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DNA alkylation promoted by an electron-rich quinone methide intermediate

Chengyun Huang,Steven E. Rokita

《化学科学与工程前沿（英文）》 2016年 第10卷 第2期   页码 213-221 doi: 10.1007/s11705-015-1541-3

摘要： Biological application of conjugates derived from oligonucleotides and quinone methides have previously been limited by the slow exchange of their covalent self-adducts and subsequent alkylation of target nucleic acids. To enhance the rates of these processes, a new quinone methide precursor with an electron donating substituent has been prepared. Additionally, this substituent has been placed to the nascent -methylene group of the quinone methide for maximum effect. A conjugate made from this precursor and a 5'-aminohexyloligonucleotide accelerates formation of its reversible self-adduct and alkylation of its complementary DNA as predicted from prior model studies.

关键词： quione methide     DNA alkylation     reversible covalent reaction     bioconjugation     target-directed modification of nucleic acids    

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Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions

Liaoran Cao,Hong Ren,Jing Miao,Wei Guo,Yan Li,Guohui Li

《化学科学与工程前沿（英文）》 2016年 第10卷 第2期   页码 203-212 doi: 10.1007/s11705-016-1572-4

摘要： Modeling structural and thermodynamic properties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge redistribution and induced dipole into account, and have been proved to be reliable to model small molecules, polypeptides and proteins, but their use on nucleic acids is still rather limited. In this article, the interactions between nucleic acids and a small molecule or ion were modeled by AMOEBAbio09, a modern polarizable force field, and conventional non-polarizable AMBER99sb and CHARMM36 force fields. The resulting intermolecular interaction energies were compared with those calculated by ab initio quantum mechanics methods. Although the test is not sufficient to prove the reliability of the polarizable force field, the results at least validate its capability in modeling energetics of static configurations, which is one basic component in force field parameterization.

关键词： nucleic acid     polarizable force field     AMOEBA    

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Invading target cells: multifunctional polymer conjugates as therapeutic nucleic acid carriers

Ulrich L?CHELT, Ernst WAGNER

《化学科学与工程前沿（英文）》 2011年 第5卷 第3期   页码 275-286 doi: 10.1007/s11705-011-1203-z

摘要： Polymer-based conjugates are an interesting option and challenge for the design of nano-sized drug-delivery systems, as they require advanced conjugation chemistry and precise engineering. In the case of nucleic acid therapy, non-viral carriers face several biological barriers during the delivery process, namely 1) protection of the cargo from extracellular degradation, 2) avoidance of non-specific interactions with non-targeted tissues, 3) efficient entry into the target cells, 4) intracellular trafficking to the site of action and 5) cargo release. To take on these obstacles, multifunctional conjugates can act as “smart polymers” with microenvironment-sensing dynamics to facilitate the separate delivery steps. Synthesis of defined polymer architectures with precise functionalization enables structure-activity relationships to be investigated and the integration of key functions for efficient delivery. Thus bioresponsive polymer conjugates, which are equipped with molecular devices responding to the certain microenvironments within the delivery pathway (e.g. pH, redox potential, enzymes) can be assembled. This review focuses on the modular engineering and conjugation of multifunctional polymeric structures for the utilization as “tailor-made” nucleic acid carriers.

关键词： conjugate     DNA     gene transfer     polymer     RNA     targeting    

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Advances in the study of directed evolution for cellulases

Hailong LIN, Weiguang LI, Changhong GUO, Sihang QU, Nanqi REN

《环境科学与工程前沿（英文）》 2011年 第5卷 第4期   页码 519-525 doi: 10.1007/s11783-011-0326-2

摘要： If cellulose can be effectively hydrolyzed into glucose by cellulase, the production costs of hydrogen, ethanol or other chemicals from cellulosic materials will be greatly decreased, and economically viable production of biohydrogen and bioethanol will become feasible. Cellulose is degraded into glucoses by multi-component enzyme systems. Nowadays cellulases are widely used in brewing, food, bioenergy, fodder, textiles, paper, pharmaceuticals, environmental protection and other industries. However, existing cellulases have several problems that limit their wider applications, including the low turnover number for solid cellulosic materials, and low stability in adapting to various application conditions. For example, high temperature, low pH, and so on. Application of directed evolution technology may be one of the most effective ways for improving the characteristics of cellulases. This paper presents a brief review of the cellulose hydrolysis mechanism by cellulase, advances in cellulases (endoglucanase and -glucosidase) improvement by directed evolution for several characteristics (for instance, thermal stability, pH adaptability and enzyme activity), limitations of directed evolution for cellulases, and the outlook for directed evolution for cellulase.

关键词： biohydrogen     bioethanol     cellulase     cellulose     directed evolution    

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Bile acids and their effects on diabetes

Cynthia Rajani, Wei Jia

《医学前沿（英文）》 2018年 第12卷 第6期   页码 608-623 doi: 10.1007/s11684-018-0644-x

摘要： Diabetes is a widespread, rapidly increasing metabolic disease that is driven by hyperglycemia. Early glycemic control is of primary importance to avoid vascular complications including development of retinal disorders leading to blindness, end-stage renal disease, and accelerated atherosclerosis with a higher risk of myocardial infarction, stroke and limb amputations. Even after hyperglycemia has been brought under control, “metabolic memory,” a cluster of irreversible metabolic changes that allow diabetes to progress, may persist depending on the duration of hyperglycemia. Manipulation of bile acid (BA) receptors and the BA pool have been shown to be useful in establishing glycemic control in diabetes due to their ability to regulate energy metabolism by binding and activating nuclear transcription factors such as farnesoid X receptor (FXR) in liver and intestine as well as the G-protein coupled receptor, TGR5, in enteroendocrine cells and pancreatic -cells. The downstream targets of BA activated FXR, FGF15/21, are also important for glucose/insulin homeostasis. In this review we will discuss the effect of BAs on glucose and lipid metabolism and explore recent research on establishing glycemic control in diabetes through the manipulation of BAs and their receptors in the liver, intestine and pancreas, alteration of the enterohepatic circulation, bariatric surgery and alignment of circadian rhythms.

关键词： bile acids     metabolic memory     diabetes     circadian rhythm     bariatric surgery    

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Design of nanocarriers for efficient cellular uptake and endosomal release of small molecule and nucleic

Vaibhav Mundra, Ram I. Mahato

《化学科学与工程前沿（英文）》 2014年 第8卷 第4期   页码 387-404 doi: 10.1007/s11705-014-1457-3

摘要： There are many challenges in developing efficient and target specific delivery systems of small molecule and nucleic acid drugs. Cell membrane presents one of the major barriers for the penetration of hydrophilic macromolecules across the plasma membrane. Nanocarriers have been designed to enhance their cellular uptake via endocytosis but following their cellular uptake, endosomal escape is the rate limiting step which restricts the value associated with the enhanced uptake by nanocarriers. Viruses are an excellent model for efficient cytosolic delivery by nanocarriers. Viruses exploit intracellular cues to release the genome to cytosol. In this review, we first discuss different endocytic uptake pathways and endosomal escape mechanisms. We then summarize the existing tools for studying the intracellular trafficking of nanocarriers. Finally, we highlight the important design elements of recent virus-based nanocarriers for efficient cellular uptake and endosomal escape.

关键词： nanocarrier     cellular uptake     endosomal release     nucleic acid drug    

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Unnormalized and normalized forms of gefura measures in directed and undirected networks

Raf GUNS,Ronald ROUSSEAU

《信息与电子工程前沿（英文）》 2015年 第16卷 第4期   页码 311-320 doi: 10.1631/FITEE.1400425

摘要： In some networks nodes belong to predefined groups (e.g., authors belong to institutions). Common network centrality measures do not take this structure into account. Gefura measures are designed as indicators of a node’s brokerage role between such groups. They are defined as variants of betweenness centrality and consider to what extent a node belongs to shortest paths between nodes from different groups. In this article we make the following new contributions to their study: (1) We systematically study unnormalized gefura measures and show that, next to the ‘structural’ normalization that has hitherto been applied, a ‘basic’ normalization procedure is possible. While the former normalizes at the level of groups, the latter normalizes at the level of nodes. (2) Treating undirected networks as equivalent to symmetric directed networks, we expand the definition of gefura measures to the directed case. (3) It is shown how Brandes’ algorithm for betweenness centrality can be adjusted to cover these cases.

关键词： Networks subdivided in groups     Partitions     Gefura measures     Q-measures     Brokerage role     Directed and undirected networks     Brandes’     algorithm    

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Controllability analysis of second-ordermulti-agent systemswith directed andweighted interconnection

Di GUO,Rong-hao ZHENG,Zhi-yun LIN,Gang-feng YAN

《信息与电子工程前沿（英文）》 2015年 第16卷 第10期   页码 838-847 doi: 10.1631/FITEE.1500069

摘要： This article investigates the controllability problem of multi-agent systems. Each agent is assumed to be governed by a second-order consensus control law corresponding to a directed and weighted graph. Two types of topology are considered. The first is concerned with directed trees, which represent the class of topology with minimum information exchange among all controllable topologies. A very simple necessary and sufficient condition regarding the weighting scheme is obtained for the controllability of double integrator multi-agent systems in this scenario. The second is concerned with a more general graph that can be reduced to a directed tree by contracting a cluster of nodes to a component. A similar necessary and sufficient condition is derived. Finally, several illustrative examples are provided to demonstrate the theoretical analysis results.

关键词： Multi-agent systems     Controllability     Directed tree    

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Catalytic conversion of biomass-derived compounds to various amino acids: status and perspectives

《化学科学与工程前沿（英文）》 2023年 第17卷 第7期   页码 817-829 doi: 10.1007/s11705-022-2254-z

摘要： Amino acids are important nitrogen-containing chemicals that have a variety of applications. Currently, fermentation is the widely employed method to produce amino acids; however, the products are mostly limited to natural amino acids in the L-configuration. Catalytic synthesis is an alternative approach for the synthesis of amino acids with different types and configurations, where the use of renewable biomass-based feedstocks is highly attractive. To date, several lignocellulose and triacylglycerol-derived intermediates, typically α-keto acids and α-hydroxyl acids, have been transformed into amino acids via the amination reaction in the presence of additional nitrogen sources (i.e., NH3·H2O). Making full use of inherent nitrogen in biomass (i.e., chitin and protein) to produce amino acids avoids the use of extra nitrogen sources and meets the requirements of green chemistry, which is attracting increasing attention. In this review, we summarize different chemical-catalytic systems for the transformation of biomass to amino acids. An outlook on the challenges and opportunities for more effective production of amino acids from biomass by catalytic methods is provided.

关键词： biomass     amino acids     chitin     nitrogen-containing compounds     lignocellulose    

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Ionic strength directed self-assembled polyelectrolyte single-bilayer membrane for low-pressure nanofiltration

《化学科学与工程前沿（英文）》 2022年 第16卷 第5期   页码 699-708 doi: 10.1007/s11705-021-2093-3

摘要： Layer-by-layer assembly is a versatile technique for fabricating nanofiltration membranes, where multiple layers of polyelectrolytes are usually required to achieve reasonable separation performance. In this work, an ionic strength directed self-assembly procedure is described for the preparation of nanofiltration membranes consisting of only a single bilayer of poly(diallyldimethylammoniumchloride) and poly(sodium-4-styrenesulfoate). The influence of background ionic strength as well as membrane substrate properties on the formation of single-bilayer membranes are systematically evaluated. Such a simplified polyelectrolyte deposition procedure results in membranes having outstanding separation performance with permeating flux of 14.2 ± 1.5 L∙m–2∙h–1∙bar–1 and Na2SO4 rejection of 97.1% ± 0.8% under a low applied pressure of 1 bar. These results surpass the ones for conventional multilayered polyelectrolyte membranes. This work encompasses an investigation of ionic strength induced coiling of the polyelectrolyte chains and emphasizes the interplay between-polyelectrolyte chain configuration and substrate pore profile. It thus introduces a new concept on the control of membrane fabrication process toward high performance nanofiltration.

关键词： layer-by-layer self-assembly     single bilayer     nanofiltration membrane     desalination    

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Anaerobic digestion of sludge by different pretreatments: Changes of amino acids and microbial community

《环境科学与工程前沿（英文）》 2022年 第16卷 第2期 doi: 10.1007/s11783-021-1458-7

摘要：

•Tryptophan protein, and aromatic protein I/II were the key identified proteins.

关键词： Sludge pretreatments     Dissolved organic nitrogen     Proteins     Amino acids     Structural equation model     Metagenomic sequencing analysis.    

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Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom

Wen Zhang,Jack W. Szostak,Zhen Huang

《化学科学与工程前沿（英文）》 2016年 第10卷 第2期   页码 196-202 doi: 10.1007/s11705-016-1565-3

摘要： X-ray crystallography is a powerful strategy for 3-D structure determination of macromolecules, such as nucleic acids and protein-nucleic acid complexes. However, the crystallization and phase determination are the major bottle-neck problems in crystallography. Recently we have successfully developed synthesis and strategy of selenium-derivatized nucleic acids (SeNA) for nucleic acid crystallography. SeNA might not only provide the rational strategies to solve the phase determination problem, but also offer a potential strategy to explore crystallization solutions.

关键词： selenium     DNA     RNA     nucleic acid     crystallization    

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Characterization of soil low-molecular-weight organic acids in the Karst rocky desertification region

Xiaoliang LI, Xiaomin CHEN, Xia LIU, Lianchuan ZHOU, Xinqiang YANG

《环境科学与工程前沿（英文）》 2012年 第6卷 第2期   页码 195-203 doi: 10.1007/s11783-012-0391-1

摘要： Soil low-molecular-weight (LMW) organic acids play important roles in the soil-forming process and the cycling of nutrients in Karst regions. In this study, we quantified the contents of LMW organic acids (including lactate, acetate, formate, malate, and oxalate) in soil solution over the Karst region of Guizhou Province, China using ion chromatography. The concentration of total LMW organic acids in topsoil solution ranged from 0.358 to 1.823 μmol·g , with an average of 0.912 μmol·g . The mean concentrations of lactate, acetate, formate, malate, and oxalate were 0.212±0.089, 0.302±0.228, 0.301±0.214, 0.014±0.018 and 0.086±0.118 μmol·g , respectively. There were also significant difference in the contents of these acids among four phases of rocky desertification, and their concentrations decreased with the aggravation of rocky desertification. The concentrations of the LMW organic acids were significantly positive correlated each other. Significant positive correlations were also observed among individual LMW organic acids in soil solution, and between them and soil available P, available K, exchangeable Ca, respectively. Furthermore, the concentrations of LMW organic acids were significantly positively correlated with inorganic anions (chlorides, nitrates, and sulfates) in Karst topsoil solution. Therefore, the concentrations of soil LMW organic acids might be one of driving force in the Karst rock desertification process in Guizhou Province.

关键词： Karst rocky desertification     low-molecular-weight (LMW) organic acids     distribution characteristics     soil    

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Optimization of pretreatment of Jatropha oil with high free fatty acids for biodiesel production

Supriyono SUWITO, Giuliano DRAGONE, Hary SULISTYO, Bardi MURACHMAN, Suryo PURWONO, José TEIXEIRA

《化学科学与工程前沿（英文）》 2012年 第6卷 第2期   页码 210-215 doi: 10.1007/s11705-012-1282-5

摘要： A central composite rotatable design and response surface methodology were used in order to investigate the individual and combined effects of the ethanol-to-oil ratio, H SO concentration, temperature and time of reaction on the reduction of free fatty acid (FFA) in jatropha oil. A quadratic polynomial model relating the reaction variables with FFA reduction was developed, presenting a good coefficient of determination ( = 0.893). For reducing FFA to less than 1%, the optimal combination was found to be 0.62 v·v ethanol-to-oil ratio (14.9 v·v ethanol-to-FFA ratio), 1.7% v·v H SO concentration, and 79 min reaction time at a reaction temperature of 54°C. These results are of great relevance to maximize methyl esters formation by transesterification using an alkaline catalyst.

关键词： biodiesel     biofuel     esterification     free fatty acids     jatropha curcas oil    

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Mild and highly regioselective synthesis of biaryl acids via Rh(I)-catalyzed cross-dehydrogenative couplingof benzoic acids using sodium chlorite as oxidant

Yun Liu, Youquan Zhu, Chaojun Li

《化学科学与工程前沿（英文）》 2018年 第12卷 第1期   页码 3-8 doi: 10.1007/s11705-017-1693-4

摘要： A mild and efficient synthesis for the biaryl acids via rhodium-catalyzed cross-dehydrogenative coupling reaction has been developed. This novel protocol with sodium chlorite as an oxidant featured many advantages such as mild reaction conditions, high regioselectivity, tolerance of various functional groups, and good to excellent yields.

关键词： biaryl acids     cross-dehydrogenative coupling     rhodium-catalyzed    

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标题 作者 时间 类型 操作

DNA alkylation promoted by an electron-rich quinone methide intermediate

Chengyun Huang,Steven E. Rokita

期刊论文

Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions

Liaoran Cao,Hong Ren,Jing Miao,Wei Guo,Yan Li,Guohui Li

期刊论文

Invading target cells: multifunctional polymer conjugates as therapeutic nucleic acid carriers

Ulrich L?CHELT, Ernst WAGNER

期刊论文

Advances in the study of directed evolution for cellulases

Hailong LIN, Weiguang LI, Changhong GUO, Sihang QU, Nanqi REN

期刊论文

Bile acids and their effects on diabetes

Cynthia Rajani, Wei Jia

期刊论文

Design of nanocarriers for efficient cellular uptake and endosomal release of small molecule and nucleic

Vaibhav Mundra, Ram I. Mahato

期刊论文

Unnormalized and normalized forms of gefura measures in directed and undirected networks

Raf GUNS,Ronald ROUSSEAU

期刊论文

Controllability analysis of second-ordermulti-agent systemswith directed andweighted interconnection

Di GUO,Rong-hao ZHENG,Zhi-yun LIN,Gang-feng YAN

期刊论文

Catalytic conversion of biomass-derived compounds to various amino acids: status and perspectives

期刊论文

Ionic strength directed self-assembled polyelectrolyte single-bilayer membrane for low-pressure nanofiltration

期刊论文

Anaerobic digestion of sludge by different pretreatments: Changes of amino acids and microbial community

期刊论文

Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom

Wen Zhang,Jack W. Szostak,Zhen Huang

期刊论文

Characterization of soil low-molecular-weight organic acids in the Karst rocky desertification region

Xiaoliang LI, Xiaomin CHEN, Xia LIU, Lianchuan ZHOU, Xinqiang YANG

期刊论文

Optimization of pretreatment of Jatropha oil with high free fatty acids for biodiesel production

Supriyono SUWITO, Giuliano DRAGONE, Hary SULISTYO, Bardi MURACHMAN, Suryo PURWONO, José TEIXEIRA

期刊论文

Mild and highly regioselective synthesis of biaryl acids via Rh(I)-catalyzed cross-dehydrogenative couplingof benzoic acids using sodium chlorite as oxidant

Yun Liu, Youquan Zhu, Chaojun Li

期刊论文