bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solubilization of Biomolecules in Carbon Dioxide Based Supercritical Fluids
Authors: Wong J. M. , Johnston K. P. 
Published: December 2008

AbstractSupercritical fluid (SF) carbon dioxide offers several advantages compared with organic liquid solvents for separations and reaction processes of thermally labile biomolecules.A major limitation is that the even moderately polar biomolecules are only slightly soluble. Experimental solubility and vapor pressure data were obtained for cholesterol, stigmasterol, and ergosterol in SF CO2 with and without co‐solvents over a pressure range of 100 to 350 bar. Small concentrations of certain co‐solvents can increase solubilities of particular sterols by one or two orders of magnitude, but have little effect on other sterols due to complexes formed in the solid phase. The experimental data were correlated using component solubility parameters to obtain the unlike‐pair attraction constant used in a modified van der Waals equation of state.
Multimembrane Bioreactor For Extractive Fermentation
Authors: Cho T. , Shuler M. L. 
Published: December 2008

AbstractA multimembrane reactor is described. Four layers (gas, cells, nutrient, and solvent) are separated by membranes. This structure prevents solvent emulsification in the fermentation broth. The system was tested for ethyl alcohol production from glucose using yeast. Tributyl phosphate (TBP) was chosen as the extractant. Experiments demonstrate for the first time a successful extractive fermentation with a practical solvent. Prevention of emulsification removes the toxic effect of TBP on yeast metabolism.
High Capacity Aeration in a Very Tall Tank
Authors: Jackson M. L. 
Published: December 2008

AbstractA tall tank (13 m high by 1.8 m diameter) with four orifice air inlets showed linear relationships among air input rate, gas phase holdup, and volumetric oxygen transfer coefficient. The established performance of the tall tank aeration system may be used for reference in design when scaling from laboratory to industrial size equipment.
Evaluation of Supercritical Fluid Extraction in the Pharmaceutical Industry
Authors: Larson Karen A. , King Michael L. 
Published: December 2008

AbstractVarious steroids precipitate from supercritical CO2 as very small particles but still retain their crystallinity. This suggests that SCFE in this industry could be
utilized as a size reduction method as an alternative to milling. The application
of SCFE as a separation technique is demonstrated by the simultaneous extraction and reaction of mevinolin, a metabolite of the fungus Aspergillus terreus.
Simulation of Secondary Metabolite Production By Immobilized Living Cells: Penicillin Production
Authors: Okita W. B. , Kirwan D. J. 
Published: December 2008

AbstractThe production of secondary metabolites by immobilized living microorganisms was investigated by simulation techniques. The behavior of free cell and immobilized cell reactors for the production of penicillin by P. chrysogenum was compared. This system was chosen as a model system because literature data on growth and production kinetics are available. Simulation results for bioreactors containing P. chrysogenum immobilized by adsorptive techniques demonstrates a potential advantage in productivity for such reactors over conventional fed batch operation. Realization of this advantage requires an understanding of growth and product formation kinetics for immobilized cells as well as development of immobilization technology that will provide stable, high cell loadings.
Hemoglobin‐based oxygen carrier enhanced tumor oxygenation: A novel strategy for cancer therapy
Authors: Gundersen Sharon I. , Palmer Andre F. 
Published: December 2008

AbstractA tumor's low oxygen tension is a major obstacle to current chemo‐ and radio‐therapies. By increasing oxygen transport to hypoxic tumor regions it is possible to make tumors more susceptible to current cancer treatment strategies. This article theoretically investigates the possibility of supplementing human blood with hemoglobin‐based oxygen carriers (HBOCs) in an attempt to target oxygen delivery specifically to the low oxygen tension regions present in tumors. In this work, we develop a mathematical model that describes oxygen transport in a cylindrical annulus of cancerous tissue fed by a single cylindrical capillary. The oxygen transport model was used to evaluate mixtures of red blood cells and six types of HBOCs that consisted of two polymerized hemoglobins, two liposome‐encapsulated hemoglobins, and two hydrogel‐encapsulated hemoglobins. These HBOCs span a wide range of oxygen affinities (P50s) ranging from 5 to 54 mm Hg to study the effect of P50 on the ability to target oxygen delivery to hypoxic regions of a tumor and hence improve tumor oxygenation. The results of these simulations indicate that each HBOC has an effective pO2 range in which it unloads the most oxygen, which is dependent on the HBOC's P50. Although it would seem that the HBOC with the lowest P50 (5 mm Hg) should be the best option for O2 delivery to hypoxic tumors, our results indicate that when this is the case, the lowest P50 HBOC yielded insufficient O2 delivery to normoxic tissues (inlet pO2 ∼ 95 mm Hg). Because HBOCs would be transfused into a patient's blood stream before initiating a particular cancer therapy, sufficient oxygen must be delivered to both normoxic and cancerous tissues to maintain normal tissue functions when oxygenating the tumor. Human blood supplemented with a hydrogel‐encapsulated Hb with a P50 of 10 mm Hg was found to deliver sufficient oxygen to normoxic tissue while increasing oxygen delivery to hypoxic regions of tumorgenic tissue. Taken together, this work represents a novel strategy for enhancing the efficacy of existing cancer therapies.
Propagation of embryonic stem cells in stirred suspension without serum
Authors: Kehoe Daniel E. , Lock Lye T. , Parikh Abhirath , Tzanakakis Emmanuel S. 
Published: December 2008

AbstractEmbryonic stem cells (ESCs) with their unlimited capacity for self‐renewal and ability to differentiate along multiple cell lineages are a superb starting material for biotechnology applications and cellular therapies. However, realization of the potential of ESCs requires the development of scalable systems for their production in large quantities and in a regulated manner. Here, we describe a methodology for the expansion of mouse ESCs (mESCs) as pluripotent aggregates in a stirred suspension bioreactor and in medium without serum. Initially, the culture of feeder cell‐independent mESCs in dishes was adapted to serum‐free conditions. Also, we explored whether spinner flasks equipped with a triangle‐shaped impeller and baffles support the culture of mESC aggregates. Serum‐free culture in these vessels resulted in an almost 20‐fold increase in the live mESC concentration over 4 days without significant loss of cell viability. Even after consecutive passages, mESCs retained high expression of pluripotency markers Oct3/4, Rex1 and SSEA‐1. More importantly, when differentiation was induced these cells adopted fates of all three germ layers namely neuroectoderm, cardiac mesoderm and definitive endoderm. These findings demonstrate that stem cells can be propagated under serum‐free conditions in a scalable stirred‐suspension culture without loss of their pluripotency.
In vivo dynamics of glycolysis in Escherichia coli shows need for growth‐rate dependent metabolome analysis
Authors: Schaub Jochen , Reuss Matthias 
Published: December 2008

AbstractMetabolomics emerges to become an important profiling technique in bio(techno)logical systems. In addition to intracellular metabolite concentrations at (quasi) stationary conditions, stimulus‐response experiments provide information on the dynamic behavior of metabolic pathways. These data are relevant for bioprocess analysis on the level of metabolism and for application of metabolic engineering principles aiming at a metabolic redesign of producer cells. However, even for the well‐studied bacteria Escherichia coli only limited growth‐rate dependent intracellular metabolite information is currently available, thereby impeding comprehensive metabolome analysis. Here, we present intracellular metabolite concentration data of representative glycolytic intermediates in E. coli cultivated in glucose‐limited chemostats, (i) at systematic variation of growth‐rate (D = 0.1, 0.2, 0.3, and 0.4 h−1) and (ii) at both steady‐state and after a glucose pulse applying a recently introduced integrated sampling procedure and LC‐MS analytical method. Whereas intracellular steady‐state concentrations of upper part glycolytic intermediates FBP and DHAP+GAP increased 2.3‐fold, respectively 2.8‐fold, when specific growth‐rate is raised from μ = 0.1 h−1 to μ = 0.4 h−1, the opposite trend was observed for 2PG+3PG and PEP pools with a decrease by a factor of 2.1, respectively 1.9. In glucose pulse experiments FBP and DHAP+GAP showed a 3.3 (1.8)‐fold, respectively 2.8 (2.0)‐fold, increase relative to the steady‐state level at μ = 0.1 (0.4) h−1. Also, the dynamics changed with growth‐rate for these two metabolite pools. In contrast, 2PG+3PG and PEP were characterized by decreased concentrations in response to a glucose pulse and the relative changes related to steady‐state values were significantly smaller compared with FBP and DHAP+GAP. The observed growth‐rate dependency of our data clearly indicates the necessity for metabolome studies covering a broader range of physiological growth conditions.
Screening of a human antibody phage display library against a peptide antigen using stimuli‐responsive bioconjugates
Authors: Stocker Gisela , Dumoulin Dorothée , Vandevyver Caroline , Hilbrig Frank , Freitag Ruth 
Published: December 2008

AbstractA synthetic antibody phage library (ETH‐2) was screened against the MUC‐1 peptide. Two standard methods were used, namely screening on immunotubes coated with the peptide antigen and on streptavidin‐coated paramagnetic particles together with a biotinylated MUC‐1 peptide. The results were compared with those obtained using a novel approach based on a stimuli‐responsive bioconjugate of avidin and poly‐(N‐isopropylacrylamide), also in combination with the biotinylated peptide. The poly‐(N‐isopropylacrylamide)‐based bioconjugate is soluble below a temperature of 30°C in the aqueous solutions pertinent to this study, but precipitates rapidly once this temperature is surpassed. The process is reversible, and the bioconjugate redissolves once the temperature is lowered again. The stimuli‐responsive bioconjugate was used to isolate specific phage from the library in several rounds of panning, consisting of repeated thermoprecipitation/redissolution cycles in a procedure known as “affinity precipitation.” As far as we know, this is the first time a compound as big as a viral particle has been specifically captured by a stimuli‐responsive bioconjugate. Compared to the two other investigated screening techniques, affinity precipitation of the phage led to a greater variety of genetically different specific phage, while the process was easy to handle and required no dedicated equipment safe for a centrifuge and a thermostated water bath.
Estimation of transgene copy number in transformed citrus plants by quantitative multiplex real‐time PCR
Authors: Omar Ahmad A. , Dekkers Marty G. H. , Graham James H. , Grosser Jude W. 
Published: December 2008

AbstractQuantitative real‐time PCR (qRT‐PCR) was adapted to estimate transgene copy number of the rice Xa21 gene in transgenic citrus plants. This system used TaqMan qRT‐PCR and the endogenous citrus gene encoding for lipid transfer protein (LTP). Transgenic “Hamlin” sweet orange plants were generated using two different protoplast‐GFP transformation systems: cotransformation and single plasmid transformation. A dilution series of genomic DNA from one of the transgenic lines was used to generate a standard curve for the endogenous LTP and the transgene Xa21. This standard curve was used for relative quantification of the endogenous gene and the transgene. Copy numbers of the transgene Xa21 detected from qRT‐PCR analysis correlated with that from Southern blot analysis (r = 0.834). Thus, qRT‐PCR is an efficient means of estimating copy number in transgenic citrus plants. This analysis can be performed at much earlier stages of transgenic plant development than southern blot analysis, which expedites investigation of transgenes in slow‐growing woody plants.
Automated microfluidic assay system for autoantibodies found in autoimmune diseases using a photoimmobilized autoantigen microarray
Authors: Matsudaira Takahiro , Tsuzuki Saki , Wada Akira , Suwa Akira , Kohsaka Hitoshi , Tomida Maiko , Ito Yoshihiro 
Published: December 2008

AbstractAutoimmune diseases such as rheumatoid arthritis, multiple sclerosis, and autoimmune diabetes are characterized by the production of autoantibodies that serve as useful diagnostic markers, surrogate markers, and prognostic factors. We devised an in vitro system to detect these clinically pivotal autoantibodies using a photoimmobilized autoantigen microarray. Photoimmobilization was useful for preparing the autoantigen microarray, where autoantigens are covalently immobilized on a plate, because it does not require specific functional groups of the autoantigens and any organic material can be immobilized by a radical reaction induced by photoirradiation. Here, we prepared the microarray using a very convenient method. Aqueous solutions of each autoantigen were mixed with a polymer of poly(ethylene glycol) methacrylate and a photoreactive crosslinker, and the mixtures were microspotted on a plate and dried in air. Finally, the plate was irradiated with an ultraviolet lamp to obtain immobilization. In the assay, patient serum was added to the microarray plate. Antigen‐specific IgG adsorbed on the microspotted autoantigen was detected by peroxidase‐conjugated anti‐IgG antibody. The chemical luminescence intensities of the substrate decomposed by the peroxidase were detected with a sensitive CCD camera. All autoantigens were immobilized stably by this method and used to screen antigen‐specific IgG. In addition, the plate was covered with a polydimethylsiloxane sheet containing microchannels and automated measurement was carried out.
Development and application of an excitation ratiometric optical pH sensor for bioprocess monitoring
Authors: Badugu Ramachandram , Kostov Yordan , Rao Govind , Tolosa Leah 
Published: December 2008

AbstractThe development of a fluorescent excitation ratiometric pH sensor (AHQ‐PEG) using a novel allylhydroxyquinolinium (AHQ) derivative copolymerized with polyethylene glycol dimethacrylate (PEG) is described. The AHQ‐PEG sensor film is shown to be suitable for real‐time, noninvasive, continuous, online pH monitoring of bioprocesses. Optical ratiometric measurements are generally more reliable, robust, inexpensive, and insensitive to experimental errors such as fluctuations in the source intensity and fluorophore photobleaching. The sensor AHQ‐PEG in deionized water was shown to exhibit two excitation maxima at 375 and 425 nm with a single emission peak at 520 nm. Excitation spectra of AHQ‐PEG show a decrease in emission at the 360 nm excitation and an increase at the 420 nm excitation with increasing pH. Accordingly, the ratio of emission at 420:360 nm excitation showed a maximum change between pH 5 and 8 with an apparent pKa of 6.40. The low pKa value is suitable for monitoring the fermentation of most industrially important microorganisms. Additionally, the AHQ‐PEG sensor was shown to have minimal sensitivity to ionic strength and temperature. Because AHQ is covalently attached to PEG, the film shows no probe leaching and is sterilizable by steam and alcohol. It shows rapid (∼2 min) and reversible response to pH over many cycles without any photobleaching. Subsequently, the AHQ‐PEG sensor film was tested for its suitability in monitoring the pH of S. cereviseae (yeast) fermentation. The observed pH using AHQ‐PEG film is in agreement with a conventional glass pH electrode. However, unlike the glass electrode, the present sensor is easily adaptable to noninvasive monitoring of sterilized, closed bioprocess environments without the awkward wire connections that electrodes require. In addition, the AHQ‐PEG sensor is easily miniaturized to fit in microwell plates and microbioreactors for high‐throughput cell culture applications.
Bioprocess optimization using design‐of‐experiments methodology
Authors: Mandenius Carl‐Fredrik , Brundin Anders 
Published: December 2008

AbstractThis review surveys recent applications of design‐of‐experiments (DoE) methodology in the development of biotechnological processes. Methods such as factorial design, response surface methodology, and (DoE) provide powerful and efficient ways to optimize cultivations and other unit operations and procedures using a reduced number of experiments. The multitude of interdependent parameters involved within a unit operation or between units in a bioprocess sequence may be substantially refined and improved by the use of such methods. Other bioprocess‐related applications include strain screening evaluation and cultivation media balancing. In view of the emerging regulatory demands on pharmaceutical manufacturing processes, exemplified by the process analytical technology (PAT) initiative of the United States Food and Drug Administration, the use of experimental design approaches to improve process development for safer and more reproducible production is becoming increasingly important. Here, these options are highlighted and discussed with a few selected examples from antibiotic fermentation, expanded bed optimization, virus vector transfection of insect cell cultivation, feed profile adaptation, embryonic stem cell expansion protocols, and mammalian cell harvesting.
Assessment of potential life‐cycle energy and greenhouse gas emission effects from using corn‐based butanol as a transportation fuel
Authors: Wu May , Wang Michael , Liu Jiahong , Huo Hong 
Published: December 2008

AbstractSince advances in the ABE (acetone‐butanol‐ethanol) fermentation process in recent years have led to significant increases in its productivity and yields, the production of butanol and its use in motor vehicles have become an option worth evaluating. This study estimates the potential life‐cycle energy and emission effects associated with using bio‐butanol as a transportation fuel. It employs a well‐to‐wheels (WTW) analysis tool: the Greenhouse Gases, Regulated Emissions, and Energy Use in Transportation (GREET) model. The estimates of life‐cycle energy use and greenhouse gas (GHG) emissions are based on an Aspen Plus® simulation for a corn‐to‐butanol production process, which describes grain processing, fermentation, and product separation. Bio‐butanol‐related WTW activities include corn farming, corn transportation, butanol production, butanol transportation, and vehicle operation. In this study, we also analyzed the bio‐acetone that is coproduced with bio‐butanol as an alternative to petroleum‐based acetone. We then compared the results for bio‐butanol with those of conventional gasoline. Our study shows that driving vehicles fueled with corn‐based butanol produced by the current ABE fermentation process could result in substantial fossil energy savings (39%–56%) and avoid large percentage of the GHG emission burden, yielding a 32%–48% reduction relative to using conventional gasoline. On energy basis, a bushel of corn produces less liquid fuel from the ABE process than that from the corn ethanol dry mill process. The coproduction of a significant portion of acetone from the current ABE fermentation presents a challenge. A market analysis of acetone, as well as research and development on robust alternative technologies and processes that minimize acetone while increase the butanol yield, should be conducted.
A hybrid model of anaerobic E. coli GJT001: Combination of elementary flux modes and cybernetic variables
Authors: Kim Jin Il , Varner Jeffery D. , Ramkrishna Doraiswami 
Published: December 2008

AbstractFlux balance analysis (FBA) in combination with the decomposition of metabolic networks into elementary modes has provided a route to modeling cellular metabolism. It is dependent, however, on the availability of external fluxes such as substrate uptake or growth rate before estimates can become available of intracellular fluxes. The framework classically does not allow modeling of metabolic regulation or the formulation of dynamic models except through dynamic measurement of external fluxes. The cybernetic modeling approach of Ramkrishna and coworkers provides a dynamic framework for modeling metabolic systems because of its focus on describing regulatory processes based on cybernetic arguments and hence has the capacity to describe both external and internal fluxes. In this article, we explore the alternative of developing hybrid models combining cybernetic models for the external fluxes with the flux balance approach for estimation of the internal fluxes. The approach has the merit of the simplicity of the early cybernetic models and hence computationally facile while also providing detailed information on intracellular fluxes. The hybrid model of this article is based on elementary mode decomposition of the metabolic network. The uptake rates for the various elementary modes are combined using global cybernetic variables based on maximizing substrate uptake rates. Estimation of intracellular metabolism is based on its stoichiometric coupling with the external fluxes under the assumption of (pseudo‐) steady state conditions. The set of parameters of the hybrid model was estimated with the aid of nonlinear optimization routine, by fitting simulations with dynamic experimental data on concentrations of biomass, substrate, and fermentation products. The hybrid model estimations were tested with FBA (based on measured substrate uptake rate) for two different metabolic networks (one is a reduced network which fixes ATP contribution to the biomass and maintenance requirement of ATP, and the other network is a more complex network which has a separate reaction for maintenance.) for the same experiment involving anaerobic growth of E. coli GJT001. The hybrid model estimated glucose consumption and all fermentation byproducts to better than 10%. The FBA makes similar estimations of fermentation products, however, with the exception of succinate. The simulation results show that the global cybernetic variables alone can regulate the metabolic reactions obtaining a very satisfactory fit to the measured fermentation byproducts. In view of the hybrid model's ability to predict biomass growth and fermentation byproducts of anaerobic E. coli GJT001, this reduced order model offers a computationally efficient alternative to more detailed models of metabolism and hence useful for the simulation of bioreactors.