bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening of Insect Cell Lines for the Production of Recombinant Proteins and Infectious Virus in the Baculovirus Expression System
Authors: Wickham T. J. , Davis T. , Granados R. R. , Shuler M. L. , Wood H. A.
Published: March 2005

Eight cell lines derived from the insects Spodoptera frugiperda, Trichoplusia ni, Mamestra brassicae, and Estigmene acrea were evaluated for recombinant β‐galac‐tosidase and infectious virus production following infection with the baculovirus Autographa californica multiple nuclear polyhedrosis virus (AcMNPV). Production was assessed on a specific (per cell and per microgram of uninfected cellular protein) and on a volumetric (per milliliter) basis. Cell density was found to be an important factor in comparing the cell lines due to a density‐dependent inhibition of specific protein and virus production that appeared to result from cell‐cell contact. After infection of cells at low‐density specific β‐galactosidase production per cell would drop between β‐ and 6‐fold in five of the eight cell lines when plated on tissue culture plates at near‐confluent and confluent cell densities. The cell lines Sf 21 and Sf 9 were least sensitive to cell density. After accounting for cell density effects and differences in cell size, two cell lines, BTI Tn 5B1‐4 and BTI TnM, were identified that were superior to the other cell lines, including Sf 21 and Sf 9, in β‐galactosidase production. Optimal volumetric and specific β‐galactosidase production from Tn 5B1‐4 and TnM cells was 2‐fold and 5‐fold higher, respectively, in both cell lines than the optimal production from Sf 9 or Sf 21 cells. The Tn 5B1‐4 cell line also had the highest viability of all the cell lines at 3 days postinfection and could be adapted to serum‐free media. Specific (per microgram of cellular protein) infectious virus production between cell lines varied by less than 2‐fold between cell lines after cell size differences were taken into account. No correlation was found between recombinant protein and NOV production although both were found to decrease similarly with increasing cell density.
Fluctuations in Continuous Mammalian Cell Bioreactors with Retention
Authors: Vits Hugo , Hu Wei‐Shou
Published: March 2005

Continuous flow bioreactors with cell retention have been increasingly used for the cultivation of mammalian cells. The potential advantages of such bioreactors are high cell concentrations and volumetric productivities. In many reported cases, these systems have shown fluctuations in cell concentrations of various frequency and magnitude. To analyze the dynamics of the fluctuations, a model‐based approach is followed. Simulations showed that large fluctuations in biomass resulted in response to fluctuations in the retention ratio when the system is operated at high dilution rate and high cell retention. The dependence of cell concentration fluctuations on variations in dilution rate and retention ratio was established by a cross‐correlation statistical analysis on available experimental data. The slower dynamics and the fluctuation propensity of retention systems suggest that continuous culture without retention is more convenient for kinetic studies. In all likelihood, continuous culture with retention can be stabilized by controlling both the retention ratio and the dilution rate.
Inactivation of Saccharomyces cerevisiae by Supercritical and Subcritical Carbon Dioxide
Authors: Lin Ho‐Mu , Yang Zhiying , Chen Li‐Fu
Published: March 2005

Yeast cells were inactivated by carbon dioxide at subcritical and supercritical temperatures over the pressure range of 1000–3000 psi. A static apparatus was developed for the experiments. The results showed that a maximum of 15 min, depending on the pressure, was sufficient to inactivate yeast cells by 107‐fold under supercritical conditions. Subcritical carbon dioxide was found to be much less effective. It took 30–40 min to achieve inactivation of 104‐fold and more than 1 h to achieve inactivation of 107‐fold. There are two distinct mechanisms in the deactivation of yeast cells. The rate of cell inactivation is slow at first and increases drastically at the later stage, suggesting that the penetration of CO2 into microbial cells was a primary controlling factor of the inactivation process. The inactivation rate was enhanced remarkably by a series of pressure release/recompression of CO2 in the midst of a complete experiment. Other methods to improve the efficiency of inactivation are discussed.
Mass Transfer in an Airlift Reactor with a Net Draft Tube
Authors: Wu Wen‐Teng , Wu Jiumn‐Yih , Jong Jian‐Zhong
Published: March 2005

Gas–liquid mass transfer in an airlift reactor with net draft tube is investigated. The effects of both the ratio of draft tube to reactor diameter and the reactor pressure on oxygen transfer are considered. The value of the volumetric mass transfer coefficient, kLa, increases with a decreasing diameter ratio at higher air flow rates. The correlation of volumetric mass transfer coefficient with respect to the true superficial air velocity under different reactor pressures is determined. The kLa value decreases with increasing reactor pressure.
On‐Line Assessment of Metabolic Activities Based on Culture Redox Potential and Dissolved Oxygen Profiles During Aerobic Fermentation
Authors: Kwong Simon C. W. , Randers Lisa , Rao Govind
Published: March 2005

We report here on the utility of on‐line culture redox potential and dissolved oxygen measurements to identify metabolic changes in fermentation by Corynebacterium glutamicum under aerobic conditions. Metabolic changes were identified by observing discrepancies in the profile of culture redox potential and dissolved oxygen. On the basis of these measurements, we can identify the end of the lag phase, threonine exhaustion, and glucose exhaustion during fermentation.
Altered Distribution of Mitochondria and Actin Fibers in 3T3 Cells Cultured on Microcarriers
Authors: Laney Tracey V.Du , Cherry Robert S. , Coppinger Justine A. , Truskey George A.
Published: March 2005

The mitochondria and actin fibers of 3T3 fibroblasts cultured on microcarriers in spinner flasks were visualized using fluorescent stains. In contrast to cells grown on planar surfaces under static or steady laminar flow conditions, cells exposed to higher levels of turbulent agitation do not form actin stress fibers. Greater agitation also leads to a more diffuse appearance of the mitochondria and a wider distribution of them throughout the cytoplasm. This response may indicate damaged mitochondria, as similar results have been reported for chemical toxins.
A Correlation for the Effective Strength of Escherichia coli during Homogenization
Authors: Middelberg Anton P. J. , O'Neill Brian K.
Published: March 2005

A new model for high‐pressure homogenization has been previously developed. A key model parameter, the mean effective cell strength, can be correlated with average cell length and peptidoglycan cross‐linkage. In this article, we develop a correlation for mean effective strength based on a statistical thermodynamic approach to fracture. The final correlation provides an unbiased estimate. While it offers no numerical advantage over a previous empirical correlation, it is based on a modeling approach and an understanding of wall structure. The variable groupings are therefore justifiable.
Complex Coacervate Microcapsules for Mammalian Cell Culture and Artificial Organ Development
Authors: Matthew Howard W. , Salley Steven O. , Peterson Ward D. , Klein Michael D.
Published: March 2005

A number of combinations of anionic and cationic polymers, the majority being polysaccharides, were screened to determine their suitability for the development of alternative microcapsule formulations capable of supporting cells. The capsules were taken through a limited optimization and then evaluated on the bases of rupture strength, permeability to albumin, and ability of their components to promote the attachment, aggregation, and function of encapsulated rabbit hepatocytes. The widely used alginate—polylysine capsules were employed as a comparative standard in all tests. A number of the new formulations compared favorably with the standard, and some exhibited superior performance in specific areas. Hepatocyte function, as evaluated by the rate of urea synthesis, showed no significant differences between formulations over a 24‐h test period. One formulation, composed of the polysaccharides (carboxymethyl) cellulose, chondroitin sulfate A, chitosan, and polygalacturonate, was found to be superior to alginate—polylysine capsules in the areas investigated and supported the long‐term survival and growth of liver endothelial cells.
Production of Poly(hydroxybutyrate) Homopolymer and Copolymer from Ethanol and Propanol in a Fed‐Batch Culture
Authors: Alderete Jason E. , Karl Daniel W. , Park Chang‐Ho
Published: March 2005

Production of poly (hydroxy butyrate) (PHB) homopolymer and poly(hydroxybutyrate‐valerate) (PHBV) copolymer by a mutant strain of Alcaligenes eutrophus was studied in a 7‐L fed‐batch fermentor using ethanol and propan‐1‐o1 as sole carbon sources. Decreasing the initial phosphate concentration to 20% of the original Repaske medium allowed exhaustion of the phosphate during logarithmic growth and was an effective means of PHB(V) induction. Up to 74% PHB by weight was obtained with 63 g/L of dry cell mass. The copolymer content increased with a higher fraction of propan‐1‐o1 in the feed and reached a maximum of 35.2 mol % from pure propan‐1‐o1. Gradual oxygen limitation during the late log phase induced 21.9% PHB by weight.
Sustaining Protein Synthesis in the Absence of Rapid Cell Division: An Investigation of Plasmid‐Encoded Protein Expression inEscherichia coliduring Very Slow Growth
Authors: Flickinger Michael C. , Rouse Michael P.
Published: March 2005

The minimum growth rate capable of supporting plasmid‐encoded gene expression is determined using continuous cultures ofEscherichia coliMZ9387 at dilution rates (D) as low as 5% of the maximum specific growth rate. Expression from a low copy number plasmid, pMPR166, encoding cyanase under the control of Placis investigated in order to study plasmid‐encoded gene expression under conditions approaching starvation. Plasmid copy number was stabilized by selection in the presence of 500 μg/raL chloramphenicol by constitutive expression of chloramphenicol acetyl transferase (CAT). Plasmid retention was determined by dot‐blot hybridization and chloramphenicol resistance. The contribution of plasmid maintenance and cyanase expression to the maximum cell yield (Y′x/s) and the maintenance coefficient (ms) was determined for MZ9387 and MZ9387: pMPR166 under uninduced and IPTG‐induced conditions. The values ofYx/sand msfor non‐plasmid‐bearing cultures were 0.56 g of cell dry mass (DCM)/g of glucose and 0.26 g of glucose/g of DCM·h, respectively. The cell yield for plasmid‐bearing cultures under uninduced conditions (Y′x/s) was 0.28 g of DCM/g of glucose, with m°s= 0.08 g of glucose/g of DCM·h. These values decreased following induction of cyanase expression. Glucose consumption in the presence of IPTG was linearly related to the growth rate atD< 0.28 h−1but nonlinear at dilution rates greater than 50% of the maximum specific growth rate, indicating that cyanase expression alters metabolism and glucose consumption. The fraction of plasmid‐free cells decreased with decreasing Damköhler number (Da). These data confirm the usefulness ofDafor predicting the relationship between plasmid‐free and plasmid‐bearing cells where plasmids are stabilized by concentrations of antibiotic greater than the minimum plasmid‐free host cell growth inhibitory concentration. Specific cyanase expression increased as the dilution rate decreased toD= 0.15 h−1. BetweenD= 0.15 h−1andD= 0.14 h−1, expression decreased 7‐fold. At very low dilution rates (D≤ 0.06 h−1), nonseptated filamentous cells appeared. The appearance of filamentous cells could be reversed by increasing the dilution rate. These data are evidence that when plasmid copy number is stabilized by chloramphenicol resistance, a minimum dilution rate exists below which stringent regulation of protein synthesis dramatically reduces gene expression.
Effect of Water Content on the Glass Transition and Caking of Fish Protein Hydrolyzates
Authors: Aguilera Jose M. , Levi Guy , Karel Marcus
Published: March 2005

The glass transition temperature (Tg) and structure collapse (volumetric shrinkage) of a freeze‐dried fish protein hydrolyzate (HFP) were studied. An increase in the water activity from 0 to 0.64 reduced the Tg of HFP from 79.1 to −42.8 °C. The Gordon—Taylor equation was a good predictor for the plasticizing effect of water on Tg. At room temperature (19 °C), collapse was initiated at aw = 0.44 corresponding to a T — Tg value of 35.8 °C, and browning was evident above aw = 0.55. Above these critical values several structural changes occurred: shrinkage, collapse, browning, and setting into a sticky, high‐viscosity brown liquid. The viscosity of the matrix at the onset of collapse was 105–107 Pa·s, as estimated using the Williams—Landel—Ferry equation.
Effects of Abrupt and Gradual Osmotic Stress on Antibody Production and Content in Hybridoma Cells That Differ in Production Kinetics
Authors: Reddy Sridhar , Miller William M.
Published: March 2005

AB2‐143.2 cells exhibit non‐growth‐associated antibody production (constant specific antibody production rate (qAb) throughout batch culture), while IND1 cells exhibit growth‐associated production (decrease in qAb during stationary phase). AB2‐143.2 cells increase qAb following abrupt batch osmotic stress. Enhanced antibody production in IND1 cells after batch osmotic shock is evidenced as maintenance of the higher exponential phase QAb into the stationary phase. AB2‐143.2 cells also increase qAb in response to gradual osmotic stress in continuous culture. In contrast, IND1 cells decrease 9Ab during gradual osmotic stress. Although the two cell lines differ in antibody production, they have very similar intracellular antibody content profiles. Both show (1) constant antibody content during the exponential phase in control culture with a decrease as cells enter stationary phase; (2) maintenance of exponential‐phase antibody content into the stationary phase after batch osmotic shock; and (3) no change in antibody content in response to gradual osmotic stress.
Characterization and Polyelectrolyte Precipitation of β‐Galactosidase Containing Genetic Fusions of Charged Polypeptides
Authors: Niederauer Mark Q. , Suominen Ilari , Rougvie Malcolm A. , Ford Clark F. , Glatz Charles E.
Published: March 2005

Genetically engineered versions of β‐galactosidase were constructed through the addition of charged polypeptide fusion tails for the purpose of enhancing polyelectrolyte precipitation. Negatively charged aspartic acid tails and positively charged poly(arginine) tails were added to β‐galactosidase from Escherichia coli. These fusion proteins were all shown to possess specific activity equal to that of the native enzyme. Gel permeation and ion‐exchange chromatography provided evidence concerning the integrity of the tails as well as their altered charge characteristics. All enzymes containing charged tails displayed enhanced polyelectrolyte precipitation over the native enzyme. An optimal number of charged residues, beyond which no further enhancement of precipitation was observed, was found to be approximately 10 residues for each type of tail. No interference from nucleic acids was observed in the precipitation of positively tailed β‐galactosidase.
Effect of Sodium Hydroxide on the Solubilities of L‐Isoleucine, L‐Leucine, and L‐Valine
Authors: Brown Marena Gatewood , Rousseau Ronald W.
Published: March 2005

The solubilities of L‐isoleucine, L‐leucine, and L‐valine in aqueous solutions containing sodium hydroxide were determined. In all cases, the solubility increased as the solution pH was increased above the isoelectric point, and then it decreased sharply with further additions of base, after 1 mol of NaOH/mol of amino acid was added to the solution.
Effects of Carbon Dioxide, Air Flow Rate, and Inoculation Density on the Batch Growth of Catharanthus roseus Cell Suspensions in Stirred Fermentors
Authors: Van Gulik Walter M. , Nuutila Anna Maria , Vinke Ko L. , Ten Hoopen Hens J. G. , Heijnen Joseph J.
Published: March 2005

A high reproducibility of batch growth of Catharanthus roseus could only be achieved by using identical inoculum material. It was found that the initial growth rate of the cells increased with increasing inoculation density, whereas the maximum growth rate was not affected. Withdrawal of the conditioned medium from the inoculum resulted in a strong decline in the initial growth rate, indicating that conditioning factors affected the initial growth rate. Neither increasing the air flow rate from 0.5 to 1.5 volume of air per volume of broth‐min−1 (vvm) nor CO2 enrichment of the aeration gas had any effect on the growth of the cells.
In Pursuit of the Optimal Fed‐Batch Process for Monoclonal Antibody Production
Authors: Bibila Theodora A. , Robinson David K.
Published: March 2005

Fed‐batch culture currently represents the most attractive choice for large scale production of monoclonal antibodies (MAbs), due to its operational simplicity, reliability, and flexibility for implementation in multipurpose facilities. Development of highly productive cell lines, maximization of cell culture longevity, and maintenance of high specific antibody secretion rates through genetic engineering techniques, nutrient supplementation, waste product minimization, and control of environmental conditions are important for the design of high‐yield fed‐batch processes. Initially simple supplementation protocols have evolved into sophisticated serum‐free multi‐nutrient feeds that result in MAb titers on the order of 1–2 g/L. Limited research has been published to date on the effects of various culture parameters on potentially important quality issues, such as MAb glycosylation and stability. Although most fed‐batch protocols to date have relied on relatively simple control schemes, increasingly sophisiticated algorithms must be applied in order to take full advantage of the potentially additive effects of manipulating nutrient and environmental parameters to maximize fed‐batch process productivity.
Protective Effects of Polymer Additives on Animal Cells Exposed to Rapidly Falling Liquid Films
Authors: Wu Jianyong , Daugulis Andrew J. , Faulkner Peter , Goosen Mattheus F. A.
Published: March 2005

The protective effects of polymer additives on insect cells against fluid mechanical damage was investigated in a falling film‐flow device. The falling liquid film creates rapidly moving air&β;liquid interfaces and high fluid shear stress, mimicking the characteristics of a bursting bubble in aerated cell culture. The additives tested included a group of surface‐active polymers, (i. e., Pluronic F68, poly(ethylene glycol)s, and Tween 80) and a group of viscosity‐enhancing polymers (i. e., dextrans, methyl‐cellulose, and (carboxymethyl)cellulose). We found that methylcellulose, which was previously considered a viscosity‐enhancing polymer, actually had significant surface‐active properties. All of the surface‐active polymers exhibited significant protective effects, with Pluronic F68 and the higher molecular weight poly(ethylene glycol), PEG 20M, providing the best protection. In contrast, the viscosity‐enhancing polymers, with the exception of methylcellulose, showed little or no protection for insect cells in the film flow. All of the protective polymers had surface‐active properties, even though some of them did not change the surface tension in the actual insect cell medium. There was no correlation between the protective effect and the changes in liquid viscosity and surface tension due to the polymer additives. The level of protection was shown to be dependent upon the type of polymer, its concentration in the culture medium, and the polymer molecular weight. We concluded that the mechanism of protection of these surface‐active polymers was through interaction of the polymer molecules with the cell plasma membranes: a fast‐acting biological mechanism.
Improved Homogenization of Recombinant Escherichia coli following Pretreatment with Guanidine Hydrochloride
Authors: Bailey Stuart M. , Blum Paul H. , Meagher Michael M.
Published: March 2005

Pretreatment of recombinant Escherichia coli, expressing human growth hormone inclusion bodies, with guanidine hydrochloride and Triton X‐100 prior to high‐pressure homogenization has been investigated. Homogenates were analyzed for protein release, viscosity, and particle size. We were able to reduce the number of passes required for cell disruption and the number of downstream processing steps required for the recovery of protein from inclusion bodies by pretreating cells with guanidine HCl and Triton X‐100. Pretreatment of exponential growth phase cells with 1.5 M guanidine HCl and 1.5% Triton X‐100 gave adequate disruption after one pass at 41 MPa with a particle size distribution similar to that for untreated cells disrupted after one pass at 62 MPa. This combination of guanidine HCl and Triton X‐100 was also selected so as to wash the inclusion bodies without solubilization of the human growth hormone. Pretreatment of cells with 4 M guanidine HCl produced cell debris that was substantially smaller than the debris from untreated cells and partially solubilized the inclusion bodies. Cells harvested in the stationary growth phase were more resistant to high‐pressure homogenization and pretreatment.
Evaluation of UNIFAC for the Prediction of Partitioning in Two‐Phase Aqueous‐Organic Systems Containing Amino Acids and Oligomers
Authors: Roberts Jason D. , Daugulis Andrew J.
Published: March 2005

Ternary liquid‐liquid equilibria were predicted by the UNIFAC method for organic/aqueous biphasic systems containing amino acids and amino acid oligomers composed of glycine, alanine, phenylalanine, and tyrosine. UNIFAC was used to screen solvents for use as potential extractants, and UNIFAC‐calculated distribution coefficients were compared to data obtained experimentally. UNIFAC identified some novel extractants from a larger database of solvents. Distribution into the organic phase generally increased with the degree of polymerization of the oligomers. The presence of nonpolar residues in oligomers was found to decrease extraction over hydrophobic species alone. It was concluded that the polarity of the amide backbone and the zwitterion effects were significant in reducing the hydrophobicity of the side chains.
Grain fracture in 3D numerical simulations of granular shear
Authors: Abe Steffen , Mair Karen
Published: March 2005

We present a new method to implement realistic grain fracture in 3D numerical simulations of granular shear. We use a particle based model that includes breakable bonds between individual particles allowing the simulation of fracture of large aggregate grains during shear. Grain fracture simulations produce a comminuted granular material that is texturally comparable to natural and laboratory produced fault gouge. Our model is initially characterized by monodisperse large aggregate grains and gradually evolves toward a fractal distribution of grain sizes with accumulated strain. Comminution rate and survival of large grains is sensitive to applied normal stress. The fractal dimension of the resultant grain size distributions (2.3 ± 0.3 and 2.9 ± 0.5) agree well with observations of natural gouges and theoretical results that predict a fractal dimension of 2.58.
Myricetin, quercetin and catechin-gallate inhibit glucose uptake in isolated rat adipocytes
Authors: STROBEL Pablo , ALLARD Claudio , PEREZ-ACLE Tomás , CALDERON Rosario , ALDUNATE Rebeca , LEIGHTON Federico
Published: March 2005

The facilitative glucose transporter, GLUT4, mediates insulin-stimulated glucose uptake in adipocytes and muscles, and the participation of GLUT4 in the pathogenesis of various clinical conditions associated with obesity, visceral fat accumulation and insulin resistance has been proposed. Glucose uptake by some members of the GLUT family, mainly GLUT1, is inhibited by flavonoids, the natural polyphenols present in fruits, vegetables and wine. Therefore it is of interest to establish if these polyphenolic compounds present in the diet, known to be effective antioxidants but also endowed with several other biological activities such as protein-tyrosine kinase inhibition, interfere with GLUT4 function. In the present study, we show that three flavonoids, quercetin, myricetin and catechin-gallate, inhibit the uptake of methylglucose by adipocytes over the concentration range of 10–100 μM. These three flavonoids show a competitive pattern of inhibition, with Ki=16, 33.5 and 90 μM respectively. In contrast, neither catechin nor gallic acid inhibit methylglucose uptake. To obtain a better understanding of the interaction among GLUT4 and flavonoids, we have derived a GLUT4 three-dimensional molecular comparative model, using structural co-ordinates from a GLUT3 comparative model and a mechanosensitive ion channel [PDB (Protein Data Bank) code 1MSL] solved by X-ray diffraction. On the whole, the experimental evidence and computer simulation data favour a transport inhibition mechanism in which flavonoids and GLUT4 interact directly, rather than by a mechanism related to protein-tyrosine kinase and insulin signalling inhibition. Furthermore, the results suggest that GLUT transporters are involved in flavonoid incorporation into cells.
Interaction of the endothelial nitric oxide synthase with the CAT-1 arginine transporter enhances NO release by a mechanism not involving arginine transport
Authors: LI Chunying , HUANG Wei , HARRIS M. Brennan , GOOLSBY Jonathan M. , VENEMA Richard C.
Published: March 2005

eNOS (endothelial nitric oxide synthase) catalyses the conversion of L-arginine into L-citrulline and NO. Evidence has been presented previously that eNOS is associated with the CAT (cationic amino acid transporter)-1 arginine transporter in endothelial caveolae, and it has been proposed that eNOS–CAT-1 association facilitates the delivery of extracellular L-arginine to eNOS. Definitive proof of a protein–protein interaction between eNOS and CAT-1 is lacking, however, and it is also unknown whether the two proteins interact directly or via an adaptor protein. In the present study, we raised a polyclonal antibody against CAT-1, and show using reciprocal co-immunoprecipitation protocols that eNOS and CAT-1 do indeed form a complex in BAECs (bovine aortic endothelial cells). In vitro binding assays with GST (glutathione S-transferase)–CAT-1 fusion proteins and eNOS show that the two proteins interact directly and that no single CAT-1 intracellular domain is sufficient to mediate the interaction. Overexpression of CAT-1 in BAECs by adenoviral-mediated gene transfer results in significant increases in both L-arginine uptake and NO production by the cells. However, whereas increased L-arginine transport is reversed completely by the CAT-1 inhibitor, L-lysine, increased NO release is unaltered, suggesting that NO production in this in vitro model is independent of CAT-1-mediated transport. Furthermore, eNOS enzymic activity is increased in lysates of CAT-1-overexpressing cells accompanied by increased phosphorylation of eNOS at Ser-1179 and Ser-635, and decreased association of eNOS with caveolin-1. Taken together, these data suggest that direct interaction of eNOS with CAT-1 enhances NO release by a mechanism not involving arginine transport.
Structure-based mutagenesis studies of the peptide substrate binding fragment of type I heat-shock protein 40
Authors: LI Jingzhi , SHA Bingdong
Published: March 2005

Ydj1 is the major type I Hsp40 (heat-shock protein 40) family member in yeast. Ydj1 can pair with yeast Hsp70 Ssa1 to facilitate protein translocation and protein folding. Ydj1 itself can also function as a molecular chaperone to bind the non-native polypeptides and suppress protein aggregations in vitro. The crystal structure of Ydj1 complexed with its peptide substrate GWLYEIS reveals that a hydrophobic pocket located on Ydj1 domain I may play a major role in mediating the interactions between Ydj1 and the peptide substrate. To understand the mechanism by which Ydj1 interacts with non-native polypeptide, we have mutated the residues forming the hydrophobic pocket, based on the structural information. We have also constructed deletion mutations of the zinc-finger motifs within Ydj1. We have examined the functional consequences of these Ydj1 mutants by in vivo and in vitro assays. The results indicated that the hydrophobic pocket located on Ydj1 plays a critical role in its molecular chaperone activity by mediating interactions with the non-native polypeptides.
Manganese toxicity and Saccharomyces cerevisiae Mam3p, a member of the ACDP (ancient conserved domain protein) family
Authors: YANG Mei , JENSEN Laran T. , GARDNER Allison J. , CULOTTA Valeria C.
Published: March 2005

Manganese is an essential, but potentially toxic, trace metal in biological systems. Overexposure to manganese is known to cause neurological deficits in humans, but the pathways that lead to manganese toxicity are largely unknown. We have employed the bakers' yeast Saccharomyces cerevisiae as a model system to identify genes that contribute to manganese-related damage. In a genetic screen for yeast manganese-resistance mutants, we identified S. cerevisiae MAM3 as a gene which, when deleted, would increase cellular tolerance to toxic levels of manganese and also increased the cell's resistance towards cobalt and zinc. By sequence analysis, Mam3p shares strong similarity with the mammalian ACDP (ancient conserved domain protein) family of polypeptides. Mutations in human ACDP1 have been associated with urofacial (Ochoa) syndrome. However, the functions of eukaryotic ACDPs remain unknown. We show here that S. cerevisiae MAM3 encodes an integral membrane protein of the yeast vacuole whose expression levels directly correlate with the degree of manganese toxicity. Surprisingly, Mam3p contributes to manganese toxicity without any obvious changes in vacuolar accumulation of metals. Furthermore, through genetic epistasis studies, we demonstrate that MAM3 operates independently of the well-established manganese-trafficking pathways in yeast, involving the manganese transporters Pmr1p, Smf2p and Pho84p. This is the first report of a eukaryotic ACDP family protein involved in metal homoeostasis.
Positron beam studies of argon-irradiated polycrystal α-Zr
Authors: Zhou Chunlan , Liu Xiaoyang , Ma Chuangxin , Wang Baoyi , Zhang Zhiming , Wei Long
Published: March 2005

Doppler broadening spectroscopy was performed using a variable-energy positron beam to investigate the effect of defects induced by 150-keV Ar-ion-irradiated α-Zr bulk material. S parameter in the damaged layer of the as-irradiated sample induced by ion irradiation increased with the increasing implantation dose. Isochronal annealing between 350 and 800°C in vacuum studies was carried out to investigate the thermal stability of defects in the oxide surface and damaged layer for low-dose (1×1014cm2) and high-dose (1×1016cm2) irradiated samples. The results of S-W plot measured at different annealing temperatures showed that the positron-trapping center had changed. The Ar-decorated voids or vacancies, which formed in high-dose implantation samples by Ar ions combining with open-volume defects, are stable and do not recover until at high annealing temperatures. Comparing the annealing behavior of the high-dose and low-dose implantation samples show that the recovery process of open-volume defects such as vacancies and voids will be delayed by the excess Ar concentration.
Ultrafast far-infrared dynamics probed by terahertz pulses: A frequency domain approach. I. Model systems
Authors: Němec H. , Kadlec F. , Surendran S. , Kužel P. , Jungwirth P.
Published: March 2005

Time-resolved terahertz spectroscopy has become a widely used experimental tool for the investigation of ultrafast dynamics of polar systems in the far infrared. We have recently proposed an analytical method for the extraction of a transient two-dimensional susceptibility from the experimental data [Němec, Kadlec, and Kužel, J. Chem. Phys. 117, 8454 (2002)]. In the present paper the methodology of optical pump-terahertz probe experiments is further developed for direct application in realistic experimental situations. The expected two-dimensional transient response function is calculated for a number of model cases (including Drude dynamics of free carriers, harmonic and anharmonic oscillator modes); these results serve as a basis for the interpretation of experimental results. We discuss also the cases where only partial (one-dimensional) information about the system dynamics can be experimentally obtained.
Polymerization dynamics of double-stranded biopolymers: Chemical kinetic approach
Authors: Stukalin Evgeny B. , Kolomeisky Anatoly B.
Published: March 2005

The polymerization dynamics of double-stranded polymers, such as actin filaments, is investigated theoretically using simple chemical kinetic models that explicitly take into account some microscopic details of the polymer structure and the lateral interactions between the protofilaments. By considering all possible molecular configurations, the exact analytical expressions for the growth velocity and dispersion for two-stranded polymers are obtained in the case of the growing at only one end, and for the growth from both polymer ends. Exact theoretical calculations are compared with the predictions of approximate multilayer models that consider only a finite number of the most relevant polymer configurations. Our theoretical approach is applied to analyze the experimental data on the growth and fluctuations dynamics of individual single actin filaments.
Proton conduction along a chain of water molecules. Development of a linear model and quantum dynamical investigations using the multiconfiguration time-dependent Hartree method
Authors: Vendrell Oriol , Meyer Hans-Dieter
Published: March 2005

Proton transfer along a chain of water molecules is discussed. A linear model for such a chain is developed and its parameters are determined by comparison to quantum chemistry calculations. Fully quantum mechanical dynamical simulations on the translocation process are performed for different chain lengths, with up to five water molecules. We found that tunneling is important for the proton-transfer process. Furthermore, translocation is accomplished through a strongly correlated motion involving both hydrogen and oxygen atoms. An approximate treatment, which limits or even neglects this correlation, may lead to severely incorrect results.
Polarity effect of electromigration on kinetics of intermetallic compound formation in Pb-free solder V-groove samples
Authors: Gan H. , Tu K. N.
Published: March 2005

Intermetallic compound (IMC) formation is critical for the reliability of microelectronic interconnections, especially for flip chip solder joints. In this article, we investigate the polarity effect of electromigration on kinetics of IMC formation at the anode and the cathode in solder V-groove samples. We use V-groove solder line samples, with width of 100 μm and length of 500–700 μm, to study interfacial IMC growth between Cu electrodes and Sn-3.8Ag-0.7Cu (in wt %) solder under different current density and temperature settings. The current densities are in the range of 103 to 104A∕cm2 and the temperature settings are 120, 150, and 180 °C. While the same types of IMCs, Cu6Sn5 and Cu3Sn, form at the solder∕Cu interfaces independent of the passage of electric current, the growth of the IMC layer has been enhanced by electric current at the anode and inhibited at the cathode, in comparison with the no-current case. We present a kinetic model, based on the Cu mass transport in the sample, to explain the growth rate of IMC at the anode and cathode. The growth of IMC at the anode follows a parabolic growth rule, and we propose that the back stress induced in the IMC plays a significant role. The model is in good agreement with our experimental data. We then discuss the influence of both chemical force and electrical force, and their combined effect on the IMC growth with electric current.
The effect of Fe substitution on pyroelectric properties of 0.62Pb(Mg1∕3Nb2∕3)O3–0.38PbTiO3 single crystals
Authors: Wan Xinming , Chew K.-H. , Chan H. L. W. , Choy C. L. , Zhao Xiangyong , Luo Haosu
Published: March 2005

Fe-doped 0.62Pb(Mg1∕3Nb2∕3)O3–0.38PbTiO3 (PMN–0.38PT) single crystals with two different dopant concentrations, 0.2 and 1.0mol%, were grown by a modified Bridgman technique. The effect of Fe substitution on dielectric and pyroelectric properties was examined. The dielectric constant of the 0.2mol% Fe-doped PMN–0.38PT single crystal was controlled successfully, indicating the possibility of tuning the dielectric properties by doping with a small concentration of iron ions. The mechanism of doping effect was also discussed based on the principles of crystal chemistry. The pyroelectric response of the single crystals was measured using a dynamic method from 20to50°C. Compared with the 1.0mol% Fe-doped single crystal, the 0.2mol% Fe-doped sample possesses the better pyroelectric properties. At room temperature, the pyroelectric coefficient and detectivity figure of merit (FD) for the 0.2mol% Fe-doped sample are 568μC∕m2K and 53μPa−1∕2, respectively, and they increase slightly with temperature increasing. These excellent pyroelectric properties as well as being able to produce large-size and high-quality single crystals make this kind of single crystal a promising candidate for high-performance infrared detectors and other pyroelectric applications.
Microbeam high-resolution x-ray diffraction in strained InGaAlAs-based multiple quantum well laser structures grown selectively on masked InP substrates
Authors: Sirenko A. A. , Kazimirov A. , Huang R. , Bilderback D. H. , O’Malley S. , Gupta V. , Bacher K. , Ketelsen L. J. P. , Ougazzaden A.
Published: March 2005

Structural and optical properties of the InGaAlAs-based multiple quantum well (MQW) 1.3μm laser structures produced on InP (001) substrates by metal organic vapor phase epitaxy (MOVPE) technique in the regime of selective area growth (SAG) have been studied. An x-ray beam of 10μm diameter generated by a microbeam high-resolution x-ray diffraction (μ-HRXRD) setup based on an imaging one-bounce capillary optic and a three-bounce channel cut Si(004) analyzer crystal has been utilized to measure the diffraction curves from MQW structures grown between oxide mask stripes. The high angular resolution achieved in our experiments allowed accurate measurements of θ–2θ scans over a broad range of angles that was necessary for utilization of fitting algorithms for quantitative analysis of the strain and thickness of individual layers in the MQW structures. The thickness and strain variations in the quantum well and the barrier layers of the MQW SAG structure have been analyzed as a function of the oxide mask width in the range of 15–140μm with the gap between the oxide masks in the range of 15–80μm. Dramatic structural changes from the perfect quality MQW’s in the SAG structures with the narrow oxide masks (less than 45μm) to the strain relaxed MQW’s in the SAG regime with the wide oxide masks (more than 50μm) have been experimentally detected. The spontaneous photoluminescence emission between 1.3 and 1.51μm from the simultaneously grown InGaAlAs-based MQW SAG laser structures have been measured. Using a combination of μ-HRXRD results with the microphotoluminescence data, the optimal SAG mask parameters for the growth of integrated InGaAlAs-based optoelectronic light-emitting components and devices have been determined.
Charge transport and recombination in bulk heterojunction solar cells studied by the photoinduced charge extraction in linearly increasing voltage technique
Authors: Mozer A. J. , Sariciftci N. S. , Lutsen L. , Vanderzande D. , Österbacka R. , Westerling M. , Juška G.
Published: March 2005

Charge carrier mobility and recombination in a bulk heterojunction solar cell based on the mixture of poly[2-methoxy-5-(3,7-dimethyloctyloxy)-phenylene vinylene] (MDMO-PPV) and 1-(3-methoxycarbonyl)propyl-1-phenyl-(6,6)-C61 (PCBM) has been studied using the novel technique of photoinduced charge carrier extraction in a linearly increasing voltage (Photo-CELIV). In this technique, charge carriers are photogenerated by a short laser flash, and extracted under a reverse bias voltage ramp after an adjustable delay time (tdel). The Photo-CELIV mobility at room temperature is found to be μ=2×10−4cm2V−1s−1, which is almost independent on charge carrier density, but slightly dependent on tdel. Furthermore, determination of charge carrier lifetime and demonstration of an electric field dependent mobility is presented.
Kerr detected time average of magnetization precession in ferromagnetic resonance
Authors: Meckenstock R. , Möller M. , Spoddig D.
Published: March 2005

In ferromagnetic resonance (FMR), the magnetization precesses around its equilibrium orientation. A conventional magneto-optical Kerr effect (MOKE) setup, was used to detect the time average of the precession of the magnetization. The microwave power was adjusted to the linear precession regime. The different components of the high-frequency magnetization can be discriminated by the choice of the plane of incidence of the light. The use of a conventional FMR cavity setup ensures well defined homogeneous excitation of the magnetization and allows angle dependent measurements. A further benefit of the MOKE detection is the spatial resolution for FMR on a micrometer scale. The samples under investigation were (001)-Fe films on ZnSe covered by ZnSe, which were characterized by conventional angle and frequency dependent FMR as well.
Enhanced performance of bipolar cascade light-emitting diodes by doping the aluminum oxide apertures
Authors: Siskaninetz W. J. , Ehret J. E. , Lott J. A. , Griffith J. C. , Nelson T. R.
Published: March 2005

Performance improvements in multiple-stage, single-cavity bipolar cascade light-emitting diodes including reduced operating voltages, enhanced light generation, and reduced device heating are obtained by doping intracavity aluminum oxide apertures with silicon. This doping results in a reduced electron energy barrier and, therefore, a reduced series resistance which leads to better power and heating characteristics. Nearly 50% reductions in operating voltages, 200% increases in light power, and increased operating range are demonstrated. We discuss the direct implications of these results for the design of bipolar cascade vertical-cavity surface-emitting lasers.
Planned Burn-Piedmont. A local operational numerical meteorological model for tracking smoke on the ground at night: model development and sensitivity tests
Authors: Achtemeier Gary L.
Published: March 2005

Smoke from both prescribed fires and wildfires can, under certain meteorological conditions, become entrapped within shallow layers of air near the ground at night and get carried to unexpected destinations as a combination of weather systems push air through interlocking ridge–valley terrain typical of the Piedmont of the Southern United States. Entrapped smoke confined within valleys is often slow to disperse. When moist conditions are present, hygroscopic particles within smoke may initiate or augment fog formation. With or without fog, smoke transported across roadways can create visibility hazards. Planned Burn (PB)-Piedmont is a fine scale, time-dependent, smoke tracking model designed to run on a PC computer as an easy-to-use aid for land managers. PB-Piedmont gives high-resolution in space and time predictions of smoke movement within shallow layers at the ground over terrain typical of that of the Piedmont. PB-Piedmont applies only for weather conditions when smoke entrapment is most likely to occur––at night during clear skies and light winds. This paper presents the model description and gives examples of model performance in comparison with observations of entrapped smoke collected during two nights of a field project. The results show that PB-Piedmont is capable of describing the movement of whole smoke plumes within the constraints for which the model was designed.
Simulation of the Big Elk Fire using coupled atmosphere - fire modeling
Authors: Coen Janice L.
Published: March 2005

Models that simulate wildland fires span a vast range of complexity; the most physically complex present a difficult supercomputing challenge that cannot be solved fast enough to become a forecasting tool. Coupled atmosphere–fire model simulations of the Big Elk Fire, a wildfire that occurred in the Colorado Front Range during 2002, are used to explore whether some factors that make simulations more computationally demanding (such as coupling between the fire and the atmosphere and fine atmospheric model resolution) are needed to capture wildland fire parameters of interest such as fire perimeter growth. In addition to a Control simulation, other simulations remove the feedback to the atmospheric dynamics and use increasingly coarse atmospheric resolution, including some that can be computed in faster than real time on a single processor. These simulations show that, although the feedback between the fire and atmosphere must be included to capture accurately the shape of the fire, the simulations with relatively coarse atmospheric resolution (grid spacing 100–500 m) can qualitatively capture fire growth and behavior such as surface and crown fire spread and smoke transport. A comparison of the computational performance of the model configured at these different spatial resolutions shows that these can be performed faster than real time on a single computer processor. Thus, although this model still requires rigorous testing over a wide range of fire incidents, it is computationally possible to use models that can capture more complex fire behavior (such as rapid changes in intensity, large fire whirls, and interactions between fire, weather, and topography) than those used currently in the field and meet a faster-than-real-time operational constraint.
Fire spread in chaparral—'go or no-go?'
Authors: Weise David R. , Zhou Xiangyang , Sun Lulu , Mahalingam Shankar
Published: March 2005

Current fire models are designed to model the spread of a linear fire front in dead, small-diameter fuels. Fires in predominantly living vegetation account for a large proportion of annual burned area in the United States. Prescribed burning is used to manage living fuels; however, prescribed burning is currently conducted under conditions that result in marginal burning. We do not understand quantitatively the relative importance of the fuel and environmental variables that determine spread in live vegetation. To address these weaknesses, laboratory fires have been burned to determine the effects of wind, slope, moisture content and fuel characteristics on fire spread in fuel beds of common chaparral species. Four species (Adenostoma fasciculatum, Ceanothus crassifolius, Quercus berberidifolia, Arctostaphylos parryana), two wind velocities (0 and 2 m s−1) and two fuel bed depths (20 and 40 cm) were used. Oven-dry moisture content of fine fuels (<0.63 cm diameter) ranged from 0.09 to 1.06. Seventy of 125 fires successfully propagated the length (2.0 m) of the elevated fuel bed. A logistic model to predict the probability of successful fire spread was developed using stepwise logistic regression. The variables selected to predict propagation were wind velocity, slope percent, moisture content, fuel loading, species and air temperature. Air temperature and species terms were removed from the model for parsimony. The final model correctly classified 94% of the observations. Comparison of results with an empirical decision matrix for prescribed burning in chaparral suggested some agreement between the laboratory data and the empirical tool.