A QM/MM study of the catalytic mechanism of aspartate ammonia lyase

Aspartate ammonia lyase (Asp) is one of three types of ammonia lyases specific for aspartate or its derivatives as substrates, which catalyzes the reversible reaction of l-aspartate to yield fumarate and ammonia. In this paper, the catalytic mechanism of Asp has been studied by using combined quantum-mechanical/molecular-mechanical (QM/MM) approach. The calculation results indicate that the overall reaction only contains two elementary steps. The first step is the abstraction of C_β proton of l-aspartate by Ser318, which is calculated to be rate limiting. The second step is the cleavage of C_αN bond of l-aspartate to form fumarate and ammonia. Ser318 functions as the catalytic base, whereas His188 is a dispensable residue, but its protonation state can influence the active site structure and the existing form of leaving amino group, thereby influences the activity of the enzyme, which can well explain the pH dependence of enzymatic activity. Mutation of His188 to Ala only changes the active site structure and slightly elongates the distance of C_β proton of substrate with Ser318, causing the enzyme to remain significant but reduced activity.     

Leakage current in a Si-based nanopore structure and its influence on noise characteristics

We have measured leakage current in a silicon substrate-based nanopore membrane device immersed in an aqueous environment which typically shows the current level of few nA. This current level is compared with the measured current density (400 nA/cm² at 1 V) from the pristine Si wafer (p-type, 10¹⁶/cm³ boron doping) indicating that the exposed Si surface in a nanopore membrane device acts as an electrochemical reaction site. The leakage current is drastically reduced from >10 nA to <100 pA at 1 V by the deposition of a dielectric layer to the Si-based nanopore membrane device. We also noted that the root-mean-square noise of the ionic current is also reduced from 38 to 28 pA in correlation with the reduction of leakage current, indicating that electrochemical reaction provides one of the major sources of noise.     

Synthesis and swelling properties of poly[acrylamide-co-(crotonic acid)] superabsorbents

Superabsorbent polymers of acrylamide (AAm)/crotonic acid (CA) were synthesized by foamed polymerization in an aqueous solution of AAm with CA as a comonomer, initiated by an initiator couple of ammonium persulfate and N,N,N′N′-tetramethylethylenediamine. A crosslinking agent N,N′-methylenebisacrylamide, a foaming agent sodium bicarbonate, and a foam stabilizer, a triblock copolymer of polyoxyethylene/polyoxypropylene/polyoxyethylene, were used in the polymerization. The influences of the relative contents of CA, crosslinking agent, and initiator, on the swelling properties of the superabsorbent polymer systems were examined. The superabsorbent polymer synthesized with an AAm/CA ratio of 98:2 by mole, 0.5 wt.% of N,N′-methylenebisacrylamide and 1 wt.% of ammonium persulfate at 250 rpm and 50 °C for 30 min of polymerization time produced the highest water absorption of 211 ± 9 times its dried weight and could absorb water up to 162 ± 4 g g⁻¹ of the dry copolymer within 10 min. The electrochemical reaction for acrylamide–crotonic acid polymerization was investigated by cyclic voltammetry. The anodic current indicated that acrylamide acting as an electron donor whereas crotonic acid performed as an electron receiver, then providing the cathodic current. The diffusion of water into the superabsorbent polymer was non-Fickian (case II and anomalous). Acrylamide–crotonic acid superabsorbents containing various crosslinker concentrations had a water swelling in the range of 79–289 g g⁻¹. The diffusion coefficients varied between 6.9 × 10⁻⁹ and 5.1 × 10⁻⁸ cm² s⁻¹. Adsorption of the basic dye by the superabsorbent was a monolayer evaluated by the Langmuir isotherm. The superabsorbents can thus be used to adsorb cationic dyes in textile industry.     

Efficient Gene Transfection into Mammalian Cells Mediated by Cross-linked Polyethylenimine

25 kDa branched polyethylenimine (PEI) has successfully been used for in vitro and in vivo gene delivery approaches, but it is cytotoxic. Smaller PEIs are usually non-cytotoxic but less efficient. In order to enhance the gene delivery efficiency and minimize cytotoxicity of PEI, we explored to synthesize cross-linked PEIs with degradable bonds by reacting amines of small branched 2000 Da PEI with small diacrylate (1,4-butanediol diacrylate or ethyleneglycol dimethacrylate) for 2–6 hours. The efficiency of the cross-linked PEIs during in vitro delivering plasmid containing enhanced green fluorescent protein (EGFP) gene reporter and their cytotoxicity were assessed in melanoma B16F10 cell and other cell lines. In vivo gene delivery efficiency was evaluated by direct injection delivery of the EGFP plasmid/cross-linked PEI complexes into mice and by estimating the EGFP expression in animal muscles. Compared to commercially available 25-kDa branched PEI, the cross-linked PEIs reported here could mediate more efficient expression of reporter gene than the 25-kDa PEI control, 19-fold more efficiently in B16F10 cells, 17-fold in 293T cells, 2.3-fold in 3T3 cells, and they exhibited essentially nontoxic at their optimized condition for gene delivery. Furthermore the transfection activity of polyplexs was preserved in the presence of serum proteins. The muscle transfected with the cross-linked PEI prepared here exhibited normal morphology and excellent gene expression. The cross-linked PEIs reported here were evidently more efficient than the commercial 25-kD PEI control and had less cytotoxicity in gene delivery in vitro and in vivo.     

应用基因组重排技术提高普那霉素产量

将普那霉素产生菌——始旋链霉菌ND-23的孢子和原生质体经紫外线诱变后获得高产突变菌株,其中高产突变株SP-S73的产量达到356 mg/L,比出发菌株提高了31%.在上述增产突变株中选取4株作为基因组重排的出发亲本,对它们进行了4轮基因组重排育种,筛选得到了高产重排菌株,其中1株重排菌株G-211的普那霉素产量为832 mg/L,比产量最高的亲本菌株提高了134%,比原始出发菌株ND-23(272 mg/L)提高了206%.通过研究高产菌株和出发菌株ND-23在5 L罐上的发酵过程,发现普那霉素产生菌的生物合成属于非生长耦合型;其高产菌株G-211在合成产物的时期对还原糖和氨基氮的消耗量均大于原始菌株ND-23,这些结果将为高产菌株发酵条件优化和发酵放大研究提供有价值的参考.     

Sex phermone components of mulberry looper,Hemerophila atrilineata butler (lepidoptera: Geometridae)

(6Z-9S, 10R)-Epoxy-octadecene (SR-1) and (3Z, 6Z-9S, 10R)-epoxy-octadecadiene (SR-2) are sex pheromone components of the mulberry looper (MBL),Hemerophila atrilineata Butler. Compounds extracted from female MBL pheromone glands were identified by coupled gas chromatographic-electroantennographic detection (GC-EAD) and GC-mass spectrometry. In field experiments in China,SR-2,RS-2, or both combined were hardly attractive, butSR-2 in combination withSR-1 attracted significant numbers of MBL males. Synergistic behavioral activity ofSR-1 plusSR-2, but not of corresponding antipode mixtures, indicates enantiospecificity of MBL pheromone communication. Because blends of racemic and enantiospecific (SR)1 plus2 were similarly attractive, racemic1 plus2 may have potential for mass trapping or confusion of MBL males in commercial mulberry plantations.     

酶工程：从人工设计到人工智能

计算机在酶工程中的应用使得酶的序列空间探索度不断被扩大。随着不同分子力场参数的建立,涌现出诸多以计算分子能量为基础的算法,并被用于酶的催化活性、稳定性、底物特异性等的改造与筛选。伴随计算机硬件的提升与算法的优化,从头设计全新功能的人工酶取得成功并得以发展。近年来,人工智能在蛋白质结构预测上不断获得突破,同时也被应用到酶的设计中。介绍了分子力场基础和酶设计与筛选的算法,重点阐述了从头设计的方法和成功案例,以及机器学习设计酶的流程和最新的研究进展,展望了人工智能在酶工程领域的未来发展,为酶的改造与全新功能的生物催化剂的设计助力。     

Improving classification-based diagnosis of batch processes through data selection and appropriate pretreatment

This work considers the application of classification algorithms for data-driven fault diagnosis of batch processes. A novel data selection methodology is proposed which enables online classification of detected disturbances without requiring the estimation of unknown (future) process behavior, as is the case in previously reported approaches.The proposed method is benchmarked in two case studies using the Pensim process model of Birol et al. (2002) implemented in RAYMOND. Both a simple k Nearest Neighbors (k-NN) and complex Least Squares Support Vector Machine (LS-SVM) are employed for classification to demonstrate the generic nature of the proposed approach. In addition, the influence of different data pretreatment methods on the classification performance is discussed, together with a motivation for selecting the correct pretreatment steps. Finally, the influence of the number of available training batches is studied.The results demonstrate that a good classification performance can be achieved with the proposed data selection method even with a low number of faulty training batches by exploiting knowledge on the nature of the to-be-diagnosed faults in the data pretreatment. This provides a proof of concept for classification-based batch diagnosis and demonstrates the importance of incorporating process insight in the construction of data-driven process monitoring and diagnosis tools.