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  • 1995-1999  (14,578)
  • 1995  (14,578)
  • Chemistry  (11,922)
  • Life and Medical Sciences  (2,263)
  • Atomic, Molecular and Optical Physics  (370)
  • Genetics  (327)
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Years
  • 1995-1999  (14,578)
Year
Keywords
  • 1
    ISSN: 1432-5233
    Keywords: Maturity-onset diabetes of the young (MODY) ; Genetics ; Diabetes mellitus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Genetic linkage studies of families with earlyonset type 2 diabetes have facilitated the identification of diabetes-susceptibility genes. In order to assess the feasibility of using linkage approaches to identify genes responsible for the development of type 2 diabetes in Japanese subjects, we examined our clinical records for multigenerational families suitable for genetic studies. We identified 16 families in which at least one subject was diagnosed with type 2 diabetes before 25 years of age. Seven of these families had a pattern of inheritance consistent with a diagnosis of maturity-onset diabetes of the young (MODY) and nine families showed a complex pattern of inheritance of type 2 diabetes with transmission of diabetes-susceptibility genes from both parents. The glucokinase and mitochondrial tRNALeu(UUR) genes were screened for mutations in at least one affected subject from each family in order to assess the contribution of mutations in these genes to the development of the diabetes. No mutations were found, which suggests that the diabetes in these families resulted from mutations in other genes.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 90 (1995), S. 380-388 
    ISSN: 1432-2242
    Keywords: Genetics ; Breeding ; Sorghum bicolor Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The objective of this study was to use restriction fragment length polymorphisms (RFLPs) to determine the genetic location and effects of genomic regions controlling plant height in sorghum. F2 plants (152) from the cross CK60 x PI229828 were used. Genomic and cDNA clones (106) identified 111 loci distributed among ten linkage groups covering 1299 cM. Interval mapping identified four regions, each in a separate linkage group. These regions may correspond to loci (dw) previously identified by alleles with qualitative effects. Also, these regions identified in sorghum may be orthologous to those previously reported for plant height in maize. Gene effects and gene action varied among genomic regions. In each region, PI229828 alleles resulted in increased plant height. Each region accounted for 9.2–28.7% of the phenotypic variation. Positive, additive effects ranged from 15 to 32cm. Tallness was dominant or overdominant and conferred by alleles from PI229828 for three quantitative trait loci (QTL). At the fourth QTL, PI229828 contributed to increased plant height, but short stature was partially dominant. One digenic interaction was significant. The presence of a PI229828 allele at one region diminished the effects of the other region. A multiple model indicated that these four regions collectively accounted for 63.4% of the total phenotypic variation. The utility of this information for germplasm conversion through backcross breeding is discussed.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-0533
    Keywords: Primitive neuroepithelial tumor ; Desmoplastic small cell tumor ; Brain tumor of infancy Immunocytochemistry ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We describe a case of a desmoplastic brain tumor which was initially resected from the right fronto-temporal region in a 2 year-old boy. This nodular, calcified tumor was vascularized by the internal carotid artery and the middle meningeal artery branches. Grossly, it contained several mucoid cysts. Light microscopy showed cords or nests of small cuboidal cells surrounded by a loose connective tissue and desmoplasic areas containing fibers and spindle cells. The cuboidal cells expressed epithelial, neuronal and neuroendocrine markers. Some foci of spindle cells showed glial differentiation. The tumor recurred 16 months later and displayed some characteristics of the small cell neuroepithelial component, mitoses being conspicuous. Electron microscopy revealed undifferentiated clear cells, some containing neurosecretory granules. Karyotyping demonstrated the following formula: 〈 15 〉 46, t(8;11) (a13; q11). The chromosome 11 breakpoint was different from that described in Ewing's sarcoma. This isolated translocation has not been previously reported to our knowledge. These unusual features lead us to report this case and to discuss its pathogenesis.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    European journal of pediatrics 154 (1995), S. 654-657 
    ISSN: 1432-1076
    Keywords: Key words Fetal development ; Brain diseases ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We report two female siblings with the fetal brain disruption sequence. Extensive investigation of both children failed to define a definitive aetiology but clinical and laboratory findings are consistent with a hitherto unknown storage disease. We postulate that the accumulation of a neurotoxic metabolite may be responsible for the disease phenotype observed. This is the first report of recurrence of the fetal brain disruption sequence and supports the existence of a genetic form of this condition. Previous reports have emphasized possible environmental aetiologies. Infants with fetal brain disruption sequence should be investigated exhaustively and, in the absence of definitive evidence of an environmental cause, the possibility of a genetic aetiology should be considered. In some families the recurrence risk may be as high as one in four.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1432-1076
    Keywords: Key words Floating-Harbor ; syndrome ; Growth retardation ; Dysmorphology ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The Floating-Harbor syndrome is a growth retardation syndrome with delayed bone age, speech development, and typical facial features. The face is triangular with deep-set eyes, long eyelashes, bulbous nose, wide columella, short philtrum, and thin lips. We present an additional patient and review 16 cases from the literature. The possible phenotype in the patient's mother suggests a dominant mode of inheritance for the syndrome. Conclusion The Floating Harbor syndrome is a growth deficiency syndrome characterized by proportionate short stature, characteristic face and delayed speech development. Inheritance is possibly autosomal dominant.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-1076
    Keywords: Key words Osteogenesis imperfecta ; Collagen I ; Mosaicism ; Genetics ; Recurrence risk
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Osteogenesis imperfecta (OI), a dominantly inherited connective tissue disorder, is usually caused by defects in collagen I. There is growing evidence for parental mosaicism that results in affected children born to unaffected parents. This situation poses a difficult task for the geneticist because a mosaic parent may appear clinically healthy while carrying the mutation in a fraction of her or his gonadal cells. To illustrate this problem, we report a Swiss couple whose first child was affected with severe OI. The unexpected recurrence of the disorder in the second child raised the suspicion of a recessive trait or, rather, of parental mosaicism. We identified the responsible collagen mutation in the COL1A2 gene (Gly688Ser in the α2(I)-chain) in both children and demonstrated the father to be a somatic mosaic for this mutation and to have subtle clinical signs such as soft skin and short stature that may be a result of his mosaic state.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    European journal of pediatrics 154 (1995), S. 654-657 
    ISSN: 1432-1076
    Keywords: Fetal development ; Brain diseases ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We report two female siblings with the fetal brain disruption sequence. Extensive investigation of both children failed to define a definitive aetiology but clinical and laboratory findings are consistent with a hitherto unknown storage disease. We postulate that the accumulation of a neurotoxic metabolite may be responsible for the disease phenotype observed. This is the first report of recurrence of the fetal brain disruption sequence and supports the existence of a genetic form of this condition. Previous reports have emphasized possible environmental aetiologies. Infants with fetal brain disruption sequence should be investigated exhaustively and, in the absence of definitive evidence of an environmental cause, the possibility of a genetic aetiology should be considered. In some families the recurrence risk may be as high as one in four.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1432-1076
    Keywords: Floating-Harbor syndrome ; Growth retardation ; Dysmorphology ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Abstract The Floating-Harbor syndrome is a growth retardation syndrome with delayed bone age, speech development, and typical facial features. The face is triangular with deep-set eyes, long eyelashes, bulbous nose, wide columella, short philtrum, and thin lips. We present an additional patient and review 16 cases from the literature. The possible phenotype in the patient's mother suggests a dominant mode of inheritance for the syndrome. Conclusion The Floating Harbor syndrome is a growth deficiency syndrome characterized by proportionate short stature, characteristic face and delayed speech development. Inheritance is possibly autosomal dominant.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Der Hautarzt 46 (1995), S. 394-399 
    ISSN: 1432-1173
    Keywords: Schlüsselwörter Malignes Melanom ; Genetische Instabilität ; Genetik ; Syndrom der dysplastischen Nävi ; Xeroderma pigmentosum ; Key words Malignant melanoma ; Genetic instability ; Genetics ; Dysplastic nevus syndrome ; Xeroderma pigmentosum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Summary Exposure of the skin to ultraviolet irradiation is an important risk factor for the development of malignant melanoma, with UVA possibly playing an important role. Hereditary factors are also relevant. In the dysplastic nevus syndrome a genetic instability has been shown by different methods. In xeroderma pigmentosum the DNA repair defect is thought to be responsible for the high incidence of malignant melanoma. Frequent and non-random changes in certain chromosomes have been demonstrated in melanoma cells. These might contain sequences that control melanoma growth or melanoma suppressor genes. Especially the short arm of chromosome 9 is thought to contain one of these genes. This hypothesis is supported by a genetic linkage analysis in melanoma families and the demonstration of a germ line deletion of the locus 9p21 in a patient with eight primary melanomas. Changes in known tumor suppressor genes and oncogenes have also been reported in melanoma, but no consistent sequence of genetic events is known.
    Notes: Zusammenfassung Die Exposition der Haut mit ultravioletten Strahlen ist ein wichtiger Risikofaktor für die Entwicklung eines malignen Melanoms. Möglicherweise spielt hierbei UVA-A eine besondere Rolle. Daneben sind hereditäre Faktoren von Bedeutung. Während beim Syndrom der dysplastischen Nävi eine genetische Instabilität mit verschiedenen Methoden nachgewiesen wurde, wird bei Xeroderma pigmentosum der DNA-Reparaturdefekt für die hohe Melanominzidenz verantwortlich gemacht. In Melanomzellen sind überzufällig häufig karyotypische Veränderungen in bestimmten Chromosomen gefunden worden. Diese enthalten möglicherweise Melanomwachstumsregulierende Sequenzen oder Melanom-Suppressorgene. Insbesondere der kurze Arm des Chromosoms 9 steht in Verdacht, eines dieser Gene zu enthalten. Diese Hypothese wird auch unterstützt durch eine genetische Kopplungsanalyse an Melanomfamilien und dem Nachweis einer Keimbahndeletion des Lokus 9p21 bei einer Patientin mit 8 primären Melanomen. Veränderungen an bereits bekannten Tumorsuppressorgenen oder Onkogenen sind ebenfalls in Melanomen beschrieben worden, ohne daß jedoch eine konsistente Reihenfolge von genetischen Ereignissen bekannt wäre.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 90 (1995), S. 146-149 
    ISSN: 1432-2242
    Keywords: Capsicum chinense ; Resistance gene ; Genetics ; Pepper ; Tomato spotted wilt virus ; Tospoviruses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Pepper (Capsicum chinense Jacq.) has been reported to be an important reservoir of resistance genes to tomato spotted wilt virus (TSWV). The genes for TSWV resistance present in three C. chinense lines (‘PI 152225’, ‘PI 159236’ and ‘Panca’) were investigated for allelism. All resistant lines were crossed with each other. Parents, F1, backcrosses and F2 populations (including reciprocals) developed from those crosses were mechanically inoculated with a highly virulent TSWV isolate. Susceptible C. annuum cv ‘Magda’ was used to check inoculum virulence. Fifty plants of the F1 hybrids; ‘Magda’ x ‘PI 152225’, ‘Magda’ x ‘PI 159236’, and ‘Magda’ x 'Panca, were also inoculated with the TSWV isolate. The resistance response in all C. chinense sources was associated with a localized, hypersensitive-like reaction that was phenotypically expressed as a prompt formation of large local lesions accompanied by premature leaf abscission. All F1 generations presented a final score of resistant; indicating that the expression of resistance to TSWV is conditioned by a dominant gene regardless of the source. The absence of segregation for resistance to TSWV that was observed in all generations of the crosses between C. chinense lines indicated that either a tightly linked group of genes exists or that the resistance is governed by the same single major gene (probably the already described Tsw gene). Previous reports have indicated that the Tsw gene is not effective against tospovirus members of serogroup II, i.e. tomato chlorotic spot virus (TCSV) and groundnut ring spot virus (GRSV). In the assay described here, all of the C. chinense lines showed, after mechanical inoculation, an identical susceptibility response to the TCSV and GRSV isolates.
    Type of Medium: Electronic Resource
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  • 11
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 90 (1995), S. 707-713 
    ISSN: 1432-2242
    Keywords: Mineral stress ; Nutrient efficiency ; Aluminium tolerance ; Inheritance ; Genetics ; Breeding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Brazilian tropical adapted soybeans contains, in addition to superior morphological characters, genetic factors for tolerance to cultivation in acidic, mineral-stressed soils. However, the selection process for these hindrances has been empirical, and information on the genetics of mineral element uptake by the plant is necessary. The objective of this investigation was to identify the mode of inheritance for the absorption of phosphorus, potassium, calcium, magnesium, iron, aluminium, manganese, zinc and copper in a 9 × 9 diallel cross. General combining ability (GCA) was higher than specific combining ability (SCA), with the exception of copper, manganese and zinc, indicating predominantly additive effects. The ratios of GCA/SCA varied between 3.4 (calcium) and 8.5 (magnesium). The regression of covariance (Wr) on variance (Vr) showed that the additive-dominance model explained the genetic differences in this germ plasm. However, the detection of overdominance could be related to possible heterozygosity in the parental varieties for mineral absorption. Broad-sense heritability values were higher than narrow sense heritability values for aluminium, iron, potassium, calcium and magnesium, being in the range of 67.9–86.9% and 42.0–56.6%, respectively. This is an indication that soybeans can be further improved to efficient utilisation of nutrients and to tolerate toxic factors in the soil.
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  • 12
    ISSN: 1432-2072
    Keywords: Opioid ; Genetics ; Self-administration ; CXBK/ByJ ; Reinforcement
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract It is commonly thought thatμ-receptors play an important role in the reinforcing effects of opioids. In the present study, inbred strains widely divergent in CNS opiate receptor densities were used to investigate the influence of genetic variation in receptor concentration on opioid-reinforced behavior. In particular, the CXBK/ByJ mice were used as an investigative tool because of their significantly lower number of CNSμ opioid receptors. The behavioral pharmacology of opioids in theμ-deficient CXBK/ByJ mice was compared to other commonly used inbred mouse strains, C57BL/6J and BALB/cJ, and the opiate receptor rich CXBH/ByJ mice. Operant opioid reinforced behavior, opioid-induced locomotor stimulation, analgesia and respiratory depression were investigated in all four inbred strains. To assess the acquisition and maintenance of opioid reinforced behavior, oral self-administration of the potent benzimidazole opioid, etonitazene, was determined using an operant fixed-ratio schedule of reinforcement (FR 8). Acquisition of etonitazene-reinforced behavior was established in all four strains including theμ-deficient CXBK/ByJ mice. However, there were significant genetic differences in the amount of drug intake during the maintenance of opioid-reinforced behavior and extinction behavior following vehicle substitution. For example, drug intake was significantly greater in the BK versus BH mice during the maintenance phase and an extinction burst was seen in the BH but not the BK mice following vehicle substitution. Thus,μ-receptor density may not account for individual variability in the acquisition of opioid-reinforced behavior under these conditions. Sensitivity to etonitazene-induced respiratory depression, stimulation of locomotor activity and analgesia were unrelated to drug intake during self-administration sessions across these four inbred strains. These data indicate that inherited differences in CNSμ-opiate receptor concentrations do not affect acquisition of etonitazene-reinforced behavior.
    Type of Medium: Electronic Resource
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  • 13
    ISSN: 1432-2072
    Keywords: Cocaine ; Quantitative trait loci ; Seizure ; Recombinant inbred strains ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Among inbred mice, genetic factors mediate differences in sensitivity to the convulsant properties of cocaine; however, the gene(s) underlying cocaine's effects have not been identified. To help elucidate the gene(s) responsible for cocaine seizure susceptibility, we used recombinant inbred-quantitative trait loci (RI-QTL) analyses to identify chromosomal loci associated with cocaine-induced seizures. RI-QTL analyses seek to identify associations between a quantitative measure of a particular phenotype and one or more previously mapped marker genes across a panel of RI strains. This report describes an RI-QTL analysis of cocaine seizure susceptibility among 26 BXD RI strains. These strains showed a skewed, bimodal range of seizure susceptibility which could be the result of one or more modifying genes acting in concert with a major gene to influence cocaine sensitivity. Correlating the percent seizures displayed by each strain following 60 mg/kg cocaine with chromosomal marker data for these strains revealed a number of significant correlations clustered in two regions on chromosomes 12 and 6. This is the first identification of putative chromosomal loci associated with a cocaine-related phenotype and should facilitate identification of the gene(s) underlying cocaine toxicity and other cocaine-related phenotypes.
    Type of Medium: Electronic Resource
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  • 14
    Electronic Resource
    Electronic Resource
    Springer
    Sexual plant reproduction 8 (1995), S. 129-132 
    ISSN: 1432-2145
    Keywords: Sex control ; Disomic segregation ; Dioecy Kiwifruit ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The sex segregation ratio was checked in bi-parental families of Actinidia deliciosa (2n=6x=174) obtained by crossing four females (A12, Mo3, Br4, Hw1) with two males (T2, M1) and one fruiting male (M3h, subandroecious) according to a factorial mating design. The M3h fruiting male was also selfed. The sex ratio was checked in maternal families of A. kolomikta (2n=2x) and A. chinensis (2n=2x) as well as in A. deliciosa. Seedlings of both diploid species took 3–4 years to progress beyond juvenility, whereas a noticeable number of seedlings from biparental crosses of A. deliciosa involving A12 and Hw1 as seed parents were still non-flowering after seven growing seasons. Open-pollinated families of both diploid and hexaploid species as well as most families from biparental crosses showed a sex segregation ratio approaching 1∶1. Subandroecious lines with different degrees of ovary and pistil development appeared in proportions of 0–4.2%, depending on the cross, but only 6 of the 2567 male vines checked were capable of setting fruit. No case of self-fertility or apomixis was detected among 1866 bagged female vines. Selfed M3h progenies gave only female and male phenotypes in a ratio of 1 female to 3 males. No off-type vines were found among these progenies. The same disomic sex segregation ratio seems to be operating at different ploidy levels in the genus Actinidia. Since selfed fruiting males produced both female and male individuals, the male sex appears to be the heterogametic one. Such evidence indicates that a monofactorial system based on one or more linked genes or on an X/Y chromosome set must be controlling sex expression. How a monofactorial sex-determining mechanism could operate in polyploids to give a 1∶1 female: male ratio is discussed. Minor modifying gene(s) seem to be responsible for the feminization of males, and their expression appears enhanced by environmental conditions. Masculinizing gene(s) seem to be lacking in female genotypes.
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  • 15
    Electronic Resource
    Electronic Resource
    Springer
    Astrophysics and space science 224 (1995), S. 81-84 
    ISSN: 1572-946X
    Keywords: Chemistry ; Depletions ; Shocks ; IRAS 05338-0624 ; NGC 1333 IRAS 4
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract High resolution interferometer and single-dish observations of young, deeply embedded stellar systems reveal a complex chemistry in the circumstellar environments of low to intermediate mass stars. Depletions of gas-phase molecules, grain mantle evaporation, and shock interactions actively drive chemical processes in different regions around young stars. We present results for two systems, IRAS 05338-0624 and NGC 1333 IRAS 4, to illustrate the behavior found and to examine the physical processes at work.
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  • 16
    Electronic Resource
    Electronic Resource
    Springer
    Astrophysics and space science 233 (1995), S. 125-137 
    ISSN: 1572-946X
    Keywords: Interstellar Medium ; Dark Clouds ; Chemistry ; Bistability ; C-shock Waves
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract Shock waves perturb the chemical state of the interstellar gas. We consider the effects of C-shocks on the composition of molecular clouds, for a range of values of the pre-shock gas density and magnetic induction. The time required to re-establish equilibrium in the post-shock gas depends on the initial conditions and can become very large. The significance of the two known chemical phases of dark clouds and of bistability is considered in this context.
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  • 17
    Electronic Resource
    Electronic Resource
    Springer
    Astrophysics and space science 233 (1995), S. 161-164 
    ISSN: 1572-946X
    Keywords: Stars ; Chemistry ; Diffusion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We have assessed the role of diffusion in determining chemical abundances in molecular interface regions. Chemical models have been developed which include the appropriate diffusion terms and that are appropriate to a narrow diffusion region (∼0.01pc) that may exist at the interface between a dark core and a hot, shocked T-Tauri wind. We have assumed pressure balance throughout and have calculated the chemical abundances as functions of time and position through the interface. The results show that significant enhancements of detectable molecules/transitions are expected (e.g. CO J=6→5, OH and CH). Using a realistic value of the diffusion coefficient a diffusive region of dimension 0.01pc may be established within about 104 years. In general it seems likely that diffusion processes are highly significant on these and smaller lengthscales.
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  • 18
    ISSN: 1432-1440
    Keywords: Adrenergic receptors ; Human genetics ; Restriction fragment length polymorphism ; Chromosome mapping ; Linkage ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We have genetically mapped the genes encoding four human adrenergic receptors (ARs) of subtypes α1C, α2A, α2B, and β1, which are prototypic G protein coupled receptors that mediate the physiological effects of neurotransmitters, hormones, and drugs. We placed these genes onto the Cooperative Human Linkage Center (CHLC) and Genethon framework maps, within confidence intervals with greater than 1000∶1 odds. With multipoint analysis the α1C gene (locus ADRA1C) mapped to the interval between NEFL and D8S283; α2-C4, the gene encoding the α2C AR (locus ADRA2C), mapped to the interval between D4S126 and D4S62; and the α2-C10 (α2A AR)/β1 haplotype (loci ADRA2A/ ADRB1) mapped to the interval between D10S259 and D10S187. A fifth AR gene, β2, yielded significant LOD scores with markers on the long arm of chromosome 5; however, this locus (ADRB2) could not be mapped to any specific interval with odds of greater than 1000∶1. The two AR genes that are completely linked, α2-C10 and β1, were oriented on their shared 225-kb genomic fragment relative to the direction of transcription, with β1 being 5′ to α2-C10. The positioning of these genes on high-density framework maps allows them to be tested as candidates in a spectrum of diseases that might involve AR dysfunction.
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  • 19
    ISSN: 1432-1440
    Keywords: Atherosclerosis ; Hypertension ; Type 2 diabetes ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract In the search for new risk factors for diabetic macroangiopathy the insertion/deletion (I/D) polymorphism in the angiotensin-converting enzyme gene was studied in 237 consecutive patients (125 men and 112 women) with non-insulin-dependent diabetes. The female population showed an excess of ischemic electro-cardiographic changes or definite myocardial infarctions in the patients homozygous for the deletion [D/D; odds ratio (OR) 2.8; 95% confidence interval (CI) 1.4–5.3] and in the insertion/deletion heterozygotes (I/D; OR 1.8; CI 1.1–3.1) compared with the patients homozygous for the insertion (I/I). In the total series coronary heart disease, cerebrovascular disease, and claudication were more often observed in the patients with I/D (OR 1.5; CI 1.0–2.2) or the D/D genotype patients (OR 1.7; CI 1.1–2.6) than in those with the genotype I/I. The systolic blood pressure was lower in patients with genotype I/I (138±19 mmHg) than in those with the genotype I/D (149±22 mmHg) or D/D (150±21 mmHg; P〈0.02). The prevalence of hypertension and the median urinary albumin excretion rate also tended to be lowest in the I/I genotype patients. Multiple logistic analysis revealed that in women the angiotensin-converting enzyme D/D genotype is independently associated with coronary heart disease. Our findings suggest that variation at the angiotensin-converting enzyme gene locus is one of the factors involved in the predisposition of diabetic patients to the development of arterial disease and hypertension.
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  • 20
    Electronic Resource
    Electronic Resource
    Springer
    Journal of neurology 242 (1995), S. 508-511 
    ISSN: 1432-1459
    Keywords: Dystonia ; Torticollis ; Blepharospasm ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The inheritance of focal dystonias was investigated in 43 families containing 43 index cases with torticollis (n = 21), blepharospasm (n = 18) and writer's cramp (n = 4). They generated a potential population of 235 first-degree relatives, and 168 out of 179 living first-degree relatives were examined. Ten relatives with dystonia were identified in ten families. Another two parents from two of the same group of ten families were affected according to the family history. The majority of the secondary cases (six patients, five siblings, and one child) were not aware of any dystonia. The tendency for affected relatives to have the same type of dystonia as index patients was observed only for torticollis. Overall, 23% of index patients had relatives with dystonia. Segregation analysis suggested the presence of an autosomal dominant gene or genes with reduced penetrante underlying focal dystonia.
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  • 21
    Electronic Resource
    Electronic Resource
    Springer
    Rheumatology international 15 (1995), S. 89-93 
    ISSN: 1437-160X
    Keywords: SLE Lupus ; BBV transformation ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Epstein-Barr-virus (EBV)-transformed lymphoblastoid B-cell lines were generated from peripheral blood lymphocytes of 55 patients with systemic lupus erythematosus (SLE) and 44 healthy relatives. All donors have previously been extensively characterized with regard to clinical, serologic, and genetic parameters. Here, peripheral blood lymphocytes and lines were characterized for cell surface antigens. Furthermore, autoantibody production and proliferation rate of the cell lines were monitored. A significant difference between patients and relatives was the lower proliferation rate of EBV-transformed cell lines of the SLE patients. All SLE cell lines are available for interested researches and can be obtained from the European Cell Bank, Salisbury, UK.
    Type of Medium: Electronic Resource
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  • 22
    Electronic Resource
    Electronic Resource
    Springer
    Journal of industrial microbiology and biotechnology 14 (1995), S. 355-364 
    ISSN: 1476-5535
    Keywords: Transformation ; Fungi ; Yeast ; Genetics ; Biotechnology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary The genetic investigation of fungi has been extended substantially by DNA-mediated transformation, providing a supplement to more conventional genetic approaches based upon sexual and parasexual processes. Initial transformation studies with the yeastSaccharomyces cerevisiae provided the model for transformation systems in other fungi with regard to methodology, vector construction and selection strategies. There are, however, certain differences betweenS. cerevisiae and filamentous fungi with regard to type of genomic insertion and the availability of shuttle vectors. Single-site linked insertions are common in yeast due to the high level of homology required for recombination between vectored and genomic sequences, whereas mycelial fungi often show a high frequency of heterologous and unlinked insertions, often in the form of random and multiple-site integrations. While extrachromosomally-maintained or replicative vectors are readily available for use with yeasts, such vectors have been difficult to construct for use with filamentous fungi. The development of vectors for replicative transformation with these fungi awaits further study. It is proposed that replicative vectors may be inherently less efficient for use with mycelial fungi relative to yeasts, since the mycelium, as an extended and semicontinuous network of cells, may delimit an adequate diffusion of the vector carrying the selectable gene, thus leading to a high frequency of abortive or unstable transformants.
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    Theoretical medicine and bioethics 16 (1995), S. 347-373 
    ISSN: 1573-1200
    Keywords: Genetics ; human research ; adolescence ; child ; informed consent ; decision making ; medical ethics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine , Philosophy
    Notes: Abstract The participation of adolescents in genetic research engenders unusual problems concerning the nature of their informed consent. In this study we analyze 70 consent documents collected from genetics investigators in the United States who conduct research with children and adolescents. We find that many consent documents do not reflect either the current or the developing ethical and legal standards for research with adolescents and that in many cases the documents are simply confusing or unclear. We make recommendations for change to reflect more adequately the changing perspective concerning the autonomous decision-making capacity of adolescents.
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  • 24
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    Environmental biology of fishes 43 (1995), S. 1-27 
    ISSN: 1573-5133
    Keywords: Conservation ; Extinction ; Rarity ; Biodiversity ; Breeding guilds ; Endemism ; Speciation ; Habitat degradation ; Environmental management ; Invasive fishes ; Genetics ; Ecology ; Stenotopy ; Captive propagation ; Legislation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis The conservation status and factors threatening fishes worldwide are reviewed in order to introduce a series of one-page articles on ‘Threatened fishes of the world’, and to encourage the incorporation of information on threatened fishes into international conservation programmes. Information on fish extinction and threat rates are compared with those of other animal groups, and the unique characteristics of fish conservation problems are highlighted. At present 979 species of fishes are listed as threatened in the IUCN Red List and at least 36 species and three subspecies are listed as recently extinct. It is argued that these figures are probably gross underestimates and that they may mislead conservation authorities and resource users about the seriousness of the situation. Freshwater fishes may be the most threatened group of vertebrates after the Amphibia. Urgent action is required to save many narrowly endemic, stenotopic species from extinction, especially in Africa, Asia and South America. The conservation of common species that drive essential ecological processes is also important. Anthropogenic pressures, especially habitat degradation, the introduction of invasive species and pollution, on inland and coastal waters are particularly severe and many major fish communities are threatened with elimination throughout the world. The conservation of marine fishes is complicated by the fact that it is difficult to ascertain their rarity. The importance of the retention of genetic variation is highlighted, and both orthodox and innovative conservation measures are encouraged. Further research on minimum viable populations, genetics, and the factors that cause fishes to become vulnerable to extinction, is urgently required.
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  • 25
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    Theoretical and applied genetics 91 (1995), S. 639-646 
    ISSN: 1432-2242
    Keywords: Gene introgression ; Genetics ; Linkage ; Taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The wild tetraploid (2n=28) oat species Avena magna and A. murphyi have been domesticated by having been transferred from the common oat, A sativa (2n=42), the characteristics of non-shedding spikelets glabrous and yellow lemma, and reduced awn formation. Domestication has been achieved by crossing the common oat with either of the tetraploid species and then backcrossing the pentaploid hybrids with pollen of the tetraploid wild parent. Among the BC plants obtained only a few produced some seeds. Fertile tetraploids exhibiting the domesticated syndrome have been selected for in the F2 generation. Although morphologically they were almost indistinguishable from the common oat, they were tetraploids. Wild x domesticated A. magna hybrids were vigorous and fertile. They retained their spikelets at maturity, lemma color and pubescence were intermediate between the parental lines, and awns were formed only on the lower floret of the spikelet. Each of these characteristics segregated in a 3∶1 fashion, indicating single gene control, as in the common oat. These four characteristics formed a linkage group in one F2 family and two linkage groups in the other two families. The usefulness of the domesticated tetraploids for oat research and production has been discussed. Taxonomically, the domesticated tetraploids were ranked as subspecies: A. magna ssp. domestica, and A. murphyi ssp. rigida.
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  • 26
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    Cell Motility and the Cytoskeleton 30 (1995), S. 1-7 
    ISSN: 0886-1544
    Keywords: actin ; cytoskeleton ; contractile ring ; microinjection ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Cofilin is a small actin-binding protein which reguiates actin polymerization in a pH-dependent manner. Immunofluorescence microscopy with a monoclonal antibody for cofilin revealed that this protein is temporarily concentrated at the contractile ring during cytokinesis. Cofilin appeared to accumulate rapidly at the contractile ring during late stages of furrowing, and was finally enriched at the midbody. The concentration of cofilin at the contractile ring was observed in several kinds of cultured cells. Furthermore, cofilin introduced into living cells by a microinjection method was also concentrated at the contractile ring. These results suggest that cofilin is involved in actin reorganization during cytokinesis. © 1995 Wiley-Liss, Inc.
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  • 27
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    Cell Motility and the Cytoskeleton 30 (1995), S. 38-49 
    ISSN: 0886-1544
    Keywords: Listeria monocytogenes ; actin ; profilin ; DNase I ; vitamin D-binding protein ; phalloidin ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Infection of host cells by Listeria monocytogenes results in the recruitment of cytoplasmic actin into a tail-like appendage that projects from one end of the bacterium. Each filamentous actin tail progressively lengthenes, providing the force which drives the bacterium in a forward direction through the cytoplasm and later results in Listeria cell-to-cell spread. Host cell actin monomers are incorporated into the filamentous actin tail at a discrete site, the bacterial-actin tail interface. We have studied the consequences of microinjecting three different actin monomer-binding proteins on the actin tail assembly and Listeria intracellular movement. Introduction of high concentrations of profilin (estimated injected intracellular concentration 11-22 m̈M) into infected PtK2 cells causes a marked slowing of actin tail elongation and bacterial migration. Lower intracellular concentrations of two other injected higher affinity monomer-sequenstering proteins, Vitamin D-binding protein (DBP; 1-2 m̈M) and DNase I (6-7 m̈M) completely block bacterial-induced actin assembly and bacterial migration. The onset of inhibition by each protein is gradual (10-20 min) indicating that the mechanisms by which these proteins interfere with Listeria-induced actin assembly are likely to be complex. To exclude the possibility that Listeria recruits preformed actin filaments to generate the tails and that these monomer-binding proteins act by depolymerizing such performed actin filaments, living infected cells have been injected with fluorescently labeled phalloidin (3 m̈M). Although the stress fibers are labeled, no fluorescent phalloidin is found in the tails of the moving bacteria. These results demonstrate that Listeria-induced actin assembly in PtK2 cells is the result of assembly of actin monomers into new filaments and that Listeria's ability to recruit polymerization competent monomeric actin is very sensitive to the introduction of exogenous actin monomer-binding proteins. © 1995 Wiley-Liss, Inc.
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  • 28
    ISSN: 0886-1544
    Keywords: microfilamentous cytoskeleton ; actin binding proteins ; actin polymerization ; annealing ; non-muscle cells ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Gelsolin, a Ca++ activated, 90 kd actin binding protein, can regulate actin polymerization in polymorphonuclear leukocytes (PMNs) via severing of filaments to dissolve gels or by capping of filament ends to limit polymerization. In Triton-lysed PMNs, 30% of gelsolin is bound to the Triton-soluble F-actin (TSF) pool and none is bound to the Triton-insoluble F-actin (TIF) pool. Calcium-activated PMNs exhibit concurrent temporal and quantitative TIF growth and TSF and total F-actin loss. To determine if gelsolin plays a role in regulating TSF pool size, we monitored gelsolin-actin interactions and TIF, TSF and G-actin content at 5 second intervals in PMNs activated with the calcium ionophore, ionomycin. Actin pools were measured by NBDphallacidin binding and by gel scans and expressed relative to basal; gelsolin-actin interactions were measured as change in the amount of EGTA-resistant gelsolin:actin (G:A) complexes and by immunoblot quantification of gelsolin in actin pools. In basal PMNs, 33% of PMN gelsolin is bound in 1:1 EGTA-resistant G:A complexes and TSF and TIF retain 30% and 0% of PMN gelsolin, respectively. By 20 seconds after ionomycin addition, TSF decreases, TIF increases and a fraction of gelsolin repartitions from the TSF to the TIF pool. At maximum change (60 seconds), total F-actin (TIF + TSF) and TSF decrease and TIF increases by 25%; gelsolin is bound to both TSF and TIF (35% of total gelsolin in each pool), and 1:1 EGTA-resistant G:A complexes increase from 33% to 70%. No changes occur in cells activated by ionomycin in the absence of Ca++. The data show Ca++ activated TIF growth and TSF loss are temporally and quantitatively associated with an increase in the percent of gelsolin bound to actin and the translocation of gelsolin from TSF to TIF. This is unique, since no other PMN activator is known to repartition gelsolin into TIF actin. Further, the Ca++ activated initial increase in TIF concurrent with a fall in TSF without a change in total F-actin or G-actin content suggest that TIF grows initially only by TSF annealing/cross-linking to TIF. Gelsolin may regulate these events. © 1995 Wiley-Liss, Inc.
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  • 29
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    Cell Motility and the Cytoskeleton 30 (1995), S. 153-163 
    ISSN: 0886-1544
    Keywords: colchicine binding site ; MTC ; cod microtubules ; bovine microtubules ; MAPs ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Isolated microtubules from cod (Gadus morhua) are apparently more stable to colchicine than bovine microtubules. In order to further characterize this difference, the effect of the colchicine analogue 2-methoxy-5-(2,3,4-trimethoxyphenyl)-2,4,6-cyclo heptatrien-1-one (MTC) was studied on assembly, as measured by turbidity and sedimentation analysis, and on polymer morphology. MTC has the advantage to bind fast and reversible to the colchicine binding site of tubulin even at low temperatures. It was found to bind to one site in cod brain tubulin, with affinity (6.5 ± 1.5) × 105M 1at both low or high temperature, similarly to bovine brain tubulin. However, the effect of the binding differed. At substoichiometric concentrations of MTC bovine brain microtubule assembly was almost completely inhibited, while less effect was seen on the mass of polymerized cod microtubule proteins. A preformed bovine tubulin-colchicine complex inhibited the assembly of both cod and bovine microtubules at substoichiometric concentrations, but the effect on the assembly of cod microtubules was less. At higher concentrations (5 × 10-5 to 1 × 10-3M), MTC induced a large amount of cold-stable spirals of cod proteins, whereas abnormal polymers without any defined structure were formed from bovine proteins. Spirals of cod microtubule proteins were only formed in the presence of microtubule associated proteins (MAPs), indicating that the morphological effect of MTC can be modulated by MAPs. The effects of colchicine and MTC differed. At 10-5M colchicine no spirals were formed, while at 10-4M and 10-3M, a mixture of spirals and aggregates was found. The morphology of the spirals differed both from vinblastine spirals and from the spirals previously found when cod microtubule proteins polymerize in the presence of high Ca2concentrations. The present data show that even if the colchicine binding site is conserved between many different species, the bindings have different effects which seem to depend on intrinsic properties of the different tubulins. © 1995 Wiley-Liss, Inc.
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    Cell Motility and the Cytoskeleton 31 (1995), S. 34-44 
    ISSN: 0886-1544
    Keywords: microtubule ; MTOC ; mitosis ; MPM-2 ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In diverse cell types, monoclonal antibody MPM-2 recognizes a class of phosphorylated proteins related to microtubule organizing centers and abundant during mitosis. We have used this antibody in an attempt to identify the spatial and temporal localization of putative microtubule organizing centers in endosperm cells of the higher plant Haemanthus. Our results show that MPM-2 recognized epitope is present in interphase cells and enriched in mitotic cells. In interphase the antibody usually stains cytoplasmic granules. During the interphase-prophase transition immunoreactive material appears in the nucleus, at the nuclear envelope, and in association with microtubules. Concomitantly, we observed an increase of immunoreactivity of the cytoplasm. During mitosis the phosphorproteins recognized by MPM-2 are detected in the cytoplasm, in association with microtubules of the spindle, the phragmoplast, and in the newly-formed cell plate. After completion of mitosis, only the cell plate and cytoplasmic granules are MPM-2 positive. Extraction of the cells with Triton X-100 prior to fixation removes staining of the cytoplasm by MPM-2. The detergent resistant immunoreactive material remains associated with surrounding the nucleus microtubules of the prophase spindle, the core of kinetochore fibers, and the phragmoplast. In the phragmoplast, however, segments of microtubules which are distal to the cell plate are depleted of MPM-2.These data demonstrate that microtubule arrays of endosperm cells are phosphorylated during mitosis. Thus, similar to animal cells, interphase and mitotic microtubules of higher plants have different properties. Additionally, the localization of detergent resistant MPM-2 antigen points to the difference in microtubule nucleation/organization between higher plant and animal cells.
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    Cell Motility and the Cytoskeleton 31 (1995), S. 59-65 
    ISSN: 0886-1544
    Keywords: flagella ; cane-shaped bend ; principal bend ; calcium ; membrane depolarization ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: To investigate the mechanism of the flagellar quiescence in sperm, we examined the effect of electric stimulation of individual spermatozoa of the sea urchin, Hemicentrotus pulcherrimus. Stimulation with a suction electrode attached to the sperm head elicited a flagellar quiescence response, in which the sperm showed a typical cane-shaped bend in the proximal region of the flagellum when the electrode was used as anode. Cathodic stimulation also induced quiescence, but was much less effective than anodic stimulation. During the quiescence response, which lasted for 1-3 s, no new bend was initiated, and subsequently the flagellum resumed normal beating. The quiescence response required the presence of Ca2+ (〉2 mM) in sea water, and was inhibited by Co2+ and La3+. At low Ca2+ concentrations (2-5 mM), the angle of the cane-shaped bend was smaller than that at 10 mM Ca2+; thus the angle of the cane-shaped bend, characteristic of the quiescence response is dependent on Ca2+ concentration. These results suggest membrane, followed by an influx of Ca2+ into the flagellum through Ca2+ channels. The increase in Ca2+ concentration within the flagellum affects the amount of sliding and thus produces a cane-shaped proximal bend of various angles, white inhibiting both the propagation of the proximal bend (principal bend) and the formation of a new reverse bend.
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  • 32
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    Cell Motility and the Cytoskeleton 30 (1995), S. 285-300 
    ISSN: 0886-1544
    Keywords: microtubule dynamics ; β-tubulin ; mitosis ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Microtubule (MT) dynamics vary both spatially and temporally within cells and are thought to be important for proper MT cellular function. Because MT dynamics appear to be closely tied to the guanosine triphosphatase (GTPase) activity of β-tubulin subunits, we examined the importance of MT dynamics in the budding yeast S. cerevisiae by introducing a T107K point mutation into a region of the single β-tubulin gene, TUB2, known to affect the assembly-dependent GTPase activity of MTs in vitro. Analysis of MT dynamic behavior by video-enhanced differential interference contrast microscopy, revealed that T107K subunits slowed both the growth rates and catastrophic disassembly rates of individual MTs in vitro. In haploid cells tub2-T107K is lethal; but in tub2-T107K/tub2-590 heterozygotes the mutation is viable, dominant, and slows cell-cycle progression through mitosis, without causing wholesale disruption of cellular MTs. The correlation between the slower growing and shortening rates of MTs in vitro, and the slower mitosis in vivo suggests that MT dynamics are important in budding yeast and may regulate the rate of nuclear movement and segregation. The slower mitosis in mutant celis did not result in premature cytokinesis and cell death, further suggesting that cell-cycle control mechanisms “sense” the mitotic slowdown, possibly by monitoring MT dynamics directly. © 1995 Wiley-Liss, Inc.
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  • 33
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    Cell Motility and the Cytoskeleton 30 (1995), S. 310-323 
    ISSN: 0886-1544
    Keywords: mitosis ; mitotic apparatus ; sea urchin ; immunofluorescence ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: A protein component of 62-kDa (p62) in the mitotic apparatus of the sea urchin embryo has been shown to be important for the proper progression of mitosis [Dinsmore and Sloboda, 1989: Cell 57:127-134]. To study the subcellular distribution of p62 during the cell cycle of sea urchin embryos, indirect immunofluorescence microscopy was used coupled to a modified detergent extraction procedure. The improved fluorescent images obtained by this procedure provide new information concerning the subcellular localization of p62 during the cell cycle that could not be obtained with previous conventional staining procedures [Johnston and Sloboda, 1992: J. Cell Biol. 119:843-854]. Using affinity purified antibodies to p62, we observed a cell cycle-dependent localization of p62 to the chromosomes/chromatin. Prior to nuclear envelope breakdown of the first or second cell cycle, p62 localizes to chromatin in the nucleus. During mitosis, p62 associates with the region of the spindle occupied by the microtubules of the mitotic apparatus. As anaphase proceeds, but before the nuclear envelope reforms, p62 becomes progressively associated with the chromosomes. Thus, p62 is incorporated into the forming interphase nucleus due to its association with chromosomes during late anaphase, rather than by active translocation into the newly formed daughter nuclei through the nuclear pores. The protein is not unique to marine embryos, as demonstrated by immunofluorescence of Y-1 cells, a mouse adrenal tumor cell line In these cells, the localization of p62 is similar to the localization of the protein in echinoderm embryos, suggesting its possible function in mitotic progression in mammalian somatic cells as well. © 1995 Wiley-Liss, Inc.
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  • 34
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    Cell Motility and the Cytoskeleton 31 (1995), S. 45-58 
    ISSN: 0886-1544
    Keywords: colcemid ; kinesin ; actin ; topographic guidance ; micromachined substrata ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Fibroblats cultured on grooved substrata align themselves and migrate in the direction of the grooves, a phenomenon called contact guidance. Microtubules have been deemed important for cell polarization, directed locomotion, and contact guidance. Because microtubules were the first cytoskeletal element to align with the grooves when fibroblasts spread on grooved substrata, we investigated the consequences of eliminating the influence of microtubules by seeding fibro-blasts onto smooth and grooved micromachined substrata in the presence of colcemid. Fibroblasts were examined by time-lapse cinematography and epifluorescence or confocal microscopy to determine cell shape and orientation and the distribution of cytoskeletal or associated elements including actin filaments, vinculin, intermediate filaments, microtubules, and kinesin.As expected, cells spreading on smooth surfaces in the presence of colcemid did not polarize or locomote. Surprisingly however, by 24 hours, cells spread on grooves in the presence of colcemid were morphologically indistinguishable from controls spread on grooves. Both groups were aligned and polarized with the direction of the grooves and demonstrated directional locomotion along the grooves. In the absence of microtubules, kinesin localized to some of the aligned stress fibers and to leading edges of cells spreading on grooves. The grooved substratum compensated for the microtubule deficiency by organizing and maintaining an aligned actin filament framework. Thus, microtubules are not required to establish or maintain stable, polarized cell shapes or directed locomotion, provided an alternate oriented cytoskeletal component is available.
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    Cell Motility and the Cytoskeleton 31 (1995), S. 255-258 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 36
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    Cell Motility and the Cytoskeleton 31 (1995), S. 207-214 
    ISSN: 0886-1544
    Keywords: flagella ; Chlamydomonas ; mutant ; high-frequency vibration ; nanometer-scale measurement ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The flageliar axoneme of the mutant pf18 lacking the central pair does not beat, but undergoes a nanometer-scale, high-frequency oscillation (hyper-oscillation) in the presence of ATP [Yagi et al., 1994: Cell Motil, Cytoskeleton 29:177-185]. The present study demonstrates that the amplitude of the hyper-oscillation increases significantly in the simultaneous presence of ATP and ADP. In addition, the hyper-oscillation under these conditions sometimes takes on an exceptionally simple asymmetric pattern, in which the maximal shearing velocity exceeds 50 μm/sec, much higher than the maximal velocity of ordinary dynein-microtubule sliding. The asymmetric oscillation thus appears to be at least partly driven by an internal elastic force. Its amplitude suggests that the axoneme has an elastic component that can be stretched by as long as 0.1 μm. Analyses of the asymmetric pattern further suggests that the axonemal dyneins have a tendency to attach to and detach from the doublets cooperatively and that the mechanochemical cycle of dynein has an inherent refractory period of about 2 msec, during which dynein cannot interact with microtubules.
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  • 37
    ISSN: 0886-1544
    Keywords: Ascaris sperm ; motility ; computer-assisted motion analysis ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Computer-assisted methods have been employed to obtain a high resolution description of pseudopod expansion, cellular translocation, and the subcellular dynamics of MSP fiber complexes in the motile sperm of the nematode Ascaris suum. Although Ascaris sperm translocating in a straight line or along a curved path do not retract their pseudopod or significantly alter pseudopod shape, they move in a cyclic fashion, with an average period between velocity peaks of 0.35 × 0.05 min, which is independent of the forward velocity of sperm translocation. Expansion is confined to a central zone at the distal edge of the pseudopod for sperm translocating in a straight line and to a left-handed or right-handed lateral zone in the direction of turning, for sperm translocating along a curved path. For cells translocating in a straight line, the branch points and kinks of MSP fiber complexes move in a retrograde direction in relation to the substratum at an average velocity of 11 μm per min which is independent of the forward velocity of sperm translocation. The distal (anterior) end of a fiber complex, however, moves distally at the speed of sperm translocation when it emanates from the expansion zone, but when it is displaced to a nonexpanding surface of the pseudopod, it stops moving distally. When a cell is anchored to the substratum and is, therefore, nonmotile, the velocity of fiber complexes moving in a retrograde direction doubles. The unique aspects of pseudopod and MSP fiber complex dynamics in Ascaris are compared to the dynamics of pseudopod formation and actin filament dynamics in traditional actin-based amoeboid cells, and the treadmill model for MSP polymerization is reassessed in light of the discovery that fiber complex branch points move proximally (posteriorly) at a fixed rate.
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    Cell Motility and the Cytoskeleton 31 (1995), S. 323-332 
    ISSN: 0886-1544
    Keywords: adherens junction ; cytoskeleton ; intercellular junction ; tight junction ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We previously reported the expression of ZO-1 in cell types that do not form tight junctions. Here we compare the molecular environments of ZO-1 in epithelial cells, primary cultures of astrocytes and in the non-epithelial S180 sarcoma cell line. ZO-1 co-localizes with a subset of actin filament in all cell types. In astrocytes, ZO-1 is found concentrated in discrete bands at points of cell-cell contact. Indirect immunofluorescent microscopy shows that these bands of ZO-1 co-localize with the adherens junction proteins vinculin and α-actinin, and with the antigen recognized by a pan-cadherin antibody. In contrast, ZO-1 in S180 cells, which exhibit limited cell-cell interactions, is diffusely distributed over the plasma membrane, with concentrations in lamellipodia where actin filaments accumulate. ZO-1 does not co-localize with vinculin at focal adhesions in this cell type. Analysis of ZO-1 immunoprecipitation profiles from different cell types, performed under conditions previously demonstrated to maintain interactions between ZO-1, ZO-2 and p130 from the MDCK epithelial cell line, show that the proteins which co-precipitate with ZO-1 vary with cell type. Precipitation of polypeptides at 165 kDa, potentially ZO-2, and 65 kDa occurs in both a mouse kidney tubule epithelial cell line and the non-epithelial S180 cells. No proteins specifically associate with ZO-1 immunoprecipitated from astrocytes. Spectrin, α-actinin, vinculin and cadherin are not detected in immunoblots of ZO-1 immunoprecipitates from any cell type. © 1995 Wiley-Liss, Inc.
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  • 39
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    Cell Motility and the Cytoskeleton 32 (1995), S. 26-36 
    ISSN: 0886-1544
    Keywords: microtubules ; motor proteins ; axonal transport ; mitosis ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We report the cloning and sequencing of genomic DNA encoding a cytoplasmic dynein heavy chain from the nematode Caenorhabditis elegans. In a contiguous stretch of 35,103 bp of DNA from the left arm of linkage group I, we have found a gene that is predicted to encode a protein of 4,568 amino acids. This gene is composed of 15 exons and 14 relatively short introns, and it has significant homology of the other dynein heavy chains in the databases. The deduced molecular mass of the derived polypeptide is 512,624 Da. As with other dynein heavy chains that have been sequenced to date, it contains four GXXGXGK(S/T) motifs that form part of the consensus sequence for nucleotide triphosphate-binding domains. Comparison of axonemal and cytoplasmic dynein heavy chains shows that regions of homology among all dyneins are clustered in the carboxyl terminal two-thirds of the polypeptide, whereas the amino terminal one-third of the heavy chains may contain domains that specify functions that differ between axonemal and cytoplasmic forms of the dynein heavy chain. © 1995 Wiley-Liss, Inc.
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    Cell Motility and the Cytoskeleton 32 (1995) 
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    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Cell Motility and the Cytoskeleton 32 (1995), S. 95-97 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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    Cell Motility and the Cytoskeleton 32 (1995), S. 106-109 
    ISSN: 0886-1544
    Keywords: Chlamydomonas ; cilia and flagella ; protein kinase and phosphatase ; dynein-driven microtubule sliding ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The following is a summary of physiological and pharmacological studies of the regulation of dynein-driven microtubule sliding in Chlamydomonas flagella. The experimental basis for the study is described, and data indicating that an axonemal cAMP-dependent protein kinase can regulate inner arm dynein activity are reviewed. In addition, preliminary data are summarized indicating that an axonemal type 1 phosphatase can also regulate dynein-drive microtubule sliding velocity. It is predicted that the protein kinase, phosphatase, and an inner dynein arm component form a regulatory complex in the axoneme.
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    Cell Motility and the Cytoskeleton 32 (1995), S. 129-132 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 44
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    Cell Motility and the Cytoskeleton 32 (1995), S. 151-161 
    ISSN: 0886-1544
    Keywords: membrane localization ; ATPase activity ; actin binding ; calmodulin ; motility ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Although the specific functions of myosin I motors are not known, their localization to membrane structures suggests a function in membrane motility. Different myosin I isoforms in the same cell or in different cells can possess different localizations. To determine if the localization and biochemical activity of the best-characterized mammalian myosin I, chicken intestinal epithelium brush border myosin I, was dependent on determinants of the membrane or actin cytoskeleton specific to epithelial cells, we transfected the cDNA for the heavy chain of this myosin into COS cells. Transient transfection of COS cells with the chicken brush border myosin I heavy chain resulted in the production of recombinant myosin I. Recombinant brush border myosin I localized to protrusions of the plasma membrane, particularly at spreading cell edges, and also to unknown cytoplasmic structures. Some cells expressing particularly high levels of brush border myosin I possessed a highly irregular surface. Recombinant brush border myosin I purified from COS cells bound to actin filaments in an ATP-dependent manner and decorated actin filaments to form a characteristic appearance. The recombinant myosin also catalyzed calcium-sensitive, actin-activated MgATPase activity similar to that of the native enzyme. Thus, any cellular factor required for the general membrane localization or biochemical activity of brush border myosin I is present in COS cells as well as intestinal epithelium.
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  • 45
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    Cell Motility and the Cytoskeleton 32 (1995), S. 1-9 
    ISSN: 0886-1544
    Keywords: review ; fascin ; actin ; actin bundling proteins ; filopodia ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Fascin is an actin-bundling protein that was first isolated from cytoplasmic extracts of sea urchin eggs [Kane, 1975: J. Cell Biol. 66:305-315] and was the first bundling protein to be charactrized in vitro. Subsequent work has shown that fascin bundles actin filaments in fertilized egg microvilli and filopodia of phagocytic coelomocytes [Otto et al., 1980: Cell Motil. 1:31-40; Otto and Bryan, 1981: Cell Motil. 1:179-192]. Fifteen years later, the molecular cloning of sea urchin fascin [Bryan et al., 1993: Proc. Natl. Acad. Sci. U.S.A. 90:9115-9119] has led to the identification and characterization of homologous proteins in Drosophila [Cant et al., 1994: J. Cell Biol. 125:369-380], Xenopus [Holthuis et al., 1994: Biochim. Biophys. Acta. 1219:184-188], rodents [Edwards et al., 1995: J. Biol. Chem. 270:10764-10770], and humans [Duh et al., 1994: DNA Cell Biol. 13:821-827; Mosialos et al., 1994: J. Virol. 68:7320-7328] that bundle actin filaments into structures which stabilize cellular processes ranging from mechanosensory bristles to the filopodia of nerve growth cones. Fascin has emerged from relative obscurity as an exotic invertebrate egg protein to being recognized as a widely expressed protein found in a broad spectrum of tissues and organisms. This purpose of this review is to relate the early studies done on sea urchin and HeLa cell fascins to the recent molecular biology that defines a family of bundling proteins, and discuss the current state of knowledge regarding fascin structure and function. © 1995 Wiley-Liss, Inc.
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  • 46
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    Cell Motility and the Cytoskeleton 32 (1995), S. 173-186 
    ISSN: 0886-1544
    Keywords: microtubule dynamics ; microinjection ; centripetal transport ; pinocytotic vesicles ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The Study of microtubule (MT) dynamics in cells has largely been restricted to events occurring over relatively short periods in nonmotile or stationary cell in culture. By using the antioxidant, Oxyrase, we have reduced the sensitivity of fluorescent MTs to photodamage and this has allowed us to image fluorescent MTs with good temporal resolution over much longer periods of time. We have used our enhanced imaging capabilities to examine MT dynamics in fibroblasts moving directionally into a wound. We found that MTs in these cells exhibited dynamic instability similar to that reported for other cells. More interestingly, we found a novel dynamic behavior of the MTs in wihch entire MTs were moved inward from the leading edge toward the cell nucleus. This centripetal transport (CT) of MTs only occurred to those MTs that were oriented with their long axis parallel to the leading edge; radially oriented MTs were not transported centripetally. Both small bundles of MTs and individual MTs were observed to undergo CT at a rate of 0.63 × 0.37 μm/min. This rate was similar to the rate of CT of latex beads applied to the cell surface and of endogenous pinocytotic vesicles in the cytoplasm. When we imaged both MTs and pinocytotic vesicles, we found that the pinocytotic vesicles were ensheathed by a small group of parallel MTs that moved centripetally in concert with the vesicles. Conversely, we found many instances of MTs moving centripetally without associated vesicles. When cells were treated with nocodazole to depolymerize MTs rapidly, the rate of pinocytotic vesicle CT was inhibited by 75%. This suggests that centripetal transport of MTs may be involved in the movement of pinocytotic vesicles in cells. In conclusion, our results show that MTs in motile cells are redistributed by a novel mechanism, CT, that does not require changes in polymer length. The centripetally transported MTs may play a role in transporting pinocytotic vesicles in the cell. © 1995 Wiley-Liss, Inc.
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  • 47
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    Cell Motility and the Cytoskeleton 32 (1995), S. 233-243 
    ISSN: 0886-1544
    Keywords: caldesmon ; over-expression ; cell cycle ; motility ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Caldesmon is an actin, calmodulin, tropomyosin, and myosin binding protein implicated in the regulation of actomyosin interactions. We have invesigated the effect of overexpression of the higher molecular weight smooth muscle isoform of caldesmon on mouse L cell physiology. Mouse L(TK-) cell were transfected stably with plasmids carrying the TK+ gene and a full length human smooth muscle caldesmon cDNA under control of the adenovirus major late promoter. Two clones displaying four and eight times the level of the endogenous mouse high molecular weight caldesmon were isolated. These cells acquire a distinct phenotype characterized by an altered morphology, including an increased number of processes and larger area due to enhanced cell spreading, and a significantly slower growth rate than that of untransfected control cells, or cells transfected with the TK+ gene alone. The majority of the overexpressed caldesmon appears to be active and localized on cytoskeleton structures as determined by detergent lysis. Immuno-fluorescence analysis of the clones revealed that the caldesmon is localized as punctate staining on stress-fibers and in membrane ruffles. The immunofluores-cence images suggest that caldesmon overexpressing cells have more total filaments than control cells. The effects of excess caldesmon on cell mobility are ambiguous: one clone displayed increased motility compared to the control, while the motility of the second clone was decreased relative to the control. © 1995 Wiley-Liss, Inc.
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  • 48
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    Cell Motility and the Cytoskeleton 32 (1995), S. 289-298 
    ISSN: 0886-1544
    Keywords: cytoskeleton ; intermediate filaments ; vimentin ; microtubules ; myoepithelial cells ; immunofluorescence ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Salivary gland neoplastic myoepithelial cells in culture form very thin cytoplasmic processes in which the vimentin network is well dispersed. These vimentin filaments can be individually visualized by immunofluorescence. In this study, we have analyzed the role of microtubules in the distension and organization of the vimentin filament network found in these cells. We find that vimentin filaments colocalize along microtubules; however, a significant number of filaments can also be found in microtubule-free domains. Additionally, vimentin filaments are absent from large domains of microtubule inhibitor nocodazole did not cause any retraction of the distended vimentin network. This observation suggests that the structural integrity of microtubules is not important for the stability of the vimentin network. Combining procedures for transient disruption of vimentin filaments and microtubules we observed that, in the absence of microtubules, the vimentin network could reassemble in the perinuclear region but was unable to extend toward the cell periphery. The dispersion of vimentin filaments to the peripheral regions of the cytoplasm could only be observed upon microtubule reassembly. This indicates that microtubules are not required for the stability of the vimentin network, but the dispersion of vimentin filaments to the peripheral cytoplasm depends on active interactions with microtubules. © 1995 Wiley-Liss, Inc.
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  • 49
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    Journal of Chemometrics 9 (1995), S. 197-209 
    ISSN: 0886-9383
    Keywords: proficiency test ; true value ; homogeneity robust statistic ; standard ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Profficiency tests raise two types of problems: (i) the homogeneity of a sample must be carefully checked before using it as a reference material; (ii) it is necessary to define a conventional reference value (RV) in order to rank participants. Since these topics are poorly addressed in the literature, a reference material was specially prepared in order to propose a procedure for verifying homogeneity and to establish whether the algorithms classically used to compute the conventional true value have an influence on the conclusion of the test.The homogeneity of the sample was not perfect and univariate and multivariate techniques were used to demonstrate some analytes can be suspected as heterogeneous. However, this was considered adequate for introducing the sample in a large proficiency test organized between four laboratory associations which regularly perform such tests. Altogether more than 3000 measurements were collected and eight algorithms were applied to compute the RV on 14 analytes. Thus is was possible to demonstrate that some of these algorithms are better adapted than others. It is also obvious that some analytes are better suited to proficiency testing.It can be concluded from this work that some effort towards standardization would be profitable to check homogeneity or to compute the RV, especially since the economic weight of proficiency testing is becoming even more important with the development of certification accreditation.
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  • 50
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    Journal of Chemometrics 9 (1995) 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 51
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    Journal of Chemometrics 9 (1995), S. 451-457 
    ISSN: 0886-9383
    Keywords: non-linear regression ; optimization ; robust methods ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Several robust regression methods, including a new proposal, are described and their properties discussed. Resistance to various types of outliers and non-normality is demonstrated. The techniques are applied to non-linear regression models from chemical kinetics and calibration. Optimization of the types of objective functions encountered when applying robust regression is considered.
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  • 52
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    Journal of Chemometrics 9 (1995), S. 471-481 
    ISSN: 0886-9383
    Keywords: batch prediction ; continuum regression ; multivariate calibration ; sequential prediction ; simultaneous prediction ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In analytical chemistry a single fitted calibration model is used repeatedly to predict the level of the analyte of interest for the specimens comprising the prediction set. Unlike the calibration (or training) set, which is often limited in size, the prediction set can be very large.In the case of multivariate calibration a number of methods such as PLS and PCR are commonly used to construct the calibration model. The set of instrumental measurements and the reference analyte level are available for each specimen in the calibration set. For specimens in the prediction set, only the instrumental measurements are available, since the problem is to predict the analyte level for these specimens. It is not widely recognized that predictions of the analyte levels for individual specimens can be improved by utilizing seemingly unrelated information from the instrumental measurements associated with the other members of the prediction set. In the case of PCR there exists a very straightforward procedure for doing this. A description of the various sources of prediction errors is provided to explain the ability of PCR to utilize this additional information. The use of PCR in this context is illustrated with both a synthetic and a real example.
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  • 53
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    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 54
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    Journal of Chemometrics 9 (1995), S. 21-29 
    ISSN: 0886-9383
    Keywords: Near-infrared absorbance ; Partial least squares ; Principal component regression ; Root-mean-square error of prediction ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The use of principal component regression (PCR) as a multivariate calibration method has been discussed by a number of authors. In most situations principal components are included in the regression model in sequence based on the variances of the components, and the principal components with small variances are rarely used in regression. As pointed out by some authors, a low variance for a component does not necessarily imply that the corresponding component is unimportant, especially when prediction is of primary interest. In this paper we investigate a different version of PCR, correlation principal component regression (CPCR). In CPCR the importance of principal components in terms of predicting the response variable is used as a basis for the inclusion of principal components in the regression model. Two typical examples arising from calibrating near-infrared (NIR) instruments are discussed for the comparison of the two different versions of PCR along with partial least squares (PLS), a commonly used regression approach in NIR analysis. In both examples the three methods show similar optimal prediction ability, but CPCR performs better than standard PCR and PLS in terms of the number of components needed to achieve the optimal prediction ability. Similar results are also seen in other NIR examples.
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  • 55
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    Journal of Chemometrics 9 (1995), S. i 
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    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 56
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    Journal of Chemometrics 9 (1995), S. 137-138 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 57
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    Keywords: pattern recognition ; infrared spectra ; factor analysis ; maximum likelihood method ; entropy of information ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectral region from 700 to 3600 cm-1 is subdivided into several wave number intervals. The peaks in each interval are summarized by means of three encoding algorithms. Using a factor model of kcommon factors, the total extractable variacnce (com) of a given set of intervals is calculated and correlated with the redundancy of information in all these intervals. The value of com is verified by analysis of the factor loadings aik (factor pattern). Finally, the information content of some chosen sets of intervals coded by the three selected feature algorithms will be correlated to the probability of information flow through a serial-parallel network. The encoding using only wave numbers was found to be the most effective.
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  • 58
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    Journal of Chemometrics 9 (1995), S. 211-221 
    ISSN: 0886-9383
    Keywords: diagnostics statistics ; QSAR ; MASCA ; principal component regression ; non-least squares regression ; types of multicollincarity ; flagged observations ; influential points ; high-leverage points ; outliers ; extra-carrier points ; random perturbation ; cluster correalation ; resampling ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formal application of a Hansch analysis to a series of 3-quinuclidinyl benzylates (QNBs) led to a ‘statistically significant’ QSAR equation. In contrast, the application of the MASCA model has shown that the design matrix is unsuitable for each QSAR analysis: one sample member is an outlier but not a high-leverage or influential point; another one is an influential point, a high-leverage point and an extra-carrier point. The regressors of the design matrix are multicollinear without predictive model power. The result of such flagged observation and this type of multicollinearity is a multiple cluster correlation. The QNB series is a good example for ‘sampling artifacts’ where no practically important but artificial QSARs can be found.
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  • 59
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    Journal of Chemometrics 9 (1995), S. 230-231 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 60
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    Journal of Chemometrics 9 (1995), S. 239-262 
    ISSN: 0886-9383
    Keywords: industrial experimentation ; parameter design ; quality by design ; robust design ; Taguchi method ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aim of this paper is to present a simple structured review of the different approaches to robust process design to clarify their similarities and dissimilarities. It is primarily written for practitioners who wish to understand and compare the main ideas of each approach and to apply them to their work. Two examples are used to illustrate the different approaches and their corresponding data analysis strategies: the first one is a constructed example on a pigment kneading process and the second one is real example dealing with the validation of an HPLC method. A comparison of the different approaches is provided and some practical recommendations are formulated.
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  • 61
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    Journal of Chemometrics 9 (1995), S. 323-326 
    ISSN: 0886-9383
    Keywords: partial least squares ; biased regression ; ordinary least squares ; minimum length least squares ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An algebraic proof is given that in partial least squares (PLS) regression the Euclidean length of the estimator is shrunk in comparison with the ordinary least squares estimator or with PLS estimators based on a larger number of dimensions.
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  • 62
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    Journal of Chemometrics 9 (1995) 
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    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 63
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    Journal of Chemometrics 9 (1995), S. 363-372 
    ISSN: 0886-9383
    Keywords: PLS regression ; orthogonal expansion ; optimization ; Lagrange multipliers ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple iteration algorithm that is faster and less memory-intensive than the NIPALS iteration algorithm for PLS regression is presented. The iteration algorithm is obtained by treating the orthogonal expansion or decomposition of a matrix X as an extremum problem subject to normalization and orthogonality constraint conditions and then solving the problem by use of the method of Lagrange multipliers. The main idea in this method is to find the transformation vector r. The latent variable t is expressed exactly as the linear combination of X-variables with the vector r so that the final regression coefficients can be conveniently provided. In the algorithm the recursion of the orthogonal projection is needed, which is derived by use of a matrix inverse formula. Algorithms are established from the equation for calculating the vector r that are suitable for dealing with three cases of large data sets. The first case is when the number of objects is very large, the number of variables is relatively small and the number of Y-variables is equal to or greater than the number of X-variables. The second case is when the number of objects is very large, the number of variables is relatively small and the number of X-variables is greater than the number of Y-variables. The last case is when the number of variables, either X- or Y-variables, or both, is very large and the number of objects is small.
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  • 64
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    Journal of Chemometrics 9 (1995), S. 423-430 
    ISSN: 0886-9383
    Keywords: PLS ; neural network ; training ; interpretable ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This communication describes the combination of a feedforward neural network (NN) with one hidden neuron and partial least squares (PLS) regression. Through training of the neural network with an algorithm that is a combination of a modified simplex, PLS and certain numerical restrictions, one gains an NN solution that has several feasible properties: (i) as in PLS the solution is qualitatively interpretable; (ii) it works faster than or comparably with ordinary training algorithms for neural networks; (iii) it contains the linear solution as a limiting case. Another very important aspect of this training algorithm is the fact that outlier detection as in ordinary PLS is possible through loadings, scores and residuals. The algorithm is used on a simple non-linear problem concerning fluorescence spectra of white sugar solutions.
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    Journal of Chemometrics 9 (1995), S. 439-439 
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 66
    ISSN: 0886-9383
    Keywords: PLS ; kernel algorithm ; multivariate calibration ; EM algorithm ; cross-validation ; missing data ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This is Part II of a series concerning the PLS kernel algorithm for data sets with many variables and few objects. Here the issues of cross-validation and missing data are investigated. Both partial and full crossvalidation are evaluated in terms of predictive residuals and speed and are illustrated on real examples. Two related approaches to the solution of the missing data problem are presented. One is a full EM algorithm and the second a reduced EM algorithm which applies when the number of missing values is small. The two examples are multivariate calibration data sets. The first set consists of UV-visible data measured on mixtures of four metal ions. The second example consists of FT-IR measurements on mixtures consisting of four different organic substances.
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  • 67
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    Journal of Chemometrics 9 (1995), S. 509-520 
    ISSN: 0886-9383
    Keywords: canonical variates ; discriminant analysis ; partial least squares ; principal components ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new set of derived variables is proposed for exhibiting group separation in multivariate data on for preprocessing such data prior to discriminant analysis. The technique combines optimal features of canonical variate analysis and principal component analysis: the derived variables are linear combinations of the original variables that optimize the canonical variate criterion (ratio of between-group to within-group variance) but subject to the orthogonality constraints of principal components. In this formulation the canonical variates can be derived even when the within-group matrix is singular (i.e. when there are more variables than objects in the data matrix). A simple computational algorithm for extraction of these variables is proposed. The methods are illustrated on several data sets and compared with alternative techniques such as principal component analysis and partial least squares.
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  • 68
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    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 154-167 
    ISSN: 0887-3585
    Keywords: iron-sulfur proteins ; electron transfer ; oxidation-reduction potentials ; solvent accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations of Clostridium pasteurianum rubredoxin in the oxidized and reduced forms have been performed. Good agreement between both forms and crystal data has been obtained (rms deviation of backbone atoms of 1.06 and 1.42 Å, respectively), which was due in part to the use of explicit solvent and counterions. The reduced form exhibits an unexpected structural change: the redox site becomes much more solvent-accessible, so that water enters a channel between the surface and the site, but with little actual structural rearrangement (the rms deviation of backbone atoms between the oxidized and reduced is 0.77 Å). The increase in solvent accessibility is also seen, although to a much lesser extent, between the oxidized and reduced crystal structures of Pyrococcus furiosus rubredoxin, but no high resolution crystal or nuclear magnetic resonance solution data exist for reduced C. pasteurianum rubredoxin. The electrostatic potential at the iron site and fluctuations in the potential, which contribute to both the redox and electron transfer properties, have also been evaluated for both the oxidized and the reduced simulations. These results show that the backbone plays a significant role (62-70 kcall/mol/e) and the polar sidechains contribute relatively little (0-4 kcal/mol/e) to the absolute electrostatic potential at the iron of rubredoxin for both forms. However, both groups contribute significantly to the change in redox state by becoming more polarized and more densely packed around the redox site upon reduction. Furthermore, these results show that the solvent becomes much more polarized in the reduced form than in the oxidized form, even excluding the penetrating water. Finally, the simulation indicates that the contribution of the charged side chains to the electrostatic potential is largely canceled by that of the counterions. © 1995 Wiley-Liss, Inc.
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  • 70
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 191-192 
    ISSN: 0887-3585
    Keywords: lipopolysaccharide ; lipid A ; endotoxin ; protein structure ; acyltransferase ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of UDP-N-acetylglucosamine O-acyltransferase (lpxA) fromEscherichia coli have been obtained from solutions of sodium/potassium phosphate and dimethylsulfoxide. These crystals belong to the cubic space group P213 (a = 99.0 Å), diffract X-raysto approximately 2.5 Å resolution and contain one subunit of the enzyme in the asymmetric unit. © 1995 Wiley-Liss, Inc.
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  • 71
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 187-190 
    ISSN: 0887-3585
    Keywords: cytokine ; BCRF1 ; protein structure ; crystal seeding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of recombinant human interleukin 10 have been grown from solutions of ammonium sulfate. The crystals are tetragonal, space group P41212 or P43212; the unit cell axes are a = 36.5 Å and c = 221.9 Å. There is the equivalent of one polypeptide chain in the asymmetric unit. The crystals are stable to X-rays and diffract to at least 2.5 Å resolution. © 1995 Wiley-Liss, Inc.
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  • 72
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    Keywords: hydrophobic moment ; peptide-cell ; membrane interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Multiple linear regression was used to quantify the dependence of the antimicrobial activity of 13 peptides upon three calculated or experimentally determined parameters: mean hydrophobicity, mean hydrophobic moment, and α-helix content. Mean hydrophobic moment is a measure of the amphiphilicity of peptides in an α-helical conformation. Antimicrobial activity was quantified as the reciprocal of the measured minimal inhibitory concentration (MIC) against Escherichia coli. One of the peptides was magainin 2, and the remainder were novel peptides designed for this study. The multiple linear regression results revealed that the amphiphilicity of the peptides was the most important factor governing anti-microbial activity compared to mean hydrophobicity orα-helix content. A better regression cf the data was obtained using In(1/MIC + constant) as the dependent variable than with either 1/MIC or In(1/MIC). These results should be useful in designing peptides with higher antimicrobial activity. © 1995 Wiley-Liss, Inc.
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  • 73
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 168-181 
    ISSN: 0887-3585
    Keywords: aspartic proteinase ; enzyme kinetics ; rule-based model ; chromogenic assay ; synthetic substrate ; inhibitor ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Aspartic proteinases are produced in the human body by a variety of cells. Some of these proteins, examples of which are pepsin, gastricsin, and renin, are secreted and exert their effects in the extracellular spaces. Cathepsin D and cathepsin E on the other hand are intracellular enzymes. The least characterized of the human aspartic proteinases is cathepsin E. Presented here are results of studies designed to characterize the binding specificities in the active site of human cathepsin E with comparison to othermechanistically similar enzymes. A peptide series based on Lys-Pro-Ala-Lys-Phe*Nph-Arg-Leu was generatedto elucidate the specificity in the individual binding pockets with systematic substitutions in the P5- P2 and P2′-P3′ based on charge, hydrophobicity, and hydrogen bonding. Also, to explore the S2 binding preferences, asecond series of peptides based on Lys-Pro-Ile-Glu-Phe*Nph-Arg-Leu was generated with systematic replacements in the P2 position. Kinetic parameters were determined forboth sets of peptides. The results were correlated to a rule-based structural model of human cathepsin E, constructed on the known three-dimensional structures of several highly homologous aspartic proteinases; porcine pepsin, bovine chymosin, yeast proteinase A, human cathepsin D, andmouse and human renin. Important specificity-determining interactions were found in the S3 (Glu13) and S2 (Thr-222, Gln-287, Leu-289, Ile-300)subsites. © 1995 Wiley-Liss, Inc.
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  • 74
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    Proteins: Structure, Function, and Genetics 22 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 75
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 193-196 
    ISSN: 0887-3585
    Keywords: urea cycle ; frog ; liver ; carbamyl phosphate synthetase ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Carbamoyl phosphate synthetase I (ammonia; E C 6.3.4.16) was purified from the liver of Rana catesbeiana (bullfrog). Crystals of the protein have been obtained at 22°C by the hanging drop vapor diffusion technique, with polyethylene glycol as precipitant. Tetragonal crystals of about 0.3 × 0.3 × 0.7 mm diffract at room temperature to at least 3.5 Å using a conventional source and are stable to X-radiation for about 12 h. Therefore, these crystals are suitablefor high resolution studies. The space group is P41212 (or its enantiomorph P43212), with unit cell dimensions a = b = 291.6 Å and c = 189.4 Å. Density packing considerations areconsistent with the presence of 4-6 monomers (Mr of the monomer, 160,000) in the asymmetric unit. Amino-terminal sequence of the enzyme and of a chymotryptic fragment of 73.7 kDa containing the COOH-terminus has been obtained. The extensive sequence identity with rat and human carbamoyl phosphate synthetase I indicates the relevance for mammals of structural data obtained with the frog enzyme. © 1995 Wiley-Liss, Inc.
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  • 76
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 199-209 
    ISSN: 0887-3585
    Keywords: chaperonins ; electron microscopy ; FTIR ; molecular modeling ; structure prediction ; contact prediction ; active site prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional structure of the GroES monomer and its interaction with GroEL has been predicted using a combination of prediction tools and experimental data obtained by biophysical [electron microscope (EM), Fourier transform infrared (FTIR), and nuclear magnetic resonance (NMR)] and biochemical techniques. The GroES monomer, according to the prediction, is composed of eight β-strands forming a β-barrel with loose ends. In the model, β-strands 5-8 run along the outer surface of GroES, forming an antiparallel β-sheet with β4 loosely bound to one of the edges. β-strands 1-3 would then be parallel and placed in the interior of the molecule. Loops 1-3 would face the internal cavity of the GroEL-GroES complex, and together with conserved residues in loops 5 and 7, would form the active surface interacting with GroEL. © 1995 Wiley-Liss, Inc.
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  • 77
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 226-244 
    ISSN: 0887-3585
    Keywords: photosynthesis ; protein structure ; homology modeling ; molecular mechanics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The reaction center (RC) from the photosynthetic bacterium Rhodobacter (Rb.) capsulatus has been the subject of a considerable amount of molecular biological and spectroscopic work aimed at improving our understanding of the primary steps of photosynthesis. However, no three-dimensional structure is available for this protein. We present here a model obtained by combining information from the structure of the highly homologous RC from Rhodopseudomonas (Rps.) viridis with molecular mechanics and simulated annealing calculations. In the Rb. Capsulatus model the orientations of the bacteriochlorophyll monomer and the bacteriopheophytin on the branch inactive in electron transfer differ significantly from those in the RCs of Rps. Viridis and Rb. Sphaeroides. The bacteriopheophytin orientational difference is in good accord with previous linear dichroism measurements. A comparison is made of interactions between the pigments and the protein environment that may be of functional significance in Rps. viridis, Rb. sphaeroides, and Rb. capsulatus. © 1995 Wiley-Liss, Inc.
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  • 78
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 210-225 
    ISSN: 0887-3585
    Keywords: serpin-proteinase complex ; mutants ; deamidation ; α-helix-β-sheet conversion ; homology modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The mechanism of formation and the structures of serpin-inhibitor complexes are not completely understood, despite detailed knowledge of the structures of a number of cleaved and uncleaved inhibitor, noninhibitor, and latent serpins. It has been proposed from comparison of inhibitor and noninhibitor serpins in the cleaved and uncleaved forms that insertion of strand s4A into preexisting β-sheet A is a requirement for serpin inhibitor activity. We have investigated the role of this strand in formation of serpin-proteinase complexes and in serpin inhibitor activity through homology modeling of wild type inhibitor, mutant substrate, and latent serpins, and of putative serpin-proteinase complexes. These models explain the high stability of the complexes and provide an understanding of substrate behavior in serpins with point mutations in s4A and of latency in plasmingoen activator inhibitor I. © 1995 Wiley-Liss, Inc.
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  • 79
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 259-266 
    ISSN: 0887-3585
    Keywords: homology search ; phosphodiesterases ; sequence analysis ; structure prediction ; threading ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of glycerol-3-phosphate cytidylyltransferase from B. subtilis (TagD) is about to be solved. Here, we report a testable structure prediction based on the identification by sequence analysis of a superfamily of functionally diverse but structurally similar nucleotide-binding enzymes. We predict that TagD is a member of this family. The most conserved region in this superfamily resembles the ATP-binding HiGH motif of class I aminoacyI-tRNA synthetases. The predicted secondary structure of cytidylyltransferase and its homologues is compatible with the α/β topography of the class I aminoacyl-tRNA synthetases. The hypothesis of similarity of fold is strengthened by sequence-structure alignment and 3D model building using the known structure of tyrosyl tRNA synthetase as template. The proposed 3D model of TagD is plausible both structurally, with a well packed hydrophobic core, and functionally, as the most conserved residues cluster around the putative nucleotide binding site. If correct, the model would imply a very ancient evolutionary link between class I tRNA synthetases and the novel cytidylyltransferase superfamily. © 1995 Wiley-Liss, Inc.
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  • 80
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 267-272 
    ISSN: 0887-3585
    Keywords: α-keratin ; intermediate filaments ; epidermal keratin ; vimentin ; keratinopathies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In intermediate filaments (IF) both epidermal keratin and vimentin molecules have been shown to have an eight residue head to-tail overlap between the rod domains of similarly directed molecules. In the case of the epidermal keratins this region has also been shown to have particular structural/functional significance since it represents a hot-spot for mutations in the four keratinopathies characterized to date. While there is good evidence that this head-to-tail overlap is present in IF containing Type III, IV, and V chains, as well as in the epidermal keratin IF (Ib/IIb), there are no data currently available for the hard α-keratin IF (Ia/IIa). Using a variety of data derived from X-ray diffraction and crosslinking studies, as well as theoretical modeling, it is now possible to demonstrate that the overlap region is not a feature of hard α-keratin IF. Indeed, it is shown that there is a nine residue gap between consecutive parallel molecules in the IF. An explanation for this observation is presented in terms of compensating disulfide bonds that occur both within the IF, and between the IF and the matrix in which the IF are embedded. © 1995 Wiley-Liss, Inc.
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  • 81
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 12-19 
    ISSN: 0887-3585
    Keywords: protein dynamics ; low temperature optical spectroscopy ; recombinant hemoglobin ; anharmonicity ; vibrational coupling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The thermal behavior of the Soret band relative to the carbonmonoxy derivatives of some β-chain mutant hemoglobins is studied in the temperature range 300-10 K and compared to that of wild-type carbonmonoxy hemoglobin. The band profile at various temperatures is modeled as a Voigt function that accounts for homogeneous broadening and for the coupling with high- and low-frequency vibrational modes, while inhomogeneous broadening is taken into account with a gaussian distribution of purely electronic transition frequencies. The various contributions to the overall bandwidth are singled out With this analysis and their temperature dependence, in turn, gives information on structural and dynamic properties of the system studied. In the wildtype and mutant hemoglobins, the values of homogeneous bandwidth and of the coupling constants to high-frequency vibrational modes are not modified with respect to natural human hemoglobin, thus indicating that the local electronic and vibrational properties of the heme-CO complex are not altered by the recombinant procedures. On the contrary, differences in the protein dynamic behavior are observed. The most relevant are those relative to the “polar isosteric” βVal-67(Ell) →Thr substitution, localized in the heme pocket, which results in decreased coupling with low-frequency modes and increased anharmonic motions. Mutations involving residue βLys-144(HC1) at the C-terminal and residue βCys-112(G14) at the α1β1 interface have a smaller effect consisting in an increased coupling with low-frequency modes. Mutations at the β-N-terminal and at the α1β2 interface have no effect on the dynamic properties of the heme pocket. © 1995 Wiley-Liss, Inc.
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  • 82
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 27-40 
    ISSN: 0887-3585
    Keywords: protein folding ; disulfide bonds ; three-stage multiple pathways ; kinetics ; entropic barriers ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The role of disulfide bonds in directing protein folding is studied using lattice models. We find that the stability and the specificity of the disulfide bond interactions play quite different roles in the folding process: Under some conditions, the stability decreases the overall rate of folding; the specificity, however, by yielding a simpler connectivity of intermediates, always increases the rate of folding. This conclusion is intimately related to the selection mechanism entailed by entropic driving forces, such as the loop formation probability, and entropic barriers separating the native and the many native-like metastable states. The folding time is found to be a minimum for a certain range of the effective disulfide bond interaction. Examination of a model, which allows for the formation of disulfide bonded intermediates, suggests that folding proceeds via a threestage multiple pathways kinetics. We show that there are pathways to the native state involving only native-like intermediates, as well as those that are mediated by nonnative intermediates. These findings are interpreted in terms of the appropriate energy landscape describing the barriers connecting low energy conformations. The consistency of our conclusions with several experimental studies is also discussed. © 1995 Wiley-Liss, Inc.
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  • 83
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 41-44 
    ISSN: 0887-3585
    Keywords: hydrogen exchange ; nuclear magnetic exchange ; noncovalent complex ; β-sheet ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The study of complementary protein fragments is thought to be generally useful to identify early folding intermediates. A prerequisite for these studies is the reconstitution of the native-like structure by fragment complementation. Structural analysis of the complementation of the domain-sized proteolytic fragments of E. coli thioredoxin, using a combination of H-exchange and 2D NMR experiments as a fingerprint technique, provide evidence for the extensive reconstitution of a native β-sheet, with local conformational adjustments near the cleavage site. Remarkably, the antiparallel β-strand between the fragments shows a native-like protection of the amide protons to solvent exchange. Our results indicate that these fragments can be useful to study the early events in the still little understood formation of β-sheets. © 1995 Wiley-Liss, Inc.
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  • 84
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 290-292 
    ISSN: 0887-3585
    Keywords: macroH2A ; specialized nucleosomes ; fusion protein ; crystallization ; X-ray diffraction ; noncrystal-lographic symmetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Histone macroH2A has a novel hybrid structure consisting of a large nonhistone region and a region that closely resembles a full-length histone H2A. One key to understanding macroH2A function is determining the structure and function of its nonhistone region. The nonhistone region of one of the two known macroH2A subtypes was expressed in Escherichia coli and purified using affinity and molecular sieve chromatography. Crystals of the protein suitable for structural studies were grown from polyethylene glycol solutions by vapor equilibration techniques. The crystals belong to the hexagonal space group P64 (or its enantiomorph P62) with unit cell parameters: a = b = 106.2 Å, c = 125.9 Å, α = β = 90°, and γ = 120°. There are four molecules in the asymmetric unit. Self-rotation function studies revealed three twofold noncrystallographic rotation axes related approximately by 222 symmetry. These crystals have 47% solvent content and diffract to 3.8 Å resolution. © 1995 Wiley-Liss, Inc.
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  • 85
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    Proteins: Structure, Function, and Genetics 22 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 86
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 293-297 
    ISSN: 0887-3585
    Keywords: erythrocyte membrane ; anion exchanger ; ankyrin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A cytoplasmic domain of the human erythrocyte membrane protein band 3 (Mr = 42,500), residues 1-379, expressed in and purified from E. coli, has been crystallized by the method of vapor diffusion in sitting drops with subsequent streak-seeding at room temperature. Initial crystals were grown from solutions containing 65-68% saturated ammonium sulfate at pH 4.9 and 2 mg/ml protein. Subsequent streak-seeding into solutions of 50-53% ammonium sulfate at pH 4.9 and 7 mg/ml protein produced single crystals suitable fur X-ray analysis, which contained pure protein as revealed by gel electrophoresis. The crystals belong to the monoclinic space group C2 with cell dimensions of a = 178.8 Å, b = 90.5 Å, c = 122.1 Å, and β = 131.3° and diffract at least to 2.7 Å resolution (at 100 K). A self-rotation function shows the presence of approximate 222 local symmetry. © 1995 Wiley-Liss, Inc.
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  • 87
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 68-69 
    ISSN: 0887-3585
    Keywords: microtubule motors ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The motor domain of the kinesin homolog ncd has been crystallized in the presence of MgATP by the vapor diffusion method using polyethylene glycol as the precipitant. The crystals belong to the orthorhombic space group I222 with unit cell dimensions a = 127.1 Å, b = 122.3 Å, c = 68.0 Å, and there is one ncd molecule per asymmetric unit. The crystals diffract X-ray to at least 2.3 Å and are appropriate for high-resolution structure determination. © 1995 Wiley-Liss, Inc.
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  • 88
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 40-56 
    ISSN: 0887-3585
    Keywords: zinc parameterization ; effective force-field ; four-coordination ; five-coordination ; reaction mechanism ; ligand exchange ; bond length constraint ; ligand dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A detailed parameterization is presented of a zinc ion with one histidine and two cysteinate ligands, together with one or two water, hydroxide, aldehyde, alcohol, or alkoxide ligands. The parameterization is tailored for the active site of alcohol dehydrogenase and is obtained entirely from quantum chemical computations. The force-field reproduces excellently the geometry of quantum chemically optimized zinc complexes as well as the crystallographic geometry of the active site of alcohol dehydrogenase and small organic structures. The parameterization is used in molecular dynamics simulations and molecular mechanical energy minimizations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. The active-site zinc ion seems to prefer four-coordination over five-coordination by at least 36 kJ/mol. The only stable binding site of a fifth ligand at the active-site zinc ion is opposite to the normal substrate site, in a narrow cavity behind the zinc ion. Only molecules of the size of water or smaller may occupy this site. There are large fluctuations in the geometry of the zinc coordination sphere. A four-coordinate water molecule alternates frequently (every 7 ps) between the substrate site and the fifth binding site and even two five coordinate water molecules may interchange ligation sites without prior dissociation. Ligand exchange at the zinc ion probably proceeds by a dissociative mechanism. The results show that it is essential to allow for bond stretching degrees of freedom in molecular dynamics simulations to get a correct description of the dynamics of the metal coordination sphere; bond length constraints may restrict the accessible part of the phase space and therefore lead to qualitatively erroneous results. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 70-73 
    ISSN: 0887-3585
    Keywords: cell cycle protein ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The cell cycle regulatory protein CksHs1 has been crystallized in a form suitable for X-ray studies. CksHsl crystals were grown in the presence of vanadate, a phos-phatase inhibitor, but were also obtained with phosphate or tungstate as a cofactor. They belong to the hexagonal space group P6122 with unit cell dimensions: a=b=94 Å, c=131.6 Å, and γ =120. The crystals grown in the presence of vanadate diffract X-rays to at least 2.8 Å. Molecular replacement results from the homologous human CksHs2 structure reveal that a dimer forms the crystal habit, giving the unusual Vm value of 4.4 Å3/Da or a solvent content of 72%. © 1995 Wiley-Liss, Inc.
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  • 90
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 78-81 
    ISSN: 0887-3585
    Keywords: T = 3 plant virus ; tymovirus ; protein crystallization ; X-ray diffraction ; synchrotron radiation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Turnip yellow mosaic virus (TYMV) was purified from Chinese cabbage and crystallized in a form that permits high resolution structural analysis using X-ray diffraction. The crystals have a hexagonal bipyramidal morphology and often achieve dimensions of 1.0 × 1.0 × 0.5 mm. The crystals appear to be of hexagonal space group P6222 with a = b = 525 Å, c=315 Å, but we cannot strictly rule out the possibility that the space group is P622. They appear different than any crystals of TYMV previously reported. There are three T = 3 virus particles in the unit cell, which implies that one quarter of the particle, or 45 protein subunits, comprises the asymmetric unit of the crystal. Native data have been collected using synchrotron radiation to a resolution of 3.2 Å. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 83-90 
    ISSN: 0887-3585
    Keywords: cytochrome c ; thermodynamics ; antibody binding ; microcalorimetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this paper we study the binding of two monoclonal antibodies, E3 and E8, to cytochrome c using high-sensitivity isothermal titration calorimetry. We combine the calorimetric results with empirical calculations which relate changes in heat capacity to changes in entropy which arise from the hydrophobic effect. The change in heat capacity for binding E3 is -350 ± 60 cal K-1 mol-1 while for E8 it is -165 ± 40 cal K-1 mol-1. This result indicates that the hydrophobic effect makes a much larger contribution for E3 than for E8. Since the total entropy change at 25°C is very similar for both antibodies, it follows that the configurational entropy cost for binding E3 is much larger than for binding E8 (-77 ± 15 vs. -34 ± 11 cal K-1 mol-1). These results illustrate a case of entropy compensation in which the cost of restricting conformational degrees of freedom is to a large extent compensated by solvent release. We also show that the thermodynamic data can be used to make estimates of the surface area changes that occur upon binding. The results of the present study are consistent with previous hydrogen-deuterium exchange data, detected using 2D NMR, on the two antibody-antigen interactions. The NMR study indicated that protection from exchange is limited to the binding epitope for E8, but extends beyond the epitope for E3. These results were interpreted as suggesting that a larger surface area was buried on cytochrome c upon binding to E3 than to E8, and that larger changes in configurational entropy occur upon binding of E3 than E8. These findings are confirmed by the present study using isothermal titration calorimetry. © 1995 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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  • 92
    ISSN: 0887-3585
    Keywords: transhydrogenase ; NAD binding ; prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A three-dimensional structure of the NAD site of Escerichia coli transhydrogenase has been predicted. The model is based on analysis of conserved residues among the transhydrogenases from five different sources, homologies with enzymes using NAD as cofactors or substrates, hydrophilicity profiles, and secondary structure predictions. The present model supports the hypothesis that there is one binding site, located relatively close to the N-terminus of the α-subunit. The proposed structure spans residues α145 to α287, and it includes five β-strands and five α-helices oriented in a typical open twisted α/β conformation. The amino acid sequence following the GXGXXG dinucleotide binding consensus sequence (residues α172 to α177) correlates exactly to a typical fingerprint region for ADP binding βαβ folds in dinucleotide binding enzymes. In the model, aspartic acid α195 forms hydrogen bonds to one or both hydroxyl groups on the adenosine ribose sugar moiety. Threonine α196 and alanine α256, located at the end of βB and βD, respectively, create a hydrophobic sandwich with the adenine part of NAD buried inside. The nicotinamide part is located in a hydrophobic cleft between αA and βE. Mutagenesis work has been carried out in order to test the predicted model and to determine whether residues within this domain are important for proton pumping directly. All data support the predicted structure, and no residue crucial for proton pumping Was detected. Since no three-dimensional structure of transhydrogenase has been solved, a well based tertiary structure prediction is of great value for further experimental design in trying to elucidate the mechanism of the energy-linked proton pump. © 1995 Wiley-Liss, Inc.
    Additional Material: 11 Ill.
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  • 93
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 118-126 
    ISSN: 0887-3585
    Keywords: O-glyeosylation ; Ser-conjugated substrate ; Thr-conjugated substrate ; nonapeptide ; reduced 8-D space ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The specificity of UDP-Gal-NAc:polypeptide N-acetylgalactosaminytransferase (GalNAc-transferase) is consistent with the existence of an extended site composed of nine subsites, denoted by P4, P3, P2, P1, P0, P1′, P2′, P3′, and P4′, where the acceptor at P0 is being either Ser or Thr. To predict whether a peptide will react with the enzyme to form a Ser- or Thr-conjugated glycopeptide, a vector projection method is proposed which uses a training set of amino acid sequences surrounding 90 Ser and 106 Thr O-glycosylation sites extracted from the National Biomedical Research Foundation Protein Database. The model postulates independent interactions of the 9 amino acid moieties with their respective binding sites. The high ratio of correct predictions vs. total predictions for the data in both the training and the testing sets indicates that the method is self-consistent and efficient. It provides a rapid means for predicting O-glycosylation and designing effective inhibitors of GalNAc-transferase. © 1995 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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  • 94
    ISSN: 0887-3585
    Keywords: crystals ; X-ray structure ; (α/β)8 barrel protein ; 222 molecular symmetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Sweet potato β-amylase is a tetramer of identical subunits, which are arranged to exhibit 222 molecular symmetry. Its subunit consists of 498 amino acid residues (Mr 55,880). It has been crystallized at room temperature using polyethylene glycol 1500 as precipitant. The crystals, growing to dimensions of 0.4 mm × 0.4 mm × 1.0 mm within 2 weeks, belong to the tetragonal space group P42212 with unit cell dimensions of a = b = 129.63 Å and c = 68.42 Å. The asymmetric unit contains 1 subunit of β-amylase, with a crystal volume per protein mass (VM) of 2.57 Å3/Da and a solvent content of 52% by volume. The three-dimensional structure of the tetrameric β-amylase from sweet potato has been determined by molecular replacement methods using the monomeric structure of soybean enzyme as the starting model. The refined subunit model contains 3,863 nonhydrogen protein atoms (488 amino acid residues) and 319 water oxygen atoms. The current R-value is 20.3% for data in the resolution range of 8-2.3 Å (with 2 σ cut-off) with good stereochemistry. The subunit structure of sweet potato β-amylase (crystallized in the absence of α-cyclodextrin) is very similar to that of soybean β-amylase (complexed with α-cyclodextrin). The root-mean-square (RMS) difference for 487 equivalent Cα atoms of the two β-amylases is 0.96 Å. Each subunit of sweet potato β-amylase is composed of a large (α/β)8 core domain, a small one made up of three long loops [L3 (residues 91-150), LA (residues 183-258), and L5 (residues 300-327)], and a long C-terminal loop formed by residues 445-493. Conserved Glu 187, believed to play an important role in catalysis, is located at the cleft between the (α/β)8 barrel core and a small domain made up of three long loops (L3, L4, and L5). Conserved Cys 96, important in the inactivation of enzyme activity by sulfhydryl reagents, is located at the entrance of the (α/β)8 barrel. © 1995 Wiley-Liss, Inc.
    Additional Material: 11 Ill.
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  • 95
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 214-225 
    ISSN: 0887-3585
    Keywords: photosynthetic reaction center ; quinone binding site ; D1 protein ; herbicides ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Functional identity and significant similarities in cofactors and sequence exist between the L and M reaction center proteins of the photosynthetic bacteria and the D1 and D2 photosystem-II reaction center proteins of cyanobacteria, algae, and plants. A model of the quinone (QB) binding site of the D1 protein is presented based upon the resolved structure of the QB binding pocket of the L subunit, and introducing novel quantitative notions of complementarity and contact surface between atoms. This model, built -without using traditional methods of molecular mechanics and restricted to residues in direct contact with QB, accounts for the experimentally derived functional state of mutants of the Dl protein in the region of QB. It predicts the binding of both the classical and phenol-type PSII herbicides and rationalizes the relative levels of tolerance of mutant phenotypes. © 1995 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 96
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 196-213 
    ISSN: 0887-3585
    Keywords: protein folding ; computer simulation ; molecular dynamics ; high pressure ; compressibility ; heat capacity ; amide proton exchange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Four methods are compared to drive the unfolding of a protein: (1) high temperature (T-run), (2) high pressure (P-run), (3) by imposing a gradual increase in the mean radius of the protein using a penalty function added to the physical interaction function (F-run, radial force driven unfolding), and (4) by weak coupling of the difference between the temperature of the radially outward moving atoms and the radially inward moving atoms to an external temperature bath (K-run, kinetic energy driven unfolding). The characteristic features of the four unfolding pathways are analyzed in order to detect distortions due to the size or the type of the applied perturbation, as well as the features that are common to all of them. Hen egg white lysozyme is used as a test system. The simulations are analyzed and compared to experimental data like 1H-NMR amide proton exchange-folding competition, heat capacity, and compressibility measurements. © 1995 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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  • 97
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 167-195 
    ISSN: 0887-3585
    Keywords: protein folding ; energy landscape ; folding pathway ; folding funnel ; lattice simulation ; folding thermodynamics ; folding kinetics ; protein engineering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation, that is, to the energy landscape. The statistical energy landscape approach explains when and why unique behaviors, such as specific folding pathways, occur in some proteins and more generally explains the distinction between folding processes common to all sequences and those peculiar to individual sequences. This approach also gives new, quantitative insights into the interpretation of experiments and simulations of protein folding thermodynamics and kinetics. Specifically, the picture provides simple explanations for folding as a two-state first-order phase transition, for the origin of metastable collapsed unfolded states and for the curved Arrhenius plots observed in both laboratory experiments and discrete lattice simulations. The relation of these quantitative ideas to folding pathways, to uniexponential vs. multiexponential behavior in protein folding experiments and to the effect of mutations on folding is also discussed. The success of energy landscape ideas in protein structure prediction is also described. The use of the energy landscape approach for analyzing data is illustrated with a quantitative analysis of some recent simulations, and a qualitative analysis of experiments on the folding of three proteins. The work unifies several previously proposed ideas concerning the mechanism protein folding and delimits the regions of validity of these ideas under different thermodynamic conditions. © 1995 Wiley-Liss, Inc.
    Additional Material: 12 Ill.
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  • 98
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. 111-114 
    ISSN: 0887-3585
    Keywords: replication ; amplification ; PCR ; enzyme ; thermostability ; x-ray ; diffraction ; synchrotron ; three-dimensional ; structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Thermus aquaticus DNA polymerase I is an enzyme that is of both physiological and technological interest. It carries out template-directed polymerization of DNA at elevated temperatures and is widely used in polymerase chain reaction (PCR). We have obtained crystals of the enzyme that diffracts X-rays to at least 3.0 Å resolution in a cubic space group. Determination of the three-dimensional structure of the native enzyme along with those of relevant complexes will greatly enhance our knowledge of molecular events involved in DNA replication, will permit improvements in PCR, and will add to our knowledge of the structural bases of thermo stability in proteins. © 1995 Wiley-Liss, Inc.
    Additional Material: 1 Tab.
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  • 99
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. 97-110 
    ISSN: 0887-3585
    Keywords: bovine pancreatic trypsin inhibitor ; cluster analysis ; conformational searching ; molecular dynamics ; protein tertiary structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using energy minimization and cluster analysis, we have analyzed a 1020 ps molecular dynamics trajectory of solvated bovine pancreatic trypsin inhibitor. Elucidation of conformational sub states in this way both illustrates the degree of conformational convergence in the simulation and reduces the structural data to a tractable subset. The relative movement of structures upon energy minimization was used to estimate the sizes of features on the protein potential energy surface. The structures were analyzed using their pairwise root-mean-square Cα deviations, which gave a global measure of conformational changes that would not be apparent by monitoring single degrees of freedom. At time scales of 0.1 ps, energy minimization detected sharp transitions between energy minima separated by 0.1 Å rms deviation. Larger conformational clusters containing these smaller minima and separated by 0.25 Å were seen at 1 ps time scales. Both of these small features of the conformational landscape were characterized by movements in loop regions associated with small, correlated backbone dihedral angle shifts. On a nanosecond time scale, the main features of the protein energy landscape were clusters separated by over 0.7 Å rms deviation, with only seven of these sub states visited over the 1 ns trajectory. These substates, discernible both before and after energy minimization, differ mainly in a monotonic pivot of the loop residues 11-18 over the course of the simulation. This loop contains lysine 17, which specifically binds to trypsin in the active site. The trajectory did not return to previously visited clusters, indicating that this trajectory has not been shown to have completely sampled the conformational substates available to it. Because the apparent convergence to a single region of conformation space depends on both the time scale of observation and the size of the conformational features examined, convergence must be operationally defined within the context of the simulation. © 1995 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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  • 100
    ISSN: 0887-3585
    Keywords: antibody-protein complex ; influenza virus hemagglutinin ; protein recognition ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Fab fragments from two different monoclonal antibodies (BH151 and HC45) which bind to the same antigenic region of the influenza hemagglutinin were crystallized as complexes with the hemagglutinin. The complexes crystallize in PEG 600, pH 6.0, and PEG 2000, pH 8.5, respectively. Both crystals belong to space group P321, with very similar unit cell dimensions. © 1995 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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