bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary history of vertebrate appendicular muscle
Authors: Galis Frietson 
Published: August 2002

AbstractThe evolutionary history of muscle development in the paired fins of teleost fish and the limbs of tetrapod vertebrates is still, to a large extent, uncertain. There has been a consensus, however, that in the vertebrate clade the ancestral mechanism of fin and limb muscle development involves the extension of epithelial tissues from the somite into the fin/limb bud. This mechanism has been documented in chondrichthyan, dipnoan, chondrostean and teleost fishes. It has also been assumed that in amniotes, in contrast, individual progenitor cells of muscles migrate from the somites into the limb buds. Neyt et al.(1) now present the exciting finding that in zebrafishes this presumably derived mechanism involving individual cell migration, is present. They conclude, based on data on sharks, zebrafishes, chickens, quails and mice that the derived mechanism was present in the sarcopterygians. This conclusion, however, may be premature in the light of further data available in the literature, which show a highly mosaic distribution of this character in the vertebrate clade. Furthermore, a developmental mode exists that is intermediate between the supposed ancestral and derived modes in teleosts, reptiles and possibly amphibians. BioEssays 23:383–387, 2001. © 2001 John Wiley & Sons, Inc.
A plausible function of the prion protein: conjectures and a hypothesis
Authors: Abdulla Yousef H. 
Published: August 2002

AbstractAmyloid beta precursor protein (APP) and prion protein (PrP) are cell membrane elements implicated in neurodegenerative diseases. Both proteins undergo endoproteolysis. Evidence is adduced from the literature hinting that the process in the two proteins could be related, their functions may overlap and their distributions coincide. It is proposed that PrP catalyses its own cleavage, the C‐terminal fragment functions as an α secretase and the N‐terminal segment chaperones the active site; the α secretase releases anticoagulant and neurotrophic ectodomains from APP. The proposals explain some features of spongiform encephalopathies. BioEssays 23:456–462, 2001. © 2001 John Wiley & Sons, Inc.
Mitochondria in the pathogenesis of lipodystrophy induced by anti‐HIV antiretroviral drugs: actors or bystanders?
Authors: Cossarizza Andrea , Mussini Cristina , Viganò Alessandra 
Published: August 2002

AbstractEffective therapies are now available that can stop the progression of HIV infection and significantly delay the onset of AIDS. The “highly active antiretroviral therapy” (HAART) is a combination of potent antiretroviral drugs such as viral protease inhibitors or nucleoside‐analogue reverse‐transcriptase inhibitors, that has a variety of serious side effects, including lipodystrophy, a pathology characterized by accumulation of visceral fat, breast adiposity, cervical fat‐pads, hyperlipidemia, insulin resistance as well as fat wasting in face and limbs. There is still an open debate that concerns the precise responsibility of HAART as well as metabolic pathways and mechanisms that are involved in the onset of lipodystrophy. The similarities with multiple symmetric lipomatosis (MSL), in which mitochondria impairment plays a crucial role, lead to the hypothesis that drug‐induced damages to mitochondrial DNA are able to alter mitochondria functionality to an extent that is similar to what occurs in MSL. In addition, several evidences indicate that HAART is also linked to a deregulated production of tumour necrosis factor‐α, which uses mitochondria as intracellular targets. In this paper, we review data concerning the role of mitochondria in the pathogenesis of lipodystrophy, and advance a unifying hypothesis involving either direct or indirect effects of the drugs employed during HAART. BioEssays 23:1070–1080, 2001. © 2001 John Wiley & Sons, Inc.
Functional assessment and treatment of pica: a single‐case experiment
Authors: Rapp John T. , Dozier Claudia L. , Carr James E. 
Published: August 2002

AbstractThe pica of a 6‐year‐old girl diagnosed with autism was initially shown to persist in the absence of socially mediated consequences. In an attempt to provide a competing source of oral stimulation, we used a stimulus preference assessment to identify food items that were subsequently presented noncontingently. However, the noncontingent schedule could not be thinned to a practical variation while still maintaining reductions in pica. A subsequent multielement evaluation of response blocking and verbal reprimands demonstrated that neither intervention both produced and maintained low levels of pica. Verbal reprimands were then used in conjunction with noncontingent food presentation, but this intervention did not produce significant reductions in pica. Suppression of pica was ultimately obtained in both a clinic setting and in the child's natural environment using contingent, varied auditory stimulation. The results are discussed in the context of the ‘least restrictive alternative’ model of treatment selection. Copyright © 2001 John Wiley & Sons, Ltd.
Recognizing shorter coding regions of human genes based on the statistics of stop codons
Authors: Wang Yonghong , Zhang Chun‐Ting , Dong Puxuan 
Published: August 2002

AbstractWith the quick progress of the Human Genome Project, a great amount of uncharacterized DNA sequences needs to be annotated copiously by better algorithms. Recognizing shorter coding sequences of human genes is one of the most important problems in gene recognition, which is not yet completely solved. This paper is devoted to solving the issue using a new method. The distributions of the three stop codons, i.e., TAA, TAG and TGA, in three phases along coding, noncoding, and intergenic sequences are studied in detail. Using the obtained distributions and other coding measures, a new algorithm for the recognition of shorter coding sequences of human genes is developed. The accuracy of the algorithm is tested based on a larger database of human genes. It is found that the average accuracy achieved is as high as 92.1% for the sequences with length of 192 base pairs, which is confirmed by sixfold cross‐validation tests. It is hoped that by incorporating the present method with some existing algorithms, the accuracy for identifying human genes from unannotated sequences would be increased. © 2002 John Wiley & Sons, Inc. Biopolymers 63: 207–216, 2002
Structural features of two distinct molecular complexes of copper(II) cationic porphyrin and deoxyribonucleotides
Authors: Mojzes Peter , Praus Petr , Baumruk Vladimir , Turpin Pierre‐Yves , Matousek Pavel , Towrie Michael 
Published: August 2002

AbstractThe associations of the water‐soluble cationic copper(II)‐5,10,15,20‐meso‐tetrakis(4‐N‐methylpyridyl) porphyrin (CuP) with d(pT)9 oligothymidylate and its building blocks deoxythymidine (dT) and deoxythymidine 5′‐monophosphate (dTMP) were investigated by spectrophotometric titration [absorption, nanosecond transient resonance Raman (ns‐RR) and picosecond time‐resolved resonance Raman (ps‐TR3) spectroscopies] to elucidate the structural requirements for the CuP exciplex formation in molecular complexes with unchained mononucleotides. In the d(pT)9 a factor analysis and global fit of the CuP absorption spectra revealed the formation of a single spectral species attributable to a 1 : 1 CuP · d(pT)9 complex throughout a wide range of d(pT)9/CuP ratios (0–10). Using ps‐TR3 spectroscopy, the CuP · d(pT)9 complex was shown to be fully responsible for exciplex formation. In contrast, CuP mixed with dTMP ([dTMP]/[CuP] < 3000) yielded two spectroscopically distinct types of molecular complexes with 1 : 1 (CuP · dTMP) and 1 : 2 (CuP · (dTMP)2) (or even higher for [dTMP]/[CuP] > 3000) stoichiometry, the latter being spectroscopically identical to the CuP · d(pT)9 and providing a microenvironment favorable for exciplex formation to the same extent as the oligothymidylate. On the other hand, the 1 : 1 CuP · dTMP complex (prevailing for [dTMP]/[CuP] < 100) yielded no exciplex features. Similar behavior was observed for the CuP complexed with dT. To explain the difference in the ability of the CuP · dTMP and CuP · (dTMP)2 species to form the exciplex, two types of molecular complexes were suggested and discussed, differing in the orientation of the thymine planes with respect to the porphyrin macrocycle. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 67: 278–281, 2002
Extreme stability of helices formed by water‐soluble poly‐N‐substituted glycines (polypeptoids) with α‐chiral side chains
Authors: Sanborn Tracy J. , Wu Cindy W. , Zuckermann Ronald N. , Barron Annelise E. 
Published: August 2002

AbstractPoly‐N‐substituted glycines or “peptoids” are protease‐stable peptide mimics. Although the peptoid backbone is achiral and lacks hydrogen‐bond donors, substitution with α‐chiral side chains can drive the formation of stable helices that give rise to intense CD spectra. To systematically study the solution properties and stability of water‐soluble peptoid helices with α‐chiral side chains, we have synthesized and characterized an amphipathic, 36‐residue N‐substituted glycine oligomer. CD was used to investigate effects of concentration and solvent environment on this helical peptoid. We saw no significant dependence of helical structure on concentration. Intense, “α‐helix‐like” CD spectra were observed for the 36‐mer in aqueous, 2,2,2‐trifluorethanol (TFE), and methanol solution, proving a relative insensitivity of peptoid helical structure to solvent environment. While CD spectra taken in these different solvents were fundamentally similar in shape, we did observe some interesting differences in the intensities of particular CD bands in the various solvents. For example, the addition of TFE to an aqueous solvent increases the degree of peptoid helicity, as is observed for polypeptide α‐helices. Moreover, the helical structure of peptoids appears to be virtually unaffected by heat, even in an aqueous buffer containing 8 M urea. The extraordinary resistance of these peptoid helices to denaturation is consistent with a dominant role of steric forces in their structural stabilization. The structured polypeptoids studied here may have potential as robust mimics of helical polypeptides of therapeutic interest. © 2002 John Wiley & Sons, Inc. Biopolymers 63: 12–20, 2002
Effects of various environmental conditions on the transformation of chlorinated solvents by Methanosarcina thermophila cell exudates
Authors: Baeseman Jenny L. , Novak Paige J. 
Published: August 2002

AbstractSeveral microbiologically produced biomolecules have been shown to degrade chlorinated contaminants found in groundwater systems. It was discovered that the cell‐free exudates of the methanogen Methanosarcina thermophila were capable of carbon tetrachloride (CT) and chloroform (CF) degradation. Characterization of the exudates suggested that the active agents were porphorinogen‐type molecules, possibly containing zinc. This research was performed to determine if the exudates from M. thermophila could be used for remediation purposes. The cell exudates were found to be capable of degrading CT, CF, tetrachloroethene, trichloroethene, and 1,1,1‐trichloroethane. CT degradation was used to gauge exudate activity under a variety of conditions that would be encountered in the environment. The cell exudates were active when incubated in two types of soil matrices and at temperatures ranging from 4 to 23°C. Over a 35‐day period approximately 10.2 μmoles of CT were degraded by M. thermophila exudates. To test the hypothesis that the exudates contained either a zinc porphorinogen or a quinone, experiments were performed with zinc 5,10,15,20‐tetra (4‐pyridyl)‐21 H, 23 H‐porphine tetrakis, protoporphyrin IX zinc, and juglone. The two zinc porphyrins were capable of mediating CT degradation at rates comparable to those observed with the M. thermophila exudates; however, juglone was only capable of very slow CT transformation. The electron‐transfer activity of the M. thermophila cell exudates was therefore more consistent with the activity of porphorinogens rather than quinones. Finally, in two enrichment cultures established from aquifer material and marine sediment, the possibility of excreted agents capable of degrading CT was evident. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 75: 634–641, 2001.
Why do crown ethers activate enzymes in organic solvents?
Authors: van Unen Dirk‐Jan , Engbersen Johan F. J. , Reinhoudt David N. 
Published: August 2002

AbstractOne of the major drawbacks of enzymes in nonaqueous solvents is that their activity is often dramatically low compared to that in water. This limitation can be largely overcome by crown ether treatment of enzymes. In this paper, we describe a number of carefully designed new experiments that have improved the insights into the mechanisms that are operative in the crown ether activation of enzymes in organic solvents. The enhancement of enzyme activity upon addition of 18‐crown‐6 to the organic solvent can be reconciled with a mechanism in which macrocyclic interactions of 18‐crown‐6 with the enzyme play an important role. Macrocyclic interactions (e.g., complexation with lysine ammonium groups of the enzyme) can lead to a reduced formation of inter‐ and intramolecular salt bridges and, consequently, to lowering of the kinetic conformational barriers, enabling the enzyme to refold into thermodynamically stable, catalytically (more) active conformations. This assumption is supported by the observation that the crown‐ether‐enhanced enzyme activity is retained after removal of the crown by washing with a dry organic solvent. A much stronger crown ether activation is observed when 18‐crown‐6 is added prior to lyophilization, and this can be explained by a combination of two effects: the before‐mentioned macrocyclic complexation effect, and a less specific, nonmacrocyclic, lyoprotecting effect. The magnitude of the total crown ether effect depends on the polarity and thermodynamic water activity of the solvent, the activation being highest in dry and apolar media, where kinetic conformational barriers are highest. By determination of the specific activity of crown‐ether‐lyophilized enzyme as a function of the enzyme concentration, the macrocyclic crown ether (linearly dependent on the enzyme concentration) and the nonmacrocyclic lyoprotection effect (not dependent on the enzyme concentration) could be separated. These measurements reveal that the contribution of the nonmacrocyclic effect is significantly larger than the macrocyclic refolding effect. © 2002 John Wiley & Sons, Inc. Biotechnol Bioeng 77: 248‐255, 2002.
Production of teicoplanin by Actinoplanes teichomyceticus in continuous fermentation
Authors: Vara Antonio Gonzalez , Hochkoepple Alejandro , Nielsen Jens , Villadsen John 
Published: August 2002

AbstractProduction of the potent antibiotic teicoplanin by Actinoplanes teichomyceticus was studied in batch and in chemostat cultures. It is found that the producing strain deactivates to a non‐producing strain named NP‐12. This strain is used to find the growth kinetics of the A. teichomyceticus without interference from the product teicoplanin. In batch experiments with NP‐12 grown on glucose at different initial concentrations and with different added amounts of teicoplanin, the strong inhibitory effect of teicoplanin was determined. These results obtained on NP‐12 were validated in a series of chemostat experiments with the processing strain. All experiments in batch and in chemostat cultures were well represented by Monod kinetics with respect to the carbon and energy source (glucose) and with a substantial inhibitory effect of teicoplanin. Further experiments were made with the producing strain in a continuous reactor coupled to a microfilter that delivers a cell‐free permeate. It was found that the derived kinetics almost exactly simulated the behavior of the cell recirculation reactor in addition to when the cell concentration in the reactor was more than four times higher than in the chemostat. For industrial production of teicoplanin, a continuous reactor with cell recirculation and working with a low effluent glucose concentration was by far the best mode of operation. Finally, the deactivation of the producing strain to NP‐12 was modeled by a two‐step deactivation mechanism. Deactivation was independent of dilution rate but dependendest on the inoculum preparation and on the previous history of the inoculum. © 2002 John Wiley & Sons, Inc. Biotechnol Bioeng 77: 589–598, 2002; DOI 10.1002/bit.10137
Quantitative determination of cellulase concentration as distinct from cell concentration in studies of microbial cellulose utilization: Analytical framework and methodological approach
Authors: Lynd Lee R. , Zhang Yiheng 
Published: August 2002

AbstractIn analyzing microbial cellulose utilization, it would be useful to independently measure the mass concentration of cells and cellulase enzymes. Such measurements would allow investigation of the allocation of cellular resources between synthesis of cells and cellulase, in vivo cell‐ and cellulase‐specific cellulose hydrolysis rates, and bioenergetics. Methodological protocols are not established for independent determination of cell and cellulase concentrations for the common case in which a substantial fraction of cellulase is attached to the cell surface. Alternative analytical approaches by which to develop such protocols are examined from the perspective of error minimization. For cell concentration measurement, acceptable accuracy is expected when the concentrations of a cell‐specific component (e.g., DNA) is determined or when total protein is determined in conjunction with a measurement specific to cellulase. For cellulase concentration measurement, acceptable accuracy is expected when a measurement specific to cellulase such as ELISA is used. Several analytical approaches are rejected based on large expected errors. © 2002 John Wiley & Sons, Inc. Biotechnol Bioeng 77: 467–475, 2002; DOI 10.1002/bit.10142
Effects of osmoprotectant compounds on NCAM polysialylation under hyperosmotic stress and elevated pCO2
Authors: Schmelzer Albert E. , Miller William M. 
Published: August 2002

AbstractElevated osmolality and pCO2 have been shown to alter sialylation in a protein‐specific manner. In Chinese hamster ovary (CHO)MT2‐l‐8 cells, tPA sialylation changed only slightly from 40 to 250 mm Hg pCO2, whereas neural cell adhesion molecule polysialic acid (NCAM PSA) content decreased by up to 70% at 250 mm Hg pCO2, pH 7.2. NCAM PSA content also decreased with increasing NaCl or NH4Cl concentration. This suggests that PSA content is a sensitive indicator of conditions that may alter glycosylation. Amino acids and their derivatives have been used to protect hybridoma and CHO cell growth under hyperosmotic stress. We examined the impact of osmoprotectants on NCAM PSA content in CHO MT2‐1‐8 cells under hyperosmolality (up to 545 mOsm/kg) and at 195 and 250 mm Hg pCO2. NCAM PSA content at 545 mOsm/kg was at least two‐fold greater in the presence of glycine betaine or L‐proline compared to that without osmoprotectant. Surprisingly, in the presence of 20 mM glycine betaine, PSA levels were 50–60% of the control level for osmolalities ranging from 320 to 545 mOsm/kg. Thus, glycine betaine inhibits NCAM polysialylation at osmolalities below 435 mOsm/kg and is beneficial at higher osmolalities. In contrast to glycine betaine, L‐proline increased PSA content by 25–120% relative to the unprotected culture at ≤545 mOsm/kg. The decrease in NCAM PSA levels of CHO MT2‐1‐8 cells cultured at 195 mm Hg pCO2–435 mOsm/kg was not mitigated by the presence of 25 mM glycine betaine, glycine, or L‐threonine, even though all of these compounds enhanced cell growth. At 250 mm Hg pCO2, all osmoprotectants tested (20 mM L‐threonine, L‐proline, glycine, or glycine betaine) increased NCAM polysialylation, with 20 mM glycine betaine restoring NCAM PSA to near control levels. Thus, osmoprotectants may (partially) offset changes in glycosylation, as well as the inhibition of growth, in cells under environmental stress. Supernatant β‐galactosidase levels, which increase upon alkalization of acidic organelles, did not differ significantly under elevated pCO2 and hyperosmolality from that at control conditions. © 2002 John Wiley & Sons, Inc. Biotechnol Bioeng 77: 359–368, 2002; DOI 10.1002/bit.10175
Design of transgenes for efficient expression of active chimeric proteins on mammalian cells
Authors: Liao Kuang‐Wen , Chou Wan‐Chih , Lo Yu‐Chih , Roffler Steve R. 
Published: August 2002

AbstractHeterologous proteins expressed on the surface of cells may be useful for eliciting therapeutic responses and engineering new extracellular properties. We examined factors that control the membrane targeting of α‐fetoprotein (AFP) and a single‐chain antibody (scFv). Chimeric proteins were targeted to the plasma membrane by employing the transmembrane domain (TM) and cytosolic tail of murine CD8O (B7‐1), the TM of the human platelet‐derived growth factor receptor (PDGFR), the glycosylphosphatidylinositol anchor encoded by the C‐terminal extension of decay‐accelerating factor (DAF), and the TM of the H1 subunit of the human asialoglycoprotein receptor (ASGPR). AFP chimeric proteins containing the B7, DAF, ASGPR, or PDGFR targeting domains displayed half‐lives of 12.2, 3.8, 2.4, and 1.6 h, respectively. The newly synthesized B7 chimera was rapidly transported and remained on the cell surface. Glycosylphosphatidylinositol‐anchored chimeras reached the surface more slowly and significant amounts were released into the culture medium. PDGFR TM chimeras were rapidly degraded, whereas ASGPR chimeras were retained in the endoplasmic reticulum (ER). The surface expression of both AFP and scFv chimeric proteins followed the order (highest to lowest) of B7 > DAF >> PDGFR. Introduction of a dimerization domain (hinge—CH2—CH3 region of human IgG1) between scFv and TM dramatically reduced cleavage of the chimeric protein, increased surface expression, and produced biologically active scFv. Our results indicate that transgenes designed for the expression of active scFv on cells should incorporate a TM that does not undergo endocytosis, include an intact cytoplasmic domain, and possess a spacer to reduce cleavage and retain biological activity. © 2001 John Wiley & Sons, Inc. Biotechnol Bioeng 73: 313–323, 2001.