Genetically engineered materials: Proteins and beyond

Information-rich molecules provide opportunities for evolution. Genetically engineered materials are superior in that their properties are coded within genetic sequences and could be fine-tuned. In this review, we elaborate the concept of genetically engineered materials(GEMs) using examples ranging from engineered protein materials to engineered living materials. Proteinbased materials are the materials of choice by nature. Recent progress in protein engineering has led to opportunities to tune...     

An Improvement to Conformer-Based Model for High-Accuracy Speech Feature Extraction and Learning

Owing to the loss of effective information and incomplete feature extraction caused by the convolution and pooling operations in a convolution subsampling network, the accuracy and speed of current speech processing architectures based on the conformer model are influenced because the shallow features of speech signals are not completely extracted. To solve these problems, in this study, we researched a method that used a capsule network to improve the accuracy of feature extraction in a conformer-based model, and then, we proposed a new end-to-end model architecture for speech recognition. First, to improve the accuracy of speech feature extraction, a capsule network with a dynamic routing mechanism was introduced into the conformer model; thus, the structural information in speech was preserved, and it was input to the conformer blocks via sequestered vectors; the learning ability of the conformed-based model was significantly enhanced using dynamic weight updating. Second, a residual network was added to the capsule blocks, thus, the mapping ability of our model was improved and the training difficulty was reduced. Furthermore, the bi-transformer model was adopted in the decoding network to promote the consistency of the hypotheses in different directions through bidirectional modeling. Finally, the effectiveness and robustness of the proposed model were verified against different types of recognition models by performing multiple sets of experiments. The experimental results demonstrated that our speech recognition model achieved a lower word error rate without a language model because of the higher accuracy of speech feature extraction and learning using our model architecture with a capsule network. Furthermore, our model architecture benefited from the advantage of the capsule network and the conformer encoder, and also has potential for other speech-related applications.     

Palladium-catalyzed hydrosilylation of ynones to access silicon-stereogenic silylenones by stereospecific aromatic interaction-assisted Si–H activation

Hydrosilylation is one of the most important reactions in synthetic chemistry and ranks as a fundamental method to access organosilicon compounds in industrial and academic processes. However, the enantioselective construction of chiral-at-silicon compounds via catalytic asymmetric hydrosilylation remained limited and difficult. Here we report a highly enantioselective hydrosilylation of ynones, a type of carbonyl-activated alkynes, using a palladium catalyst with a chiral binaphthyl phosphoramidite ligand. The stereospecific hydrosilylation of ynones affords a series of silicon-stereogenic silylenones with up to 94% yield, 20:1 regioselectivity and 98:2 enantioselectivity. The density functional theory(DFT) calculations were conducted to elucidate the reaction mechanism and origin of high degree of stereoselectivity, in which the powerful potential of aromatic interaction in this reaction is highlighted by the multiple C–H-π interaction and aromatic cavity-oriented enantioselectivitydetermining step during desymmetric functionalization of Si–H bond.     

Cloning,Expression, Purification,and Characterization of β-Galactosidase from Bifidobacterium longum and Bifidobacterium pseudocatenulatum

Expression and purification of β-galactosidases derived from Bifidobacterium provide a new resource for efficient lactose hydrolysis and lactose intolerance alleviation. Here, we cloned and expressed two β-galactosidases derived from Bifidobacterium. The optimal pH for BLGLB1 was 5.5, and the optimal temperature was 45 °C, at which the enzyme activity of BLGLB1 was higher than that of commercial enzyme E (300 ± 3.6 U/mg) under its optimal conditions, reaching 2200 ± 15 U/mg. The optimal pH and temperature for BPGLB1 were 6.0 and 45 °C, respectively, and the enzyme activity (0.58 ± 0.03 U/mg) under optimum conditions was significantly lower than that of BLGLB1. The structures of the two β-galactosidase were similar, with all known key sites conserved. When o-nitrophenyl-β-D-galactoside (oNPG) was used as an enzyme reaction substrate, the maximum reaction velocity (V_max) for BLGLB1 and BPGLB1 was 3700 ± 100 U/mg and 1.1 ± 0.1 U/mg, respectively. The kinetic constant (K_m) of BLGLB1 and BPGLB1 was 1.9 ± 0.1 and 1.3 ± 0.3 mmol/L, respectively. The respective catalytic constant (k_cat) of BLGLB1 and BPGLB1 was 1700 ± 40 s⁻¹ and 0.5 ± 0.02 s⁻¹, respectively; the respective k_cat/K_m value of BLGLB1 and BPGLB1 was 870 L/(mmol∙s) and 0.36 L/(mmol∙s), respectively. The K_m, k_cat and V_max values of BLGLB1 were superior to those of earlier reported β-galactosidase derived from Bifidobacterium. Overall, BLGLB1 has potential application in the food industry.     

关联规则增量式更新的改进算法

关联规则是数据挖掘中的重要研究内容之一，对在事务数据库不变，只对最小支持度和最小可信度进行改变的情况下，针对关联规则的维护问题，设计了一个增量式更新的改进算法AIUA。     

光子四维量子态隐形传输

多维量子纠缠态比二维纠缠态可加载更多的信息,多维量子系统是量子信息处理中一个很重要的资源.本文采用已实现的光子四维纠缠态,给出了光子四维量子态的张量表达式,并描述了四维量子态隐形传输的一般表示方法;通过讨论光子四维量子态系统的量子通道参数矩阵和测量矩阵的特性,得到实现完全传输和非零概率传输的充要条件.最后,本文给出在多种量子通道下的四维态的量子隐形传态方案,这一过程在张量分析表示下十分清晰明了.     

Spiking patterns of a hippocampus model in electric fields

We develop a model of CA3 neurons embedded in a resistive array to mimic the effects of electric fields from a new perspective. Effects of DC and sinusoidal electric fields on firing patterns in CA3 neurons are investigated in this study. The firing patterns can be switched from no firing pattern to burst or from burst to fast periodic firing pattern with the increase of DC electric field intensity. It is also found that the firing activities are sensitive to the frequency and amplitude of the sinusoidal electric field. Different phase-locking states and chaotic firing regions are observed in the parameter space of frequency and amplitude. These findings are qualitatively in accordance with the results of relevant experimental and numerical studies. It is implied that the external or endogenous electric field can modulate the neural code in the brain. Furthermore, it is helpful to develop control strategies based on electric fields to control neural diseases such as epilepsy.     

Construction of Enzyme-Responsive Micelles Based on Theranostic Zwitterionic Conjugated Bottlebrush Copolymers with Brush-on-Brush Architecture for Cell Imaging and Anticancer Drug Delivery

Bottlebrush copolymers with different chemical structures and compositions as well as diverse architectures represent an important kind of material for various applications, such as biomedical devices. To our knowledge, zwitterionic conjugated bottlebrush copolymers integrating fluorescence imaging and tumor microenvironment-specific responsiveness for efficient intracellular drug release have been rarely reported, likely because of the lack of an efficient synthetic approach. For this purpose, in this study, we reported the successful preparation of well-defined theranostic zwitterionic bottlebrush copolymers with unique brush-on-brush architecture. Specifically, the bottlebrush copolymers were composed of a fluorescent backbone of polyfluorene derivate (PFONPN) possessing the fluorescence resonance energy transfer with doxorubicin (DOX), primary brushes of poly(2-hydroxyethyl methacrylate) (PHEMA), and secondary graft brushes of an enzyme-degradable polytyrosine (PTyr) block as well as a zwitterionic poly(oligo (ethylene glycol) monomethyl ether methacrylate-co-sulfobetaine methacrylate) (P(OEGMA-co-SBMA)) chain with super hydrophilicity and highly antifouling ability via elegant integration of Suzuki coupling, NCA ROP and ATRP techniques. Notably, the resulting bottlebrush copolymer, PFONPN₉-g-(PHEMA₁₅-g-(PTyr₁₆-b-P(OEGMA₆-co-SBMA₆)₂)) (P₂) with a lower MW ratio of the hydrophobic side chains of PTyr and hydrophilic side chains of P(OEGMA-co-SBMA) could self-assemble into stabilized unimolecular micelles in an aqueous phase. The resulting unimolecular micelles showed a fluorescence quantum yield of 3.9% that is mainly affected by the pendant phenol groups of PTyr side chains and a drug-loading content (DLC) of approximately 15.4% and entrapment efficiency (EE) of 90.6% for DOX, higher than the other micelle analogs, because of the efficient supramolecular interactions of π–π stacking between the PTyr blocks and drug molecules, as well as the moderate hydrophilic chain length. The fluorescence of the PFONPN backbone enables fluorescence resonance energy transfer (FRET) with DOX and visualization of intracellular trafficking of the theranostic micelles. Most importantly, the drug-loaded micelles showed accelerated drug release in the presence of proteinase K because of the enzyme-triggered degradation of PTyr blocks and subsequent deshielding of P(OEGMA-co-SBMA) corona for micelle destruction. Taken together, we developed an efficient approach for the synthesis of enzyme-responsive theranostic zwitterionic conjugated bottlebrush copolymers with a brush-on-brush architecture, and the resulting theranostic micelles with high DLC and tumor microenvironment-specific responsiveness represent a novel nanoplatform for simultaneous cell image and drug delivery.     

Computational Insight into Biotransformation Profiles of Organophosphorus Flame Retardants to Their Diester Metabolites by Cytochrome P450

Biotransformation of organophosphorus flame retardants (OPFRs) mediated by cytochrome P450 enzymes (CYPs) has a potential correlation with their toxicological effects on humans. In this work, we employed five typical OPFRs including tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), tris(1-chloro-2-propyl) phosphate (TCIPP), tri(2-chloroethyl) phosphate (TCEP), triethyl phosphate (TEP), and 2-ethylhexyl diphenyl phosphate (EHDPHP), and performed density functional theory (DFT) calculations to clarify the CYP-catalyzed biotransformation of five OPFRs to their diester metabolites. The DFT results show that the reaction mechanism consists of Cα-hydroxylation and O-dealkylation steps, and the biotransformation activities of five OPFRs may follow the order of TCEP ≈ TEP ≈ EHDPHP > TCIPP > TDCIPP. We further performed molecular dynamics (MD) simulations to unravel the binding interactions of five OPFRs in the CYP3A4 isoform. Binding mode analyses demonstrate that CYP3A4-mediated metabolism of TDCIPP, TCIPP, TCEP, and TEP can produce the diester metabolites, while EHDPHP metabolism may generate para-hydroxyEHDPHP as the primary metabolite. Moreover, the EHDPHP and TDCIPP have higher binding potential to CYP3A4 than TCIPP, TCEP, and TEP. This work reports the biotransformation profiles and binding features of five OPFRs in CYP, which can provide meaningful clues for the further studies of the metabolic fates of OPFRs and toxicological effects associated with the relevant metabolites.     

Pogostone Enhances the Antibacterial Activity of Colistin against MCR-1-Positive Bacteria by Inhibiting the Biological Function of MCR-1

The emergence of the plasmid-mediated colistin resistance gene mcr-1 has resulted in the loss of available treatments for certain severe infections. Here we identified a potential inhibitor of MCR-1 for the treatment of infections caused by MCR-1-positive drug-resistant bacteria, especially MCR-1-positive carbapenem-resistant Enterobacteriaceae (CRE). A checkerboard minimum inhibitory concentration (MIC) test, a killing curve test, a growth curve test, bacterial live/dead assays, scanning electron microscope (SEM) analysis, cytotoxicity tests, molecular dynamics simulation analysis, and animal studies were used to confirm the in vivo/in vitro synergistic effects of pogostone and colistin. The results showed that pogostone could restore the bactericidal activity of colistin against all tested MCR-1-positive bacterial strains or MCR-1 mutant–positive bacterial strains (FIC < 0.5). Pogostone does not inhibit the expression of MCR-1. Rather, it inhibits the binding of MCR-1 to substrates by binding to amino acids in the active region of MCR-1, thus inhibiting the biological activity of MCR-1 and its mutants (such as MCR-3). An in vivo mouse systemic infection model, pogostone in combination with colistin resulted in 80.0% (the survival rates after monotherapy with colistin or pogostone alone were 33.3% and 40.0%) survival at 72 h after infection of MCR-1-positve Escherichia coli (E. coli) ZJ487 (blaNDM-1-carrying), and pogostone in combination with colistin led to one or more order of magnitude decreases in the bacterial burdens in the liver, spleen and kidney compared with pogostone or colistin alone. Our results confirm that pogostone is a potential inhibitor of MCR-1 for use in combination with polymyxin for the treatment of severe infections caused by MCR-1-positive Enterobacteriaceae.