Abiotic foldamer quaternary structures.

Abiotic aromatic foldamer sequences have been previously shown to fold in helix-turn-helix motifs in organic solvents. Using simple computational tools, a new helix-turn-helix motif was designed that bears additional hydrogen bond donor OH groups to promote its aggregation into a genuine, trimeric, abiotic quaternary structure. This sequence was synthesized and its self-assembly in solution was investigated by Nuclear Magnetic Resonance (NMR), Circular Dichroism (CD) and Molecular Dynamics (MD) simulations. The existence of two stable discrete aggregates was evidenced, one assigned to the initially designed trimer, the other to a dimer including multiple water molecules. The two species may be quantitatively interconverted upon changing the water content of the solution or the temperature. These results represent important steps in the design of protein-like abiotic architectures.

Forte: A suite of advanced multireference quantum chemistry methods.

Forte is an open-source library specialized in multireference electronic structure theories for molecular systems and the rapid prototyping of new methods. This paper gives an overview of the capabilities of Forte, its software architecture, and examples of applications enabled by the methods it implements.

Domain Swapping in Abiotic Foldamers.

Foldamer sequences that adopt tertiary helix-turn-helix folds mediated by helix-helix hydrogen bonding in organic solvents have been previously reported. In an attempt to create genuine abiotic quaternary structures, i.e. assemblies of tertiary structures, new sequences were prepared that possess additional hydrogen bond donors at positions that may promote an association between the tertiary folds. However, a solid state structure and extensive solution state investigations by Nuclear Magnetic Resonance (NMR) and Circular Dichroism (CD) show that, instead of forming a quaternary structure, the tertiary folds assemble into stable domain-swapped dimer motifs. Domain swapping entails a complete reorganization of the arrays of hydrogen bonds and changes in relative helix orientation and handedness that can all be rationalized.

Ultrasound assisted hot water extraction of polysaccharides from Taraxacum mongolicum: Optimization, purification, structure characterization, and antioxidant activity.

Ultrasound assisted hot water extraction (UAHWE) was applied to extraction of polysaccharides from Taraxacum mongolicum with hot water as extract solvent. Experimental factors in UAHWE process were optimized by response surface methodology. The optimal extraction parameters to achieve the highest Taraxacum mongolicum polysaccharides (TMPs) yield (12.08 ± 0.14)% by UAHWE were obtained under the ultrasound power of 200 W, extraction temperature of 62°C, solid-to-liquid ratio of 1:20 g/mL, and extraction time of 40 min, and then the crude TMPs were further purified by DEAE-52 and Sephadex G-100 chromatography to obtain a homogenous polysaccharide fraction (TMPs-1-SG). Subsequently, the structure of TMPs-1-SG was characterized by UV-vis, Fourier transform infrared spectroscopy (FT-IR), high performance gel permeation chromatography (HPGPC), high performance liquid chromatography (HPLC), scanning electron microscope (SEM), transmission electron microscopy (TEM), and Congo red test. The results display that TMPs-1-SG with an average molecular weight of 5.49 × 104 Da was comprised of mannose (Man), galactose (Gal), xylose (Xyl), and arabinose (Ara) with a molar ratio of 39.85:52.61:27.14:6.30. Moreover, TMPs-1-SG did not contain a triple helix structure. Furthermore, TMPs-1-SG and TEM presented a sheet-like, rod-shaped, and irregular structure. Finally, the antioxidant activity of TMPs-1-SG was evaluated by in vitro experiment. The IC50 values of scavenging DPPH and OH radicals for TMPs-1-SG achieved 0.71 mg/mL and 0.75 mg/mL, respectively. The findings can provide an effective method for extracting polysaccharides from natural resources.

Research on the coupling coordination relationship between the digital economy and high-quality energy development: Evidence from China.

The deep integration of the digital economy and high-quality energy development is a vital breakthrough in promoting the digital transformation and upgrading of energy, and it is also a critical path to achieving green and low-carbon development. However, the degree of integration of the two has yet to be discovered. This article measures the coupling coordination degree of the digital economy and high-quality energy development using panel data from 30 provinces in China from 2013 to 2020, explores the spatiotemporal evolution characteristics of the coupling coordination degree, and further analyzes the driving factors of the coupling coordination degree. The results show that:(1) The coupling coordination degree shows an upward trend, but there are apparent gradient differences and spatial non-equilibrium features in the coupling coordination degree among provinces. (2) The coupling coordination degree shows a "parabolic" spatial trend of "high east and low west" in the east-west direction and an "inverted U-shaped" spatial trend in the north-south direction. (3) The center of gravity of the coupling coordination degree moves to the southwest, clustering in the northeast-southwest direction and showing a spreading trend in the southeast-northwest direction. (4) The coupling coordination degree has a significant positive spatial correlation, and the cold-hot spot gradually develops into a distribution pattern with the Yangtze River Delta in China as the agglomeration center. (5) Economic development, industrial structure, government behavior, environmental regulation, urbanization, technological innovation, and external openness significantly impact the coupling coordination degree. In addition, economic development and human capital have a positive spatial spillover effect on the coupling coordination degree. Urbanization level and technological innovation have a negative spatial spillover effect on the coupling coordination degree. Accordingly, to promote the coupling and interaction between the digital economy and high-quality energy development, the government should take effective measures in optimizing the industrial structure, scientifically promoting the urbanization process, and enhancing the scientific and technological innovation capacity.

Enhancement of Macrophage Immunity against Chlamydial Infection by Natural Killer T Cells.

Lung macrophage (LM) is vital in host defence against bacterial infections. However, the influence of other innate immune cells on its function, including the polarisation of different subpopulations, remains poorly understood. This study examined the polarisation of LM subpopulations (monocytes/undifferentiated macrophages (Mo/Mφ), interstitial macrophages (IM), and alveolar macrophages (AM)). We further assessed the effect of invariant natural killer T cells (iNKT) on LM polarisation in a protective function against Chlamydia muridarum, an obligate intracellular bacterium, and respiratory tract infection. We found a preferentially increased local Mo/Mφ and IMs with a significant shift to a type-1 macrophage (M1) phenotype and higher expression of iNOS and TNF-α. Interestingly, during the same infection, the alteration of macrophage subpopulations and the shift towards M1 was much less in iNKT KO mice. More importantly, functional testing by adoptively transferring LMs isolated from iNKT KO mice (iNKT KO-Mφ) conferred less protection than those isolated from wild-type mice (WT-Mφ). Further analyses showed significantly reduced gene expression of the JAK/STAT signalling pathway molecules in iNKT KO-Mφ. The data show an important role of iNKT in promoting LM polarisation to the M1 direction, which is functionally relevant to host defence against a human intracellular bacterial infection. The alteration of JAK/STAT signalling molecule gene expression in iNKT KO-Mφ suggests the modulating effect of iNKT is likely through the JAK/STAT pathway.

Development and validation of a prognostic nomogram model incorporating routine laboratory biomarkers for preoperative patients with endometrial cancer.

BACKGROUND: Some biomarkers collected from routine laboratory tests have shown important value in cancer prognosis. The study aimed to evaluate the prognostic significance of routine laboratory biomarkers in patients with endometrial cancer (EC) and to develop credible prognostic nomogram models for clinical application. METHODS: A total of 727 patients were randomly divided into a training set and a validation set. Cox proportional hazards models were used to evaluate each biomarker's prognostic value, and independent prognostic factors were used to generate overall survival (OS) and progression-free survival (PFS) nomgrams. The efficacy of the nomograms were evaluated by Harrell's concordance index (C-index), receiver operating characteristic (ROC) curves, decision curve analysis (DCA), calibration curves, X-tile analysis and Kaplan‒Meier curves. RESULTS: Ten significant biomarkers in multivariate Cox analysis were integrated to develop OS and PFS nomograms. The C-indices of the OS- nomogram in the training and validation sets were 0.885 (95% confidence interval (CI), 0.810-0.960) and 0.850 (95% CI, 0.761-0.939), respectively; those of the PFS- nomogram in the training and validation sets were 0.903 (95% CI, 0.866-0.940) and 0.825 (95% CI, 0.711-0.939), respectively. ROC, DCA and calibration curves showed better clinical application value for the nomograms incorporating routine laboratory biomarkers. X-tile analysis and Kaplan‒Meier curves showed that the nomograms were stable and credible in evaluating patients at different risks. CONCLUSIONS: Nomogram models incorporating routine laboratory biomarkers, including NLR, MLR, fibrinogen, albumin and AB blood type, were demonstrated to be simple, reliable and favourable in predicting the outcomes of patients with EC.

IFNγ-Producing B Cells Play a Regulating Role in Infection-Mediated Inhibition of Allergy.

The hygiene hypothesis suggests that some infections may inhibit the development of allergic diseases, but the mechanism remains unclear. Our previous study has shown that Chlamydia muridarum (Cm) lung infection can inhibit local eosinophilic inflammation induced by ovalbumin (OVA) through the modulation of dendritic cell (DC) and T cell responses in mice. In this study, we explored the role of B cells in the chlamydial-infection-mediated modulation of allergic responses. The results showed that adoptive transfer of B cells isolated from Cm-infected mice (Cm-B cells), unlike those from naïve mice (naïve B cells), could effectively inhibit allergic airway eosinophilia and mucus overproduction, as well as Th2 cytokine responses. In addition, total IgE/IgG1 and OVA-specific IgE/IgG1 antibodies in the serum were also decreased by the adoptive transfer of Cm-B cells. Intracellular cytokine analysis showed that B cells from Cm-infected mice produced higher levels of IFNγ than those from naïve mice. More interestingly, the inhibiting effect of adoptively transferred Cm-B cells on allergic reactions was virtually abolished by the simultaneous blockade of IFNγ using a monoclonal antibody. The results suggest that B cells modulated by chlamydial lung infection could play a regulatory role in OVA-induced acute allergic responses in the lung via the production of IFNγ. The results provide new insights into the targets related to the prevention and treatment of allergic diseases.

Circadian rhythm-related factors of PER and CRY family genes function as novel therapeutic targets and prognostic biomarkers in lung adenocarcinoma.

The period (PER) and cryptochrome (CRY) families play critical roles in circadian rhythms. The imbalance of circadian factors may lead to the occurrence of cancer. Expressions of PER and CRY family members decrease in various cancers. Nevertheless, expression levels, genetic variations, and molecular mechanisms of PER and CRY family members in lung adenocarcinoma (LUAD) and their correlations with prognoses and immune infiltration in LUAD patients are still unclear. In this study, to identify their biological functions in LUAD development, comprehensive high-throughput techniques were applied to analyze the relationships of expressions of PER and CRY family members with genetic variations, molecular mechanisms, and immune infiltration. The present results showed that transcription levels of PER1 and CRY2 in LUAD were significantly downregulated. High expression levels of PER2, PER3, CRY1, and CRY2 indicated longer overall survival. Some cancer signaling pathways were related to PER and CRY family members, such as cell-cycle, histidine metabolism, and progesterone-mediated oocyte maturation pathways. Expressions of PER and CRY family members significantly affected the infiltration of different immune cells. In conclusion, our findings may help better understand the molecular basis of LUAD, and provide new perspectives of PER and CRY family members as novel biomarkers for LUAD.

Exogenous Semaphorin 3E treatment protects against chlamydial lung infection in mice.

Recent studies reported that semaphorins play a significant role in various settings of the immune response. In particular, Semaphorin 3E (Sema3E), a secreted semaphorin protein, is involved in cell proliferation, migration, inflammatory responses, and host defence against infections. However, the therapeutic function of Sema3E in bacterial infection has not been investigated. Our data showed that exogenous Sema3E treatment protects mice from chlamydial infection with lower bacterial burden, reduced body weight loss, and pathological lung changes. Cytokine analysis in the lung and spleen revealed that Sema3E-Fc treated mice, compared to saline-Fc treated mice, showed enhanced production of IFN-γ and IL-17 but reduced IL-4 and IL-10 production. Cellular analysis showed that Sema3E treatment leads to enhanced Th1/Th17 response but reduced Treg response in lungs following chlamydial infection. Moreover, Sema3E treatment also enhanced the recruitment of pulmonary dendritic cells, which express higher co-stimulatory but lower inhibitory surface molecules. The data demonstrate that Sema3E plays a vital role in protective immunity against chlamydial lung infection, mainly through coordinating functions of T cells and DCs.

Genetic Characterization of Puccinia striiformis f. sp. tritici Populations from Different Wheat Cultivars Using Simple Sequence Repeats.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important fungal diseases affecting wheat (Triticum aestivum L.) worldwide. In this study, the genetic diversity and population structure of Pst isolates were analyzed using 15 microsatellite markers. Isolates were collected from five wheat cultivars with different levels of resistance from Yanting county and Fucheng district, Mianyang city, Sichuan province, China. The aim of this study was to investigate whether Pst populations are differentiated by wheat genotype or geographic origin. Seventy-six multilocus genotypes (MLGs) were identified from all 289 single uredinial isolates. In general, the genotypic diversity of Pst populations from five wheat cultivars in Fucheng was higher than that in Yanting. In addition, the genetic diversity was highest in the Pst populations from Mianmai 367, a cultivar considered to be highly resistant. The unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree, Bayesian clustering analysis, and minimum spanning network for the MLGs revealed two major genetic clusters based on geographical location. Greater differentiation was observed between the populations from the two sampling locations than between the populations from different hosts in the same location. The results suggest that geographic and environmental differences could partially explain the genetic differentiation of Pst more than wheat genotype. This study provides novel insight into the interactions between Pst populations and their hosts. The results could be helpful in designing more effective management strategies for stripe rust in wheat production.

Analytic Energy Gradients for the Driven Similarity Renormalization Group Multireference Second-Order Perturbation Theory.

We derive analytic energy gradients of the driven similarity renormalization group (DSRG) multireference second-order perturbation theory (MRPT2) using the method of Lagrange multipliers. In the Lagrangian, we impose constraints for a complete-active-space self-consistent-field reference wave function and the semicanonical orthonormal molecular orbitals. Solving for the associated Lagrange multipliers is found to share the same asymptotic scaling of a single DSRG-MRPT2 energy computation. A pilot implementation of the DSRG-MRPT2 analytic gradients is used to optimize the geometry of the singlet and triplet states of p-benzyne. The equilibrium bond lengths and angles are similar to those computed via other MRPT2s and Mukherjee's multireference coupled cluster theory. An approximate DSRG-MRPT2 method that neglects the contributions of the three-body density cumulant is found to introduce negligible errors in the geometry of p-benzyne, lending itself to a promising low-cost approach for molecular geometry optimizations using large active spaces.

Selective Anti-melanoma Effect of Phosphothioated Aptamer Encapsulated by Neutral Cytidinyl/Cationic Lipids.

BC15-31 is a DNA aptamer that targets heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), which plays a crucial role in the process of pre-RNA maturation and is also essential for the rapid proliferation of tumor cells. In this research, we modified BC15-31 with a phosphorothioate (PS) backbone, LNA, and 2-O-MOE to enhance its stability and target affinity. In addition, a neutral cytidinyl lipid (DNCA) and a cationic lipid (CLD) were mixed to encapsulate modified aptamers with the aim of improving their cell permeability with low toxicity. Under the DNCA/CLD package, aptamers are mainly distributed in the nucleus. A modified sequence WW-24 showed an excellent selective anti-melanoma (A375 cells, ∼25 nM, 80%) activity, targeted to both hnRNP A1 and hnRNP A2/B1 found by the BLI experiment, and induced more early and late apoptosis in vitro, which also showed stronger antitumor effect and longer accumulation time in vivo. These results provide a new strategy for further clinical applications.

SND1 promotes Th1/17 immunity against chlamydial lung infection through enhancing dendritic cell function.

To date, no reports have linked the multifunctional protein, staphylococcal nuclease domain-containing protein 1 (SND1), to host defense against intracellular infections. In this study, we investigated the role and mechanisms of SND1, by using SND1 knockout (SND1-/-) mice, in host defense against the lung infection of Chlamydia muridarum, an obligate intracellular bacterium. Our data showed that SND1-/- mice exhibited significantly greater body weight loss, higher organism growth, and more severe pathological changes compared with wild-type mice following the infection. Further analysis showed significantly reduced Chlamydia-specific Th1/17 immune responses in SND1-/- mice after infection. Interestingly, the dendritic cells (DCs) isolated from SND1-/- mice showed lower costimulatory molecules expression and IL-12 production, but higher IL-10 production compared with those from wild-type control mice. In the DC-T cell co-culture system, DCs isolated from SND1-/- infected mice showed significantly reduced ability to promote Chlamydia-specific IFN-γ producing Th1 cells but enhanced capacity to induce CD4+T cells into Foxp3+ Treg cells. Adoptive transfer of DCs isolated from SND1-/- mice, unlike those from wild-type control mice, failed to protect the recipients against challenge infection. These findings provide in vivo evidence that SND1 plays an important role in host defense against intracellular bacterial infection, and suggest that SND1 can promote Th1/17 immunity and inhibit the expansion of Treg cells through modulation of the function of DCs.

Semaphorin 3E Protects against Chlamydial Infection by Modulating Dendritic Cell Functions.

Recent studies have identified semaphorin 3E (Sema3E) as a novel mediator of immune responses. However, its function in immunity to infection has yet to be investigated. Using a mouse model of chlamydial lung infection, we show that Sema3E plays a significant role in the host immune response to the infection. We found that Sema3E is induced in the lung after chlamydial infection, and Sema3E deficiency has a detrimental impact on disease course, dendritic cell (DC) function, and T cell responses. Specifically, we found that Sema3E knockout (KO) mice exhibited higher bacterial burden, severe body weight loss, and pathological changes after Chlamydia muridarum lung infection compared with wild-type (WT) mice. The severity of disease in Sema3E KO mice was correlated with reduced Th1/Th17 cytokine responses, increased Th2 response, altered Ab response, and a higher number of regulatory CD4 T cells. Moreover, DCs isolated from Sema3E KO mice showed lower surface expression of costimulatory molecules and production of IL-12, but higher expression of PD-L1, PD-L2, and IL-10 production. Functional DC-T cell coculture studies revealed that DCs from infected Sema3E KO mice failed to induce Th1 and Th17 cell responses compared with DCs from infected WT mice. Upon adoptive transfer, mice receiving DCs from Sema3E KO mice, unlike those receiving DCs from WT mice, were not protected against challenge infection. In conclusion, our data evidenced that Sema3E acts as a critical factor for protective immunity against intracellular bacterial infection by modulating DC functions and T cell subsets.

NK cells modulate T cell responses via interaction with dendritic cells in Chlamydophila pneumoniae infection.

Protective immune response to chlamydial infection is largely dependent on cell-mediated immune responses with IFN-γ production. Recent studies have shown the critical role of NK cells in bridging innate and adaptive immune responses. In this study, we investigated the effect of NK cells on T cell responses during Chlamydophila pneumoniae (Cpn) lung infection. The results showed that NK cells play a protective role in Cpn infection and influence T cell immunity largely though modulating dendritic cells (DCs) function. Specifically, we found that NK depletion significantly impaired type 1 T cell responses, but enhanced FOXP3+Treg cells and IL-10-producing CD4+T cells. The alteration of T cell responses was associated with more disease severity and higher chlamydial growth in the lung. Further analysis of DC phenotype and cytokine profile found that DCs from NK cell-depleted mice expressed lower levels of co-stimulatory molecules and produced higher levels of IL-10 than those from control IgG-treated mice. More importantly, the adoptive transfer of DCs from NK cell-depleted mice induced a much lower degree of type 1 T cell responses but a higher amount of FOXP3+ Treg cells and IL-10-producing CD4+T cells in the recipient mice than DCs from IgG-treated mice. In contrast to the strong protective effect observed in recipients of DCs from IgG-treated mice, the recipients of DCs from NK cell-depleted mice failed to be protected against Cpn infection. The data suggest that NK cells play a critical role in coordinating innate and adaptive immunity in Cpn lung infection by modulating the DC function to influence T cell responses.

Overcoming the delivery barrier of oligonucleotide drugs and enhancing nucleoside drug efficiency: The use of nucleolipids.

With the rapid development of synthetic technology and biological technology, many nucleic acid-based drugs have entered the clinical trials. However, their inherent disabilities in actively and efficiently penetrating cell membranes still severely restrict their further application. The main drawback of cationic lipids, which have been widely used as nonviral vectors of nucleic acids, is their high cytotoxicity. A series of nucleoside-based or nucleotide-based nucleolipids have been reported in recent years, due to their oligonucleotide delivery capacity and low toxicity in comparison with cationic lipids. Lipophilic prodrugs of nucleoside analogs have extremely similar structures with nucleolipid vectors and are thus helpful for improving the transmembrane ability. This review introduces the progress of nucleolipids and provides new strategies for improving the delivery efficiency of nucleic acid-based drugs, as well as lipophilic prodrugs of nucleosides or nucleotides for antiviral or anticancer therapies.