bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wnt signalling: a theme with nuclear variations
Authors: Sharpe Colin , Lawrence Nicola , Arias Alfonso Martinez 
Published: August 2002

AbstractWnt proteins are involved in a large number of events during development and disease. The crucial element in the transduction of the signal elicited by Wnt is the state and activity of β‐catenin. There are two pools of β‐catenin, one associated with cadherins at the cell surface and a soluble one in the cytolasm, whose state and concentration are critical for Wnt signalling. In the absence of Wnt, the cytoplasmic pool is low due to targetted degradation of β‐catenin. Upon Wnt signalling, β‐catenin is stabilized. As a consequence, it can access the nucleus where it interacts with members of the Tcf family of transcription factors to modulate the expression of defined targets. Recent reports indicate that, in addition to Tcfs, β‐catenin can interact with other nuclear proteins raising the possibility that Wnt signalling has a wider modulatory effect on transcription than is mediated by its interactions with Tcfs. BioEssays 23:311–318, 2001. © 2001 John Wiley & Sons, Inc.
Therefore, what are recombination proteins there for?
Authors: Courcelle Justin , Ganesan Ann K. , Hanawalt Philip C. 
Published: August 2002

AbstractThe order of discovery can have a profound effect upon the way in which we think about the function of a gene. In E. coli, recA is nearly essential for cell survival in the presence of DNA damage. However, recA was originally identified, as a gene required to obtain recombinant DNA molecules in conjugating bacteria. As a result, it has been frequently assumed that recA promotes the survival of bacteria containing DNA damage by recombination in which DNA strand exchanges occur. We now know that several of the processes that interact with or are controlled by recA, such as excision repair and translesion synthesis, operate to ensure that DNA replication occurs processively without strand exchanges. Yet the view persists in the literature that recA functions primarily to promote recombination during DNA repair. With the benefit of hindsight and more than three decades of additional research, we reexamine some of the classical experiments that established the concept of DNA repair by recombination, and we consider the possibilities that recombination is not an efficient mechanism for rescuing damaged cells, and that recA may be important for maintaining processive replication in a manner that does not generally promote recombination. BioEssays 23:463–470, 2001. © 2001 John Wiley & Sons, Inc.
Master regulatory genes; telling them what to do
Authors: Baker Nicholas E. 
Published: August 2002

AbstractIn 1995, the eyeless (ey) gene was dubbed the “master‐regulator” of eye development in Drosophila. Not only is ey required for eye development, but its misexpression can convert many other tissues into eye, including legs, wings and antennae.(1) ey is remarkable for its ability to drive coordinate differentiation of the multiple cell types that have to differentiate in a very precise pattern to construct the fly eye, and for its power to override the previous differentiation programs of many other diverse tissues. Even more remarkable, the ey homolog Pax6 and homologs of other eye determination genes from Drosophila are also required for eye development in vertebrates,(2,3) prompting reassessment of the evolution of vision throughout the animal kingdom.(4,5) Now Kumar and Moses have published a study that throws a new light on ey function in Drosophila.(6) According to their work, ey becomes a master regulator of eye development much later than previously thought, and is regulated by signalling through the Notch and EGFR signaling pathways. BioEssays 23:763–766, 2001. © 2001 John Wiley & Sons, Inc.
Extended analysis and treatment of self‐injurious behavior
Authors: Healey John J. , Ahearn William H. , Graff Richard B. , Libby Myrna E. 
Published: August 2002

AbstractIn experiment 1, an extended functional analysis of self‐injury was conducted with a 21‐year‐old male diagnosed with autism and profound mental retardation. The multielement phase yielded undifferentiated results. Subsequent blocking of conditions plus the addition of a component allowing access to multiple sensory stimuli suggested that self‐injury was unrelated to programmed positive or negative reinforcement contingencies. The behavior appeared to be automatically reinforced; its occurrence decreased when access to alternative sensory stimuli was provided. Experiment 2 evaluated a treatment condition in which response‐independent access to these sensory stimuli was provided within the participant's everyday environment. Baseline and treatment frequencies of self‐injury were compared in a combined, multiple‐baseline‐across‐settings and ABAB design. The level of self‐injury decreased substantially during treatment. These results support the use of extended analog analyses of aberrant behavior in instances in which undifferentiated responding occurs in the initial analogue analysis. Additionally, a procedure is described for generalizing the intervention derived from the experimental analysis into the participant's everyday environment. Copyright © 2001 John Wiley & Sons, Ltd.
Behavioral treatments for sleep problems in autism: empirically supported or just universally accepted?
Authors: Schreck Kimberly A. 
Published: August 2002

AbstractWith health maintenance organizations and insurance companies requiring proof of treatment efficacy, clinicians must determine whether research supports commonly used treatment methods. To determine the effectiveness of applied behavior analysis (ABA) for treating sleep problems in children with autism, a computer search of all relevant literature was conducted. The resulting articles revealed four basic themes of behavioral techniques for treating sleep disorders for children with autism: bedtime routines, extinction, stimulus fading, and faded bedtimes. Research on each technique was evaluated based on the Chambless criteria of treatment efficacy (Chambless and Hollon, 1998; Lonigan, Elbert, and Johnson, 1998). Of the ABA methods, only research on extinction provided sufficient evidence for a possibly efficacious intervention for sleep problems in children with autism. However, the lack of available research indicates significantly more research must be conducted before endorsing other ABA methods. Copyright © 2001 John Wiley & Sons, Ltd.
Molecular dynamics simulations of α2 → 8‐linked disialoside: Conformational analysis and implications for binding to proteins
Authors: Vasudevan Sheeja V. , Balaji Petety V. 
Published: August 2002

AbstractComputational methods have played a key role in elucidating the various three‐dimensional structures of oligosaccharides. Such structural information, together with other experimental data, leads to a better understanding of the role of oligosaccharide in various biological processes. The disialoside Neu5Ac‐α2→8‐Neu5Ac appears as the terminal glycan in glycoproteins and glycolipids, and is known to play an important role in various events of cellular communication. Neurotoxins such as botulinum and tetanus require Neu5Ac‐α2 → 8‐Neu5Ac for infecting the host. Glycoconjugates containing this disialoside and the enzymes catalyzing their biosynthesis are also regulated during cell growth, development, and differentiation. Unlike other biologically relevant disaccharides that have only two linkage bonds, the α2→8‐linked disialoside has four: C2—O, O—C8′, C8′—C7′, and C7′—C6′. The present report describes the results from nine 1 ns MD simulations of α2→8‐linked disialoside (Neu5Ac‐α2→8‐Neu5Ac); simulations were run using GROMOS96 by explicitly considering the solvent molecules. Conformations around the O—C8′ bond are restricted to the +sc/+ap regions due to stereochemical reasons. In contrast, conformations around the C2—O and C8′—C7′ bonds were found to be largely unrestricted and all the three staggered regions are accessible. The conformations around the C7′—C6′ bond were found to be in either the −sc or the anti region. These results are in excellent agreement with the available NMR and potential energy calculation studies. Overall, the disaccharide is flexible and adopts mainly two ensembles of conformations differing in the conformation around the C7′—C6′ bond. The flexibility associated with this disaccharide allows for better optimization of intermolecular contacts while binding to proteins and this may partially compensate for the loss of conformational entropy that may be incurred due to disaccharide′s flexibility. © 2002 John Wiley & Sons, Inc. Biopolymers 63: 168–180, 2002; DOI 10.1002/bip.10019
Chemotaxonomy of mints of genus Mentha by applying Raman spectroscopy
Authors: Rösch P. , Kiefer W. , Popp J. 
Published: August 2002

AbstractThe characterization of mints is often problematic because Mentha is a taxonomically complex genus. In order to provide a fast and easy characterization method, we use a combination of micro‐Raman spectroscopy and hierarchical cluster analysis. A classification trial of different mint taxa is possible for one collection time. For spectra measured at different points during the growing season, a more sophisticated pretreatment of the data is necessary to receive good discrimination between the species, as well as between the subspecies and varieties of the mints. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 67: 358–361, 2002
DNA persistence length revisited
Authors: Lu Yongjun , Weers Brock , Stellwagen Nancy C. 
Published: August 2002

AbstractDNA restriction fragments ranging from 79 to 789 base pairs in length have been characterized by transient electric birefringence (TEB) measurements at various temperatures between 4 and 43°C. The DNA fragments do not contain runs of four or more adenine residues in a row and migrate with normal electrophoretic mobilities in polyacrylamide gels, indicating that they are not intrinsically curved or bent. The low ionic strength buffers used for the measurements contained 1 mM Tris Cl, pH 8.0, EDTA, and variable concentrations of Na+ or Mg2+ ions. The rotational relaxation times were obtained by fitting the TEB field‐free decay signals with a nonlinear least‐squared fitting program; the decay of the birefringence was monoexponential for fragments ≤ 241 base pair (bp) in length and multiexponential for larger fragments. The terminal relaxation times, characteristic of the end‐over‐end rotation of the DNA molecules, were then used todetermine the persistence length (p) and hydrodynamic radius (r) of DNA as a function of temperature and ionic strength, using several different hydrodynamic models. The specific values obtained for p and r are model dependent. The wormlike chain model of P. J. Hagerman and B. H. Zimm (Biopolymers 1981, Vol. 20, pp. 1481–1502) combined with the revised Broersma equation (J. Newman et al., Journal of Mol Biol 1997, Vol. 116, pp. 593–606) appears to be the most suitable for describing the flexibility of DNA in low ionic strength solutions. The values of p and r obtained from the global least squares fitting of this equation are independent of DNA length, and the deviations of the individual values from the average are reasonably small. The consensus r value calculated for DNA in various low ionic strength solutions containing 1 mM Tris buffer is 14.7 ± 0.4 Å at 20°C. The consensus p values decrease from 814 ∼ 564 Å in solutions containing 1 mM Tris buffer plus 0.2–1 mM NaCl and decrease still further to 440 Å in solutions containing 0.2 mM Mg2+ ions. The persistence length exhibits a shallow maximum at 20°C and decreases slowly upon either increasing or decreasing the temperature, regardless of the model used to fit the data. By contrast, the consensus values of the hydrodynamic radius are independent of temperature. The calculated persistence lengths and hydrodynamic radii are compared with other data in the literature. © 2002 Wiley Periodicals, Inc. Biopolymers 61: 261–275, 2002
Using ATP bioluminescence technique for monitoring microbial activity in sludge
Authors: Chu C. P. , Lee D. J. , Chang Bea‐Ven , Liao C. S. 
Published: August 2002

AbstractThis study demonstrates, for the first time, that the presence of suspended solids in waste‐activated sludge interferes with adenosine triphosphate (ATP) bioluminescence tests. The sludge subject to acid/alkaline treatment represented the test sample. Without consideration of the effect of solid concentrations, one would erroneously estimate the density levels of heterotrophic bacteria in the sludge using ATP data. A light blockage model was proposed to evaluate the luminescence reading without the interference of suspended solids. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 75: 469–474, 2001.
Optimal temperature policy for immobilized enzyme packed bed reactor performing reversible Michaelis–Menten kinetics using the disjoint policy
Authors: Faqir Naim M. , Attarakih Menwer M. 
Published: August 2002

AbstractThe optimal temperature policy that maximizes the time‐averaged productivity of a continuous immobilized enzyme packed bed reactor is determined. This optimization study takes into consideration the enzyme thermal deactivation with substrate protection during the reactor operation. The general case of reversible Michaelis–Menten kinetics under constant reactor feed flow rate is assumed. The corresponding nonlinear optimization problem is solved using the calculus of variations by applying the disjoint policy. This policy reduces the optimization problem into a differential‐algebraic system, DAE. This DAE system defines completely the optimal temperature–time profiles. These profiles depend on the kinetic parameters, feed substrate concentration, operating period, and the residence time and are characterized by increasing form with time. Also, general analytical expressions for the slopes of the temperature and residual enzyme activity profiles are derived. An efficient solution algorithm is developed to solve the DAE system, which results into a one‐dimensional optimization problem with simple bounds on the initial feed temperature. The enzymatic isomerization of glucose into fructose is selected as a case study. The computed productivities are very close to that obtained by numerical nonlinear optimization with simpler problem to solve. Moreover, the computed conversion profiles are almost constant over 90% of the operating periods, thus producing a homogeneous product. © 2002 John Wiley & Sons, Inc. Biotechnol Bioeng 77: 163–173, 2002.
A microfabricated array bioreactor for perfused 3D liver culture
Authors: Powers Mark J. , Domansky Karel , Kaazempur‐Mofrad Mohammad R. , Kalezi Artemis , Capitano Adam , Upadhyaya Arpita , Kurzawski Petra , Wack Kathryn E. , Stolz Donna Beer , Kamm Roger , Griffith Linda G. 
Published: August 2002

AbstractWe describe the design, fabrication, and performance of a bioreactor that enables both morphogenesis of 3D tissue structures under continuous perfusion and repeated in situ observation by light microscopy. Three‐dimensional scaffolds were created by deep reactive ion etching of silicon wafers to create an array of channels (through‐holes) with cell‐adhesive walls. Scaffolds were combined with a cell‐retaining filter and support in a reactor housing designed to deliver a continuous perfusate across the top of the array and through the 3D tissue mass in each channel. Reactor dimensions were constructed so that perfusate flow rates meet estimated values of cellular oxygen demands while providing fluid shear stress at or below a physiological range (<2 dyne cm2), as determined by comparison of numerical models of reactor fluid flow patterns to literature values of physiological shear stresses. We studied the behavior of primary rat hepatocytes seeded into the reactors and cultured for up to 2 weeks, and found that cells seeded into the channels rearranged extensively to form tissue like structures and remained viable throughout the culture period. We further observed that preaggregation of the cells into spheroidal structures prior to seeding improved the morphogenesis of tissue structure and maintenance of viability. We also demonstrate repeated in situ imaging of tissue structure and function using two‐photon microscopy. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 257–269, 2002.
Control of the redox potential by oxygen limitation improves bacterial leaching of chalcopyrite
Authors: Third K. A. , Cord‐Ruwisch R. , Watling H. R. 
Published: August 2002

AbstractShake flask and stirred tank bioleaching experiments showed that the dissolution of chalcopyrite is inhibited by ferric ion concentrations as low as 200 mg L−1 and redox potentials >420 mV (vs. Ag/AgCl). Chemical leaching of chalcopyrite (4% suspension, surface area 2.3 m2 g−1) was enhanced fourfold in the presence of 0.1 M ferrous sulphate compared with 0.1 M ferric sulphate. A computer‐controlled reactor was designed to function as a “potentiostat”‐bioreactor by arresting the air supply to the reactor when the redox potential in solution was greater than a designated setpoint. Leaching at a low, constant redox potential (380 mV vs. Ag/AgCl) achieved final copper recoveries of 52%–61%, which was twice that achieved with a continuous supply of oxygen (<30% extraction). The bacterial populations were observed to continue growing under oxygen limitation but in a controlled manner that was found to improve chalcopyrite dissolution. As the control mechanism is easily established and is likely to decrease production cost, the use of this technology may find application in industry. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 433–441, 2002.
Optimizing the heterologous production of epothilone D in Myxococcus xanthus
Authors: Lau Janice , Frykman Scott , Regentin Rika , Ou Sally , Tsuruta Hiroko , Licari Peter 
Published: August 2002

AbstractThe heterologous production of epothilone D in Myxococcus xanthus was improved by 140‐fold from an initial titer of 0.16 mg/L with the incorporation of an adsorber resin, the identification of a suitable carbon source, and the implementation of a fed‐batch process. To reduce the degradation of epothilone D in the basal medium, XAD‐16 (20 g/L) was added to stabilize the secreted product. This greatly facilitated its recovery and enhanced the yield by three‐fold. The potential of using oils as a carbon source for cell growth and product formation was also evaluated. From a screen of various oils, methyl oleate was shown to have the greatest impact. At the optimal concentration of 7 mL/L in a batch process, the maximum cell density was increased from 0.4 g dry cell weight (DCW)/L to 2 g DCW/L. Product yield, however, depended on the presence of trace elements in the production medium. With an exogenous supplement of trace metals to the basal medium, the peak epothilone D titer was enhanced eight‐fold. This finding demonstrates the significant role of metal ions in cell metabolism and in epothilone biosynthesis. To further increase the product yield, a continuous fed‐batch process was used to promote a higher cell density and to maintain an extended production period. The optimized fed‐batch cultures consistently yielded a cell density of 7 g DCW/L and an average production titer of 23 mg/L. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 280–288, 2002.
Variations in the enantioselectivity of salt‐activated subtilisin induced by lyophilization
Authors: Hsu Wei‐Ting , Clark Douglas S. 
Published: August 2002

AbstractIncluding excess salt during lyophilization has been shown to increase the activity of freeze‐dried subtilisin Carlsberg (SC) in anhydrous media by over 20,000‐fold [Ru et al. (1999) Biotechnol Bioeng 63:233–241]. In the present study, salt‐activated SC (KCl‐SC) showed a 30% enhancement in enantioselectivity compared to the salt‐free enzyme in a variety of organic solvents. Activity toward both enantiomers of N‐acetyl‐phenylalanine methyl ester (APME) increased in tandem by 2–3 orders of magnitude in all solvents, indicating that the mechanism of salt activation is inherent to the enzyme and does not strongly favor one enantiomer over the other. However, activity and enantioselectivity of salt‐activated SC could be manipulated through changes in the lyophilization conditions. Variations in lyophilization time, initial KCl concentration, and initial lyophilization volume altered enantioselectivity over 2‐fold. The changes in enantioselectivity reflected the activity for the L enantiomer, while the activity toward the D enantiomer was mostly unaffected. The results indicate that the lyophilization time and final water content of the KCl‐SC are important determinants of enzyme activity for the L enantiomer, suggesting that the favored reaction is more sensitive to the structural integrity of the salt‐activated enzyme. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 73: 231–237, 2001.
Characterization of monoclonal antibody fragments produced by plant cells
Authors: Sharp Janet M. , Doran Pauline M. 
Published: August 2002

AbstractProduction of a murine IgG1 was investigated using hairy roots, shooty teratomas, and suspended cells of transgenic tobacco. In all cases, in addition to complete assembled antibody, two to four major antibody fragments accumulated in the biomass. A range of protease inhibitors, protein‐stabilizing agents, inhibitors of N‐glycosylation and protein secretion, glycan‐reactive agents, and affinity probes was used to characterize these fragments and investigate their sites and mechanisms of formation. The fragments were not experimental artifacts caused by antibody degradation during tissue homogenization and sample preparation, nor did they represent glycosylation variants. All of the molecules were actively secreted into the culture media and some showed evidence of Golgi‐associated glycan processing, indicating they were not assembly intermediates. Antibody fragments of 50 and 80 kDa were identified mainly as the products of extracellular degradation in the root and shoot apoplast; the 80‐kDa fragment was also present in cell suspension medium, and in suspended cell biomass toward the end of the growth phase. Larger 120‐ and 135‐kDa fragments were most likely produced by proteolytic degradation along the secretory pathway outside of the endoplasmic reticulum (ER) and Golgi apparatus; the carbohydrate residues of the 135‐kDa antibody suggest formation between these organelles. Inhibition of protein secretion and retention of antibody in the ER and/or Golgi reduced fragmentation and increased antibody accumulation levels, probably by reducing exposure to the principal sites of protease activity. This work highlights the importance of foreign protein degradation in plant tissues as a mechanism for posttranslational product loss. Identifying the nature of these degradative processes is a first step toward alleviating their effects, improving protein yields, and enhancing the feasibility of plants as a commercial means for large‐scale protein production. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 73: 338–346, 2001.
Integrated flow‐injection processing for on‐line quantification of plasmid DNA during cultivation of E. coli
Authors: Nandakumar M. P. , Karlsson E. Nordberg , Mattiasson B. 
Published: August 2002

AbstractAn integrated flow‐injection processing (FIP) system for the quantification of plasmids during cultivation is described. The system performs on‐line sampling, cell lysis, and quantification of plasmids in an integrated manner during cultivation of E. coli. The system was operated by using a miniaturized expanded‐bed column which can be used for handling samples containing cells and cell debris without interfering with the binding analysis. Two types of detectors (one measuring UV absorbance at 254 nm and a fluorometer) are used for on‐line plasmid detection. The system was developed using standard solutions and it was successfully applied in monitoring plasmid contents during a cultivation of E. coli. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 73: 406–411, 2001.