Publications by authors named "Xiaoqing You"

44 Publications

Nitrate dose-responsive transcriptome analysis identifies transcription factors and small secreted peptides involved in nitrogen response in Tartary buckwheat.

Plant Physiol Biochem 2021 May 25;162:1-13. Epub 2021 Feb 25.

Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China. Electronic address:

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an economically important pseudocereal crop, which can adapt well to extreme environments, including low nitrogen (LN) stress. However, little is known regarding the associated molecular mechanisms. In this study, the molecular mechanism of Tartary buckwheat roots in response to different doses of nitrate was investigated by combining physiological changes with transcriptional regulatory network. LN improved elongation and branching of lateral roots, indicating that the plasticity of lateral roots drives the adaption of Tartary buckwheat under LN condition. The roots of the seedlings that were cultivated under four N conditions were selected for RNA-Seq analysis. In total 1686 nitrate dose-responsive genes were identified. Of these genes, 16 genes encoding N transporters showed response to N availability, and they may play important roles in N transport and root system architecture in Tartary buckwheat roots. 108 transcription factors (TFs) showed dose-response to N availability, and they may regulate N response and root growth under varied N conditions by modulating the expression of N transporters. A NIN-like protein, FtNLP7, was identified and it may contribute to the transcriptional regulation of N transporters. Furthermore, 81 N-responsive genes were identified as the small secreted peptides (SSPs). 48 N-responsive SSPs were annotated as hypothetical proteins and they may be the species-specific proteins of Tartary buckwheat. This paper provides useful information for further investigation of the mechanisms underlying the adaptation of Tartary buckwheat under N-deficient condition.
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http://dx.doi.org/10.1016/j.plaphy.2021.02.027DOI Listing
May 2021

ERRα inhibitor acts as a potential agonist of PPARγ to induce cell apoptosis and inhibit cell proliferation in endometrial cancer.

Aging (Albany NY) 2020 11 10;12(22):23029-23046. Epub 2020 Nov 10.

Department of Gynecology and Obstetrics, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, China.

Two transcriptional factors, peroxisome proliferator-activated receptor-γ (PPARγ) and estrogen-related receptor-α (ERRα), have been reported to be key regulators of cellular energy metabolism. However, the relationship between ERRα and PPARγ in the development of endometrial cancer (EC) is still unclear. The expression levels of PPARγ and ERRα in EC were evaluated by quantitative real-time PCR, western blot, tissue array and immunohistochemistry. A significant negative correlation was identified between PPARγ and ERRα expression in women with EC (ρ=-0.509, P<0.001). Bioinformatics analyses showed that PPARγ and ERRα can activate or inhibit the same genes involved in cell proliferation and apoptosis through a similar ModFit. ERRα activation or PPARγ inhibition could promote proliferation and inhibit apoptosis through the Bcl-2/Caspase3 pathways. Both PPARγ and ERRα can serve as serum tumor markers. Surprisingly, as evaluated by receiver operating characteristic (ROC) curves and a logistic model, a PPARγ/ERRα ratio≤1.86 (area under the ROC curve (AUC)=0.915, Youden index=0.6633, P<0.001) was an independent risk factor for endometrial carcinogenesis (OR=14.847, 95% CI= 1.6-137.748, P=0.018). EC patients with PPARγ(-)/ERRα(+) had the worst overall survival and disease-free survival rates (both P<0.001). Thus, a dynamic imbalance between PPARγ and ERRα leads to endometrial carcinogenesis and predicts the EC prognosis.
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http://dx.doi.org/10.18632/aging.104049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7746384PMC
November 2020

Flame synthesized nanoscale catalyst (CuCeWTi) with excellent Hg oxidation activity and hydrothermal resistance.

J Hazard Mater 2021 Apr 1;408:124427. Epub 2020 Nov 1.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, Beijing 100084, China.

In view of poor hydrothermal resistance of impregnation prepared catalysts (Cu5Ce5W9Ti-I), this paper aims to enhance thermal and hydrothermal resistance of Cu/Ce based catalysts for Hg oxidation via flame synthesis technology. The result found that the flame synthesis method could form nanoscale Cu10Ce10W9Ti-F particles with smaller lattice size (8-25 nm), more stable carrier structure and more oxygen vacancies. The inter-doping and inter-substitution of Ce, Cu and Ti oxides created more oxygen vacancies (Ce) and L-sites (O). Furthermore, the carrier TiO of Cu10Ce10W9Ti-F existed in form of highly thermostable rutile rather than anatase. High Hg oxidation efficiency (MOE) of 83.9-99.7% at 100-450 °C proved excellent oxidation activity of Cu10Ce10W9Ti-F catalyst. Moreover, the thermal and hydrothermal treatment (700 °C) only decreased MOE by less than 5% since L-sites kept fine thermostability of Cu10Ce10W9Ti-F. The flame synthesis was proven to be a promising catalyst preparation method to enhance thermal and hydrothermal resistance.
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http://dx.doi.org/10.1016/j.jhazmat.2020.124427DOI Listing
April 2021

Recipient-specific T-cell repertoire reconstitution in the gut following murine hematopoietic cell transplant.

Blood Adv 2020 09;4(17):4232-4243

Blood and Marrow Transplantation.

Graft-versus-host disease (GVHD) is a complication of hematopoietic cell transplantation (HCT) caused by alloreactive T cells. Murine models of HCT are used to understand GVHD and T-cell reconstitution in GVHD target organs, most notably the gastrointestinal (GI) tract where the disease contributes most to patient mortality. T-cell receptor (TCR) repertoire sequencing was used to measure T-cell reconstitution from the same donor graft (C57BL/6 H-2b) in the GI tract of different recipients across a spectrum of matching, from syngeneic (C57BL/6), to minor histocompatibility (MHC) antigen mismatch BALB.B (H-2b), to major MHC mismatched B10.BR (H-2k) and BALB/c (H-2d). Although the donor T-cell pools had highly similar TCR, the TCR repertoire after HCT was very specific to recipients in each experiment independent of geography. A single invariant natural killer T clone was identifiable in every recipient group and was enriched in syngeneic recipients according to clonal count and confirmatory flow cytometry. Using a novel cluster analysis of the TCR repertoire, we could classify recipient groups based only on their CDR3 size distribution or TCR repertoire relatedness. Using a method for evaluating the contribution of common TCR motifs to relatedness, we found that reproducible sets of clones were associated with specific recipient groups within each experiment and that relatedness did not necessarily depend on the most common clones in allogeneic recipients. This finding suggests that TCR reconstitution is highly stochastic and likely does not depend on the evaluation of the most expanded TCR clones in any individual recipient but instead depends on a complex polyclonal architecture.
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http://dx.doi.org/10.1182/bloodadvances.2019000977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7479954PMC
September 2020

Reaction kinetics of hydrogen addition reactions to methyl butenoate.

Phys Chem Chem Phys 2020 Mar;22(9):5286-5292

Center for Combustion Energy, Tsinghua University, Beijing 100084, China. and Key Laboratory for Thermal Science and Power Engineering of the Ministry of Education, Tsinghua University, Beijing 100084, China.

To investigate the kinetics of hydrogen addition reactions of unsaturated methyl esters, we selected two representative molecules that are isomers with C[double bond, length as m-dash]C double bonds at different locations, i.e. methyl 2-butenoate and methyl 3-butenoate for study. An appropriate quantum chemical method was determined to compute the potential energy surfaces. The high-pressure limit rate constants were computed by applying multi-structural canonical variational transition state theory including tunneling by the multi-dimensional small-curvature tunneling approximation. The master equation analysis was followed to study the pressure-dependence of the rate constants of H addition and the subsequent dissociation reactions. The results show that it is easier for the H atom to add to the C[double bond, length as m-dash]C than to the C[double bond, length as m-dash]O bond because of the lower barrier heights, and the hydrogen addition reactions are faster for both methyl 2-butenoate and methyl 3-butenoate, except that the hydrogen abstraction is dominant at above 1700 K for methyl 2-butenoate. Using our computed rate constants, the prediction for methyl propanoate mole fraction agreed better with experimental data of methyl 2-butenoate combustion.
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http://dx.doi.org/10.1039/c9cp06570aDOI Listing
March 2020

Promoting SO Resistance of a CeO(5)-WO(9)/TiO Catalyst for Hg Oxidation via Adjusting the Basicity and Acidity Sites Using a CuO Doping Method.

Environ Sci Technol 2020 02 14;54(3):1889-1897. Epub 2020 Jan 14.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment , Tsinghua University , Beijing 100084 , China.

The competition between SO and elemental mercury (Hg) for active sites was an important factor for suppressing the Hg oxidation properties of catalysts. There were obvious differences in properties of basicity and acidity between SO and Hg. Raising the SO resistance via adjusting the basicity and acidity sites of catalysts was promising for reducing the competition between SO and Hg. This study aimed to form multiple active sites with different basicities via Cu, Fe, Mn, and Sn doping. The results indicated that Cu doping had the best modification performance. Five percent CuO doping could significantly improve the SO resistance of CuO(5)-CeO(5)-WO(9)/TiO and increase the mercury oxidation efficiency (MOE) from 54.7 to 85.5% in the condition (6% O, 100 ppm NO, 100 ppm NH, and 100 ppm SO). CO temperature-programmed desorption analysis showed that CuO(5)-CeO(5)-WO(9)/TiO exhibited weak basic sites (CeO), medium-strong basic sites (Cu-O-Ce), and strong basic sites (CuO). Therefore, the CuO in the Ce-O-Cu structure was prioritized for the reaction with acid gas SO and protected CeO from SO poisoning. This study prepared a highly SO-resistant catalyst for Hg oxidation. This research and development will be conducive for use in Hg oxidation in actual coal-fired flue gases.
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http://dx.doi.org/10.1021/acs.est.9b04465DOI Listing
February 2020

Peroxide-mediated site-specific C-H methylation of imidazo[1,2-a]pyridines and quinoxalin-2(1H)-ones under metal-free conditions.

Org Biomol Chem 2020 01;18(2):205-210

Department of Chemistry, Nanchang University, No. 999, Xuefu Rd., Nanchang, 330031, P. R. China.

An effective approach to realize the direct methylation of imidazo[1,2-a]pyridines and quinoxalin-2(1H)-ones with peroxides under metal-free conditions is described. In this protocol, peroxides serve as both the radical initiator and methyl source. Methylated imidazopyridines and quinoxalin-2(1H)-ones were smoothly synthesized in moderate to good yields. A free radical reaction mechanism was proposed to describe the methylation process.
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http://dx.doi.org/10.1039/c9ob02328cDOI Listing
January 2020

On the Prediction of Standard Enthalpy of Formation of C2-C4 Oxygenated Species.

J Phys Chem A 2019 Dec 17;123(51):11004-11011. Epub 2019 Dec 17.

In this study, to determine an efficient and accurate method for predicting standard enthalpy of formation (Δ) of oxygenated species, we calculated Δ for several typical C2-C4 oxygenated species using atomization and isodesmic reactions in combination with various quantum chemical methods, including six density functional theory methods, three compound methods, and CCSD(T)/CBS. Compared with experimental values, at the same quantum chemical level, Δ values predicted by using isodesmic reactions are more accurate than those using atomization reactions. Comparing various quantum chemical methods when isodesmic reactions are used, the performance of G4 is the best with a mean unsigned deviation (MUE) of 0.3 kcal/mol and a standard deviation (SD) of 0.3 kcal/mol, while M06-2X can predict Δ efficiently and accurately with an MUE of 0.6 kcal/mol and SD of 0.5 kcal/mol. Using the best methods we have found, we calculated the enthalpies of formation and other thermodynamic properties for dimethyl carbonate (DMC) and its associated species and then applied them in a DMC combustion model for predicting ignition delay times. Better agreement with the experiments is achieved when the newly computed thermodynamic properties are adopted.
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http://dx.doi.org/10.1021/acs.jpca.9b08516DOI Listing
December 2019

Energy transfer in intermolecular collisions of polycyclic aromatic hydrocarbons with bath gases He and Ar.

J Chem Phys 2019 Jul;151(4):044301

Dassault Systèmes, BIOVIA, 334, Cambridge Science Park, Cambridge CB4 0WN, United Kingdom.

Classical trajectory simulations of intermolecular collisions were performed for a series of polycyclic aromatic hydrocarbons interacting with the bath gases helium and argon for bath gas temperature from 300 to 2500 K. The phase-space average energy transferred per deactivating collision, ⟨∆E⟩, was obtained. The Buckingham pairwise intermolecular potentials were validated against high-level quantum chemistry calculations and used in the simulations. The reactive force-field was used to describe intramolecular potentials. The dependence of ⟨∆E⟩ on initial vibrational energy is discussed. A canonical sampling method was compared with a microcanonical sampling method for selecting initial vibrational energy at high bath gas temperatures. Uncertainties introduced by the initial angular momentum distribution were identified. The dependence of the collisional energy transfer parameters on the type of bath gas and the molecular structure of polycyclic aromatic hydrocarbons was examined.
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http://dx.doi.org/10.1063/1.5094104DOI Listing
July 2019

Kinetics of Hydrogen Abstraction Reactions of Methyl Palmitate and Octadecane by Hydrogen Atoms.

J Phys Chem A 2019 Apr 29;123(14):3058-3067. Epub 2019 Mar 29.

Center for Combustion Energy , Tsinghua University , Beijing 100084 , China.

Hydrogen abstractions play a crucial role in the consumption of fuel molecules during fuel pyrolysis and combustion processes. In this study, a generalized energy-based fragmentation approach was used to obtain CCSD(T)-F12a/cc-pVTZ energy barriers of hydrogen abstraction reactions by hydrogen atoms from methyl palmitate (CHCOOCH), a key component of biodiesel. The accuracy of M06-2X/6-311++G(d,p) for obtaining the energy barriers was evaluated against the CCSD(T) results. Based on the quantum chemical results, the high-pressure-limit rate constants for CHCOOCH + H were calculated and compared with those of octadecane ( n-CH) reacting with H. The treatment of hindered internal rotations for such long-chain molecules was discussed and the rate rules for different abstraction sites were summarized. The results show that in the CHCOOCH + H system, the α hydrogen abstraction no longer plays a dominant role as in small methyl esters, and the hydrogen atoms of CH groups far away from the ester group are more easily abstracted than those near the ester group.
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http://dx.doi.org/10.1021/acs.jpca.8b08802DOI Listing
April 2019

Effect of hindered internal rotation treatments on predicting the thermodynamic properties of alkanes.

Phys Chem Chem Phys 2019 Jan;21(4):1928-1936

Center for Combustion Energy, Tsinghua University, Beijing 100084, China.

When considering hindered internal rotation, we usually have several options, including (i) single structure harmonic oscillator (SS-HO) approximation that considers the lowest-energy conformer only and approximates all molecular vibrations as harmonic oscillations, (ii) one-dimensional (1-D) internal rotation treatment that replaces the corresponding vibrational mode with one-dimensional torsion, and (iii) the multistructural method with torsional anharmonicity (MS-T) that considers the multiple-structure and torsional anharmonicity. These methods differ greatly in computational cost and accuracy. To evaluate the effect of different treatments on predicting thermodynamic properties, we calculated enthalpy, entropy, and heat capacity for a series of normal and branched alkanes using six different methods, including the SS-HO treatment, three 1-D methods, the MS-T method, and the group additivity (GA) method. The comparison of the computational results with experimental data shows that GA and two 1-D methods proposed in this study are more suitable for reliable and rapid predictions of thermodynamic properties for large hydrocarbons with many carbon-carbon single bonds.
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http://dx.doi.org/10.1039/c8cp07308bDOI Listing
January 2019

Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum).

BMC Plant Biol 2019 Jan 8;19(1):15. Epub 2019 Jan 8.

College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030, China.

Background: Leaf mold, one of the major diseases of tomato caused by Cladosporium fulvum (C. fulvum), can dramatically reduce the yield and cause multimillion dollar losses annually worldwide. Mapping the resistance genes (R genes) of C. fulvum and devising MAS based strategies for breeding new cultivars is an effective approach to improve the resistance in tomato. Up to now, many C. fulvum genes or QTLs have been mapped using different genetic materials, but few studies focused on Cf-10 gene positioning.

Results: In this study, we investigated the genetic rules for Cf-10 and used a novel combinatorial strategy to rapidly map the Cf-10 gene. Initially, the performance of F, F and BCF individuals after infection, demonstrated that the resistance against C. fulvum was controlled by a single dominant gene. Two pools of resistant and susceptible individuals from F population were investigated, using mapping by sequencing approach and Cf-10 was found to be localized to 3.35 Mb and 3.74 Mb on chromosome 1, employing SNP/InDel index methods, respectively. After accounting for overlapping regions, these two algorithms yielded a total length of 3.29 Mb, narrowing down the target region. We further developed five serviceable KASP markers for this region based on sequencing data and conducted local QTL mapping using individuals from the F population, except for mapping by sequencing as mentioned above. Finally Cf-10 gene was mapped spanning a region of 790 kb, where only one gene (Solyc01g007130.3) was annotated as probable receptor protein kinase TMK1 with a LRR motif, a common R gene characteristic. The RT-qPCR analysis further confirmed the localization and the relative expression of Solyc01g007130.3 in Ontario 792 and was found to be significantly higher than that in Moneymaker at 9 dpi and 12 dpi, respectively.

Conclusion: This study proposed a novel combinatorial strategy by combining SNP-index, InDel-index analyses and local QTL mapping using KASP genotyping approach to rapidly map genes responsible for specific traits and provided a robust base for cloning the Cf-10 gene. Furthermore, these analyses suggest that Solyc01g007130.3 is a potential candidate to be regarded as Cf-10 gene.
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http://dx.doi.org/10.1186/s12870-018-1616-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325758PMC
January 2019

Dimerization of Polycyclic Aromatic Hydrocarbon Molecules and Radicals under Flame Conditions.

J Phys Chem A 2018 Nov 30;122(44):8701-8708. Epub 2018 Oct 30.

Center for Combustion Energy, Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Department of Energy and Power Engineering , Tsinghua University , Beijing 100084 , China.

This work presents a dynamic and kinetic study on the dimerization of polycyclic aromatic hydrocarbon (PAH) molecules and radicals under flame conditions using reactive force field (ReaxFF) molecular dynamics (MD) simulations. The accuracy of the ReaxFF force field is evaluated through comparing with quantum chemistry (QC) calculations of the barrier heights and species concentrations of PAHs reacting with H and OH radicals. A series of homobinary collisions between PAH molecules/radicals are performed to reveal the influence of temperature, molecular size, PAH composition, and the number of radical sites on the dynamics and kinetics of PAH dimerization. Instead of directly forming the strong covalent bonds, the majority of the binary collisions between PAH radicals are bound with weak intermolecular interactions. Effects of oxygen on PAH radical dimerization are also investigated, which indicates that the oxygenated PAH radicals are less likely to contribute to soot nucleation. In addition, the temperature, PAH characteristic, and radical site dependent collision efficiency for PAH radical-radical combinations is extracted from this study.
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http://dx.doi.org/10.1021/acs.jpca.8b07102DOI Listing
November 2018

Physiological and RNA-seq analyses provide insights into the response mechanism of the Cf-10-mediated resistance to Cladosporium fulvum infection in tomato.

Plant Mol Biol 2018 Mar 30;96(4-5):403-416. Epub 2018 Jan 30.

College of Horticulture and Landscape Architecuture, Northeast Agricultural University, Harbin, 150030, China.

Key Message: Based on the physiological and RNA-seq analysis, some progress has been made in elucidating the Cf-10-mediated resistance responses to C. fulvum infection in tomato. GO and KEGG enrichment analysis revealed that the DEGs were significantly associated with defense-signaling pathways like oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Leaf mold, caused by the fungus Cladosporium fulvum, is one of the most common diseases affecting tomatoes worldwide. Cf series genes including Cf-2, Cf-4, Cf-5, Cf-9 and Cf-10 play very important roles in resisting tomato leaf mold. Understanding the molecular mechanism of Cf gene-mediated resistance is thus the key to facilitating genetic engineering of resistance to C. fulvum infection. Progress has been made in elucidating two Cf genes, Cf -19 and Cf -12, and how they mediate resistance responses to C. fulvum infection in tomato. However, the mechanism of the Cf-10- mediated resistance response is still unclear. In the present study, RNA-seq was used to analyze changes in the transcriptome at different stages of C. fulvum infection. A total of 2,242 differentially expressed genes (DEGs) responsive to C. fulvum between 0 and 16 days post infection (dpi) were identified, including 1,501 upregulated and 741 downregulated genes. The majority of DEGs were associated with defense-signaling pathways including oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Four DEGs associated with plant-pathogen interaction were uniquely activated in Cf-10 tomato and validated by qRT-PCR. In addition, physiological indicators including reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were measured at 0-21 dpi, and hormone expression [Jasmonic acid (JA) and salicylic acid (SA)] was estimated at 0 and 16 dpi to elucidate the mechanism of the Cf-10-mediated resistance response. C. fulvum infection induced the activities of POD, CAT and SOD, and decreased ROS levels. JA was determined to participate in the resistance response to C. fulvum during the initial infection period. The results of this study provide accountable evidence for the physiological and transcriptional regulation of the Cf-10-mediated resistance response to C. fulvum infection, facilitating further understanding of the molecular mechanism of Cf-10-mediated resistance to C. fulvum infection.
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http://dx.doi.org/10.1007/s11103-018-0706-0DOI Listing
March 2018

Reaction kinetics of hydrogen abstraction from polycyclic aromatic hydrocarbons by H atoms.

Phys Chem Chem Phys 2017 Nov;19(45):30772-30780

Center for Combustion Energy, Tsinghua University, Beijing, 100084, China.

Hydrogen abstraction reactions of polycyclic aromatic hydrocarbons (PAH) by H atoms play a very important role in both PAH and soot formation processes. However, large discrepancies up to a few orders of magnitude exist among the literature rate constant values. To increase the reliability of the computed rate constants, it is critical to obtain highly accurate potential energy surfaces. For this purpose, we have investigated the energetics of hydrogen abstraction from benzene and naphthalene using both high level-of-theory quantum chemistry methods and a series of density functional theory (DFT) methods, among which M06-2X/6-311g(d,p) has the best performance with a mean unsigned deviation from the CCSD(T)/CBS calculations of 1.0 kcal mol for barrier heights and reaction energies. Thus, M06-2X/6-311g(d,p) has then been applied to compute the potential energy surfaces of the hydrogen abstraction reactions of a series of larger PAH. Based on the quantum chemistry calculations, rate constants are computed using the canonical transition state theory. The effects of the PAH size, structure, and reaction site on the energetics and rate constants are examined systematically. Finally, the hydrogen abstraction rate constants for application in PAH and soot surface chemistry models are recommended.
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http://dx.doi.org/10.1039/c7cp04964aDOI Listing
November 2017

Retinoid X receptor ligand regulates RXRα/Nur77-dependent apoptosis via modulating its nuclear export and mitochondrial targeting.

Int J Clin Exp Pathol 2017 1;10(11):10770-10780. Epub 2017 Nov 1.

Department of Cell Biology and Genetics/Center for Cell and Developmental Biology, School of Basic Medical Sciences, Fujian Medical University Fuzhou 350122, Fujian, China.

Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder disease in elderly. It is characterized by the formation of amyloid plaques and nerve cells apoptosis in the brain. This study focuses on the association between nerve cells apoptosis and nuclear receptors within AD. Thus, we detected the changes of the expression and subcellular localization of RXRα/Nur77 and the apoptotic rate of neuroblastoma cells, SH-SY5Y cells and nerve cells in C57BL/6 mouse hippocampus in Alzheimer's disease pathologic condition, and investigated the effect of RXRα exporting inhibition caused by 9-cis-RA on the apoptosis of neurons. We demonstrated that Aβ peptide and HO treatment could result in the translocation of RXRα and Nur77 from the nucleus to the mitochondria, and the ligand of RXR, 9-cis-RA, treatment can block the above phenomenon. More importantly, 9-cis-RA treatment could reduce the apoptotic rate of neurons caused by HO or Aβ stimulation via enhancing the expression level of Bcl-2 protein. Therefore, our studies revealed a critical role of RXRα/Nur77 in 9-cis-RA-mediated anti-apoptosis in nerve cells and provided novel information for better management of AD.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6965856PMC
November 2017

Effect of retinoid X receptor-α nuclear export inhibition on apoptosis of neurons in vivo and in vitro.

Mol Med Rep 2017 Aug 14;16(2):2037-2044. Epub 2017 Jun 14.

Department of Cell Biology and Genetics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China.

Alzheimer's disease (AD), which is characte-rized by excessive apoptosis of neurons, is considered to be a global public health crisis. Retinoid-induced apoptosis is dependent on the orphan nuclear receptor Nur77, a transcription factor that is expressed predominantly in brain tissues. Nur77 nuclear export requires retinoid X receptor‑α (RXRα) as a carrier. However, the involvement of Nur77 in mediating β‑amyloid (Aβ)‑induced neuronal apoptosis has not yet been elucidated. The primary aim of the present study was to investigate the potential of Nur77 in Aβ‑induced neuron apoptosis, and to evaluate the effect of RXRα nuclear export inhibition on neuronal apoptosis. Mouse neuroblastoma Neuro‑2a (N2a) cells and mouse hippocampi were treated with Aβ25‑35 or Aβ25‑35 combined with a RXRα ligand, 9‑cis‑retinoid acid (9‑cis‑RA), while untreated cells and mice served as controls. The expression of RXRα and Nur77 was determined using western blotting and reverse transcription‑quantitative polymerase chain reaction analyses, and the translocation of RXRα and Nur77 was detected using confocal microscopy. In addition, the apoptosis and viability of N2a cells was detected using flow cytometry and MTT assays, respectively, and the expression of B cell lymphoma 2 (Bcl‑2) and Bcl‑2 associated X (Bax) was quantified by western blotting. No significant alterations in the protein or mRNA expression levels of RXRα and Nur77 in N2a cells or mouse hippocampi among the three groups were observed. Aβ25‑35 treatment resulted in elevated cytoplasmic protein ratios of RXRα and Nur77 in N2a cells when compared with controls, while combined treatment with Aβ25‑35 and 9‑cis‑RA reduced cytoplasmic protein ratios of RXRα and Nur77 to 6.67 and 5.44% in N2a cells, respectively. The MTT assay results revealed a significant reduction in the viability of N2a cells following treatment with Aβ25‑35 for 24 h when compared with the controls, while the viability of N2a cells treated with Aβ25‑35 plus 9‑cis‑RA significantly increased from 53.65 to 84.10%. Western blotting revealed elevated Bax expression and reduced Bcl‑2 expression in Aβ25‑35‑treated N2a cells when compared with controls, while combined treatment with Aβ25‑35 and 9‑cis‑RA recovered Bcl‑2 expression from 0.46‑fold in cells treated with Aβ25‑35 alone to 2.44‑fold (relative to the control) and decreased Bax expression from 2.52‑fold in cells treated with Aβ25‑35 alone to 0.99‑fold (relative to the control). Flow cytometry analysis revealed that the apoptotic rate of untreated N2a cells was 4.36%, while a 15.1% apoptotic rate was detected in cells exposed to Aβ25‑35 for 24 h and a ~5.31% apoptotic rate was observed in N2a cells treated with Aβ25‑35 plus 9‑cis‑RA. In conclusion, treatment with Aβ25‑35 or Aβ25‑35 plus 9‑cis‑RA demonstrated no significant effect on the protein and mRNA expression levels of RXRα and Nur77. In addition, inhibition of RXRα nuclear export reduced neuronal apoptosis. The results of the present study may provide novel insight into the development of novel anti-AD agents.
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http://dx.doi.org/10.3892/mmr.2017.6766DOI Listing
August 2017

Kinetics and branching fractions of the hydrogen abstraction reaction from methyl butenoates by H atoms.

Phys Chem Chem Phys 2017 Jun;19(25):16563-16575

Center for Combustion Energy, Tsinghua University, Beijing, 100084, China.

In order to explore the hydrogen abstraction reaction kinetics of unsaturated methyl esters by hydrogen atoms, we selected two molecules for study, in particular methyl 3-butenoate and methyl 2-butenoate, whose C[double bond, length as m-dash]C double bonds are at different locations. We first determined an accurate and efficient electronic structure method for the investigation by considering eight hydrogen abstraction reactions and comparing their barrier heights and reaction energies computed using several exchange-correlation density functionals to those obtained from CCSD(T)-F12a/jun-cc-pVTZ coupled cluster calculations. In this way, we found the M06-2X/ma-TZVP method to have the best performance with a mean unsigned deviation from the CCSD(T) calculations of 0.51 kcal mol. Based on quantum-chemical calculations by using the M06-2X/ma-TZVP method, we then computed rate constants for 298-2500 K by direct dynamics calculations using multi-structural canonical variational transition state theory including tunneling by the multi-dimensional small-curvature tunneling approximation (MS-CVT/SCT). The computed transmission coefficients were compared with those obtained using the zero-curvature tunneling (ZCT) and one-dimensional Eckart tunneling (ET) approximations. We employed the multi-structural torsional method (MS-T) to include the multiple-structure and torsional potential anharmonic effects. The results show that the variational recrossing transmission coefficients range from 0.6 to 1.0, and the multi-structural torsional anharmonicity introduces a factor of 0.5-2.5 into the rate constant, while the tunneling transmission coefficients obtained by SCT can be as large as 17.4 and differ considerably from those determined by the less accurate ZCT and ET approximations. In addition, independent of the location of the C[double bond, length as m-dash]C double bond, the dominant hydrogen abstraction reactions occur at the allylic sites.
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http://dx.doi.org/10.1039/c7cp01686gDOI Listing
June 2017

Obtaining effective rate coefficients to describe the decomposition kinetics of the corannulene oxyradical at high temperatures.

Phys Chem Chem Phys 2017 May;19(18):11064-11074

Center for Combustion Energy, Tsinghua University, Beijing, 100084, China.

Unimolecular reactions play an important role in combustion kinetics. An important task of reaction kinetic analysis is to obtain the phenomenological rate coefficients for unimolecular reactions based on the master equation approach. In most cases, the eigenvalues of the transition matrix describing collisional internal energy relaxation are of much larger magnitude than and well separated from the chemically significant eigenvalues, so that phenomenological rate coefficients may be unequivocally derived for incorporation in combustion mechanisms. However, when dealing with unimolecular reactions for a large molecule, especially at high temperatures, the large densities of states of the reactant cause the majority of the population distribution to lie at very high energy levels where the microcanonical reaction rate constants are large and the relaxation and chemical eigenvalues overlap, so that well-defined phenomenological rate coefficients cannot be determined. This work attempts to analyze the effect of overlapping eigenvalues on the high-temperature kinetics of a large oxyradical, based on microcanonical reaction rates and population distributions as well as the eigenvalue spectrum of the transition matrix from the master equation. The aim is to provide a pragmatic method for obtaining the most effective rate coefficients for competing elimination, dissociation, and bimolecular reactions for incorporation in combustion mechanisms. Our approach is demonstrated with a representative example, thermal decomposition and H addition reactions of the corannulene oxyradical.
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http://dx.doi.org/10.1039/c7cp00639jDOI Listing
May 2017

Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use.

J Mol Diagn 2017 01 1;19(1):72-83. Epub 2016 Nov 1.

Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California. Electronic address:

Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. For controls and patients with GVHD, replicate sequencing of the same T-cell receptor β (TRB) libraries was highly reproducible. Higher variability was observed in sequencing of different TRB libraries made from the same DNA stock. Variability was increased in patients with GVHD compared with controls; patients with GVHD also had lower diversity than controls. In the T-cell repertoire of a healthy person, approximately 99.6% of the CDR3 clones were in low abundance, with frequency <10. A single library could identify >93% of the clones with frequency ≥10 in the repertoire. Sequencing in duplicate increased the average detection rate to >97%. This work demonstrates that NGS reliably and robustly characterizes TRB populations in healthy individuals and patients with GVHD with frequency ≥10 and provides a methodologic framework for applying NGS immune repertoire methods to clinical testing applications beyond MRD.
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http://dx.doi.org/10.1016/j.jmoldx.2016.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225307PMC
January 2017

An adaptive distance-based group contribution method for thermodynamic property prediction.

Phys Chem Chem Phys 2016 Sep 15;18(34):23822-30. Epub 2016 Aug 15.

State Key Laboratory of Automotive Safety and Energy, Tsinghua University, Beijing 100084, China.

In the search for an accurate yet inexpensive method to predict thermodynamic properties of large hydrocarbon molecules, we have developed an automatic and adaptive distance-based group contribution (DBGC) method. The method characterizes the group interaction within a molecule with an exponential decay function of the group-to-group distance, defined as the number of bonds between the groups. A database containing the molecular bonding information and the standard enthalpy of formation (Hf,298K) for alkanes, alkenes, and their radicals at the M06-2X/def2-TZVP//B3LYP/6-31G(d) level of theory was constructed. Multiple linear regression (MLR) and artificial neural network (ANN) fitting were used to obtain the contributions from individual groups and group interactions for further predictions. Compared with the conventional group additivity (GA) method, the DBGC method predicts Hf,298K for alkanes more accurately using the same training sets. Particularly for some highly branched large hydrocarbons, the discrepancy with the literature data is smaller for the DBGC method than the conventional GA method. When extended to other molecular classes, including alkenes and radicals, the overall accuracy level of this new method is still satisfactory.
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http://dx.doi.org/10.1039/c6cp02929aDOI Listing
September 2016

Theoretical Analysis of the Effect of C═C Double Bonds on the Low-Temperature Reactivity of Alkenylperoxy Radicals.

J Phys Chem A 2016 Aug 27;120(30):5969-78. Epub 2016 Jul 27.

Center for Combustion Energy, Tsinghua University , Beijing 100084, China.

Biodiesel contains a large proportion of unsaturated fatty acid methyl esters. Its combustion characteristics, especially its ignition behavior at low temperatures, have been greatly affected by these C═C double bonds. In this work, we performed a theoretical analysis of the effect of C═C double bonds on the low-temperature reactivity of alkenylperoxy radicals, the key intermediates from the low-temperature combustion of biodiesel. To understand how double bonds affect the fate of peroxy radicals, we selected three representative peroxy radicals from heptane, heptene, and heptadiene having zero, one, and two double C═C bonds, respectively, for study. The potential energy surfaces were explored at the CBS-QB3 level, and the reaction rate constants were computed using canonical/variational transition state theories. We have found that the double bond is responsible for the very different bond dissociation energies of the various types of C-H bonds, which in turn affect significantly the reaction kinetics of alkenylperoxy radicals.
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http://dx.doi.org/10.1021/acs.jpca.6b05399DOI Listing
August 2016

Benchmark Calculations for Bond Dissociation Enthalpies of Unsaturated Methyl Esters and the Bond Dissociation Enthalpies of Methyl Linolenate.

J Phys Chem A 2016 Jun 1;120(23):4025-36. Epub 2016 Jun 1.

Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States.

It is important to determine an appropriate computational method for obtaining accurate thermochemical properties of large biodiesel molecules such as methyl linolenate. In this study, we use Kohn-Sham density functional theory (DFT) and coupled cluster theory to calculate bond dissociation enthalpies (BDEs) of seven fragment molecules of methyl linolenate, in particular, propene, methyl formate, cis-3-hexene, 1,4-pentadiene, 1-pentene, butane, and methyl butanoate. The results are compared to BDEs obtained from experiments and to Oyeyemi et al.'s multireference averaged coupled pair functional (MRACPF2) calculations. We found that with extrapolation to the complete basis set (CBS) limit, the BDEs derived from coupled cluster calculations with single, double, and triple excitations (CCSDT) and from CCSDT with a perturbative treatment of connected quadruple excitations, CCSDT(2)Q/CBS, are closer to the available experimental values than those obtained by MRACPF2 for propene and methyl formate. The CCSDT/CBS calculations were chosen as the reference for validating the DFT methods. Among the density functionals, we found that M08-HX has the best performance with a mean unsigned deviation (MUD) from CCSDT/CBS of only 1.0 kcal/mol, whereas the much more expensive MRACPF2 has an MUD of 1.1 kcal/mol. We then used the most successfully validated density functionals to calculate the BDEs of methyl linolenate and compared the results with the MRACPF2 BDEs. The present study identifies several Kohn-Sham exchange-correlation functionals that should be useful for modeling ester combustion, especially the M08-HX, M06-2X, M05-2X, M08-SO, and MPWB1K global-hybrid meta functionals, the M11 and MN12-SX range-separated-hybrid meta functionals, the ωB97 range-separated hybrid gradient approximation functional, and the SOGGA11-X global-hybrid gradient approximation functional.
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http://dx.doi.org/10.1021/acs.jpca.6b02600DOI Listing
June 2016

Thermal decomposition of graphene oxyradicals under the influence of an embedded five-membered ring.

Phys Chem Chem Phys 2016 04;18(17):12149-62

School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.

In this study, we examined the influence of an embedded five-membered ring on the thermal decomposition of graphene oxyradicals. Their decomposition potential energy surfaces were explored at the B3LYP/6-311g(d,p) level. The temperature and pressure dependence of the rate coefficients was computed by master equation modeling. The results suggest that the embedded five-membered ring leads to a generally slower decomposition rate for CO elimination than that of graphene oxyradicals with only six-membered rings, but the impact of the embedded five-membered ring diminishes when it is two layers away from the edge. Well-behaved first-order kinetics was demonstrated at 1500 K, but collisional relaxation was incomplete on the dissociation timescale at higher temperatures. The ways of determining the effective rate coefficient were discussed and the influence of the uncertainty in rate constants on the predictions of species profiles was also estimated by performing kinetic modeling.
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http://dx.doi.org/10.1039/c6cp00917dDOI Listing
April 2016

Role of Carbon-Addition and Hydrogen-Migration Reactions in Soot Surface Growth.

J Phys Chem A 2016 Feb 1;120(5):683-9. Epub 2016 Feb 1.

Center for Combustion Energy, Tsinghua University , Beijing 100084, China.

Using density functional theory and master equation modeling, we have studied the kinetics of small unsaturated aliphatic molecules reacting with polycyclic aromatic hydrocarbon (PAH) molecules having a diradical character. We have found that these reactions follow the mechanism of carbon addition and hydrogen migration (CAHM) on both spin-triplet and open-shell singlet potential energy surfaces at a rate that is about ten times those of the hydrogen-abstraction-carbon-addition (HACA) reactions at 1500 K in the fuel-rich postflame region. The results also show that the most active reaction sites are in the center of the zigzag edges of the PAHs. Furthermore, the reaction products are more likely to form straight rather than branched aliphatic side chains in the case of reacting with diacetylene. The computed rate constants are also found to be independent of pressure at conditions of interest in soot formation, and the activation barriers of the CAHM reactions are linearly correlated with the diradical characters.
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http://dx.doi.org/10.1021/acs.jpca.5b10306DOI Listing
February 2016

Role of Spin-Triplet Polycyclic Aromatic Hydrocarbons in Soot Surface Growth.

J Phys Chem Lett 2015 Feb 21;6(3):477-81. Epub 2015 Jan 21.

†Center for Combustion Energy, Tsinghua University, Meng Minwei Science Technology Building, Zhishan Road, Beijing 100084, China.

Using density functional theory, a possible pathway of soot surface growth is studied in the low-temperature, postflame region in which spin-triplet polycyclic aromatic hydrocarbon (PAH) molecules with a small singlet-triplet energy gap react with unsaturated aliphatics such as acetylene via the carbon-addition-hydrogen-migration (CAHM) reaction. Results show that a PAH-core-aliphatic-shell structure is formed and the mass growth rate of this triplet soot surface growth reaction is one order of magnitude larger than that of the surface hydrogen-abstraction-carbon-addition (HACA) reaction at temperatures below 1500 K.
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http://dx.doi.org/10.1021/jz502635tDOI Listing
February 2015

All-trans-retinoic acid reduces BACE1 expression under inflammatory conditions via modulation of nuclear factor κB (NFκB) signaling.

J Biol Chem 2015 Sep 3;290(37):22532-42. Epub 2015 Aug 3.

From the Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee 38163,

Insulin resistance and neuroinflammation have emerged as two likely key contributors in the pathogenesis of Alzheimer disease (AD), especially in those sporadic AD cases compromised by diabetes or cardiovascular disease. Amyloid-β (Aβ) deposition and its associated inflammatory response are hallmarks in sporadic AD brains. Elevated expression and activity of β-secretase 1 (BACE1), the rate-limiting enzyme responsible for the β-cleavage of amyloid precursor proteins to Aβ peptides, are also observed in sporadic AD brains. Previous studies have suggested that there is therapeutic potential for retinoic acid in treating neurodegeneration based on decreased Aβ. Here we discovered that BACE1 expression is elevated in the brains of both Tg2576 transgenic mice and mice on high fat diets. These conditions are associated with a neuroinflammatory response. We found that administration of all-trans-retinoic acid (atRA) down-regulated the expression of BACE1 in the brains of Tg2576 mice and in mice fed a high fat diet. Moreover, in LPS-treated mice and cultured neurons, BACE1 expression was repressed by the addition of atRA, correlating with the anti-inflammatory efficacy of atRA. Mutations of the NFκB binding site in BACE1 promoter abolished the suppressive effect of atRA. Furthermore, atRA disrupted LPS-induced nuclear translocation of NFκB and its binding to BACE1 promoter as well as promoting the recruitment of the corepressor NCoR. Our findings indicate that atRA represses BACE1 gene expression under inflammatory conditions via the modulation of NFκB signaling.
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http://dx.doi.org/10.1074/jbc.M115.662908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4566228PMC
September 2015

Effects of Intravenous Injection of Porphyromonas gingivalis on Rabbit Inflammatory Immune Response and Atherosclerosis.

Mediators Inflamm 2015 3;2015:364391. Epub 2015 May 3.

School and Hospital of Stomatology, Fujian Medical University, and Stomatological Key Laboratory of Fujian College and University, Fuzhou 350000, China ; Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing 210000, China.

The effects of intravenous injection of Porphyromonas gingivalis (Pg) on rabbit inflammatory immune response and atherosclerosis were evaluated by establishing a microamount Pg bacteremia model combined with high-fat diet. Twenty-four New Zealand rabbits were randomly divided into Groups A-D (n = 6). After 14 weeks, levels of inflammatory factors (C-reactive protein (CRP), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and monocyte chemoattractant protein-1 (MCP-1)) in peripheral blood were detected by ELISA. The aorta was subjected to HE staining. Local aortic expressions of toll-like receptor-2 (TLR-2), TLR-4, TNF-α, CRP, IL-6, matrix metallopeptidase-9, and MCP-1 were detected by real-time PCR, and those of nuclear factor-κB (NF-κB) p65, phospho-p38 mitogen-activated protein kinase (MAPK), and phospho-c-Jun N-terminal kinase (JNK) proteins were detected by Western blot. Intravenous injection of Pg to the bloodstream alone induced atherosclerotic changes and significantly increased systemic and local aortic expressions of inflammatory factors, NF-κB p65, phospho-p38-MAPK, and JNK, especially in Group D. Injection of microamount Pg induced inflammatory immune response and accelerated atherosclerosis, in which the NF-κB p65, p38-MAPK, and JNK signaling pathways played important roles. Intravenous injection of Pg is not the same as Pg from human periodontitis entering the blood stream. Therefore, our results cannot be extrapolated to human periodontitis.
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http://dx.doi.org/10.1155/2015/364391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4433690PMC
February 2016

Hyperlipidemia causes changes in inflammatory responses to periodontal pathogen challenge: implications in acute and chronic infections.

Arch Oral Biol 2014 Oct 21;59(10):1075-84. Epub 2014 Jun 21.

Institute and Hospital of Stomatology, Nanjing University Medical School, Nanjing, Jiangsu 210008, China. Electronic address:

Objective: In this study, the effect of hyperlipidemia on immune responses to periodontal bacterial infections was investigated.

Methods: Sixty male New Zealand white rabbits were equally assigned to normal diet (ND) and high-fat diet (HFD) for 6 weeks. Every six rabbits with ND or HFD were orally inoculated with live Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis three times a week for 8 weeks. Also every six rabbits with ND or HFD rabbits were injected intravenously with A. actinomycetemcomitans and P. gingivalis LPS. Periodontal disease severity was quantified by macroscopic and radiographical evaluation. Serum cytokines were examined by enzyme-linked immunosorbent assay. In vitro, peripheral mononuclear cells were collected and stimulated with LPS. Quantitative real-time polymerase chain reaction was used to determine the changes in gene expression of macrophages.

Results: In the early stages of infection, HFD rabbits were exposed to oral infection and systemic infection developed a weak inflammatory response to the reduced cytokine expression compared with ND rabbits. However, HFD rabbits exhibited higher inflammatory cytokine expression during long-term infections. Moreover, the pronounced changes in inflammatory cytokine expression elicited a significantly increase in bone loss in HFD rabbits with oral infection. Peripheral macrophages harvested from HFD rabbits and exposed to LPS exhibited reduced levels of pro-inflammatory cytokines compared with those from ND rabbits in vitro.

Conclusion: These data indicated that hyperlipidemia interfered with immune responses differently. The mechanism is possibly associated with immune paralysis in the acute phase and accumulation of inflammatory mediators in the chronic period.
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http://dx.doi.org/10.1016/j.archoralbio.2014.06.004DOI Listing
October 2014
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