Publications by authors named "Dong Liu"

2,065 Publications

  • Page 1 of 1

Immune Microenvironment Terms Signature Robustly Predicts the Prognosis and Immunotherapy Response in Bladder Cancer Based on Large Population Cohorts.

Front Genet 2022 9;13:872441. Epub 2022 May 9.

Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China.

Immune microenvironment is implicated in cancer progression. However, the role of immune microenvironment in bladder cancer has not been fully explored. Open-accessed datasets GSE120736, GSE128959, GSE13507, GSE31684, GSE32548, GSE48075, GSE83586, and The Cancer Genome Atlas (TCGA) database were enrolled in our study. Single-sample gene set enrichment analysis (ssGSEA) was used to quantify 53 immune terms in combined BLCA cohorts. The top 10 important immune terms were identified through random forest algorithm for model establishment. Our model showed satisfactory efficacy in prognosis prediction. Furthermore, we explored clinical and genomic feature differences between high- and low-risk groups. The results indicated that the patients in the high-risk group might be associated with worse clinical features. Gene set enrichment analysis showed that epithelial-mesenchymal translational, mTORC1 signaling, mitotic spindle, glycolysis, E2F target, and G2M checkpoint pathways were aberrantly activated in high-risk patients, partially explaining its worse prognosis. Patients in the low-risk group showed better immunotherapy response according to TIDE and TCIA analysis, indicating that our model could effectively predict the immunotherapy response rate. KCNH4, UGT1A1, TPO, SHANK1, PITX3, MYH1, MYH13, KRT3, DEC1, and OBP2A genes were identified as feature genes in the high- and low-risk patients. CMAP analysis was performed to identify potential compounds targeting the riskscore.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2022.872441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9126043PMC
May 2022

Is Required for Zebrafish Lateral Line Development Through Regulation of Mitogen-Activated Protein Kinase and Cellular Senescence Signaling Pathways.

Front Mol Neurosci 2022 5;15:844668. Epub 2022 May 5.

Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China.

Cingulin, a cytoplasmic element of tight junctions (TJs), is involved in maintenance of the integrity of epithelial and endothelial cells. However, the role of cingulin in the development of auditory organs remains unclear. Zebrafish is popular as a model organism for hearing research. Using the whole mount hybridization (WISH) experiment, we detected the expression of in the posterior lateral line system (PLLs) of zebrafish. We traced the early development progress of zebrafish PLLs from 36 hpf to 72 hpf, and found that inhibition of by target morpholinos resulted in severe developmental obstruction, including decreased number of neuromasts, reduced proliferative cells in the primordium, and repressed hair cell differentiation in the neuromasts. To examine the potential mechanism of in the development of zebrafish PLL neuromasts, we performed RNA-seq analysis to compare the differently expressed genes (DEGs) between knockdown samples and the controls. The KEGG enrichment analysis revealed that MAPK signaling pathway and cellular senescence were the key pathways with most DEGs in -MO morphants compared to the Control-MO embryos. Furthermore, quantitative RT-PCR analysis confirmed the findings by RNA-seq that the transcript levels of cell cycle negative regulators such as and , were remarkably upregulated after inhibition of . Our results therefore indicated an important role of in the development of auditory organs, and MAPK signaling pathway was inhibited while cellular senescence pathway was activated after downregulation of . We bring forward new insights of cingulin by exploring its function in auditory system.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fnmol.2022.844668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9119177PMC
May 2022

A humanized murine model, demonstrating dominant progressive hearing loss caused by a novel KCNQ4 mutation (p.G228D) from a large Chinese family.

Clin Genet 2022 May 22. Epub 2022 May 22.

ENT institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China.

The pathogenic variants in KCNQ4 cause DFNA2 nonsyndromic hearing loss. However, the understanding of genotype-phenotype correlations between KCNQ4 and hearing is limited. Here, we identified a novel KCNQ4 mutation p.G228D from a Chinese family, including heterozygotes characterized by high-frequency hearing loss that is progressive across all frequencies and homozygotes with more severe hearing loss. We constructed a novel murine model with humanized homologous Kcnq4 mutation. The heterozygotes had mid-frequency and high-frequency hearing loss at 4 weeks, and moved toward all frequencies hearing loss at 12 weeks, while the homozygotes had severe-to-profound hearing loss at 8 weeks. The degeneration of outer hair cells (OHCs) was observed from basal to apical turn of cochlea. The reduced K currents and depolarized resting potentials were revealed in OHCs. Remarkably, we observed the loss of inner hair cells (IHCs) in the region corresponding to the frequency above 32 kHz at 8-12 weeks. The results suggest the degeneration of OHCs and IHCs may contribute to high-frequency hearing loss in DFNA2 over time. Our findings broaden the variants of KCNQ4 and provide a novel mouse model of progressive hearing loss, which contributes to an understanding of pathogenic mechanism and eventually treatment of DFNA2 progressive hearing loss. This article is protected by copyright. All rights reserved.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/cge.14164DOI Listing
May 2022

Modification-Free Fluorescent Biosensor for CEA Based on Polydopamine-Coated Upconversion Nanoparticles.

J Fluoresc 2022 May 21. Epub 2022 May 21.

School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China.

Upconversion nanoparticles (UCNPs) have achieved considerable success in protein sensing in vitro. And aptamer is one of the most frequently used biomolecules to modify the nanoparticles for protein assay. However, the complicated process of modifying UCNPs with DNA and the susceptibility of the phosphate groups of DNA backbone to adsorb on the surface of UCNPs have limited their practical applications. To overcome these limitations, a modification-free fluorescent biosensor based on polydopamine-coated upconversion nanoparticles ([email protected]) is proposed. It consists of [email protected] and CEA aptamer-functionalized AuNPs (AuNPs-CEA aptamer). The CEA aptamer on AuNPs can be adsorbed onto the surface of [email protected] due to the interactions of π-π stacking and hydrogen bonding, triggering the process of fluorescence resonance energy transfer (FRET) from [email protected] to AuNPs-CEA aptamer. In the presence of CEA, the AuNPs-CEA aptamer departs from [email protected] due to the stronger affinity of CEA with its aptamer. Therefore, the recovery of upconversion fluorescence can sensitively quantify the concentration of CEA. This biosensor provides a linear range from 0.1 to 100 ng/mL for CEA with a LOD of 0.031 ng/mL in an aqueous solution. In spiked human serum samples, the same linear range is acquired with a slightly higher LOD of 0.055 ng/mL, demonstrating the great potential of the biosensor in practical application.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10895-022-02973-8DOI Listing
May 2022

SHR1032, a novel STING agonist, stimulates anti-tumor immunity and directly induces AML apoptosis.

Sci Rep 2022 May 20;12(1):8579. Epub 2022 May 20.

Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai, 200245, China.

Stimulator of interferon genes (STING) activation induces type I interferons and pro-inflammatory cytokines which stimulate tumor antigen cross presentation and the adaptive immune responses against tumor. The first-generation of STING agonists, cyclic di-nucleotide (CDN), mimicked the endogenous STING ligand cyclic guanosine monophosphate adenosine monophosphate, and displayed limited clinical efficacy. Here we report the discovery of SHR1032, a novel small molecule non-CDN STING agonist. Compared to the clinical CDN STING agonist ADU-S100, SHR1032 has much higher activity in human cells with different STING haplotypes and robustly induces interferon β (IFNβ) production. When dosed intratumorally, SHR1032 induced strong anti-tumor effects in the MC38 murine syngeneic tumor model. Pharmacodynamic studies showed induction of IFNβ, tumor necrosis factor α (TNFα) and interleukin-6 (IL-6) in the tumors and, to a lower extent, in the plasma. More importantly, we found SHR1032 directly causes cell death in acute myeloid leukemia (AML) cells. In conclusion, our findings demonstrate that in addition to their established ability to boost anti-tumor immune responses, STING agonists can directly eradicate AML cells, and SHR1032 may present a new and promising therapeutic agent for cancer patients.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-022-12449-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9122897PMC
May 2022

Highly efficient acousto-optic modulation using nonsuspended thin-film lithium niobate-chalcogenide hybrid waveguides.

Light Sci Appl 2022 May 20;11(1):145. Epub 2022 May 20.

Guangdong Provincial Key Laboratory of Optoelectronic Information Processing Chips and Systems, Sun Yat-sen University, 510275, Guangzhou, China.

A highly efficient on-chip acousto-optic modulator is as a key component and occupies an exceptional position in microwave-to-optical conversion. Homogeneous thin-film lithium niobate is preferentially employed to build the suspended configuration for the acoustic resonant cavity, with the aim of improving the modulation efficiency of the device. However, the limited cavity length and complex fabrication recipe of the suspended prototype restrain further breakthroughs in modulation efficiency and impose challenges for waveguide fabrication. In this work, based on a nonsuspended thin-film lithium niobate-chalcogenide glass hybrid Mach-Zehnder interferometer waveguide platform, we propose and demonstrate a built-in push-pull acousto-optic modulator with a half-wave-voltage-length product VL as low as 0.03 V cm that presents a modulation efficiency comparable to that of a state-of-the-art suspended counterpart. A microwave modulation link is demonstrated using our developed built-in push-pull acousto-optic modulator, which has the advantage of low power consumption. The nontrivial acousto-optic modulation performance benefits from the superior photoelastic property of the chalcogenide membrane and the completely bidirectional participation of the antisymmetric Rayleigh surface acoustic wave mode excited by the impedance-matched interdigital transducer, overcoming the issue of low modulation efficiency induced by the incoordinate energy attenuation of acoustic waves applied to the Mach-Zehnder interferometer with two arms in traditional push-pull acousto-optic modulators.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41377-022-00840-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9122937PMC
May 2022

Highly diastereoselective synthesis of benzothiazolo[3,2-]pyridines [4 + 2] annulation reaction of 2-vinylbenzothiazoles and azlactones.

Org Biomol Chem 2022 May 20. Epub 2022 May 20.

College of Pharmacy, Third Military Medical University, Shapingba, Chongqing 400038, China.

An efficient AgOTf-catalyzed [4 + 2] annulation reaction of 2-vinylbenzothiazoles and azlactones was successfully performed under mild reaction conditions. With this approach, a series of novel benzothiazolo[3,2-]pyridine derivatives was readily obtained in good to excellent yields (68-96%), with high diastereoselectivities and tolerating quite a broad scope of substituents. By using chiral phosphoric acid catalyst, the desired products were obtained in high enantioselectivities, up to -94%. This methodology provides a rapid and useful method for constructing fused benzothiazole derivatives.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/d2ob00618aDOI Listing
May 2022

Principles and Protocols For Post-Cryopreservation Quality Evaluation of Stem Cells in Novel Biomedicine.

Front Pharmacol 2022 3;13:907943. Epub 2022 May 3.

Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China.

Stem cell therapy is a thriving topic of interest among researchers and clinicians due to evidence of its effectiveness and promising therapeutic advantage in numerous disease conditions as presented by novel biomedical research. However, extensive clinical application of stem cells is limited by its storage and transportation. The emergence of cryopreservation technology has made it possible for living organs, tissues, cells and even living organisms to survive for a long time at deep low temperatures. During the cryopreservation process, stem cell preparations are subject to three major damages: osmotic damage, mechanical damage, and peroxidative damage. Therefore, Assessing the effectiveness and safety of stem cells following cryopreservation is fundamental to the quality control of stem cell preparations. This article presents the important biosafety and quality control parameters to be assessed during the manufacturing of clinical grade stem cell products, highlights the significance of preventing cryodamage. and provides a reference for protocols in the quality control of stem cell preparations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fphar.2022.907943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9113563PMC
May 2022

Modulation of biological motion perception in humans by gravity.

Nat Commun 2022 May 19;13(1):2765. Epub 2022 May 19.

State Key Laboratory of Brain and Cognitive Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Psychology, Chinese Academy of Sciences, Beijing, China.

The human visual perceptual system is highly sensitive to biological motion (BM) but less sensitive to its inverted counterpart. This perceptual inversion effect may stem from our selective sensitivity to gravity-constrained life motion signals and confer an adaptive advantage to creatures living on Earth. However, to what extent and how such selective sensitivity is shaped by the Earth's gravitational field is heretofore unexplored. Taking advantage of a spaceflight experiment and its ground-based analog via 6° head-down tilt bed rest (HDTBR), we show that prolonged microgravity/HDTBR reduces the inversion effect in BM perception. No such change occurs for face perception, highlighting the particular role of gravity in regulating kinematic motion analysis. Moreover, the reduced BM inversion effect is associated with attenuated orientation-dependent neural responses to BM rather than general motion cues and correlated with strengthened functional connectivity between cortical regions dedicated to visual BM processing (i.e., pSTS) and vestibular gravity estimation (i.e., insula). These findings suggest that the neural computation of gravity may act as an embodied constraint, presumably implemented through visuo-vestibular interaction, to sustain the human brain's selective tuning to life motion signals.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-022-30347-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9120521PMC
May 2022

Treatment of unresectable intrahepatic cholangiocarcinoma using transarterial chemoembolisation with irinotecan-eluting beads: analysis of efficacy and safety.

Cardiovasc Intervent Radiol 2022 May 19. Epub 2022 May 19.

Department of Interventional Therapy, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, 100039, China.

Purpose: This retrospective study evaluated the efficacy, safety, and factors affecting the prognosis of transarterial chemoembolisation with irinotecan-eluting beads with CalliSpheres (DEB-TACE) for intrahepatic cholangiocarcinoma (ICC).

Materials And Methods: We retrospectively collected data on 39 patients with unresectable ICC who received DEB-TACE therapy. We assessed the indicators of tumour response, progression-free survival (PFS), overall survival (OS), and the incidence of adverse events. PFS and OS were analysed using Kaplan-Meier curves, while Cox analysis was used to identify factors affecting the prognosis.

Results: The 3-month objective response rate (ORR) and disease control rate (DCR) of the 39 patients with unresectable ICC were 35.9% and 56.4%, respectively, while the 6-month ORR and DCR were 23.0% and 40.9%, respectively. The median OS and PFS were 11.0 months and 8.0 months, respectively. Cox analysis demonstrated that combined therapy (adjuvant sorafenib after DEB-TACE) and a low cancer antigen (CA) 125 level (≤ 35 U/ml) were independent favourable prognostic factors. Transient elevation of the aminotransferase level, nausea, vomiting, abdominal pain, fever, and hyper-bilirubinaemia were common adverse events in patients with unresectable ICC treated with DEB-TACE with CalliSphere beads (CBs). Hepatic abscess was the most serious complication, observed in one patient.

Conclusions: DEB-TACE with CBs is a safe and well-tolerated therapy in patients with unresectable ICC with a low incidence of adverse events and relatively prolonged survival. Combined therapy and low CA125 are prognostic factors associated with longer survival.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00270-022-03108-zDOI Listing
May 2022

Lysine Acetylation/Deacetylation Modification of Immune-Related Molecules in Cancer Immunotherapy.

Front Immunol 2022 2;13:865975. Epub 2022 May 2.

Department of Thoracic Surgery, Tangdu Hospital, The Air Force Military Medical University, Xi'an, China.

As major post-translational modifications (PTMs), acetylation and deacetylation are significant factors in signal transmission and cellular metabolism, and are modulated by a dynamic process two pivotal categories of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs). In previous studies, dysregulation of lysine acetylation and deacetylation has been reported to be associated with the genesis and development of malignancy. Scientists have recently explored acetylation/deacetylation patterns and prospective cancer therapy techniques, and the FDA has approved four HDAC inhibitors (HDACi) to be used in clinical treatment. In the present review, the most recent developments in the area of lysine acetylation/deacetylation alteration in cancer immunotherapy were investigated. Firstly, a brief explanation of the acetylation/deacetylation process and relevant indispensable enzymes that participate therein is provided. Subsequently, a multitude of specific immune-related molecules involved in the lysine acetylation/deacetylation process are listed in the context of cancer, in addition to several therapeutic strategies associated with lysine acetylation/deacetylation modification in cancer immunotherapy. Finally, a number of prospective research fields related to cancer immunotherapy concepts are offered with detailed analysis. Overall, the present review may provide a reference for researchers in the relevant field of study, with the aim of being instructive and meaningful to further research as well as the selection of potential targets and effective measures for future cancer immunotherapy strategies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fimmu.2022.865975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9108232PMC
May 2022

PD-1+ T-Cells Correlate with Nerve Fiber Density as a Prognostic Biomarker in Patients with Resected Perihilar Cholangiocarcinoma.

Cancers (Basel) 2022 Apr 27;14(9). Epub 2022 Apr 27.

Department of Surgery and Transplantation, University Hospital RWTH Aachen, 52074 Aachen, Germany.

Background And Aims: Perihilar cholangiocarcinoma (pCCA) is a hepatobiliary malignancy, with a dismal prognosis. Nerve fiber density (NFD)-a novel prognostic biomarker-describes the density of small nerve fibers without cancer invasion and is categorized into high numbers and low numbers of small nerve fibers (high vs low NFD). NFD is different than perineural invasion (PNI), defined as nerve fiber trunks invaded by cancer cells. Here, we aim to explore differences in immune cell populations and survival between high and low NFD patients.

Approach And Results: We applied multiplex immunofluorescence (mIF) on 47 pCCA patients and investigated immune cell composition in the tumor microenvironment (TME) of high and low NFD. Group comparison and oncological outcome analysis was performed. CD8+PD-1 expression was higher in the high NFD than in the low NFD group (12.24 × 10 vs. 1.38 × 10 positive cells by overall cell count, = 0.017). High CD8+PD-1 expression was further identified as an independent predictor of overall (OS; Hazard ratio (HR) = 0.41; = 0.031) and recurrence-free survival (RFS; HR = 0.40; = 0.039). Correspondingly, the median OS was 83 months (95% confidence interval (CI): 18-48) in patients with high CD8+PD-1+ expression compared to 19 months (95% CI: 5-93) in patients with low CD8+PD-1+ expression ( = 0.018 log rank). Furthermore, RFS was significantly lower in patients with low CD8+PD-1+ expression (14 months (95% CI: 6-22)) compared to patients with high CD8+PD-1+ expression (83 months (95% CI: 17-149), = 0.018 log rank).

Conclusions: PD-1+ T-cells correlate with high NFD as a prognostic biomarker and predict good survival; the biological pathway needs to be investigated.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/cancers14092190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9103905PMC
April 2022

The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as mA readers in cancer.

Int J Biol Sci 2022 28;18(7):2744-2758. Epub 2022 Mar 28.

College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China.

RNA can be modified by over 170 types of distinct chemical modifications, and the most abundant internal modification of mRNA in eukaryotes is N6-methyladenosine (mA). The mA modification accelerates mRNA process, including mRNA splicing, translation, transcript stability, export and decay. mA RNA modification is installed by methyltransferase-like proteins (writers), and potentially removed by demethylases (erasers), and this process is recognized by mA-binding proteins (readers). Notably, alterations of mA-modified proteins (writers, erasers and readers) are involved in the tumorigenesis, progression and metastasis. Importantly, the fate of mA-methylated mRNA is mediated mostly through mA readers, and among these readers, insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) are unique RNA-binding proteins (RBPs) that stabilize their targets mRNA via mA modification. In this review, we update the writers, erasers and readers, and their cross-talks in mA modification, and briefly discuss the oncogenic role of IGF2BPs in cancer. Most importantly, we mainly review the up-to-date knowledges of IGF2BPs (IGF2BP1/2/3) as mA readers in an mA-modified manner in cancer progression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7150/ijbs.70458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9066119PMC
May 2022

Comparison between trabectedin and doxorubicin in soft-tissue sarcomas-reply letter.

Ann Transl Med 2022 Apr;10(7):426

Department of Orthopedic Surgery, Xijing Hospital, the Fourth Military Medical University, Xi'an, China.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.21037/atm-2022-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073790PMC
April 2022

Extracellular vesicles rich in HAX1 promote angiogenesis by modulating ITGB6 translation.

J Extracell Vesicles 2022 May;11(5):e12221

Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China.

Tumour-associated angiogenesis plays a critical role in metastasis, the main cause of malignancy-related death. Extracellular vesicles (EVs) can regulate angiogenesis to participate in tumour metastasis. Our previous study showed that EVs rich in HAX1 are associated with in metastasis of nasopharyngeal carcinoma (NPC). However, the mechanism by which HAX1 of EVs promotes metastasis and angiogenesis is unclear. In this study, we demonstrated that EVs rich in HAX1 promote angiogenesis phenotype by activating the FAK pathway in endothelial cells (ECs) by increasing expression level of ITGB6. The expression level of HAX1 is markedly correlated with microvessel density (MVDs) in NPC and head and neck cancers based on an analysis of IHC. In addition to a series of in vitro cellular analyses, in vivo models revealed that HAX1 was correlated with migration and blood vessel formation of ECs, and metastasis of NPC. Using ribosome profiling, we found that HAX1 regulates the FAK pathway to influence microvessel formation and promote NPC metastasis by enhancing the translation efficiency of ITGB6. Our findings demonstrate that HAX1 can be used as an important biomarker for NPC metastasis, providing a novel basis for antiangiogenesis therapy in clinical settings.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jev2.12221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9077140PMC
May 2022

Prediction of DNA-Binding Protein-Drug-Binding Sites Using Residue Interaction Networks and Sequence Feature.

Front Bioeng Biotechnol 2022 20;10:822392. Epub 2022 Apr 20.

College of Computer and Information Engineering, Henan Normal University, Xinxiang, China.

Identification of protein-ligand binding sites plays a critical role in drug discovery. However, there is still a lack of targeted drug prediction for DNA-binding proteins. This study aims at the binding sites of DNA-binding proteins and drugs, by mining the residue interaction network features, which can describe the local and global structure of amino acids, combined with sequence feature. The predictor of DNA-binding protein-drug-binding sites is built by employing the Extreme Gradient Boosting (XGBoost) model with random under-sampling. We found that the residue interaction network features can better characterize DNA-binding proteins, and the binding sites with high betweenness value and high closeness value are more likely to interact with drugs. The model shows that the residue interaction network features can be used as an important quantitative indicator of drug-binding sites, and this method achieves high predictive performance for the binding sites of DNA-binding protein-drug. This study will help in drug discovery research for DNA-binding proteins.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fbioe.2022.822392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9065339PMC
April 2022

Micro-flower like Core-shell structured [email protected]@1T-2H-MoS composites for broadband electromagnetic wave absorption and photothermal performance.

J Colloid Interface Sci 2022 Jan 31;622:261-271. Epub 2022 Jan 31.

State Key Laboratory of Separation Membranes and Membrane Processes, School of Textile Science and Engineering, Tiangong University, Tianjin 300387, China.

Core-shell structure has been receiving extensive attention to enhance the electromagnetic wave (EMW) absorption performance due to its unique interface effect. In this paper, a micro-flower like [email protected]@1T-2H-MoS was prepared through MOF self-template method. The introduction 1T-2H-MoS shell helps optimize impedance matching of the [email protected] particles to improve the EMW absorption ability. The minimal reflection loss (RL) value of [email protected]@1T-2H-MoS is -35.83 dB with a thickness of 5.0 mm at 5.83 GHz and the effective absorption (RL < -10 dB) bandwidth up to 4.56 GHz at 2.0 mm thickness. Meanwhile, the overall effective absorption bandwidth (OEAB) can reach up to 13.44 GHz from 4.56 to 18.0 GHz. Moreover, ultrafast photothermal performances are also achieved, which can guarantee the normal functioning of [email protected]@1T-2H-MoS materials in cold conditions. The excellent EMW absorption and photothermal performance are attributed to the unique structure designed with the core of magnetic [email protected] rhombic dodecahedral and the shell of dielectric micro-flower like 1T-2H-MoS optimize impedance matching.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jcis.2022.01.179DOI Listing
January 2022

Nuclear Progestin Receptor Mediated Linkage of Blood Coagulation and Ovulation.

Endocrinology 2022 May 2. Epub 2022 May 2.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.

Ovulation is a dramatic remodeling process that includes rupture of blood capillaries and clotting, but coagulation is not thought to directly regulate this process. Herein, we report remarkable increases of coagulation factors V (f5, ~3145-fold) and tissue factor (f3a, ~120-fold) in zebrafish ovarian follicle cells during ovulation. This increase was mediated through the nuclear progestin receptor (Pgr), which is essential for ovulation in zebrafish, and was totally abolished in ovarian follicular cells from pgr-/- mutants. In addition, promoter activities of f5 and f3a were significantly enhanced by progestin (DHP) via Pgr. Similar regulation of human F5 promoter activity was induced via human PGRB, suggesting a conserved mechanism. Site-directed mutagenesis of the zebrafish f5 promoter further demonstrated a direct regulation of coagulation factors via progestin response elements. Moreover, a stark increase of erythrocytes occurred in capillaries meshed in wildtype preovulatory follicles but was absent in pgr-/- mutants. Interestingly, anticoagulants significantly inhibited ovulation both in vitro and in vivo, respectively. Furthermore, reduced fecundity was observed in f5+/- female zebrafish. Taken together, our study provides plausible evidence for steroid regulation of coagulation factors, and a new hypothesis for blood clotting triggered ovulation in vertebrates.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1210/endocr/bqac057DOI Listing
May 2022

Attribute Artifacts Removal for Geometry-Based Point Cloud Compression.

IEEE Trans Image Process 2022 11;31:3399-3413. Epub 2022 May 11.

Geometry-based point cloud compression (G-PCC) can achieve remarkable compression efficiency for point clouds. However, it still leads to serious attribute compression artifacts, especially under low bitrate scenarios. In this paper, we propose a Multi-Scale Graph Attention Network (MS-GAT) to remove the artifacts of point cloud attributes compressed by G-PCC. We first construct a graph based on point cloud geometry coordinates and then use the Chebyshev graph convolutions to extract features of point cloud attributes. Considering that one point may be correlated with points both near and far away from it, we propose a multi-scale scheme to capture the short- and long-range correlations between the current point and its neighboring and distant points. To address the problem that various points may have different degrees of artifacts caused by adaptive quantization, we introduce the quantization step per point as an extra input to the proposed network. We also incorporate a weighted graph attentional layer into the network to pay special attention to the points with more attribute artifacts. To the best of our knowledge, this is the first attribute artifacts removal method for G-PCC. We validate the effectiveness of our method over various point clouds. Objective comparison results show that our proposed method achieves an average of 9.74% BD-rate reduction compared with Predlift and 10.13% BD-rate reduction compared with RAHT. Subjective comparison results present that visual artifacts such as color shifting, blurring, and quantization noise are reduced.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TIP.2022.3170722DOI Listing
May 2022

[Effect of high-intensity interval exercise on depression-related behavior in mice].

Sheng Li Xue Bao 2022 Apr;74(2):165-176

School of Life Science, Nantong University, Nantong 226001, China.

This paper was aimed to clarify the effect of high-intensity interval training (HIIT) on depression. Animal running platforms were used to establish HIIT exercise models, depression models were prepared by chronic unpredictable mild stress (CUMS), and depression-related behaviors were detected by behavioral experiments. The results showed that HIIT exercise improved depression-related behavior in CUMS model mice. Western blot and ELISA results showed that in the hippocampus, medial prefrontal cortex (mPFC) and amygdala of the CUMS model mice, glucocorticoid receptor (GR) protein expression was down-regulated, and the content of tumor necrosis factor α (TNF-α) was increased, compared with those in the control group, whereas HIIT exercise could effectively reverse these changes in CUMS model mice. These results suggest that HIIT exercise can exert antidepressant effect, which brings new ideas and means for the clinical treatment of depressive diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
April 2022

Continuous Production of Human Epidermal Growth Factor Using Biofilm.

Front Microbiol 2022 12;13:855059. Epub 2022 Apr 12.

State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.

Increasing demand for recombinant proteins necessitates efficient protein production processes. In this study, a continuous process for human epidermal growth factor (hEGF) secretion by was developed by taking advantage of biofilm formation. Genes , , and that have proved to facilitate biofilm formation and some genes , , , and potentially involved in biofilm formation were examined for their effects on hEGF secretion as well as biofilm formation. Finally, biofilm-based fermentation processes were established, which demonstrated the feasibility of continuous production of hEGF with improved efficiency. The best result was obtained from -disruption that showed a 28% increase in hEGF secretion over the BL21(DE3) wild strain, from 24 to 32 mg/L. Overexpression of also showed great potential in continuous immobilized fermentation. Overall, the biofilm engineering here represents an effective strategy to improve hEGF production and can be adapted to produce more recombinant proteins in future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2022.855059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9039743PMC
April 2022

Circadian activities of the brain MNK-eIF4E signalling axis contribute to diurnal rhythms of some cognitive functions.

Eur J Neurosci 2022 Apr 28. Epub 2022 Apr 28.

Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA.

Although it is well recognized that the circadian timing system profoundly influences cognitive performance, the underlying molecular mechanisms remain poorly defined. Our previous work has found that the mitogen-activated protein kinase-interacting kinase (MNK)-eukaryotic translation initiation factor 4E (eIF4E) axis, a conserved cellular signalling pathway regulating mRNA translation, modulates the function of the suprachiasmatic nucleus (SCN), the master circadian clock. Here, with the use of a combination of genetic, biochemical and behavioural approaches, we investigated the distribution and temporal regulation of eIF4E phosphorylation in the brain and its role in regulating the diurnal oscillations of some aspects of cognition in mice. We found that activities of the MNK-eIF4E axis, as indicated by the level of eIF4E phosphorylation at Ser209, exhibited significant circadian oscillations in a variety of brain regions, including but not limited to the prefrontal cortex, the hippocampus, the amygdala and the cerebellum. Phosphorylated eIF4E was enriched in neurons but not in astrocytes or microglia. Mice lacking eIF4E phosphorylation (eIF4E ) or the MNKs (Mnk ), the kinases that phosphorylate eIF4E, exhibited impaired diurnal variations of novel object recognition, object location memory, Barnes maze learning and ambulatory activities. Together, these results suggest that circadian activities of the MNK-eIF4E axis contribute to the diurnal rhythms of some cognitive functions, highlighting a role for rhythmic translational control in circadian regulation of cognitive performance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/ejn.15678DOI Listing
April 2022

Chlorinated metabolites with antibacterial activities from a deep-sea-derived fungus.

RSC Adv 2021 Sep 3;11(47):29661-29667. Epub 2021 Sep 3.

State Key Laboratory of Natural and Biomimetic Drugs, Peking University Beijing 100191 P. R. China

Chromatographic separation of the solid cultures of a deep-sea-derived fungus (MCCC 3A00308) resulted in the isolation of eight compounds. Their structures were identified on the basis of the spectroscopic data. Compounds 1-8 are classified as depsidone-type (1-4), isocoumarin-type (5 and 6), and benzothiazole-type (7 and 8), of which 1-7 are new compounds and 1-3 along with 5 and 6 are chlorinated. Compound 3 is characterized by trichlorination and shows potent activities against Gram-positive pathogenic bacteria including ATCC 25923, ATCC 10792, and CMCC 63501, with minimum inhibitory concentration (MIC) values ranging from 0.5 to 1.0 μg mL. This study extends the chemical diversity of chlorinated natural products from marine-derived fungi and provides a promising lead for the development of antibacterial agents.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/d1ra05736gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041095PMC
September 2021

Characterizing warm atmospheric boundary layer over land by combining Raman and Doppler lidar measurements.

Opt Express 2022 Mar;30(7):11892-11911

PBL plays a critical role in the atmosphere by transferring heat, moisture, and momentum. The warm PBL has a distinct diurnal cycle including daytime convective mixing layer (ML) and nighttime residual layer developments. Thus, for PBL characterization and process study, simultaneous determinations of PBL height (PBLH) and ML height (MLH) are necessary. Here, new approaches are developed to provide reliable PBLH and MLH to characterize warm PBL evolution. The approaches use Raman lidar (RL) water vapor mixing ratio (WVMR) and Doppler lidar (DL) vertical velocity measurements at the Southern Great Plains (SGP) atmospheric observatory, which was established by the Atmospheric Radiation Measurement (ARM) user facility. Compared with widely used lidar aerosol measurements for PBLH, WVMR is a better trace for PBL vertical mixing. For PBLH, the approach classifies PBL water vapor structures into a few general patterns, then uses a slope method and dynamic threshold method to determine PBLH. For MLH, wavelet analysis is used to re-construct 2-D variance from DL vertical wind velocity measurements according to the turbulence eddy size to minimize the impacts of gravity wave and eddy size on variance calculations; then, a dynamic threshold method is used to determine MLH. Remotely-sensed PBLHs and MLHs are compared with radiosonde measurements based on the Richardson number method. Good agreements between them confirm that the proposed new algorithms are reliable for PBLH and MLH characterization. The algorithms are applied to warm seasons' RL and ML measurements at the SGP site for five years to study warm season PBL structure and processes. The weekly composited diurnal evolutions of PBLHs and MLHs in warm climate were provided to illustrate diurnal and seasonal PBL evolutions. This reliable PBLH and MLH dataset will be valuable for PBL process study, model evolution, and PBL parameterization improvement.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1364/OE.451728DOI Listing
March 2022

Simulation and optimization of Fe resonance fluorescence lidar performance for temperature-wind measurement.

Opt Express 2022 Apr;30(8):13278-13293

Fe resonance fluorescence lidar (Fe lidar) is considered an ideal candidate for temperature and wind measurement in the mesosphere and lower thermosphere region. However, considering the complexity of it, only a few Fe lidars have been operated in a few locations. To develop a Fe lidar with high performance, simulation work is the first important step. A simulation model is built in this paper. The expressions for the temperature-wind uncertainties are derived using the error propagation method. Within the limit of saturation effect, an index decomposition of the lidar and atmospheric parameters are performed. When the dwell time and central frequency shift are optimized to 0.205 and 932 MHz at night and 0.212 and 687 MHz during the day, night and daytime calibration curves are acquired, and after confirming the simulation parameters, the performance of Fe lidar is also evaluated. The simulation model could provide a valuable guidance for Fe lidar design.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1364/OE.455189DOI Listing
April 2022

Unusual Deformation and Fracture in Gallium Telluride Multilayers.

J Phys Chem Lett 2022 May 25;13(17):3831-3839. Epub 2022 Apr 25.

Center for Device Thermography and Reliability (CDTR), H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K.

The deformation and fracture mechanism of two-dimensional (2D) materials are still unclear and not thoroughly investigated. Given this, mechanical properties and mechanisms are explored on example of gallium telluride (GaTe), a promising 2D semiconductor with an ultrahigh photoresponsivity and a high flexibility. Hereby, the mechanical properties of both substrate-supported and suspended GaTe multilayers were investigated through Berkovich-tip nanoindentation instead of the commonly used AFM-based nanoindentation method. An unusual concurrence of multiple pop-in and load-drop events in loading curve was observed. Theoretical calculations unveiled this concurrence originating from the interlayer-sliding mediated layers-by-layers fracture mechanism in GaTe multilayers. The van der Waals force dominated interlayer interactions between GaTe and substrates was revealed much stronger than that between GaTe interlayers, resulting in the easy sliding and fracture of multilayers within GaTe. This work introduces new insights into the deformation and fracture of GaTe and other 2D materials in flexible electronics applications.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpclett.2c00411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9082608PMC
May 2022

Regulates Zebrafish Vascular Patterning and Motor Neuronal Axon Growth in Spinal Cord.

Front Mol Neurosci 2022 7;15:854556. Epub 2022 Apr 7.

Nantong Laboratory of Development and Diseases, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, School of Life Science, Second Affiliated Hospital, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.

Vessels and nerves are closely associated in anatomy as well as functions. Accumulating evidences have demonstrated that axon-guiding signals may affect endothelial cells migration and path finding, which is crucial for the patterning of both the complex vascular network and neural system. However, studies regarding the functional overlap between vascular and neuronal orchestrating are still incomplete. Semaphorin6D (Sema6D) belongs to the Semaphorin family and has been identified as an important regulating factor in diverse biological processes. Its roles in vascular development are still unclear. Here, we confirmed that is enriched in neural system and blood vessels of zebrafish embryos by hybridization. Then, the deficiency of caused by specific antisense morpholino-oligonucleotides (MO) led to dramatic path finding defects in both intersegmental vessels (ISVs) and primary motor neurons (PMNs) of spinal cord in zebrafish embryos. Furthermore, these defective phenotypes were confirmed in F0 generation of knockouts and rescue experiments by overexpression of mRNA in morphants. These data collectively indicate that regulates zebrafish vascular patterning and motor neuronal axon growth in the spinal cord, which might be of great therapeutical use to regulate vessel and nerve guidance in the relevant diseases that affect both systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fnmol.2022.854556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9021825PMC
April 2022

Ordered structure constructed from -symmetric hexa--hexabenzocoronene linked with oligo(dimethylsiloxane).

Soft Matter 2022 May 4;18(17):3430-3436. Epub 2022 May 4.

Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, and College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.

The preparation of sub-5-nm ordered structures is very important to the development of today's nanotechnology. Block molecules have the potential to form structures with significantly small characteristic dimensions. Herein two novel organic-inorganic block molecules composed of a hexa--hexabenzocoronene (HBC) core and two oligo(dimethylsiloxane) (ODMS) tails with symmetry are reported. A hierarchical lamello-columnar structure with a two-dimensional rectangular lattice where HBC cores adopt a tilted arrangement was obtained from their bulk self-assembly. The feature sizes are all below 5 nm and can be regulated the number of ODMS chains. Sub-5-nm line structures were obtained through spin-coating of the block molecules onto silicon substrates modified with poly(dimethylsiloxane). As organic-inorganic hybrid materials, these block molecules may be further applied in sub-5-nm nanopatterning.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/d2sm00059hDOI Listing
May 2022

GBP2 facilitates the progression of glioma via regulation of KIF22/EGFR signaling.

Cell Death Discov 2022 Apr 18;8(1):208. Epub 2022 Apr 18.

Department of Neurosurgery, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi Province, P. R. China.

Identifying the mechanism of glioma progression is critical for diagnosis and treatment. Although studies have shown that guanylate-binding protein 2(GBP2) has critical roles in various cancers, its function in glioma is unclear. In this work, we demonstrate that GBP2 has high expression levels in glioma tissues. In glioma cells, depletion of GBP2 impairs proliferation and migration, whereas overexpression of GBP2 enhances proliferation and migration. Regarding the mechanism, we clarify that epidermal growth factor receptor (EGFR) signaling is regulated by GBP2, and also demonstrate that GBP2 interacts directly with kinesin family member 22(KIF22) and regulates glioma progression through KIF22/EGFR signaling in vitro and in vivo. Therefore, our study provides new insight into glioma progression and paves the way for advances in glioma treatment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41420-022-01018-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9016070PMC
April 2022

Nexmifa Regulates Axon Morphogenesis in Motor Neurons in Zebrafish.

Front Mol Neurosci 2022 31;15:848257. Epub 2022 Mar 31.

Division of Brain Science, Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China.

Nexmif is mainly expressed in the central nervous system (CNS) and plays important roles in cell migration, cell to cell and cell-matrix adhesion, and maintains normal synaptic formation and function. Nevertheless, it is unclear how nexmif is linked to motor neuron morphogenesis. Here, we provided hybridization evidence that nexmifa (zebrafish paralog) was localized to the brain and spinal cord and acted as a vital regulator of motor neuron morphogenesis. Nexmifa deficiency in zebrafish larvae generated abnormal primary motor neuron (PMN) development, including truncated Cap axons and decreased branches in Cap axons. Importantly, RNA-sequencing showed that nexmifa-depleted zebrafish embryos caused considerable CNS related gene expression alterations. Differentially expressed genes (DEGs) were mainly involved in axon guidance and several synaptic pathways, including glutamatergic, GABAergic, dopaminergic, cholinergic, and serotonergic synapse pathways, according to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. In particular, when compared with other pathways, DEGs were highest (84) in the axon guidance pathway, according to Organismal Systems. Efna5b, bmpr2b, and sema6ba were decreased markedly in nexmifa-depleted zebrafish embryos. Moreover, both overexpression of efna5b mRNA and sema6ba mRNA could partially rescued motor neurons morphogenesis. These observations supported nexmifa as regulating axon morphogenesis of motor neurons in zebrafish. Taken together, nexmifa elicited crucial roles during motor neuron development by regulating the morphology of neuronal axons.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fnmol.2022.848257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9009263PMC
March 2022
-->