Publications by authors named "Jinpeng Wang"

151 Publications

Machine learning guided aptamer refinement and discovery.

Nat Commun 2021 04 22;12(1):2366. Epub 2021 Apr 22.

Aptitude Medical Systems Inc., Santa Barbara, CA, USA.

Aptamers are single-stranded nucleic acid ligands that bind to target molecules with high affinity and specificity. They are typically discovered by searching large libraries for sequences with desirable binding properties. These libraries, however, are practically constrained to a fraction of the theoretical sequence space. Machine learning provides an opportunity to intelligently navigate this space to identify high-performing aptamers. Here, we propose an approach that employs particle display (PD) to partition a library of aptamers by affinity, and uses such data to train machine learning models to predict affinity in silico. Our model predicted high-affinity DNA aptamers from experimental candidates at a rate 11-fold higher than random perturbation and generated novel, high-affinity aptamers at a greater rate than observed by PD alone. Our approach also facilitated the design of truncated aptamers 70% shorter and with higher binding affinity (1.5 nM) than the best experimental candidate. This work demonstrates how combining machine learning and physical approaches can be used to expedite the discovery of better diagnostic and therapeutic agents.
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http://dx.doi.org/10.1038/s41467-021-22555-9DOI Listing
April 2021

Piccolo is essential for the maintenance of mouse retina but not cochlear hair cell function.

Aging (Albany NY) 2021 Apr 21;13. Epub 2021 Apr 21.

School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China.

Piccolo is a presynaptic protein with high conservation among different species, and the expression of Piccolo is extensive in vertebrates. Recently, a small fragment of Piccolo (Piccolino), arising due to the incomplete splicing of intron 5/6, was found to be present in the synapses of retinas and cochleae. However, the comprehensive function of Piccolo in the retina and cochlea remains unclear. In this study, we generated knockout mice using CRISPR-Cas9 technology to explore the function of Piccolo. Unexpectedly, whereas no abnormalities were found in the cochlear hair cells of the mutant mice, significant differences were found in the retinas, in which two layers (the outer nuclear layer and the outer plexiform layer) were absent. Additionally, the amplitudes of electroretinograms were significantly reduced and pigmentation was observed in the fundoscopy of the mutant mouse retinas. The expression levels of Bassoon, a homolog of Piccolo, as well as synapse-associated proteins CtBP1, CtBP2, Kif3A, and Rim1 were down-regulated. The numbers of ribbon synapses in the retinas of the mutant mice were also reduced. Altogether, the phenotype of -/- mice resembled the symptoms of retinitis pigmentosa (RP) in humans, suggesting might be a candidate gene of RP and indicates knockout mice are a good model for elucidating the molecular mechanisms of RP.
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http://dx.doi.org/10.18632/aging.202861DOI Listing
April 2021

Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander.

Hortic Res 2020 Apr 1;7(1):55. Epub 2020 Apr 1.

Center for Genomics and Biocomputing/College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063210, China.

Coriander (Coriandrum sativum L.), also known as cilantro, is a globally important vegetable and spice crop. Its genome and that of carrot are models for studying the evolution of the Apiaceae family. Here, we developed the Coriander Genomics Database (CGDB, http://cgdb.bio2db.com/) to collect, store, and integrate the genomic, transcriptomic, metabolic, functional annotation, and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants. Using these data sets in the CGDB, we intriguingly found that seven transcription factor (TF) families showed significantly greater numbers of members in the coriander genome than in the carrot genome. The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15, followed by those for tubby protein (TUB) and heat shock factors. As a demonstration of CGDB applications, we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses. RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander. CGDB allows bulk downloading, significance searches, genome browser analyses, and BLAST searches for comparisons between coriander and other plants regarding genomics, gene families, gene collinearity, gene expression, and the metabolome. A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions. CGDB will be continuously updated, and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.
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http://dx.doi.org/10.1038/s41438-020-0261-0DOI Listing
April 2020

Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle.

Genomics 2021 Mar 23;113(3):1491-1503. Epub 2021 Mar 23.

Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China; College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China. Electronic address:

Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds that led to their divergence from India-origin zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (≥1800 m) and low-altitude adapted breeds (<1500 m) revealed candidate genes (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 ACSS2-knockout analyses suggest that the up-regulation of ACSS2 expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.
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http://dx.doi.org/10.1016/j.ygeno.2021.03.023DOI Listing
March 2021

HDAC3 protects against atherosclerosis through inhibition of inflammation via the microRNA-19b/PPARγ/NF-κB axis.

Atherosclerosis 2021 Apr 20;323:1-12. Epub 2021 Feb 20.

Department of Cardiology, the Second Hospital of Jilin University, Changchun, 130041, PR China. Electronic address:

Background And Aims: Atherosclerosis (AS) is one of the leading causes of cardiovascular diseases. Studies have revealed critical roles of microRNAs (miRNAs) in the progression of AS. This study was conducted to elucidate the role and mechanism by which miR-19b influences AS.

Methods: Human umbilical vein endothelial cells (HUVECs) were treated with oxidized-low-density lipoprotein (ox-LDL), and an AS mouse model was generated with the help of ApoE mice using a high-fat diet regimen. The expression patterns of peroxisome proliferator-activated receptor γ (PPARγ), nuclear factor κB (NF-κB)/p65, miR-19b and histone deacetylase 3 (HDAC3) were then characterized by reverse transcription quantitative polymerase chain reaction and Western blot analysis. In addition, the relationship among PPARγ, NF-κB/p65, miR-19b and HDAC3 was evaluated by co-immunoprecipitation, chromatin immunoprecipitation and dual-luciferase reporter gene assays. Gain- and loss-of-function experiments were also performed to examine their functional significance on ox-LDL-induced inflammation in HUVECs. Enzyme-linked immunosorbent assay was applied to determine the expression patterns of inflammatory factors in AS mice.

Results: PPARγ and HDAC3 were poorly expressed, while miR-19b and NF-κB/p65 were highly expressed in ox-LDL-induced HUVECs and arterial tissues of AS mice. PPARγ inhibited ox-LDL-induced inflammation in HUVECs by ubiquitination and degradation of NF-κB/p65. miR-19b, downregulated by HDAC3, targeted PPARγ and negatively-regulated its expression. Upregulated PPARγ or HDAC3 or downregulated miR-19b or NF-κB/p65 reduced TNF-α and IL-1β expression levels in ox-LDL-induced HUVECs and AS mice.

Conclusions: Collectively, the results show that HDAC3 upregulation prevents inflammation to inhibit AS by inactivating NF-κB/p65 via upregulation of miR-19b-mediated PPARγ, providing a basic therapeutic consideration for AS treatment.
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http://dx.doi.org/10.1016/j.atherosclerosis.2021.02.013DOI Listing
April 2021

Optimize the preparation of FeO-modified magnetic mesoporous biochar and its removal of methyl orange in wastewater.

Environ Monit Assess 2021 Mar 10;193(4):179. Epub 2021 Mar 10.

School of Architecture and Civil Engineering, Anhui Polytechnic University, Wuhu, 241000, China.

In this paper, Eichhornia Crassipes stems were used as biomass feedstock, and Fe was used as the precursor solution to prepare FeO-modified magnetic mesoporous biochar (FeO@BC). By using Box-Behnken design (BBD) response surface methodology, the influences of three preparation parameters (X = Fe concentration, X = pyrolysis temperature and X = pyrolysis time) on the adsorption of methyl orange (MO) by FeO@BC were investigated, and a reliable response surface model was constructed. The results show that XX and XX have a significant influence on the adsorption of MO by FeO@BC. The surface area and pore volume of FeO@BC are controlled by all preparation parameters. The increase of pyrolysis time will significantly reduce the -OH on the surface of FeO@BC and weaken its MO adsorption capacity. Through the numerical optimization of the constructed model, the optimal preparation parameters of FeO@BC can be obtained as follows: Fe concentration = 0.27 mol/L, pyrolysis temperature = 405 °C, and pyrolysis time = 3.2 h. The adsorption experiment shows that the adsorption of FeO@BC to MO is a spontaneous exothermic process, and the adsorption capacity is maximum when pH = 4. The adsorption kinetics and adsorption isotherms of FeO@BC to MO conform to the pseudo-second-order kinetics and Sips model, respectively. Mechanism analysis shows that electrostatic interaction and H bond formation are the main forces for FeO@BC to adsorb MO. This research not only realizes a new way of resource utilization of Eichhornia Crassipes biomass but also enriches the preparation research of magnetic biochar.
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http://dx.doi.org/10.1007/s10661-021-08971-wDOI Listing
March 2021

EGCG Regulates Cell Apoptosis of Human Umbilical Vein Endothelial Cells Grown on 316L Stainless Steel for Stent Implantation.

Drug Des Devel Ther 2021 11;15:493-499. Epub 2021 Feb 11.

Department of Nutrition and Food Hygiene, School of Public Health, Jilin University, Changchun, 130021, People's Republic of China.

Background: Nowadays, medical grade 316L stainless steel (316L SS) is being widely used for intravascular stents, and the drug-eluting stent (DES) system is able to significantly reduce the occurrences of in-stent restenosis. But the drugs and the polymer coating used in DES potentially induce the forming of late stent thrombosis. In order to reduce the occurrence of ISR after stent implantation, the development of novel drugs for DESs is urgently needed.

Methods: This study aimed to investigate the potential mechanisms of epigallocatechin-3-gallate (EGCG) on human umbilical vein endothelial cells (HUVEC) grown on 316L stainless steel (316L SS) using flow cytometry and Q-PCR methods.

Results: Our results showed that EGCG (12.5, 25, 50, 100 μmol/L) significantly inhibited HUVEC proliferation. Flow cytometry analysis indicated that EGCG (25, 50, 100 μmol/L) induced apoptosis. Moreover, qRT-PCRrevealed that genes associated with cell apoptosis (caspase-3, 8, 9, Fas) and autophagy (Atg 5, Atg 7, Atg 12) were up-regulated after EGCG treatment.

Conclusion: These findings indicate that EGCG possesses chemo preventive potential in stent coating which may serve as a novel new drug for stent implantation.
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http://dx.doi.org/10.2147/DDDT.S296548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7886104PMC
February 2021

Amygdala-hippocampal innervation modulates stress-induced depressive-like behaviors through AMPA receptors.

Proc Natl Acad Sci U S A 2021 Feb;118(6)

Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of People's Republic of China, IDG/McGovern Institute for Brain Research at Peking University, 100083 Beijing, People's Republic of China;

Chronic stress is one of the most critical factors in the onset of depressive disorders; hence, environmental factors such as psychosocial stress are commonly used to induce depressive-​like traits in animal models of depression. Ventral CA1 (vCA1) in hippocampus and basal lateral amygdala (BLA) are critical sites during chronic stress-induced alterations in depressive subjects; however, the underlying neural mechanisms remain unclear. Here we employed chronic unpredictable mild stress (CUMS) to model depression in mice and found that the activity of the posterior BLA to vCA1 (pBLA-vCA1) innervation was markedly reduced. Mice subjected to CUMS showed reduction in dendritic complexity, spine density, and synaptosomal AMPA receptors (AMPARs). Stimulation of pBLA-vCA1 innervation via chemogenetics or administration of cannabidiol (CBD) could reverse CUMS-induced synaptosomal AMPAR decrease and efficiently alleviate depressive-like behaviors in mice. These findings demonstrate a critical role for AMPARs and CBD modulation of pBLA-vCA1 innervation in CUMS-induced depressive-like behaviors.
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http://dx.doi.org/10.1073/pnas.2019409118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8017726PMC
February 2021

Synthesis of polyethylene glycol functional bonded silica gel for selective recognition and separation of α-cyclodextrin.

J Chromatogr A 2021 Feb 20;1639:461917. Epub 2021 Jan 20.

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu Province, 214122, China. Electronic address:

In this work, we for the first time synthesized the polyethylene glycol (PEG) bonded silica gel via KH-560 as a silane coupling reagent for column chromatography by a solid/liquid surface continuous reaction method. The molecular interaction, structure, morphology, and thermostability was characterized by fourier transform infrared spectroscopy (FTIR), elemental analysis (EA), scanning electronic microscope (SEM) and thermogravimetric analysis (TGA). Given that PEG is capable to self-assemble with α-CD, the PEG bonded silica gel was used as packing of column chromatography to achieve the selective separation of α-cyclodextrin (α-CD) at room temperature and atmospheric pressure. The bonded silica gel column could realize the effective separation of α-CD in the enzymatic hydrolysis mixture, which provides support for industrial separation of α-CD.
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http://dx.doi.org/10.1016/j.chroma.2021.461917DOI Listing
February 2021

Pyroptosis in Osteoblasts: A Novel Hypothesis Underlying the Pathogenesis of Osteoporosis.

Front Endocrinol (Lausanne) 2020 8;11:548812. Epub 2021 Jan 8.

Department of Orthopaedics, First Affiliated Hospital of China Medical University, Shenyang, China.

Osteoporosis has become a worldwide disease characterized by a reduction in bone mineral density and the alteration of bone architecture leading to an increased risk of fragility fractures. And an increasing number of studies have indicated that osteoblasts undergo a large number of programmed death events by many different causes in osteoporosis and release NLRP3 and interleukin (e.g., inflammatory factors), which play pivotal roles in contributing to excessive differentiation of osteoclasts and result in exaggerated bone resorption. NLRP3 is activated during pyroptosis and processes the precursors of IL-1β and IL-18 into mature forms, which are released into the extracellular milieu accompanied by cell rupture. All of these compounds are the classical factors of pyroptosis. The cellular effects of pyroptosis are commonly observed in osteoporosis. Although many previous studies have focused on the pathogenesis of these inflammatory factors in osteoporosis, pyroptosis has not been previously evaluated. In this review, pyroptosis is proposed as a novel hypothesis of osteoporosis pathogenesis for the first time, thus providing a new direction for the treatment of osteoporosis in the future.
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http://dx.doi.org/10.3389/fendo.2020.548812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821870PMC
January 2021

The relationship between 24-hour indicators and mortality in patients with exertional heat stroke.

Endocr Metab Immune Disord Drug Targets 2021 Jan 22. Epub 2021 Jan 22.

Medical School of Chinese PLA, Beijing 100853. China.

Background: Exertional heat stroke (EHS) is a life-threatening illness that can lead to multiple organ damage in the early stage.

Objective: This study aimed to investigate the relationship between 24-hour indicators and mortality in patients with EHS.

Methods: The records of EHS patients hospitalized were collected and divided into the death group and the survival group. We then analyzed the demographic characteristics and APACHE II scores and laboratory results of the participants in the blood within the first 24 h after hospitalization, and assessed whether these candidate indicators differed between the death group and the survival group. Cox regression analysis of the survival data was performed to explore the relationship between early indicators and prognosis.

Results: The levels of plasma PT, APTT, TT, and INR were significantly higher in the death group than in the survival group. The blood PLT count and the levels of PTA and Fb were significantly lower in the death group than in the survival group, while the levels of BU, SCr, ALT, AST, TBil, and DBil were significantly higher in the death group than in the survival group. Furthermore, the levels of Mb, LDH, TNI, and NT-proBNP were significantly higher in the death group than in the survival group, while there was no significant difference in CK levels between the two groups.

Conclusion: Patients with EHS often had multiple organ injuries in the early stage (within 24 h), while those cases in the death group were more severe.
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http://dx.doi.org/10.2174/1871530321666210122153249DOI Listing
January 2021

Near-infrared hyperspectral imaging for detection and visualization of offal adulteration in ground pork.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Mar 15;249:119307. Epub 2020 Dec 15.

College of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China.

Hyperspectral imaging (HSI) technique was investigated to explore a feasible protocol for detecting the potential offal (lung) adulteration in ground pork. Tested samples (176 adulterated and 2 controls) were first prepared with adulterant of ground lung in range of 0%-100% (w/w) at 10% intervals. After hyperspectral images were acquired and calibrated in reflectance mode (400-1000 nm), full spectra were extracted from identified regions of interests (ROIs) and then transformed into absorbance and Kubelka-Munck spectral units, respectively. Partial least squares regression (PLSR) models based on full spectra showed that raw reflectance spectra with no preprocessings performed best with coefficient of determination (R) of 0.98, root mean square error (RMSEP) of 4.25%, and ratio performance deviation (RPD) of 7.53 in prediction set. To reduce the high dimensionality of spectra, data was further explored using principal component loadings, two-dimensional correlation spectroscopy (2D-COS), and regression coefficients (RC), respectively. The optimal performance of established simplified PLSR model were acquired using eleven featured wavelengths selected by PC loadings with R of 0.98, RMSEP of 4.47% and RPD of 7.16. Finally, the limit of detection (LOD) was calculated to be a satisfactory 7.58%, and readily discernible visualization procedure using preferred simplified PLSR model yielded satisfactory spatial distribution of adulteration situation. Control samples with known distribution were also visualized to successfully prove the validity. Consequently, this research offers an alternative assay for visually and rapidly detecting offal of lung adulteration in ground pork.
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http://dx.doi.org/10.1016/j.saa.2020.119307DOI Listing
March 2021

Donkey genomes provide new insights into domestication and selection for coat color.

Nat Commun 2020 12 8;11(1):6014. Epub 2020 Dec 8.

BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.

Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.
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http://dx.doi.org/10.1038/s41467-020-19813-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723042PMC
December 2020

Study on Novel Nanoparticle Slow-Release Drugs for Moyamoya Disease.

J Nanosci Nanotechnol 2021 Feb;21(2):1008-1017

Department of Neurosurgery, Weifang People's Hospital, Weifang City, 261000, China.

Spontaneous basilar artery occlusive disease is a disease characterized by thickening of the intima of the bilateral internal carotid artery and the anterior and middle cerebral arteries, gradually narrowing the arterial diameter, and compensatory dilatation of the perforating artery at the base of the brain. Aspirin (acetylsalicylic acid), as a classic non-steroidal anti-inflammatory drug, has been proven to have antiplatelet, anti-inflammatory, and immune-regulating effects. But how to achieve long-term sustained release of aspirin and achieve anti-platelet aggregation remains to be studied. This study intends to build a microsphere sustained-release system to achieve long-term stable and slow release of aspirin drug, thereby achieving a more ideal anti-platelet aggregation effect. The therapeutic effects of three groups of nanoparticle sustained-release drug regimens on platelet aggregation were compared. The results showed that the platelet inhibition rate and NIHSS scores before treatment were compared between the three groups; compared with the other groups, the PLGA group had higher AA and ADP pathway-induced platelet inhibition rates after treatment and lower plasma Lp-PLA2 and NIHSS scores. This shows that aspirin nanoparticle slow-release drugs can effectively increase platelet inhibition rate and improve the antiplatelet ability of patients with spontaneous basilar artery occlusive disease, which is beneficial to promoting prognosis recovery.
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http://dx.doi.org/10.1166/jnn.2021.18682DOI Listing
February 2021

Paleo-polyploidization in Lycophytes.

Genomics Proteomics Bioinformatics 2020 06 4;18(3):333-340. Epub 2020 Nov 4.

Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China; National Key Laboratory for North China Crop Improvement and Regulation, Agriculture University of Hebei, Baoding 071001, China. Electronic address:

Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13-15 million years ago (MYA) and another about 125-142 MYA, during the evolution of the genome of Selaginella moellendorffii, a model lycophyte. In addition, comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleo-polyploidization events than seed plants. Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages-lycophytes and seed plants-of vascular plants.
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http://dx.doi.org/10.1016/j.gpb.2020.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801247PMC
June 2020

Effect of functional single nucleotide polymorphism g.-572 A > G of apolipoprotein A1 gene on resistance to ketosis in Chinese Holstein cows.

Res Vet Sci 2021 Mar 20;135:310-316. Epub 2020 Oct 20.

Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan 250131, China. Electronic address:

The ketosis has negative effects on the high-yielding dairy cows during early lactation. Apolipoprotein A1 (APOA1) is a component of high-density lipoprotein. However, the association of APOA1 gene with ketosis, and the molecular mechanisms of expression of APOA1 gene are not fully understood in dairy cows. In this study, expression of APOA1 in the liver and blood was investigated by RT-qPCR and immunohistochemistry, and genetic variation in the 5'-flanking region of the AOPA1 gene was also screened and identified. In addition, correlation of the single nucleotide polymorphisms (SNPs) of APOA1 gene with blood ketone characters, and activity of APOA1 promoter were analyzed in dairy cows. The results showed that ApoA1 protein was expressed in the liver, and the mRNA level of APOA1 was significantly higher in the cows with ketosis comparing to the healthy cows. In addition, a novel SNP (g.-572 A > G) in the core promoter of the APOA1 gene was identified between base g.-714 and g.-68 through transient transfection in both HepG2 cell and FFb cell, and luciferase report assay. Moreover, there was lower concentration of blood β-hydroxybutyrate in cows with genotype GG comparing to the cows with genotypes AA and AG. This study reported for the first time that the genetic variant g.-572 A > G in the core promoter region of APOA1 gene was associated with the ketosis in Chinese Holstein cows, and g.-572 A > G may be used as a genetic marker for ketosis prevention.
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http://dx.doi.org/10.1016/j.rvsc.2020.10.006DOI Listing
March 2021

Application of copper tailings combined with persulfate for better removing methyl orange from wastewater.

Water Sci Technol 2020 Oct;82(8):1676-1686

School of Architecture and Civil Engineering, Anhui Polytechnic University, Wuhu 241000, China E-mail:

In this paper, wasted copper tailings (CT) were used to activate persulfate (PS) to degrade azo dye methyl orange (MO). The results show that a large amount of FeS contained in CT can slowly release Fe in the aqueous solution to activate PS to generate reactive oxygen species to degrade MO. When the dosage of CT and PS was 2 g/L and 3 mM respectively, the MO degradation efficiency of 20 mg/L in the CT/PS system was 96.52% within 60 min. At the same time, it is found that CT has a certain adsorption capacity for MO, and the intra-particle diffusion model can well describe the adsorption process of MO by CT. The effects of related reaction parameters (CT dosage, PS dosage, initial MO concentration and solution pH) on MO degradation in CT/PS system were investigated. Compared with the direct addition of an equal amount of Fe as in the CT/PS system, for homogeneous activated PS to degrade MO (Fe/PS), the results showed that the degradation efficiency of Fe/PS system for MO was lower than that of CT/PS system due to excessive Fe consumption of SO. By comparing the Fe and Fe concentrations in the two systems, it was found that the CT/PS system could maintain a low Fe concentration during the reaction process, and the Fe released by CT could be used by PS to degrade MO more efficiently. The free radical scavenging experiments showed that the reactive oxygen species in the CT/PS system was mainly SO. This study not only proposed a new CT utilization approach, but also solved the problem of reduced degradation efficiency of organic pollutants caused by excessive Fe in the Fenton-like reaction.
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http://dx.doi.org/10.2166/wst.2020.419DOI Listing
October 2020

The celery genome sequence reveals sequential paleo-polyploidizations, karyotype evolution and resistance gene reduction in apiales.

Plant Biotechnol J 2021 04 18;19(4):731-744. Epub 2020 Nov 18.

School of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China.

Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high-quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences, with 62.12% of 31 326 annotated genes confined to the terminal 20% of chromosomes. Simultaneous bursts of shared long-terminal repeats (LTRs) in different Apiaceae plants suggest inter-specific exchanges. Two ancestral polyploidizations were inferred, one shared by Apiales taxa and the other confined to Apiaceae. We reconstructed 8 Apiales proto-chromosomes, inferring their evolutionary trajectories from the eudicot common ancestor to extant plants. Transcriptome sequencing in three tissues (roots, leaves and petioles), and varieties with different-coloured petioles, revealed 4 and 2 key genes in pathways regulating anthocyanin and coumarin biosynthesis, respectively. A remarkable paucity of NBS disease-resistant genes in celery (62) and other Apiales was explained by extensive loss and limited production of these genes during the last ~10 million years, raising questions about their biotic defence mechanisms and motivating research into effects of chemicals, for example coumarins, that give off distinctive odours. Celery genome sequencing and annotation facilitates further research into important gene functions and breeding, and comparative genomic analyses in Apiales.
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http://dx.doi.org/10.1111/pbi.13499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8051603PMC
April 2021

Supplementation of Diet With Different n-3/n-6 PUFA Ratios Ameliorates Autistic Behavior, Reduces Serotonin, and Improves Intestinal Barrier Impairments in a Valproic Acid Rat Model of Autism.

Front Psychiatry 2020 9;11:552345. Epub 2020 Sep 9.

Department of Developmental Pediatrics, The Second Hospital of Jilin University, Changchun, China.

The implication of different dietary n-3/n-6 polyunsaturated fatty acids (PUFAs) ratios has been investigated in some neurodevelopmental disorders (including autism and depression). However, the mechanisms underlying the effects of different PUFAs ratios on the autism are still poorly understood. In the present study, a valproic acid (VPA) rat model of autism was used to study the effects of diet with different n-3/n-6 PUFA ratios on the autism, and the underlying mechanisms explored. Our results showed that rats with prenatal administration of VPA took less response time to sniff three odorants in the olfactory habituation/dishabituation tests, had lower frequency of pinning and following patterns, and had decreased hippocampal 5-hydroxytryptamine (5-HT), increased serum 5-HT and downregulated expression of tight junction protein (occludin and claudin-1) in the colon. However, supplementation of n-3/n-6 PUFAs (1:5) in the VPA treated rats ameliorated the autistic behaviors, increased hippocampal 5-HT and tight junction expression in the colon, and decreased serum 5-HT. In conclusion, dietary supplementation of n-3/n-6 PUFAs (1:5) significantly improves VPA-induced autism-like behaviors in rats, which may be, at least partially, related to the increased hippocampal 5-HT. Furthermore, this diet can increase the expression of tight junction proteins to improve intestinal barrier impairment.
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http://dx.doi.org/10.3389/fpsyt.2020.552345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509584PMC
September 2020

Upregulation of long non-coding RNA LOC284454 may serve as a new serum diagnostic biomarker for head and neck cancers.

BMC Cancer 2020 Sep 24;20(1):917. Epub 2020 Sep 24.

Department of Stomatology, NHC Key Laboratory of Carcinogenesis, Xiangya Hospital, Central South University, No.88 Xiangya Road, Changsha, Hunan, P. R. China, 410078.

Background: Identification of effective diagnostic and prognostic biomarkers of cancer is necessary for improving precision medicine. Long non-coding RNAs (lncRNAs) play an important regulatory role in tumor initiation and progression. The lncRNA LOC284454 is distinctly expressed in various head and neck cancers (HNCs), as demonstrated by our previous bioinformatics analysis. However, the expression levels and functions of LOC284454 in cancer are still unclear.

Methods: We investigated the dysregulation of lncRNAs in HNCs using the GEO database and found that LOC284454 was highly expressed in HNCs. Serum samples from 212 patients with HNCs and 121 normal controls were included in this biomarker study. We measured the expression of LOC284454 in the sera of HNC patients and normal controls using RT-qPCR. Receiver operating characteristics (ROC) analysis is an important statistical method that is widely used in clinical diagnosis and disease screening. ROC was used to analyze the clinical value of LOC284454 in the early diagnosis of HNCs.

Results: LOC284454 was significantly upregulated in the sera of patients with nasopharyngeal carcinoma, oral cancer, and thyroid cancer. LOC284454 upregulation had good clinical diagnostic value in these cancers, as evaluated by area under the ROC curve values of 0.931, 0.698, and 0.834, respectively.

Conclusions: LOC284454 may be a valuable serum biomarker for HNCs facilitating the early diagnosis of malignant cancers. Further studies are needed to elucidate the mechanisms underlying the involvement of LOC284454 in HNCs. This study provides the first evidence that LOC284454 may be a serum biomarker for HNCs.
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http://dx.doi.org/10.1186/s12885-020-07408-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7517628PMC
September 2020

In Situ Self-Assembly of Nanoparticles into Waxberry-Like Starch Microspheres Enhanced the Mechanical Strength, Fatigue Resistance, and Adhesiveness of Hydrogels.

ACS Appl Mater Interfaces 2020 Oct 30;12(41):46609-46620. Epub 2020 Sep 30.

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.

Owing to the diminishing resources and growing awareness of environmental issues, significant scientific attention has been paid to the development of physical gel materials using renewable and low-cost natural resources. Inspired by the strengthened mechanism of double-network and nanocomposite (NC) gels, we report a facile and green method to realize a mechanically stiff, fatigue-resistant, and adhesive-debranched waxy corn starch/poly(vinyl alcohol) double-crosslinked NC gel (W-Gel) skeleton material with dynamic noncovalent bonds. The in situ formation of debranched starch nanoparticles leads to self-assembly into three-dimensional waxberry-like microspheres, which act as physical cross-linkers by embedding themselves within network skeleton structures. The resulting hydrogel exhibited an excellent mechanical behavior, including a good stretchability over 1200% strain, a maximum compressive strength of up to 780.7 ± 27.8 kPa, and the ability to sustain as much weight as 4.6 kg (about 2000 times its own weight). Notably, the recovery efficiency exceeded 93% after the 60th compressive successive loading-unloading cycle at 50% strain. The hydrogel successfully adhered onto soft and hard substrates, such as skins, plastics, gauzes, glasses, and metals, manifesting in long-term, stable, sustained release of epigallocatechin gallate (EGCG). The EGCG-loaded W-Gels exhibited predominant antibacterial activity against both Gram-positive bacteria () and Gram-negative bacteria ( and ).
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http://dx.doi.org/10.1021/acsami.0c10327DOI Listing
October 2020

Simultaneous Detection of Three Foodborne Pathogens Based on Immunomagnetic Nanoparticles and Fluorescent Quantum Dots.

ACS Omega 2020 Sep 3;5(36):23070-23080. Epub 2020 Sep 3.

School of Public Health, Jilin University, Changchun 130021, China.

This paper presents a peptide-mediated immunomagnetic separation technique and an immunofluorescence quantum dot technique for simultaneous and rapid detection of , , and . First, three peptides that can specifically recognize the three foodborne pathogens were combined with magnetic nanoparticles to form an immunomagnetic nanoparticle probe for capturing three kinds of target bacteria and then added three quantum dot probes (quantum dots-aptamer), which formed a sandwich composite structure. When the three quantum dot probes specifically combined with the three pathogenic bacteria, the remaining fluorescent signal in the supernatant will be reduced by magnetic separation. Therefore, the remaining fluorescent signal in the supernatant can be measured with a fluorescence spectrophotometer to indirectly determine the three pathogens in the sample. The linear range of the method was 10-10 cfu/mL, and in the buffer, the detection limits of , , and were 2.460, 5.407, and 3.770 cfu/mL, respectively. In the tap water simulation, the detection limits of , , and were 2.730, 1.990 × 10, and 4.480 cfu/mL, respectively. In the milk simulation sample, the detection limits of , , and were 6.660, 1.070 × 10, and 2.236 × 10 cfu/mL, respectively. The method we presented can detect three kinds of foodborne pathogens at the same time, and the entire experimental process did not exceed 4 h. It has high sensitivity and low detection limit and may be used in the sample detection of other pathogens.
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http://dx.doi.org/10.1021/acsomega.0c02833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7495797PMC
September 2020

Adsorption characteristics and mechanism of norfloxacin in water by γ-FeO@BC.

Water Sci Technol 2020 Jul;82(2):242-254

College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu 241000, China.

Using waste pomelo peel as raw material, pomelo peel-based biochar (BC) was prepared by pyrolysis at 400 °C, and the pomelo peel-based biochar was prepared by loading γ-FeO onto the surface of the pomelo peel-based biochar by unlimited oxygen chemical precipitation. The results showed that the pomelo peel biochar loaded with γ-FeO had higher specific surface area and larger pore volume. The load of γ-FeO gives γ-FeO@BC excellent magnetic separation ability, and its magnetic saturation intensity is as high as 30.60 emu/g. BC and γ-FeO@BC were applied to remove norfloxacin (NOR) from a water body. It was found that the adsorption of NOR by both of them followed the pseudo-second-order kinetic model. The adsorption isotherm mainly conforms to the Sips model, and the adsorption process of NOR is a spontaneous endothermic reaction. The pH and ionic strength have a great influence on the adsorption of NOR by BC and γ-FeO@BC, and they play a role mainly by influencing the morphology of NOR in water. The adsorption mechanism showed that cation exchange and hydrogen bonding were the main forces for BC to adsorb NOR. Moreover, the γ-FeO particles enhanced the hydrophobicity of the pomelo peel-based biochar, making the hydrophobicity become the main force for the adsorption of NOR by the γ-FeO@BC. The adsorption-desorption experiment showed that after four cycles of recycling, the adsorption capacity of γ-FeO@BC for NOR was still up to 61.43% of the initial adsorption capacity, and it had a good recycling property.
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http://dx.doi.org/10.2166/wst.2020.078DOI Listing
July 2020

Illegitimate Recombination Between Homeologous Genes in Wheat Genome.

Front Plant Sci 2020 21;11:1076. Epub 2020 Jul 21.

School of Life Sciences, North China University of Science and Technology, Tangshan, China.

Polyploidies produce a large number of duplicated regions and genes in genomes, which have a long-term impact and stimulate genetic innovation. The high similarity between homeologous chromosomes, forming different subgenomes, or homologous regions after genome repatterning, may permit illegitimate DNA recombination. Here, based on gene colinearity, we aligned the (sub)genomes of common wheat (, AABBDD genotype) and its relatives, including (AA), (DD), and ssp. dicoccoides (AABB) to detect the homeologous (paralogous or orthologous) colinear genes within and between (sub)genomes. Besides, we inferred more ancient paralogous regions produced by a much ancient grass-common tetraploidization. By comparing the sequence similarity between paralogous and orthologous genes, we assumed abnormality in the topology of constructed gene trees, which could be explained by gene conversion as a result of illegitimate recombination. We found large numbers of inferred converted genes (>2,000 gene pairs) suggested long-lasting genome instability of the hexaploid plant, and preferential donor roles by DD genes. Though illegitimate recombination was much restricted, duplicated genes produced by an ancient whole-genome duplication, which occurred millions of years ago, also showed evidence of likely gene conversion. As to biological function, we found that ~40% catalytic genes in colinearity, including those involved in starch biosynthesis, were likely affected by gene conversion. The present study will contribute to understanding the functional and structural innovation of the common wheat genome.
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http://dx.doi.org/10.3389/fpls.2020.01076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7396543PMC
July 2020

MicroRNA-200a Inhibits Inflammation and Atherosclerotic Lesion Formation by Disrupting EZH2-Mediated Methylation of STAT3.

Front Immunol 2020 23;11:907. Epub 2020 Jun 23.

Department of Cardiology, The Second Hospital of Jilin University, Changchun, China.

Endothelial inflammation and dysfunction are critical to the process of atherosclerosis. Emerging evidence demonstrates that upregulation of miR-200a reduces VCAM-1 expression and prevents monocytic cell adhesion onto the aortic endothelium. However, limited information is available about the role of microRNA-200a (miR-200a) in facilitating atherosclerotic lesion formation. We investigated the anti-inflammatory and anti-atherosclerotic actions of miR-200a. Human umbilical vein endothelial cells (HUVECs) were cultured in the presence of oxidized low-density lipoprotein (ox-LDL), and their viability and apoptosis were evaluated using CCK-8 assays and flow cytometric analysis. The enhancer of zeste homolog 2 (EZH2) promoter activity was evaluated in the presence of miR-200a by dual luciferase reporter gene assay. EZH2-mediated methylation of signal transducer and activator of transcription 3 (STAT3) was validated by ChIP and IP assays. ApoE mice were given a 12-week high-fat diet and developed as atherosclerotic models. miR-200a was downregulated but EZH2 and HMGB1 were upregulated in ox-LDL-treated HUVECs and the aorta tissues of atherosclerotic mouse models. Elevated miR-200a was shown to protect HUVECs against ox-LDL-induced apoptosis and inflammation. EZH2 was verified as a target of miR-200a. The protective effects of miR-200a were abrogated upon an elevation of EZH2. EZH2 methylated STAT3 and enhanced STAT3 activity by increased tyrosine phosphorylation of STAT3, thereby increasing apoptosis and release of pro-inflammatory cytokines in ox-LDL-treated HUVECs. An anti-atherosclerotic role of miR-200a was also demonstrated in atherosclerotic mouse models. Our study demonstrates that miR-200a has anti-inflammatory and anti-atherosclerotic activities dependent on the EZH2/STAT3 signaling cascade.
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http://dx.doi.org/10.3389/fimmu.2020.00907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7324475PMC
April 2021

ISG15 induces ESRP1 to inhibit lung adenocarcinoma progression.

Cell Death Dis 2020 07 2;11(7):511. Epub 2020 Jul 2.

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 Medical University, 300060, Tianjin, China.

Our previous work demonstrated that Epithelial Splicing Regulatory Protein 1 (ESRP1) could inhibit the progression of lung adenocarcinoma (ADC). When ESRP1 was upregulated, the interferon (IFN) pathway was activated and Interferon-stimulated gene 15 (ISG15) expression increased exponentially in our microarray result. In this study, we aim to explore the function of ISG15 and its interactions with ESRP1 and to provide new insights for ADC treatment. ISG15 expression in lung ADC tissues was determined by immunohistochemistry (IHC) staining. The effect of ISG15 on lung ADC progression was examined by in vitro and in vivo assays. The mechanism of action on ESRP1 regulating ISG15 was investigated using Western blotting, RT-qPCR, immunofluorescence staining, chromatin immunoprecipitation, and a dual luciferase reporter system. The ISGylation between ISG15 and ESRP1 was detected by co-immunoprecipitation. Patients with high ISG15 expression were associated with higher survival rates, especially those with ISG15 expression in the nucleus. In vitro and in vivo experiments showed that upregulation of ISG15 inhibited EMT in lung ADC. ESRP1 upregulated the expression of ISG15 through CREB with enriched ISG15 in the nucleus. Importantly, ISG15 promoted ISGylation of ESRP1 and slowed the degradation of ESRP1, which demonstrated that ESRP1 and ISG15 formed a positive feedback loop and jointly suppressed EMT of lung ADC. In conclusion, ISG15 serves as an independent prognostic marker for long-term survival in lung ADC patients. We have revealed the protective effect of ISG15 against lung ADC progression and the combinatorial benefit of ISG15 and ESRP1 on inhibiting EMT. These findings suggest that reconstituting ISG15 and ESRP1 may have the potential for treating lung ADC.
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http://dx.doi.org/10.1038/s41419-020-2706-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7343783PMC
July 2020

Real-Time Monitoring of a Protein Biomarker.

ACS Sens 2020 07 13;5(7):1877-1881. Epub 2020 Jul 13.

Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.

The ability to monitor protein biomarkers continuously and in real-time would significantly advance the precision of medicine. Current protein-detection techniques, however, including ELISA and lateral flow assays, provide only time-delayed, single-time-point measurements, limiting their ability to guide prompt responses to rapidly evolving, life-threatening conditions. In response, here we present an electrochemical aptamer-based sensor (EAB) that supports high-frequency, real-time biomarker measurements. Specifically, we have developed an electrochemical, aptamer-based (EAB) sensor against Neutrophil Gelatinase-Associated Lipocalin (NGAL), a protein that, if present in urine at levels above a threshold value, is indicative of acute renal/kidney injury (AKI). When deployed inside a urinary catheter, the resulting reagentless, wash-free sensor supports real-time, high-frequency monitoring of clinically relevant NGAL concentrations over the course of hours. By providing an "early warning system", the ability to measure levels of diagnostically relevant proteins such as NGAL in real-time could fundamentally change how we detect, monitor, and treat many important diseases.
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http://dx.doi.org/10.1021/acssensors.0c01085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8088336PMC
July 2020

Theoretical Study on CL-20-Based Cocrystal Energetic Compounds in an External Electric Field.

ACS Omega 2020 Jun 11;5(24):14767-14775. Epub 2020 Jun 11.

College of Safety Science and Engineering, Nanjing Tech University, Nanjing 211816, China.

An external electric field has great effects on the sensitivity of cocrystal energetic materials. In order to find out the relationship between the external electric field and sensitivity of cocrystals 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane/benzotrifuroxan (CL-20/BTF), 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane/3,4-dinitropyrazole (CL-20/DNP), and 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane/1-methyl-3,5-dinitro-1,2,4-triazole (CL-20/MDNT), density functional theory at B3LYP-D3/6-311+G(d,p) and M062X-D3/ma-def2 TZVPP levels was employed to calculate frontier molecular orbitals, atoms in molecules (AIM) electron density values, bond dissociation energies (BDEs) of the N-NO bond, impact sensitivity (), electrostatic potentials (ESPs), and nitro group charges ( ) in this work. The results show that a smaller highest occupied molecular orbital-lowest unoccupied molecular orbital gap and the BDEs, as well as , tend to have a larger sensitivity along with the positive directions in the external electric field. Moreover, a smaller local positive ESP () leads to better stability in the negative electric field. The sensitivity of cocrystal molecules decreases gradually in the negative external electric field with the increase of negative nitro group charges. Finally, the change in the bond lengths, AIM electron density values, and nitro group charges correlate well with the external electric field strengths.
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http://dx.doi.org/10.1021/acsomega.0c01643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315606PMC
June 2020