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http://dx.doi.org/10.1016/j.intimp.2021.107857DOI Listing
June 2021

[Evaluation of digital technology for orthognathic surgery in 25 patients].

Shanghai Kou Qiang Yi Xue 2021 Apr;30(2):219-224

Department of Oral and Maxillofacial Surgery, Qingdao University Affiliated Hospital. Qingdao 266000, China.

Purpose: To use three-dimensional reconstruction measurement, preoperative diagnosis, surgical design, surgical simulation, guide plate production, navigation verification and effect evaluation of orthognathic surgery assisted by digital technology, in order to explore more scientific and reasonable programs and procedures of orthognathic surgery.

Methods: Twenty-five patients with congenital dental and maxillofacial deformity were selected as the experimental subjects, craniofacial spiral CT was conducted before surgery and CT data were imported into Mimics 20.0 software to establish a 3D head digital model. The bone landmarks in three-dimensional reconstruction digital model were selected, measured, analyzed and diagnosed, and the design of the surgical plan and the production of the guide plates were performed. Surgical navigation system was used to confirm the maxillary position, verify the bone retention and guide precise bone grinding during operation. Craniofacial spiral CT was conducted 1 week after surgery for postoperative validation of the surgical design protocol. Statistical analysis was performed using SPSS 24.0 software package.

Results: All 25 patients were operated according to the digital orthognathic surgery design and procedure.There were no significant differences in X, Y and Z three-dimensional directions in 10 actual landmarks between the postoperative actual head model and the preoperative predictive head model(P>0.05).

Conclusions: Orthognathic surgery assisted by digital technology has the advantages of precision and minimal invasiveness.
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April 2021

Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers.

BMC Plant Biol 2021 Jun 7;21(1):264. Epub 2021 Jun 7.

Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.

Background: Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus.

Results: Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P < 0.001), and might be used in the future selection and breeding.

Conclusion: A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future.
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http://dx.doi.org/10.1186/s12870-021-03037-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8186225PMC
June 2021

Preclinical metabolic characterization of mefunidone, a novel anti-renal fibrosis drug.

Life Sci 2021 Sep 2;280:119666. Epub 2021 Jun 2.

Research Institute of Drug Metabolism and Pharmacokinetics, School of Xiangya Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China. Electronic address:

Aims: The preclinical evaluation of innovative drugs plays an important role in the new drugs development. As a derivative of pirfenidone (PFD), mefunidone (MFD) has shown better anti-fibrosis and anti-inflammatory activity in both cell lines and animal models. To support the clinical investigations of MFD, the metabolic characterization of MFD was initially evaluated in preclinical models.

Main Methods: The potential metabolites of MFD were analyzed by LC-MS/MS methods. The induction effect of MFD on CYP1A2, CYP2B6, and CYP3A4 was performed in primary human hepatocytes, and the inhibition of CYP enzymes by MFD was also evaluated in human liver microsomes. Finally, the pharmacokinetic profiles of MFD were assessed in SD rats after the rats had received multiple doses (62.5 mg/kg) of MFD.

Key Findings: MFD was metabolized in three pathways including oxidation, N-demethylation, and hydroxylation. Except for slight inhibition on the activity of CYP2D6, MFD exerted no effect on other CYP enzymes. Moreover, drug accumulation of MFD was not observed in rats after repeated dosing of MFD.

Significance: MFD was first discovered in preclinical investigations without inducing and inhibiting metabolic enzymes. This work provides some important information about the metabolic characterization of MFD for its further clinical investigations.
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http://dx.doi.org/10.1016/j.lfs.2021.119666DOI Listing
September 2021

PSII Activity Was Inhibited at Flowering Stage with Developing Black Bracts of Oat.

Int J Mol Sci 2021 May 17;22(10). Epub 2021 May 17.

Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.

The color of bracts generally turns yellow or black from green during cereal grain development. However, the impact of these phenotypic changes on photosynthetic physiology during black bract formation remains unclear. Two oat cultivars ( L.), 'Triple Crown' and 'Qinghai 444', with yellow and black bracts, respectively, were found to both have green bracts at the heading stage, but started to turn black at the flowering stage and become blackened at the milk stage for 'Qinghai 444'. Their photosynthetic characteristics were analyzed and compared, and the key genes, proteins and regulatory pathways affecting photosynthetic physiology were determined in 'Triple Crown' and 'Qinghai 444' bracts. The results show that the actual PSII photochemical efficiency and PSII electron transfer rate of 'Qinghai 444' bracts had no significant changes at the heading and milk stages but decreased significantly ( < 0.05) at the flowering stage compared with 'Triple Crown'. The chlorophyll content decreased, the LHCII involved in the assembly of supercomplexes in the thylakoid membrane was inhibited, and the expression of and was downregulated at the flowering stage. During this critical stage, the expression of and was upregulated, and the biosynthetic pathway of -coumaric acid using tyrosine and phenylalanine as precursors was also enhanced. Moreover, the key upregulated genes (, and ) of anthocyanin biosynthesis might complement the impaired PSII activity until recovered at the milk stage. These findings provide a new insight into how photosynthesis alters during the process of oat bract color transition to black.
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http://dx.doi.org/10.3390/ijms22105258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8156022PMC
May 2021

3-Methyladenine but not antioxidants to overcome BACH2-mediated bortezomib resistance in mantle cell lymphoma.

Cancer Cell Int 2021 May 26;21(1):279. Epub 2021 May 26.

Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan, China.

Background: Bortezomib (BTZ) is an inhibitor of the proteasome that has been used to treat patients with mantle cell lymphoma (MCL), but the resistance to BTZ in clinical cases remains a major drawback. BACH2 is a lymphoid-specific transcription repressor recognized as a tumor suppressor in MCL. Reduced BACH2 levels contribute to BTZ resistance; however, the molecular events underlying BACH2-mediated BTZ resistance are largely unclear.

Methods: We silenced BACH2 in MCL cells using a lentiviral shRNA-mediated knockdown system. Bioinformatic, real-time RT-PCR, immunoblotting and a series of functional assays were performed to describe the molecular mechanisms underlying BTZ resistance in MCL. The therapeutic effects of chemicals were evaluated on numerous cellular and molecular processes in resistant MCL cell lines and xenografts.

Results: In resistant cells, BTZ-triggered mild oxidative stress induced a strong activation of PI3K-AKT signaling, which further blocked nuclear translocation of BACH2. Defective nuclear translocation of BACH2 or silencing BACH2 removed its transcriptional repression on HMOX1, leading to upregulation of heme oxygenase-1 (HO-1). Increased HO-1 further maintained reactive oxygen species (ROS) within a minimal tumor-promoting level and enhanced cytoprotective autophagy. Interestingly, although mild increase in ROS exhibited a pro-tumorigenic effect on resistant cells, simply blocking ROS by antioxidants did not lead to cell death but aggravated BTZ resistance via stabilizing BACH1, the other member of BACH family. Instead, 3-methyladenine (3-MA), a dual inhibitor to suppress PI3K signaling and autophagosome formation, sensitized resistant MCL cells to BTZ, both in vitro and in vivo.

Conclusion: Our results dissected the interconnected molecular network in resistant MCL cells in which 3-MA represents an effective therapeutic strategy to overcome BTZ resistance. Notably, BACH1 and BACH2, albeit from the same family, are likely to play opposite roles in pathogenesis and progression of MCL.
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http://dx.doi.org/10.1186/s12935-021-01980-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8157467PMC
May 2021

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Res Sq 2021 May 19. Epub 2021 May 19.

The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.
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http://dx.doi.org/10.21203/rs.3.rs-515215/v1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8142659PMC
May 2021

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

bioRxiv 2021 May 11. Epub 2021 May 11.

The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.
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http://dx.doi.org/10.1101/2021.05.10.443524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8132225PMC
May 2021

Practical considerations for using K3 cameras in CDS mode for high-resolution and high-throughput single particle cryo-EM.

J Struct Biol 2021 May 11;213(3):107745. Epub 2021 May 11.

Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States. Electronic address:

Detector technology plays a pivotal role in high-resolution and high-throughput cryo-EM structure determination. Compared with the first-generation, single-electron counting direct detection camera (Gatan K2), the latest K3 camera is faster, larger, and now offers a correlated-double sampling mode (CDS). Importantly this results in a higher DQE and improved throughput compared to its predecessor. In this study, we focused on optimizing camera data collection parameters for daily use within a cryo-EM facility and explored the balance between throughput and resolution. In total, eight data sets of murine heavy-chain apoferritin were collected at different dose rates and magnifications, using 9-hole image shift data collection strategies. The performance of the camera was characterized by the quality of the resultant 3D reconstructions. Our results demonstrated that the Gatan K3 operating in CDS mode outperformed standard (nonCDS) mode in terms of reconstruction resolution in all tested conditions with 8 electrons per pixel per second being the optimal dose rate. At low magnification (64kx) we were able to achieve reconstruction resolutions of 149% of the physical Nyquist limit (1.8 Å with a 1.346 Å physical pixel size). Low magnification allows more particles to be collected per image, aiding analysis of heterogeneous samples requiring large data sets. At moderate magnification (105kx, 0.834 Å physical pixel size) we achieved a resolution of 1.65 Å within 8-h of data collection, a condition optimal for achieving high-resolution on well behaved samples. Our results also show that for an optimal sample like apoferritin, one can achieve better than 2.5 Å resolution with 5 min of data collection. Together, our studies validate the most efficient ways of imaging protein complexes using the K3 direct detector and will greatly benefit the cryo-EM community.
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http://dx.doi.org/10.1016/j.jsb.2021.107745DOI Listing
May 2021

Identification of T Cell Epitopes in the Spike Glycoprotein of Severe Acute Respiratory Syndrome Coronavirus 2 in Rhesus Macaques.

J Immunol 2021 06 12;206(11):2527-2535. Epub 2021 May 12.

Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China;

The T cell response is an important detection index in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine development. The present study was undertaken to determine the T cell epitopes in the spike (S) protein of SARS-CoV-2 that dominate the T cell responses in SARS-CoV-2-infected patients. PBMCs from rhesus macaques vaccinated with a DNA vaccine encoding the full-length S protein were isolated, and an ELISPOT assay was used to identify the recognized T cell epitopes among a total of 158 18-mer and 10-aa-overlapping peptides spanning the full-length S protein. Six multipeptide-based epitopes located in the S1 region, with four of the six located in the receptor-binding domain, were defined as the most frequently recognized epitopes in macaques. The conservation of the epitopes across species was also verified, and peptide mixtures for T cell response detection were established. Six newly defined T cell epitopes were found in the current study, which may provide a novel potential target for T cell response detection and the diagnosis and vaccine design of SARS-CoV-2 based on multipeptide subunit-based epitopes.
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http://dx.doi.org/10.4049/jimmunol.2000922DOI Listing
June 2021

TRIB3 promotes proliferation, migration, and invasion of retinoblastoma cells by activating the AKT/mTOR signaling pathway.

Cancer Biomark 2021 ;31(4):307-315

Department of Fundus Disease, Huainan Chenguang Eye Hospital, Huainan, Anhui, China.

Background: Tribbles pseudokinase 3 (TRIB3) is a member of the tribbles-related family, which has been determined in various cancers, including renal cell carcinoma, acute promyelocytic leukemia, colorectal cancer, endometrial cancer, and glioma. However, its role in retinoblastoma (RB) has not yet been explored.

Methods: The expression level of TRIB3 was detected in RB tissues and cell lines using qRT-PCR. The effects of TRIB3 on cell proliferation and invasion capacities were analyzed with MTT, crystal violet, and transwell assays. Western blot and rescue assays were conducted to explore the underlying mechanism.

Results: This study found that TRIB3 was upregulated in human RB tissues compared to adjacent normal tissues both at the mRNA and protein levels. Overexpression of TRIB3 significantly promoted cell proliferation and invasion of RB cells, while TRIB3 knockdown inhibited these processes. Moreover, the mechanism deciphering experiments showed that TRIB3 overexpression can increase AKT and mTOR phosphorylation. Conversely, TRIB3 knockdown decreased the phosphorylation of AKT and mTOR. Additionally, MK2206, a potent AKT inhibitor, blocked the promotive effects of TRIB3 in RB cells.

Conclusion: This study demonstrated that TRIB3 acts as an oncogene and plays a crucial role in the proliferation and invasion of RB cells via regulating the AKT/mTOR signaling pathway. Therefore, TRIB3 may serve as a potential target in the diagnosis and/or treatment of RB.
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http://dx.doi.org/10.3233/CBM-200050DOI Listing
January 2021

Isovitexin Depresses Osteoarthritis Progression via the Nrf2/NF-κB Pathway: An in vitro Study.

J Inflamm Res 2021 13;14:1403-1414. Epub 2021 Apr 13.

The Third Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, 310005, People's Republic of China.

Purpose: Osteoarthritis (OA) is a multifactorial joint disease and inflammatory processes contribute to joint destruction. Isovitexin (IVX) is a flavone component found in passion flower, Cannabis and, and the palm that is known for its anti-inflammatory properties.

Materials And Methods: This study investigated in vitro the role and underlying mechanism used by IVX in its regulation of OA development. Effects of IVX on the viability of chondrocytes were measured by CCK-8 assays. The phenotypes of extracellular matrix (ECM) degeneration and inflammation were measured by qPCR, Western blot, and ELISA; and NF-κB pathway was detected by immunofluorescence and Western blot. Molecular docking was applied to predict the interacting protein of IVX, while Nrf2 was knocked down by siRNAs to confirm its role.

Results: We demonstrated that IVX suppressed ECM degeneration and suppressed pro-inflammatory factors in IL-1β-treated chondrocytes. Additionally, IVX impact on NF-κB signaling in IL-1β-exposed chondrocytic cells; Mechanistically, it was also demonstrated in molecular docking and knock down studies that IVX might bind to Nrf2 to suppress NF-κB pathway.

Conclusion: Our data suggest that IVX halts OA disease advancement through the Nrf2/NF-κB axis, suggesting a possibility of IVX as a target for OA therapy.
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http://dx.doi.org/10.2147/JIR.S299557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8053716PMC
April 2021

Early immune responses and prognostic factors in children with COVID-19: a single-center retrospective analysis.

BMC Pediatr 2021 04 17;21(1):181. Epub 2021 Apr 17.

Department of Hematology, Wuhan Children's Hospital (Wuhan Medical Care Center for Women and Children), Tongji College, Huazhong University of Science and Technology, Wuhan, Hubei, China.

Background: Early diagnostic indicators and the identification of possible progression to severe or critical COVID-19 in children are unknown. To investigate the immune characteristics of early SARS-CoV-2 infection in children and possible key prognostic factors for early identification of critical COVID-19, a retrospective study including 121 children with COVID-19 was conducted. Peripheral blood lymphocyte subset counts, T cell-derived cytokine concentrations, inflammatory factor concentrations, and routine blood counts were analyzed statistically at the initial presentation.

Results: The T lymphocyte subset and natural killer cell counts decreased with increasing disease severity. Group III (critical cases) had a higher Th/Tc ratio than groups I and II (common and severe cases); group I had a higher B cell count than groups II and III. IL-6, IL-10, IFN-γ, SAA, and procalcitonin levels increased with increasing disease severity. Hemoglobin concentration, and RBC and eosinophil counts decreased with increasing disease severity. Groups II and III had significantly lower lymphocyte counts than group I. T, Th, Tc, IL-6, IL-10, RBC, and hemoglobin had relatively high contribution and area under the curve values.

Conclusions: Decreased T, Th, Tc, RBC, hemoglobin and increased IL-6 and IL-10 in early SARS-CoV-2 infection in children are valuable indices for early diagnosis of severe disease. The significantly reduced Th and Tc cells and significantly increased IL-6, IL-10, ferritin, procalcitonin, and SAA at this stage in children with critical COVID-19 may be closely associated with the systemic cytokine storm caused by immune dysregulation.
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http://dx.doi.org/10.1186/s12887-021-02561-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8052550PMC
April 2021

Variations in Env at amino acids 328 and 330 affect HIV-1 replicative fitness and entry inhibitor sensitivity.

Virus Res 2021 Jul 18;299:198424. Epub 2021 Apr 18.

Unit of HIV Molecular Epidemiology and Virology, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. Electronic address:

While the variations in the HIV-1 Env V3 loop have been the focus of much research to explore its functional effect, how specific mutations of certain amino acids in the V3 loop affect viral fitness remains unclear. In this study, we evaluated a series of natural polymorphisms at positions 328 and 330 with different combinations of adjacent glycosylation sites in the HIV-1 subtype B backbone to address their role in replicative fitness and sensitivity to entry inhibitors based on analysis of env sequence frequency at the population level. Pairwise growth competition experiment showed that wild-type virus with major consensus amino acids obviously had higher replicative fitness (P < 0.001). A change at position 328 to a less frequently occurring amino acid, K, together with a mutated N332 glycosylation site harbored lower fitness and became more sensitive to coreceptor antagonists (AMD3100), fusion inhibitors (T20) and sCD4. A change at position 330 to a less frequently occurring amino acid, Y, together with a mutated N332 glycosylation site resulted in higher fitness and less sensitivity to entry inhibitors (T20, AMD3100, and sCD4), and viruses containing both changes showed intermediate activity. It seems that the H330Y mutation compensated for the reduced replicative capacity caused by the Q328 K mutation. Moreover, viruses that showed lower replicative fitness also exhibited slower entry kinetics, lower levels of replication intermediates and protein packaging, and a lower ability to replicate in primary peripheral blood mononuclear cells (PBMCs). The findings highlight the functional effect of variations at 328 and 330 in the V3 loop on replicative fitness and may benefit HIV-1 treatment by helping predict the sensitivity to entry inhibitors.
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http://dx.doi.org/10.1016/j.virusres.2021.198424DOI Listing
July 2021

Synthesis and biological evaluation of 2-(4-alkoxy-3-cyano)phenylpyrimidine derivatives with 4-amino or 4-hydroxy as a pharmacophore element binding with xanthine oxidase active site.

Bioorg Med Chem 2021 May 2;38:116117. Epub 2021 Apr 2.

Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China. Electronic address:

Xanthine oxidase is the rate-limiting enzyme critical for the synthesis of uric acid, and therefore xanthine oxidase inhibitors are considered as one of the promising therapies for hyperuricemia and gout. In our previous study, series of 2-(4-alkoxy-3-cyano)phenyl-6-oxo-1,6-dihydropyrimidine-5-carboxylic acids and 2-(4-alkoxy-3-cyano)phenyl-6-imino-1,6-dihydropyrimidine-5-carboxylic acids were synthesized that presented excellent in vitro xanthine oxidase inhibitory potency. Interestingly, molecular docking studies revealed that the interaction behavior of these compounds with xanthine oxidase was changed after the conversion from a hydroxy group to amine group. To further investigate the structure-activity relationships of these pyrimidine-containing xanthine oxidase inhibitors and explore the contribution of amino or hydroxy group on xanthine oxidase inhibitory potency, several 2-phenylpyrimidine derivatives with amino or hydroxy functional group were designed and synthesized. Thereafter, the structure-activity research and molecular modeling study proved that hydroxy and amino groups could be used as pharmacophore elements for the design of 2-phenylpyrimidines xanthine oxidase inhibitors. Particularly, the optimized compound, 2-(3-cyano-4-isopentoxy)phenylpyrimidine-4-ol, emerged the strongest xanthine oxidase inhibitor potency, with an IC value of 0.046 µM, which was approximately 120-fold more potent than that of allopurinol (IC = 5.462 µM). Additionally, Lineweaver-Burk plot analysis revealed that the optimized compound acted as a mixed-type inhibitor. Furthermore, the in vivo hypouricemic effect of the optimized compound was investigated in a hyperuricemia rat model induced by potassium oxonate, and the results showed that the optimized compound could effectively reduce serum uric acid levels at an oral dose of 30 mg/kg.
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http://dx.doi.org/10.1016/j.bmc.2021.116117DOI Listing
May 2021

The emerging regulatory roles of long non-coding RNAs implicated in cancer metabolism.

Mol Ther 2021 Jul 26;29(7):2209-2218. Epub 2021 Mar 26.

Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, People's Republic of China; Suzhou Cancer Center, Gusu School of Nanjing Medical University Suzhou, Jiangsu, People's Republic of China. Electronic address:

Compared to normal cells, cancer cells exhibit specific metabolic characteristics that facilitate the growth and metastasis of cancer. It is now widely appreciated that long non-coding RNAs (lncRNAs) exert extensive regulatory effects on a spectrum of biological processes through diverse mechanisms. In this review, we focus on the rapidly advancing field of lncRNAs and summarize the relationship between the dysregulation of lncRNAs and cancer metabolism, with a particular emphasis on the specific roles of lncRNAs in glycolysis, mitochondrial function, glutamine, and lipid metabolism. These investigations reveal that lncRNAs are a key factor in the complexity of malignant cancer metabolism. Only through understanding the relevance between lncRNAs and cancer metabolic reprogramming can we open a new chapter in the history of carcinogenesis, one that promises to alter the methods of cancer diagnosis and treatment.
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http://dx.doi.org/10.1016/j.ymthe.2021.03.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261164PMC
July 2021

Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge.

NPJ Digit Med 2021 Mar 19;4(1):53. Epub 2021 Mar 19.

Institute for Computing and Information Sciences, Radboud University, Nijmegen, The Netherlands.

Consumer wearables and sensors are a rich source of data about patients' daily disease and symptom burden, particularly in the case of movement disorders like Parkinson's disease (PD). However, interpreting these complex data into so-called digital biomarkers requires complicated analytical approaches, and validating these biomarkers requires sufficient data and unbiased evaluation methods. Here we describe the use of crowdsourcing to specifically evaluate and benchmark features derived from accelerometer and gyroscope data in two different datasets to predict the presence of PD and severity of three PD symptoms: tremor, dyskinesia, and bradykinesia. Forty teams from around the world submitted features, and achieved drastically improved predictive performance for PD status (best AUROC = 0.87), as well as tremor- (best AUPR = 0.75), dyskinesia- (best AUPR = 0.48) and bradykinesia-severity (best AUPR = 0.95).
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http://dx.doi.org/10.1038/s41746-021-00414-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7979931PMC
March 2021

Elucidation of the Pathogenicity-Associated Regulatory Network in Xanthomonas oryzae pv. oryzae.

mSystems 2021 Mar 9;6(2). Epub 2021 Mar 9.

State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China

is a notorious plant pathogen causing serious diseases in hundreds of plant hosts. species are equipped with an array of signal transduction systems that regulate gene expression to survive in various harsh environments and successfully infect hosts. Although certain pathogenicity-associated regulators have been functionally characterized, signal transduction systems always function as a regulatory network which remains to be elucidated in This study used a systematic approach to characterize all identified pathogenicity-associated regulators in pv. oryzae (Xoo), including a transcriptional regulator with unknown function, and their interactive regulatory network. RNA sequencing was used in elucidating the patterns of the 10 pathogenicity-associated regulators identified. Results revealed that each pathogenicity-associated regulator has cross talk with others and all these regulators function as a regulatory network, with VemR and PXO_RS20790 being the master pathogenicity-associated regulators and HrpX being the final executant. Moreover, regulome analysis showed that numerous genes other than genes in pathogenicity islands are finely regulated within the regulatory network. Given that most of the pathogenicity-associated regulators are conserved in , our findings suggest a global network of gene regulation in this evolutionarily conserved pathogen. In conclusion, our study provides essential basic information about the regulatory network in Xoo, suggesting that this complicated regulatory network is one of the reasons for the robustness and fitness of spp. The host plant infection process of pathogenic bacteria is a coordinating cellular behavior, which requires dynamic regulation at several levels in response to variations in host plants or fluctuations in the external environment. As one of the most important genera of plant-pathogenic bacteria, has been studied as a model. Although certain pathogenicity-associated regulators have been functionally characterized, interactions among them remain to be elucidated. This study systematically characterized pathogenicity-associated regulators in Xoo and revealed that cross talk exists among pathogenicity-associated regulators and function as a regulatory network in which a hierarchy exists among the regulators. Our study elucidated the landscape of the pathogenicity-associated regulatory network in , promoting understanding of the infection process of pathogenic bacteria.
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http://dx.doi.org/10.1128/mSystems.00789-20DOI Listing
March 2021

Circular RNA circVAPA promotes chemotherapy drug resistance in gastric cancer progression by regulating miR-125b-5p/STAT3 axis.

World J Gastroenterol 2021 Feb;27(6):487-500

Department of Ophthalmology, The First Affiliated Hospital of China Medical University, Shenyang 110001, Liaoning Province, China.

Background: Gastric cancer (GC) is a prevalent malignancy, leading to a high incidence of cancer-associated death. Cisplatin (DDP)-based chemotherapy is the principal therapy for clinical GC treatment, but DDP resistance is a severe clinical challenge and the mechanism remains poorly understood. Circular RNAs (circRNAs) have been identified to play crucial roles in modulating the chemoresistance of gastric cancer cells.

Aim: To explore the effect of circVAPA on chemotherapy resistance during GC progression.

Methods: The effect of circVAPA on GC progression and chemotherapy resistance was analyzed by MTT assay, colony formation assay, Transwell assay, wound healing assay, and flow cytometry analysis in GC cells and DDP resistant GC cell lines, and tumorigenicity analysis in nude mice . The mechanism was investigated by luciferase reporter assay, quantitative real-time PCR, and Western blot analysis.

Results: CircVAPA expression was up-regulated in clinical GC tissues compared with normal samples. CircVAPA depletion inhibited proliferation, migration, and invasion and increased apoptosis of GC cells. The expression of circVAPA, STAT3, and STAT3 downstream genes was elevated in DDP resistant SGC7901/DDP cell lines. CircVAPA knockdown attenuated the DDP resistance of GC cells. Mechanically, circVAPA was able to sponge miR-125b-5p, and miR-125b-5p could target STAT3 in the GC cells. MiR-125b-5p inhibitor reversed circVAPA depletion-enhanced inhibitory effect of DDP on GC cells, and STAT3 knockdown blocked circVAPA overexpression-induced proliferation of DDP-treated SGC7901/DDP cells. The depletion of STAT3 and miR-125b-5p inhibitor reversed circVAPA depletion-induced GC cell apoptosis. Functionally, circVAPA contributed to the tumor growth of SGC7901/DDP cells .

Conclusion: CircVAPA promotes chemotherapy resistance and malignant progression in GC by miR-125b-5p/STAT3 signaling. Our findings present novel insights into the mechanism by which circVAPA regulates chemotherapy resistance of GC cells. CircVAPA and miR-125b-5p may be considered as the potential targets for GC therapy.
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http://dx.doi.org/10.3748/wjg.v27.i6.487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7896438PMC
February 2021

Characterization of follicular T helper cells and donor-specific T helper cells in renal transplant patients with de novo donor-specific HLA-antibodies.

Clin Immunol 2021 05 24;226:108698. Epub 2021 Feb 24.

Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany. Electronic address:

T follicular helper (T) cells are a heterogeneous subset of immunocompetent T helper (T) cells capable of augmenting B cell responses in lymphoid tissues. In transplantation, exposure to allogeneic tissue activates T cells increasing the risk of the emergence of de novo donor-specific HLA-antibodies (dnDSA). These can cause antibody-mediated rejection (AMR) and allograft loss. Follicular regulatory T (T) cells counteract T cell activity. Here, we investigated the implications of T and T cells on dnDSA formation after renal transplantation (RTX). Considering T cells to be CXCR5 and IL-21, we found by flow cytometry that patients with dnDSA produced IL-21 more abundantly compared to healthy volunteers. In in vitro alloreactivity assays, patients with dnDSA featured an enhanced alloreactive T cell pool in response to donor-specific HLA antigens. Besides, longitudinal investigations suggested enhanced alloreactivity shortly after transplantation increasing the risk of dnDSA development. Taken together, in spite of continuous immunosuppression we report a strong IL-21 response in T cells and an expanded reservoir of donor-specific memory T cells in patients with dnDSA. This warrants further investigations if aberrant T cell activation may precede the formation of dnDSA promoting AMR.
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http://dx.doi.org/10.1016/j.clim.2021.108698DOI Listing
May 2021

Perioperative treatment compliance, anxiety and depression of elderly patients with ophthalmic surgery and the influential factors.

Ann Palliat Med 2021 Feb 22;10(2):2115-2122. Epub 2021 Feb 22.

Department of Operation, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, China.

Background: Ophthalmic surgery is invasive, and treatment efficacy is affected by a variety of factors. We aimed to analyze perioperative treatment compliance, anxiety and depression of elderly patients undergoing ophthalmic surgery and the influential factors.

Methods: The study group comprised 119 elderly patients undergoing ophthalmic surgery between March 2018 and March 2020. Clinical and treatment compliance data of all patients were collected. The self-rating anxiety scale (SAS) and self-rating depression scale (SDS) were administered to all patients, and logistic regression analysis was used for multivariate analysis.

Results: During the perioperative period the 119 elderly patients had a mean SAS score of 65.13±14.36, and SDS score of 61.94±17.39. Treatment compliance was as follows: 76 cases of complete compliance, 25 of incomplete compliance, and 18 of complete non-compliance. Economic status, complications, treatment options and levels of TNF-α, IL-6, and IL-8 are independent risk factors that affected the compliance of elderly patients undergoing ophthalmology surgery (P<0.05). Education level, marital status, economic status, complications, treatment options and levels of TNF-α, IL-6, and IL-8 were independent risk factors affecting perioperative anxiety and depression.

Conclusions: There are many factors affecting the perioperative treatment compliance, anxiety and depression of elderly patients undergoing ophthalmic surgery. Effective intervention measures should be taken to improve patients' compliance, reduce their negative emotions, and improve the surgical efficacy.
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http://dx.doi.org/10.21037/apm-21-37DOI Listing
February 2021

Two Cyc2CL transcripts (Cyc2CL-1 and Cyc2CL-2) may play key roles in the petal and stamen development of ray florets in chrysanthemum.

BMC Plant Biol 2021 Feb 19;21(1):105. Epub 2021 Feb 19.

Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.

Background: Chrysanthemum morifolium is one of the most popular ornamental crops. The capitulum, which is the main ornamental part of chrysanthemum plants, consists of ligulate marginal ray florets, an attractive corolla (petals), and radially hermaphroditic disc florets, but no stamens. In Asteraceae species, the zygomorphic ray florets evolved from the actinomorphic disc florets. During this process, the zygomorphic ligulate corolla arose and the stamens were aborted. Although molecular genetic research has clarified ray floret development to some extent, the precise molecular mechanism underlying ray floret development in chrysanthemum remained unclear.

Results: A CYC2-like gene, Cyc2CL, was cloned from C. morifolium 'Fenditan'. Subsequent analyses revealed that the alternative splicing of Cyc2CL, which occurred in the flower differentiation stage, resulted in the production of Cyc2CL-1 and Cyc2CL-2 in the apical buds. Prior to this stage, only Cyc2CL-1 was produced in the apical buds. A fluorescence in situ hybridization analysis of labeled Cyc2CL-1 and Cyc2CL-2 RNA indicated that Cyc2CL-2 was first expressed in the involucre tissue during the final involucre differentiation stage, but was subsequently expressed in the receptacle and floret primordia as the floral bud differentiation stage progressed. Moreover, Cyc2CL-2 was highly expressed in the inflorescence tissue during the corolla formation stage, and the expression remained high until the end of the floral bud differentiation stage. Furthermore, the overexpression of Cyc2CL-1 and Cyc2CL-2 in transgenic Arabidopsis inhibited stamen and petal development. Therefore, both Cyc2CL-1 and Cyc2CL-2 encode candidate regulators of petal development and stamen abortion and are important for the ray floret development in chrysanthemum.

Conclusion: In this study, we characterized the alternatively spliced transcripts of the CYC2-like gene that differ subtly regarding expression and function. The data presented herein will be useful for clarifying the regulatory mechanisms associated with the CYC2-like gene and may also be important for identifying the key genes and molecular mechanisms controlling the development of ray florets in chrysanthemum.
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http://dx.doi.org/10.1186/s12870-021-02884-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893774PMC
February 2021

Integrating genome-wide CRISPR immune screen with multi-omic clinical data reveals distinct classes of tumor intrinsic immune regulators.

J Immunother Cancer 2021 Feb;9(2)

Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA

Background: Despite approval of immunotherapy for a wide range of cancers, the majority of patients fail to respond to immunotherapy or relapse following initial response. These failures may be attributed to immunosuppressive mechanisms co-opted by tumor cells. However, it is challenging to use conventional methods to systematically evaluate the potential of tumor intrinsic factors to act as immune regulators in patients with cancer.

Methods: To identify immunosuppressive mechanisms in non-responders to cancer immunotherapy in an unbiased manner, we performed genome-wide CRISPR immune screens and integrated our results with multi-omics clinical data to evaluate the role of tumor intrinsic factors in regulating two rate-limiting steps of cancer immunotherapy, namely, T cell tumor infiltration and T cell-mediated tumor killing.

Results: Our studies revealed two distinct types of immune resistance regulators and demonstrated their potential as therapeutic targets to improve the efficacy of immunotherapy. Among them, PRMT1 and RIPK1 were identified as a dual immune resistance regulator and a cytotoxicity resistance regulator, respectively. Although the magnitude varied between different types of immunotherapy, genetically targeting and sensitized tumors to T-cell killing and anti-PD-1/OX40 treatment. Interestingly, a RIPK1-specific inhibitor enhanced the antitumor activity of T cell-based and anti-OX40 therapy, despite limited impact on T cell tumor infiltration.

Conclusions: Collectively, the data provide a rich resource of novel targets for rational immuno-oncology combinations.
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http://dx.doi.org/10.1136/jitc-2020-001819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7887353PMC
February 2021

Catalytic Conversion of a ≥ 200 °C Fraction Separated from Low-Temperature Coal Tar into Light Aromatic Hydrocarbons.

ACS Omega 2021 Feb 1;6(5):4062-4073. Epub 2021 Feb 1.

School of Chemical Engineering, International Science & Technology Cooperation Base of MOST for Clean Utilization of Hydrocarbon Resources, Chemical Engineering Research Center of the Ministry of Education for Advanced Use Technology of Shanbei Energy, Shaanxi Research Center of Engineering Technology for Clean Coal Conversion, Northwest University, Taibai North Road 229, 710069 Xi'an, Shaanxi, China.

A ≥ 200 °C fraction (CT200F) of low-temperature coal tar was prepared by a rotary film evaporator. The catalytic conversion experiments of CT200F and six model compounds were conducted on the pyrolysis gas chromatography-mass spectrometer. The yields of catalytic conversion products benzene, toluene, xylene, and naphthalene (BTXN) were analyzed by semi-quantitative analysis according to the chromatographic peak areas. Additionally, the possible formation pathways and mechanisms of the target products BTXN generated over different catalysts were investigated. The results show that the yield of aromatic hydrocarbons increases and the yield of acid compounds decreases during CT200F pyrolysis over ZSM-5, HY, USY, and β-zeolite compared with that of its non-catalytic pyrolysis, especially the yields of BTXN obtained over USY and β-zeolite increase by 128 and 108%, respectively. The pore structure of ZSM-5 is suitable to produce BTX, while the suitable acidity and pore structure of USY, HY, and β-zeolite are more beneficial for the selective preparation of naphthalene than that of ZSM-5. The conversion pathways of six model compounds into BTXN over zeolites were obtained, and the following conclusions can be drawn: The dehydroxylation effect of zeolites shows the order of ZSM-5 > HY > USY > β-zeolite. The catalytic effect of zeolites on the cracking and ring opening of PAHs in CT200F shows the order of β-zeolite > USY > HY > ZSM-5. The catalytic effect of catalysts on the cracking and aromatization of aliphatic compounds shows the order of ZSM-5 > β-zeolite > USY > HY. β-zeolite has an outstanding catalytic performance in the conversion of PAHs into naphthalene. ZSM-5 and HY can effectively remove phenolic hydroxyl groups in phenol and naphthol. During the catalytic conversion processes of the coal tar fraction and model compounds, the catalytic effect of the pore constructions of zeolites is more important than their acidities, which determines whether large molecules can enter and whether acid sites in non-micropores can be effectively utilized.
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http://dx.doi.org/10.1021/acsomega.0c06123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7876866PMC
February 2021

Oceanomicrobium pacificus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from seawater of tropical western Pacific.

Antonie Van Leeuwenhoek 2021 Mar 6;114(3):303-311. Epub 2021 Feb 6.

Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.

The Gram-stain-negative, aerobic, ovoid or rod-shaped bacterial strain, designated KN286, was isolated from seawater of tropical western Pacific. Growth occurred between 15 and 40 °C (optimally at 30-35 °C), pH 6-9 (optimally at 7.0) and in the presence of 0.5-5.0% (w/v) NaCl (optimally between 2.0 and 3.0%). Strain KN286 contained Q-10 as the major respiratory quinone. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, three phospholipids, three glycolipids, and three unidentified polar lipids. The predominant cellular fatty acid was summed feature 8 (composed of Cω7c and/or Cω6c). Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain KN286 was a member of the family Rhodobacteraceae and formed a distinct lineage. Strain KN286 has a genome size of 3.25 Mbp and a G + C content of 65.0 mol%. It encoded with some genes for carbohydrate-active enzymes, such as GH20 (Glycoside Hydrolase Family 20) and PL1 (Polysaccharide Lyase Family 1) and did not encode with a set of genes for reduction of nitrate to nitrite (nitrate reductase gamma subunit, respiratory nitrate reductase alpha N-terminal and respiratory nitrate reductase beta C-terminal). Based on phylogenetic analyses with single-copy orthologous clusters, low isDDH value (19.6%), low ANI (72.4%) and low AAI (65.7%) results, differential chemotaxonomic and physiological properties, strain KN286 represents a novel species of a novel genus of the family Rhodobacteraceae, for which the name Oceanomicrobium pacificus gen. nov., sp. nov. is proposed. The type strain of Oceanomicrobium pacificus is KN286 (=CGMCC 1.17118 = KCTC 72430).
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http://dx.doi.org/10.1007/s10482-021-01523-9DOI Listing
March 2021
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