Publications by authors named "Yong Yu"

748 Publications

A deep learning approach to identify gene targets of a therapeutic for human splicing disorders.

Nat Commun 2021 06 7;12(1):3332. Epub 2021 Jun 7.

Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA.

Pre-mRNA splicing is a key controller of human gene expression. Disturbances in splicing due to mutation lead to dysregulated protein expression and contribute to a substantial fraction of human disease. Several classes of splicing modulator compounds (SMCs) have been recently identified and establish that pre-mRNA splicing represents a target for therapy. We describe herein the identification of BPN-15477, a SMC that restores correct splicing of ELP1 exon 20. Using transcriptome sequencing from treated fibroblast cells and a machine learning approach, we identify BPN-15477 responsive sequence signatures. We then leverage this model to discover 155 human disease genes harboring ClinVar mutations predicted to alter pre-mRNA splicing as targets for BPN-15477. Splicing assays confirm successful correction of splicing defects caused by mutations in CFTR, LIPA, MLH1 and MAPT. Subsequent validations in two disease-relevant cellular models demonstrate that BPN-15477 increases functional protein, confirming the clinical potential of our predictions.
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http://dx.doi.org/10.1038/s41467-021-23663-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8185002PMC
June 2021

[Construction of Escherichia coli cell factories].

Sheng Wu Gong Cheng Xue Bao 2021 May;37(5):1564-1577

Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin 300308, China.

As an important model industrial microorganism, Escherichia coli has been widely used in pharmaceutical, chemical industry and agriculture. In the past 30 years, a variety of new strategies and techniques, including artificial intelligence, gene editing, metabolic pathway assembly, and dynamic regulation have been used to design, construct, and optimize E. coli cell factories, which remarkably improved the efficiency for biotechnological production of chemicals. In this review, three key aspects for constructing E. coli cell factories, including pathway design, pathway assembly and regulation, and optimization of global cellular performance, are summarized. The technologies that have played important roles in metabolic engineering of E. coli, as well as their future applications, are discussed.
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http://dx.doi.org/10.13345/j.cjb.200716DOI Listing
May 2021

A Novel Biosorbent From Hardwood Cellulose Nanofibrils Grafted With Poly(-Aminobenzene Sulfonate) for Adsorption of Cr(VI).

Front Bioeng Biotechnol 2021 17;9:682070. Epub 2021 May 17.

Department of Paper Science and Engineering, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, South Korea.

Cellulose from different lignocellulosic biomass can be used to prepare various materials. In this work, the cellulose nanofibrils were produced from hardwood bleached kraft pulp. Then, a novel biosorbent from cellulose nanofibrils grafted with poly(-aminobenzene sulfonate) (PABS) was prepared for effective detoxification and adsorption of Cr(VI) in an aqueous medium. 6,6-tetramethylpiperidine-1-oxyl (TEMPO)-oxidized cellulose nanofibrils (TOCNF) with a high aspect ratio was used as an adsorbent matrix. PABS, an amine-rich conductive polymer, was grafted onto TOCNF via a successive two-step reaction. The analyses of Fourier transform infrared (FT-IR) spectroscopy and X-ray photoelectron spectroscopy (XPS) confirmed the successful grafting reaction between TOCNF and PABS. The biosorbent from TOCNF-bonded PABS with the nitrogen content of 7.0% was synthesized. It exhibited excellent Cr(VI) adsorption capacity at a solution pH below 3, and almost 100% Cr(VI) can be removed. The adsorption of Cr(VI) on the biosorbent was described by a pseudo-second-order model and obeyed the Langmuir model. The Cr(VI) adsorption capacity of the biosorbent from TOCNF-bonded PABS was almost 10 times higher than that of TOCNF. It was interesting to note that part of Cr(VI) ions had been reduced to Cr(III) during the adsorption process. It indicated that the biosorbent from TOCNF grafted with PABS could detoxify and adsorb Cr(VI) synchronously.
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http://dx.doi.org/10.3389/fbioe.2021.682070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166254PMC
May 2021

Correction to: Evaluation of lifestyle risk factor differences in global patterns of breast cancer mortality and DALYs during 1990-2017 using hierarchical age-period-cohort analysis.

Environ Sci Pollut Res Int 2021 May 31. Epub 2021 May 31.

Department of Epidemiology and Biostatistics, School of Health Sciences, Wuhan University, Wuhan, 430071, China.

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http://dx.doi.org/10.1007/s11356-021-14448-7DOI Listing
May 2021

Entropy engineering promotes thermoelectric performance in p-type chalcogenides.

Nat Commun 2021 May 28;12(1):3234. Epub 2021 May 28.

Shenzhen Key Laboratory of Thermoelectric Materials, Department of Physics, Southern University of Science and Technology, Shenzhen, China.

We demonstrate that the thermoelectric properties of p-type chalcogenides can be effectively improved by band convergence and hierarchical structure based on a high-entropy-stabilized matrix. The band convergence is due to the decreased light and heavy band energy offsets by alloying Cd for an enhanced Seebeck coefficient and electric transport property. Moreover, the hierarchical structure manipulated by entropy engineering introduces all-scale scattering sources for heat-carrying phonons resulting in a very low lattice thermal conductivity. Consequently, a peak zT of 2.0 at 900 K for p-type chalcogenides and a high experimental conversion efficiency of 12% at ΔT = 506 K for the fabricated segmented modules are achieved. This work provides an entropy strategy to form all-scale hierarchical structures employing high-entropy-stabilized matrix. This work will promote real applications of low-cost thermoelectric materials.
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http://dx.doi.org/10.1038/s41467-021-23569-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8163856PMC
May 2021

The comparison of epidemiological characteristics between confirmed and clinically diagnosed cases with COVID-19 during the early epidemic in Wuhan, China.

Glob Health Res Policy 2021 05 28;6(1):18. Epub 2021 May 28.

Department of Epidemiology and Biostatistics, School of Health Sciences, Wuhan University, 430071, Wuhan, China.

Background: To put COVID-19 patients into hospital timely, the clinical diagnosis had been implemented in Wuhan in the early epidemic. Here we compared the epidemiological characteristics of laboratory-confirmed and clinically diagnosed cases with COVID-19 in Wuhan.

Methods: Demographics, case severity and outcomes of 29,886 confirmed cases and 21,960 clinically diagnosed cases reported between December 2019 and February 24, 2020, were compared. The risk factors were estimated, and the effective reproduction number (Rt) of SARS-CoV-2 was also calculated.

Results: The age and occupation distribution of confirmed cases and clinically diagnosed cases were consistent, and their sex ratio were 1.0 and 0.9, respectively. The epidemic curve of clinical diagnosis cases was similar to that of confirmed cases, and the city centers had more cumulative cases and higher incidence density than suburbs in both of two groups. The proportion of severe and critical cases (21.5 % vs. 14.0 %, P < 0.0001) and case fatality rates (5.2 % vs. 1.2 %, P < 0.0001) of confirmed cases were all higher than those of clinically diagnosed cases. Risk factors for death we observed in both of two groups were older age, male, severe or critical cases. Rt showed the same trend in two groups, it dropped below 1.0 on February 6 among confirmed cases, and February 8 among clinically diagnosed cases.

Conclusions: The demographic characteristics and spatiotemporal distributions of confirmed and clinically diagnosed cases are roughly similar, but the disease severity and clinical outcome of clinically diagnosed cases are better than those of confirmed cases. In cases when detection kits are insufficient during the early epidemic, the implementation of clinical diagnosis is necessary and effective.
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http://dx.doi.org/10.1186/s41256-021-00200-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8161348PMC
May 2021

Wrinkling of liquid-crystal elastomer disks caused by light-driven dynamic contraction.

Phys Rev E 2021 Apr;103(4):L041002

Department of Civil Engineering, Anhui Jianzhu University, Hefei, Anhui Province 230601, People's Republic of China.

The trigger time of light-driven wrinkling is very critical for accurate active control in photo-powered machines. In this paper, the wrinkling of liquid-crystal elastomer disks caused by light-driven dynamic contraction is theoretically studied, and the critical times for appearance and disappearance of the wrinkles are numerically calculated. The light-driven prebuckling stress can be significantly adjusted by changing the contraction coefficient, while controlled within a certain limit by tuning the light intensity and illumination time. There exists a critical contraction coefficient for triggering the wrinkling of the disk, and the second-order mode of wrinkling is the most unstable mode, which is most easily induced for the illumination radius ratio 0.69. The critical times for the appearance and disappearance of wrinkling can be significantly changed by the contraction coefficient, while regulated only within a certain range by the light intensity and the illumination radius ratio. These results have potential applications for accurate active control in the fields of soft robotics, active microlens, smart windows, and tunable surface patterns.
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http://dx.doi.org/10.1103/PhysRevE.103.L041002DOI Listing
April 2021

Co-treatment of electroplating sludge, copper slag, and spent cathode carbon for recovering and solidifying heavy metals.

J Hazard Mater 2021 May 5;417:126020. Epub 2021 May 5.

Engineering Research Center of Metallurgical Energy Conservation and Emission Reduction, Ministry of Education, Kunming University of Science and Technology, Kunming, China; National Local Joint Engineering Research Center of Energy Saving and Environmental Protection Technology in Metallurgy and Chemical Engineering Industry, Kunming University of Science and Technology, Kunming, China; State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization, Kunming University of Science and Technology, Kunming, China; Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming, China.

Electroplating sludge, a hazardous solid waste product of the electroplating industry, presents a serious environmental pollution risk. In this study, an environmentally friendly process for solidifying and recovering heavy metals from electroplating sludge using copper slag and spent cathode carbon is proposed. Combining the results of toxicity characteristic leaching procedure tests, thermodynamic analysis, chemical analysis, X-ray diffraction analysis, and electron probe microanalysis, the Cr, Ni, Cu, Fe, and F transformation mechanisms were first probed during vitrification. Under optimal experimental conditions, the Cr, Ni, and Cu recovery ratios reached 75.56 wt%, 98.41 wt%, and 99.25 wt%, and they increased by 40%, 5%, and 5%, respectively compared with the currently utilized technique. Moreover, the toxicity leaching results of the slag indicate that the Cr, F, and Cu are stable, while Ni is easily leached from the (Fe,Ni)(Fe,Cr)O and alloy phases. Under the optimal metal recovery conditions, the leaching concentrations of Cr, Cu, F, and Ni were 0.57 mg/L, 4.45 mg/L, 1.52 mg/L, and 1.85 mg/L, respectively, which can be reused in other materials, minimizing the environmental risk. The electroplating sludge, copper slag, and spent cathode carbon co-treatment process achieves waste disposal with waste and significantly reduces electroplating sludge processing costs.
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http://dx.doi.org/10.1016/j.jhazmat.2021.126020DOI Listing
May 2021

Multiplex ligation-dependent probe amplification identifies copy number changes in normal and undetectable karyotype MDS patients.

Ann Hematol 2021 May 15. Epub 2021 May 15.

Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China.

Chromosomal abnormalities play an important role in classification and prognostication of myelodysplastic syndrome (MDS) patients. However, more than 50% of low-risk MDS patients harbor a normal karyotype. Recently, multiplex ligation-dependent probe amplification (MLPA) has emerged as an effective and robust method for the detection of cytogenetic aberrations in MDS patients. To characterize the subset of MDS with normal karyotype or failed chromosome banding analysis, we analyzed 144 patient samples with normal karyotype or undetectable through regular chromosome banding analysis, which were subjected to parallel comparison via fluorescence in situ hybridization (FISH) and MLPA. MLPA identifies copy number changes in 16.7% of 144 MDS patients, and we observed a significant difference in overall survival (OS) (median OS: undefined vs 27 months, p=0.0071) in patients with normal karyotype proved by MLPA versus aberrant karyotype cohort as determined by MLPA. Interestingly, patients with undetectable karyotype via regular chromosome banding indicated inferior outcome. Collectively, MDS patients with normal or undetectable karyotype via chromosome banding analysis can be further clarified by MLPA, providing more prognostic information that benefit for individualized therapy.
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http://dx.doi.org/10.1007/s00277-021-04550-8DOI Listing
May 2021

Comparison of LBM and FVM in the estimation of LAD stenosis.

Proc Inst Mech Eng H 2021 May 13:9544119211016912. Epub 2021 May 13.

School of Medicine, Tsinghua University, Beijing, P. R. China.

The finite volume method (FVM)-based computational fluid dynamics (CFD) technology has been applied in the non-invasive diagnosis of coronary artery stenosis. Nonetheless, FVM is a time-consuming process. In addition to FVM, the lattice Boltzmann method (LBM) is used in fluid flow simulation. Unlike FVM solving the Navier-Stokes equations, LBM directly solves the simplified Boltzmann equation, thus saving computational time. In this study, 12 patients with left anterior descending (LAD) stenosis, diagnosed by CTA, are analysed using FVM and LBM. The velocities, pressures, and wall shear stress (WSS) predicted using FVM and LBM for each patient is compared. In particular, the ratio of the average and maximum speed at the stenotic part characterising the degree of stenosis is compared. Finally, the golden standard of LAD stenosis, invasive fractional flow reserve (FFR), is applied to justify the simulation results. Our results show that LBM and FVM are consistent in blood flow simulation. In the region with a high degree of stenosis, the local flow patterns in those two solvers are slightly different, resulting in minor differences in local WSS estimation and blood speed ratio estimation. Notably, these differences do not result in an inconsistent estimation. Comparison with invasive FFR shows that, in most cases, the non-invasive diagnosis is consistent with FFR measurements. However, in some cases, the non-invasive diagnosis either underestimates or overestimates the degree of stenosis. This deviation is caused by the difference between physiological and simulation conditions that remains the biggest challenge faced by all CFD-based non-invasive diagnostic methods.
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http://dx.doi.org/10.1177/09544119211016912DOI Listing
May 2021

Influences and mechanisms of nanoparticles on pentachloronitrobenzene accumulation by earthworms.

Environ Sci Pollut Res Int 2021 May 13. Epub 2021 May 13.

Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.

Pesticides and nanoparticles may coexist in soil; however, influences of nanoparticles on accumulation of pesticides in terrestrial organisms are still unclear. This study aims to investigate the influences and mechanisms of metal oxide nanoparticles (nano ZnO and nano CuO) on accumulation of pentachloronitrobenzene (PCNB) in earthworms and their combined toxicity. The earthworms were cultivated in the soil spiked with nanoparticles (10, 50, 250 mg/kg) and PCNB (100 μg/kg) for 21 days. The concentrations of PCNB in earthworms in binary exposure treatments (PCNB + ZnO and PCNB + CuO) reached 2.47 and 3.13 times of that in individual PCNB exposure treatment, indicating that nanoparticles facilitated the accumulation of PCNB in earthworms. The contents of reactive oxygen species (ROS) in earthworms in treatments PCNB + ZnO 250 and PCNB + CuO 250 reached 379 and 316 fluorescence intensity/mg Protein, respectively, which were significantly higher than that in control group (183 fluorescence intensity/mg protein), indicating that nanoparticles would cause oxidative stress to earthworms. Earthworm coelomocytes were extracted from healthy earthworms and cultivated in culture media in cytotoxicity tests. Changes of intracellular ROS contents and cell viability suggested that PCNB and nanoparticles caused serious oxidative damage to earthworm coelomocytes, thus leading to the damage of cell membrane and cell death. In in vivo tests, changes of biomarkers (ROS and malondialdehyde) demonstrated that these pollutants injured the earthworms. Increased accumulation of PCNB in binary exposure treatments was due to the damage of body cavity caused by nanoparticles. This study provides a novel hypothesis for nanoparticles facilitating organic pollutants entering terrestrial organisms and determines whether nanoparticles would bring about greater environmental risks of other pollutants.
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http://dx.doi.org/10.1007/s11356-021-14368-6DOI Listing
May 2021

BPV associated with imaging features of SSI on MRI.

Brain Behav 2021 May 7:e02155. Epub 2021 May 7.

Department of Neurology, Weihai Central Hospital Affiliated to Qingdao University, Weihai, China.

Objectives: A retrospective study was performed to investigate the relationship between blood pressure variability (BPV) and imaging features of single small infarction (SSI) on magnetic resonance imaging (MRI).

Materials And Methods: Two hundreds and five patients with SSI and 120 healthy subjects matched with age and sex as the control group were enrolled into this study. All subjects came from the Affiliated Hospital to Qingdao University and Qingdao Municipal Hospital from October 2011 to June 2016. Research subjects were classified into different groups. Blood pressure was measured once a day and recorded during the hospitalization period (7-10 days). The followed up data of patients after discharging from hospital was collected from the follow-up records.

Results: Twenty-four hours BPV (SBP , DSBP , DSBP , NDBP , NDBP and DDBP ), day-to-day, and visit-to-visit BPV (SBP , SBP , DBP and DBP ) in the SSI group were significantly higher than that in control group. Compared with the giant lacunar group, day-to-day BPV (SBP , SBP , SBP , SBP , DBP , DBP , DBP ), and visit-to-visit BPV (SBP , SBP , SBP , DBP , DBP , DBP ) were significantly higher in the small lacunar infarct group (p < .05). The 24 hr BPV (SBP , DDBP , DDBP ), day-to-day BPV (SBP , SBP , SBP ), and visit-to-visit SBP in nonround lesion group were significantly higher than that in round group (p < .05). Compared with nondeep lesion group, some parameters in day-to-day BPV and visit-to-visit BPV were significantly higher in the deep small lesion group (p < .05).

Conclusion: Increased BPV parameters such as day-to-day and visit-to-visit (SBP , SBP , DBP ) were related to the SSI characterized by small lesion in deep brain region.
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http://dx.doi.org/10.1002/brb3.2155DOI Listing
May 2021

Heavy Metals in Indoor Dust Across China: Occurrence, Sources and Health Risk Assessment.

Arch Environ Contam Toxicol 2021 Jul 4;81(1):67-76. Epub 2021 May 4.

College of Chemistry, Changchun Normal University, Changchun, 130032, China.

In this study, the occurrence of heavy metals including cadmium (Cd), chromium (Cr), copper (Cu), lead (Pb), and zinc (Zn) was investigated in indoor dust samples collected from 33 urban and rural areas in 11 provinces, China. The concentrations of the selected heavy metals were determined by an inductively coupled plasma mass spectrometry. The mean concentrations of Zn (166 mg kg), Pb (40.7 mg kg), Cr (19.8 mg kg), Cu (16.9 mg kg), and Cd (2.29 mg kg) in indoor dust are in low or moderate levels compared with other countries or regions. Cd was significantly enriched with the highest enrichment factor of 23.7, followed by Zn, Pb, Cu, and Cr, which were all lower than 3. The concentrations of Pb from Northern China (61.4 mg kg) were significantly higher than those from Southern China (8.88 mg kg). The concentrations of heavy metals in indoor dusts from rural areas were higher than those from urban areas except for Cu. The multivariate analysis of variance revealed that wall cover, fuel types, and air conditioning were dominant factors influencing the levels of heavy metals in indoor dust. Principal component analysis showed that outdoor dust and wall paint were main factors for the high concentrations of Cd, Pb, and Cr, accounting for 40.6% of the total contribution; traffic sources contributed to the high levels of Cu and Zn explained 20.6% of the total variance. The hazard indexes of selected heavy metals were less than 1 and carcinogenic risk value of Cr were between 1.01 × 10 and 1 × 10, indicating minor noncarcinogenic and carcinogenic risks from heavy metals in indoor dust for residents in China. Pb contributed 72.0% and 86.9% to the sum of noncarcinogenic risk values of selected heavy metals for adults and children, respectively. The carcinogenic risk value of Cr was approximately 13-fold higher than that of Cd for both adults and children. Children endured higher risks from heavy metals in indoor dust compared with adults.
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http://dx.doi.org/10.1007/s00244-021-00849-9DOI Listing
July 2021

Evaluation of lifestyle risk factor differences in global patterns of breast cancer mortality and DALYs during 1990-2017 using hierarchical age-period-cohort analysis.

Environ Sci Pollut Res Int 2021 May 3. Epub 2021 May 3.

Department of Epidemiology and Biostatistics, School of Health Sciences, Wuhan University, Wuhan, 430071, China.

Background: Statistical evidence on breast cancer (BC) burden related to health and lifestyle risk factors are valuable for health policy-making. This study aimed to compare the trends in BC mortality and disability adjusted life years (DALYs) attributable to various health and life style risk factors among different world's regions according to sociodemographic index (SDI).

Methods: We extracted the age-standardized and age-specific rate of mortality and DALYs of women BC during 1990-2017 using the comparative risk assessment framework of the 2017 global burden of disease (GBD) study. We performed hierarchical age-period-cohort analysis to estimate age- and time-related trends, and effect of interactions between different risk factors on BC risk.

Results: During 1990-2017, the age-standardized rate of mortality and DALYs of women BC was increasing in less developed and under developing regions. The risk factor alcohol use [RR 51.3(95%CI 17.6-149.7)] and smoking [5.9(2.0-17.3)] were significantly highly contributor to increased mortality risk in high SDI region. Whereas in the low-SDI region, the greater mortality risk was observed in alcohol use [6.9(2.4-17)] and high FPG [2.7(1.5-3.1)]-related deaths. The adjusting for individual age, period, and risk factor effects, the significant interaction effect between metabolic risk factors and older ages were observed in all SDI regions and globally as well. However, an increasing cohort effect of alcohol, high fasting plasma glucose (FPG) and smoking-related death, and DALYs was observed during 1960 to 1985 cohorts among low-SDI regions.

Conclusions: The age-standardized rates of mortality and DALYs due to BC has been increasing in low-SDI region. Alcohol consumption, high body mass index (BMI), high FPG, and smoking are potential BC risk factors particularly in older ages that leading to adverse disease outcomes. Therefore, rapid aging and prevalence of these prospective risk factors may strengthen the increasing mortality and DALYs of BC in low-SDI region. Hence, preventive measure along with strict action against concerned BC risk factors should be taken to reduce the disease burden specifically among lower-SDI regions.
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http://dx.doi.org/10.1007/s11356-021-14165-1DOI Listing
May 2021

Three body photodissociation of the water molecule and its implications for prebiotic oxygen production.

Nat Commun 2021 04 30;12(1):2476. Epub 2021 Apr 30.

State Key Laboratory of Molecular Reaction Dynamics and Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.

The provenance of oxygen on the Earth and other planets in the Solar System is a fundamental issue. It has been widely accepted that the only prebiotic pathway to produce oxygen in the Earth's primitive atmosphere was via vacuum ultraviolet (VUV) photodissociation of CO and subsequent two O atom recombination. Here, we provide experimental evidence of three-body dissociation (TBD) of HO to produce O atoms in both D and P states upon VUV excitation using a tunable VUV free electron laser. Experimental results show that the TBD is the dominant pathway in the VUV HO photochemistry at wavelengths between 90 and 107.4 nm. The relative abundance of water in the interstellar space with its exposure to the intense VUV radiation suggests that the TBD of HO and subsequent O atom recombination should be an important prebiotic O-production, which may need to be incorporated into interstellar photochemical models.
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http://dx.doi.org/10.1038/s41467-021-22824-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8087761PMC
April 2021

Five long non-coding RNAs establish a prognostic nomogram and construct a competing endogenous RNA network in the progression of non-small cell lung cancer.

Authors:
Yong Yu Kaiming Ren

BMC Cancer 2021 Apr 23;21(1):457. Epub 2021 Apr 23.

Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.

Background: Accumulating evidence has revealed that long non-coding RNAs (lncRNAs) play vital roles in the progression of non-small cell lung cancer (NSCLC). But the relationship between lncRNAs and survival outcome of NSCLC remains to be explored. Therefore, we attempt to figure out their survival roles and molecular connection in NSCLC.

Methods: By analyzing the transcriptome profiling of NSCLC from TCGA databases, we divided patients into three groups, and identified differentially expressed lncRNAs (DELs) of each group. Next, we explored the prognostic roles of common DELs by univariate and multivariate Cox analysis, Lasson, and Kaplan-Meier analysis. Additionally, we assessed and compared the prognostic accuracy of 5 lncRNAs through ROC curves and AUC values. Ultimately, we detected their potential function by enrichment analysis and molecular connection through establishing a competing endogenous RNA (ceRNA) network.

Results: One hundred ninety-seven common DELs were spotted. And we successfully screened out 5 lncRNAs related to the patient's survival, including LINC01833, AC112206.2, FAM83A-AS1, BANCR, and HOTAIR. Combing with age and AJCC stage, we constructed a nomogram that prognostic prediction was superior to the traditional parameters. Furthermore, 275 qualified mRNAs related to 5 lncRNAs were spotted. Functional analysis indicates that these lncRNAs act key roles in the progression of NSCLC, such as P53 and cell cycle signaling pathway. And ceRNA network also suggests that these lncRNAs are tightly connected with tumor progression.

Conclusions: A nomogram and ceRNA network based on 5 lncRNAs indicate that there can effectively predict the overall survival of NSCLC and potentially serve as a therapeutic guide for NSCLC.
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http://dx.doi.org/10.1186/s12885-021-08207-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067646PMC
April 2021

Effects of polystyrene microplastics on uptake and toxicity of phenanthrene in soybean.

Sci Total Environ 2021 Aug 10;783:147016. Epub 2021 Apr 10.

Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China. Electronic address:

Microplastics (MPs) can influence the availability of contaminants in the soil and have adverse effects on plants. Up to now, the effects of MPs on the uptake of organic pollutants by leguminous plants are still unclear. In this study, we explored the impacts and mechanisms of polystyrene MPs of different sizes on the uptake of phenanthrene (Phe) by soybean seedlings. The results showed that MPs decreased the uptake of Phe in soybean roots and leaves. Micron-size MPs showed a higher inhibition of Phe uptake in roots than nano-size MPs (4.83 mg/kg) at the beginning with concentrations of 1.89 mg/kg, 3.40 mg/kg, and 0.72 mg/kg in groups 1 μm, 10 μm, and 100 μm MPs/Phe, respectively. The combined toxicity of micron-size MPs and Phe to soybean plants was higher than that of nano-size MPs and Phe, and 100 μm MPs and Phe co-contaminant show the highest toxicity to soybean. The activities of antioxidative enzymes and their gene expression showed that micron-size MPs induced higher genotoxic and oxidative damage to soybean roots than nano-size MPs, which decreased the activity of roots, thus leading to the lower uptake of Phe by soybean roots and leaves. This study highlights that the combined exposure to MPs and Phe causes harmful effects on soybean plants and MPs inhibit the uptake of organic pollutants by higher plants.
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http://dx.doi.org/10.1016/j.scitotenv.2021.147016DOI Listing
August 2021

Complete genome sequence of Marinomonas arctica BSI20414, a giant antifreeze protein-producing bacterium isolated from Arctic sea ice.

Mar Genomics 2021 Jun 2;57:100829. Epub 2020 Nov 2.

Key Laboratory for Polar Science, MNR, Polar Research Institute of China, 451 Jinqiao Road, Shanghai 200136, China.

Sea ice in the polar oceans is a dynamic and challenging environment for life to survive, with extreme gradients of temperature, salinity and nutrients etc., as well as formation of ice crystals. Bacteria surviving in sea ice attract broad attention from academia and industry, due to fascinating mechanisms for adaptation. Here we described the complete genome sequence of Marinomonas arctica BSI20414, isolated from Arctic sea ice. The strain tolerated high salinity and low temperature. Genetic features commonly related to adaptation to oxidative stress, osmotic stress and cold stress were detected in the genome. In addition, a large adhesion protein containing a putative antifreeze protein (AFP) domain was detected in the genome, similar with the giant AFP MpIBP from M. primoryensis. The presence of the putative AFP could facilitate M. arctica BSI20414 to bind to sea ice for favorable conditions and protect it from freezing. The genome sequence and the AFP reported here can provide insights into adaptation to sea ice and can be explored further for biotechnological applications.
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http://dx.doi.org/10.1016/j.margen.2020.100829DOI Listing
June 2021

GAS5 regulates viability and apoptosis in TGF-β1-stimulated bronchial epithelial cells by regulating miR-217/HDAC4 axis.

Genes Genomics 2021 Apr 17. Epub 2021 Apr 17.

Department of Pediatrics, Heping Hospital Affiliated to Changzhi Medical College, No. 110, Yanan Sourth Road, Changzhi, 046000, Shanxi Province, China.

Background: Asthma is a serious respiratory disease that affects the physical and mental health of children. Airway epithelial apoptosis concomitantly mediated by transforming growth factor-β1 (TGF-β1) is a crucial component of asthma pathogenesis. LncRNA growth Arrest Specific 5 (GAS5), microRNA-217 (miR-217) and Histone deacetylase 4 (HDAC4) shown a close relationship with TGF-β1-induced injury of airway epithelial. However, the mechanism underlying TGF-β1-induced injury of airway epithelial in asthma still needs to be investigated.

Objective: We aimed to investigate the effect and underlying mechanism of GAS5/miR-217/HDAC4 axis in TGF-β1-stimulated bronchial epithelial cells.

Methods: The levels of were detected by quantitative real-time polymerase chain reaction (RT-qPCR). All protein levels were determined by western blot. Cell viability and apoptosis rate were assessed by Methyl thiazolyl tetrazolium (MTT) and Flow cytometry, respectively. The targeting relationship between miR-217 and GAS5 or HDAC4 was examined with dual-luciferase reporter assay.

Results: TGF-β1, GAS5, HDAC4 were up-regulated, while miR-217 was down-regulated in bronchial mucosal tissues of asthmatic children and TGF-β1-treated BEAS-2B cells. TGF-β1 could reduce cell viability and induce apoptosis, while these effects could be reversed by downregulation of GAS5 or HDAC4. Mechanically, GAS5 acted as a sponge for miR-217 to regulate the expression of HDAC4. Furthermore, overexpression of HDAC4 rescued the effects of GAS5 knockdown on viability and apoptosis of TGF-β1-induced BEAS-2B cells. GAS5 knockdown induced cell viability and hampered cell apoptosis in TGF-β1-stimulated BEAS-2B cells by regulating the miR-217/HDAC4 axis.

Conclusions: The lncRNA GAS5/miR-217/HDAC4 axis played an important role in regulating TGF-β1-induced bronchial epithelial cells injury, thus contributing to asthma.
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http://dx.doi.org/10.1007/s13258-021-01092-1DOI Listing
April 2021

Infection-provoked psoriasis: Induced or aggravated (Review).

Exp Ther Med 2021 Jun 29;21(6):567. Epub 2021 Mar 29.

Department of Dermatology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China.

Psoriasis is a common chronic, immune-mediated, inflammatory skin disorder, with a reported prevalence of 0.0-2.1% among children and 0.91-8.50% among adults, worldwide. Psoriasis is induced by several environmental factors, including infection, alcohol consumption, drugs, trauma, acute withdrawal of systemic or potent topical corticosteroids, body mass index and endocrine disorders. Increasing evidence suggest that a variety of microorganisms play key roles in the induction and exacerbation of psoriasis. Pathogens, such as and are considered causal factors, presumably via superantigen activation of skin-seeking T cells. In addition, fungal pathogens, such as and , and viral agents, such as human immunodeficiency virus, hepatitis C virus infection and human papillomavirus, are also closely associated with psoriasis. Recently, several types of pathogens, such as infection, virus and scabies, have been reported to potentially trigger psoriasis. The present review discusses the underlying molecular mechanisms by which these infections influence psoriasis to provide a better understanding of the pathogenesis of psoriasis.
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http://dx.doi.org/10.3892/etm.2021.9999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027725PMC
June 2021

Establishment and characterization of 38 novel patient-derived primary cancer cell lines using multi-region sampling revealing intra-tumor heterogeneity of gallbladder carcinoma.

Hum Cell 2021 May 4;34(3):918-931. Epub 2021 Apr 4.

Department of Biliary I, Shanghai Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438, China.

Gallbladder carcinoma (GBC) is a lethal biliary tract malignant neoplasm. Patient-derived primary cancer cell lines (PDPCs) are appropriate models to explore biological characteristics and potential therapeutics; however, there is a lack of PDPCs in GBC. In this study, we aimed to establish and characterize the GBC PDPCs, and further investigated the intra-tumor heterogeneity (ITH). Multi-region sampling (3-9 regions) of the operable tumor tissue samples was used to establish PDPCs. Short tandem repeat genotyping for cell authentication and karyotyping was performed, followed by whole-exome sequencing and RNA sequencing to assess the ITH at the genetic and transcriptional levels, respectively. Thirty-eight PDPCs were successfully established from seven GBC patients and characterized. ITH was observed with a median of 38.3% mutations being heterogeneous (range, 26.6-59.4%) across all patients. Similar with other tumor types, TP53 mutations were always truncal. In addition, there were three genes, KMT2C, CDKN2A, and ARID1A, with truncal mutations in at least two patients. A median of 370 differentially expressed genes (DEGs) was identified per patient. Distinct expression patterns were observed between major histocompatibility complex (MHC) class I and II genes. We found the expression of MHC class II genes in the PDPC samples was closely regulated by CIITA, while that of MHC class I genes were not correlated with CIITA expression. The PDPCs established from GBC patients can serve as novel in vitro models to identify the ITH, which may pave a crucial molecular foundation for enhanced understanding of tumorigenesis and progression.
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http://dx.doi.org/10.1007/s13577-021-00492-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8057967PMC
May 2021

Modulating oxidative stress counteracts specific antigen-induced regulatory T-cell apoptosis in mice.

Eur J Immunol 2021 Apr 3. Epub 2021 Apr 3.

Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen University School of Medicine, Shenzhen, P. R. China.

Treg are known to have a central role in orchestrating immune responses, but less is known about the destiny of Treg after being activated by specific Ags. This study aimed to investigate the role of superoxide dismutase, an active molecule in the regulation of oxidative stress in the body, in the prevention of Treg apoptosis induced by specific Ags. Ag-specific Tregs were isolated from the DO11.10 mouse intestine. A food allergy mouse model was developed with ovalbumin as the specific Ag and here, we observed that exposure to specific Ag induced Treg apoptosis through converting the precursor of TGF-β to its mature form inside the Tregs. Oxidative stress was induced in Tregs upon exposure to specific Ags, in which Smad3 bound the latency-associated peptide to induce its degradation, converting the TGF-β precursor to its mature form, TGF-β. Suppressing oxidative stress in Tregs alleviated the specific Ag-induced Treg apoptosis in in vitro experiments and suppressed experimental food allergy by preventing the specific Ag-induced Treg apoptosis in the intestine. In conclusion, exposure to specific Ags induces Treg apoptosis and it can be prevented by upregulating superoxide dismutase or suppressing reactive oxidative species in Tregs.
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http://dx.doi.org/10.1002/eji.202049112DOI Listing
April 2021

HOG1 has an essential role in the stress response, virulence and pathogenicity of .

Exp Ther Med 2021 May 12;21(5):476. Epub 2021 Mar 12.

Department of Dermatology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China.

() is a lethal pathogen that causes the majority of cryptococcosis cases in previously healthy individuals. This pathogen poses an increasing threat to global public health, but the mechanisms underlying the pathogenesis have remained to be fully elucidated. In the present study, the role of high-osmolarity glycerol (HOG)1 in the stress reaction and virulence control of was characterized by deleting the HOG1 gene using the clinical isolate strain CZ2012, and finally, the virulence and pathogenic traits of the deletion strain were defined. Deletion of the HOG1 gene resulted in notable growth defects under stress conditions (high salt and antifungal drugs), but different traits were observed under oxidative stress conditions (hydrogen peroxide). Similarly, the strains (deletion of ) also displayed decreased capsule production and melanin synthesis. Furthermore, mice infected with the strain had longer survival times than those infected with the wild-type strain and the reconstituted strain. The strain recovered from infected organs exhibited significant growth defects in terms of decreased colony count and size. The present results suggested that HOG1 has a significant role in the virulence of and these results may help to elucidate the pathogenesis of .
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http://dx.doi.org/10.3892/etm.2021.9907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7976431PMC
May 2021

Notes on the species of Abrostola Ochsenheimer, 1816 (Lepidoptera, Noctuidae, Plusiinae) from China, with the description of a new species.

Zootaxa 2021 Mar 11;4942(1):zootaxa.4942.1.9. Epub 2021 Mar 11.

Lepidoptera Research Group, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.

This paper deals with seven species of Abrostola from China, among which one is new to science. The new species, Abrostola wanglangensis sp. nov., resembles Abrostola korbi Dufay, 1958 (known from Russia) and Abrostola pacifica Dufay, 1960 (known from Russia, Korean Peninsula and Japan). Adults and genitalia are illustrated.
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http://dx.doi.org/10.11646/zootaxa.4942.1.9DOI Listing
March 2021

MiR-340-3p-HUS1 axis suppresses proliferation and migration in lung adenocarcinoma cells.

Life Sci 2021 Jun 9;274:119330. Epub 2021 Mar 9.

Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China. Electronic address:

Aims: The functions and molecular mechanisms of miR-340-3p in lung adenocarcinoma (LUAD) progression remain unclear. On the other hand, the role of HUS1 in LUAD progression should be further explored.

Main Methods: Data from cancer database were subjected to bioinformatics analysis. Quantitative real-time PCR and western blot were performed to detect gene expression. Colony formation and MTT assay were performed to examine cell growth in vitro. Wound healing assays and transwell assays were performed to examine cell migration.

Key Findings: Here, our results showed that miR-340-3p was lower expressed in LUAD tissues and LUAD-derived cell lines. And miR-340-3p suppressed the proliferation and migration ability of LUAD cells. Further, miR-340-3p inhibits HUS1 expression, which was higher expressed in LUAD tissues and promoted the proliferation and migration ability of LUAD cells. Moreover, higher HUS1 expression was associated with poor survival rate and shorter survival time in patients with LUAD, and HUS1 expression was negative correlated with that of miR-340-3p in clinical samples. In addition, overexpression of HUS1 counteracted the downregulation of cell growth by miR-340-3p.

Significance: The study mainly indicated that miR-340-3p may play a tumor suppressor role in the progression of LUAD, with the function of restraining HUS1 expression, highlighting a potential therapeutic target for LUAD.
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http://dx.doi.org/10.1016/j.lfs.2021.119330DOI Listing
June 2021

Regulation of the Migration of Distinct Dendritic Cell Subsets.

Front Cell Dev Biol 2021 19;9:635221. Epub 2021 Feb 19.

Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Science, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.

Dendritic cells (DCs), a class of antigen-presenting cells, are widely present in tissues and apparatuses of the body, and their ability to migrate is key for the initiation of immune activation and tolerogenic immune responses. The importance of DCs migration for their differentiation, phenotypic states, and immunologic functions has attracted widespread attention. In this review, we discussed and compared the chemokines, membrane molecules, and migration patterns of conventional DCs, plasmocytoid DCs, and recently proposed DC subgroups. We also review the promoters and inhibitors that affect DCs migration, including the hypoxia microenvironment, tumor microenvironment, inflammatory factors, and pathogenic microorganisms. Further understanding of the migration mechanisms and regulatory factors of DC subgroups provides new insights for the treatment of diseases, such as infection, tumors, and vaccine preparation.
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http://dx.doi.org/10.3389/fcell.2021.635221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7933215PMC
February 2021

Effect of current density and pH on the electrochemically generated active chloro species for the rapid mineralization of p-substituted phenol.

Chemosphere 2021 Jul 24;275:129848. Epub 2021 Feb 24.

School of Environment Science and Spatial Informatics, China University of Mining and Technology Xuzhou City, Jiangsu, 221116, PR China.

The aim of present study is increasing the degradation and mineralization of 4-chlorophenol (4-CP) during electrochemical oxidation with Ti/RuO anodes. Innovatively, the evolution of chlorine-related species and the formations of various inorganic ions were investigated by electrolytic analysis in order to set up whether the formation and consumption of these byproducts associated with either chemical or electrochemical reactions. The effect of operating parameters such as current density, solution pH, treatment time, and electrolyte concentration has been studied. The formation of Cl, chlorite (ClO), and chlorate (ClO) were detected by adding the known concentration of Cl ions at different pH and current densities. Concentration trends of active chloro-species indicate that the degradation of 4-CP and chemical oxygen demand (COD) removal was formed maximum at pH 6 and j of 225.2 Am in presence of 0.0085 M NaCl. Thus, the 4-CP degradation mainly depends on the radicals and active chlorine formation and a mineralization mechanism was proposed based on intermediates byproducts formation such as catechol, hydroquinone, 1, 4-benzoquinone, and organic acids identify by using the GC-MS and HPLC analysis at the optimum treatment condition. Total organic carbon (TOC) at different pH and current density, mass balance analysis of carbon and inorganic species formation were determined at the optimum treatment conditions of 4-CP. The degradation kinetic of 4-CP was followed the pseudo-first order kinetic model during the each parameters optimization. Specific energy consumption and current efficiency were also used to identify the technical feasibility of the process.
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http://dx.doi.org/10.1016/j.chemosphere.2021.129848DOI Listing
July 2021

Fusion Gene Involved Early T-Cell Precursor Acute Lymphoblastic Leukemia in Adult with B Marker Expression.

Int J Gen Med 2021 25;14:659-664. Epub 2021 Feb 25.

Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, People's Republic of China.

Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is rare and associated with poor clinical outcome especially in adults. ETP tumor cells that express cross-lineage antigens or lack pan T markers usually pose big challenges to diagnosis, and their prognostic implications are therefore more uncertain. This study reports the unique case of a 44-year-old woman with breast mass as the initial presentation of acute leukemia possessing both T- and B-cell features (cytoplasmic CD3CD7CD19CD79a). Despite the presence of gene rearrangements of and probably in a small amount of B cells, the patient was diagnosed with T-ALL mainly according to WHO criteria, and further ETP-ALL rather than mixed phenotype ALL based on additional positive expression of stem/myeloid lineage antigens (CD34CD13CD33HLA-DR). Moreover, in spite of normal karyotype, gene fusion is identified, which has not been described in ETP-ALL with bi-phenotype. After intensive chemotherapy, the patient achieved short-term morphologic complete remission but relapsed within one month. This report may expand immunophenotype and clinical behavior of ETP-ALL in adults. Comprehensive evaluations are emphasized in making a differential diagnosis and distinguishing subtypes of acute leukemia.
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http://dx.doi.org/10.2147/IJGM.S294715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7920624PMC
February 2021

Effect of drying methods on the solubility and amphiphilicity of room temperature soluble gelatin extracted by microwave-rapid freezing-thawing coupling.

Food Chem 2021 Jul 9;351:129226. Epub 2021 Feb 9.

College of Food Science, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400715, China. Electronic address:

The effect of three drying methods (hot air, freeze and spray drying) on the solubility and amphiphilicity of gelatin were investigated and compared. Results showed spray drying gelatin (SDG) and hot air drying gelatin (HDG) showed the lowest and best solubility, respectively. This phenomenon was attributed to the degree of subunits degradation and hydrophobicity. The HDG showed an obvious degradation during the hot air drying and displayed the strongest hydrophilicity, while SDG showed a slight degradation and strongest hydrophobicity. The results of wettability showed that SDG had a better amphiphilicity (92.48°) in comparison with HDG (57.7°) and freeze drying gelatin (VDG, 77.53°), which can effectively reduce the interfacial tension of gelatin, thus significantly improving the stability of foam and emulsion (p < 0.05). These results suggested the drying methods can adjust the amphiphilicity of gelatin, and the SDG displayed a better amphiphilicity, showing good potential applications in foam and emulsion.
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http://dx.doi.org/10.1016/j.foodchem.2021.129226DOI Listing
July 2021

Metal oxide nanoparticles facilitate the accumulation of bifenthrin in earthworms by causing damage to body cavity.

Environ Pollut 2020 Aug 19;263(Pt A):114629. Epub 2020 Apr 19.

Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China. Electronic address:

In this study, we explored the influence of two metal oxide nanoparticles, nano CuO and nano ZnO (10, 50, 250 mg/kg), on accumulation of bifenthrin (100 μg/kg) in earthworms (Eisenia fetida) and its mechanism. The concentrations of bifenthrin in earthworms from binary exposure groups (bifenthrin + CuO and bifenthrin + ZnO) reached up to 23.2 and 28.9 μg/g, which were 2.65 and 3.32 times of that in bifenthrin exposure group without nanoparticles, respectively, indicating that nanoparticles facilitated the uptake of bifenthrin in earthworms. The contents of biomarkers (ROS, SOD, and MDA) in earthworms indicated that nanoparticles and bifenthrin caused damage to earthworms. Ex vivo test was utilized to investigate the toxic effects of the pollutants to cell membrane of earthworm coelomocytes and mechanism of increased bifenthrin accumulation. In ex vivo test, cell viability in binary exposure groups declined up to 30% and 21% compared to the control group after 24 h incubation, suggesting that coelomocyte membrane was injured by the pollutants. We conclude that nanoparticles damage the body cavity of earthworms, and thus lead to more accumulation of bifenthrin in earthworms. Our findings provide insights into the interactive accumulation and toxicity of nanoparticles and pesticides to soil organisms.
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http://dx.doi.org/10.1016/j.envpol.2020.114629DOI Listing
August 2020