Computational determination of the S1(Ã1A″) absorption spectra of HONO and DONO using full-dimensional neural network potential energy surfaces.

The Ã1A″ ← X̃1A' absorption spectra of HONO and DONO were simulated by a full six-dimensional quantum mechanical method based on the newly constructed potential energy surfaces for the ground and excited electronic states, which were represented by the neural network method utilizing over 36 000 ab initio energy points calculated at the multireference configuration interaction level with Davidson correction. The absorption spectrum of HONO/DONO comprises a superposition of the spectra from two isomers, namely, trans- and cis-HONO/DONO, due to their coexistence in the ground X̃1A' state. Our calculated spectra of both HONO and DONO were found to be in fairly good agreement with the experiment, including the energy positions and widths of the peaks. The dominant progression was assigned to the N=O stretch mode (20n) associated with trans-HONO/DONO, which can be attributed to the promotion of an electron to the π* orbital of N=O. Specifically, the resonances with higher vibrational quanta were found to be in the domain of the Feshbach-type resonances. The assignments of the spectra and mode specificity therein are discussed.

Quantum state-to-state nonadiabatic dynamics of the charge transfer reaction H+ + NO(X2Π) → H + NO+(X1Σ+): Influence of ro-vibrational excitation of NO.

Quantum state-to-state nonadiabatic dynamics of the charge transfer reaction H+ + NO(X2Π, vi = 1, 3, ji = 0, 1) → H + NO+(X1Σ+) has been studied based on the recently constructed diabatic potential energy matrix. It was found that the vibrational excitation of reactant NO inhibits the reactivity, while the rotational excitation of reactant NO has little effect on the reaction probability. These attributes were also observed in the semi-classical trajectory calculations employed in the adiabatic representation. Such an inhibitory effect of the vibrational excitation of reactant NO was owing to lower accessibility of the conical intersection and avoided crossing regions, which are located in the wells with respect to the Π diabat, as evidenced by the analysis of the population of the time-independent wave functions. Calculated vibrational state distributions of the product show that the decrease of the reaction mainly leads to the less formation of low vibrational states (vf < 6), and the product vibrational state distributions are more evenly populated for vi = 1 and 3, suggesting a non-statistical behavior. However, the overall shapes of the product rotational distributions remain unchanged, indicating that the redistribution of energy into the rotation of product NO is sufficient in the charge transfer process between H+ and NO. While the reaction is dominated by the forward and backward scattering in differential cross sections (DCSs), consistent with the complex-forming mechanism, a clear forward bias in the DCSs appears, indicating that the occurrence of the reaction is not sufficiently long to undergo the whole phase space of the interaction configurations.

Full-dimensional potential energy surface for the photodissociation of HNCO via its S1 band.

A full-dimensional potential energy surface (PES) for the first excited state S1(1A'') of HNCO has been built up by the neural network method based on more than 36 000 ab initio points, which were calculated at the multireference configuration interaction level with Davidson correction using the augmented correlation consistent polarized valence triple zeta basis set. It was found that two minima, namely, trans and cis isomers of HNCO, and another seven stationary points exist on the S1 PES for the two dissociation pathways: HNCO(S1) → H + NCO/NH + CO. Particularly, a new out-of-plane transition state between the two minima was found in this work, thanks to including all the degree of freedoms for this system. The adiabatic excitation energy of the S1(1A'') ← S0(1A') transition and dissociation energies D0(HNCO → H + NCO) and D0((HNCO →NH(a1Δ) + CO) calculated on the PES are in good agreement with experimental results. In addition, based on the newly constructed S1 PES, the percentage of products H + NCO in the photodissociation of HNCO(S1) was obtained by a quasi-classical trajectory method at the photon wavelengths ranging from 190 to 225 nm, which is in reasonably good agreement with earlier theoretical and experimental results. For the dissociation lifetimes of the trajectories, they were calculated to be less than 5 ps, which is also consistent with experimental observations.

Nonadiabatic quantum dynamics of the charge transfer reaction H+ + NO(X2Π) → H + NO+(X1Σ+).

Nonadiabatic quantum dynamics of the charge transfer (CT) reaction H+ + NO(X2Π) → H + NO+(X1Σ+) is investigated on a new diabatic potential energy matrix (PEM) including the 12A' and 22A' states of HNO+/HON+ at the multireference configuration interaction level with Davidson correction using a large basis set. The diabatization of the two coupled states was achieved by the adiabatic-to-diabatic transformation with a mixing angle and the final diabatic PEM was obtained by fitting each matrix element separately using a three-dimensional cubic spline interpolation including more than 22 000 ab initio points. The reaction was found to be dominated by the resonances supported by the double well associated with HNO+ and HON+ species, manifested by the oscillatory structures in the reaction probabilities and product rotational distributions. The product vibrational states were highly excited due to the large exothermicity of the reaction. Consistent with the complex-forming mechanism, the differential cross sections (DCSs) were found to be dominated by the forward and backward scatterings. A clear forward bias in the vibrational state resolved DCSs suggests that the non-statistical behavior of the reaction mainly comes from the low vibrational states of the product. In addition, the rate constants of the reaction in the temperature range from 50 to 500 K were computed for the first time and found to be in fairly good agreement with the available experimental results at 300 K. In particular, compared to other reactions involving neutral species in this system including N, O, and H atoms, such a CT reaction was found to be much more reactive, which has rate constants more than thirty times larger.

Compositional alterations of the gut microbiota in acute myocardial infarction patients with type 2 diabetes mellitus.

Background: Type 2 diabetes mellitus (T2DM) is a risk factor for acute myocardial infarction (AMI) and a common comorbidity in patients with AMI. T2DM doubles the fatality rate of patients with AMI in the acute phase of AMI and the follow-up period. However, the mechanisms by which T2DM increases the fatality rate remain unknown. This study sought to investigate changes in the gut microbiota of patients with AMI and T2DM (AMIDM) to extend understandings of the relative mechanisms from the aspects of gut microbiota. Methods: Patients were recruited and divided into 2 groups comprising 15 patients with AMIDM and 15 patients with AMI but without T2DM (AMINDM). Their stool samples and clinical information were collected. 16S ribosomal DNA sequencing was used to analyze the structure and composition of the gut microbiota based on the operational taxonomic units. Results: A significant difference was observed in the gut microbiota ß diversity between the 2 groups. At the phylum level, the AMIDM patients showed an increase in the abundance of Firmicutes and a decrease in the abundance of Bacteroidetes compared to the AMINDM patients. At the genus level, the AMIDM patients showed an increase in the abundance of Companilactobacillus, Defluvitaleaceae UCG-011 and UCG-009, and a decrease in the abundance of Phascolarctobacterium and CAG 56 compared to the AMINDM patients. At the species level, the AMIDM patients showed an increase in the abundance of species unclassified NK4A214 group, Bacteroides clarus, Coprococcus comes, unclassified Defluviltaleaceae UCG-011, uncultured rumen bacterium, unclassified CAG 56, Barnesiella intestinihominis, Lachnospiraceae bacterium, Bacteroides nordii, unclassified UCG-009, and the Family XIII AD3011 group compared to the AMINDM patients. The gut microbiota function predictions indicated that the nucleotide metabolism-related pathway was significantly more increase in the patients with AMIDM than those with AMINDM. Additionally, the patients with AMIDM showed an increase in gram-positive bacteria and a decrease in the proportion of gram-negative bacteria. Our correlation analysis results on the gut microbiota and clinical parameters might extend understandings of the progression of AMI. Conclusions: Changes in the gut microbiota composition of patients with AMIDM affect the severity of the metabolic disturbance and may be responsible for poorer clinical outcomes and worse disease progression in patients with AMIDM compared to those with AMINDM.

Nonadiabatic heavy atom tunneling in 1nσ*-mediated photodissociation of thioanisole.

The 1nσ*-mediated photodissociation dynamics of thioanisole is investigated quantum mechanically using a three-dimensional model based on a newly constructed diabatic potential energy matrix. The lifetimes of the low-lying S1(1ππ*) resonances are determined and found to accord well with available experimental data. Specifically, our theoretical results demonstrate that the photodissociation of thioanisole at the low-lying S1(1ππ*) levels takes place via the heavy atom tunneling due to the higher S1/S2 conical intersection and two equivalent out-of-plane saddle points appearing on the dissociation path. The isotopic effect on the lifetimes is found to be pronounced, manifesting the nature of the tunneling process. Moreover, the geometric phase effect around the S1/S2 conical intersection is found to slightly impact the lifetimes due to the weak destructive or constructive interferences in this heavy atom tunneling, which differs significantly from the scenario in the nonadiabatic hydrogen atom tunneling. Importantly, the quantum mechanical treatment is essentially required to accurately describe the 1nσ*-mediated photodissociation dynamics of thioanisole owing to involving quantum tunneling and geometric phase effects near the conical intersection.

Identification and Validation of Potential Candidate Genes of Colorectal Cancer in Response to Fusobacterium nucleatum Infection.

Objective: Recent investigations revealed the relationship between Fusobacterium nucleatum (Fn) infection and colorectal cancer (CRC). However, how the host genes changes contribute to CRC in response to Fn infection remains largely unknown. Materials and methods: In the present study, we aimed to comprehensively analyze microarray data obtained from a Caco-2 infection cell model using integrated bioinformatics analysis and further identify and validate potential candidate genes in Fn-infected Caco-2 cells and CRC specimens. Results: We identified 10 hub genes potentially involved in Fn induced tumor initiation and progression. Furthermore, we demonstrated that the expression of centrosomal protein of 55 kDa (CEP55) is significantly higher in Fn-infected Caco-2 cells. Knocking down of CEP55 could arrest the cell cycle progression and induce apoptosis in Fn-infected Caco-2 cells. The expression of CEP55 was positively correlated with the Fn amount in Fn-infected CRC patients, and these patients with high CEP55expression had an obviously poorer differentiation, worse metastasis and decreased cumulative survival rate. Conclusion: CEP55 plays an important role in Fn-infected colon cancer cell growth and cell cycle progression and could be used as a new diagnostic and prognostic biomarker for Fn-infected CRC.

Quantum Chemical Simulation of the Qy Absorption Spectrum of Zn Chlorin Aggregates for Artificial Photosynthesis.

Zn chlorin (Znchl) is easy to synthesize and has similar optical properties to those of bacteriochlorophyll c in the nature, which is expected to be used as a light-harvesting antenna system in artificial photosynthesis. In order to further explore the optical characteristics of Znchl, various sizes of a parallel layered Znchl-aggregate model and the THF-Znchl explicit solvent monomer model were constructed in this study, and their Qy excited state properties were simulated by using time-dependent density functional theory (TDDFT) and exciton theory. For the Znchl monomer, with a combination of the explicit solvent model and the implicit solvation model based on density (SMD), the calculated Qy excitation energy agreed very well with the experimental one. The Znchl aggregates may be simplified to a Zn36 model to reproduce the experimental Qy absorption spectrum by the Förster coupling theory. The proposed Znchl aggregate model provides a good foundation for the future exploration of other properties of Znchl and simulations of artificial light-harvesting antennas. The results also indicate that J-aggregrates along z-direction, due to intermolecular coordination bonds, are the dominant factor in extending the Qy band of Znchl into the near infrared region.

Low circadian clock genes expression in cancers: A meta-analysis of its association with clinicopathological features and prognosis.

BACKGROUND: Per1, Per2, Per3, Cry1, Cry2, Bmal1, Npas2 and CLOCK genes are the eight core circadian clock genes. Low expression of these circadian clock genes plays an important role in the progression of cancers. However, its clinicopathological and prognostic value in patients with cancers remains controversial and inconclusive. We performed a meta-analysis of studies assessing the clinicopathological and prognostic significance of low expression of these genes in cancers. METHODS: Relevant studies were searched from the Cochrane Central Register of Controlled Trials, Embase, EBSCO, Ovid, PubMed, Science Direct, Wiley Online Library database, CNKI and Wan Fang database. The meta-analysis was performed by using STATA version 12 software. A random-effect model was employed to evaluate all pooled hazard ratios (HRs) and odd ratios (ORs). RESULTS: A total of 36 studies comprising 7476 cases met the inclusion criteria. Meta-analysis suggested that low expression of Per1 was associated with poor differentiation (Per1: OR=2.30, 95%CI: 1.36∼3.87, P=0.002) and deeper invasion depth (Per1: OR=2.12, 95%CI: 1.62∼2.77, Ρ<0.001); low Per2 expression was correlated with poor differentiation (Per2: OR=2.41, 95%CI: 1.53∼3.79, Ρ<0.001), worse TNM stage (Per2:OR=3.47, 95%CI: 1.88∼6.42, P<0.001) and further metastasis (Per2:OR=2.35, 95%CI: 1.35∼4.11, Ρ=0.003). Furthermore, the results revealed that low expressions of Per1 and Per2 were also correlated with poor overall survival of cancers (Per1: HR=1.35, 95%CI: 1.06∼1.72, P=0.014; Per2: HR=1.43, 95%CI: 1.10∼1.85, P=0.007). Subgroup analysis indicated that low Per1 and Per2 expressions were especially associated with poor prognosis of gastrointestinal caners (Per1: HR=1.33, 95%CI: 1.14∼1.55, Ρ<0.001, Ι2=4.2%; Per2: HR=1.62, 95%CI: 1.25∼2.18, P<0.001, I2=0.0%). CONCLUSIONS: Our study suggested that low Per1, Per2 and Npas2 expression played a distinct and crucial role in progression of cancers. Low expressions of Per1 and Per2 could serve as unfavorable indicators for cancers prognosis, especially for gastrointestinal cancers.

Dual interference with novel genes mfgl2 and mTNFR1 ameliorates murine hepatitis virus type 3-induced fulminant hepatitis in BALB/cJ mice.

Our studies and those of many others have implicated hepatocyte necrosis and apoptosis mediated by fibrinogen-like protein-2 (fgl2) prothrombinase and tumor necrosis factor receptor (TNFR) in the development of fulminant viral hepatitis, a disease with a mortality rate greater than 80% in cases lacking immediate organ transplantation. This study was designed to explore the efficacy of dual short hairpin RNA (shRNA) interference with fgl2 and TNFR1 in the treatment of murine hepatitis virus strain 3 (MHV-3)-induced fulminant hepatitis in mice. Plasmids p-mfgl2shRNA and p-mTNFR1shRNA, complementary to the sequences for mfgl2 and mTNFR1, were constructed. Plasmids pEGFP-mfgl2 and pEGFP-mTNFR1 expressing mfgl2-EGFP (enhanced green fluorescent protein) and mTNFR1-EGFP fusion proteins were also constructed to screen the inhibitory effect of p-mfgl2shRNA and p-mTNFR1shRNA on mfgl2 and mTNFR1 expression. Cotransfection of individual shRNA plasmids and pcDNA3.0-mfgl2 and pcDNA3.0-mTNFR1 expression constructs into Chinese hamster ovary (CHO) cells significantly inhibited mfgl2 and mTNFR1 gene expression, as evidenced by fluorescence microscopy, reverse transcription-polymerase chain reaction, and Western blotting. In vivo hydrodynamic delivery of dual-interference shRNA plasmids for mfgl2 and mTNFR1 significantly decreased mfgl2 and mTNFR1 expression; markedly ameliorated fibrin deposition, hepatocyte necrosis, and apoptosis; and prolonged survival against fulminant viral hepatitis induced by MHV-3 in BALB/cJ mice compared with mfgl2 or TNFR1 single-gene interference. These results indicate that in vivo interference with genes for more than one key target provides superior treatment efficacy compared with single-gene interference.

[Construction of the p-mfgl2shRNA and its effect on mfgl2 expression in vitro].

OBJECTIVE: To construct the siRNA plasmid for mfgl2 gene, which has been reported to be involved in a variety of disease developments including fulminant viral hepatitis, acute rejection of allo/zero transplantation and fetal loss syndrome, and to investigate its inhibitory effects on mfgl2 expression in vitro. METHODS: A plasmid p-mfgl2shRNA complimentary to the sequence responsible for the functional domain of mouse fgl2 (mfgl2) was constructed. The pcDNA3.1 mfgl2 expression construct was able to show a satisfactory fgl2 protein expression. The plasmid expression pEGFP and a construct expressing irrelevant shRNA with a random combination of the p-mfgl2shRNA sequence were used as controls. A pEGFP-mfgl2 expressing mfgl2-EGFP fusion protein was also constructed for screening of the effect of p-mfgl2shRNA on the mfgl2 expression. RESULTS: Cotransfection of p-mfgl2shRNA with pEGFP-mfgl2 decreased green fluorescent cells and the lightness of fluorescence within the cells at the 24 h, 48 h and 72 h post-transfection when compared with that in the control groups which were solely transfected with pEGFP-mfgl2. Furthermore the mfgl2 expression was significantly reduced when the pcDNA3.1 mfgl2 expression construct was cotransfected with p-mfgl2shRNA both at mRNA level by RT-PCR and protein level by RT-PCR, immunohistochemistry staining and FACS in both CHO cell and Hela cell lines. CONCLUSIONS: The study demonstrated that the construct of p-mfgl2shRNA successfully interfered in the mfgl2 expression in vitro. It provides a basis for a further investigation of effect in vivo.

[The study of cis-element HNF4 in the regulation of mfg12 prothrombinase/fibroleukin gene expression in response to nucleocapsid protein of MHV-3].

OBJECTIVE: To identify the transcription factor(s) that is essential for activation of mfgl2 prothrombinase/fibroleukin gene in response to nucleocapsid protein of murine hepatitis virus type 3 (MHV-3). METHODS: Western blotting was performed to investigate whether HNF4 is expressed in macrophages of Ba1b/c mice where mfgl2 is expressed. Confocus microscope immunofluorescence was performed to show whether N protein of MHV enters into the nucleus of infected cells, which is a critical step for the N protein to facilitate its transactivation property. To facilitate the identification of three candidate factor(s) including hepatocyte nuclear factor 4 (HNF4)/liver factor A1 (LF-A1), cytomegalovirus immediate early gene 1.2 (IE1.2) regulatory element and granulocyte- macrophage colony stimulating factor (GM-CSF) in response to mfgl2 activation upon the stimulation of MHV-A59 N protein, gel mobility shift assay (GMSA), competition experiments and site directed mutagenesis were performed. RESULTS: Western blotting displayed that HNF4 was constitutively expressed in macrophages and did not show significant change under the stimulation of different MHV. Confocus microscope immunofluorescence clearly showed that N protein of MHV entered into the nucleus of infected cells. GMSA and competition experiments demonstrated binding to both HNF4 and IE1.2 fragments could be competed with the cold specific oligonucleotides but not with the same amount of non-specific oligos nucleotides. A super shift band was observed when HNF4 antibody was pre-incubated with the nuclear extracts indicating the interaction between the HNF4 element and mfgl2 promoter. Site directed mutagenesis of cis-elements HNF4 (pfgl2HNF4mut) and HNF4/IE1.2 (pfgl2HNF4/IE1.2mut) mutations abolished over 75% of transcription from wild-type mfgl2 promoter. However the pfgl2IE1.2mut displayed almost wild-type promoter activity (75% approximately 80%). CONCLUSIONS: The factor HNF4 binds to mfgl2 promoter and serves as an essential transcription factor for mfgl2/fibroleukin expression in response to MHV-3 N protein.

Induction of prothrombinase fgl2 by the nucleocapsid protein of virulent mouse hepatitis virus is dependent on host hepatic nuclear factor-4 alpha.

Fibrinogen-like protein 2/fibroleukin (Fgl2) plays a pivotal role in the pathogenesis of both experimental and human fulminant hepatic failure. We have reported recently that the nucleocapsid (N) protein from strains of murine hepatitis virus (MHV-3, MHV-A59), which cause massive hepatocellular necrosis but not from strains (MHV-JHM, MHV-2) which do not produce serious liver disease, induces transcription of fgl2. The purpose of the present study was to characterize both viral and host factor(s) necessary for viral induced transcription of fgl2. Mutation of residues Gly-12, Pro-38, Asn-40, Gln-41, and Asn-42 within domain 1 of the N protein of MHV-A59 to their corresponding residues found in MHV-2 abrogated fgl2 transcription, whereas mutation of other N protein domains, including a protein expressed from an internal reading frame (I protein), did not affect fgl2 gene transcription. We then examined the -372 to -306 sequence within the 1.3-kb fgl2 promoter region upstream from the transcription start site that was previously identified as necessary for N protein-induced gene transcription. We demonstrated that the -331/-325 HNF4 cis-element and its cognate transcription factor, HNF4alpha, are necessary for virus-induced fgl2 gene transcription. In uninfected macrophages and macrophages infected with MHV-2, an unidentified protein occupies the HNF4 cis-element. Following stimulation with MHV-A59, it was shown by electrophoretic mobility shift assay that HNF4alpha binds the HNF4 cis-element in the fgl2 promoter. We further report the unprecedented presence of HNF4alpha in peritoneal macrophages. Collectively, the results of this study define both viral and host factors necessary for induction of fgl2 prothrombinase gene transcription in MHV infection and may provide an explanation for the hepatotrophic nature of MHV-induced fulminant hepatic failure.