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  • 1995-1999  (3,489)
  • 1998  (3,489)
  • Polymer and Materials Science  (2,108)
  • Engineering  (644)
  • Theoretical, Physical and Computational Chemistry  (583)
  • Genetics  (153)
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  • 1995-1999  (3,489)
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  • 1
    ISSN: 1534-4681
    Keywords: Breast cancer ; Genetics ; Prophylactic mastectomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Background: The discovery of a cadre of breast cancer susceptibility genes has resulted in an increase in the number of women seeking information about prophylactic breast surgery, but virtually no large-scale prospective databases exist to assist women considering prophylactic mastectomy. Methods: The authors constructed a National Prophylactic Mastectomy Registry comprised of a volunteer population of 817 women from 43 states who have undergone prophylactic mastectomy. Results: In the registry, 370 women had undergone bilateral prophylactic mastectomy. Twenty-one (5%) women expressed regrets about the procedure. The median follow-up was 14.6 years (mean 14.8 years; range 0.2–51 years). Those with regrets were subsetted into those with major (n=10) or minor (n=7) regrets. Regrets were more common in those women with whom discussion about prophylactic mastectomy was initiated by a physician (19/255), compared with patients who initiated the discussion themselves (2/108;P〈.05). Conclusions: The overall satisfaction rate of 95% reported here may be explained by the voluntary nature of this registry. The most important factor that predicts an unfavorable outcome following bilateral prophylactic mastectomy is a physician-initiated discussion.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1364-6753
    Keywords: Key words Alzheimer disease ; Risk factors ; Parental age ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: ABSTRACT We compared the parental age at birth of patients with Alzheimer disease (AD) with that of cognitively healthy control subjects. Within 206 carefully diagnosed AD patients, two groups were distinguished according to the likelihood of carrying a major gene for AD (MGAD). This likelihood was calculated by applying a Bayesian approach which incorporates data on aggregation of the disease, age at onset, and "censoring" ages within the family. All AD patients were ranked by MGAD probability. According to the sample's quartiles, two subgroups were defined representing the 52 individuals with the lowest and the 52 with the highest MGAD probability. Age at onset of dementia, education, and apolipoprotein E ε  4 allele frequencies were not statistically different between the two groups. Fathers of patients with a low MGAD probability were significantly older (35.7±8.1 years) than fathers of both other groups (high MGAD probability 31.3±6.9 years, P =0.004; controls 32.6±6.8 years, P =0.04, n=50). The differences for mothers were less pronounced and not statistically significant. These findings suggest that increased paternal age is a risk factor for AD in the absence of a major gene, whereas increased maternal age and AD are associated only weakly and independently of genetic disposition.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular medicine 76 (1998), S. 303-309 
    ISSN: 1432-1440
    Keywords: Key words Autosomal recessive polycystic kidney disease ; Linkage study ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Autosomal recessive polycystic kidney disease (ARPKD) is a rare inherited disorder which usually becomes clinically manifest in early childhood, although the spectrum of ARPKD is much more variable than generally known. Presentation of ARPKD at later ages and survival into adulthood have been observed in many cases. The responsible gene has been mapped to chromosome 6p. Thus there is no evidence of genetic heterogeneity. The most important indication for DNA diagnosis is the prenatal diagnosis in families with at least one affected child. The critical region has been narrowed with the use of recombinant families of about 4 cM. Several possible candidate genes have been excluded.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Monatsschrift Kinderheilkunde 146 (1998), S. 86-91 
    ISSN: 1433-0474
    Keywords: Schlüsselwörter Geschlechtliche Differenzierung ; Androgenrezeptor ; Genetik ; Genotyp-Phänotyp-Korrelation ; Key words Sexual differentiation ; Androgen receptor ; Genetics ; Genotype-phenotype-correlation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Summary The determination of the genetic background of sexual development has not only assisted in the explanation of intersex disorders, but also in the diagnosis and clinical management of affected individuals. The possibilities and limitations of molecular genetic studies can be illustrated by the example of androgen insensitivity syndromes. The search for the underlying mutations within the androgen receptor gene is technically possible even for large numbers of patients. The characterization of mutations can be performed with high specificity and sensitivity. While large gene defects are associated with complete loss of function of the receptor, point mutations with subsequent amino acid changes are responsible for the phenotypic variability of the disease. Type and location of the amino acid substitution may influence the clinical appearance of the individual patient, but the phenotype can be highly variable even with the same underlying mutation. This is probably due to regulation mechanisms within the cell of which the androgen receptor is only one, although important, part. Therefore, results of molecular genetic testing have to be interpreted only in connection with clinical and laboratory findings. Further research will focus on the elucidation of the cellular mechanisms of androgen action in order to introduce the results into the clinical management of patients with androgen insensitivity.
    Notes: Zusammenfassung Die Aufdeckung der genetischen Grundlagen von Störungen der Geschlechtsentwicklung hat neue Möglichkeiten nicht nur in der Erklärung dieser Erkrankungen, sondern auch für die Diagnostik und den klinischen Umgang mit betroffenen Individuen eröffnet. Am Beispiel der Androgenresistenz können die Erfolge, aber auch die Grenzen molekulargenetischer Untersuchungen aufgezeigt werden. Die Suche nach den zugrundeliegenden genetischen Veränderungen im Androgenrezeptorgen ist heute technisch auch zur Analyse größerer Patientenzahlen anwendbar. Der Nachweis von Mutationen kann mit hoher Sensitivität und Spezifität in großen Genabschnitten durchgeführt werden. Während größere Gendefekte mit einem völligen Funktionsverlust des Rezeptors einhergehen, sind Punktmutationen, die zu Veränderungen der Aminosäuresequenz führen, für das große phänotypische Spektrum der Androgenresistenz verantwortlich. Zwar wird das klinische Erscheinungsbild durch Art und Ort der Aminosäuresubstitution mitbestimmt, dennoch kann der Phänotyp auch bei gleicher Mutation sehr variabel sein. Dies ist mit großer Wahrscheinlichkeit auf zelluläre Regulationsmechanismen zurückzuführen, in deren Wirkungskette der Androgenrezeptor nur ein Glied, wenn auch ein wichtiges, darstellt. Daher müssen molekulargenetische Befunde immer in Zusammenhang mit den anamnestischen, klinischen und laborchemischen Parametern gesehen werden. Ziel wissenschaftlicher Untersuchungen ist es, die zellulären Mechanismen der Androgenwirkung weiter aufzuklären, um diese Erkenntnisse dann möglicherweise in die therapeutischen Entscheidungen bei Patienten mit Androgenresistenz einfließen zu lassen.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Archives of dermatological research 290 (1998), S. 463-476 
    ISSN: 1432-069X
    Keywords: Key words Psoriasis ; Genetics ; HLA ; Linkage ; Epidemiology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Non-pustular psoriasis consists of two disease subtypes, type I and type II, which demonstrate distinct characteristics. Firstly the disease presents in different decades of life, in type I before the age of 40 years and later in type II. Secondly, contrasting frequencies of HLA alleles are found: type I patients express predominantly HLA-Cw6, -B57, and -DR7, whereas in type II patients HLA-Cw2 is overrepresented. Finally, familial inheritance is found in type I but not in type II psoriasis. The study of concomitant diseases in psoriasis contributes to deciphering the distinct patterns of the disease. Defence against invading microorganisms seems better developed in psoriatics than in controls. This evolutionary benefit may have caused the overall high incidence of psoriasis of 2%. Psoriasis is a multifactorial and heterogenetically inherited disease. The heterogeneity is evident by the diversity of genetically linked markers. The multifactorial component results from the observation of external trigger mechanisms, such as the Koebner phenomenon, stress and the intake of certain drugs. Twin studies have shown that environmental factors contribute to the onset of the disease. In type I psoriasis, special extended haplotypes such as EH57.1 (HLA-Cw6-B57-DRB1*0701-DQA1*0201-DQBl*0303) and EH65.1 (HLA-Cw8-B65-DRB1*0102-DQB1*0501) have been found to be increased. The application of microsatellite techniques has identified distinct positions on several chromosomes at which putative psoriasis genes may be located. Disease susceptibility genes are thought to be present on chromosomes 4q, 6p, 16q, 17q and 20p. Moreover, on chromosome 1q, genes regulating epidermal differentiation have been identified. Linkage to this area has been proposed. Furthermore, psoriasis gene loci on chromosomes 2, 8 and 20 have been suggested.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Neurogenetics 1 (1998), S. 153-163 
    ISSN: 1364-6753
    Keywords: Key words Epilepsy ; Genetics ; Linkage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: ABSTRACT Despite several lines of evidence indicating a strong genetic influence in the etiology of idiopathic epilepsies, progress in the mapping and identification of human epilepsy genes has been limited until recently. In addition to the localisation and/or isolation of several genes causing progressive epilepsies associated with cerebral degeneration, at least seven human genomic regions (6p, 8q, 10q, 15q, 16p, 19q, 20q) are now known to harbour genes implicated in idiopathic epilepsies. In the case of nocturnal frontal lobe epilepsy, mutations in a nicotinic acetylcholine receptor subunit gene have been identified. Systematic studies of rare epileptic disorders inherited as monogenic Mendelian traits, as well as studies on more complex polygenic idiopathic epilepsies, are still needed in order to identify all the epilepsy genes. This will allow better diagnosis and genetic counseling in families of affected individuals, a better understanding of both the pathophysiology of epilepsies and normal brain functioning, and the design of new pharmacological and genetic therapies.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomedical science 5 (1998), S. 28-30 
    ISSN: 1423-0127
    Keywords: Genetics ; Schizophrenia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Evidence for genetic factors in schizophrenia is reviewed with regard to family, twin and adoption studies, and recent advances in molecular genetic technology are applied to explore possible gene loci susceptible to schizophrenia. Application of neuropsychological and neuroimaging methodologies are also reviewed with an aim to develop criteria for defining phenotypes for genetic studies.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1432-1076
    Keywords: Key words Febrile seizures ; Genetics ; Family ; Risk factors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract To quantify the risk of febrile seizures (FS) in relatives of children with FS and to predict the risk of FS in siblings, we calculated cumulative risks of FS in first degree relatives of 129 children with FS. The study was conducted as a prospective follow up study of FS recurrences at the outpatient clinic of the Sophia Children's Hospital in Rotterdam. Thirteen parents and 12 siblings had experienced FS, accounting for a 6-year cumulative risk of 7%. The risk of FS was increased in relatives of children with recurrent FS (12%). The risk of FS in siblings (10%) in our study was more than twice the average risk in a similar population (4%). A positive FS history in a parent, young age at onset in the proband, and recurrences in the proband were selected in a multivariable prediction model. If two or more of these risk factors were present, the risk of West European siblings to develop FS was 46% (hazard ratio 5.4). Conclusion The cumulative risk of FS in siblings of children with FS is increased. The age attained risk of FS can be estimated using a practical model incorporating three readily available risk factors.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of comparative physiology 182 (1998), S. 489-500 
    ISSN: 1432-1351
    Keywords: Key words Honey bee ; Behavior ; Genetics ; Neurobiology ; Foraging
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Honey bee foragers were tested for their proboscis extension response (PER) to water and varying solutions of sucrose. Returning pollen and nectar foragers were collected at the entrance of a colony and were assayed in the laboratory. Pollen foragers had a significantly higher probability of responding to water and to lower concentrations of sucrose. Bees derived from artificially selected high- and low-pollen-hoarding strains were also tested using the proboscis extension assay. Returning foragers were captured and tested for PERs to 30% sucrose. Results demonstrated a genotypic effect on PERs of returning foragers. The PERs of departing high- and low-strain foragers were consistent with those of returning foragers. The PERs were related to nectar and water reward perception of foragers. High strain bees were more likely to return with loads of water and lower concentrations of sucrose than foragers from the low pollen strain. Low-strain bees were more likely to return empty. We identified a previously mapped genomic region that contains a variable quantitative trait locus that appears to influence sucrose response thresholds. These studies demonstrate a gene-brain-behavior pathway that can be altered as a consequence of colony-level selection for quantities of stored food.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Acta diabetologica 35 (1998), S. 109-111 
    ISSN: 1432-5233
    Keywords: Key words BB rat ; Diabetes ; Genetics ; Crossing study
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Several crossing studies with diabetic BB rats have shown that in addition to the lymphopenia (Iddm1) and the MHC class II genes of the RT1u haplotype (Iddm2) there are further non-MHC genes essential for diabetes development. Because diabetes-resistant inbred rat strains may be homozygous for one of the diabetogenic non-MHC genes, masking the expression of diabetogenic genes and leading to an underestimation of the number of diabetogenic genes, we crossed wild and diabetic BB/OK rats. The F1 hybrids were backcrossed onto diabetic female (BC1W-F, n=97) and male BB/OK rats (BC1W-M, n=98) transferred to a specified-pathogen-free environment and studied for the frequency and age at onset of diabetes up to an age of 30 weeks. Comparing the results of these BC1 W hybrids with similarly derived hybrids using diabetes-resistant DA rats (BC1DA-F, n=113; BC1DA-M, n=216), the diabetes frequency in total was comparable indicating the action of three recessive genes. The percentage of diabetics in Iddm1 and Iddm2 homozygotes confirmed the existence of the third gene, Iddm3, but there were some sex differences; significantly more male than female BC1W-F and significantly more BC1DA-M than BC1DA-F males were diabetic. Regarding the age at onset, the BC1W-F hybrids manifested not only significantly earlier, but also more uniformly than BC1DA-F and BC1-M hybrids.
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  • 11
    ISSN: 1432-5233
    Keywords: Key words Non-insulin-dependent diabetes mellitus ; MODY ; Hepatocyte nuclear factor-1α ; Genetics ; Microsatellite polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Recently, hepatocyte nuclear factor-1α (HNF-1α, which is encoded by the TCF1 gene) mutations were reported in a subset of patients with maturity onset diabetes of the young (MODY3). We studied the contribution of TCF1 to genetic susceptibility to common non-insulin-dependent diabetes mellitus (type 2) in Japanese subjects by investigating allelic association with type 2 diabetes use of three markers. We also studied the frequency of the G191D mutation, the only mutation of TCF1 reported so far in late-onset type 2 diabetes. A total of 356 subjects were studied. There were no significant differences in allele frequency of the three markers between patients with type 2 diabetes and control subjects. A G191D mutation was not found in the subjects studied, giving a frequency of less than 0.4% in common type 2 diabetes. The lack of association of type 2 diabetes with three markers in and near TCF1 suggests that mutations in TCF1 derived from a limited number of founders are not a major cause of common type 2 diabetes even in the genetically homogeneous Japanese population. The data also indicate that the G191D mutation in TCF1 plays little, if any, role in susceptibility to common type 2 diabetes in the Japanese.
    Type of Medium: Electronic Resource
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  • 12
    ISSN: 1432-2242
    Keywords: Key words Cupressus sempervirens ; Cytology ; Megasporogenesis ; Megagametogenesis ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The processes of megasporogenesis and early megagametogenesis were cytologically investigated in Cupressus sempervirens L. in order to elucidate, at the cellular level, the origin of the megagametophyte. After pollination, sporogenous tissue developed in the chalazal region of the nucellus, but only one megaspore mother cell differentiated and divided meiotically without cell-wall formation. This led to the development of a cell with four nuclei which directly functioned as a megaspore. The C. sempervirens megagametophyte is thus tetrasporic, in contrast to the majority of conifers where the megagametophyte is monosporic. The consequenses of this observation are discussed from a genetics point of view.
    Type of Medium: Electronic Resource
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  • 13
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 97 (1998), S. 1269-1278 
    ISSN: 1432-2242
    Keywords: Key words Simple sequence repeat (SSR) ; Microsatellites ; Molecular markers ; Genetics ; Kiwifruit
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  We have isolated and sequenced 263 microsatellite-containing clones from two small insert libraries of Actinidia chinensis enriched for (AC/GT) and (AG/CT) repeats, respectively. Primer pairs were designed for 203 microsatellite loci and successfully amplified from both plasmid and A. chinensis genomic DNA. In this paper we report the sequences of 40 primer pairs for which we have demonstrated Mendelian segregation in the progeny from controlled crosses. The polymorphism of ten microsatellites of each type was evaluated in four diploid and six tetraploid genotypes of A. chinensis. All microsatellites proved to be polymorphic, the number of alleles per locus detected in polyacrylamide sequencing gels ranging from 9 to 17. The high degree of polymorphism in Actinidia renders these markers useful either for mapping in A. chinensis or for fingerprinting cultivars of both domesticated kiwifruit species (A. chinensis and A. deliciosa). While most primer pairs produced single amplification products, about 20% generated banding patterns consistent with the amplification of two different loci. This supports the hypothesis that diploid species of Actinidia (2n=2x=58) are polyploid in origin with a basic chromosome number x=14/15 and that chromosome duplication may have occurred during the evolution of the genus. Finally, we have assayed the cross-species transportability of primer pairs designed from A. chinensis sequences and have found extensive cross-species amplification within the genus Actinidia; 75% of primer pairs gave successful amplification in the eight species assayed (A. arguta, A. rufa, A. polygama, A. chrysantha, A. callosa, A. hemsleyana, A. eriantha, and A. deliciosa), which are representative of the four sections into which the genus is currently split.
    Type of Medium: Electronic Resource
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  • 14
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 96 (1998), S. 588-601 
    ISSN: 1432-2242
    Keywords: Key words Fruit trees ; Genetics ; Almond ; Prunus amygdalus ; Breeding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The large size and the long generation time of fruit trees generally reduce the possibilities of obtaining genetic information on the transmission and heritability of useful agronomic traits in these species. However, from breeding work carried out with fruit trees, an important amount of data is now available, although large differences are apparent among the different species. There is not much information known about almond compared to what is available on other Prunus fruit species, but more data have been accumulated on it than on most of the other nut trees, thus making almond special among all the temperate fruit and nut species. Only five qualitative traits have been described in almond, with an additional two also possibly qualitative. Heritabilities have been estimated for an important number of quantitative traits, mainly phenological times and fruit characters. Important information is available on molecular markers, including enzymes, RFLPs, RAPDs and other recently developed markers. Linkages, however, have only been established among molecular markers, allowing accurate genetic maps to be built but not yet enabling agronomical characters to be located in these maps, probably because the latter have not been sufficiently studied. The effectiveness of the application of genetic maps in plant breeding will depend on the accuracy of the study of different agronomic traits and their expression, implying more field work and recognition of this work. Ultimately, any new fruit cultivar has to be grown in the field and has to allow the grower to make a profit.
    Type of Medium: Electronic Resource
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  • 15
    Electronic Resource
    Electronic Resource
    Springer
    Behavioral ecology and sociobiology 43 (1998), S. 191-196 
    ISSN: 1432-0762
    Keywords: Key words Honeybees ; Scouting ; Division of labor ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Every recruitment system in social insects requires some individuals that serve as scouts, foragers that search independently for food sources. It is not well understood which factors influence whether an individual becomes a scout or a recruit, nor how the division of labor between the two forager groups is regulated. It is shown here for honeybees (Apis mellifera), using two different molecular techniques, that there is a genetically based difference in the probability that individuals will scout independently for food. In contrast to earlier suggestions, experimental tests showed that the age of a bee does not seem to influence its probability of becoming a scout or a recruit. Furthermore, scout bees do not search opportunistically for either pollen or nectar but, rather, individuals have preferences that are genetically based. These findings are discussed in the framework of foraging regulation by specialization in honeybees and the adaptive significance of polyandry.
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  • 16
    Electronic Resource
    Electronic Resource
    Springer
    Neurological sciences 19 (1998), S. 271-276 
    ISSN: 1590-3478
    Keywords: Neuronal ceroid lipofuscinosis ; Clinical features ; Classification ; Diagnosis ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Sommario Le ceroido lipofuscinosi neuronali (NCL) sono tra le encefalopatie progressive più freguenti nell'infanzia ed interessano, seppure più raramente, l'adulto. Clinicamente sono caratterizzate da demenza, deficit visivo, epilessia e disturbi motori. Gli aspetti patologici specifici sono rappresentati da degenerazione neuronale ed accumulo lisosomiale di lipopigmento in differenti tipi cellulari. Il difetto biochimico della malattia non e noto. La classificazione delle NCL, basata su criteri clinici, distingue sei forme classiche ed altre forme atipiche. L'elettrofisiologia e la neuroradiologia sono di importante ausilio diagnostico, ma la diagnosi si fonda sull'identificazione dell'accumulo di lipopigmento the presenta pattern ultrastrutturali specifici. Differenti difetti genetici sono stati dimostrati in diverse forme cliniche, ma il meccanismo patogenetico molecolare rimane ancora da chiarire.
    Notes: Abstract Neuronal ceroid lipofuscinoses (NCLs) are among the most common neurodegenerative diseases in childhood but rarely present in adulthood. The main symptoms are psychomotor deterioration, visual failure, epilepsy and motor disturbances. The NCLs are morphologically characterized by the accumulation of lipopigments within numerous cell types and loss of neurons. Pathogenesis is unknown. The current clinical classification recognizes six classic types of NCL and several atypical forms. Electrophysiological and neuroradiological findings may be of diagnostic significance, but disease recognition rests on the demonstration of a typical ultrastructural pattern. Genetic studies have demonstrated that several different genetic loci are involved in the pathogenesis of NCL, but the molecular mechanisms underlying neuronal death and lipopigment accumulation are not understood.
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  • 17
    Electronic Resource
    Electronic Resource
    Springer
    Behavior genetics 28 (1998), S. 265-278 
    ISSN: 1573-3297
    Keywords: Genetics ; body mass index ; adolescents ; race ; sex
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Psychology
    Notes: Abstract The present study uses a behavioral genetic design to investigate the genetic and environmental influences on variation in adolescent body mass index (BMI) and to determine whether the relative influences of genetic and environmental factors on variation in BMI are similar across racial groups and sexes. Data for the present study come from the National Longitudinal Study on Adolescent Health (Add Health), a large, nationally representative study of adolescent health and health-related behaviors. The Add Health sample contains a subset of sibling pairs that differs in levels of genetic relatedness, making it well suited for behavioral genetics analyses. The present study examines whether genetic and environmental influences on adolescent BMI are the same for males and females and for Black and White adolescents. Results indicate that genetic factors contribute substantially to individual differences in adolescent BMI, explaining between 45 and 85% of the variance in BMI. Furthermore, based on an analysis of opposite-sex sibling pairs, the genes that influence variation in adolescent BMI are similar for males and females. However, the relative importance of genetic and environmental influences on variation in BMI differs for males and females and for Blacks and Whites. Although parameter estimates could be constrained to be equal for Black and White males, they could not be constrained to be equal for Black and White females. Moreover, the best-fitting model for Black females was an ADE model, for White females it was an ACE model, and for males it was an AE model. Thus, shared environmental influences are significant for White female adolescents, but not for Black females or males. Likewise, nonadditive genetic influences are indicated for Black females, but not for White females or males. Implications of these results are discussed.
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  • 18
    Electronic Resource
    Electronic Resource
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    Journal of biological physics 24 (1998), S. 41-58 
    ISSN: 1573-0689
    Keywords: Neural networks ; Associative memory ; Brain functions ; Disordered systems ; Genetics ; Synergetics ; Self-organization ; Vitreous state
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Non-spin glasses possess a number of specific features which, in structural and dynamic aspects, are close to conditions necessary for neural networks to function. In a disordered network there exists a plurality of structural parameters and a number of two-level states defined by double-well potentials. Their characteristics are specified by the conditions of glass formation, i.e. by genesis. The thermodynamic description of glass as a self-organizing system (that does not require introducing an interacting potential model) leads to an unambiguous conclusion that its frequency spectrum is predetermined by the structure, which is characterized by zero-point entropy. Glass is a natural system of oscillators which form a disordered network. In this sense, glass conforms to a known model of a disordered neural network formed by interconnected oscillators. If one assumes that in living organisms the structure of a neural network (the brain) is inherited according to a genetic mechanism, the quickness of learning and recognition of patterns, the stability of associative memory and other capabilities have to be inherited genetically. The more ordered a neural network formed by distinguishable neurons, the better its capabilities.
    Type of Medium: Electronic Resource
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  • 19
    Electronic Resource
    Electronic Resource
    Springer
    Space science reviews 84 (1998), S. 199-206 
    ISSN: 1572-9672
    Keywords: Nuclear reactions ; Nucleosynthesis ; Abundances ; Stars:Evolution ; Interior ; Rotation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We first recall the observational and theoretical facts that constitute the so-called 3He problem. We then review the chemical anomalies that could be related to the destruction of 3He in red giants stars. We show how a simple consistent mechanism can lead to the destruction of 3He in low mass stars and simultaneously account for the low 12C/13C ratios and low lithium abundances observed in giant stars of different populations. This process should both naturally account for the recent measurements of 3He/H in galactic HII regions and allow for high values of 3He observed in some planetary nebulae. We propose a simple statistical estimation of the fraction of stars that may be affected by this process.
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  • 20
    ISSN: 0006-3525
    Keywords: folding type-specific secondary structure propensities ; amino acids ; α-helical proteins ; β sheet proteins ; α/β proteins ; α+β proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35-49, 1998
    Additional Material: 6 Ill.
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  • 21
    Electronic Resource
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    Biopolymers 45 (1998), S. 69-83 
    ISSN: 0006-3525
    Keywords: DNA branched junctions ; branch migration ; superhelical torque ; control of DNA structure ; endonuclease VII ; nanomechanical device ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA branched junctions are analogues of Holliday junction recombination intermediates. Partially mobile junctions contain a limited amount of homology flanking the branch point. A partially mobile DNA branched junction has been incorporated into a synthetic double-stranded circular DNA molecule. The junction is flanked by four homologous nucleotide pairs, so that there are five possible locations for the branch point. Two opposite arms of the branched junction are joined to form the circular molecule, which contains 262 nucleotides to the base of the junction. This molecule represents a system whereby torque applied to the circular molecule can have an impact on the junction, by relocating its branch point. Ligation of the molecule produces two topoisomers; about 87% of the product is a relaxed molecule, and the rest is a molecule with one positive supercoil. The position of the branch point is assayed by cleaving the molecule with endonuclease VII. We find that the major site of the branch point in the relaxed topoisomer is at the maximally extruded position in the relaxed molecule. Upon the addition of ethidium, the major site of the branch point migrates to the minimally extruded position. © 1998 John Wiley & Sons, Inc. Biopoly 45: 69-83, 1998
    Additional Material: 9 Ill.
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  • 22
    ISSN: 0006-3525
    Keywords: conformation ; aggregation ; κ-carrageenan ; flow field-flow fractionation ; multiangle light scattering ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relatively novel combination of flow field-flow fractionation (FFF) and multiangle light scattering (MALS) was employed to study a nondegraded κ-carrageenan in different 0.1M salt solutions. The applicability of the technique was tested, and the effects of salt type and salt composition on the molar mass and radius of gyration were studied. A conformational ordering was induced at room temperature by switching the solvent from 0.1M NaCl (coil form) to 0.1M NaI (helix form). An approximate doubling of the average molar mass and an increase in radius of gyration was then observed, in agreement with results obtained previously using size exclusion chromatography-MALS. This increase in size was attributed to conformational ordering and to the formation of double helices. Severe aggregation was observed above 40% CsI in the 0.1M mixed salt solution of CsI and NaI. This was ascribed to the association of helices into large aggregates. For these large associates, having molar masses of several millions, a reversal of the elution order in flow FFF was detected. © 1998 John Wiley & Sons, Inc. Biopoly 45: 85-96 1998
    Additional Material: 10 Ill.
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  • 23
    Electronic Resource
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    Biopolymers 45 (1998), S. 119-133 
    ISSN: 0006-3525
    Keywords: conformations of D-alanyl-D-alanine ; β-lactam ; structural overlay ; AMBER force field ; AM1 ; ab initio ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this article a conformational analysis of the D-alanyl-D-alanine dipeptide, both charged and neutral, has been carried out. The preferred conformations were determined by means of ab initio and semiempirical quantum, together with empirical force field calculations. The AMBER* force field and the 6-31 + G** and 6-31G** ab initio levels give rise to a coincident minimum energy structure, which, on the other hand, differs from that determined by AM1, 3-21 + G, and 3-21G. The solvent effect on the different charged and neutral conformations have been considered through the AMSOL semiempirical method. A quantification regarding the structural similarities between the different dipeptide conformations and the ampicillin has been performed. The results show that the best overlay is attained by the minimum structure energy obtained by using the 6-31 + G** methodology, which presents a planar amidic nitrogen. © 1998 John Wiley & Sons, Inc. Biopoly 45: 119-133, 1998
    Additional Material: 5 Ill.
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  • 24
    ISSN: 0006-3525
    Keywords: chemical oxidation ; cellulose ; conformational transition ; capillary viscosity ; microcalorimetry ; calcium ions ; gels ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational behavior of different molecular weight fractions of a synthetic C6-oxidized derivative of cellulose were investigated by means of capillary viscometry, CD, and microcalorimetric measurements. Experiments were carried out in the presence of either monovalent or divalent counterions.The experimental data indicated that C6-oxidized cellulose can assume an ordered extended conformation at low ionic strength, induced by the intrachain repulsions of negative charges. This conformation was suggested to be very similar to the fully extended structure of cellulose. In addition to this, upon increasing the ionic strength, a conformational transition of the order-to-disorder type occurred. In fact, the screening of the electrostatic repulsions introduced a number of conformational kinks into the cellulosic backbone, which enabled the polymer to assume a more coiled conformation hence producing less viscous aqueous solutions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 157-163, 1998
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  • 25
    ISSN: 0006-3525
    Keywords: conformational stability ; biological polyelectrolytes ; enthalpy ; entropy ; conformational transitions ; carrageenan ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new method is proposed for the determination of the enthalpy and entropy changes of nonionic origin upon conformational transition of linear biopolyelectrolytes in solution. For all transition midpoints, defined by given temperature and ionic strength, the total free energy change of the system is zero, which means that the nonionic contribution to the free energy change is equal in value and opposite in sign to the polyelectrolytic one. The counterion condensation theory of linear polyelectrolytes provides for the appropriate analytical expression to be used in such calculations. Linear plots of the proper functions of the calculated free energy changes vs the proper functions of temperature allows for the determination of the enthalpic and entropic terms of the nonionic free energy change of transition.The method has been applied to the extensive available data of the ion-induced conformational change of κ-carrageenan, a linear sulfated galactan extracted from seaweeds. The method has proved very successful, with the results showing a remarkable convergency of the enthalpy values for different monovalent counterions. On the other hand, the above approach has made it possible to explain the known effect of counterion specificity on the transition by a small difference in the nonionic entropic contributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 203-216, 1998
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  • 26
    ISSN: 0006-3525
    Keywords: uv resonance Raman spectroscopy ; Raman cross section ; hypochromism ; DNA ; deoxynucleoside ; protein ; aromatic amino acid ; virus assembly ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ultraviolet resonance Raman (UVRR) spectra of H2O and D2O solutions of the nucleoside (dA, dG, dC, dT) and aromatic amino acid (Phe, Trp, Tyr) constituents of DNA viruses have been obtained with laser excitation wavelengths of 257, 244, 238, and 229 nm. Using the 981 cm-1 marker of Na2SO4 as an internal standard, Raman frequencies and scattering cross sections were evaluated for all prominent UVRR bands at each excitation wavelength. The results show that UVRR cross sections of both the nucleosides and amino acids are strongly dependent on excitation wavelength and constitute sensitive and selective probes of the residues. The results provide a library of UVRR marker bands for structural analysis of DNA viruses and other nucleoprotein assemblies. © 1998 John Wiley & Sons, Inc. Biopoly 45: 247-256, 1998
    Additional Material: 4 Ill.
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  • 27
    ISSN: 0006-3525
    Keywords: hemoglobin ; hexagonal bilayer ; Lumbricus ; electron microscopy ; three-dimensional reconstruction ; small-angle x-ray scattering ; three-dimensional models ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The quaternary structure of Lumbricus terrestris hemoglobin was investigated by small-angle x-ray scattering (SAXS). Based on the SAXS data from several independent experiments, a three-dimensional (3D) consensus model was established to simulate the solution structure of this complex protein at low resolution (about 3 nm) and to yield the particle dimensions. The model is built up from a large number of small spheres of different weights, a result of the two-step procedure used to calculate the SAXS model. It accounts for the arrangement of 12 subunits in a hexagonal bilayer structure and for an additional central unit of cylinder-like shape. This model provides an excellent fit of the experimental scattering curve of the protein up to h = 1 nm-1 and a nearly perfect fit of the experimental distance distribution function p(r) in the whole range. Scattering curves and p(r) functions were also calculated for low-resolution models based on 3D reconstructions obtained by cryoelectron microscopy (EM). The calculated functions of these models also provide a very good fit of the experimental scattering curve (even at h 〉 1 nm-1) and p(r) function, if hydration is taken into account and the original model coordinates are slightly rescaled. The comparison of models reveals that both the SAXS-based and the EM-based model lead to a similar simulation of the protein structure and to similar particle dimensions. The essential differences between the models concern the hexagonal bilayer arrangement (eclipsed in the SAXS model, one layer slightly rotated in the EM model), and the mass distribution, mainly on the surface and in the central part of the protein complex. © John Wiley & Sons, Inc. Biopoly 45: 289-298, 1998
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  • 28
    ISSN: 0006-3525
    Keywords: conformational changes ; vicinal glycosylation ; branched α-l-Rhap(1-2)[β-d-Galp(1-3)]-β-d-Glc1-OMe trisaccharide ; parent disaccharides ; hydrogen bond ; isotope effect ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformations of the α-l-Rhap(1-2)-β-d-Glc1-OMe and β-d-Galp(1-3)-β-d-Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d6 solution by 1H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An “isotopomer-selected NOE” method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular Φ,Ψ-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the Φ,Ψ grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1→2 and 1→3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average Φ,Ψ values of 38°, 17° for the 1→2 and 48°, 1° for the 1→3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues. © 1998 John Wiley & Sons, Inc. Biopoly 46: 417-432, 1998
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  • 29
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    Biopolymers 46 (1998), S. 489-492 
    ISSN: 0006-3525
    Keywords: refractive index increment ; proteins ; solvent ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The refractive index increment of a protein solution is a property not only of the protein, but also of the solvent. This is demonstrated theoretically and confirmed experimentally using analytical interferometry. © 1998 John Wiley & Sons, Inc. Biopoly 46: 489-492, 1998
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  • 30
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    Biopolymers 47 (1998), S. 1-1 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 31
    ISSN: 0006-3525
    Keywords: hepatitis A ; synthetic peptides ; CD ; liposomes ; computational study ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present study was undertaken to examine the structural features that may be important to explain the immunogenicity of the (110-121) peptide sequence (FWRGDLVFDFQV) of VP3 capsid protein of hepatitis A virus. A conformational analysis of the preferred conformations by CD and molecular mechanics was carried out. Present results suggest that the interaction with liposomes as biomembrane model induces and stabilizes the amphipathic β-structure of the peptide.To study the contribution of amino acid replacements at the RGD tripeptide as well as the influence of the peptide chain length on peptide conformation, solid-phase peptide synthesis of several peptide analogs was carried out and the peptide conformation was studied using CD spectroscopy. The results show that the RGD sequence is necessary to induce the β-structure in the presence of liposomes. © 1998 John Wiley & Sons, Inc. Biopoly 45: 479-492, 1998
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  • 32
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    Biopolymers 46 (1998), S. 31-37 
    ISSN: 0006-3525
    Keywords: DNA liquid crystals ; DNA fragments ; screened Coulomb interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The critical volume fractions pertaining to the formation of DNA liquid crystals were obtained from polarization microscopy, 31P-nmr, and phase separation experiments. The DNA length (approximately one to two times the persistence length 50 nm), ionic strength, and counterion variety dependencies are reported. The cholesteric-isotropic transition is interpreted in terms of the coexistence equations, which are derived from the solution free energy including orientational entropy and excluded volume effects. With the wormlike chain as reference system, the electrostatic contribution to the free energy is evaluated as a thermodynamic perturbation in the second virial approximation with a Debye-Hückel potential of mean force. The hard core contribution has been evaluated with scaled particle theory and/or a simple generalization of the Carnahan-Starling equation of state for hard spheres. For sufficiently high ionic strengths, the agreement is almost quantitative. At lower amounts of added salt deviations are observed, which are tentatively attributed to counterion screening effects. The contour length dependence agrees with a DNA persistence length 50 nm. © 1998 John Wiley & Sons, Inc. Biopoly 46: 31-37, 1998
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  • 33
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    Biopolymers 46 (1998), S. 245-252 
    ISSN: 0006-3525
    Keywords: gelatin ; gelation ; atomic force microscopy ; interfacial rheology ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Gelation of gelatin under various conditions has been followed by atomic force microscopy (AFM) with the objective of understanding more fully the structure formed during the gelation process. AFM images were obtained of the structures formed from both the bulk sol and in surface films during the onset of gelation. While gelation occurred in the bulk sol, the extent of helix formation was monitored by measurements of optical rotation, and the molecular aggregation was imaged by AFM. Interfacial gelatin films formed at the air-water interface were also studied. Measurements of surface tension and surface rheology were made periodically and Langmuir-Blodgett films were drawn from the interface to allow AFM imaging of the structure of the interfacial layer as a function of time. Structural studies reveal that at low levels of helical content the gelatin molecules assemble into aggregates containing short segments of dimensions comparable to those expected for gelatin triple helices. With time larger fibrous structures appear whose dimensions suggest that they are bundles of triple helices. As gelation proceeds, the number density of fibers increases at the expense of the smaller aggregates, eventually assembling into a fibrous network. The gel structure appears to be sensitive to the thermal history, and this is particularly important in determining the structure and properties of the interfacial films. © 1998 John Wiley & Sons, Inc. Biopoly 46: 245-252, 1998
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  • 34
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    Biopolymers 48 (1998), S. 65-81 
    ISSN: 0006-3525
    Keywords: nucleotide analogue interference mapping ; phosphorothioate ; group I intron ; interference suppression ; RNA ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I will outline several chemogenetic approaches used to determine the chemical basis of large ribozyme function and structure. The term chemogenetics was first used to describe site-specific functional group modification experiments in the analysis of DNA-protein interactions. Within the past few years equivalent experiments have been performed on large catalytic RNAs using both single-site substitution and interference mapping techniques with nucleotide analogues. While functional group mutagenesis is an important aspect of a chemogenetic approach, chemical correlates to genetic revertants and suppressors must also be realized for the genetic analogy to be intellectually valid and experimentally useful. Several examples of functional group revertants and suppressors have now been obtained within the Tetrahymena group I ribozyme. These experiments define an ensemble of tertiary hydrogen bonds that have made it possible to construct a detailed model of the ribozyme catalytic core. The model includes a functionally important monovalent metal ion binding site, a wobble-wobble receptor motif for helix-helix packing interactions, and a minor groove triple helix. © 1998 John Wiley & Sons, Inc. Biopoly 48: 65-81, 1998
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  • 35
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    Biopolymers 48 (1998), S. 83-96 
    ISSN: 0006-3525
    Keywords: nucleic acid ; disulfide cross-link ; structure ; dynamics ; stability ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids. © 1998 John Wiley & Sons, Inc. Biopoly 48: 83-96, 1998
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  • 36
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    Biopolymers 48 (1998), S. 113-135 
    ISSN: 0006-3525
    Keywords: divalent cations ; magnesium ; RNA ; ion binding ; RNA folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Divalent cations, like magnesium, are crucial for the structural integrity and biological activity of RNA. In this article, we present a picture of how magnesium stabilizes a particular folded form of RNA. The overall stabilization of RNA by Mg2+ is given by the free energy of transferring RNA from a reference univalent salt solution to a mixed salt solution. This term has favorable energetic contributions from two distinct modes of binding: diffuse binding and site binding. In diffuse binding, fully hydrated Mg ions interact with the RNA via nonspecific long-range electrostatic interactions. In site binding, dehydrated Mg2+ interacts with anionic ligands specifically arranged by the RNA fold to act as coordinating ligands for the metal ion. Each of these modes has a strong coulombic contribution to binding; however, site binding is also characterized by substantial changes in ion solvation and other nonelectrostatic contributions. We will show how these energetic differences can be exploited to experimentally distinguish between these two classes of ions using analyses of binding polynomials. We survey a number of specific systems in which Mg2+-RNA interactions have been studied. In well-characterized systems such as certain tRNAs and some rRNA fragments these studies show that site-bound ions can play an important role in RNA stability. However, the crucial role of diffusely bound ions is also evident. We emphasize that diffuse binding can only be described rigorously by a model that accounts for long-range electrostatic forces. To fully understand the role of magnesium ions in RNA stability, theoretical models describing electrostatic forces in systems with complicated structures must be developed. © 1999 John Wiley & Sons, Inc. Biopoly 48: 113-135, 1998
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  • 37
    ISSN: 0006-3525
    Keywords: 1H-nmr ; molecular modeling ; peptaibol ; peptide-lipid interaction ; sodium dodecyl sulfate micelles ; trichorzianin TA VII ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Trichorzianin TA VII, Ac0 U1 A2 A3 U4 J5 Q6 U7 U8 U9 S10 L11 U12 P13 V14 U15 I16 Q17 Q18 Fol19, is a nonadecapeptide member of the peptaibol antibiotics biosynthesized by Trichoderma soil fungi, which is characterized by a high proportion of the α,α-dialkylated amino acids, α-aminoisobutyric acid (Aib, U) and isovaline (Iva, J), an acetylated N-terminus and a C-terminal phenylalaninol (Pheol, Fol). The main interest in such peptides stems from their ability to interact with phospholipid bilayers and form voltage-dependent transmembrane channels in planar lipid bilayers. In order to provide insights into the lipid-peptide interaction promoting the voltage gating, the conformational study of TA VII in the presence of perdeuterated sodium dodecyl sulfate (SDS-d25) micelles has been carried out. 1H sequential assignments have been performed with the use of two-dimensional homo- and -heteronuclear nmr techniques including double quantum filtered correlated spectroscopy, homonuclear Hartmann-Hahn, nuclear Overhauser effect spectroscopy, 1H-13C heteronuclear single quantum correlation, and heteronuclear multiple bond correlation. Conformational parameters, such as 3JNHCαH coupling constants, temperature coefficients of amide protons (Δδ/ΔTNH) and quantitative nuclear Overhauser enhancement data, lead to detailed structural information. Ninety-eight three-dimensional structures consistent with the nmr data were generated from 231 interproton distances and six Φ dihedral angle restraints, using restrained molecular dynamics and energy minimization calculations. The average rms deviation between the 98 refined structures and the energy-minimized average structure is 0.59 Å for the backbone atoms. The structure of trichorzianin TA VII associated with SDS micelles, as determined by these methods, is characterized by two right-handed helical segments involving residues 1-8 and 11-19, linked by a β-turn that leads to an angle about 90°-100° between the two helix axes; residues 18 and 19 at the end of the C-terminal helix exhibit multiple conformations. © 1998 John Wiley & Sons, Inc. Biopoly 46: 75-88, 1998
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  • 38
    ISSN: 0006-3525
    Keywords: 9-hydroxyellipticine ; DNA ; CD ; linear dichroism ; resonance light scattering ; intercalation ; drug-drug interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of 9-hydroxyellipticine to calf thymus DNA, poly[d(A-T)]2, and poly-[d(G-C)]2 has been studied in detail by means of CD, linear dichroism, resonance light scattering, and molecular dynamics. The transition moment polarizations of 9-hydroxyelliptiycine were determined in polyvinyl alcohol stretched film. Spectroscopic solution studies of the DNA/drug complex are combined with theoretical CD calculations using the final 50 ps of a series of molecular dynamics simulations as input. The spectroscopic data shows 9-hydroxyellipticine to adopt two main binding modes, one intercalative and the other a stacked binding mode involving the formation of drug oligomers in the DNA major groove. Analysis of the intercalated binding mode in poly[d(A-T)]2 suggests the 9-hydroxyellipticine hydroxyl group lies in the minor groove and hydrogen bonds to water with the pyridine ring protruding into the major groove. The stacked binding mode was examined using resonance light scattering and it was concluded that the drug was forming small oligomer stacks rather than extended aggregates. Reduced linear dichroism measurements suggested a binding geometry that precluded a minor groove binding mode where the plane of the drug makes a 45° angle with the plane of the bases. Thus it was concluded that the drug stacks in the major groove. No obvious differences in the mode of binding of 9-hydroxyellipticine were observed between different DNA sequences; however, the stacked binding mode appeared to be more favorable for calf thymus DNA and poly[d(G-C)]2 than for poly[d(A-T)]2, an observation that could be explained by the slightly greater steric hindrance of the poly[d(A-T)]2 major groove. A strong concentration dependence was observed for the two binding modes where intercalation is favored at very low drug load, with stacking interactions becoming more prominent as the drug concentration is increased. Even at DNA : drug mixing ratios of 70:1 the stacked binding mode was still important for GC-rich DNAs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 127-143, 1998
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  • 39
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    Biopolymers 46 (1998), S. 169-179 
    ISSN: 0006-3525
    Keywords: macromolecular carriers ; drug targeting and delivery ; branched chain synthetic polypeptides ; membrane-synthetic polypeptide interaction ; lipid monolayers/bilayers ; polymer therapeutics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The surface properties at the air/water interface and the interaction of branched chain polymeric polypeptides with a general formula poly[Lys-(DL-Alam-X1)], where X = Π (AK), Ser (SAK), or Glu (EAK), with phospholipids were investigated. Polylysine derivatives with polycationic (SAK, AK) or amphoteric (EAK) were capable to spread and form stable monomolecular layers. The stability of monolayers at the air/water interface was dependent on the side-chain terminal amino acid residue of polymers and can be described by SAK 〈 AK 〈 EAK order. The area per amino acid residue values calculated from compression isotherms were in the same range as compared to those of linear poly-α-amino acids and proteins. Moreover, these polymers interact with phospholipid monomolecular layers composed of dipalmitoyl phosphatidyl choline (DPPC) or DPPC/PG (PG: phosphatidyl glycerol; 95/5, mol/mol). Data obtained from compression isotherms of phospholipids spread on aqueous polymer solutions at different initial surface pressure indicated that insertion into lipid monolayers for SAK or AK is more pronounced than for EAK. The interaction between branched polypeptides and phospholipid membranes was further investigated using lipid bilayers with DPPC/PG and fluorescent probes located either at the polar surface [1-(4-trimethylammonium-phenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH) sodium anilino naphthalene sulfonate (ANS)] or within the hydrophobic core (DPH) of the liposome. Changes in fluorescence intensity and in polarization were observed when TMA-DPH or ANS, but not DPH were used. Comparative data also indicate that all three polymers interact only with the outer surface of the bilayer, but even the most marked penetration of polycationic polypeptide (SAK) did not result in alteration of the ordered state of the alkyl chains in the bilayer. Taken together, data obtained from mono- or bilayer experiments suggest that the interaction between branched polymers and phospholipids are highly dependent on the charge properties (Ser vs Glu) and on the identity (Ser vs Ala) of side-chain terminating amino acids. The binding of polymers to the model membranes could be mainly driven by electrostatic forces, but the significant role of hydrophilic properties in case of SAK cannot be excluded. © 1998 John Wiley & Sons, Inc. Biopoly 46: 169-179, 1998
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  • 40
    ISSN: 0006-3525
    Keywords: Cα,α-dialkylated glycines ; molecular dynamics ; geometry and conformation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between the local backbone conformation and bond angles at Cα of symmetrically substituted Cα,α-dialkylated glycines (Cα,α-dimethylglycine or α-aminoisobutyric acid, Aib; Cα,α-diethylglycine, Deg; Cα,α-di-n-propylglycine, Dpg) has been investigated by molecular dynamics (MD) simulation adopting flat bottom harmonic potentials, instead of the usual harmonic restraints, for the Cα bond angles. The MD simulations show that the Cα bond angles are related to the local backbone conformation, irrespectively of the side-chain length of Aib, Deg, and Dpg residues. Moreover, the N-Cα-C′ (τ) angle is the most sensitive conformational parameter and, in the folded form, is always larger and more flexible than in the extended one. © 1998 John Wiley & Sons, Inc. Biopoly 46: 239-244, 1998
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  • 41
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    Biopolymers 46 (1998), S. 319-327 
    ISSN: 0006-3525
    Keywords: methionine ligation ; parathyroid hormones ; biomimetic ligation ; S-methylation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In biological systems, both proteolysis and aminolysis of amide bonds produce activated intermediates through acyl transfer reactions either inter- or intramolecularly. Protein splicing is an illustrative example that proceeds through a series of catalyzed acyl transfer reactions and culminates at an O- or S-acyl intermediate. This intermediate leads to an uncatalyzed acyl migration to form an amide bond in the spliced product. A ligation method mimicking the uncatalyzed final steps in protein splicing has been developed utilizing the acyl transfer amide-bond feature for the blockwise coupling of unprotected, free peptide segments at methionine (Met). The latent thiol moiety of Met can be exploited using homocysteine at the α-amino terminal position of a free peptide for transthioesterification with another free peptide containing an α-thioester to give an S-acyl intermediate. A subsequent, proximity-driven S- to N-acyl migration of this acyl intermediate spontaneously rearranges to form a homocysteinyl amide bond. S-methylation with excess p-nitrobenezensulfonate yields Met at the ligation site. The methionine ligation is selective and orthogonal, and is usually completed within 4 h when performed at slightly basic pH and under strongly reductive conditions. No side reactions due to acylation were observed with any other α-amines of both peptide segments as seen in the synthesis of parathyroid hormone peptides. Furthermore, cyclic peptide can also be obtained through the same strategy by placing both homocysteine at the amino terminus and the thioester at the carboxyl terminus in an unprotected peptide precursor. These biomimetic ligation strategies hold promise for engineering novel peptides and proteins. © 1998 John Wiley & Sons, Inc. Biopoly 46: 319-327, 1998
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  • 42
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    Biopolymers 46 (1998), S. 359-373 
    ISSN: 0006-3525
    Keywords: boundary element method ; DNA electrophoresis ; electrophoretic mobility of DNA ; free solution electrophoretic mobility of DNA ; ion relaxation, DNA electrophoresis ; modeling electrophoresis of polyions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Boundary element methods are used to model the free solution electrophoretic mobility of short DNA fragments. The Stern surfaces of the DNA fragments are modeled as plated cylinders that reproduce translational and rotational diffusion constants. The solvent-accessible and ion-accessible surfaces are taken to be coincident with the Stern surface. The mobilities are computed by solving simultaneously the coupled Navier-Stokes, Poisson, and ion-transport equations. The equilibrium electrostatics are treated at the level of the full Poisson-Boltzmann equation and ion relaxation is included. For polyions as highly charged as short DNA fragments, ion relaxation is substantial. At .11 M KCl, the simulated mobilities of a 20 base pair DNA fragment are in excellent agreement with experiment. At .04 M Tris acetate, pH = 8.0, the simulated mobilities are about 10-15% higher than experimental values and this discrepancy is attributed to the relatively large size of the Tris counterion. The length dependence of the mobility at .11 M KCl is also investigated. Earlier mobility studies on lysozyme are reexamined in view of the present findings. In addition to electrophoretic mobilities, the effective polyion charge measured in steady state electrophoresis and its relationship to the preferential interaction parameter γgG is briefly considered. © 1998 John Wiley & Sons, Inc. Biopoly 46: 359-373, 1998
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  • 43
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    Biopolymers 45 (1998), S. 341-346 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
    Additional Material: 5 Ill.
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  • 44
    ISSN: 0006-3525
    Keywords: diffusional encounter ; Brownian dynamics ; average Boltzmann factor ; acetylcholinesterase ; Poisson-Boltzmann ; electrostatics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The utility of the average Boltzmann factor around the active site of an enzyme as the predictor of the electrostatic enhancement of the substrate binding rate is tested on a set of data on wild-type acetylcholinesterase and 18 charge mutants recently obtained by Brownian dynamics simulations. A good correlation between the average Boltzmann factors and the substrate binding rate constants is found. The effects of single charge mutations on both the Boltzmann factor and the substrate binding rate constant are modest, i.e., 〈5 fold increase or decrease. This is consistent with the experimental results of Shafferman et al. but does not support their suggestion that the overall rate of the catalytic reaction is not limited by the diffusional encounter of acetylcholinesterase and its substrate. © 1998 John Wiley & Sons, Inc. Biopoly 45: 355-360, 1998
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  • 45
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    Biopolymers 45 (1998), S. 469-478 
    ISSN: 0006-3525
    Keywords: molecular dynamics ; hydrated proteins ; crystal structures ; density distributions ; globular proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpendicular radial distribution functions for water molecules around globular proteins. These universal functions may be used to reconstruct the unique three-dimensional solvent density distribution around every individual protein with a modest error. We discuss potential applications of this solvent treatment in protein x-ray crystallographic refinements and in theoretical modeling. We also present a fast, grid-based algorithm for construction of the perpendicular solvent density distributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 469-478, 1998
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  • 46
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    Biopolymers 47 (1998), S. 23-29 
    ISSN: 0006-3525
    Keywords: independently folded polypeptide motifs ; miniproteins ; natural target domains ; BBA motif ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper we present a redesign strategy for the development of uniquely folded polypeptide motifs of less than 40 residues. These mini proteins are based on natural target domains, including the zinc finger domains (BBA motif) Nomenclature corresponds to the defined elements of secondary structure, beginning at the N-terminus of the peptide. Roman lettering refers to a specific motif while Greek characters correspond to the elements of secondary structure within that motif. and the disulfide-rich snake and scorpion toxins (BBB motif). These motifs are designed to act as the molecular framework for the construction of novel functional polypeptides. We will explore the structural determinants of the folded BBA motif, inspired by the zinc finger peptides, in relation to the redesign process. © 1998 John Wiley & Sons, Inc. Biopoly 47: 23-29, 1998
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  • 47
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    Biopolymers 47 (1998), S. 75-81 
    ISSN: 0006-3525
    Keywords: ion channel ; synthetic peptide ; de novo design ; template-assembled synthetic proteins ; supramolecular assembly ; membrane protein ; planer lipid bilayers ; amphiphilic peptide ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To create ion channel function by synthetic peptides is a challenge in the de novo design of artificial membrane proteins. Amphiphilic α-helical motifs of ∼ 20 amino acid residues to span lipid bilayers are most often used for the creation of peptide ion channels. Template molecules to tether helical peptides have been employed to obtain more organized pore structures. Approaches to form molecular assembly of peptides in the membranes by hydrogen bonding have been also investigated. We have developed approaches to assemble helices with individual amino acid sequences to construct artificial helical proteins. Using one of these approaches, four helices corresponding to the voltage sensor segments (S4 in repeat I-IV) of the sodium channel were assembled on a peptide template to give a protein having ion channel activity with rectification. © 1998 John Wiley & Sons, Inc. Biopoly 47: 75-81, 1998
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  • 48
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    Biopolymers 47 (1998), S. 127-142 
    ISSN: 0006-3525
    Keywords: collagen mimetics ; triple helix ; peptoid ; template ; biophysics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Collagen peptidomimetics have been synthesized as an alternative to natural collagen. The incorporation of unnatural residues such as peptoids in the collagen sequences can demonstrate potent and specific biological activity and enhance the biostability against enzymatic degradation. Furthermore, the use of achiral peptoids simplifies synthetic strategies by reducing racemization problems. The peptoid residue N-isobutylglycine (Nleu) has been successfully incorporated into a series of collagen mimetics composed of Gly-Pro-Nleu, Gly-Nleu-Pro, and Gly-Nleu-Nleu. The discovery of template-assembled collagen mimetics and metal binding ability has laid the foundation for new opportunities in the design of novel collagen mimetic complexes. This review summarizes the synthesis and integrated biophysical analyses of the structures of these collagen mimetics. Solid phase segment condensation techniques have been utilized for the synthesis of the single chain and template-assembled analogues. The characterization of the collagen-like structures has been established by temperature-dependent optical rotation measurements, CD, NMR spectroscopy, and molecular modelling simulations. © 1998 John Wiley & Sons, Inc. Biopoly 47: 127-142, 1998
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  • 49
    ISSN: 0006-3525
    Keywords: non-natural amino acid ; peptide ; squarylium dye ; thin film ; poly(3-methylthiophene) ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We designed a polypeptide that behaves as a photodevice by using a non-natural amino acid with replacement of an α-hydrogen by a squarylium dye and succeeded in syntheses of the non-natural amino acid derivative containing a squarylium and its peptide with trialanine Ala-Ala-Ala. Strong dye-dye interactions were confirmed by absorption and CD spectra for the peptide in 2,2,2-trifluoroethanol solution and in water suspension. The non-natural amino acid derivative could be deposited onto a PMeT/Au electrode by the micelle disruption method. © 1998 John Wiley & Sons, Inc. Biopoly 47: 179-183, 1998
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  • 50
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    Biopolymers 47 (1998), S. 263-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 51
    ISSN: 0006-3525
    Keywords: electrostatically driven Monte Carlo method ; cluster analysis ; global energy minimum ; perturbed conformations ; conformational space ; lowest energy conformations ; polypeptide chain ; melittin, membrane-bound portion ; Empirical Conformational Energy Program for Peptides 3 ; annealing methods ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatically driven Monte Carlo (EDMC) method has been greatly improved by adding a series of new features, including a procedure for cluster analysis of the accepted conformations. This information is used to guide the search for the global energy minimum. Alternative procedures for generating perturbed conformations to sample the conformational space were also included. These procedures enhance the efficiency of the method by generating a larger number of low-energy conformations.The improved EDMC method has been used to explore the conformational space of a 20-residue polypeptide chain whose sequence corresponds to the membrane-bound portion of melittin. The ECEPP/3 (Empirical Conformational Energy Program for Peptides) algorithm was used to describe the conformational energy of the chain. After an exhaustive search involving 14 independent runs, the lowest energy conformation (LEC) (-91.0 kcal/mol) of the entire study was encountered in four of the runs, while conformations higher in energy by no more than 1.8 kcal/mol were found in the remaining runs with the exception of one of them (run 8). The LEC is identical to the conformation found recently by J. Lee, H.A. Scheraga, and S. Rackovsky [(1998) “Conformational Analysis of the 20-Residue Membrane-Bound Portion of Melittin by Conformational Space Annealing,” Biopolymers, Vol. 46, pp. 103-115] as the lowest energy conformation obtained in their study using the conformational space annealing method. These results suggest that this conformation corresponds to the global energy minimum of the ECEPP/3 potential function for this specific sequence; it also appears to be the conformation of lowest free energy. © 1998 John Wiley & Sons, Inc. Biopoly 46: 117-126, 1998
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  • 52
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    Biopolymers 46 (1998), S. 195-200 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 53
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    Biopolymers 46 (1998), S. 201-214 
    ISSN: 0006-3525
    Keywords: band broadening ; dispersion ; DNA ; gels ; electrophoresis ; fluorescence recovery ; photobleaching ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We determined quantitatively the band broadening effect during gel electrophoresis by measuring the longitudinal dispersion coefficient Dx, with a fluorescence recovery after photobleaching setup, coupled to an electrophoretic cell. We carried out measurements as a function of the electric field, the average pore size, and the molecular length of DNA fragments. Our results are in good agreement with the predictions of the biased reptation model with fluctuations described by T. A. Duke et al. [(1992) Physics Review Letters, vol. 69, pp. 3260-3263]. This agreement is observed on single-stranded DNA [persistence length ≅ 4 nm; B. Tinland et al. (1997) Macromolecules, vol. 30, pp. 5763-5765] in polyacrylamide gels and on double-stranded DNA (persistence length ≅ 50 nm) in agarose gels, two systems where the ratio between the average pore size and the Kuhn length is larger than 1. © 1998 John Wiley & Sons, Inc. Biopoly 46: 201-214, 1998
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  • 54
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    Biopolymers 46 (1998), S. 403-415 
    ISSN: 0006-3525
    Keywords: molecular dynamics ; DNA curvature ; DNA flexibility ; TATA box functionality ; TATA box binding protein (TBP) ; TBP recognition ; TBP binding ; TBP transcriptional activation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Four 1.5 ns molecular dynamics (MD) simulations were performed on the d(GCTATAAAAGGG) · d(CCCTTTTATAGC) double helix dodecamer bearing the Adenovirus major late promoter TATA element and three iso-composition mutants for which physical and biochemical data are available from the same laboratory. Three of these DNA sequences experimentally induce tight binding with the TATA box binding protein (TBP) and induce high transcription rates; the other DNA sequence induces much lower TBP binding and transcription. The x-ray crystal structures have previously shown that the duplex DNA in DNA-TBP complexes are highly bent. We performed and analyzed MD simulations for these four DNAs, whose experimental structures are not available, in order to address the issue of whether inherent DNA structure and flexibility play a role in establishing these observed preferences. A comparison of the experimental and simulated results demonstrated that DNA duplex sequence-dependent curvature and flexibility play a significant role in TBP recognition, binding, and transcriptional activation. © 1998 John Wiley & Sons, Inc. Biopoly 46: 403-415, 1998
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  • 55
    ISSN: 0006-3525
    Keywords: vibrational CD ; solution conformation ; alanine oligopeptides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution conformation of a number of small, linear alanine oligomers was investigated via ir (or vibrational) CD (VCD). We find that these oligopeptides assume distinct solution conformations that depend primarily on chain lengths, and to a lesser degree on temperature, ionic strength, and pH. As expected, the longer chain oligomers exhibit more distinct VCD features and, presumably, more stable solution structures. At the level of the hexamer, however, aggregation of the peptide occurs. The fast time scale of VCD allows solution structures to be detected that may not be observable using slower techniques such as various forms of nmr spectroscopy. The VCD results reported here confirm that it is generally possible to obtain conformational information for small, linear homo- and heterooligopeptides via VCD spectroscopy. In this respect, the sensitivity of VCD is similar to that of electronic CD. Furthermore, the temperature dependence of the VCD results indicate that at elevated temperatures, the increasing number of conformational states results in a loss of discernible conformers, and consequently, a broadening and weakening of the VCD features. © 1998 John Wiley & Sons, Inc. Biopoly 46: 455-463, 1998
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  • 56
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    Biopolymers 47 (1998), S. 5-22 
    ISSN: 0006-3525
    Keywords: hemoproteins ; model systems ; miniaturized proteins ; mimochromes ; helix structures ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present paper highlights and reviews current research in the field of hemoprotein models. Hemoproteins have been extensively studied in order to understand structure-function relationships, and to design new molecules with desired functions. A wide number of synthetic analogues have been developed, using quite different approaches. They differ in molecular structures, ranging from simple meso-substituted tetraaryl-metalloporphyrins and peptide-porphyrin conjugates.In this paper we summarize the state of the art on peptide based hemoprotein models. We also report here the approach used by us to develop a new class of molecules, named mimochromes. They can be regarded as miniaturized hemoproteins, because mimochromes are low molecular weight compounds with some structural and functional properties common to those of the parent high molecular weight protein. The basic structure of mimochromes is a deuteroporphyrin ring covalently linked to two helical peptide chains. Two molecules of this series have been fully characterized. All the information derived from their structural analysis has been applied to the design of new analogues with additional functions. © 1998 John Wiley & Sons, Inc. Biopoly 47: 5-22, 1998
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  • 57
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    Biopolymers 46 (1998), S. 503-516 
    ISSN: 0006-3525
    Keywords: discrete charge model of DNA ; dielectric cylinder in water ; effective dielectric constant ; salt effects ; Debye shielding factor ; potential variations in DNA surface ; Boltzmann averaged bending angles ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied electrostatic properties of DNA with a discrete charge model consisting of a cylindrical dielectric core with a radius of 8 Å and a dielectric constant Di = 4, surrounded by two helical strings of phosphate point charges at 10 Å from the axis, immersed in an aqueous medium with dielectric constant Dw = 78.54. Eliminating the dielectric core makes potentials in the phosphate surface less negative by about 0.5 kT/e. Salt effects are evaluated for the model without a dielectric core, using the shielded Coulomb potential. Smearing the phosphate charges increases their potential by about 2.5 kT/e, due mostly to the self-potential of the smeared charge. Potentials in the center of the minor and major grooves vary less than 0.02 kT/e along their helical path. The potential in the center of the minor groove is from 1.0 to 1.7 kT/e, more negative than in the center of the major groove, depending on dielectric core and salt concentration. So multivalent cations and also larger cationic ligands, such as some antibiotics, are likely to adsorb in the minor groove, in agreement with earlier computations by A. and B. Pullman. Dielectric effects on the surface potential and the local potential variations are found to be relatively small. Bending of DNA is studied by placing a multivalent cation, MZ+, in the center of the minor or major groove, curving DNA around it for a certain length, and calculating the free energy difference between the bent and the straight configuration. Boltzmann averaged bending angles, 〈β〉, are found to be maximal in 0.03M monovalent salt, for a length of about 50 or 25 Å of curved DNA when an MZ+ ion is adsorbed in the minor or the major groove, respectively. When the dielectric constant of water is used throughout the calculation, we find maximal bends of 〈β〉 = 11° for M2+ and 〈β〉 = 16° for M3+ in the minor groove, 〈β〉 = 13° for M3+ in the major groove. The absence of bends in DNA adsorbed to mica in the presence of Mg salts supports the role of Mg2+ in “ion bridging” between DNA and mica. The treatment of the effective dielectric constant between two points outside a dielectric cylinder in water is appended. © 1998 John Wiley & Sons, Inc. Biopoly 46: 503-516, 1998
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  • 58
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    Biopolymers 47 (1998), S. 63-73 
    ISSN: 0006-3525
    Keywords: protein de novo design ; novel macromolecules ; topological templates ; Template Assembled Synthetic Proteins (TASP) ; biosensors ; protein folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ultimate goal in protein de novo design is the creation of novel macromolecules with tailor-made receptor, sensory, and catalytic functions. Despite considerable progress in understanding basic rules of secondary structure formation and protein stability, the well-known protein folding problem is still far from being solved and, in general, only a limited number of designed proteins are folded uniquely. In this article the state-of-the-art in protein design is demonstrated on some selected examples, indicating that the construction of protein-like macromolecules mimicking some essential features of natural proteins seems to be within reach. Thus, protein design and mimicry has become an interdisciplinary challenge with most intriguing perspectives. © 1998 John Wiley & Sons, Inc. Biopoly 47: 63-73, 1998
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  • 59
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    Biopolymers 47 (1998), S. 451-463 
    ISSN: 0006-3525
    Keywords: bacteria ; antibiotics ; linear amphipathic α-helical antimicrobial peptides ; peptide-lipid interactions ; membrane permeation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The increasing resistance of bacteria to conventional antibiotics resulted in a strong effort to develop antimicrobial compounds with new mechanisms of action. Antimicrobial peptides seem to be a promising solution to this problem. Many studies aimed at understanding their mode of action were described in the past few years. The most studied group includes the linear, mostly α-helical peptides. Although the exact mechanism by which they kill bacteria is not clearly understood, it has been shown that peptide-lipid interactions leading to membrane permeation play a role in their activity. Membrane permeation by amphipathic α-helical peptides can proceed via either one of the two mechanisms: (a) transmembrane pore formation via a “barrel-stave” mechanism; and (b) membrane destruction/solubilization via a “carpet-like” mechanism. The purpose of this review is to summarize recent studies aimed at understanding the mode of action of linear α-helical antimicrobial peptides. This review, which is focused on magainins, cecropins, and dermaseptins as representatives of the amphipathic α-helical antimicrobial peptides, supports the carpet-like rather the barrel-stave mechanism. That these peptides vary with regard to their length, amino acid composition, and net positive charge, but act via a common mechanism, may imply that other linear antimicrobial peptides that share the same properties also share the same mechanism. © 1999 John Wiley & Sons, Inc. Biopoly 47: 451-463, 1998
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  • 60
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    Biopolymers 48 (1998), S. 39-55 
    ISSN: 0006-3525
    Keywords: modified nucleotides ; site-specific probes ; RNA structure ; RNA function ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Modified nucleotides can be incorporated site specifically into RNA by the use of total chemical synthesis as well as by use of a variety of recombinant RNA techniques. The range of nucleotide analogues includes modifications to base, sugar, and phosphate for structure-function analysis and for cross-linking studies as well as to answer specific mechanistic questions in RNA catalysis. We describe how RNA containing site-specific modifications are prepared, concentrating in particular on routes involving chemically synthesized oligoribonucleotides, and give examples of their application in studies of the hammerhead and hairpin ribozymes. © 1998 John Wiley & Sons, Inc. Biopoly 48: 39-55, 1998
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  • 61
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    Biopolymers 48 (1998), S. 29-37 
    ISSN: 0006-3525
    Keywords: amide synthase ; catalytic antibodies ; Diels-Alderase ; ideal catalyst platform ; in vitro selection ; Lewis acid ; modified uridines ; modified RNA ; ribozymes ; SELEX ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this manuscript the catalytic ability of RNA is examined and compared to other biopolymers. Despite having considerably fewer catalytically enabling properties when compared to proteins, the power of in vitro selection has allowed for RNA and DNA catalysts to be isolated. RNA catalysis has been expanded by incorporating modified bases to enrich the structural and functional diversity of RNA. Successful examples of new RNA chemistry using base modifications include carbon-carbon bond forming reactions and creation of highly specific active sites that are capable of recognizing small organic molecules without the need for nucleic acid templating or intercalation. In fact, the scope of functional modifications available for use in the RNA platform may eventually surpass those that are found in proteins and there are already hints that well chosen modifications allow nucleic acid catalysts to take advantage of mechanisms not available to selected protein catalysts for similar reactions. The chemical versatility of RNA is just emerging and future research directions will likely entail more creative methods for functional modification that will lead to new catalysts. © 1998 John Wiley & Sons, Inc. Biopoly 48: 29-37, 1998
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  • 62
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    Biopolymers 48 (1998), S. 137-153 
    ISSN: 0006-3525
    Keywords: RNA ; pseudoknot ; Turnip Yellow Mosaic Virus ; Mouse Mammary Tumor Virus ; Beet Western Yellows Virus ; Simian Retrovirus type-1 ; Hepatitis Delta Virus ; translational frameshifting ; ribozyme ; nmr ; x-ray diffraction ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently, several high-resolution structures of RNA pseudoknots have become available. Here we review the progress in this area. The majority of the structures obtained belong to the classical or H-type pseudoknot family. The most complicated pseudoknot structure elucidated so far is the Hepatitis Delta Virus ribozyme, which forms a nested double pseudoknot. In particular, the structure-function relationships of the H-type pseudoknots involved in translational frameshifting have received much attention. All molecules considered show interesting new structural motifs. © 1999 John Wiley & Sons, Inc. Biopoly 48: 137-153, 1998
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  • 63
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1-24 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We study the large time asymptotics of solutions u(x, t) of the wave equation with time-harmonic force density f(x)e-iωt, ω≥0, in the semi-strip Ω= (0, ∞)×(0, 1) for a given f∊C∞0(Ω). We assume that u satisfies the initial condition u=(∂/∂t)u=0 for t=0 and the boundary conditions u=0 for x2=0 and x2=1, and (∂/∂x1)u=αu for x1=0, with given α, -π≤α〈∞. Let Dα be the self-adjoint realization of -Δ in Ω with this boundary condition. For -π≤α〈0, Dα has eigenvalues λj=π2j2-α2, j=1, 2, … For j≥2 these eigenvalues are embedded in the continuous spectrum of Dα, σc(Dα)=[π2, ∞]. For α≥0, Dα has no eigenvalues. We consider the asymptotic behaviour of u(x, t), t→∞, as a function of α. In the case α=0 resonances of order √t at ω=πj, j=1, 2, …, were found in References 5 and 10. We prove that for α=-π there is a resonance of order t2 for ω=0 and resonances of order t for every ω〉0 (note that 0 is an eigenvalue of D-π). Moreover, for -π〈α〈0 there are resonances of order t at ω=√λj. The resonance frequencies are continuous functions of α for -π〈α〈0 and tend to πj, j=1, 2, … as α goes to zero.On the contrary in the case α〉0 there are no real resonances in the sense that the solution remains bounded in time as t→∞. Actually in this case, the limit amplitude principle is valid for all frequencies ω≥0. This rather striking behaviour of the resonances is explained in terms of the extension of the resolvent R(κ)=(Dα-κ2)-1 as a meromorphic function of κ into an appropriate Riemann surface. We find that as α crosses zero the real poles of R(κ) associated with the eigenvalues remain real, but go into a second sheet of the Riemann surface. This behaviour under perturbation is rather different from the case of complex resonances which has been extensively studied in the theory of many-body Schrödinger operators where the (real) eigenvalues embedded in the continuous spectrum turn under a small perturbation into complex poles of the meromorphic extension of the resolvent, as a function of the spectral parameter κ2. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 117-128 
    ISSN: 0170-4214
    Keywords: third-grade fluid ; existence ; uniqueness ; classical solution ; Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The global existence and uniqueness of classical solution of steady motions of a third-grade fluid provided assumptions on positivness of μ (coefficient of viscosity) and α1, γ (material coefficients) is proved. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 227-249 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: Integral equations associated with the basic boundary value problems for the Laplace and Stokes equations are considered. The integral operators for these integral equations are interpreted as the pseudodifferential operators, and their principal symbols are calculated. The symbols are obtained in terms of the principal curvatures and the coefficients of the first quadratic form of the boundary. As a consequence, the initial approximation is suggested for the iterative methods solving the integral equations. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 327-359 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The boundary integral equation method is used to prove the convergence of the Drude-Born-Fedorov equations with variable coefficients, possibly non-smooth, to Maxwell's equations as chirality admittance tends to zero. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 565-588 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: New explicit stability conditions are derived for a linear integro-differential equation with periodic operator coefficients. The equation under consideration describes oscillations of thin-walled viscoelastic structural members driven by periodic loads. To develop stability conditions two approaches are combined. The first is based on the direct Lyapunov method of constructing stability functionals. It allows stability conditions to be derived for unbounded operator coefficients, but fails to correctly predict the critical loads for high-frequency excitations. The other approach is based on transforming the equation under consideration in such a way that an appropriate ‘differential’ part of the new equation would possess some reserve of stability. Stability conditions for the transformed equation are obtained by using a technique of integral estimates. This method provides acceptable estimates of the critical forces for periodic loads, but can be applied to equations with bounded coefficients only. Combining these two approaches, we derive explicit stability conditions which are close to the Floquet criterion when the integral term vanishes. These conditions are applied to the stability problem for a viscoelastic bar compressed by periodic forces. The effect of material and structural parameters on the critical load is studied numerically. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 653-664 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In order to maintain spectrally accurate solutions, the grids on which a non-linear physical problem is to be solved must also be obtained by spectrally accurate techniques. The purpose of this paper is to describe a pseudospectral computational method of solving integro-differential systems with quadratic performance index. The proposed method is based on the idea of relating grid points to the structure of orthogonal interpolating polynomials. The optimal control and the trajectory are approximated by the m th degree interpolating polynomial. This interpolating polynomial is spectrally constructed using Legendre-Gauss-Lobatto grid points as the collocation points, and Lagrange polynomials as trial functions. The integrals involved in the formulation of the problem are calculated by Gauss-Lobatto integration rule, thereby reducing the problem to a mathematical programming one to which existing well-developed algorithms may be applied. The method is easy to implement and yields very accurate results. An illustrative example is included to confirm the convergence of the pseudospectral Legendre method, and a comparison is made with an existing result in the literature. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 701-718 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This article establishes the existence of a trapped-mode solution to a linearized water-wave problem. The fluid occupies a symmetric horizontal channel that is uniform everywhere apart from a confined region which either contains a thin vertical plate spanning the depth of the channel or has indentations in the channel walls; the forces of gravity and surface tension are operative. A trapped mode corresponds to an eigenvalue of the composition of an inverse differential operator and a Neumann-Dirichlet operator for an elliptic boundary-value problem in the fluid domain. The existence of such an eigenvalue is established by extending previous results dealing with the case when surface tension is absent. © 1998 B.G. Teubner Stuttgart-John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 501-517 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper an initial-boundary-value problem in one-space dimension is studied for the Broadwell model extended to a gas mixture undergoing bimolecular reactions. Techniques of semigroup of bounded positive operators in a suitable Banach space are used to prove existence and uniqueness of the solution on bounded time intervals whose length depends on the initial data. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 685-700 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In the present work, the problem of electromagnetic wave propagation in three-dimensional stratified media is studied. The method of decoupling the electric and magnetic fields is implemented, and the spectral approach is adopted, componentwise, to the vector equation involving the electric field. Operational calculus of self-adjoint, positive operators in suitable Hilbert spaces is used to solve the corresponding initial value problems. The spectral families of these operators for the cases of the whole space and of a finite layer are constructed. A discussion on the applicability of the obtained results to physical problems is also included. © 1998 B.G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 757-780 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we prove under the assumption of small initial data the global existence of a classical solution to the equations in viscoelasticity, associated with a free damping boundary condition. We also show that if we choose the initial data large enough, blow up will occur in finite time. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 797-821 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider the thermoelastic plate system,utt-γΔutt+Δ2u+αΔθ=0,θt-κΔθ-αΔut=0 and we make a comparison between the models in which γ=0 and γ〉0. We conclude that in the first case the plate system is of a parabolic type, while when γ〉0 the corresponding system has a hyperbolic behaviour. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 883-894 
    ISSN: 0170-4214
    Keywords: solitary wave ; stability ; long wave-short wave resonance equations ; Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This paper concerns the orbital stability for solitary waves of the Long Wave-Short Wave resonance equations. Since the abstract results of Grillakis et al. [7, 8] cannot be applied directly, we can extend the abstract stability theory and use the detailed spectral analysis to obtain the stability of the solitary waves. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1049-1066 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider particle transport in a three-dimensional convex region V, bounded by the regular surface ∂V. We assume that particles are specularly reflected by ∂V and that a source q is assigned on ∂V; more general non-homogeneous boundary conditions are also discussed. The problem is non-linear because the boundary condition is not homogeneous. We prove existence of a unique strict solution and by using the theory of semigroups we derive the explicit expression of such a solution in terms of the boundary source q. In the appendix, we indicate how some properties of affine operators can be used to derive the solution. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1085-1105 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: A phase-field model based on the Coleman-Gurtin heat flux law is considered. The resulting system of non-linear parabolic equations, associated with a set of initial and Neumann boundary conditions, is studied. Existence, uniqueness, and regularity results are proved. An asymptotic analysis is also carried out, in the case where the coefficient of the interfacial energy term tends to 0. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1115-1148 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We apply the Child-Langmuir asymptotics of the Vlasov-Poisson system to the case of a bipolar diode, i.e. a vacuum diode where two species of particles of opposite electric charge are flowing. This leads to a simplified model which, if at least one of the two injected currents is not too large, has a unique solution. Moreover, in that case, the currents flowing inside the diode are limited by the so-called bipolar Child-Langmuir currents. In the case of large currents, other solutions may appear, and the formation of virtual electrodes may occur inside the diode. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1107-1113 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we consider the Cauchy problem for the equation∂u/∂t + u ∂u/∂x + u/x = 0 for x 〉 0, t ≥ 0, with u(x, 0) = u0-(x) for x 〈 x0, u(x, 0) = u0+(x) for x 〉 x0, u0-(x0) 〉 u0+(x0). Following the ideas of Majda, 1984 and Lax, 1973, we construct, for smooth u0- and u0+, a global shock front weak solution u(x, t) = u-(x, t) for x 〈 φ(t), u(x, t) = u+(x, t) for x 〉 φ(t), where u- and u+ are the strong solutions corresponding (respectively) to u0- and u0+ and the curve t → φ(t) is defined by dφ/dt (t) = 1/2[u-(φ(t), t) + u+(φ(t), t)], t ≥ 0 and φ(0) = x0.© 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1195-1206 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: A variational approach to a non-linear non-local identification problem related to the non-linear transport equation is studied. Introducing a similarity transformation, the problem is formulated as an identification problem for a non-linear differential equation of second order with an additional non-local condition. For the solution of the forward problem stability in H1-norm with respect to the identification parameter is obtained. Using this result the existence of a solution to the identification problem is proved. Some results of computational experiments are given. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1233-1267 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider the plate equation in a polygonal domain with free edges. Its resolution by boundary integral equations is considered with double layer potentials whose variational formulation was given in Reference 25. We approximate its solution (u, (∂u/∂n)) by the Galerkin method with approximated spaces made of piecewise polynomials of order 2 and 1 for, respectively, u and (∂u/∂n). A prewavelet basis of these subspaces is built and equivalences between some Sobolev norms and discrete ones are established in the spirit of References 14, 16, 30 and 31. Further, a compression procedure is presented which reduces the number of nonzero entries of the stiffness matrix from O(N2) to O(N log N), where N is the size of this matrix. We finally show that the compressed stiffness matrices have a condition number uniformly bounded with respect to N and that the compressed Galerkin scheme converges with the same rate than the Galerkin one. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1287-1296 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The relativistic Vlasov-Maxwell-Fokker-Planck system is used in modelling distribution of charged particles in plasma. It consists of a transport equation coupled with the Maxwell system. The diffusion term in the equation models the collisions among particles, whereas the viscosity term signifies the dynamical frictional forces between the particles and the background reservoir. In the case of one space variable and two momentum variables, we prove the existence of a classical solution when the initial density decays fast enough with respect to the momentum variables. The solution which shares this same decay condition along with its first derivatives in the momentum variables is unique. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1415-1439 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider reactive mixtures of dilute polyatomic gases in full vibrational non-equilibrium. The governing equations are derived from the kinetic theory and possesses an entropy. We recast this system of conservation laws into a symmetric conservative form by using entropic variables. Following a formalism developed by the authors in a previous paper, the system is then rewritten into a normal form, that is, in the form of a quasilinear symmetric hyperbolic-parabolic system. Using a result of Vol'pert and Hudjaev, we prove local existence and uniqueness of a bounded smooth solution to the Cauchy problem. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1479-1494 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: Approximate solutions of the non-linear Boltzmann equation, which have the structure of the linear combination of three global Maxwellians with arbitrary hydrodynamical parameters, are considered. Some sufficient conditions which allow the error between the left- and the right-hand sides of the equation tend to zero, and which are calculated either in the mixed metric or in the pure integral metric, are obtained. The class of the distributions, which minimized this error for the arbitrary Knudsen number, is found. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1519-1542 
    ISSN: 0170-4214
    Keywords: non-hyperbolic systems ; two-phase flows ; dispersion terms ; symmetrization ; Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The paper considers a system of partial differential equations of convection dispersion type, modelling a stratified two-phase fluid flow. Local existence in time is proved for a sufficiently smooth initial data, given in the set of physically admissible states. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1559-1569 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we study the motion of an elastic conducting wire in a magnetic field. The motion of the conductor induces a current in the wire (Faraday's law) which, in turn produces a force on the wire. We consider the linear equation obtained by linearizing the resulting equations of motion about an equilibrium solution. This is a hyperbolic partial differential equation with a non-local term. We prove existence and uniqueness of a weak solution of an initial-boundary value problem for this equation. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1637-1654 
    ISSN: 0170-4214
    Keywords: generalized Stokes equations ; incompressible flow ; least-squares ; finite element method ; Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we are concerned with a weighted least-squares finite element method for approximating the solution of boundary value problems for 2-D viscous incompressible flows. We consider the generalized Stokes equations with velocity boundary conditions. Introducing the auxiliary variables (stresses) of the velocity gradients and combining the divergence free condition with some compatibility conditions, we can recast the original second-order problem as a Petrovski-type first-order elliptic system (called velocity-stress-pressure formulation) in six equations and six unknowns together with Riemann-Hilbert-type boundary conditions. A weighted least-squares finite element method is proposed for solving this extended first-order problem. The finite element approximations are defined to be the minimizers of a weighted least-squares functional over the finite element subspaces of the H1 product space. With many advantageous features, the analysis also shows that, under suitable assumptions, the method achieves optimal order of convergence both in the L2-norm and in the H1-norm. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 1619-1635 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider the two-parameter non-linear Sturm-Liouville problems. By using the variational method on general level sets, the variational eigenvalues are obtained. The purpose of this paper is to study the properties of these variational eigenvalues with respect to the parameter of general level sets. © 1998 B. G. Teubner Stuttgart - John Wiley & Sons, Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 187-226 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We study the limit behaviour of solution of Poisson's equation in a class of thin two-dimensional domains, both simply connected or single-hollowed, as its thickness becomes very small. The method is based on a transformation of the original problem into another posed on a fixed domain, obtention of a priori estimates and convergence results when thickness parameter tends to zero. As an important application of abstract results we obtain the limit expressions for functions appearing in elastic beam theories as torsion and warping functions. In this way, we provide a mathematical justification and a correct definition of torsion, warping and Timoshenko functions and constants that should be used in the open and closed thin-walled elastic beam theories. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 269-279 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The generalized Möbius function and Möbius inversion formula are applied to a multiplicative semigroup. A general mathematical method based on this Möbius inversion is presented to solve inversion problems of expansions with unequally weighted terms. By this method, all the inverse lattice problems in physics can be solved concisely. The solutions of four inverse lattice problems: the Fibonacci structure, the square lattice structure, the bcc and the hcp lattice structures are given. These are difficult to be solved by other methods. © 1998 by B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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    Mathematical Methods in the Applied Sciences 21 (1998), S. 361-374 
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    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We use the eigenfunction expansion of Green's function of Dirichlet problems to obtain sampling theorems. The analytic properties of the sampled integral transforms as well as the uniform convergence of the sampling series are proved without any restrictions on the integral transforms. We obtain a one- and multi-dimensional versions of sampling theorems. In both cases the sampling series are written in terms of Lagrange-type interpolation expansions. Some examples and the truncation error as well as the stability of the obtained sampling expansions are discussed at the end of the paper. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
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  • 91
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    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 393-416 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider a dynamical von Kármán system in the presence of thermal effects. Our model includes the possibility of a rotational inertia term in the system. We show that the total energy of the solution of such system decays exponentially as t→+∞. The decay rates we obtain are uniform on bounded sets of the energy space. The main ingredients of our method of proof are suitable properties of a decoupled system, the energy method and the compactness of the nonlinear map associated to the von Kármán system. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Type of Medium: Electronic Resource
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  • 92
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    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 479-488 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This short article discusses the spectrum of the Neumann Laplacian in the infinite domain Ω⊂∝n, n ≥2 created by inserting a compact obstacle P into the uniform cylinder Ω0 =(-∞, ∞)×Ω′. The main result is the existence of at least one embedded eigenvalue when P is an (n -2)-dimensional surface whose unit normal is parallel to Ω′ at each point of P . The special case when P is symmetric about {0}×Ω′ is also treated. It is shown that there is at least one symmetric eigenvector and, when P is sufficiently long, at least one antisymmetric eigenvector. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Additional Material: 2 Ill.
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  • 93
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    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 551-564 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We prove the existence of solutions to the three-dimensional elastoplastic problem with Hencky's law and Neumann boundary conditions by elliptic regularization and the penalty method, both for the case of a smooth boundary and of an interior two dimensional crack. It is shown, in particular, that the variational solution satisfies all boundary conditions. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Type of Medium: Electronic Resource
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  • 94
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    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 251-268 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The propagation of Hölder regularity of the solutions to the 3D Euler equations is discussed. Our method is a special semi-linearization of the vorticity equation combined with the classical Schauder interior estimates. © 1998 by B.G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Type of Medium: Electronic Resource
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  • 95
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    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 433-461 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This paper is concerned with the solution of Maxwell equations in the modelling of the scattering of a time-harmonic electromagnetic wave by an obstacle located in a two-layered medium. The use of the Silver-Müller radiation condition in each layer is shown to provide a well-posed scattering problem. The analysis is based on the study of the Green tensor, which allows to relate the radiation condition to an integral representation formula. The analyticity properties of the scattering problem with respect to the frequency are then investigated. This gives rise to a limiting absorption principle and furnishes a characterization of the resonances. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Additional Material: 2 Ill.
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  • 96
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    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 489-499 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We apply our recently developed distributional technique [2, 3] to study time-domain asymptotics. This enables us to present a rigorous mathematical discussion and extensions of the results given by Chapman [1] and subsequent workers in this field. The present analysis is facilitated by defining functions which are distributionally small at infinity. We find that one of the advantages of using this technique is that multidimensional extensions can be derived very easily. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Type of Medium: Electronic Resource
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  • 97
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    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 519-549 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This paper is concerned with a specific finite element strategy for solving elliptic boundary value problems in domains with corners and edges. First, the anisotropic singular behaviour of the solution is described. Then the finite element method with anisotropic, graded meshes and piecewise linear shape functions is investigated for such problems; the schemes exhibit optimal convergence rates with decreasing mesh size. For the proof, new local interpolation error estimates for functions from anisotropically weighted spaces are derived. Finally, a numerical experiment is described, that shows a good agreement of the calculated approximation orders with the theoretically predicted ones. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Additional Material: 9 Ill.
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  • 98
    Electronic Resource
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    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 605-617 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: This paper presents a general method of analysis for investigating the whirl stability of a rotor-bearing system whose appendage is flexibly attached to the spinning shaft. Sufficient conditions of asymptotic stability involving system different parameters are derived based on Liapunov's theory. An inclusive analysis of the effect of the combined flexibilities of the elastic attachment of the appendage to the shaft and the two end bearings coupled with the other various parameters of the system on the dynamic stability is presented. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Additional Material: 9 Ill.
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  • 99
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    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 665-684 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We investigate the steady compressible Navier-Stokes equations near the equilibrium state v = 0, ρ = ρ0 (v the velocity, ρ the density) corresponding to a large potential force. We introduce a method of decomposition for such equations: the velocity field v is split into a non-homogeneous incompressible part u (div (ρ0u) = (0) and a compressible (irrotational) part ∇φ. In such a way, the original complicated mixed elliptic-hyperbolic system is split into several ‘standard’ equations: a Stokes-type system for u, a Poisson-type equation for φ and a transport equation for the perturbation of the density σ = ρ - ρ0. For ρ0 = const. (zero potential forces), the method coincides with the decomposition of Novotny and Padula [21]. To underline the advantages of the present approach, we give, as an example, a ‘simple’ proof of the existence of isothermal flows in bounded domains with no-slip boundary conditions. The approach is applicable, with some modifications, to more complicated geometries and to more complicated boundary conditions as we will show in forthcoming papers. © 1998 B.G. Teubner Stuttgart-John Wiley & Sons Ltd.
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  • 100
    Electronic Resource
    Electronic Resource
    Chichester, West Sussex : Wiley-Blackwell
    Mathematical Methods in the Applied Sciences 21 (1998), S. 619-651 
    ISSN: 0170-4214
    Keywords: Engineering ; Numerical Methods and Modeling
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider acoustic scattering from an obstacle inside an inhomogeneous structure. We prove in the paper that if the outside inhomogeneity is known then the obstacle and possible inside inhomogeneity are uniquely determined by the fixed energy far field data. The proof is based on new mapping properties of layer potentials in spaces that specify one point. © 1998 B. G. Teubner Stuttgart-John Wiley & Sons Ltd.
    Type of Medium: Electronic Resource
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