Publications by authors named "Xin Yan"

794 Publications

Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.

Theor Appl Genet 2021 Jun 12. Epub 2021 Jun 12.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Key Message: Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.
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http://dx.doi.org/10.1007/s00122-021-03885-0DOI Listing
June 2021

A poplar B-box protein PtrBBX23 modulates the accumulation of anthocyanins and proanthocyanidins in response to high light.

Plant Cell Environ 2021 Jun 10. Epub 2021 Jun 10.

Laboratory of Forest Symbiology, Asian Natural Environmental Science Center, The University of Tokyo, 1-1-8 Midori-cho, Nishitokyo, Tokyo, Japan.

Flavonoids, which modulate plant resistance to various stresses, can be induced by high light. B-box (BBX) transcription factors (TFs) play crucial roles in the transcriptional regulation of flavonoids biosynthesis, but limited information is available on the association of BBX proteins with high light. We present a detailed overview of 45 Populus trichocarpa BBX TFs. Phylogenetic relationships, gene structure, tissue-specific expression patterns, and expression profiles were determined under 10 stress or phytohormone treatments to screen candidate BBX proteins associated with the flavonoid pathway. Sixteen candidate genes were identified, of which five were expressed predominantly in young leaves and roots, and BBX23 showed the most distinct response to high light. Overexpression of BBX23 in poplar activated expression of MYB TFs and structural genes in the flavonoid pathway, thereby promoting accumulation of proanthocyanidins and anthocyanins. CRISPR/Cas9-generated knockout of BBX23 resulted in the opposite trend. Furthermore, the phenotype induced by BBX23 overexpression was enhanced under exposure to high light. BBX23 was capable of binding directly to the promoters of proanthocyanidin- and anthocyanin-specific genes, and its interaction with HY5 enhanced activation activity. We identified novel regulators of flavonoid biosynthesis in poplar, thereby enhancing our general understanding of the transcriptional regulatory mechanisms involved. This article is protected by copyright. All rights reserved.
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http://dx.doi.org/10.1111/pce.14127DOI Listing
June 2021

Association between NF-kB polymorphism and age-related macular degeneration in a high-altitude population.

PLoS One 2021 8;16(6):e0251931. Epub 2021 Jun 8.

Department of Ophthalmology, Qinghai Provincial People's Hospital, Xining, Qinghai Province, China.

Objective: To investigate the association between the nuclear factor kappa B (NF-kB) gene polymorphism and age-related macular degeneration (AMD) in a high-altitude population.

Methods: Fifty-five patients with AMD and 57 control subjects were recruited from the Qinghai Provincial People's Hospital, China. Genomic DNA was extracted from the blood sample of each participant. Four NF-kB polymorphisms (rs3774959, rs3774932, rs3774937, and rs230526) were genotyped using a MassARRAY system. The genotype and allele frequencies were compared between the case and control groups using the chi-squared test or Fisher's exact test.

Results: There was no significant difference in sex, age, hypertension, diabetes, blood lipid level or smoking and drinking status between the AMD and control groups (P > 0.05). The genotype distributions of four NF-kB polymorphisms were in accordance with Hardy-Weinberg equilibrium in the control group (P > 0.05). The frequencies of genotype AA of rs3774932 and genotype CC of rs3774937 were nominally significantly higher in the AMD group than in the control group (P = 0.046 and 0.023, respectively), although these associations did not survive the Bonferroni correction (corrected P > 0.05). Genotype distributions of rs3774959 and rs230526 were not significantly different between the two groups (P = 0.08 and 0.16, respectively). No significant difference in the allele frequencies of the four polymorphisms was found between the AMD and control groups (P > 0.05).

Conclusions: Genotype AA of rs3774932 and genotype CC of rs3774937 in NF-kB might be risk factors for AMD.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0251931PLOS
June 2021

A metabolically engineered spin-labeling approach for studying glycans on cells.

Chem Sci 2020 Oct 20;11(46):12522-12532. Epub 2020 Oct 20.

Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA

Metabolic glycan engineering (MGE) coupled with nitroxide spin-labeling (SL) was utilized to investigate the heterogeneous environment of cell surface glycans in select cancer and normal cells. This approach exploited the incorporation of azides into cell surface glycans followed by a click reaction with a new nitroxide spin label. Both sialic acid and -acetylglucosamine (GlcNAc) were targeted for spin labelling. Although each of these moieties experiences a diverse and heterogeneous glycan environment, their EPR spectra and hence mobility are both characterized as a linear combination of two distinct spectra where one component reflects a highly mobile or uncrowded micro-environment with the second component reflecting more restricted motion, reflective of increased crowding and packing within the glycocalyx. What differs among the spectra of the targeted glycans is the relative percentage of each component, with sialic acid moieties experiencing on average an ∼80% less crowded environment, where conversely GlcNAc/GalNAz labeled sites reported on average a ∼50% more crowded environment. These distinct environments are consistent with the organization of sugar moieties within cellular glycans where some residues occur close to the cell membrane/protein backbone ( more restricted) and others are more terminal in the glycan ( more mobile). Strikingly, different cell lines displayed varied relative populations of these two components, suggesting distinctive glycan packing, organization, and composition of different cells. This work demonstrates the capability of SDSL EPR to be a broadly useful tool for studying glycans on cells, and interpretation of the results provides insights for distinguishing the differences and changes in the local organization and heterogeneity of the cellular glycocalyx.
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http://dx.doi.org/10.1039/d0sc03874aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8162880PMC
October 2020

A Highly Sensitive Refractive Index Sensor Based on a V-Shaped Photonic Crystal Fiber with a High Refractive Index Range.

Sensors (Basel) 2021 May 29;21(11). Epub 2021 May 29.

State Key Laboratory of Synthetical Automation for Process Industries, College of Information Science and Engineering, Northeastern University, Shenyang 110819, China.

This paper proposes a highly sensitive surface plasmon resonance (SPR) refractive index sensor based on the photonic crystal fiber (PCF). The optical properties of the PCF are investigated by modulating the refractive index of a liquid analyte. The finite element method (FEM) is used to calculate and analyze the PCF structure. After optimization, the fiber can achieve high linearity of 0.9931 and an average refractive index sensitivity of up to 14,771.4 nm/RIU over a refractive index range from 1.47 to 1.52, with the maximum wavelength sensitivity of 18,000.5 nm/RIU. The proposed structure can be used in various sensing applications, including biological monitoring, environmental monitoring, and chemical production with the modification and analysis of the proposed structure.
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http://dx.doi.org/10.3390/s21113782DOI Listing
May 2021

Switchable and Dual-Tunable Multilayered Terahertz Absorber Based on Patterned Graphene and Vanadium Dioxide.

Micromachines (Basel) 2021 May 27;12(6). Epub 2021 May 27.

State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing 100876, China.

In this paper, a switchable and dual-tunable terahertz absorber based on patterned graphene and vanadium dioxide is proposed and analyzed. By controlling the Fermi level of graphene and the temperature of vanadium dioxide, the device's function can be switched and its absorbing properties can be tuned. When the vanadium dioxide is in an insulator state, the device can be switched from near-total reflection (>97%) to ultra-broadband absorption (4.5-10.61 THz) as the Fermi level of graphene changes from 0 to 0.8 eV. When the vanadium dioxide is changed to a metal state, the device can act as a single-band absorber (when the Fermi level of graphene is 0 eV) and a dual-band absorber with peaks of 4.16 THz and 7.3 THz (when the Fermi level of graphene is 0.8 eV). Additionally, the absorber is polarization-insensitive and can maintain a stable high-absorption performance within a 55° incidence angle. The multilayered structure shows great potential for switchable and tunable high-performance terahertz devices.
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http://dx.doi.org/10.3390/mi12060619DOI Listing
May 2021

Structure, Biological Activities and Metabolism of Flavonoid Glucuronides.

Mini Rev Med Chem 2021 May 21. Epub 2021 May 21.

Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia 750004, China.

Background: Flavonoid glucuronides are a kind of natural products which present a flavone linked directly with one or several glucuronides through O-glycoside bond. They had become of interest in natural product research in the past decades for their antioxidant, anti-inflammatory, and anti-bacteria activities. In particular, the compound breviscapine has a notable effect on cardio-cerebrovascular diseases. Several other compounds even have antitumor activity.

Methods: Through searching the database and reading a large number of documents, we summarized the related findings of flavonoid glucuronides.

Results: We summarized 211 naturally occurring flavonoid glucuronides in 119 references with their chemical structures, biological activities, and metabolism. A total of 220 references from 1953 to 2020 were cited in this paper according to literature databases such as CNKI, Weipu, Wanfang data, Elsevier, Springer, Wiley, NCBI, PubMed, EmBase, etc..

Conclusion: Flavonoid glucuronides are a class of compounds with various chemical structures and a diverse range of biological activities. And they are thought to be potential candidates for drug discovery, but the specific study on their mechanisms is still limited until now. We hope this article can provide references for natural product researchers and draw more attention to flavonoid glucuronides' biological activities and mechanisms.
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http://dx.doi.org/10.2174/1389557521666210521221352DOI Listing
May 2021

AaMYB15, an R2R3-MYB TF in Artemisia annua, acts as a negative regulator of artemisinin biosynthesis.

Plant Sci 2021 Jul 24;308:110920. Epub 2021 Apr 24.

Joint International Research Laboratory of Metabolic and Developmental Sciences, Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. Electronic address:

Artemisinin is a secondary metabolite extracted from Artemisia annua. As an effective antimalarial component certified by WHO, artemisinin has extensive economical values. Numerous studies about transcription factors positively regulating artemisinin biosynthesis have been published while negative regulators are rarely reported. In the present study, we identified AaMYB15 as the first R2R3-MYB that negatively regulates artemisinin biosynthesis in A. annua. Experimental evidences showed that AaMYB15 is a transcription factor within nucleus and predominantly expressed in glandular secretory trichomes (GSTs) in A. annua where artemisinin is synthesized and accumulated. The expression of AaMYB15 was induced by dark and JA treatment. Overexpression of AaMYB15 led to a significant decline in the expression levels of key enzyme genes ADS, CYP, DBR2, and ALDH1 and a significant decrease in the artemisinin contents of transgenic A. annua. AaMYB15 directly bound to the promoter of AaORA, a reported positive regulator of artemisinin biosynthesis in JA signaling pathway, to repress its transcriptional activity, thus downregulating the expression levels of downstream key enzyme genes and negatively regulating the artemisinin biosynthesis. Our study provides candidate gene for improvement of A. annua germplasm and new insights into the artemisinin biosynthesis regulation network mediated by light and JA.
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http://dx.doi.org/10.1016/j.plantsci.2021.110920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8174473PMC
July 2021

Microstructured optical fiber temperature sensor based on the self-phase modulation effect.

Opt Express 2021 May;29(10):15653-15663

In this paper, we proposed a highly sensitive temperature sensor based on self-phase modulation (SPM) in an in-house fabricated microstructured optical fiber (MOF) which had three rings of air holes. The temperature sensing performance was evaluated by detecting the 3 dB bandwidth of SPM spectrum with the variation of temperature at different pump wavelengths and average pump power. At the pump wavelength of 1400 nm with the average pump power of 600 mW, the temperature sensitivity was obtained to be as high as 1.296 nm/°C. Moreover, the theoretical simulation was carried out, the results of which corresponded well with the experiment. To the best of our knowledge, this is the first experimental study concerning SPM-based temperature sensing. This work proves experimentally and theoretically a new temperature sensing mechanism drawing on the SPM effect in optical fibers, which is expected to develop temperature sensors of low cost, simple structure and high sensitivity.
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http://dx.doi.org/10.1364/OE.425863DOI Listing
May 2021

No-core optical fiber sensor based on surface plasmon resonance for glucose solution concentration and temperature measurement.

Opt Express 2021 Apr;29(9):12930-12940

The accuracy of the surface plasmon resonance (SPR) optical fiber sensor is affected by the change of ambient temperature. Therefore, we propose a simple dual channel SPR optical fiber sensor, which can measure both glucose concentration and ambient temperature. The proposed sensor is a two-channel structure based on a no-core optical fiber (NCF): one channel is coated with gold film and polydimethylsiloxane (PDMS) to sense the ambient temperature, and the other is coated with silver film to sense glucose concentration. The experimental results show that the sensor's sensitivity for sensing glucose concentration is 2.882 nm / %, and for sensing temperature is -2.904 nm / °C. By monitoring the real-time temperature, the accuracy of glucose concentration detection was improved. The proposed sensor has a simple and compact structure, and it is suitable for sensing glucose solution or other analyte solutions that need temperature compensation.
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http://dx.doi.org/10.1364/OE.423307DOI Listing
April 2021

In Situ Oil Separation and Collection from Water under Surface Wave Condition.

Langmuir 2021 May 12;37(20):6257-6267. Epub 2021 May 12.

Beijing Key Laboratory of Multiphase Flow and Heat Transfer for Low Grade Energy Utilization, North China Electric Power University, Beijing 102206, China.

Removal of oil from water is strongly desired due to environmental pollution, and related studies are mainly limited to the material itself. Here, we propose an oil-water separation device, called a floating well, which includes a container for oil collection and a modified mesh screen for oil separation. The mesh screen is superhydrophilic to oil and superhydrophobic to water. The oil removal experiment was performed in a basin. Under the calm surface condition, the oil collection efficiency is shown to be 42-69%. The inadequate oil collection is explained by the breakdown of a thin oil film above water to form an oil-free area, preventing direct contact between the separator and the oil. Sustained by a wave generator, we are surprised to find that with a low-frequency surface wave, the oil collection efficiency is increased to 98%, and the collection speed reaches 2.5 times that under the calm surface condition. The almost complete collection is due to the sustained contact between the separator and the oil, under which the surface wave continuously drives the oil film toward the separator from elsewhere, thus the oil-free area cannot be formed. Our work presents a new clue for large-scale in situ applications, in which the nature wave energy of river/sea can be the driving force for continuous oil separation and collection.
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http://dx.doi.org/10.1021/acs.langmuir.1c00585DOI Listing
May 2021

Platinum(II) Metallatriangle: Construction, Coassembly with Polypeptide, and Application in Combined Cancer Photodynamic and Chemotherapy.

Inorg Chem 2021 Jun 11;60(11):7627-7631. Epub 2021 May 11.

School of Chemistry and Chemical Engineering, Nantong University, Nantong, Jiangsu 226019, P.R. China.

The development of the supramolecular coordination complex with different shapes and dimensionalities lays the basis for its application in different areas. In this study, a porphyrin-based 3D organo-Pt(II) metallatriangle () was fabricated through the reported method termed as "coordination driven self-assembly". P NMR, H NMR, HR-MS, and theoretical calculation were employed to characterize the resultant fully. Furthermore, the fabricated nanocomposite through coassembly of and an amphiphilic polypeptide () could generate singlet oxygen (O) under the NIR irradiation and release a Pt drug under a low-pH microenvironment. O and the Pt drug can both damage the cancer cells, which improves the efficiency of cancer therapies. The fabrication of a Pt-porphyrin metallatriangle expands the topological structures, and the Pt-porphyrin metallatriangle can be applied to the combined cancer therapies. Moreover, various stimuli-responsive groups can be modified to the triangle, so a new method is created to develop high-performance biosupramolecular materials.
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http://dx.doi.org/10.1021/acs.inorgchem.1c00962DOI Listing
June 2021

ERK/Drp1-dependent mitochondrial fission contributes to HMGB1-induced autophagy in pulmonary arterial hypertension.

Cell Prolif 2021 Jun 4;54(6):e13048. Epub 2021 May 4.

Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.

Objectives: High-mobility group box-1 (HMGB1) and aberrant mitochondrial fission mediated by excessive activation of GTPase dynamin-related protein 1 (Drp1) have been found to be elevated in patients with pulmonary arterial hypertension (PAH) and critically implicated in PAH pathogenesis. However, it remains unknown whether Drp1-mediated mitochondrial fission and which downstream targets of mitochondrial fission mediate HMGB1-induced pulmonary arterial smooth muscle cells (PASMCs) proliferation and migration leading to vascular remodelling in PAH. This study aims to address these issues.

Methods: Primary cultured PASMCs were obtained from male Sprague-Dawley (SD) rats. We detected RNA levels by qRT-PCR, protein levels by Western blotting, cell proliferation by Cell Counting Kit-8 (CCK-8) and EdU incorporation assays, migration by wound healing and transwell assays. SD rats were injected with monocrotaline (MCT) to establish PAH. Hemodynamic parameters were measured by closed-chest right heart catheterization.

Results: HMGB1 increased Drp1 phosphorylation and Drp1-dependent mitochondrial fragmentation through extracellular signal-regulated kinases 1/2 (ERK1/2) signalling activation, and subsequently triggered autophagy activation, which further led to bone morphogenetic protein receptor 2 (BMPR2) lysosomal degradation and inhibitor of DNA binding 1 (Id1) downregulation, and eventually promoted PASMCs proliferation/migration. Inhibition of ERK1/2 cascade, knockdown of Drp1 or suppression of autophagy restored HMGB1-induced reductions of BMPR2 and Id1, and diminished HMGB1-induced PASMCs proliferation/migration. In addition, pharmacological inhibition of HMGB1 by glycyrrhizin, suppression of mitochondrial fission by Mdivi-1 or blockage of autophagy by chloroquine prevented PAH development in MCT-induced rats PAH model.

Conclusions: HMGB1 promotes PASMCs proliferation/migration and pulmonary vascular remodelling by activating ERK1/2/Drp1/Autophagy/BMPR2/Id1 axis, suggesting that this cascade might be a potential novel target for management of PAH.
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http://dx.doi.org/10.1111/cpr.13048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168414PMC
June 2021

Recent advances on 2'-fucosyllactose: physiological properties, applications, and production approaches.

Crit Rev Food Sci Nutr 2020 Dec 1:1-10. Epub 2020 Dec 1.

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.

The trisaccharide, 2'-fucosyllactose (Fucα1-2Galβ1-4Glc; 2'-FL), is the most abundant oligosaccharide in human milk. It has numerous significant biological properties including prebiotics, antibacterial, antiviral, and immunomodulating effects, and has been approved as "generally recognized as safe" (GRAS) by the Food and Drug Administration (FDA) and as a novel food (NF) by the European Food Safety Authority (EFSA). 2'-FL not only serves as a food ingredient added in infant formula, but also as a dietary supplement and medical food material in food bioprocesses. There is considerable commercial interest in 2'-FL for its irreplaceable nutritional applications. This review aims at systematically elaborating key functional properties of 2'-FL as well as its applications. In addition, several approaches for 2'-FL production are described in this review, including chemical, chemo-enzymatical, and cell factory approaches, and the pivotal research results also have been summarized. With the rapid development of metabolic engineering and synthetic biology strategies, using the engineered cell factory for 2'-FL large-scale production might be a promising approach. From an economic and safety point of view, microbial selection for cell factory engineering in 2'-FL bioprocess also should be taken into consideration.
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http://dx.doi.org/10.1080/10408398.2020.1850413DOI Listing
December 2020

MicroRNA-210-3p Promotes Chondrogenic Differentiation and Inhibits Adipogenic Differentiation Correlated with HIF-3 Signalling in Bone Marrow Mesenchymal Stem Cells.

Biomed Res Int 2021 10;2021:6699910. Epub 2021 Apr 10.

Sports Medicine Department, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Beijing, China.

Cartilage injury of the knee joint is very common. Due to the limited self-healing ability of articular cartilage, osteoarthritis is very likely to occur if left untreated. Bone marrow mesenchymal stem cells (BMMSCs) are widely used in the study of cartilage injury due to their low immunity and good amplification ability, but they still have disadvantages, such as heterogeneous undifferentiated cells. MicroRNAs can regulate the chondrogenic differentiation ability of MSCs by inhibiting or promoting mRNA translation and degradation. In this research, we primarily investigated the effect of microRNA-210-3p (miR-210-3p) on chondrogenic and adipogenic differentiation of BMMSCs in vitro. Our results demonstrate that miR-210-3p promoted chondrogenic differentiation and inhibited adipogenic differentiation of rat BMMSCs, which was related to the HIF-3 signalling pathway. Additionally, miR-210-3p promotes mRNA and protein levels of the chondrogenic expression genes COLII and SOX9 and inhibits mRNA and protein levels of the adipogenic expression genes PPAR and LPL. Thus, miR-210-3p combined with BMMSCs is a candidate for future clinical applications in cartilage regeneration and could represent a promising new therapeutic target for OA.
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http://dx.doi.org/10.1155/2021/6699910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8055413PMC
May 2021

UNC13D mutation in a patient with juvenile polymyositis with recurrent macrophage activation syndrome.

Rheumatology (Oxford) 2021 Apr 30. Epub 2021 Apr 30.

Division of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.

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http://dx.doi.org/10.1093/rheumatology/keab391DOI Listing
April 2021

Inorganic-Ligand Quantum Dots Meet Inorganic-Ligand Semiconductor Nanoplatelets: A Promising Fusion to Construct All-Inorganic Assembly.

Inorg Chem 2021 May 30;60(10):6994-6998. Epub 2021 Apr 30.

School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.

By the reaction of inorganic-ligand CdS/Cd quantum dots (QDs) with inorganic-ligand CdSe/CdS/S nanoplatelets (NPLs), semiconductor CdS QDs were fused with CdSe/CdS NPLs to yield all-inorganic assemblies, accompanied by great photoluminescence-enhancement. These all-inorganic assemblies facilitate charge transport between each other and open up interesting prospects with electronic and optoelectronic nanodevices.
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http://dx.doi.org/10.1021/acs.inorgchem.1c00880DOI Listing
May 2021

Photonic Crystal Fiber SPR Liquid Sensor Based on Elliptical Detective Channel.

Micromachines (Basel) 2021 Apr 7;12(4). Epub 2021 Apr 7.

State Key Laboratory of Synthetical Automation for Process Industries, College of Information Science and Engineering, Northeastern University, Shenyang 110819, China.

This paper proposes a Photonic Crystal Fiber (PCF) refractive index sensor model based on the surface plasmon resonance effect. The proposed PCF model also uses the full vector finite element method to transfer the structure under the anisotropic Perfect Matching Layer (PML) boundary condition. Numerical calculations were carried out on the sensor characteristics. The calculation results show that the elliptical air hole on the left side of the PCF core is coated with a gold-nano film which serves as a Surface Plasmon Resonance (SPR) sensing channel to detect the refractive index of liquid materials. Compared with other structures, the resonant peak generated by the excited SPR effect from the elliptical sensing channel has a high sensitivity to the change of the refractive index of the liquid to be measured. With the help of this attribute, it is relatively easy to adjust the sensitivity. The refractive index range of this structure is within 1.43-1.49 and the sensitivity is up to 12,719.97 nm·RIU. The linearity is good; = 0.99927, which is very suitable for liquid sensing.
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http://dx.doi.org/10.3390/mi12040408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067755PMC
April 2021

LncRNA MAFG-AS1 Suppresses the Maturation of miR-34a to Promote Glioblastoma Cell Proliferation.

Cancer Manag Res 2021 22;13:3493-3501. Epub 2021 Apr 22.

Department of Neurosurgery, Zibo Central Hospital, Zibo City, Shandong Province, 255036, People's Republic of China.

Purpose: LncRNA MAFG-AS1 plays critical roles in several types of cancer, while its role in glioblastoma (GBM) is unknown. By analyzing the TCGA dataset, we observed the upregulation of MAFG-AS1 in GBM. This study aimed to investigate the involvement of MAFG-AS1 in GBM cancer.

Methods: The expression levels of MAFG-AS1, mature miR-34a, and miR-34a precursor in GBM and paired non-tumor tissues of 56 GBM patients were determined by RT-qPCR. Correlations are analyzed using linear regression. Overexpression of MAFG-AS1 was achieved in GBM cells, followed by measurement of the expression levels of mature miR-34a, miR-34a precursor, DICER and Drosha by RT-qPCR. The roles of MAFG-AS1 and miR-34a in regulating GBM cell proliferation were evaluated by CCK-8 assay. Flow cytometry was performed to explore the role of MAFG-AS1 and miR-34a in regulating the apoptosis and cell cycle of GBM cells. Cell scratch experiment was performed to determine the role of MAFG-AS1 and miR-34a in regulating the migration of GBM cells. Subcutaneous tumor animal model was used for in vivo study. The expressions levels of BCL-2 and caspase-3 were detected by Western blot analysis.

Results: MAFG-AS1 was upregulated in GBM, while mature miR-34a was downregulated in GBM. Interestingly, MAFG-AS1 was inversely correlated with mature miR-34a but not miR-34a precursor across GBM tissues. In GBM tissues, the overexpression of MAFG-AS1 did not affect the expression levels of miR-34a precursor but reduced the expression levels of mature miR-34a. MAFG-AS1 promoted the expression of DICER and Drosha in GBM cells. Moreover, the overexpression of MAFG-AS1 promoted the proliferation of GBM cells and reduced the inhibitory effects of miR-34a on cell proliferation but did not affect cell cycle, apoptosis and migration. The overexpression of MAFG-AS1 promoted the progression of GBM in vivo by promoting the proliferation of GBM cells while miR-34a reversed the effect of overexpression of MAFG-AS1.

Conclusions: MAFG-AS1 may suppress the maturation of miR-34a to promote GBM cell proliferation.
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http://dx.doi.org/10.2147/CMAR.S274615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8075183PMC
April 2021

Accelerated five-component spiro-pyrrolidine construction at the air-liquid interface.

Chem Commun (Camb) 2021 Apr 19;57(31):3757-3760. Epub 2021 Mar 19.

Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.

Multi-component reactions assemble complex molecules in a highly effective way, however, they often suffer from long reaction times. We demonstrate that acceleration of a five-component spiro-pyrrolidine construction can be achieved in microdroplets and thin films. The deposition method and mild heating are crucial factors for product formation. Three key intermediates were captured by mass spectrometry to elucidate the tandem reaction mechanism. We also found that hydrogen bonding can significantly flatten the energy barrier at the air-liquid interface.
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http://dx.doi.org/10.1039/d1cc00574jDOI Listing
April 2021

TMPyP-bound guanosine-borate supramolecular hydrogel as smart hemoperfusion device with real-time visualized/electrochemical bi-modal monitoring for selective blood lead elimination.

Biosens Bioelectron 2021 Jul 7;184:113230. Epub 2021 Apr 7.

Guangdong Provincial Engineering and Technological Research Center for Drug Carrier Development, Department of Biomedical Engineering, Jinan University, Guangzhou 510632, China. Electronic address:

Blood lead poisoning is a universal and severe health problem that greatly threatens human health in various industries. Elimination of blood lead relying on chelating agents and combination with hemoperfusion adsorbents has achieved considerable progress, but it is still suffering from the compromised selectivity of adsorbents as well as in absence of real time monitoring during treatment. Herein, we proposed a selective blood lead adsorbent integrated with real-time visualized/electrochemical bi-modal monitoring based on TMPyP-bound guanosine-borate (GB) supramolecular hydrogel as potential smart hemoperfusion device. The GB hydrogel possessed stability in physiological environment, self-healing ability resistant to fluid shear, blood compatibility, selective adsorption of lead ions superior to conventional adsorbents, anti-fouling performance to blood components and renewability. Benefiting from binding with TMPyP and the intrinsic conductivity, GB hydrogel was endowed with the ability to qualitatively diagnose the presence of blood lead via simple color change and quantitatively reflect the amount of adsorbed lead from blood accurately through electrochemical technique. This work puts forward an integrated treatment/monitoring hemoperfusion device with high selectivity, simple fabrication and low-cost, providing a paradigm for next generation design of intelligent, monitorable theranostic hemopurification system, which is also an extensible platform for the other research fields such as environmental monitoring and remediation.
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http://dx.doi.org/10.1016/j.bios.2021.113230DOI Listing
July 2021

Transcriptomic analysis reveals the parallel transcriptional regulation of UV-B-induced artemisinin and flavonoid accumulation in Artemisia annua L.

Plant Physiol Biochem 2021 Jun 6;163:189-200. Epub 2021 Apr 6.

Joint International Research Laboratory of Metabolic & Developmental Sciences, Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. Electronic address:

UV-B radiation is a pivotal photomorphogenic signal and positively regulates plant growth and metabolite biosynthesis. In order to elucidate the transcriptional regulation mechanism underlying UV-B-induced artemisinin and flavonoid biosynthesis in Artemisia annua, the transcriptional responses of A. annua L. leaves to UV-B radiation were analyzed using the Illumina transcriptome sequencing. A total of 10705 differentially expressed genes (DEGs) including 533 transcription factors (TFs), were identified. Based on the expression trends of the differentially expressed TFs as well as artemisinin and flavonoid biosynthesis genes, we speculated that TFs belonging to 6 clusters were most likely to be involved in the regulation of artemisinin and/or flavonoid biosynthesis. The regulatory relationship between TFs and artemisinin/flavonoid biosynthetic genes was further studied. Dual-LUC assays results showed that AaMYB6 is a positive regulator of AaLDOX which belongs to flavonoid biosynthesis pathway. In addition, we identified an R2R3 MYB TF, AaMYB4 which potentially mediated both artemisinin and flavonoid biosynthesis pathways by activating the expression of AaADS and AaDBR2 in artemisinin biosynthesis pathway and AaUFGT in flavonoid biosynthesis pathway. Overall, our findings would provide an insight into the elucidation of the parallel transcriptional regulation of artemisinin and flavonoid biosynthesis in A. annua L. under UV-B radiation.
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http://dx.doi.org/10.1016/j.plaphy.2021.03.052DOI Listing
June 2021

PD-L1 lncRNA splice isoform promotes lung adenocarcinoma progression via enhancing c-Myc activity.

Genome Biol 2021 Apr 13;22(1):104. Epub 2021 Apr 13.

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China.

Background: Although using a blockade of programmed death-ligand 1 (PD-L1) to enhance T cell immune responses shows great promise in tumor immunotherapy, the immune-checkpoint inhibition strategy is limited for patients with solid tumors. The mechanism and efficacy of such immune-checkpoint inhibition strategies in solid tumors remains unclear.

Results: Employing qRT-PCR, Sanger sequencing, and RNA BaseScope analysis, we show that human lung adenocarcinoma (LUAD) all produce a long non-coding RNA isoform of PD-L1 (PD-L1-lnc) by alternative splicing, regardless if the tumor is positive or negative for the protein PD-L1. Similar to PD-L1 mRNA, PD-L1-lnc in various lung adenocarcinoma cells is significantly upregulated by IFNγ. Both in vitro and in vivo studies demonstrate that PD-L1-lnc increases proliferation and invasion but decreases apoptosis of lung adenocarcinoma cells. Mechanistically, PD-L1-lnc promotes lung adenocarcinoma progression through directly binding to c-Myc and enhancing c-Myc transcriptional activity.

Conclusions: In summary, the PD-L1 gene can generate a long non-coding RNA through alternative splicing to promote lung adenocarcinoma progression by enhancing c-Myc activity. Our results argue in favor of investigating PD-L1-lnc depletion in combination with PD-L1 blockade in lung cancer therapy.
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http://dx.doi.org/10.1186/s13059-021-02331-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042710PMC
April 2021

A calcineurin-mediated scaling mechanism that controls a K-leak channel to regulate morphogen and growth factor transcription.

Elife 2021 Apr 8;10. Epub 2021 Apr 8.

School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.

The increase in activity of the two-pore potassium-leak channel Kcnk5b maintains allometric juvenile growth of adult zebrafish appendages. However, it remains unknown how this channel maintains allometric growth and how its bioelectric activity is regulated to scale these anatomical structures. We show the activation of Kcnk5b is sufficient to activate several genes that are part of important development programs. We provide in vivo transplantation evidence that the activation of gene transcription is cell autonomous. We also show that Kcnk5b will induce the expression of different subsets of the tested developmental genes in different cultured mammalian cell lines, which may explain how one electrophysiological stimulus can coordinately regulate the allometric growth of diverse populations of cells in the fin that use different developmental signals. We also provide evidence that the post-translational modification of serine 345 in Kcnk5b by calcineurin regulates channel activity to scale the fin. Thus, we show how an endogenous bioelectric mechanism can be regulated to promote coordinated developmental signaling to generate and scale a vertebrate appendage.
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http://dx.doi.org/10.7554/eLife.60691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8110307PMC
April 2021

Technology-Based Fall Risk Assessments for Older Adults in Low-Income Settings: Protocol for a Cross-sectional Study.

JMIR Res Protoc 2021 Apr 7;10(4):e27381. Epub 2021 Apr 7.

Department of Statistics and Data Science, University of Central Florida, Orlando, FL, United States.

Background: One-third of older adults have maladaptive fall risk appraisal (FRA), a condition in which there is a discrepancy between the level of fear of falling (FOF) and physiological fall risk (balance performance). Older adults who overestimate their physiological fall risk and report a high FOF are less likely to participate in physical activity. Limited data suggest that the association among FOF, body composition, and physical activity intensity differs by fear severity.

Objective: This study aims to examine the associations among FRA, body composition, and physical activity using assistive health technology, including the BTrackS balance system, bioelectrical impedance analysis, and activity monitoring devices. This study also aims to examine the feasibility of recruitment and acceptability of technologies and procedures for use among older adults in low-income settings.

Methods: This cross-sectional study will be conducted in older adults' homes or apartments in low-income settings in Central Florida, United States. Following consent, participants will be contacted, and our team will visit them twice. The first visit includes questionnaire completion (eg, sociodemographic or FOF) and balance performance test using the BTrackS balance system. The participants will be stratified by the FRA matrix. In addition, they will perform hand grip strength and dynamic balance performance tests. Participants will then be asked to wear the ActiGraph GT9X Link wireless activity monitor on the nondominant wrist for 7 consecutive days. The second visit includes body composition testing and a structured interview about the acceptability of the technologies and procedures.

Results: Ethical approval was obtained from the institutional review board of the University of Central Florida (protocol number 2189; September 10, 2020). As of December 2020, participation enrollment is ongoing and the results are expected to be published in Summer 2022.

Conclusions: Accurate FRA is essential for implementing physical activity programs, especially in older adults with low income. This study will provide data for developing technology-based fall risk assessments to improve participation in physical activity, thus enhancing healthy longevity among older adults in low-income settings.

International Registered Report Identifier (irrid): PRR1-10.2196/27381.
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http://dx.doi.org/10.2196/27381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8060859PMC
April 2021

An extracytoplasmic function (ECF) sigma/anti-sigma factor system regulates hypochlorous acid resistance and impacts expression of the type IV secretion system in .

J Bacteriol 2021 Apr 5. Epub 2021 Apr 5.

Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China

The intracellular bacterial pathogen causes persistent infections in various mammalian species. To survive and replicate within macrophages, these bacteria must be able to withstand oxidative stresses and express the type IV secretion system (T4SS) to evade host immune responses. The extracytoplasmic function (ECF) sigma factor system is a major signal transduction mechanism in bacteria that senses environmental cues and responds by regulating gene expression. In this study, we defined an ECF σ and its cognate anti-σ factor in M28 by conserved domain analysis and a protein interaction assay. BcrS directly activates an adjacent operon, , that encodes a methionine-rich peptide and a putative methionine sulfoxide reductase system, whereas AbcS is a negative regulator of and The / and operons can be induced by hypochlorous acid and contribute to hypochlorous acid resistance Next, RNA sequencing analysis and genome-wide recognition sequence search identified the regulons of BcrS and AbcS. Interestingly, we found that BcrS positively influences T4SS expression in an AbcS-dependent manner and that AbcS also affects T4SS expression independently of BcrS. Last, we demonstrate that is required for the maintenance of persistent infection while is dispensable in a mouse infection model. Collectively, we conclude that BcrS and AbcS influence expression of multiple genes responsible for virulence traits. is a notorious intracellular pathogen that induces chronic infections in animals and humans. To survive and replicate within macrophages, these bacteria require a capacity to withstand oxidative stresses and to express the type IV secretion system (T4SS) to combat host immune responses. In this study, we characterized an extracytoplasmic function (ECF) sigma/anti-sigma factor system that regulates resistance to reactive chlorine species and T4SS expression, thereby establishing a potential link between two crucial virulence traits of Furthermore, the anti-sigma factor AbcS contributes to persistent infection of mice. Thus, this work provides novel insights into virulence regulation as well as a potential drug target for fighting infections.
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http://dx.doi.org/10.1128/JB.00127-21DOI Listing
April 2021

Correlation of Lipid Ratios With the Severity of Pulmonary Alveolar Proteinosis: A Cross-Sectional Study.

Front Nutr 2021 18;8:610765. Epub 2021 Mar 18.

Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.

Lipids are known to accumulate abnormally in the alveoli and circulate during pulmonary alveolar proteinosis (PAP). However, the relationship between lipid ratios and PAP is not clear. In this study, we investigated the lipid ratios in PAP patients and explored the relationships between lipid ratios and the severity of PAP. A total of 122 PAP patients were diagnosed and divided the mild- moderate PAP group ( = 61) and the severe PAP group ( = 61) according to the value of disease severity score (DSS). One hundred thirty healthy volunteers were classified as the control group. Routine blood examination and pulmonary function tests were performed and lipid profile were measured. Compared with the control group, patients with PAP had significantly higher TG, TC/HDL-C, TG/HDL-C, and non-HDL-C, while lower HDL-C (all < 0.05). Patients with the severe PAP had higher TC, TG, LDL-C, TC/HDL-C, and non-HDL-C, while lower HDL-C than patients with the mild- moderate PAP (all < 0.05). Binary logistic regression analysis indicated that TC/HDL-C ( = 2.322, 95% CI 1.621-3.713, = 0.024) and non-HDL-C ( = 1.797, 95% CI 1.239-3.109, = 0.036) were all significantly correlated with the severity of PAP after adjustment for other risk factors. The AUC value of TC/HDL-C for predicting the severity of PAP was larger than that of non-HDL-C. The AUROC for TC/HDL-C was 0.741 (0.654-0.828), and the optimal cut-off point for TC/HDL-C was 5.05 (sensitivity: 73.6%, specificity: 68.1%). Lipid ratios, including TC-HDL-C and non-HDL-C, were independent risk factors for the severity of PAP. TC/HDL-C is a promising biomarker for the severity of PAP.
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http://dx.doi.org/10.3389/fnut.2021.610765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8012728PMC
March 2021

FAT3 Mutation Is Associated With Tumor Mutation Burden and Poor Prognosis in Esophageal Cancer.

Front Oncol 2021 19;11:603660. Epub 2021 Mar 19.

Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China.

Objective: To explore the mutated genes in esophageal cancer (ESCA), and evaluate its relationship with tumor mutation burden (TMB) and prognosis of ESCA, and analyze the advantages of FAT3 as a potential prognostic marker in ESCA.

Methods: The somatic mutation landscape was analyzed according to ESCA samples from the TCGA and ICGC database. The differences of TMB between mutant type and wild type of frequently mutated genes were compared by Mann-Whitney U test. The association of gene mutations with prognosis was analyzed by Kaplan-Meier method. The relative abundance of 22 tumor-infiltrating lymphocyte subsets in ESCA was calculated by CIBERSORT algorithm.

Results: FAT3 was a high frequency mutation in both TCGA and ICGC samples from the somatic mutation landscape. Then, the mutation type of FAT3 had significantly higher TMB in patients with ESCA compared the wild type (<0.05). Meanwhile, the prognosis of FAT3 mutation type was significantly worse in patients with ESCA(<0.05), and the FAT3 mutation status might be an independent factor for prognosis of patients with ESCA (HR: 1.262-5.922, P=0.011). The GSEA analysis revealed the potential mechanism of FAT3 mutation on the occurrence and development of ESCA. Finally, naive B cells were significantly enriched in FAT3 mutation samples of the ESCA microenvironment (<0.05).

Conclusions: FAT3 mutation is related to TMB and poor prognosis in ESCA. FAT3 mutation may be a prognostic marker of ESCA, and reveal the potential mechanism of FAT3 mutation on ESCA.
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http://dx.doi.org/10.3389/fonc.2021.603660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8018597PMC
March 2021

A Blockchain-Based Trusted Edge Platform in Edge Computing Environment.

Sensors (Basel) 2021 Mar 18;21(6). Epub 2021 Mar 18.

Laboratory of Information Photonics and Optical Communications, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China.

Edge computing is a product of the evolution of IoT and the development of cloud computing technology, providing computing, storage, network, and other infrastructure close to users. Compared with the centralized deployment model of traditional cloud computing, edge computing solves the problems of extended communication time and high convergence traffic, providing better support for low latency and high bandwidth services. With the increasing amount of data generated by users and devices in IoT, security and privacy issues in the edge computing environment have become concerns. Blockchain, a security technology developed rapidly in recent years, has been adopted by many industries, such as finance and insurance. With the edge computing capability, deploying blockchain platforms/applications on edge computing platforms can provide security services for network edge environments. Although there are already solutions for integrating edge computing with blockchain in many IoT application scenarios, they slightly lack scalability, portability, and heterogeneous data processing. In this paper, we propose a trusted edge platform to integrate the edge computing framework and blockchain network for building an edge security environment. The proposed platform aims to preserve the data privacy of the edge computing client. The design based on the microservice architecture makes the platform lighter. To improve the portability of the platform, we introduce the Edgex Foundry framework and design an edge application module on the platform to improve the business capability of Edgex. Simultaneously, we designed a series of well-defined security authentication microservices. These microservices use the Hyperledger Fabric blockchain network to build a reliable security mechanism in the edge environment. Finally, we build an edge computing network using different hardware devices and deploy the trusted edge platform on multiple network nodes. The usability of the proposed platform is demonstrated by testing the round-trip time (RTT) of several important workflows. The experimental results demonstrate that the platform can meet the availability requirements in real-world usage scenarios.
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http://dx.doi.org/10.3390/s21062126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8003011PMC
March 2021