bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond the rotamer library: Genetic algorithm combined with the disturbing mutation process for upbuilding protein side‐chains
Authors: Liu Zhijie , Jiang Lin , Gao Ying , Liang Shide , Chen Hao , Han Yuzhen , Lai Luhua 
Published: December 2002

AbstractThe disturbing genetic algorithm, incorporating the disturbing mutation process into the genetic algorithm flow, has been developed to extend the searching space of side‐chain conformations and to improve the quality of the rotamer library. Moreover, the growing generation amount idea, simulating the real situation of the natural evolution, is introduced to improve the searching speed. In the calculations using the pseudo energy scoring function of the root mean squared deviation, the disturbing genetic algorithm method has been shown to be highly efficient. With the real energy function based on AMBER force field, the program has been applied to rebuilding side‐chain conformations of 25 high‐quality crystallographic structures of single‐protein and protein–protein complexes. The averaged root mean standard deviation of atom coordinates in side‐chains and veracities of the torsion angles of χ1 and χ1 + χ2 are 1.165 Å, 88.2 and 72.9% for the buried residues, respectively, and 1.493 Å, 79.2 and 64.7% for all residues, showing that the method has equal precision to the program SCWRL, whereas it performs better in the prediction of buried residues and protein–protein interfaces. This method has been successfully used in redesigning the interface of the Basnase‐Barstar complex, indicating that it will have extensive application in protein design, protein sequence and structure relationship studies, and research on protein–protein interaction. Proteins 2003;50:49–62. © 2002 Wiley‐Liss, Inc.
Rigid body response of base‐isolated structures
Authors: Kulkarni Jeevan A. , Jangid R. S. 
Published: December 2002

AbstractThe superstructure of a base‐isolated building is relatively rigid compared with the isolation system. This can lead to idealization of the superstructure as a rigid body, modelling the base‐isolated structure as a single‐degree‐of‐freedom system. Such analysis significantly reduces the computational efforts required to design the base‐isolated structure under seismic loading. In this study, a comparison is made of the seismic response of a multi‐storey base‐isolated building by idealizing the superstructure as rigid and flexible. Various isolation systems considered include elastomeric bearings (with and without lead cores) as well as sliding systems. The governing equations of motion of the isolated structural system are derived and the response of the system is obtained for a specified time‐history of earthquake ground motion. The top floor acceleration and bearing displacement of the system are plotted for different system parameters and compared with the corresponding response under rigid superstructure conditions to study the influence of superstructure flexibility. The comparison of the response is made under various isolation system parameters (i.e. isolation period, damping, yield strength of the elastomeric bearings and friction coefficient of sliding systems). It is observed that the bearing displacement can be accurately obtained by modelling the superstructure as a rigid body in a base‐isolated structure. Further, such approximation is also justified for floor accelerations of a relatively stiff superstructure isolated by elastomeric bearings. However, the rigid superstructure approach significantly under estimates the floor accelerations for the structure isolated by sliding systems. Copyright © 2002 John Wiley & Sons, Ltd.
A cloud‐resolving regional simulation of tropical cyclone formation
Authors: Powers Jordan G. , Davis Christopher A. 
Published: December 2002

AbstractThe development of Tropical Cyclone Diana (1984) is simulated with a mesoscale model using 1.2 km grid spacing over a regional‐scale (>1000 km) domain in the first known experiment of this kind. With only a synoptic‐scale disturbance in the initial conditions, the model first develops a mesoscale convective system along a remnant frontal zone, which yields a mesoscale vortex. After a period of quiescence, banded convection organizes about the vortex from isolated, grid‐resolved cells, with the system becoming warm‐core and intensifying into Tropical Storm Diana. Copyright © 2002 Royal Meteorological Society.
CALCIUM PUMP PHOSPHOENZYME FROM YOUNG AND OLD HUMAN RED CELLS
Authors: Romero Pedro J. , Salas Valentina , Hernández Concepción 
Published: December 2002

AbstractAn increase in intracellular Ca2+ occurs during ageing of human erythrocytes in vivo. The aged cells show a reduced capacity for active Ca2+ extrusion. Such a defect may arise from pump proteolysis, due to calpain activation by the raised intracellular Ca2+. To test this possibility, Ca2+ pump phosphorylation by [γ‐32P]ATP was studied on percoll‐separated young and old human erythrocytes. After phosphorylation for 30s with Ca2+, the amount of phosphoenzyme produced by the young cell membranes was 50% that of the old cells. With Ca2+ plus La3+, in contrast, the phosphoenzyme level was nearly the same in both preparations. After a prolonged phosphorylation period (50–90s), the phosphoenzyme reached almost identical equilibrium levels in both membrane preparations. On the other hand, a single Ca2+‐dependent radioactive band of about 150kDa was apparent in both preparations after acidic electrophoresis. Likewise, Western blotting using 5F10 monoclonal antibody also detected a single band of similar molecular weight. These results demonstrate that there is no alteration in either molecular mass or number of active Ca2+ pump units during cell ageing, thus indicating that the reduced Ca2+ pumping activity of aged cells does not arise from pump proteolysis.
CELL ADHESION DURING THE MIGRATORY SLUG STAGE OF DICTYOSTELIUM DISCOIDEUM
Authors: Bowers‐Morrow Vivienne M. , Ali Sinan O. , Williams Keith L. 
Published: December 2002

AbstractPrespore‐specific Antigen (PsA) is selectively expressed on the surface of prespore cells at the multicellular migratory slug stage of Dictyostelium discoideum development. It is a developmentally regulated glycoprotein that is anchored to the cell membrane through a glycosyl phosphatidylinositol (GPI) anchor. We present the results of an in vitro immunological investigation of the hypothesis that PsA functions as a cell adhesion molecule (CAM), and of a ligand‐binding assay indicating that PsA has cell membrane binding partner(s). This is the first evidence to implicate a direct role for a putative CAM in cell—cell adhesion during the multicellular migratory slug stage of D. discoideum development. Cell—cell adhesion assays were carried out in the presence or absence of the monoclonal antibody (mAb) MUD1 that has a single antigenic determinant: a peptide epitope on PsA. These assays showed specific inhibition of cell—cell adhesion by MUD1. Further, it was found that a purified recombinant form of PsA (rPsA), can neutralize the inhibitory effect of MUD1; the inhibitory effect on cell—cell adhesion is primarily due to the blocking of PsA by the mAb. The resistance of aggregates to dissociation in the presence of 10mM EDTA (ethylenediamintetraacetic acid) indicates that PsA mediates EDTA‐stable cell—cell contacts, and that PsA‐mediated cell adhesion is likely to be independent of divalent cations such as Ca2+ or Mg2+.
A SIMPLE NON‐ENZYMATIC METHOD FOR THE ISOLATION OF HIGH YIELDS OF FUNCTIONAL RAT HEPATOCYTES
Authors: Kravchenko L. , Petrenko A. , Shanina I. , Fuller B. 
Published: December 2002

AbstractA method for isolation of rat hepatocytes using liver perfusion by ethylenediamine tetra‐acetic acid (EDTA)‐containing sucrose solution and mechanical tissue disaggregation by controlled vibration (MVD) is described. The yields of hepatocytes produced by this method were similar to those obtained using collagenase perfusion. The cells had well preserved membrane integrity as judged by the trypan blue staining test (91±4%), ATP contents, rates of endogenous respiration and enzyme leakage that indicated they were functional cells. There was little evidence of expression of latent damage when the cells were stored either at 37°C (by pre‐incubation) or at 4°C. This method can be used to isolate high yields of functional cells from rat liver if the collagenase perfusion technique is not available.
REGULATION OF LEUKOTRIENE SYNTHESIS BY ARACHIDONIC ACID IN HUMAN POLYMORPHONUCLEAR LEUKOCYTE ADHESIVE INTERACTIONS IS DEPENDENT ON THE PRESENCE OF ALBUMIN
Authors: Pushkareva Marina A. , Turutin Denis V. , Sud'ina Galina F. 
Published: December 2002

AbstractWe have previously demonstrated that the pretreatment of polymorphonuclear leukocytes (PMNs) with the chemotherapeutic drug, Suramin, increases both cell attachment and inhibits calcium ionophore A23187‐stimulated leukotriene (LT) synthesis. Here, we examined the effects of extracellular arachidonic acid (AA) and albumin on attachment and LT synthesis in the interaction of PMNs with both collagen‐coated surfaces and human umbilical vein endothelial cell (HUVEC) monolayers. Suramin decreased the release of radiolabelled AA and 5‐lipoxygenase metabolites by [14C‐AA]‐prelabelled PMNs stimulated with A23187, with and without human serum albumin (HSA) in the culture medium. Addition of 1μM AA together with calcium ionophore stimulated the release of endogenous AA to the same level as control and Suramin‐pretreated cells, but attachment was unaffected and LT synthesis was still inhibited with Suramin treatment. Using 24μM AA, regulation of LT synthesis was dependent on the presence of HSA in the medium. Without HSA, 24μM AA induced detachment of PMNs and increased LT synthesis in Suramin‐treated cells above the control level. In the presence of HSA, 24μM AA did not influence PMN attachment or abolish Suramin‐induced inhibition of LT synthesis. These results suggest that tight attachment of PMNs to a solid surface leads to decreased LT synthesis during subsequent stimulation of the cells by A23187 in the presence or absence of exogenous substrate.
MECHANISTICS OF AMOEBOID LOCOMOTION: SIGNAL TO FORCES
Authors: Fukui Yoshio 
Published: December 2002

AbstractDictyostelium serves as an ideal model system for studying the molecular and structural properties of the actomyosin and microtubule systems. This organism also has been the vehicle on which the gene‐targeting technique was pioneered. Dictyostelium also represents a small number of organisms whose chemotactic ligand‐receptor mechanism has been well characterized. This article reviews recent advances in studies of the actin‐based cytoskeletal system in Dictyostelium, focusing on the mechanistic aspects of the amoeboid motion. Special emphasis is placed on the recently identified cell‐substrate‐anchoring structures ‘eupodia’, and the measurement of single‐cell migration forces. The recent advances in signal transduction cascade is also discussed with relevance to the mechanistics in amoeboid locomotion.
TELOMERASE‐DEPENDENT REACTIVATION OF DNA SYNTHESIS IN MACROPHAGES IMPLIES ALTERATION OF TELOMERES
Authors: Yegorov Y. E. , Kazimirchuk E. V. , Terekhov S. M. , Karachentsev D. N. , Shirokova E. A. , Khandazhinskaya A. L. , Meshcheryakova J. A. , Corey D. R. , Zelenin A. V. 
Published: December 2002

AbstractIn previous work we demonstrated that various types of cultured cells with a limited life span could not reactivate DNA synthesis in the nuclei of mouse peritoneal macrophages in heterokaryons. We now investigate the role of telomerase in the process of the macrophage nucleus reactivation in heterokaryons with immortal telomerase‐positive 3T3 Swiss mouse fibroblasts and human fibroblasts with introduced hTERT gene. We report that introduction of the hTERT gene into human diploid fibroblasts results in emergence of telomerase activity in these cells and the ability to induce the reactivation of DNA synthesis in the macrophage nuclei in heterokaryons. Inhibition of telomerase activity in heterokaryons by reverse transcriptase inhibitors (azidothymidine and guanosine polyphosphonate analogues) and by a 2′‐O‐methyl‐RNA oligonucleotide anti‐sense to the template region of telomerase RNA, block reactivation of DNA synthesis in macrophage nuclei without inhibiting DNA synthesis in the nuclei of fibroblasts. Our results suggest alterations (shortening or damage) in the macrophage telomere structure. As far as we know, heterokaryons with macrophages are the first cellular model for rapid investigation of the effects of telomerase inhibitors.
PARACRINE ACTION OF TRANSFORMING GROWTH FACTOR‐ALPHA IN RECTAL CRYPT EPITHELIUM OF HUMANS
Authors: Cameron Ivan L. , Hardman W. Elaine 
Published: December 2002

AbstractColon and rectal mucosal crypt epithelium is a rapidly renewing cell population, where cell proliferation is normally balanced by cell loss. This report concerns the putative paracrine action of transforming growth factor α(TGF‐α) in this homeostatic process. Immunohistochemical staining for proliferating cell nuclear antigen (PCNA) and TGF‐α was performed on biopsy specimens of rectal mucosa taken from consenting patients. The height of the proliferative compartment in mid‐axially sectioned crypts in each individual was determined from the distribution of PCNA stained cells. The number of TGF‐α stained cells that exhibited intense positive staining in a continuous column from the mouth down the side of the crypt was also scored in each individual patient. There was a significant positive correlation (P=0.05,n =22 patients) between the height of the proliferative compartment and the number of cells staining for TGF‐α. Non‐cellular TGF‐α reactivity was also observed in the lamina propria adjacent to the TGF‐α reactive epithelial cells, indicating secretion of TGF‐α by these epithelial cells. These findings suggest that TGF‐α is released from epithelial cells in the upper compartment of the crypt into the adjacent lamina propria and then diffuses to the epithelial cells in the lower part of the crypt, resulting in expansion of the proliferative compartment.
MODIFICATION OF OSCILLATORY BEHAVIOUR OF PROTEIN TYROSINE KINASE AND PHOSPHATASE DURING ALL‐TRANS RETINOIC ACID‐INDUCED DIFFFERENTIATION OF LEUKAEMIC CELLS
Authors: Calvert‐Evers J. L. , Hammond K. D. 
Published: December 2002

AbstractGranulocytic maturation of human acute promyelocytic leukaemic (HL‐60) cells was induced using all‐trans retinoic acid (ATRA). Time‐dependent changes in the enzyme activities of protein tyrosine phosphatase (PTP) and protein tyrosine kinase (PTK), and the total extractable protein content were monitored in proliferating and differentiating cells. The existence of periodicity was demonstrated clearly in both PTP and PTK enzyme activities and in the amount of protein extracted from the cells. Following ATRA treatment, differentiation‐induced changes in rhythmic characteristics such as period and amplitude were evident. A noticeable effect was that of ATRA on the enzyme activity of PTP, for which four distinct patterns of oscillatory behaviour were identified. This study examines these changes, in an attempt to gain insight into the role which biochemical oscillators may play in the regulation of molecular control mechanisms.
THE SIGNIFICANCE OF α5β1 INTEGRIN DEPENDENT AND INDEPENDENT ACTIN CYTOSKELTON ORGANIZATION IN CELL TRANSFORMATION AND SURVIVAL
Authors: Rajeswari J. , Pande Gopal 
Published: December 2002

AbstractCell—matrix and cell—cell interactions are important physiological determinants of cell growth, survival and transformation. Cell adhesion to the extra cellular matrix (ECM) via integrins also crucially influences the organization of the cytoskeleton. It triggers a cascade of intracellular biochemical events, which regulate cell viability and growth. We have studied the relationship between cell attachment to the substratum and cytoskeletal organization and cell survival and transformation. Our results demonstrate that in the absence of attachment to the substratum, adhesion‐dependent fibroblasts exhibit rapid loss of viability. However, a small percentage of cells survive even after remaining non‐adherent for 16h. The adherent and non‐adherent cells differ from one another both morphologically and physiologically. The latter show a loss of α5β1 integrin expression on their surface and bind non‐specifically to the substratum and ECM, thereby activating certain pathways more efficiently than adherent cells. We have also shown that non‐adherent cells grow faster and have worse cytoskeletal organization after attachment to the substratum, and do not form focal adhesions or actin stress fibres. Hence, our data suggests that rat fibroblasts in prolonged suspension exhibit some properties that are comparable to cells undergoing transformation, by adapting integrin‐dependent or independent signalling pathways for their survival.
EXOGENOUS ACTIVIN INCREASES THE PROPORTION OF INSULIN CELLS IN THE DEVELOPING CHICK PANCREAS IN CULTURE
Authors: Penny Clem , Kramer Beverley 
Published: December 2002

AbstractAs activin is believed to be a key signalling factor during early pancreatic development, its influence on the proliferation and/or determination of insulin cells in the developing chick dorsal pancreatic bud was investigated. Dorsal pancreatic buds of 5‐day‐old chick embryos were explanted on to Matrigel and cultured in serum‐free medium (Ham's F12.ITS), to which 1 or 10ng/ml activin was added. After 7 days in culture, the explants were processed for immunocytochemistry and the insulin‐positive cells were scored and expressed as a proportion of the sum of insulin and glucagon cells. When compared to the control cultures (Hams F12.ITS alone), activin treatment resulted in respective increases in the proportion of insulin cells of 1.6 and 1.9 fold. It is suggested that activin treatment favours differentiation of the insulin cell pathway relative to glucagon cells.
A revision of the species of the Rhizocarpon hochstetteri group occurring in the British Isles
Authors: Fryday Alan M. 
Published: December 2002

AbstractRhizocarpon hochstetteri s. str. is shown to be an upland/montane species with relatively large ascospores. The name Rhizocarpon infernulum is resurrected for the species with smaller ascospores previously included within R. hochstetteri, but which is probably more closely related to R. cinereovirens. Lectotypes are chosen for a number of taxa, including R. cinereovirens and R. infernulum, and descriptions provided for two new taxa with small hyaline, 1–septate ascospores: R. caesium, which occurs on damp, mildly basic rocks in oceanic areas, and R. infernulum f. sylvaticum occurring on siliceous rocks in damp deciduous woodlands. All these taxa are known also from North America. Rhizocarpon discoense is shown to be a distinct species, not a synonym of R. cinereovirens. The different ascospore dimensions reported for R. hochstetteri by British and European authors are shown to be due to confusion between R. hochstetteri and R. polycarpum. A number of morphological characters are evaluated regarding their relevance to species separation in Rhizocarpon and the name Macrocarpa-green is proposed for the olivaceous pigment present in most species of Rhizocarpon and Porpidia. A key is provided for the species of Rhizocarpon with hyaline, 1– septate ascospores.
The lichenicolous species of Odontotrema (Syn. Lethariicola) (Ascomycota, Ostropales)
Authors: Diederich Paul , Zhurbenko Mikhail , Etayo Javier 
Published: December 2002

AbstractThe genus Lethariicola is shown to be a synonym of Odontotrema. Fifteen lichenicolous species are recognized: O. bryoriae sp. nov. (on Bryoria), O. cuculare comb. nov. (on Parmeliopsis hyperopta), O. figulinum comb. nov. (on Lecanora polytropa) O. intermedium sp. nov. (on Thamnolia), O. lecanorae sp. nov. (on Lecanora), O. melaneliae sp. nov. (on Melanelia), O. ochrolechiae sp. nov. (on Ochrolechia), O. pertusariae sp. nov. (on Pertusaria hymenea), O. rhizocarpicola sp. nov. (on Rhizocarpon) O. santessonii sp. nov. (on Thamnolia), O. sipei comb. nov. (on Letharia), O. thamnoliae sp. nov. (on Thamnolia), and three undescribed species on Lecanora, Mycoblastus and Usnea. The type of O. cuculare has two distinct lichenicolous species of Odontotrema, and the name is lectotypified on the species growing on Parmeliopsis. A key is given to all lichenicolous species of Odontotrema and Paralethariicola.
Halogenated anthraquinones from the rare southern Illinois lichen Lasallia Papulosa
Authors: Cohen Peter A. 
Published: December 2002

AbstractFour anthraquinones were isolated from the foliose lichen, Lasallia papulosa (Ach.) Llano. Two of the anthraquinones are known compounds, previously isolated from Lasallia papulosa, while the other two were reported previously as secondary metabolites from laboratory-cultured Nephroma laevigatum, and are isolated here for the first time from lichens in their natural habitat. All compounds were characterized by UV spectrophotometry, mass spectrometry, 1H NMR and 13C NMR. The products were identified as 7-chloroemodin, valsarin (7-chloro-5-hydroxyemodin), 5-chloro-1-O-methylemodin and 5-chloro-1-O-methyl-ω-hydroxyemodin.
A new fertile species of Menegazzia and notes on two sorediate species from the Neotropics
Authors: Bjerke Jarle W. 
Published: December 2002

AbstractMenegazzia neotropica sp. nov. is described from upper montane forest remnants and paramos in Ecuador, Colombia and Venezuela. It is characterized by short-pedicellate apothecia with ridged margins that partly obscure the discs, and by narrow, glossy lobes with brown-black margins. Menegazzia dissecta is recorded from South America for the first time and M. terebrata is recorded from Colombia and Ecuador for the first time.
Immunological aspects of endometriosis
Authors: Dmowski W.P. 
Published: December 2002

AbstractDuring the past decade, evidence has accumulated indicating an association between endometriosis and changes in humoral and cell‐mediated immunity. However, it is not clear whether immune changes are the sequelae or play a role in the etiopathogenesis of the disease. The latter concept is supported by the observation that exposure of rhesus monkeys to radiation or immunotoxicants leads several years later to an increase in frequency and severity of endometriosis. Studies from our laboratories support the theory that endometrial cells misplaced during menses can implant in ectopic locations only in women with genetically or environmentally altered cell‐mediated immune function. Development of endometriosis may then prompt a humoral response in some women, which results in the production of autoantibodies to endometrial cells or cell‐derived antigens. These autoantibodies may cross‐react with the uterine endometrium, interfere with implantation, and cause infertility or early spontaneous abortions. We recently observed that the presence of autoantibodies in endometriosis was associated with significantly lower in vitro fertilization/embryo transfer pregnancy rates. Interestingly, in about 30% of women with unexplained infertility, immune changes characteristic of endometriosis were also present, suggesting a subclinical form of this disease. We conclude that: (1) women with unexplained infertility should have studies of the immune function to rule out subclinical form of endometriosis: (2) evaluation of infertility in women with endometriosis should include an assessment of autoantibody status: and (3) treatment methods involving autoantibody suppression should be considered in women with endometriosis positive for autoantibodies.
The impact of bone loss in women with endometriosis
Authors: Stevenson J.C 
Published: December 2002

AbstractLow peak adult bone mass in a premenopausal woman puts her at increased risk for osteoporosis postmenopausally. Episodes of hypo‐estrogenism premenopausally are associated with loss of bone density. This is seen with gonadotropin‐releasing hormone agonist therapy for endometriosis, and thus prolonged or repeated courses of such treatment may increase the future risk of osteoporosis. Danazol and related compounds do not result in any bone loss but may have certain metabolic disadvantages.