bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tools and ingredients for the biocatalytic synthesis of metabolites
Authors: Wohlgemuth Roland 
Published: September 2009

AbstractMetabolic networks have been an interesting starting point not only for the design of synthetic routes in a similar sequence of reactions, e.g., in biomimetic syntheses, but also for assembling a number of biocatalytic steps by preparing the required enzymes and auxiliary reagents. Retrosynthetic analysis involving multiple biocatalytic reactions steps therefore needs to consider the practically realized biocatalytic single steps. The opportunities for route selection are enlarged if novel synthetic reactions connecting easily available starting materials and products are found, and/or both biocatalytic and classical reactions of organic chemistry are utilized. Tools and ingredients for biocatalytic synthesis are of special interest for reactions difficult to achieve by classical organic synthesis. Densely and differentially functionalized small molecules do not allow much space for protecting or activating groups. Biocatalytic reactions have therefore performed well for a number of useful metabolites in enantiopure form to achieve full functionality. Although many well‐known metabolites from classical biochemistry have only been prepared in racemic form, it is of fundamental interest to have these available in enantiomerically pure form. Biocatalytic reactions with nature's privileged chiral catalysts appear to be a promising synthetic strategy towards these metabolites, especially when sensitive or stable‐isotope‐labeled metabolites are to be prepared. The main applications for these metabolites are as references materials in metabolomics, as enzyme substrates for the characterization of metabolic enzyme activities and as potential pharmaceuticals in biomedical research. The use of stable‐isotope‐labeled metabolites can thereby simplify in vivo applications and metabolic flux analyses.
BAK and BAX deletion using zinc‐finger nucleases yields apoptosis‐resistant CHO cells
Authors: Cost Gregory J. , Freyvert Yevgeniy , Vafiadis Annamaria , Santiago Yolanda , Miller Jeffrey C. , Rebar Edward , Collingwood Trevor N. , Snowden Andrew , Gregory Philip D. 
Published: September 2009

AbstractAnoxic and metabolic stresses in large‐scale cell culture during biopharmaceutical production can induce apoptosis. Strategies designed to ameliorate the problem of apoptosis in cell culture have focused on mRNA knockdown of pro‐apoptotic proteins and over‐expression of anti‐apoptotic ones. Apoptosis in cell culture involves mitochondrial permeabilization by the pro‐apoptotic Bak and Bax proteins; activity of either protein is sufficient to permit apoptosis. We demonstrate here the complete and permanent elimination of both the Bak and Bax proteins in combination in Chinese hamster ovary (CHO) cells using zinc‐finger nuclease‐mediated gene disruption. Zinc‐finger nuclease cleavage of BAX and BAK followed by inaccurate DNA repair resulted in knockout of both genes. Cells lacking Bax and Bak grow normally but fail to activate caspases in response to apoptotic stimuli. When grown using scale‐down systems under conditions that mimic growth in large‐scale bioreactors they are significantly more resistant to apoptosis induced by starvation, staurosporine, and sodium butyrate. When grown under starvation conditions, BAX‐ and BAK‐deleted cells produce two‐ to fivefold more IgG than wild‐type CHO cells. Under normal growth conditions in suspension culture in shake flasks, double‐knockout cultures achieve equal or higher cell densities than unmodified wild‐type cultures and reach viable cell densities relevant for large‐scale industrial protein production. Biotechnol. Bioeng. 2010; 105: 330–340. © 2009 Wiley Periodicals, Inc.
Computational study of the drag and oscillatory movement of biofilm streamers in fast flows
Authors: Taherzadeh Danial , Picioreanu Cristian , Küttler Ulrich , Simone Angelo , Wall Wolfgang A. , Horn Harald 
Published: September 2009

AbstractHydrodynamic conditions have a significant impact on the biofilm lifecycle. Not well understood is the fact that biofilms, in return, also affect the flow pattern. A decade ago, it was already shown experimentally that under fast flows, biofilm streamers form and oscillate with large amplitudes. This work is a first attempt to answer the questions on the mechanisms behind the oscillatory movement of the streamers, and whether this movement together with the special streamlined form of the streamers, have both a physical and biological benefit for biofilms. In this study, a state of the art two‐dimensional fluid–structure interaction model of biofilm streamers is developed, which implements a transient coupling between the fluid and biofilm mechanics. Hereby, it is clearly shown that formation of a Kármán vortex street behind the streamer body is the main source of the periodic oscillation of the streamers. Additionally it is shown that the formation of streamers reduces the fluid forces which biofilm surface experiences. Biotechnol. Bioeng. 2010; 105: 600–610. © 2009 Wiley Periodicals, Inc.
Comparison of Micromixing Models for Calculation of the Chemical Reaction Rate in Homogeneous Turbulent Flow
Authors: Chorny A. 
Published: September 2009

AbstractTurbulent mixing with a single second‐order isothermal reaction in a homogeneous flow is considered. A mixing model is stated using the probability density function (PDF) equation method and the concepts of mixture fraction and progress variable. Different micromixing models are compared. With the interaction exchange mean/linear square mean estimation (IEM/LSME) model, the time variation of the mixture fraction PDF contradicts the physical representation of mixing. The Langevin model describes mixing from the segregating state to the homogeneous state of a mixture. The PDF model proves to be two‐mode at intermediate mixing stages. This is also true for the multi‐zone PDF model. As compared to the multi‐zone PDF model, others reveal higher averaged progress variables over the entire time range and at all Damköhler number values. Such a difference is made by the approximations for the averaged reaction rate that should be allowed for in the modeling of turbulent mixing with chemical reaction.
A Microfluidic Approach for a Continuous Crystallization of Drug Carrier Nanoparticles
Authors: Jasch K. , Barth N. , Fehr S. , Bunjes H. , Augustin W. , Scholl S. 
Published: September 2009

AbstractSolid lipid nanoparticles (SLN) as a new generation of drug carrier systems for pharmaceutical applications are currently under intensive investigation. They can be prepared by melt‐homogenization of a matrix lipid in surfactant‐containing aqueous media. In the corresponding production sequence, the crystallization of the resulting lipid droplets to solid nanoparticles is a crucial step for reproducible product properties. Hitherto, melt crystallization in these dispersions is usually performed in a batchwise process under poorly defined cooling conditions, without much regard to the well‐known aspects of heat transfer, homogeneity in the product mixture, and precise process control. In addition, these setups often only allow the application of low cooling rates. The use of high, well‐defined cooling rates would, however, offer very interesting new possibilities for the manufacturing of such drug carrier systems. Due to their small volumes and superior heat and mass transfer performance, microfluidic devices ensure a precise setting and control of the optimum process conditions. In this study, a microfluidic process for the continuous melt crystallization of SLN suspensions is established, allowing for high and well‐defined cooling rates. For various cooling rates, the crystallized SLN were analyzed by differential scanning calorimetry, X‐ray diffraction, laser diffraction, and photon correlation spectroscopy. The samples were also analyzed after well‐defined storage times in order to investigate the stability of the suspensions.
Modulation of Excited‐State Proton Transfer of 2‐(2′‐Hydroxyphenyl)benzimidazole in a Macrocyclic Cucurbit[7]uril Host Cavity: Dual Emission Behavior and pKa Shift
Authors: Shaikh Mhejabeen , Dutta Choudhury Sharmistha , Mohanty Jyotirmayee , Bhasikuttan Achikanath C. , Nau Werner M. , Pal Haridas 
Published: September 2009

AbstractThe effect of the macrocyclic host, cucurbit[7]uril (CB7), on the photophysical properties of the 2‐(2′‐hydroxyphenyl)benzimidazole (HPBI) dye have been investigated in aqueous solution by using ground‐state absorption and steady‐state and time‐resolved fluorescence measurements. All three prototropic forms of the dye (cationic, neutral, and anionic) form inclusion complexes with CB7, with the largest binding constant found for the cationic form (K≈2.4×106 M−1). At pH≈4, the appearance of a blue emission band upon excitation of the HPBI cation in the presence of CB7 indicates that encapsulation into the CB7 cavity retards the deprotonation process of the excited cation, and hence reduces its subsequent conversion to the keto form. Excitation of the neutral form (pH≈8.5), however, leads to an increase in the keto form fluorescence, indicating an enhanced excited‐state intramolecular proton‐transfer process for the encapsulated dye. In both the ground and excited states, the two pKa values of the HPBI dye show upward shifts in the presence of CB7. The prototropic equilibrium of the CB7‐complexed dye is represented by a six‐state model, and the pH‐dependent changes in the binding constants have been analyzed accordingly. It has been observed that the calculated pKa values using this six‐state model match well with the values obtained experimentally. The changes in the pKa values in the presence of CB7 have been corroborated with the modulation of the proton‐transfer process of the dye within the host cavity.
Theoretical Study of the Cycloaddition Reaction of a Tungsten‐Containing Carbonyl Ylide
Authors: Ito Kazuta , Hara Yoshihiro , Mori Seiji , Kusama Hiroyuki , Iwasawa Nobuharu 
Published: September 2009

AbstractThe [3+2] cycloaddition reaction of a tungsten‐containing carbonyl ylide with methyl vinyl ether and the insertion reactions of the nonstabilized carbene complex intermediates produced have been investigated through the use of B3LYP density functional theory. The [3+2] cycloaddition reaction of the tungsten‐containing carbonyl ylide has been proven to proceed concertedly, reversibly, and with high endo selectivity. The intermolecular SiH insertion reactions of the carbene complex intermediates have been proven to be favored over the intramolecular CH insertion, in good agreement with experimental results. Moreover, the kinetic endo/exo ratio of the [3+2] cycloaddition reaction has been shown to determine the endo/exo selectivity of the SiH insertion products. In addition, secondary orbital interactions involving the benzene ring and the carbonyl ligand on the metal center have turned out to strongly influence the high endo selectivity of the [3+2] cycloaddition reaction with methyl vinyl ether.
The Stereochemistry of 1,2,3‐Triols Revealed by 1H NMR Spectroscopy: Principles and Applications
Authors: Freire Félix , Lallana Enrique , Quiñoá Emilio , Riguera Ricardo 
Published: September 2009

AbstractThe conformational compositions of the tris(α‐methoxy‐α‐phenylacetic acid) ester derivatives of 1,2,3‐prim,sec,sec‐triols are presented. These conformations have been determined by theoretical and experimental data (i.e., energy‐ and chemical‐shift calculations, circular dichroism (CD) experiments, coupling‐constant analysis, enantioselective deuteration experiments, and low‐temperature NMR spectroscopic studies). A detailed analysis of the anisotropic effects due to the most significant conformers in the 1H NMR spectra supported the correlation between the 1H NMR spectra (ΔδRS value of H(3′) and |Δ(ΔδRS)| parameters) and the absolute configuration of the substrate. The study also allows the identification of the pro‐R and pro‐S methylene protons from their vicinal coupling constants and relative chemical shifts.
Influence of carbonisation on selected engineering properties of carbon resin electrodes for electrochemical treatment of wastewater
Authors: Oke Isaiah Adesola 
Published: September 2009

AbstractIn this study, effects of selected factors on selected properties of carbon resin electrodes (CRE) have been investigated. CRE were developed from used dry cells and resin using non‐heat‐treatment process. Selected properties (density, electrical resistance, microstructure, hygroscopy, stability moisture content, compressive and flexural strength) of the electrodes were monitored and effects of carbonisation temperature, carbon particle size, and compaction pressure on these properties were studied.The study revealed that the density of CRE was in the range of 1.33 to 1.59 g/cm3, compressive strength ranged from 36.56 to 43.81 MN/m2, flexural strength, moisture content, and swelling were in the range of 6.76 to 8.10 MN/m2, 0.84–0.93%, and 6.04–9.30%, respectively. In all cases electrical resistance and density of CRE decreased with increasing carbonisation temperature at various operational factors (particle size, compacting pressure, and percentage of the resin used). Also, it was revealed that carbonisation of CRE from 30 to 220°C reduced specific electrical resistance and density from 1.85 to 1.29 × 10−1 Ω/cm and from 1.35 to 1.24 g/cm3, respectively, but carbonisation temperature had no significant effect on wetness, compressive and flexural strength, stability, and moisture content of the electrodes. Estimated costs revealed that cost of producing CRE was cheaper ($13.25/m) than that of heat‐treated electrodes ($33.33/m).It was concluded that carbonisation temperature, particle size, compacting pressure, and percentage of the resin used are important factors in the development of CRE with lower specific electrical resistance.
Vibrational, optical and microhardness studies of trimethoprim DL ‐malate
Authors: Franklin S. , Bhuvana K. P. , Balasubramanian T. 
Published: September 2009

AbstractTrimethoprim malate, an organic crystal, has been synthesized using slow evaporation method from its aqueous solution. Structural, optical and the mechanical properties of the grown crystal have been investigated by various characterization techniques which include FTIR spectra, single crystal XRD, UV‐Vis spectra and Vickers microhardness testing. The structure of the compound predicted by analysing the recorded FTIR spectrum compliments the structure determined using single crystal X‐ray diffraction. Single crystal X‐ray diffraction study reveals that the crystals are monoclinic [P21/c, a=12.9850 Å, b=9.3038 Å, c=15.6815 Å and β=111.065°]. The UV‐Vis spectrum exhibits maximum transparency (98%) for a wide range suggesting the suitability of the title compound for optical applications. The optical constants have been calculated and illustrated graphically. Microhardness tests have been performed on the cystal under study and the Vicker hardness number has been calculated. The work hardening coefficient is found to be 2.85 which suggest that the crystal belongs to the family of soft materials. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A simple glucose reduction route for the synthesis of sheet‐like copper dendrites
Authors: Ni Yonghong , Wang Biao , Liu Rong , Hong Jianming 
Published: September 2009

AbstractIn the current paper we designed a simple glucose reduction route for synthesis of sheet‐like Cu dendrites on a high yield, using CuSO4 as the starting material. The reaction was carried out at 180 °C for 18 h in the absence of any structure‐directing agent. The product was characterized by X‐ray powder diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM) and electron diffraction (ED). Some factors influencing the shapes of Cu microcrystals, including the reaction temperature, time, and the concentration of the starting CuSO4, were investigated. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Contribution to the study of elastic properties of KGd(WO4)2:Er3+ single crystals by Brillouin spectroscopy
Authors: Kasprowicz D. , Trzaskowska A. , Majchrowski A. , Michalski E. , Drozdowski M. , Mielcarek S. 
Published: September 2009

AbstractIn this paper we present the study of the acoustic phonons propagating in Er3+‐doped KGd(WO4)2 single crystals by Brillouin spectroscopy. For the investigated crystals the velocities of the longitudinal and transverse acoustic phonons [100], [010], [001], [101] and [110] have been determined. Moreover, the values of the elastic constants: C22, C44 and C66 of Er3+‐doped KGd(WO4)2 single crystals have been estimated. It was revealed that the presence of the Er3+‐ions in KGd(WO4)2 crystals, for the used doping concentration 1 at% does not influence their elastic properties. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Green fiber lasers: An alternative to traditional DPSS green lasers for flow cytometry
Authors: Telford William G. , Babin Sergey A. , Khorev Serge V. , Rowe Stephen H. 
Published: September 2009

AbstractGreen and yellow diode‐pumped solid‐state (DPSS) lasers (532 and 561 nm) have become common fixtures on flow cytometers, due to their efficient excitation of phycoerythrin (PE) and its tandems, and their ability to excite an expanding array of expressible red fluorescent proteins. Nevertheless, they have some disadvantages. DPSS 532‐nm lasers emit very close to the fluorescein bandwidth, necessitating optical modifications to permit detection of fluorescein and GFP. DPSS 561‐nm lasers likewise emit very close to the PE detection bandwidth and also cause unwanted excitation of APC and its tandems, requiring high levels of crossbeam compensation to reduce spectral overlap into the PE tandems. In this article, we report the development of a new generation of green fiber lasers that can be engineered to emit in the range between 532 and 561 nm. A 550‐nm green fiber laser was integrated into both a BD LSR II™ cuvette and FACSVantage DiVa™ jet‐in‐air cell sorter. This laser wavelength avoided both the fluorescein and PE bandwidths and provided better excitation of PE and the red fluorescent proteins DsRed and dTomato than a power‐matched 532 nm source. Excitation at 550 nm also caused less incidental excitation of APC and its tandems, reducing the need for crossbeam compensation. Excitation in the 550 nm range, therefore, proved to be a good compromise between 532‐ and 561‐nm sources. Fiber laser technology is, therefore, providing the flexibility necessary for precisely matching laser wavelengths to our flow cytometry applications. Published 2009 Wiley‐Liss, Inc.
Flow cytometry and the stability of phycoerythrin‐tandem dye conjugates
Authors: Hulspas Ruud , Dombkowski David , Preffer Frederic , Douglas Derick , Kildew‐Shah Brian , Gilbert John 
Published: September 2009

AbstractRoutine clinical flow cytometric procedures demand rigorous, simple, and reproducible procedures for spectral compensation. The current, often laborious, spectral compensation procedures are the result of variability in instrument settings, instrument performance, and variability in reagents. In particular, the use of tandem dye conjugates necessitates elaborate spectral compensation procedures that need to be applied frequently. Manufacturer, lot number, and handling procedures are considered the key aspects affecting the fluorescence characteristics of tandem dyes. A better understanding of how specific conditions affect the variability in emission spectra of tandem dyes can lead to a considerable increase in reliability of measurements and a potential simplification of setup procedures for routine, clinical flow cytometry. We investigated the effect of light exposure, handling, and storage conditions on the fluorescence characteristics of some common phycoerythrin tandem fluorochromes. In general, PE‐Cy5 showed the lowest degradation rates, whereas PE‐Cy7 showed the highest. During storage, long‐term degradation rates were lowest for reagents packaged using an extra light protective approach. Under these conditions, a degradation rate of 0.9%/month of a PE‐Cy7 conjugate decreased to 0.3%/month. As degradation rates were minimized, we studied the effect of slow degradation of a set of tandem dye conjugates on compensation matrix values over several months. Finally, we explored the effect of slow degradation on flow cytometric analysis using the same compensation settings for extended periods for an analysis template with preset regions and gating strategies. © 2009 International Society for Advancement of Cytometry
Selective interaction between Trf3 and Taf3 required for early development and hematopoiesis
Authors: Hart Daniel O. , Santra Manas K. , Raha Tamal , Green Michael R. 
Published: September 2009

AbstractIn zebrafish, TATA‐box‐binding protein (TBP)‐related factor 3, Trf3, is required for early development and initiation of hematopoiesis, and functions by promoting expression of a single target gene, mespa. Recent studies have shown that in murine muscle cells, TRF3 interacts with the TBP‐associated factor TAF3. Here we investigate the role of Taf3 in zebrafish embryogenesis. We find that like Trf3‐depleted zebrafish embryos, Taf3‐depleted embryos exhibit multiple developmental defects and fail to undergo hematopoiesis. Both Trf3 and Taf3 are selectively bound to the mespa promoter and are required for mespa expression. Significantly, Taf3 interacts with Trf3 but not Tbp, and a Trf3 mutant that disrupts this interaction fails to support mespa transcription, early development, and hematopoiesis. Thus, a selective interaction between Trf3 and Taf3 is required for early zebrafish development and initiation of hematopoiesis. Finally, we provide evidence that TRF3 and TAF3 are also required for hematopoiesis initiation in the mouse. Developmental Dynamics 238:2540–2549, 2009. © 2009 Wiley‐Liss, Inc.
A soft X‐ray and gamma‐ray source using laser and electron beams
Authors: Miyamoto Shuji , Amano Sho , Inoue Takahiro , Mochizuki Takayasu 
Published: September 2009

AbstractSoft X‐ray and gamma‐ray beam sources are developed by using laser and high‐energy electron beams. Laser plasma soft X‐ray source is a cryogenic Xe target irradiated by a high average power (>100 W) and high peak power (30 MW, 0.3 J/10 ns) laser. A conversion efficiency from the laser energy to the soft X‐ray (70 to 200 eV) energy of 22% was achieved. Laser Compton gamma‐ray source on a synchrotron radiation facility, New SUBARU, is a new quasi‐monochromatic high‐energy photon beam. The world's highest class gamma‐ray flux of more than 106 photons/s is generated at a photon energy range of 6 to 17 MeV. © 2009 Wiley Periodicals, Inc. Electron Comm Jpn, 92(10): 13–23, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecj.10134
Counterion Effects on the Mesomorphic Properties of Chiral Imidazolium and Pyridinium Ionic Liquids
Authors: Kohnen Gilles , Tosoni Martin , Tussetschläger Stefan , Baro Angelika , Laschat Sabine 
Published: September 2009

AbstractNovel calamitic N‐methylimidazolium and pyridinium salts with modified citronellyl side‐chains and various counterions 3–14 have been synthesised by utilising the commercially available (R)‐citronellol (15) as the starting material. Differential scanning calorimetry (DSC), polarising optical microscopy (POM) and temperature‐dependent X‐ray diffraction studies revealed smectic A (SmA) mesophases for all the series. 1H NMR studies of the N‐methylimidazolium salts have shown that there is a correlation between the mesophase dependence on the counterion and the counterion‐dependent chemical shifts of the acidic 2‐H proton.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)