Pattern universes

In this essay we explore analogies between macroscopic patterns, which result from a sequence of phase transitions/instabilities starting from a homogeneous state, and similar phenomena in cosmology, where a sequence of phase transitions in the early universe is believed to have separated the fundamental forces from each other, and also shaped the structure and distribution of matter in the universe. We discuss three distinct aspects of this analogy: (i) Defects and topological charges in macroscopic patterns are analogous to spins and charges of quarks and leptons; (ii) Defects in generic 3+1 stripe patterns carry an energy density that accounts for phenomena that are currently attributed to dark matter; (iii) Space-time patterns of interacting nonlinear waves display behaviors reminiscent of quantum phenomena including inflation, entanglement and dark energy.     

Prediction of H-Bonding Motifs for Pyrazoles and Oximes Using the Cambridge Structural Database

H-bonding motifs for pyrazoles and oximes have been examined in the Cambridge Structural Database. The accessible surface of the N atoms has been found to be useful as a discriminator to divide structures into dimer and catemer motifs for both pyrazoles and oximes. Low accessibility favors dimers and tetramers and high values favor catemers and trimers. Total molecular volume shows some correlation for oximes, while high values favor dimers. Empirical rules were successfully applied to predict the motifs of eight new structures in the subsequent release of the CSD.     

Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple‐scattering EXAFS analysis performed within the rigid‐body refinement scheme, non‐muffin‐tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye–Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K‐edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.     

In situ vaccination and gene-mediated PD-L1 blockade for enhanced tumor immunotherapy

Despite of the promising achievements of immune checkpoints blockade therapy (ICB) in the clinic, which was often limited by low objective responses and severe side effects. Herein, we explored a synergistic strategy to combine in situ vaccination and gene-mediated anti-PD therapy, which was generated by unmethylated cytosine-phosphate-guanine (CpG) and pshPD-L1 gene co-delivery. PEI worked as the delivery carrier to co-deliver the CpG and pshPD-L1 genes, the formed PDC (PEI/DNA/CpG) nanoparticles were further shielded by aldehyde modified polyethylene glycol (OHC-PEG-CHO) via pH responsive Schiff base reaction for OHC-PEG-CHO-PEI/DNA/CpG nanoparticles (P(PDC) NPs) preparation. All steps could be finished within 30 min. Such simple nanoparticles achieved the synergistic antitumor efficacy in B16F10 tumor-bearing mice, and the amplified T cell responses, together with enhanced NK cells infiltration were observed after the combined treatments. In addition, the pH responsive delivery system reduced the side effects triggered by anti-PD therapy. The facile and effective combination strategy we presented here might provide a novel treatment for tumor inhibition.     

Unraveling the Impact of Gold(I)–Thiolate Motifs on the Aggregation‐Induced Emission of Gold Nanoclusters

Aggregation‐induced emission (AIE) provides an efficient strategy to synthesize highly luminescent metal nanoclusters (NCs), however, rational control of emission energy and intensity of metal NCs is still challenging. This communication reveals the impact of surface Au^I‐thiolate motifs on the AIE properties of Au NCs, by employing a series of water‐soluble glutathione (GSH)‐coordinated Au complexes and NCs as a model ([Au₁₀SR₁₀], [Au₁₅SR₁₃], [Au₁₈SR₁₄], and [Au₂₅SR₁₈]^?, SR=thiolate ligand). Spectroscopic investigations show that the emission wavelength of Au NCs is adjustable from visible to the near‐infrared II (NIR‐II) region by controlling the length of the Au^I‐SR motifs on the NC surface. Decreasing the length of Au^I‐SR motifs also changes the origin of cluster luminescence from AIE‐type phosphorescence to Au⁰‐core‐dictated fluorescence. This effect becomes more prominent when the degree of aggregation of Au NCs increases in solution.     

Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs

High mobility group (HMG) proteins are the major architectural proteins. Among HMG proteins, High Mobility Group A (HMGA) is characterized by AT-hook (ATH) motifs, which have an affinity for AT-rich DNA. In this study, we characterized the plant HMGAs from the Poaceae family using in silico methods. The protein sequences for rice HMGAs were retrieved and the corresponding orthologs from grasses were extracted. The phylogenetic analysis identified three major evolutionary clades of grass HMGAs and their ATH motif analysis revealed that HMGAs from clade 1 and 2, except for clade 2 HMGAs, are devoid of high-affinity DNA-binding domain. The clade 2 HMGAs also displayed a highly conserved length of all the spacers and the length of the C-terminal tail following the last ATH. Moreover, the C-terminal tail in clade 2 HMGAs is smaller than HMGAs from any other clade. Unlike clade 2, other clades of Poaceae HMGAs displayed high variability in the length of spacers. Despite several differences among HMGAs of different clades in Poaceae, the H1/H5 domain was found to be highly conserved. This study has revealed the detailed analyses of Poaceae HMGAs and it will be useful for further investigation aiming at the determination of precise biological functions and molecular mechanisms of grass HMGAs.     

Synthesis and Hydrogen-Bond Patterns of Aryl-Group Substituted Silanediols and -triols from Alkoxy- and Chlorosilanes

Organosilanols typically show a high condensation tendency and only exist as stable isolable molecules under very specific steric and electronic conditions at the silicon atom. In the present work, various novel representatives of this class of compounds were synthesized by hydrolysis of alkoxy- or chlorosilanes. Phenyl, 1-naphthyl, and 9-phenanthrenyl substituents at the silicon atom were applied to systematically study the influence of the aromatic substituents on the structure and reactivity of the compounds. Chemical shifts in ²⁹Si NMR spectroscopy in solution, correlated well with the expected electronic situation induced by the substitution pattern on the Si atom. ¹H NMR studies allowed the detection of strong intermolecular hydrogen bonds. Single-crystal X-ray structures of the alkoxides and the chlorosilanes are dominated by π-π interactions of the aromatic systems, which are substituted by strong hydrogen bonding interactions representing various structural motifs in the respective silanol structures.     

Importance of NPA motifs in the expression and function of water channel aquaporin-1

The asparagine-proline-alanine sequences (NPA motifs) are highly conserved in aquaporin water channel family. Crystallographic studies of AQP1 structure demonstrated that the two NPA motifs are in the narrow central constriction of the channel, serving to bind water molecules for selective and effi-cient water passage. To investigate the importance of the two NPA motifs in the structure, function and biogenesis of aquaporin water channels, we generated AQP1 mutations with NPA1 deletion, NPA2 de-letion and NPA1,2 double deletion. The coding sequences of the three mutated cDNAs were subcloned into the mammalian expression vector pcDNA3.1 to form expression plasmids. We established stably transfected CHO cell lines expressing these AQP1 mutants. Immunofluorescence indicated that all the three mutated AQP1 proteins are expressed normally on the plasma membrane of stably transfected CHO cells, suggesting that deletion of NPA motifs does not influence the expression and intracellular processing of AQP1. Functional analysis demonstrated that NPA1 or NPA2 deletion reduced AQP1 water permeability by 49.6% and 46.7%, respectively, while NPA1,2 double deletion had little effect on AQP1 water permeability. These results provide evidence that NPA motifs are important for water per-meation but not essential for the expression, intracellular processing and the basic structure of AQP1 water channel.     

Toll-like receptor 9-mediated inhibition of apoptosis occurs through suppression of FoxO3a activity and induction of FLIP expression

Synthetic oligodeoxynucleotides (ODN) with a CpG-motif are recognized by Toll-like receptor 9 (TLR9) and pleiotropic immune responses are elicited. Stimulation of macrophages with TLR9 agonist prevented apoptosis induced by serum deprivation through increased expression of FLICE-like inhibitory protein (FLIP). CpG ODN-mediated anti-apoptosis depended on the TLR9-Akt-FoxO3a signaling pathway. Inhibition of TLR9 by small interfering (si) RNA or an inhibitor suppressed CpG ODN-mediated anti-apoptosis. Analysis of signaling pathways revealed that the anti-apoptotic effect of CpG ODN required phosphorylation of FoxO3a and its translocation from the nucleus to the cytosol. Overexpression of FoxO3a increased apoptosis induced by serum deprivation and CpG ODN blocked these effects through FLIP expression. In contrast, siRNA knock-down of FoxO3a decreased apoptosis by serum deprivation. In addition, Akt activation was involved in CpG ODN-induced phosphorylation of FoxO3a, expression of FLIP, and anti-apoptosis. Taken together, these results demonstrate the involvement of Akt-FoxO3a in TLR9-mediated anti-apoptosis and indicate that FoxO3a is a distinct regulator for FLIP expression.     

The effects of time delay on the stochastic resonance in feed-forward-loop neuronal network motifs

The dependence of stochastic resonance in the feed-forward-loop neuronal network motifs on the noise and time delay are studied in this paper. By computational modeling, Izhikevich neuron model with the chemical coupling is used to build the triple-neuron feed-forward-loop motifs with all possible motif types. Numerical results show that the correlation between the periodic subthreshold signal’s frequency and the dynamical response of the network motifs is resonantly dependent on the intensity of additive spatiotemporal noise. Interestingly, the excitatory intermediate neuron could induce intermittent stochastic resonance, whereas the inhibitory one weakens its influence on the intermittent mode. More importantly, it is found that the increasing delays can induce the intermittent appearance of regions of stochastic resonance. Based on the effects of the time delay on the stochastic resonance, the reasons and conditions of such intermittent resonance phenomenon are analyzed.