Publications by authors named "Ye Sun"

411 Publications

Regulation of the evolutionarily conserved muscle myofibrillar matrix by cell type dependent and independent mechanisms.

Nat Commun 2022 May 13;13(1):2661. Epub 2022 May 13.

Muscle Energetics Laboratory, NHLBI, NIH, Bethesda, MD, 20892, USA.

Skeletal muscles play a central role in human movement through forces transmitted by contraction of the sarcomere. We recently showed that mammalian sarcomeres are connected through frequent branches forming a singular, mesh-like myofibrillar matrix. However, the extent to which myofibrillar connectivity is evolutionarily conserved as well as mechanisms which regulate the specific architecture of sarcomere branching remain unclear. Here, we demonstrate the presence of a myofibrillar matrix in the tubular, but not indirect flight (IF) muscles within Drosophila melanogaster. Moreover, we find that loss of transcription factor H15 increases sarcomere branching frequency in the tubular jump muscles, and we show that sarcomere branching can be turned on in IF muscles by salm-mediated conversion to tubular muscles. Finally, we demonstrate that neurochondrin misexpression results in myofibrillar connectivity in IF muscles without conversion to tubular muscles. These data indicate an evolutionarily conserved myofibrillar matrix regulated by both cell-type dependent and independent mechanisms.
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http://dx.doi.org/10.1038/s41467-022-30401-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9106682PMC
May 2022

Regulation of the evolutionarily conserved muscle myofibrillar matrix by cell type dependent and independent mechanisms.

Nat Commun 2022 May 13;13(1):2661. Epub 2022 May 13.

Muscle Energetics Laboratory, NHLBI, NIH, Bethesda, MD, 20892, USA.

Skeletal muscles play a central role in human movement through forces transmitted by contraction of the sarcomere. We recently showed that mammalian sarcomeres are connected through frequent branches forming a singular, mesh-like myofibrillar matrix. However, the extent to which myofibrillar connectivity is evolutionarily conserved as well as mechanisms which regulate the specific architecture of sarcomere branching remain unclear. Here, we demonstrate the presence of a myofibrillar matrix in the tubular, but not indirect flight (IF) muscles within Drosophila melanogaster. Moreover, we find that loss of transcription factor H15 increases sarcomere branching frequency in the tubular jump muscles, and we show that sarcomere branching can be turned on in IF muscles by salm-mediated conversion to tubular muscles. Finally, we demonstrate that neurochondrin misexpression results in myofibrillar connectivity in IF muscles without conversion to tubular muscles. These data indicate an evolutionarily conserved myofibrillar matrix regulated by both cell-type dependent and independent mechanisms.
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http://dx.doi.org/10.1038/s41467-022-30401-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9106682PMC
May 2022

Insights into the Profile of the Human Expiratory Microbiota and Its Associations with Indoor Microbiotas.

Environ Sci Technol 2022 May 5;56(10):6282-6293. Epub 2022 May 5.

School of Space and Environment, Beihang University, Beijing 100191, China.

Microorganisms residing in the human respiratory tract can be exhaled, and they constitute a part of environmental microbiotas. However, the expiratory microbiota community and its associations with environmental microbiotas remain poorly understood. Here, expiratory bacteria and fungi and the corresponding microbiotas from the living environments were characterized by DNA amplicon sequencing of residents' exhaled breath condensate (EBC) and environmental samples collected from 14 residences in Nanjing, China. The microbiotas of EBC samples, with a substantial heterogeneity, were found to be as diverse as those of skin, floor dust, and airborne microbiotas. Model fitting results demonstrated the role of stochastic processes in the assembly of the expiratory microbiota. Using a fast expectation-maximization algorithm, microbial community analysis revealed that expiratory microbiotas were differentially associated with other types of microbiotas in a type-dependent and residence-specific manner. Importantly, the expiratory bacteria showed a composition similarity with airborne bacteria in the bathroom and kitchen environments with an average of 12.60%, while the expiratory fungi showed a 53.99% composition similarity with the floor dust fungi. These differential patterns indicate different relationships between expiratory microbiotas and the airborne microbiotas and floor dust microbiotas. The results here illustrated for the first time the associations between expiratory microbiotas and indoor microbiotas, showing a potential microbial exchange between the respiratory tract and indoor environment. Thus, improved hygiene and ventilation practices can be implemented to optimize the indoor microbial exposome, especially in indoor bathrooms and kitchens.
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http://dx.doi.org/10.1021/acs.est.2c00688DOI Listing
May 2022

Individualized Nutritional Support for Hospitalized Patients With Oropharyngeal Dysphagia After Stroke: A Randomized Controlled Trial.

Front Nutr 2022 13;9:843945. Epub 2022 Apr 13.

Department of Neurology, Stroke Center & Clinical Trial and Research Center for Stroke, The First Hospital of Jilin University, Changchun, China.

Objectives: Post-stroke dysphagia may cause aspiration pneumonia, malnutrition, dehydration, and other complications. However, data on the effects of nutritional supplementation and its value after stroke are insufficient. We aimed to evaluate the effect of an individualized 1-week nutrition intervention program on swallowing function and nutritional status in stroke patients with oropharyngeal dysphagia.

Methods: This study comprised the control group receiving oral nutritional support and continuous nasogastric tube feeding according to the results of the water swallow test (WST). The intervention group additionally underwent a volume-viscosity swallowing test (V-VST) and intermittent oroesophageal tube feeding based on WST. The outcomes were measured after 7 days of intervention, including the improvement of swallowing function assessment by WST, biochemical parameters, such as total serum protein, serum albumin, hemoglobin levels and body composition. This trial was registered with the Chinese Clinical Trial Registry, identifier ChiCTR 2100054054.

Results: In total, 173 participants completed the study between September 1, 2020, and April 30, 2021. Patients receiving individualized nutritional support showed a more significant improvement in the total effective rate of swallowing function (95.3% vs. 85.1%, < 0.05). After the intervention, the total serum protein level (0.97 ± 0.41 vs. -0.83 ± 0.47 g/L; < 0.05), serum albumin level (0.33 ± 0.28 vs. -1.39 ± 0.36 g/L; < 0.001) and lean tissue mass (0.13 ± 0.35 vs. -1.00 ± 0.40 g/L; < 0.05) increased in the intervention group. The decrease of hemoglobin levels in the control group was more evident (-6.17 ± 1.63 vs. -0.64 ± 1.40 g/L; 95%CI, -9.78 to -1.28; = 0.001). The difference of phase angle between the two groups was statistically significant (5.93 ± 0.88° vs. 5.77 ± 0.78°; = 0.035), but not in body fat mass.

Conclusions: In stroke patients with oropharyngeal dysphagia, the use of individualized nutritional support based on V-VST and intermittent oroesophageal tube feeding during the first week of hospitalization improved swallowing function and maintained nutritional status.

Clinical Trial Registration: https://clinicaltrials.gov/, identifier: ChiCTR 2100054054.
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http://dx.doi.org/10.3389/fnut.2022.843945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9043655PMC
April 2022

Salud Latina: feasibility of a synchronous online chat for latinos at risk for type 2 diabetes.

Inform Health Soc Care 2022 Apr 29:1-13. Epub 2022 Apr 29.

Department of Media and Communication, City University of Hong Kong, Hong Kong.

This study examined the feasibility of Salud Latina, a weekly synchronous online chat intervention, aimed at engaging Latinos in diabetes prevention conversations. Participants were Latino English- and Spanish-speaking individuals. Salud Latina comprised of six synchronous weekly online chats moderated by bilingual Latina moderators trained in diabetes and online engagement. Online chats used open-ended questions. We assessed feasibility, acceptability, and satisfaction of the intervention and qualitatively analyzed the chats to identify barriers and facilitators to healthy behaviors and identify types of support exchanged. Participants (N = 20) were mostly female and English/Spanish bilingual and 80% completed at least four chats. Salud Latina was acceptable, feasible and highly satisfactory. Four themes were identified: (1) barriers to engaging in healthy behaviors, (2) facilitators of healthy behaviors, (3) Salud Latina provides a community of support, and (4) the need to build a Latino culture of health. Participants recognized the importance of engaging in healthy behaviors to prevent or delay T2D. Findings provide insight in how a synchronous online chat intervention could be used to build a social media community within a Latino population to support healthy behaviors. Future research could explore combining synchronous online chats with in-person community or family-level interventions.
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http://dx.doi.org/10.1080/17538157.2022.2069029DOI Listing
April 2022

[email protected] Core-Shell Nanoagent Enabling Immediate Generation of Hydroxyl Radicals and Simultaneous Glutathione Deletion Free of Pre-Reaction for Chemodynamic-Photothermo-Photocatalytic Therapy with Significant Immune Response.

Adv Healthc Mater 2022 Apr 28:e2200041. Epub 2022 Apr 28.

State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China.

As a typical tumor microenvironment-responsive therapy, chemodynamic therapy (CDT), producing hydroxyl radicals ( OH) to eliminate tumor cells, has demonstrated great promise. Nevertheless, there are still major challenges: OH generated from endogenous H O is usually insufficient; the CDT effect is strongly dependent on the pre-reaction with glutathione. Addressing the challenges, [email protected] core-shell nanoagent for synergetic chemodynamic-photothermo-photocatalytic therapy combined with tetramodal imaging, including magnetic resonance imaging, computed tomography, photoacoustic, and infrared thermal imaging is reported. Distinct from the reported glutathione-depleting agents, Mn in MnSe allows immediate generation of OH, independent of pre-reaction. Meanwhile, Mn consumes glutathione by its conversion to Mn . The Au-MnSe combination promotes photothermal conversion and photocatalytic reaction, resulting in largely enhanced OH generation from endogenous H O and significant hyperthermia. Meanwhile, immune response is effectively activated: the intratumoral expression of programmed cell death-1 and proinflammatory cytokines increase to 4-7 folds; the cytotoxic and helper T lymphocytes cells in the tumor area increase to more than 2.5-folds; an evident, temporary systemic immunostimulatory effect is demonstrated. High tumor inhibition rate (≈97.3%) and greatly prolonged survival are obtained. This highly-integrated design coordinating three different therapies with four different imaging modals provide new possibilities for high-performance theranostic nanoagents.
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http://dx.doi.org/10.1002/adhm.202200041DOI Listing
April 2022

A Bioinformatic Analysis: The Overexpression and Prognostic Potential of in Lower-Grade Glioma.

Int J Gen Med 2022 21;15:4321-4337. Epub 2022 Apr 21.

School of Nursing, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, People's Republic of China.

Purpose: Glutathione peroxidase-7 () is a newly discovered non-selenium-containing protein with glutathione peroxidase activity, which mainly protects the organism from oxidative damage and is very important for basic biology studies. This study aims to reveal the expression pattern of and its prognosis potential from a pan-cancer perspective.

Methods: Expression levels of in human tumor tissues and normal tissues were evaluated using Human Protein Atlas (HPA), the Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) and UALCAN databases. The prognostic potential of for 33 TCGA tumors was evaluated by Kaplan-Meier analysis and Cox regression analysis. Subsequently, the Chinese Glioma Genome Atlas (CGGA) dataset was used to further verify the expression of and its prognostic potential in glioma. We explored the correlation between and immune infiltration, tumor mutational burden (TMB) and microsatellite instability (MSI). Furthermore, a nomogram lower-grade glioma (LGG) was constructed to verify the prognostic outcome of patients. Finally, the relationship between and treatment regimens for LGG was also explored.

Results: was overexpressed in multiple tumors. Elevated expression of was associated with poor prognosis of LGG patients (OS hazard ratio (HR) = 1.044, P < 0.0001; DFS HR = 1.035, P < 0.0001; PFS HR = 1.045, P < 0.0001). was proved to be an independent prognostic factor of LGG through univariate and multivariate Cox analysis. The nomogram confirmed a better predictability (Concordance index (C-index): 0.845; 95% CI, 0.825-0.865). was positively correlated with TMB in LGG. expression was negatively correlated with half-maximal inhibitory concentration (IC50) of temozolomide (TMZ) (= -0.59, P =1.3e-48).

Conclusion: was upregulated in multiple tumors, and it was a potential prognostic biomarker in LGG. High-expressed can predict the sensitivity of TMZ in LGG patients.
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http://dx.doi.org/10.2147/IJGM.S356850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9037894PMC
April 2022

Chinmedomics Strategy for Elucidating the Pharmacological Effects and Discovering Bioactive Compounds From Keluoxin Against Diabetic Retinopathy.

Front Pharmacol 2022 31;13:728256. Epub 2022 Mar 31.

National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Functional Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China.

Keluoxin (KLX) is an active agent in the treatment of diabetic retinopathy (DR). However, its mechanism, targets, and effective constituents against DR are still unclear, which seriously restricts its clinical application. Chinmedomics has the promise of explaining the pharmacological effects of herbal medicines and investigating the effective mechanisms. The research results from electroretinography and electron microscope showed that KLX could reduce retinal dysfunction and pathological changes by the DR mouse model. Based on effectiveness, we discovered 64 blood biomarkers of DR by nontargeted metabolomics analysis, 51 of which returned to average levels after KLX treatment including leukotriene D4 and A4, l-tryptophan, 6-hydroxymelatonin, l-phenylalanine, l-tyrosine, and gamma-linolenic acid (GLA). The metabolic pathways involved were phenylalanine metabolism, steroid hormone biosynthesis, sphingolipid metabolism, etc. Adenosine monophosphate-activated protein kinase (AMPK), extracellular signal-regulated protein kinase1/2 (ERK1/2), phosphatidylinositol-3-kinase (PI3K), and protein 70 S6 kinase (p70 S6K) might be potential targets of KLX against DR. This was related to the mammalian target of rapamycin (mTOR) signaling and AMPK signaling pathways. We applied the chinmedomics strategy, integrating serum pharm-chemistry of traditional Chinese medicine (TCM) with metabolomics, to discover astragaloside IV (AS-IV), emodin, rhein, chrysophanol, and other compounds, which were the core effective constituents of KLX when against DR. Our study was the first to apply the chinmedomics strategy to discover the effective constituents of KLX in the treatment of DR, which fills the gap of unclear effective constituents of KLX. In the next step, the research of effective constituents can be used to optimize prescription preparation, improve the quality standard, and develop an innovative drug.
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http://dx.doi.org/10.3389/fphar.2022.728256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9008273PMC
March 2022

SNP rs322931 (C>T) in miR-181b and rs7158663 (G>A) in MEG3 aggravate the inflammatory response of anal abscess in patients with Crohn's disease.

Aging (Albany NY) 2022 Apr 14;14(7):3313-3324. Epub 2022 Apr 14.

Anorectal, Shuyang County's Hospital of TCM, Shuyang Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Shuyang 223600, Jiangsu, China.

Background: The MEG3/miR-181b signaling has been implicated in the pathogenesis of several diseases including Crohn's disease. This work aimed to study the correlation between SNPs in MEG3/miR-181b and the severity of anal abscess in patients with Crohn's disease.

Methods: Quantitative real-time PCR was performed to analyze the expression of MEG3 and miR-181b. ELISA was carried out to examine the expression of TNF-α, IL-1β, IL-6, CRP, SSA, AAT, AAG and HPT in the peripheral blood of patients with Crohn's disease. Luciferase assay was performed to explore the role of miR-181b in the expression of MEG3 and TNF-α.

Results: The expression of MEG3 and miR-181b in the peripheral blood of patients with Crohn's disease was remarkably associated with the rs322931 and rs7158663 polymorphisms. rs322931 (C>T) in miR-181b and rs7158663 (G>A) in MEG3 significantly promoted the expression of TNF-α, IL-1β, IL-6, CRP, SSA, AAT, AAG and HPT. Luciferase assay demonstrated that miR-181b was capable of repressing the expression of MEG3 and TNF-α through binding to their specific binding sites. Moreover, alteration of MEG3 and miR-181b expression also showed a remarkable impact on the MEG3/miR-181b/TNF-α signaling pathway in THP-1 cells.

Conclusions: In conclusion, our study demonstrated that two SNPs, rs322931 (C>T) in miR-181b and rs7158663 (G>A) in MEG3, could aggravate the inflammatory response of anal abscess in patients with Crohn's disease via modulating the MEG3/miR-181b/TNF-α signaling pathway.
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http://dx.doi.org/10.18632/aging.204014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9037263PMC
April 2022

A Hypothesis From Metabolomics Analysis of Diabetic Retinopathy: Arginine-Creatine Metabolic Pathway May Be a New Treatment Strategy for Diabetic Retinopathy.

Front Endocrinol (Lausanne) 2022 24;13:858012. Epub 2022 Mar 24.

National Chinmedomics Research Center and National Traditional Chinese Medicine (TCM) Key Laboratory of Serum Pharmacochemistry, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China.

Diabetic retinopathy is one of the serious complications of diabetes, which the leading causes of blindness worldwide, and its irreversibility renders the existing treatment methods unsatisfactory. Early detection and timely intervention can effectively reduce the damage caused by diabetic retinopathy. Metabolomics is a branch of systems biology and a powerful tool for studying pathophysiological processes, which can help identify the characteristic metabolic changes marking the progression of diabetic retinopathy, discover potential biomarkers to inform clinical diagnosis and treatment. This review provides an update on the known metabolomics biomarkers of diabetic retinopathy. Through comprehensive analysis of biomarkers, we found that the arginine biosynthesis is closely related to diabetic retinopathy. Meanwhile, creatine, a metabolite with arginine as a precursor, has attracted our attention due to its important correlation with diabetic retinopathy. We discuss the possibility of the arginine-creatine metabolic pathway as a therapeutic strategy for diabetic retinopathy.
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http://dx.doi.org/10.3389/fendo.2022.858012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8987289PMC
April 2022

Baclofen attenuates cognitive deficits in post-cardiac arrest brain injury.

Biochem Biophys Res Commun 2022 04 28;602:135-141. Epub 2022 Feb 28.

Department of Anesthesiology, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, China. Electronic address:

Between 30% and 50% of survivors of cardiac arrest (CA) suffer from cognitive deficits. However, no effective medical intervention is available to alleviate cognitive deficits. Baclofen is known to protect damaged neurons, but researchers have still not clearly whether baclofen alleviates CA-induced cognitive deficits. The present study aimed to investigate whether baclofen protects against post-CA cognitive deficits and to reveal the protective mechanism of baclofen. Rats underwent 10 min of asphyxia to establish CA models. Intriguingly, our results indicated that baclofen improved spatial memory 72 h after CA. Baclofen increased plasticity-related protein (PSD95, and GAP43) expression in the brain after CA. Baclofen reduced microglial number and the release of inflammatory factors (IL-1β and IL-18). Furthermore, baclofen significantly reduced the expression of pyroptosis-related molecules after CA. Notably, activation of NLRP3 abolished the anti-pyroptosis effect of baclofen and reduced the expression of synaptic plasticity-related proteins after CA. Taken together, this study first shows that baclofen attenuates cognitive deficits induced by brain injury after CA. The mechanism is at least partially attributed to baclofen regulating pyroptosis by inhibition of NLRP3 activation.
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http://dx.doi.org/10.1016/j.bbrc.2022.02.106DOI Listing
April 2022

Consideration of Yarn Anisotropy in the Investigation of the Puncture Resistance of Fibrous Materials.

Polymers (Basel) 2022 Feb 23;14(5). Epub 2022 Feb 23.

Faculty of Textile Science and Technology, Shinshu University, Nagano 3860018, Japan.

High-performance yarns are widely used to produce protective fabrics, including stab-resistant materials. The most common approach to studying the mechanism of puncture prevention is to use simulation to assist analysis. However, the anisotropy of the yarn is often overlooked during simulation owing to various factors. In fact, there is a marked difference between the axial and radial properties of a yarn. This may lead to large errors in research. In the present study, a composite material with a grid structure for puncture analysis was designed to investigate the influence of yarn anisotropy on the accuracy of simulation results. The present study combined an actual experiment with a simulation. In the actual experiment, Kevlar yarn/epoxy resin was used to prepare a mesh composite with a spacing of 1 mm. In the simulation, a 1:1 simulation model of composite material was established using finite element software. A simulated puncture experiment was conducted based on the actual experimental conditions and material parameters. After considering yarn anisotropy, the simulation results were closer to the actual experimental results. The simulation revealed that the main failure modes of the mesh material were the fracture of the resin and the bending deformation of the yarns at the junctions, while the surrounding areas were almost unaffected.
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http://dx.doi.org/10.3390/polym14050883DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8912485PMC
February 2022

Prevention of Diabetes in Overweight/Obese Adults through Traditional Chinese Patent Medicine: Study Protocol for a Prospective Cohort Study.

Evid Based Complement Alternat Med 2021 8;2021:6006802. Epub 2021 Nov 8.

Department of Endocrinology, Guang' Anmen Hospital of China Academy of Chinese Medical Sciences, Beijing, China.

. Early intervention in prediabetes can prevent or delay the incidence of type 2 diabetes mellitus (T2DM). Traditional Chinese patent medicine (TCPM) is widely used in China to prevent T2DM. This study aims to evaluate the efficacy and safety of TCPMs for preventing T2DM. . This study is a multicenter, cohort study with two arms. A total of 600 participants will be recruited. The participants will be divided into either intervention or control groups according to their own desire, and the exposure factor is the application of TCPMs. All participants will be encouraged to lead a healthy lifestyle, and the intervention group also used TCPMs based on syndrome differentiation. Incident diabetes and normalization of blood glucose are indexes of end point. Safety assessments and adverse event monitoring will also be conducted. The treatment duration is set for 24 weeks, and we will follow-up for another 2 years. . This trial may provide initial evidence regarding the efficacy and safety of TCPMs plus lifestyle intervention (LI) compared to LI alone for preventing T2DM and provide a comprehensive intervention plans that choose suitable TCPMs for diabetes prevention according to syndrome differentiation. Chinese Clinical Trial Registry ID: ChiCTR1900023541, registered on 1 Jun 2019. The version identifier is 2018121702.
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http://dx.doi.org/10.1155/2021/6006802DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8592719PMC
November 2021

Chemical Constituents of the Roots of Schisandra chinensis.

Chem Biodivers 2022 Apr 15;19(4):e202100962. Epub 2022 Mar 15.

Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, 150040, P. R. China.

One new phenylpropanoid schineolignin D (1), one new sesquiterpene (-)-(7S,10S)-3,11,12,13-tetrahydroxycalamenene (2), one new quinic acid 4-(E)-O-coumaroylquinic acid ethyl ester (3), and seven known compounds 4-10 were separated from the roots of Schisandra chinensis. The chemical structures of all compounds were characterized by NMR spectroscopic experiments. All compounds were assessed for their neuroprotective effects on PC12 cell lines induced by H O . Compounds 1, 3-4, and 7 showed statistically significant neuroprotective activities with the negative control group at 12.5 μM.
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http://dx.doi.org/10.1002/cbdv.202100962DOI Listing
April 2022

Streptococcus strain C17 as a potential probiotic candidate to modulate oral health.

Lett Appl Microbiol 2022 Feb 25. Epub 2022 Feb 25.

Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, Liao Ning, People's Republic of China.

In the microbiome, probiotics modulate oral diseases. In this study, Streptococcus strain C17 was isolated from the oropharynx of a 5-year-old healthy child, and its potential probiotic properties were analysed using human bronchial epithelial cells (16-HBE) used as an in vitro oropharyngeal mucosal model. The results demonstrated that the C17 strain showed tolerance to moderate pH ranges of 4-5 and 0·5-1% bile. However, it was more tolerant to 0·5% bile than 1% bile. It also demonstrated an ability to accommodate maladaptive oropharyngeal conditions (i.e. tolerating lysozyme at 200 μg ml ). It was also resistant to hydrogen peroxide at 0·8 mM. In addition, we found out that the strain possesses inhibitory activities against various common pathogenic bacteria. Furthermore, C17 was not cytotoxic to 16-HBE cells at different multiplicities of infection. Scanning electron microscopy disclosed that C17 adhesion to 16-HBE cells. Competition, exclusion and displacement assays showed that it had good anti-adhesive effect against S. aureus. The present study revealed that Streptococcus strain C17 is a potentially efficacious oropharyngeal probiotic.
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http://dx.doi.org/10.1111/lam.13680DOI Listing
February 2022

Triglyceride-derived fatty acids reduce autophagy in a model of retinal angiomatous proliferation.

JCI Insight 2022 03 22;7(6). Epub 2022 Mar 22.

Department of Pharmacology, University of Montreal, Montreal, Quebec, Canada.

Dyslipidemia and autophagy have been implicated in the pathogenesis of blinding neovascular age-related macular degeneration (NV-AMD). VLDL receptor (VLDLR), expressed in photoreceptors with a high metabolic rate, facilitates the uptake of triglyceride-derived fatty acids. Since fatty acid uptake is reduced in Vldlr-/- tissues, more remain in circulation, and the retina is fuel deficient, driving the formation in mice of neovascular lesions reminiscent of retinal angiomatous proliferation (RAP), a subtype of NV-AMD. Nutrient scarcity and energy failure are classically mitigated by increasing autophagy. We found that excess circulating lipids restrained retinal autophagy, which contributed to pathological angiogenesis in the Vldlr-/- RAP model. Triglyceride-derived fatty acid sensed by free fatty acid receptor 1 (FFAR1) restricted autophagy and oxidative metabolism in photoreceptors. FFAR1 suppressed transcription factor EB (TFEB), a master regulator of autophagy and lipid metabolism. Reduced TFEB, in turn, decreased sirtuin-3 expression and mitochondrial respiration. Metabolomic signatures of mouse RAP-like retinas were consistent with a role in promoting angiogenesis. This signature was also found in human NV-AMD vitreous. Restoring photoreceptor autophagy in Vldlr-/- retinas, either pharmacologically or by deleting Ffar1, enhanced metabolic efficiency and suppressed pathological angiogenesis. Dysregulated autophagy by circulating lipids might therefore contribute to the energy failure of photoreceptors driving neovascular eye diseases, and FFAR1 may be a target for intervention.
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http://dx.doi.org/10.1172/jci.insight.154174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8986067PMC
March 2022

Super-Robust Xanthine-Sodium Complexes on Au(111).

Angew Chem Int Ed Engl 2022 04 23;61(16):e202200064. Epub 2022 Feb 23.

School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China.

A widely accepted theory is that life originated from the hydrothermal environment in the primordial ocean. Nevertheless, the low desorption temperature from inorganic substrates and the fragileness of hydrogen-bonded nucleobases do not support the required thermal stability in such an environment. Herein, we report the super-robust complexes of xanthine, one of the precursors for the primitive nucleic acids, with Na. We demonstrate that the well-defined xanthine-Na complexes can only form when the temperature is ≥430 K, and the complexes keep adsorbed even at ≈720 K, presenting as the most thermally stable organic polymer ever reported on Au(111). This work not only justifies the necessity of high-temperature, Na-rich environment for the prebiotic biosynthesis but also reveals the robustness of the xanthine-Na complexes upon the harsh environment. Moreover, the complexes can induce significant electron transfer with the metal as inert as Au and hence lift the Au atoms up.
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http://dx.doi.org/10.1002/anie.202200064DOI Listing
April 2022

Deferoxamine Counteracts Cisplatin Resistance in A549 Lung Adenocarcinoma Cells by Increasing Vulnerability to Glutamine Deprivation-Induced Cell Death.

Front Oncol 2021 20;11:794735. Epub 2022 Jan 20.

Department of Cell Biology, College of Integrated Chinese and Western Medical, Liaoning University of Traditional Chinese Medicine, Shenyang, China.

Glutamine, like glucose, is a major nutrient consumed by cancer cells, yet these cells undergo glutamine starvation in the cores of tumors, forcing them to evolve adaptive metabolic responses. Pharmacologically targeting glutamine metabolism or withdrawal has been exploited for therapeutic purposes, but does not always induce cancer cell death. The mechanism by which cancer cells adapt to resist glutamine starvation in cisplatin-resistant non-small-cell lung cancer (NSCLC) also remains uncertain. Here, we report the potential metabolic vulnerabilities of A549/DDP (drug-resistant human lung adenocarcinoma cell lines) cells, which were more easily killed by the iron chelator deferoxamine (DFO) during glutamine deprivation than their parental cisplatin-sensitive A549 cells. We demonstrate that phenotype resistance to cisplatin is accompanied by adaptive responses during glutamine deprivation partly higher levels of autophagic activity and apoptosis resistance characteristics. Moreover, this adaptation could be explained by sustained glucose instead of glutamine-dominant complex II-dependent oxidative phosphorylation (OXPHOS). Further investigation revealed that cisplatin-resistant cells sustain OXPHOS partly iron metabolism reprogramming during glutamine deprivation. This reprogramming might be responsible for mitochondrial iron-sulfur [Fe-S] cluster biogenesis, which has become an "Achilles' heel," rendering cancer cells vulnerable to DFO-induced autophagic cell death and apoptosis through c-Jun N-terminal kinase (JNK) signaling. Finally, studies using xenograft mouse models also confirmed the growth-slowing effect of DFO. In summary, we have elucidated the adaptive responses of cisplatin-resistant NSCLC cells, which balanced stability and plasticity to overcome metabolic reprogramming and permitted them to survive under stress induced by chemotherapy or glutamine starvation. In addition, for the first time, we show that suppressing the growth of cisplatin-resistant NSCLC cells iron chelator-induced autophagic cell death and apoptosis was possible with DFO treatment. These findings provide a solid basis for targeting mitochondria iron metabolism in cisplatin-resistant NSCLC for therapeutic purposes, and it is plausible to consider that DFO facilitates in the improvement of treatment responses in cisplatin-resistant NSCLC patients.
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http://dx.doi.org/10.3389/fonc.2021.794735DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8810525PMC
January 2022

FCER1G positively relates to macrophage infiltration in clear cell renal cell carcinoma and contributes to unfavorable prognosis by regulating tumor immunity.

BMC Cancer 2022 Feb 4;22(1):140. Epub 2022 Feb 4.

Department of Urinary Surgery, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), 700 North Moyu Road, 201805, Shanghai, China.

Background: Tumor-associated macrophages (TAMs) are closely related to unfavorable prognosis of patients with clear cell renal cell carcinoma (ccRCC). However, the important molecules in the interaction between ccRCC and TAMs are unclear.

Methods: TCGA-KIRC gene expression data of tumor tissues and normal tissues adjacent to tumor were compared to identify differentially expressed genes in ccRCC. TAMs related genes were discovered by analyzing the correlation between these differentially expressed genes and common macrophage biomarkers. Gene set enrichment analysis was performed to predict functions of TAMs related gene. The findings were further validated using RNA sequencing data obtained from the CheckMate 025 study and immunohistochemical analysis of samples from 350 patients with ccRCC. Kaplan-Meier survival curve, Cox regression analysis and Harrell's concordance index analysis were used to determine the prognostic significance.

Results: In this study, we applied bioinformatic analysis to explore TAMs related differentially expressed genes in ccRCC and identified 5 genes strongly correlated with all selected macrophage biomarkers: STAC3, LGALS9, TREM2, FCER1G, and PILRA. Among them, FCER1G was abundantly expressed in tumor tissues and showed prognostic importance in patients with ccRCC who received treatment with Nivolumab; however, it did not exhibit prognostic value in those treated with Everolimus. We also discovered that high expression levels of FCER1G are related to T cell suppression. Moreover, combination of FCER1G and macrophage biomarker CD68 can improve the prognostic stratification of patients with ccRCC from TCGA-KIRC. Based on the immunohistochemical analysis of samples from patients with ccRCC, we further validated that FCER1G and CD68 are both highly expressed in tumor tissue and correlate with each other. Higher expression of CD68 or FCER1G in ccRCC tissue indicates shorter overall survival and progression-free survival; patients with high expression of both CD68 and FCER1G have the worst outcome. Combining CD68 and FCER1G facilitates the screening of patients with a worse prognosis from the same TNM stage group.

Conclusions: High expression of FCER1G in ccRCC is closely related to TAMs infiltration and suppression of T cell activation and proliferation. Combining the expression levels of FCER1G and macrophage biomarker CD68 may be a promising postoperative prognostic index for patients with ccRCC.
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http://dx.doi.org/10.1186/s12885-022-09251-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8815209PMC
February 2022

Stimulation of Let-7 Maturation by Metformin Improved the Response to Tyrosine Kinase Inhibitor Therapy in an m6A Dependent Manner.

Front Oncol 2021 6;11:731561. Epub 2022 Jan 6.

Department of Thoracic Surgery, Department of Thoracic Surgery and Oncology, Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an City, China.

The molecular mechanism of the tyrosine kinase inhibitor (TKI) resistant lung adenocarcinoma is currently unclear, and the role of methylated adenosine at the N6 position in the resistance of cancer stem cells (CSCs) therapy is unknown. This study identified a novel and effective strategy to enhance TKIs therapy response. We first confirmed the sensitization of Metformin enforcing on Osimertinib treatment and revealed the mature miRNAs signatures of the Osimertinib resistant H1975 and HCC827 cells. Let-7b expression was stimulated when adding Metformin and then increasing the therapy sensitivity by decreasing the stem cell groups expanding. Methyltransferase-like 3 (METTL3) increased the pri-Let-7b, decreased both the pre-Let-7b and mature Let-7b, attenuating the Let-7b controlling of stem cell renewal. The addition of Metformin increased the bindings of DNA methyltransferase-3a/b (DNMT3a/b) to the METTL3 promoter. With the help of the readers of NKAP and HNRNPA2B1, the cluster mediated m6A formation on pri-Let-7b processing increased the mature Let-7b, the key player in suppressing Notch signaling and re-captivating Osimertinib treatment. We revealed that the maturation processing signaling stimulated the methylation regulation of the miRNAs, and may determine the stemness control of the therapy resistance. Our findings may open up future drug development, targeting this pathway for lung cancer patients.
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http://dx.doi.org/10.3389/fonc.2021.731561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8770959PMC
January 2022

Mesenchyme homeobox 2 has a cancer-inhibiting function in breast carcinoma via affection of the PI3K/AKT/mTOR and ERK1/2 pathways.

Biochem Biophys Res Commun 2022 02 7;593:20-27. Epub 2022 Jan 7.

Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.

A cancer-inhibiting role of mesenchyme homeobox 2 (MEOX2) has been observed in several malignancies. However, the association between MEOX2 and breast carcinoma has not been addressed. This research focused on investigating the possible relevance of MEOX2 in breast carcinoma. Initial expression analysis by TCGA data uncovered low levels of MEOX2 in breast carcinoma. We then confirmed that MEOX2 was poorly expressed in clinical tumor specimens of breast carcinoma by real-time quantitative PCR and immunoblotting assays. Moreover, low levels of MEOX2 in breast carcinoma patients were found to be correlated with reduced overall survival. A series of cellular function assays showed that the forced expression of MEOX2 had anticancer effects, including the inhibition of cell proliferation, the induction of G0-G1 phase arrest, the restraint of metastatic potential, and the enhancement of chemosensitivity. Further analysis revealed that MEOX2 negatively modulated the phosphatidyl-inositol-3 kinase (PI3K)/AKT/mammalian target of the rapamycin (mTOR) and extracellular signal-regulated kinase (ERK1/2) pathways. Reactivation of AKT by a chemical activator reversed MEOX2-mediated anticancer effects. An in vivo xenograft assay validated the anticancer function of MEOX2 in breast carcinoma. Taken together, these data show that MEOX2 exerts a cancer-inhibiting role in breast carcinoma by affecting the PI3K/AKT/mTOR and ERK1/2 pathways. This work suggests MEOX2 as a new contributor for breast carcinoma progression, which may be a candidate target for anticancer therapy development.
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http://dx.doi.org/10.1016/j.bbrc.2022.01.011DOI Listing
February 2022

Value of MRI in assessing back pain after thoracolumbar osteoporotic vertebral compression fractures and discussion on the underlying mechanisms by tissue biopsy.

Eur Spine J 2022 May 17;31(5):1147-1157. Epub 2022 Jan 17.

Department of Spine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250000, China.

Purpose: The specific radiological feature of osteoporotic vertebral compression fractures (OVCFs) is bone marrow oedema (BME) on magnetic resonance imaging (MRI). However, the relationship between BME and back pain (BP) is unclear. We investigated the value of MRI in assessing BP and discussed the relevant mechanisms by tissue biopsy.

Methods: One hundred nineteen patients with thoracolumbar OVCFs were included in this study. We divided all patients into two groups: the low-oedema group (BME ≤ 75%) and the high-oedema group (BME > 75%). To reduce the error generated in the acute phase of fracture, we separately analysed patients in phases I (within one month) and II (more than one month). We compared the differences between the groups using the Mann-Whitney U test and investigated the correlations using Spearman's correlation test.

Results: The degree of BP was significantly correlated with BME (p < 0.001; p < 0.001) and fibrous tissue content (p = 0.006; p = 0.035) in both phases. Further, the fibrous tissue content in the low-oedema group (12.49 ± 7.37%; 15.25 ± 13.28%) was significantly lower than that in the high-oedema group (25.68 ± 20.39%, p = 0.014; 23.92 ± 14.61%, p = 0.022) in both phases. The lamellar bone content was significantly correlated with BP (p = 0.021) in phase II.

Conclusions: BME signals on MRI can accurately predict the degree of BP, and the main mechanisms are related to the stimulation of fibrous tissue.
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http://dx.doi.org/10.1007/s00586-021-07095-6DOI Listing
May 2022

Bone microarchitecture and metabolism in elderly male patients with signs of intravertebral cleft on MRI.

Eur Radiol 2022 Jan 6. Epub 2022 Jan 6.

Department of Spine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250000, China.

Objectives: Intravertebral cleft (IVC) is a common but not unique imaging manifestation in Kümmell's disease. To date, great controversy exists regarding the specific mechanisms of IVC. In this study, we aimed to investigate the characteristics of microarchitecture and metabolism in patients with IVC and to analyse the correlations between degree of vertebral collapse and risk factors.

Methods: A total of 79 elderly men were included in this study. We divided all patients into two groups: the IVC group (30 patients) and the non-IVC group (49 patients). We compared the differences in microarchitecture and bone turnover marker (BTM) serum concentrations between the groups and analysed risk factors affecting vertebral collapse by using the Mann-Whitney U test and Spearman's correlation test.

Results: Quantitative analysis of the microarchitecture showed higher content of necrotic bone (p < 0.001) and lower content of lamellar bone (p < 0.001) in the IVC group. Analysis of BTMs identified lower concentration of N-terminal propeptide of type I collagen (PINP, p = 0.002) and higher concentration of β-isomerized C-terminal telopeptide (β-CTX, p < 0.001) in the IVC group. The correlation analysis showed that lamellar bone content (p < 0.001) and spine T-score (p = 0.011) were significantly correlated with the degree of vertebral collapse.

Conclusions: IVC is a radiological feature of excessive bone resorption by higher activities of osteoclasts and decreased bone remodelling ability by lower activities of osteoblasts. Histomorphological feature in patients with IVC is delayed callus mineralisation, which may increase the risk of vertebral collapse.

Key Points: • A key histomorphological feature in patients with IVC is delayed callus mineralisation, which may aggravate the degree of vertebral collapse. • We investigated bone metabolism in patients with IVC to evaluate the activities of osteoclasts and osteoblasts directly. • We propose a novel hypothesis for the pathogenesis of IVC: bone resorption by higher activity of osteoclasts and decreased callus mineralisation ability by lower activity of osteoblasts are the main mechanisms leading to IVC.
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http://dx.doi.org/10.1007/s00330-021-08458-9DOI Listing
January 2022

Understanding Human Behaviors and Injury Factors in Underground Mines using Data Analytics.

Annu Int Conf IEEE Eng Med Biol Soc 2021 11;2021:2459-2462

This study aims to understand human behaviors and associated injury causing factors in underground mines using data analytics of historical mining data. Decision tree and association rule were used to provide a statistical analysis of leading factors of hazards in underground mines. Based on the results, we were able to explore hazard feature identification using image feature recognition aiming to provide real-time monitoring for miners to secure healthy and safety operation via wearable computing.
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http://dx.doi.org/10.1109/EMBC46164.2021.9630428DOI Listing
November 2021

Erratum to: Double-edged effects caused by magnesium ions and alkaline environment regulate bioactivities of magnesium-incorporated silicocarnotite .

Regen Biomater 2021 Dec 30;8(6):rbab055. Epub 2021 Nov 30.

Shanghai Key Laboratory of Orthopedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, No. 639, Zhizaoju Road, Shanghai, Huangpu District 200011, China.

[This corrects the article DOI: 10.1093/rb/rbab016.].
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http://dx.doi.org/10.1093/rb/rbab055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8634078PMC
December 2021

[Status of HIV infection among men who have sex with men in Harbin, 2009-2018].

Zhonghua Liu Xing Bing Xue Za Zhi 2021 Mar;42(3):538-543

Harbin Center for Disease Control and Prevention, Harbin, 150056, China.

To explore the status of HIV infection, time trends and related factors of MSM in Harbin from 2009 to 2018 and provide evidences for comprehensive prevention and control strategies of MSM HIV/AIDS. From April to July during 2009-2018, continuous cross-sectional studies were conducted on MSM recruited through snowball sampling. The unified questionnaire was used to collect demographic, behavioral, and serological information. The SPSS 23.0 software was used for statistical analysis, and the Joinpoint 4.8.0.1 software was applied to the annual percent change (APC) for time trends analysis using the Joinpoint regression model. A total of 4 813 MSM were surveyed in Harbin from 2009 to 2018. The overall HIV antibody positive rate was 11.3 % ( 543/4 813). Joinpoint regression analysis showed that there was an increase in the HIV antibody positive rate from 2009 to 2015, while the segmentation point was in 2015 (=4.2, <0.05) but, there was a decrease from 2015 to 2018(=-1.3, =0.3). The positive rate of syphilis antibody was 12.9% (621/4 813). There was a decrease in the positive rate of syphilis antibodies from 2009 to 2013 (-2.80.05). There was a decrease in the positive rate of syphilis antibodies from 2013 to 2018 (=-0.7,=0.5). Results from multiple logistic aggression analysis showed that the risk factors associated with the prevalence of HIV infection including network recruitment (a=1.307, 95%: 1.057-1.617), age 30 and above (a=1.905, 95%: 1.235-2.939) and syphilis antibody positive (a=4.728, 95%: 3.751-5.961). Protective factors appeared: knowledge of HIV/AIDS (a=0.598, 95%: 0.433-0.825) and consistent use of condom during anal sex in the past six months (a=0.683, 95%: 0.550-0.850). The HIV antibody positive rate peaked in 2015 among MSM in Harbin from 2009 to 2018, first increased and then decreased. The positive rate of syphilis antibody showed a decreasing trend. Intervention models based on social media software, age 30 and above and syphilis antibody-positive need to be explored. It also promotes condom use and referral for syphilis among MSM.
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http://dx.doi.org/10.3760/cma.j.cn112338-20200328-00462DOI Listing
March 2021

Generating 3D-cultured organoids for pre-clinical modeling and treatment of degenerative joint disease.

Signal Transduct Target Ther 2021 11 12;6(1):380. Epub 2021 Nov 12.

Clinical and Translational Research Center for 3D Printing Technology, Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

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http://dx.doi.org/10.1038/s41392-021-00675-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8585871PMC
November 2021

A simple and fast LC-MS/MS method for the simultaneous determination of tenofovir alafenamide and tenofovir in human plasma.

Biomed Chromatogr 2022 Mar 8;36(3):e5273. Epub 2021 Dec 8.

Suzhou Haike Medical Technology Co. Ltd., Suzhou, China.

A simple and fast liquid chromatography-tandem mass spectrometry method was established and validated for the simultaneous determination of tenofovir alafenamide (TAF) and tenofovir (TNF) in human plasma. A simple protein precipitation procedure was employed to extract analytes from plasma. Chromatographic separation was performed on an Eclipse Plus C column utilizing a fast gradient elution starting with 2% of 2 mM ammonium acetate-formic acid (100/0.1, v/v) followed by increasing the percentage of acetonitrile. Detection was performed on a tandem mass spectrometer equipped with an electrospray ionization source operated in the positive ionization mode, using the transitions m/z 477.2 → m/z 346.1 for TAF and m/z 288.1 → m/z 176.1 for TNF. TAF-d and TNF-d were used as the internal standard of TAF and TNF, respectively. The method was validated in the concentration ranges 1.25-500 ng/mlfor TAF and 0.300-15.0 ng/ml for TNF with acceptable accuracy and precision.
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http://dx.doi.org/10.1002/bmc.5273DOI Listing
March 2022

Isosinensetin alleviates the injury of human bronchial epithelial cells induced by PM.

Exp Ther Med 2021 Dec 11;22(6):1435. Epub 2021 Oct 11.

Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, Liaoning 110034, P.R. China.

Flavonoids which are extracted from citrus peel and pulp have been reported to have multiple beneficial effects on human health. Isosinensetin (ISO) is a type of flavonoid compound, which has several protective effects including anticancer, antioxidant, antiviral, anti-inflammatory and bacteriostatic. However, the molecular mechanism of its antioxidant and anti-inflammatory effects remain unclear. The present study aimed to investigate the intervention effect and possible mechanism of ISO on human bronchial epithelial cells injured by fine particular matter ≤2.5 µm in diameter (PM). In the present study, the cell viability was detected by Cell Counting Kit-8 method. The levels of pro-inflammatory cytokines were analyzed by ELISA. The level of reactive oxygen species (ROS) was detected by fluorescence probe. The expression levels of proliferating cell nuclear antigen (PCNA), nuclear factor erythroid 2-related factor 2 (Nrf2) and nuclear factor кΒ (NF-кB) proteins were detected by western blotting. The results revealed that ISO evidently increased the viability of 16-HBE cells and sharply decreased the levels of pro-inflammatory factors in cell culture supernatant. ISO significantly inhibited ROS release caused by PM. Moreover, the expression levels of PCNA, Nrf2 and NF-кB proteins were downregulated after ISO incubation. These results indicated that ISO alleviated 16-HBE-cell injury by PM through the ROS-Nrf2/NF-кB signaling pathway.
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http://dx.doi.org/10.3892/etm.2021.10870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8543438PMC
December 2021

Chromosome-scale genome assembly of Castanopsis tibetana provides a powerful comparative framework to study the evolution and adaptation of Fagaceae trees.

Mol Ecol Resour 2022 Apr 2;22(3):1178-1189. Epub 2021 Nov 2.

Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.

Fagaceae species are increasingly used as models to elucidate the process and mechanism of adaptation and speciation by integrating ecology, evolution and genomics. The genus Castanopsis belongs to the family Fagaceae and is mainly distributed across subtropical and tropical Asia. In the present study, we reported the first chromosome-scale genome assembly of Castanopsis tibetana, a common species of evergreen broadleaved forests in subtropical China. The combination of Nanopore sequencing and Hi-C technologies enabled a high-quality genome assembly. The final assembled genome size of C. tibetana was 878.6 Mb (97.6% of the estimated genome size), consisting of 477 contigs with an N50 length of 3.3 Mb. The benchmarking universal single-copy orthologue (BUSCO) assessment indicated a completeness of 93.0%. Hi-C scaffolding generated 12 pseudochromosomes, representing 98.7% of the assembled genome. Subsequently, 40,937 protein-coding genes were predicted and 90.04% of them were functionally annotated. More than 476.9 Mb of repetitive sequences (54.3% of the genome) were identified, and the percentage of the genome covered by TE elements was 39.98%. Comparative genomics analysis revealed that C. tibetana was most closely related to Castanea mollissima and diverged at 18.48 Ma, and that C. tibetana has undergone considerable gene family expansion and contraction. Evidence of positive selection was detected in 53 genes, which showed different arrangement pattern compared to Quercus robur. The chromosome-scale genome assembly of C. tibetana will expand Fagaceae genome resources across the family and provide a powerful comparative framework to study the adaptation and evolution of Fagaceae trees.
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http://dx.doi.org/10.1111/1755-0998.13539DOI Listing
April 2022
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