bluuebunny/crossref_metadata_2025_split huggingface dataset:
Debottlenecking recombinant protein production in Bacillus megaterium under large‐scale conditions—targeted precursor feeding designed from metabolomics
Authors: Korneli Claudia , Bolten Christoph Josef , Godard Thibault , Franco‐Lara Ezequiel , Wittmann Christoph 
Published: January 2012

AbstractIn the present work the impact of large production scale was investigated for Bacillus megaterium expressing green fluorescent protein (GFP). Specifically designed scale‐down studies, mimicking the intermittent and continuous nutrient supply of large‐ and small‐scale processes, were carried out for this purpose. The recombinant strain revealed a 40% reduced GFP yield for the large‐scale conditions. In line with extended carbon loss via formation of acetate and carbon dioxide, this indicated obvious limitations in the underlying metabolism of B. megaterium under the large‐scale conditions. Quantitative analysis of intracellular amino acids via validated fast filtration protocols revealed that their level strongly differed between the two scenarios. During cultivation in large‐scale set‐up, the availability of most amino acids, serving as key building blocks of the recombinant protein, was substantially reduced. This was most pronounced for tryptophan, aspartate, histidine, glutamine, and lysine. In contrast alanine was increased, probably related to a bottleneck at the level of pyruvate which also triggered acetate overflow metabolism. The pre‐cursor quantifications could then be exploited to verify the presumed bottlenecks and improve recombinant protein production under large‐scale conditions. Addition of only 5 mM tryptophan, aspartate, histidine, glutamine, and lysine to the feed solution increased the GFP yield by 100%. This rational concept of driving the lab scale productivity of recombinant microorganisms under suboptimal feeding conditions emulating large scale can easily be extended to other processes and production hosts. Biotechnol. Bioeng. 2012; 109:1538–1550. © 2012 Wiley Periodicals, Inc.
Glucose/O2 biofuel cell based on enzymes, redox mediators, and Multiple‐walled carbon nanotubes deposited by AC‐electrophoresis then stabilized by electropolymerized polypyrrole
Authors: Ammam Malika , Fransaer Jan 
Published: January 2012

AbstractIn this study, we developed an automated strategy to manufacture an enzyme BFC powered by glucose/O2. The bioanode consists of GOx enzyme and PQQ redox mediator adsorbed over night on MWCNTs then deposited by means of AC‐electrophoresis at 30 Hz and 160 Vp–p and, finally stabilized by electropolymerized polypyrrole. The biocathode is constructed from LAc enzyme and ABTS redox mediator adsorbed over night on MWCNTs, then electrophoretically deposited under AC‐electric field at 30 Hz and 160 Vp–p and, finally stabilized by electrodeposited polypyrrole. The BFC was studied under air in phosphate buffer solution pH 7.4 containing 10 mM glucose and in human serum with 5 mM glucose addition at the physiological temperature of 37°C. Under these conditions, the maximum power density reaches 1.1 µW · mm−2 at a cell voltage of 0.167 V in buffer solution and 0.69 µW · mm−2 at cell voltage of 0.151 V in human serum. Such automated BFCs have a great potential to be optimized, miniaturized to micro and nanoscale devices suitable for in vivo studies. Biotechnol. Bioeng. 2012; 109:1601–1609. © 2012 Wiley Periodicals, Inc.
BESSICC, a COSMO‐RS based tool for in silico solvent screening of biocatalyzed reactions
Authors: Braiuca P. , Khaliullin I. , Švedas V. , Knapic L. , Fermeglia M. , Halling P.J. , Gardossi L. 
Published: January 2012

AbstractMany enzymatic reactions are near‐equilibrium reactions. This often limits final yield and hence application of biocatalyzed processes in the industrial production. The most widely applied strategy to overcome this issue is solvent selection. It must be underlined that measuring the equilibrium position experimentally is a difficult and time‐consuming procedure and any tool for predicting the solvent effect on the reaction equilibrium can be very valuable. The present work reports on the development of BESSICC, an algorithm to calculate the effect of medium composition on biocatalyzed reactions equilibrium. It is based on COSMO‐RS calculation of activity coefficients of all the species in the reaction mixture and minimization of Gibbs free energy of the reaction. Starting from one single experimental measurement of the equilibrium position for a given biocatalyzed reaction it can predict the yield of the reaction in any other solvent or solvent mixture. Predictions are accurate, the errors of prediction are in average below 25% for the esterification of dodecanoic acid with menthol and below 65% for esterification of 1‐dodecanoic acid with 1‐dodecanol. The best predictions show an error well below 5%. Biotechnol. Bioeng. 2012; 109:1864–1868. © 2012 Wiley Periodicals, Inc.
Continuum heterogeneous biofilm model—A simple and accurate method for effectiveness factor determination
Authors: Gonzo Elio Emilio , Wuertz Stefan , Rajal Veronica B. 
Published: January 2012

AbstractWe present a novel analytical approach to describe biofilm processes considering continuum variation of both biofilm density and substrate effective diffusivity. A simple perturbation and matching technique was used to quantify biofilm activity using the steady‐state diffusion–reaction equation with continuum variable substrate effective diffusivity and biofilm density, along the coordinate normal to the biofilm surface. The procedure allows prediction of an effectiveness factor, η, defined as the ratio between the observed rate of substrate utilization (reaction rate with diffusion resistance) and the rate of substrate utilization without diffusion limitation. Main assumptions are that (i) the biofilm is a continuum, (ii) substrate is transferred by diffusion only and is consumed only by microorganisms at a rate according to Monod kinetics, (iii) biofilm density and substrate effective diffusivity change in the x direction, (iv) the substrate concentration above the biofilm surface is known, and (v) the substratum is impermeable. With this approach one can evaluate, in a fast and efficient way, the effect of different parameters that characterize a heterogeneous biofilm and the kinetics of the rate of substrate consumption on the behavior of the biological system. Based on a comparison of η profiles the activity of a homogeneous biofilm could be as much as 47.8% higher than that of a heterogeneous biofilm, under the given conditions. A comparison of η values estimated for first order kinetics and η values obtained by numerical techniques showed a maximum deviation of 1.75% in a narrow range of modified Thiele modulus values. When external mass transfer resistance, is also considered, a global effectiveness factor, η0, can be calculated. The main advantage of the approach lies in the analytical expression for the calculation of the intrinsic effectiveness factor η and its implementation in a computer program. For the test cases studied convergence was achieved quickly after four or five iterations. Therefore, the simulation and scale‐up of heterogeneous biofilm reactors can be easily carried out. Biotechnol. Bioeng. 2012; 109:1779–1790. © 2012 Wiley Periodicals, Inc.
Differential in‐gel electrophoresis (DIGE) analysis of CHO cells under hyperosmotic pressure: Osmoprotective effect of glycine betaine addition
Authors: Kim Jee Yon , Kim Yeon‐Gu , Lee Gyun Min 
Published: January 2012

AbstractThe use of glycine betaine combined with hyperosmolality is known to be an efficient means for achieving high protein production in recombinant Chinese hamster ovary (rCHO) cells. In order to understand the intracellular events and identify the key factors in rCHO cells cultivated with glycine betaine under hyperosmotic conditions, two‐dimensional differential in‐gel electrophoresis (2D‐DIGE) followed by mass spectrometric analysis was applied. Differentially expressed 19 protein spots were selected and 16 different kinds of proteins were successfully identified. The identified proteins were associated with cellular metabolism (PEPCK, GAPDH, and PK), cellular architecture (β‐tubulin and β‐actin), protein folding (GRP78 and OSP94), mRNA processing (Rbm34, ACF, and IPMK), and protein secretion (γ‐COP). 2D‐Western blot analysis of β‐tubulin, GAPDH, Peroxidoxin‐1, and GRP78 confirmed the proteomic findings. The proteins identified from this study, which are related to cell growth and antibody production, can be applied to cell engineering for maximizing the efficacy of the use of glycine betaine combined with hyperosmolality in rCHO cells. Biotechnol. Bioeng. 2012; 109:1395–1403. © 2012 Wiley Periodicals, Inc.
Topographic cues of nano‐scale height direct neuronal growth pattern
Authors: Baranes Koby , Chejanovsky Nathan , Alon Noa , Sharoni Amos , Shefi Orit 
Published: January 2012

AbstractWe study the role of nano‐scale cues in controlling neuronal growth. We use photolithography to fabricate substrates with repeatable line‐pattern ridges of nano‐scale heights. We find that neuronal processes, which are of micron size, have strong interactions with ridges even as low as 10 nm. The interaction between the neuronal process and the ridge leads to a deflection of growth direction and a preferred alignment with the ridges. The interaction strength clearly depends on the ridges' height. For 25 nm ridges approximately half of the neuronal processes are modified, while at 100 nm the majority of neurites change their original growth direction post interaction. In addition, the effect on growth correlates with the incoming angle between the neuronal process and the ridge. We underline the adhesion as a key mechanism in directing neuronal growth. Our study highlights the sensitivity of growing neurites to nano‐scale cues thus opens a new avenue of research for pre‐designed neuronal growth and circuitry. Biotechnol. Bioeng. 2012; 109:1791–1797. © 2012 Wiley Periodicals, Inc.
Generation of a cholesterol‐independent, non‐GS NS0 cell line through chemical treatment and application for high titer antibody production
Authors: Li Jincai , Gu Wei , Edmondson Diane G. , Lu Connie , Vijayasankaran Natarajan , Figueroa Bruno , Stevenson Dave , Ryll Thomas , Li Feng 
Published: January 2012

AbstractNS0 cells require exogenous cholesterol for growth. The non‐glutamine synthetase (GS) cholesterol‐dependent NS0 host was treated with 5‐azacytidine (5azaC), a demethylation drug, and adapted to grow in cholesterol‐free, chemically defined medium. Within 7 weeks, a stable, cholesterol‐independent NS0 host (NS0.CF) was obtained. The new NS0.CF host, as well as the original cholesterol auxotroph host, was transfected with the same mAb expression plasmid, and the top producing clone from both hosts were compared side‐by‐side in the enhanced platform fed‐batch cultures using chemically defined media. The NS0.CF derived clone significantly out‐performed the cholesterol‐dependent clone, with titer reaching 4.5 g/L versus 3.0 g/L, respectively, mainly due to higher specific productivity, while key product quality attributes remained comparable. This work demonstrated an effective and rapid approach to generate a cholesterol‐independent NS0 host, and its application in recombinant protein production. Biotechnol. Bioeng. 2012; 109:1685–1692. © 2012 Wiley Periodicals, Inc.
Differentiation of PC12 cells in three‐dimensional collagen sponges with micropatterned nerve growth factor
Authors: Oh Hwan Hee , Lu Hongxu , Kawazoe Naoki , Chen Guoping 
Published: January 2012

AbstractMicropatterning of biological cues is important for the guided formation of neuronal outgrowth and neuronal differentiation. Nerve growth factor (NGF) was micropatterned in a three‐dimensional collagen sponges by using micropatterned ice lines that were composed of collagen and NGF. The micropatterned ice lines were prepared by a dispersing machine. PC12 cells were cultured in the NGF‐micropatterned collagen sponges and showed micropatterned neurite outgrowth. The neurite outgrowth followed the micropattern of NGF with more neurite outgrowth in the collagen/NGF lines than in the regions between the collagen/NGF lines. The micropattern of the NGF and the neurite network of the PC12 cells can be manipulated by controlling the micropattern of the NGF. The three‐dimensional porous scaffolds prepared by this method will have a potential application for the regeneration and repair of the nervous system. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012
Chemical Constituents and Some Biological Activities of Plants from the Genus Ceriops
Authors: Wang Hui , Li Min‐Yi , Wu Jun 
Published: January 2012

AbstractIn this review, the literature data on phytochemical and biological investigations of the genus Ceriops are compiled. The Ceriops species are mangrove plants widely distributed along the sea coasts of Africa, Madagascar, South Asia, and South Pacific islands. To date, 43 diterpenes and 29 triterpenes have been reported from the embryos, fruits, hypocotyls, roots, stems, and twigs of C. tagal and C. decandra. Diterpenoids and triterpenoids are the main constituents of this genus. The isolated terpenes showed an enormous structural diversity and exhibited various biological properties, such as antitumor, antibacterial, and larvicidal activities.
Phenolic Compounds from the Branches of Eucalyptus maideni
Authors: Tian Li‐Wen , Xu Min , Li Yan , Li Xing‐Yao , Wang Dong , Zhu Hong‐Tao , Yang Chong‐Ren , Zhang Ying‐Jun 
Published: January 2012

AbstractThree new phenolic compounds, eucalmaidin F (1), (3S)‐5‐guaiacyl‐3‐hydroxypentanoic acid (2), and 8‐β‐C‐glucopyranosyl‐5,7‐dihydroxy‐2‐isobutylchromone (3), were isolated from the branches of E. maideni, together with 30 known compounds, including four phenylpropanoids, three lignans, four phloroglucinol glucosides, five dihydroflavonoids, seven simple phenolic compounds, six terpenoids, and glycerol. The new structures were established by spectroscopic studies (MS, and 1D‐ and 2D‐NMR), chemical degradation, and modified Mosher's method. Compounds 3, guaiacylglycerol, 3‐hydroxy‐1‐(4‐hydroxyphenyl)propan‐1‐one, caffeic acid, (2E)‐3‐(4‐hydroxyphenyl)prop‐2‐enoic acid, (7′S,8R,8′R)‐lyoniresinol, (+)‐lyoresinol 3α‐O‐α‐L‐rhamnopyranoside, garcimangosone, phlorocetophenone 2′‐glucopyranoside, (+)‐taxifolin 3α‐O‐α‐L‐rhamnopyranoside, (+)‐aromadendrin, (+)‐taxifolin, resveratrol, piceatannol, 3,4,5‐trihydroxyphenol. Tachiaside, gallic acid, macrocapals A und G, and oleuropeic acid were evaluated for their cytotoxicities against five human cancer cell lines. Resveratrol, piceatannol, gallic acid, and macrocapal G exhibited moderate inhibitory effects on human myeloid heukemia HL‐60 cell, with IC50 values of 22.05, 22.05, 7.75, and 31.93 μM, respectively; and only macrocapal G showed inhibitory effect on hepatocellular carcinoma SMMC‐7721 cell, with an IC50 value of 26.75 μM.
Inhibitory Effects of Terpenoids from the Fermented Broth of the Ascomycete Stilbohypoxylon elaeicola YMJ173 on Nitric Oxide Production in RAW264.7 Macrophages
Authors: Wang Guei‐Jane , Liang Wen‐Li , Ju Yu‐Ming , Yang Wen‐Bin , Chang Ya‐Wen , Lee Tzong‐Huei 
Published: January 2012

AbstractA series of six isopimarane‐type diterpene glycosides, along with an eremophilane‐type sesquiterpene, i.e., elaeicolasides A–C (1–3, resp.), 16‐(α‐D‐mannopyranosyloxy)isopimar‐7‐en‐19‐oic acid (4), hymatoxin K (5), hymatoxin L (6), and elaeicolalactone (7), were isolated from the AcOEt extract of the fermented broth of Stilbohypoxylon elaeicola YMJ173. Among these, 1–3 and 7 are new compounds based on their spectroscopic data and sugar composition analysis. The effects of 1–7 on the inhibition of nitric oxide (NO) production in lipopolysaccharide (LPS)‐activated murine macrophage RAW264.7 cells were evaluated. All these compounds inhibited NO production, detected as nitrite in the culture medium, in activated macrophages without any cytotoxicity at a concentration of 100 μM. Among these compounds, 2 showed a significant activity with the average maximum inhibition (Emax) and median inhibitory concentration (IC50) values of 93.3±0.5% and 79.3±0.4 μM, respectively.
Studies of the Activity of Peroxidase‐Like DNAzyme by Modifying 3′‐ or 5′‐End of Aptamers
Authors: Zhang Ming , Li Haiqun , Deng Minggang , Weng Xiaocheng , Ma Heng , Feng Shuo , Zhou Yangyang , Zhou Xiang 
Published: January 2012

AbstractIn the presence of hemin and under appropriate conditions, some modalities of G‐quadruplexes can form a peroxidase‐like DNAzyme that has been widely used in biology. Structurefunction studies on the DNAzyme revealed that its catalytic ability may be dependent on the unimolecular parallel G‐quadruplex. In this report, we present the preliminary investigation on the relationship between the structure and function of DNAzymes through a terminal oligo modification in G‐quadruplex sequences by adding different lengths of oligo‐dT to the 3′‐ or 5′‐end of the aptamers. The results suggested that adding dTn to the 5′‐end of the DNA sequence of the enzyme improved the ability of hemin to bind with DNA, but the addition of dTn to the 3′‐end decreased the binding ability of hemin for DNA. The increased stability of the assembled DNAzyme would lead to more favorable binding between the enzyme and substrate (H2O2), facilitating higher peroxidase activity; on the contrary, with lower stability of the DNAzyme complex, we observed reduced peroxidase activity.
Essential Oils in the Ranunculaceae Family: Chemical Composition of Hydrodistilled Oils from Consolida regalis, Delphinium elatum, Nigella hispanica, and N. nigellastrum Seeds
Authors: Kokoska Ladislav , Urbanova Klara , Kloucek Pavel , Nedorostova Lenka , Polesna Lucie , Malik Jan , Jiros Pavel , Havlik Jaroslav , Vadlejch Jaroslav , Valterova Irena 
Published: January 2012

AbstractIn this study, we analyzed the chemical composition of volatile oils hydrodistilled from seeds of Consolida regalis, Delphinium elatum, Nigella hispanica, and N. nigellastrum using GC and GC/MS. In C. regalis, octadecenoic (77.79%) and hexadecanoic acid (8.34%) were the main constituents. Similarly, the oils from D. elatum and N. hispanica seeds consisted chiefly of octadecadienoic (42.83 and 35.58%, resp.), hexadecanoic (23.87 and 28.59%, resp.), and octadecenoic acid (21.67 and 19.76%, resp.). Contrastingly, the monoterpene hydrocarbons α‐pinene (34.67%) and β‐pinene (36.42%) were the main components of N. nigellastrum essential oil. Our results confirm the presence of essential oils in the family Ranunculaceae and suggest chemotaxonomical relationships within the representatives of the genera Consolida, Delphinium, and Nigella. In addition, the presence of various bioactive constituents such as linoleic acid, (−)‐β‐pinene, squalene, or carotol in seeds of D. elatum, N. hispanica, and N. nigellastrum indicates a possible industrial use of these plants.
The Importance of Peripheral Sequences in Determining the Metal Selectivity of an in Vitro‐Selected Co2+‐Dependent DNAzyme
Authors: Nelson Kevin E. , Ihms Hannah E. , Mazumdar Debapriya , Bruesehoff Peter J. , Lu Yi 
Published: January 2012

AbstractDNAzymes are catalytically active DNA molecules that use metal cofactors for their enzymatic functions. While a growing number of DNAzymes with diverse functions and metal selectivities have been reported, the relationships between metal ion selectivity, conserved sequences and structures responsible for selectivity remain to be elucidated. To address this issue, we report biochemical assays of a family of previously reported in vitro selected DNAzymes. This family includes the clone 11 DNAzyme, which was isolated by positive and negative selection, and the clone 18 DNAzyme, which was isolated by positive selection alone. The clone 11 DNAzyme has a higher selectivity for Co2+ over Pb2+ compared with clone 18. The reasons for this difference are explored here through phylogenetic comparison, mutational analysis and stepwise truncation. A novel DNAzyme truncation method incorporated a nick in the middle of the DNAzyme to allow for truncation close to the nicked site while preserving peripheral sequences at both ends of the DNAzyme. The results demonstrate that peripheral sequences within the substrate binding arms, most notably the stem loop, loop II, are sufficient to restore its selectivity for Co2+ over Pb2+ to levels observed in clone 11. A comparison of these sequences' secondary structures and Co2+ selectivities suggested that metastable structures affect metal ion selectivity. The Co2+ selectivity of the clone 11 DNAzyme showed that the metal ion binding and selectivities of small, in vitro selected DNAzymes may be more complex than previously appreciated, and that clone 11 may be more similar to larger ribozymes than to other small DNAzymes in its structural complexity and behavior. These factors should be taken into account when metal‐ion selectivity is required in rationally designed DNAzymes and DNAzyme‐based biosensors.
Mixed Colloidal Suspensions of Reduced Graphene Oxide and Layered Metal Oxide Nanosheets: Useful Precursors for the Porous Nanocomposites and Hybrid Films of Graphene/Metal Oxide
Authors: Lee Yu Ri , Kim In Young , Kim Tae Woo , Lee Jang Mee , Hwang Seong‐Ju 
Published: January 2012

AbstractHomogeneously mixed colloidal suspensions of reduced graphene oxide, or RGO, and layered manganate nanosheets have been synthesized by a simple addition of the exfoliated colloid of RGO into that of layered MnO2. The obtained mixed colloidal suspensions with the RGO/MnO2 ratio of ≤0.3 show good colloidal stability without any phase separation and a negatively charged state with a zeta (ζ) potential of −30 to −40 mV. The flocculation of these mixed colloidal suspensions with lithium cations yields porous nanocomposites of Li/RGO‐layered MnO2 with high electrochemical activity and a markedly expanded surface area of around 70–100 m2 g−1. Relative to the Li/RGO and Li/layered MnO2 nanocomposites (≈116 and ≈167 F g−1), the obtained Li/RGO‐layered MnO2 nanocomposites deliver a larger capacitance of approximately 210 F g−1 with good cyclability of around 95–97 % up to the 1000th cycle, thus indicating the positive effect of hybridization on the electrode performances of RGO and lithium manganate. Also, an electrophoretic deposition of the mixed colloidal suspensions makes it possible to easily fabricate uniform hybrid films composed of graphene and manganese oxide. The obtained films show a distinct electrochemical activity and a homogeneous distribution of RGO and MnO2. The present experimental findings clearly demonstrate that the utilization of the mixed colloidal suspensions as precursors provides a facile and universal methodology to synthesize various types of graphene/metal oxide hybrid materials.