bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic flux analysis in Escherichia coli by integrating isotopic dynamic and isotopic stationary 13C labeling data
Authors: Schaub Jochen , Mauch Klaus , Reuss Matthias 
Published: October 2007

AbstractThe novel concept of isotopic dynamic 13C metabolic flux analysis (ID‐13C MFA) enables integrated analysis of isotopomer data from isotopic transient and/or isotopic stationary phase of a 13C labeling experiment, short‐time experiments, and an extended range of applications of 13C MFA. In the presented work, an experimental and computational framework consisting of short‐time 13C labeling, an integrated rapid sampling procedure, a LC‐MS analytical method, numerical integration of the system of isotopomer differential equations, and estimation of metabolic fluxes was developed and applied to determine intracellular fluxes in glycolysis, pentose phosphate pathway (PPP), and citric acid cycle (TCA) in Escherichia coli grown in aerobic, glucose‐limited chemostat culture at a dilution rate of D = 0.10 h−1. Intracellular steady state concentrations were quantified for 12 metabolic intermediates. A total of 90 LC‐MS mass isotopomers were quantified at sampling times t = 0, 91, 226, 346, 589 s and at isotopic stationary conditions. Isotopic stationarity was reached within 10 min in glycolytic and PPP metabolites. Consistent flux solutions were obtained by ID‐13C MFA using isotopic dynamic and isotopic stationary 13C labeling data and by isotopic stationary 13C MFA (IS‐13C MFA) using solely isotopic stationary data. It is demonstrated that integration of dynamic 13C labeling data increases the sensitivity of flux estimation, particularly at the glucose‐6‐phosphate branch point. The identified split ratio between glycolysis and PPP was 55%:44%. These results were confirmed by IS‐13C MFA additionally using labeling data in proteinogenic amino acids (GC‐MS) obtained after 5 h from sampled biomass. Biotechnol. Bioeng. 2008;99: 1170–1185. © 2007 Wiley Periodicals, Inc.
Amphotropic retrovirus transduction is inhibited by high doses of particle‐associated envelope proteins
Authors: Landázuri Natalia , Le Doux Joseph M. 
Published: October 2007

AbstractUsing a panel of amphotropic murine leukemia virus packaging cell lines that differed only in their levels of envelope protein (gp70) expression, we examined the relationship between transduction and the number of envelope proteins per virus. We generated virus stocks that contained different levels of virus‐associated envelope proteins, purified them from gp70 that was not associated with the viruses, quantified their titers, and measured the efficiency with which they transduced NIH 3T3, TE671, and HeLa cells. As expected, titers increased monotonically with viral envelope protein number. Titers are measured using highly dilute virus, however, and are often not predictive of gene transfer when high doses of virus are used, as is done in gene therapy protocols. Interestingly, when we used high doses of virus, we observed significantly different trends: gene transfer increased, reached a maximum, and then declined sharply as the number of envelope proteins per virus increased. The highest levels of gene transfer occurred when cells were transduced with a moderate dose of virus that contained low levels of envelope protein. Our results indicate that transduction is inhibited when viruses that contain large numbers of envelope proteins are used. This is most likely because each virus, when it binds to a cell, delivers a large payload of envelope proteins that occupy or inactivate multiple virus receptors, reducing or eliminating the susceptibility of the cell to being transduced by additional viruses. The implications of our findings for the design of improved retroviral vectors for human gene therapy are discussed. Biotechnol. Bioeng. 2008;99: 1205–1215. © 2007 Wiley Periodicals, Inc.
Biorecovery of gold by Escherichia coli and Desulfovibrio desulfuricans
Authors: Deplanche K. , Macaskie L.E. 
Published: October 2007

AbstractMicrobial precipitation of gold was achieved using Escherichia coli and Desulfovibrio desulfuricans provided with H2 as the electron donor. No precipitation was observed using H2 alone or with heat‐killed cells. Reduction of aqueous Au(III) ions by both strains was demonstrated at pH 7 using 2 mM HAuCl4 solution and the concept was successfully applied to recover 100% of the gold from acidic leachate (115 ppm of Au(III)) obtained from jewellery waste. Bioreductive recovery of gold from aqueous solution was achieved within 2 h, giving crystalline Au(0) particles (20–50 nm), in the periplasmic space and on the cell surface, and small intracellular nanoparticles. The nanoparticle size was smaller (red suspension) at acidic pH (2.0) as compared to that obtained at pH 6.0 and 7.0 (purple) and 9.0 (dark blue). Comparable nanoparticles were obtained from Au(III) test solutions and jewellery leachate. Biotechnol. Bioeng. 2008;99: 1055–1064. © 2007 Wiley Periodicals, Inc.
Using nanovibrations to monitor biofouling
Authors: Pereira Ana , Mendes Joaquim , Melo Luis F. 
Published: October 2007

AbstractThe article proposes the use of the mechatronic surface sensor (MSS) to detect surface contamination. This methodology is based on the analysis of the vibration response of the monitored surface. In the present work a comparison between the responses of the MSS to different structural deposits build‐up (Pseudomonas fluorescens biofilm—formed under turbulent and laminar flow and a silica deposit) were made. The results showed that the MSS response depends not only on the amount but also on the viscoelasticity of the attached deposit—different responses were obtained for the deposits according to their viscoelasticity. Another important conclusion is that the MSS response is not highly affected by solids that are not really attached to its surface. Biotechnol. Bioeng. 2008;99: 1407–1415. © 2007 Wiley Periodicals, Inc.
Scale‐up of Escherichia coli growth and recombinant protein expression conditions from microwell to laboratory and pilot scale based on matched kLa
Authors: Islam R.S. , Tisi D. , Levy M.S. , Lye G.J. 
Published: October 2007

AbstractFermentation optimization experiments are ideally performed at small scale to reduce time, cost and resource requirements. Currently microwell plates (MWPs) are under investigation for this purpose as the format is ideally suited to automated high‐throughput experimentation. In order to translate an optimized small‐scale fermentation process to laboratory and pilot scale stirred‐tank reactors (STRs) it is necessary to characterize key engineering parameters at both scales given the differences in geometry and the mechanisms of aeration and agitation. In this study oxygen mass transfer coefficients are determined in three MWP formats and in 7.5 L and 75 L STRs. kLa values were determined in cell‐free media using the dynamic gassing‐out technique over a range of agitation conditions. Previously optimized culture conditions at the MWP scale were then scaled up to the larger STR scales on the basis of matched kLa values. The accurate reproduction of MWP (3 mL) E. coli BL21 (DE3) culture kinetics at the two larger scales was shown in terms of cell growth, protein expression, and substrate utilization for kLa values that provided effective mixing and gas–liquid distribution at each scale. This work suggests that kLa provides a useful initial scale‐up criterion for MWP culture conditions which enabled a 15,000‐fold scale translation in this particular case. This work complements our earlier studies on the application of DoE techniques to MWP fermentation optimization and in so doing provides a generic framework for the generation of large quantities of soluble protein in a rapid and cost‐effective manner. Biotechnol. Bioeng. 2008;99: 1128–1139. © 2007 Wiley Periodicals, Inc.
A perfusable 3D cell–matrix tissue culture chamber for in situ evaluation of nanoparticle vehicle penetration and transport
Authors: Ng Chee Ping , Pun Suzie Hwang 
Published: October 2007

AbstractA key factor in gene or drug therapy is the development of carriers that can efficiently reach targeted cells from a distal administration. In many gene/drug delivery studies, results obtained in 2D cultures fail to translate to similar results in vivo. In this work, we developed a perfusable 3D chamber for studying nanoparticle penetration and transport in cell–gel soft tissue cultures. The compartmented chamber is made of a polydimethylsiloxane (PDMS) top layer with the chamber features, created using micromachined lithography, bonded to a bottom glass coverslip. A solution of cells embedded in a hydrogel is loaded in the chamber between PDMS posts that serve as anchors to the cell–matrix at the gel‐media interface. The chamber offers the following unique features: (i) rapid fabrication and simplicity in assembly, (ii) direct in situ cell imaging in a plane normal to the direction of flow or action, (iii) an easily configurable and controllable environment conducive cell culture under static or interstitial flow conditions, and (iv) facile recovery of live cells from chambers for post‐experimental analysis. To assess the chamber, we delivered fluorescently labeled nanoparticles of three distinct sizes to cells‐embedded Matrigels in the 3D chamber under flow and static conditions. Penetration of nanoparticles were enhanced under interstitial flow while live cell imaging and flow cytometry of recovered cells revealed particle size restrictions to efficient delivery. Although designed for delivery studies, the chamber is versatile and can be easily modified. Thus it may have broad applications for biological, tissue engineering, and therapeutic studies. Biotechnol. Bioeng. 2008;99: 1490–1501. © 2007 Wiley Periodicals, Inc.
A compact computational model for cell construct development in perfusion culture
Authors: Chung C.A. , Chen C.P. , Lin T.H. , Tseng C.S. 
Published: October 2007

AbstractA problem nowadays tissue engineers encounter in developing sizable tissue implants is the nonuniform spread of cells and/or extracellular matrices. Research shows such a nutrients transport restriction may be improved by employing hydrodynamic culture systems. We propose a compact model for the simulation of cell growth in a porous construct under direct perfusion. Unlike the previous model proposed in the literature, which composes a cellular scaffold sandwiched between two culture media layers, the current model includes only the scaffold layer to simplify the mathematical and computational complex. Results show the present single‐layer model can predict cell spreads and the nutrient and metabolic waste distribution as accurately as does the three‐layer model. Only if the hydrodynamic aspects such as the pressure and viscous stress are prominent to know, should the more sophisticated analyses with the three‐layer model be employed. The compact model provides comparable investigations for the tissue‐engineering construct developments. Biotechnol. Bioeng. 2008;99: 1535–1541. © 2007 Wiley Periodicals, Inc.
Linear copolymeric poly(thia‐alkanedioates) by lipase‐catalyzed esterification and transesterification of 3,3′‐thiodipropionic acid and its dimethyl ester with α,ω‐alkanediols
Authors: Fehling E. , Klein E. , Vosmann K. , Bergander K. , Weber N. 
Published: October 2007

AbstractLinear copolymeric polyesters (polyoxoesters) containing thioether functions [poly(3,3′‐thiodipropionic acid‐co‐α,ω‐alkanediols)] were formed in good yield by esterification of an equimolar mixture of 3,3′‐thiodipropionic acid (4‐thiaheptane‐1,7‐dioic acid) and 1,6‐hexanediol (weight average molecular mass, MW >600 Da: ∼81% after 6 h) or 1,12‐dodecanediol (MW > 900 Da: ∼90% after 6 h) catalyzed by immobilized lipase B from Candida antarctica (Novozym 435) for up to 336 h in moderate vacuo without a solvent or drying reagent in the reaction mixture. Poly (3,3′‐thiodipropionic acid‐co‐1,6‐hexanediol) and poly (3,3′‐thiodipropionic acid‐co‐1,12‐dodecanediol) were extracted from the reaction mixtures using tetrahydrofurane and precipitated from tetrahydrofurane—iso‐hexane (1:1, v/v) at ∼0°C. The precipitate of poly(3,3′‐thiodipropionic acid‐co‐1,6‐hexanediol) showed a maximum molecular weight of 6 × 105 Da corresponding to a MW of ∼24,200 Da and a degree of polymerization of up to 2,150 monomer units. The precipitated poly(3,3′‐thiodipropionic acid‐co‐1,12‐dodecanediol) showed a maximum molecular weight of 8 × 105 Da corresponding to a MW of ∼27,200 Da and a maximum degree of polymerization of up to 2,200 monomer units. The chemical structures of both polyesters containing thioether functions were confirmed by chemical derivatization and NMR spectrometry. The chemical structures of various low‐molecular weight reaction intermediates of the esterification of 3,3′‐thiodipropionic acid with 1,6‐hexanediol were elucidated by GC–MS. Biotechnol. Bioeng. 2008;99: 1074–1084. © 2007 Wiley Periodicals, Inc.
A microplate‐based evaluation of complex denaturation pathways: Structural stability of Escherichia coli transketolase
Authors: Aucamp Jean P. , Martinez‐Torres Ruben J. , Hibbert Edward G. , Dalby Paul A. 
Published: October 2007

AbstractWe have previously developed a rapid microplate‐based approach for measuring the denaturation curves by intrinsic tryptophan fluorescence for simple monomeric and two‐state unfolding proteins. Here we demonstrate that it can accurately resolve the multiple conformational transitions that occur during the denaturation of a complex multimeric and cofactor associated protein. We have also analyzed the effect of two active‐site mutations, D381A and Y440A upon the denaturation pathway of transketolase using intrinsic fluorescence measurements, and we compare the results from classical and microplate‐based instrumentation. This work shows that the rapid assay is able to identify changes in the denaturation pathway, due to mutations or removal of cofactors, which affect the stability of the native and intermediate states. This would be of significant benefit for the directed evolution of protein stability, optimizing enzyme stability under biocatalytic process conditions, and also for engineering specific transitions in protein unfolding pathways. Biotechnol. Bioeng. 2008;99: 1303–1310. © 2007 Wiley Periodicals, Inc.
Systematic review of minimally invasive resection for gastro-oesophageal cancer
Authors: Gemmill E H , McCulloch P 
Published: October 2007

Abstract

Background
This article reviews the evidence on the safety and efficacy of minimally invasive surgery for gastric and oesophageal cancer.

Methods
An electronic search of the literature between 1997 and 2007 was undertaken to identify primary studies and systematic reviews; studies were retrieved and analysed using predetermined criteria. Information on the safety and efficacy of minimally invasive surgery for gastric and oesophageal cancer was recorded and analysed.

Results
From 188 abstracts reviewed, 46 eligible studies were identified, 23 on oesophagectomy and 23 on gastrectomy. There were 35 case series, eight case-matched studies and three randomized controlled trials. Compared with the contemporary results of open surgery, reports on minimally invasive surgery indicate potentially favourable outcomes in terms of operative blood loss, recovery of gastrointestinal function and hospital stay. However, the quality of the data was generally poor, with many potential sources of bias.

Conclusion
Minimally invasive surgery is feasible but evidence of benefit is currently weak.
Probing Hydroxyl Radicals and Their Imaging in Living Cells by Use of FAM–DNA–Au Nanoparticles
Authors: Tang Bo , Zhang Ning , Chen Zhenzhen , Xu Kehua , Zhuo Linhai , An Liguo , Yang Guiwen 
Published: October 2007

AbstractThe incorporation of gold nanoparticles (Au NPs) as quencher modules in fluorescent probes for DNA damage caused by intracellular hydroxyl radicals (HO.) is reported. Au NPs of 15 nm diameter were decorated with DNA oligomers terminating in thiol functions in their 3′ positions and possessing 5′ fluorophore modifications. The Au NPs, which have high extinction coefficients, functioned as excellent fluorescent quenchers in the fluorophore–Au NP composites. FRET is switched off as a factor of HO.‐induced strand breakage in the single‐stranded DNAs, restoring the fluorescence of the quenched fluorophores, which can be followed by spectrofluorimetry. In vitro assays with HO.‐generating Fenton reagent demonstrated increases in fluorescence intensity with a linear range from 8.0 nM to 1.0 μM and a detection limit as low as 2.4 nM. Confocal microscopic imaging of macrophages and HepG2 revealed that the probe is cell‐permeable and intracellular HO.‐responsive. The unique combination of good selectivity and high sensitivity establishes the potential value of the probe for facilitating investigations of HO.‐mediated cellular homeostasis and injury.
Synthesis, Spectroscopic and Electrochemical Characterization, and DFT Study of Seventeen C70(CF3)n Derivatives (n=2, 4, 6, 8, 10, 12)
Authors: Popov Alexey A. , Kareev Ivan E. , Shustova Natalia B. , Lebedkin Sergey F. , Strauss Steven H. , Boltalina Olga V. , Dunsch Lothar 
Published: October 2007

AbstractEight new C70(CF3)n derivatives (n=2, 6, 10, 12) have been synthesized and characterized by UV/Vis and 19F NMR spectroscopy, cyclic voltammetry, and quantum chemical calculations at the DFT level of theory. Nine previously known derivatives of C70(CF3)n with n=2–12 were also studied by cyclic voltammetry (and seven of them by UV/Vis spectroscopy for the first time). Most of the 17 compounds exhibited two or three reversible reductions at scan rates from 20 mV s−1 up to 5.0 V s−1. In general, reduction potentials for the 0/− couple are shifted anodically relative to the C700/− couple. However, the 0/− E1/2 values for a given composition are strongly dependent on the addition pattern of the CF3 groups. The data show that the addition pattern is as important, if not more important in some cases, than the number of substituents, n, in determining E1/2 values. An analysis of the DFT‐predicted LUMOs indicates that addition patterns that have non‐terminal double bonds in pentagons result in derivatives that are strong electron acceptors.
Asymmetric Iodocyclization Catalyzed by Salen–CrIIICl: Its Synthetic Application to Swainsonine
Authors: Kwon Hyo Young , Park Chul Min , Lee Sung Bae , Youn Joo‐Hack , Kang Sung Ho 
Published: October 2007

AbstractThe previously developed enantioselective iodocyclization of γ‐hydroxy‐cis‐alkenes required 30 mol % of (R,R)‐salen–CoII complex as chiral catalyst and 0.75 equivalent of N‐chlorosuccinimide (NCS) as activator to produce 2‐substituted tetrahydrofurans with 61 to 90 % ee. Due to the considerable loading amount of the CoII complex, another more effective catalyst was pursued by screening (R,R)‐salen–transition metal complexes. When 10 mol % of the catalysts were applied with 0.5 equivalent of NCS, a higher level of stereoselectivity was attained with the corresponding CrIIICl (84 % ee), MnIICl (52 % ee) and CoII complexes (66 % ee). Refinement of the conditions established a novel catalytic enantioselective iodocyclization protocol using iodine in the presence of 7 mol % of (R,R)‐salen–CrIIICl complex activated by 0.7 equivalent of NCS in toluene to induce 74 to 93 % ee.
Isomeric Control of Protein Recognition with Amino Acid‐ and Dipeptide‐Functionalized Gold Nanoparticles
Authors: You Chang‐Cheng , Agasti Sarit S. , Rotello Vincent M. 
Published: October 2007

AbstractAmino acid and dipeptide‐functionalized gold nanoparticles (NPs) possessing L/D‐leucine and/or L/D‐phenylalanine residues have been constructed in order to target the surfaces of α‐chymotrypsin (ChT) and cytochrome c (CytC). Isothermal titration calorimetry (ITC) was conducted to evaluate the binding thermodynamics and selectivity of these NP–protein interactions. The chirality of the NP end‐groups substantially affects the resultant complex stability, with up to 20‐fold differences seen between particles of identical hydrophobicity, demonstrating that structural information from the ligands can be used to control protein recognition.
Strontium Tetrafluoridoborate and Barium Tetrafluoridoborate.
Authors: Bunic Tina , Tavcar Gasper , Goreshnik Evgeny , Zemva Boris 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
An Efficient Route to Vinylsubstituted Oxadiazoles and Triazoles Using Phenylselanyl Derivatives as Precursor.
Authors: Wang Yu‐Guang , Huang Xian , Wu Yu‐Zhou 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Efficient Regio‐ and Stereoselective Cleavage of Aziridines and Epoxides Using an Ionic Liquid as Reagent and Reaction Medium.
Authors: Ranu Brindaban C. , Adak Laksmikanta , Banerjee Subhash 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
A Simple Reduction Method of Azo‐Compounds to Amines Using Fe Powder in the Presence of NH4Cl.
Authors: Mobinikhaledi Akbar , Foroughifar Naser , Jirandehi Hasan Fathinejad 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Behavior of 3(3‐Indolylmethylene)‐5‐aryl‐2(3H)‐furanones as Alkylating Agents: Intra‐ versus Intermolecular Alkylation.
Authors: Abou‐Elmagd Wael S. I. 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Hybrid Organic‐Inorganic Materials Derived from a Monosilylated Hoveyda‐Type Ligand as Recyclable Diene and Enyne Metathesis Catalysts.
Authors: Elias Xavier , Pleixats Roser , Man Michel Wong Chi , Moreau Joel J. E. 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
[(NHC)Au(I)]‐Catalyzed Formation of Conjugated Enones and Enals: An Experimental and Computational Study.
Authors: Marion Nicolas , Carlqvist Peter , Gealageas Ronan , de Fremont Pierre , Maseras Feliu , Nolan Steven P. 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Alkylation of Active Methylene Compounds with Alcohols Catalyzed by an Iridium Complex.
Authors: Morita Masao , Obora Yasushi , Ishii Yasutaka 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
L‐Proline‐Derived Triamine as a Highly Stereoselective Organocatalyst for Asymmetric Michael Addition of Cyclohexanone to Nitroolefins.
Authors: Chen Haibin , Wang Yu , Wei Siyu , Sun Jian 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Synthesis of C,N‐Diaryl Nitrones from the Reduction of Nitroarene with Aromatic Aldehydes Promoted by Metallic Samarium.
Authors: Jia Xueshun , Li Dafeng , Huang Qing , Zhu Li , Li Jian 
Published: October 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.