PEPpy: A tool to generate bacterial peptidoglycan scaffolds for coarse-grained simulations

Peptidoglycan (PG), also known as murein, is an essential component in both Gram-positive and Gram-negative bacteria. However, even if the chemical structure has been well-known for long, the great tertiary structure remains not clear due to its variability and complicated cross-link mechanism. And it inevitably raises the huge challenge for computational simulations. Against the background, here we present a method for building a solvated peptidoglycan system at coarse-grained level as required. The method is named PEPpy, which represents a Peptidoglycan python code. It reads in the user’s parameters in sequence and automatically generates a topological file and a structure file in the meantime. With these files generated, molecular dynamics simulations and a series of analyses can be easily performed afterwards

DIVERSIFIED REACTIONS OF ENOL DIAZOACETATE IN CHEMICAL CATALYSIS

Silylated enol diazoacetates, prepared by the selective O-silylation of diazoacetoacetates in the presence of a mild base, are extremely valuable in synthesizing noval heterocyclic compounds. The incorporation of a silyl enol unit in the α-diazoacetate moiety creates a unique molecule that displays multifaceted reactivities under the catalysis of conceptually different catalytic systems. Upon catalytic dinitrogen extrusion of silylated enol diazoacetate by dirhodium catalysis, the corresponding rhodium bound enol carbene intermediate resembles a metallo-1,3-dipolar species and undergoes a formal dearomatizing [3+3]-cycloaddition with isoquinolinium/pyridinium methylides that furnishes substituted quinolizidines. The development of the catalytic asymmetric variant of this cycloaddition reaction by catalysis with the previously unreported chiral dirhodium carboxylate catalyst−Rh2(S-PTIL)4 has allowed convenient access to highly enantioenriched quinolizidines. Coordination of the Lewis basic methylides to dirhodium(II) prompts the rearrangement of the enol carbene that is bound to dirhodium to produce a donor−acceptor cyclopropene which undergoes a diastereoselective [3+2]-cycloaddition with isoquinolinium/pyridinium methylides. With the overall reaction outcome controlled by the amount of catalyst used, an increase in the mol % of catalyst loading suppresses the [3+2]-cycloaddition pathway. In a reaction that proceeds under mild conditions with remarkable functional group tolerance, catalytically generated rhodium enol carbene intermediate reacts with nucleophilic silylated ketene imines and produced structurally diverse 3-amino-2-cyclopentenones bearing a quaternary carbon at the 4-position in high efficiency. The key step for the overall transformation emanates from the [3+2]-cycloaddition of silylated ketene imine and rhodium enol carbene with the nucleophilic silylated ketene imine attacking the vinylogous position of rhodium enol carbene. Under Lewis acid catalysis, silylated enol diazoacetates participates in diastereoselective [3+2]-cycloaddition reactions with azomethine imines to produce highly functionalized β-methylene-β-silyloxy-β-amido-α-diazoacetates. Catalyst-directed selectivity of competitive 1,2-C→C, -O→C and -N→C migrations from the β-methylene-β-silyloxy-β-amido-α-diazoacetates demonstrates that the differential selectivities rely on the control of the stereoelectronic property of the catalytically generated metal carbenes

Infer Implicit Contexts in Real-time Online-to-Offline Recommendation

Understanding users' context is essential for successful recommendations, especially for Online-to-Offline (O2O) recommendation, such as Yelp, Groupon, and Koubei. Different from traditional recommendation where individual preference is mostly static, O2O recommendation should be dynamic to capture variation of users' purposes across time and location. However, precisely inferring users' real-time contexts information, especially those implicit ones, is extremely difficult, and it is a central challenge for O2O recommendation. In this paper, we propose a new approach, called Mixture Attentional Constrained Denoise AutoEncoder (MACDAE), to infer implicit contexts and consequently, to improve the quality of real-time O2O recommendation. In MACDAE, we first leverage the interaction among users, items, and explicit contexts to infer users' implicit contexts, then combine the learned implicit-context representation into an end-to-end model to make the recommendation. MACDAE works quite well in the real system. We conducted both offline and online evaluations of the proposed approach. Experiments on several real-world datasets (Yelp, Dianping, and Koubei) show our approach could achieve significant improvements over state-of-the-arts. Furthermore, online A/B test suggests a 2.9% increase for click-through rate and 5.6% improvement for conversion rate in real-world traffic. Our model has been deployed in the product of "Guess You Like" recommendation in Koubei.Comment: 9 pages,KDD,KDD201

Possible Luttinger liquid behavior of edge transport in monolayer transition metal dichalcogenide crystals.

In atomically-thin two-dimensional (2D) semiconductors, the nonuniformity in current flow due to its edge states may alter and even dictate the charge transport properties of the entire device. However, the influence of the edge states on electrical transport in 2D materials has not been sufficiently explored to date. Here, we systematically quantify the edge state contribution to electrical transport in monolayer MoS2/WSe2 field-effect transistors, revealing that the charge transport at low temperature is dominated by the edge conduction with the nonlinear behavior. The metallic edge states are revealed by scanning probe microscopy, scanning Kelvin probe force microscopy and first-principle calculations. Further analyses demonstrate that the edge-state dominated nonlinear transport shows a universal power-law scaling relationship with both temperature and bias voltage, which can be well explained by the 1D Luttinger liquid theory. These findings demonstrate the Luttinger liquid behavior in 2D materials and offer important insights into designing 2D electronics

14-3-3 Protein of Neospora caninum Modulates Host Cell Innate Immunity Through the Activation of MAPK and NF-κB Pathways

Neospora caninum is an obligate intracellular apicomplexan parasite, the etiologic agent of neosporosis, and a major cause of reproductive loss in cattle. There is still a lack of effective prevention and treatment measures. The 14-3-3 protein is a widely expressed acidic protein that spontaneously forms dimers within apicomplexan parasites. This protein has been isolated and sequenced in many parasites; however, there are few reports about the N. caninum 14-3-3 protein. Here, we successfully expressed and purified a recombinant fusion protein of Nc14-3-3 (rNc14-3-3) and prepared a polyclonal antibody. Immunofluorescence and immunogold electron microscopy studies of tachyzoites or N. caninum-infected cells suggested that 14-3-3 was localized in the cytosol and the membrane. Western blotting analysis indicated that rNc14-3-3 could be recognized by N. caninum-infected mouse sera, suggesting that 14-3-3 may be an infection-associated antigen that is involved in the host immune response. We demonstrated that rNc14-3-3 induced cytokine expression by activating the MAPK and AKT signaling pathways, and inhibitors of p38, ERK, JNK, and AKT could significantly decrease the production of IL-6, IL-12p40, and TNF-α. In addition, phosphorylated nuclear factor-κB (NF-κB/p65) was observed in wild-type peritoneal macrophages (PMs) treated with rNc14-3-3, and the protein level of NF-κB/p65 was reduced in the cytoplasm but increased correspondingly in the nucleus after 2 h of treatment. These results were also observed in deficient in TLR2-/- PMs. Taken together, our results indicated that the N. caninum 14-3-3 protein can induce effective immune responses and stimulate cytokine expression by activating the MAPK, AKT, and NF-κB signaling pathways but did not dependent TLR2, suggesting that Nc14-3-3 is a novel vaccine candidate against neosporosis

Extracellular Vesicles Secreted by Neospora caninum Are Recognized by Toll-Like Receptor 2 and Modulate Host Cell Innate Immunity Through the MAPK Signaling Pathway

Neospora caninum is an obligate intracellular parasite, which causes significant economic losses in the cattle industry. However, the immune mechanism of the parasite–host interaction is not yet fully understood. Extracellular vesicles (EVs) have emerged as a ubiquitous mechanism by which almost all cells, especially immune and tumor cells, participate in intercellular communications. Although studies have indicated that EVs secreted by Toxoplasma gondii or Trypanosoma brucei promote exchanges of biological molecules important for the host–parasite interplay, however, EVs and their biological activities in N. caninum is not clear. Here, we used multiple methods, including electron microscopy, nanoparticle tracking analysis, RT-PCR, immunofluorescence, western blot, proteomics, and cytokine analyses, to examine the properties of N. caninum EVs. We found that N. caninum produced EVs that are similar to mammalian exosomes, which generally range from 30 to 150 nm in diameter. It was shown that N. caninum EVs could remarkably increase the production of pro-inflammatory cytokines IL-12p40, TNF-α, IL-1β, IL-6, and IFN-γ by wild-type (WT) mouse bone marrow-derived macrophages (BMDMs) whereas the secretion of IL-12p40, TNF-α, and IFN-γ was very strongly downregulated in TLR2−/− mouse BMDMs. The levels of IL-6 were not affected, but the secretion of IL-10 was upregulated. We found that the phosphorylation levels of P38, ERK, and JNK were significantly reduced in the TLR2−/− cells compared with those in WT mouse BMDMs and that treatment with chemical inhibiters of P38, ERK, and JNK resulted in upregulation of IL-6, IL-12p40, and IL-10 production. Together, these results demonstrated that N. caninum EVs could be rapidly internalized to deliver proteins to the host cells and modulate the host cell immune responses through MAPK signaling pathway in a TLR2-dependent manner. Our study is the first to reveal potential roles for N. caninum EVs in host communication and immune response in parasite–host interactions

TLR3 Regulated Poly I:C-Induced Neutrophil Extracellular Traps and Acute Lung Injury Partly Through p38 MAP Kinase

Acute lung injury (ALI) is the leading cause of morbidity and mortality in critically ill patients. Neutrophil extracellular traps (NETs) have been well documented in the ALI model of bacterial infection. In the present study, we demonstrated that poly I:C could induce pulmonary NETs. Upon poly I:C intratracheal inoculation, neutrophil infiltration in the bronchoalveolar lavage fluid (BALF) was significantly increased. Furthermore, the inflammatory cytokines IL-1β, IL-6, and TNF-α in the lung were also significantly elevated. Neutrophil depletion abolished NETs and decreased both neutrophil infiltration and IL-1β in the lung. As expected, DNase I, an inhibitor of MPO and NADPH, decreased pulmonary inflammation and NETs. Blocking of the poly I:C receptor TLR3 reduced lung inflammation and NETs. The MAPK kinase inhibitor p38 diminished the formation of NETs and restored the expression of the tight junction protein claudin-5 in the mouse lung when challenged with poly I:C. In summary, poly I:C induced the formation of pulmonary NETs and ALI, which may be associated with the activation of p38 MAPK and the decreased expression of claudin-5

Small-Molecule RORγt Antagonists Inhibit T Helper 17 Cell Transcriptional Network by Divergent Mechanisms

SummaryWe identified three retinoid-related orphan receptor gamma t (RORγt)-specific inhibitors that suppress T helper 17 (Th17) cell responses, including Th17-cell-mediated autoimmune disease. We systemically characterized RORγt binding in the presence and absence of drugs with corresponding whole-genome transcriptome sequencing. RORγt acts as a direct activator of Th17 cell signature genes and a direct repressor of signature genes from other T cell lineages; its strongest transcriptional effects are on cis-regulatory sites containing the RORα binding motif. RORγt is central in a densely interconnected regulatory network that shapes the balance of T cell differentiation. Here, the three inhibitors modulated the RORγt-dependent transcriptional network to varying extents and through distinct mechanisms. Whereas one inhibitor displaced RORγt from its target loci, the other two inhibitors affected transcription predominantly without removing DNA binding. Our work illustrates the power of a system-scale analysis of transcriptional regulation to characterize potential therapeutic compounds that inhibit pathogenic Th17 cells and suppress autoimmunity

MicroRNA-192 targeting retinoblastoma 1 inhibits cell proliferation and induces cell apoptosis in lung cancer cells

microRNAs play an important roles in cell growth, differentiation, proliferation and apoptosis. They can function either as tumor suppressors or oncogenes. We found that the overexpression of miR-192 inhibited cell proliferation in A549, H460 and 95D cells, and inhibited tumorigenesis in a nude mouse model. Both caspase-7 and the PARP protein were activated by the overexpression of miR-192, thus suggesting that miR-192 induces cell apoptosis through the caspase pathway. Further studies showed that retinoblastoma 1 (RB1) is a direct target of miR-192. Over-expression of miR-192 decreased RB1 mRNA and protein levels and repressed RB1-3′-UTR reporter activity. Knockdown of RB1 using siRNA resulted in a similar cell morphology as that observed for overexpression of miR-192. Additionally, RB1-siRNA treatment inhibited cell proliferation and induced cell apoptosis in lung cancer cells. Analysis of miRNA expression in clinical samples showed that miR-192 is significantly downregulated in lung cancer tissues compared to adjacent non-cancerous lung tissues. In conclusion, our results demonstrate that miR-192 is a tumor suppressor that can target the RB1 gene to inhibit cell proliferation and induce cell apoptosis in lung cancer cells. Furthermore, miR-192 was expressed at low levels in lung cancer samples, indicating that it might be a promising therapeutic target for lung cancer treatment

Critical current density: Measurements vs. reality

Different experimental techniques are employed to evaluate the critical current density (Jc), namely transport current measurements and two different magnetisation measurements forming quasi-equilibrium and dynamic critical states. Our technique-dependent results for superconducting YBa 2Cu3O7 (YBCO) film and MgB2 bulk samples show an extremely high sensitivity of Jc and associated interpretations, such as irreversibility fields and Kramer plots, which lose meaning without a universal approach. We propose such approach for YBCO films based on their unique pinning features. This approach allows us to accurately recalculate the magnetic-field-dependent Jc obtained by any technique into the Jc behaviour, which would have been measured by any other method without performing the corresponding experiments. We also discovered low-frequency-dependent phenomena, governing flux dynamics, but contradicting the considered ones in the literature. The understanding of these phenomena, relevant to applications with moving superconductors, can clarify their dramatic impact on the electric-field criterion through flux diffusivity and corresponding measurements. © Copyright EPLA, 2013