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  • Polymer and Materials Science  (17,124)
  • Ecology
  • Industrial Chemistry
  • 1980-1984  (15,163)
  • 1950-1954  (3,313)
  • 1935-1939
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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Environmental management 4 (1980), S. 111-124 
    ISSN: 1432-1009
    Keywords: Carolinian ; Ecology ; Ideology ; Policy ; Rondeau ; Technology ; Wildland Management ; Parks
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: Abstract This is a critical examination of some of the basic concepts that have guided management of parks and related reserves, often termed wildlands. Study is focussed on Rondeau Provincial Park, Ontario, and on concepts such as wilderness, primeval forest, and the Carolinian forest. Deer culling and other management policies and practices have been based upon the idea that the highly valued sassafras, tulip, and other species of the Carolinian forest are decreasing due to browsing. Field mapping and analysis of historic vegetation records indicate that this trend is not in fact occurring. Historic research also reveals difficulties in defining the Carolinian or other perceived types of forest for management purposes. A major reassessment of ideology and management policy and practice seem to be required in Rondeau and other wildlands. Vague or general concepts such as wilderness or preservation should be strongly complemented and supported by more precise statements of objectives, a learning attitude, and experimentation and research. As a result of the technical uncertainties and value judgments frequently involved, management should also be based upon the expressed preferences and continuing involvement of citizens.
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  • 2
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    Environmental management 5 (1981), S. 495-505 
    ISSN: 1432-1009
    Keywords: Suitability analysis ; Land-use assessment ; Ecology ; Planning ; Human ecology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: Abstract Beginning with the passage of the National Environmental Policy Act in 1969, the federal government of the United States has enacted numerous pieces of legislation intended to protect or conserve the environment. Other national governments have also enacted environmental legislation during the past two decades. State and local governments have also adopted policies concerned with environmental planning and management. Multiple laws and overlapping governmental agency responsibilities have confused development and resource management efforts. A comprehensive methodology that integrates the legal mandates and the agency missions into a common and unified framework is needed. Ecological planning offers such a method. Application of the method allows planners and resource managers to better understand the nature and character of the land and/or resource and therefore make better decisions about its appropriate use or management. The steps taken in an ecological planning process—1) goal setting, 2) inventory and analysis of data, 3) suitability analysis, 4) developing alternatives, 5) implementation, 6) administration, and 7) evaluation—are outlined and explained. Hand-drawn overlays and computer programs as techniques for handling ecological planning information are compared. Observations and suggestions for further research are offered.
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  • 3
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    Archives of microbiology 131 (1982), S. 107-111 
    ISSN: 1432-072X
    Keywords: Cyanophyta ; Cyanobacteria ; Oscillatoria rubescens ; Photosynthetic pathways ; Photosynthetic enzymes ; Ecology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Short term14C labelling experiments and enzymatic activities related to primary pathways of photosynthesis have been studied in the cyanophytaOscillatoria rubescens D.C. from axenic cyclostat cultures. Responses of samples from cultures with different amounts of nitrogen are presented and compared. Variations in photosynthetic pigments are used to quantify the degree of nitrogen starvation at different levels. PEPcarboxylase activity remains low and is not affected by nitrogen starvation. RuBPcarboxylase activity is lowered to nearly two thirds of its normal metabolic rate by starvation but PEPcarboxykinase and aspartate aminotransferase activities are significantly higher in this case. Malate dehydrogenase is slightly altered and malic enzyme is never active. Starved algae replaced in fresh complete media fix rapidly14C in nitrogen compounds such as amino acids. Results are discussed in regard to both physiological and ecological characteristics ofO. rubescens. PEPcarboxykinase can play a role in making efficient use of HCO 3 - .
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  • 4
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    Archives of microbiology 139 (1984), S. 351-354 
    ISSN: 1432-072X
    Keywords: Aerobic denitrification ; Thiosphaera pantotropha ; Nitrate reduction ; Bacterial selection ; Ecology ; Oxygen
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract During studies on the denitrifying mixotroph, Thiosphaera pantotropha, it has been found that this organism is capable of simultaneously utilizing nitrate and oxygen as terminal electron acceptors in respiration. This phenomenon, termed aerobic denitrification, has been found in cultures maintained at dissolved oxygen concentrations up to 90% of air saturation. The evidence for aerobic denitrification was obtained from a number of independant experiments. Denitrifying enzymes were present even in organisms growing aerobically without nitrate. Aerobic yields on acetate were higher (8.1 g protein/mol) without than with (6.0 g protein/mol) nitrate, while the anaerobic yield with nitrate was even lower (4 g protein/mol). The maximum specific growth rate of Tsa. pantotropha was higher (0.34 h-1) in the presence of both oxygen (〉80% air saturation) and nitrate than in similar cultures not supplied with nitrate (0.27 h-1), indicating that the rate of electron transport to oxygen was limiting. This was confirmed by oxygen uptake experiments which showed that although the rate of respiration on acetate was not affected by nitrate, the total oxygen uptake was reduced in its presence. The original oxygen uptake could be restored by the addition of denitrification inhibitors.
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  • 5
    ISSN: 1432-072X
    Keywords: Bacillus tusciae ; New species ; Taxonomy ; Ecology ; Chemolithoautotrophy ; Hydrogen oxidation ; Hydrogenase ; Thermophily ; Geothermal manifestation ; Solfatara
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A thermophilic, chemolithoautotrophic, hydrogen-oxidizing sporeformer has been isolated from ponds in a solfatara in the geothermal area of Tuscany (Italy). Some physicochemical parameters of the habitat were determined. The habitat was characterized by the presence of molecular hydrogen in the escaping gases, a very low content of phosphate and organic matter. Temperature and water level in the ponds varied widely. The organism formed oval, subterminal spores, which swelled distinctly the sporangium. Optimal growth occured between pH 4.2 and 4.8 at 55°C. It grew best under autotrophic conditions, but organic substrates including short chain fatty acids, amino acids and alcohols could also support heterotrophic growth. Sugars were not metabolized. The hydrogenase was soluble but did not reduce pyridine nucleotides. Based on its morphological and biochemical features, the organism belongs to the genus Bacillus, but differs from all the previously described species. It is therefore proposed as constituting a new species, Bacillus tusciae.
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  • 6
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    Journal of mathematical biology 12 (1981), S. 343-354 
    ISSN: 1432-1416
    Keywords: Ecology ; Periodic differential equations ; Optimization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Summary The theory developed here applies to populations whose size x obeys a differential equation, $$\dot x = r(t)xF(x,t)$$ in which r and F are both periodic in t with period p. It is assumed that the function r, which measures a population's intrinsic rate of growth or intrinsic rate of adjustment to environmental change, is measurable and bounded with a positive lower bound. It is further assumed that the function F, which is determined by the density-dependent environmental influences on growth, is such that there is a closed interval J, with a positive lower bound, in which there lies, for each t, a number K(t) for which $$F(K(t),t) = 0$$ and, as functions on J × ℝ, F is continuous, while ∂F/∂x is continuous, negative, and bounded. Because x(t) = 0, 〉 0, or 〈 0 in accord with whether K(t) = x(t), K(t) 〉 x(t), or K(t) 〈 x(t), the number K(t) is called the “carrying capacity of the environment at time t”. The assumptions about F imply that the number K(t) is unique for each t, depends continuously and periodically on t with period P, and hence attains its extrema, K min and K max. It is, moreover, easily shown that the differential equation for x has precisely one solution x * which has its values in J and is bounded for all t in ℝ; this solution is of period p, is asymptotically stable with all of J in its domain of attraction, and is such that its minimum and maximum values, x min * and x max * , obey $$K_{min} \leqslant x_{min}^* \leqslant x_{max}^* \leqslant K_{max}^* .$$ The following question is discussed: If the function F is given, and the function r can be chosen, which choices of r come close to maximizing, x min * ? The results obtained yield a procedure for constructing, for each F and each ɛ 〉 0, a function r such that x min * 〉 K max − ɛ.
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  • 7
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    Journal of mathematical biology 18 (1983), S. 255-280 
    ISSN: 1432-1416
    Keywords: Population dyamics ; Ecology ; Periodic solutions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract A model of the competition of n species for a single essential periodically fluctuating nutrient is considered. Instead of the familiar Michaelis-Menten kinetics for nutrient uptake, we assume only that the uptake rate functions are positive, increasing and bounded above. Sufficient conditions for extinction are given. The existence of a nutrient threshold under which the Principle of Competitive Exclusion holds, is proven. For two species systems the following very general result is proven: All solutions of a τ-periodic, dissipative, competitive system are either τ-periodic or approach a τ-periodic solution. A complete description of the geometry of the Poincaré operator of the two species system is given.
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  • 8
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    Plant ecology 44 (1981), S. 13-24 
    ISSN: 1573-5052
    Keywords: Aceri-Fagetum ; Alpine timberline ; Dynamics of stands ; Ecology ; Fagus silvatica ; Morphogenesis ; Polycormons ; Vegetative regeneration
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In the Central Europaean mountain ranges, the alpine timberline is usually formed by Picea abies or by other conifers (Larix decidua, Pinus mugo, Pinus cembra). Unlike in the East Europaean mountains, the Balkan Peninsula, the Europaean Mediterranean and Les Vosges, Fagus silvatica occurs sporadically on the alpine timberline in this area where it forms very specific woods. This type of the alpine timberline is bound to the association Aceri-Fagetum (Bartsch 1940, Moor 1952). This association is found on the highest sites of the Fagion alliance in the subalpine vegetation zone. Within this zone, the association is bound to localities with heavy snowfall and a submaritime climat. It occupies larger areas in the Swiss Jura and in Les Vosges. In other Central Europaean mountains (the Alps, Schwarzwald, Krkonoše etc.) it occus in isolated areas only. Many trunk deformations and bush forms are found with Fagus on a large scale in the snow impacted localities (steep slopes, periphery of corries, avalanche slopes etc.). Crawling and sliding snow causes these growth deformations in the Fagus seedlings since their first year. The general increase of the vegetative propagation is a remarkable and exceptional response of Fagus in adapting to these extreme growth conditions. Under alpine timberline conditions, the generative propagation is very limited. The vegetative shoots with adventitious root systems are formed mainly from branches layering in the humus. The typical monocormonal tree-form of Fagus from lower altitudes turns in this way into a polycormon. From an evolutionary point of view, it is a suitable substitution; but from the ecological viewpoint, however, it is a sturdy growth form. In its typical form, the polycormon is formed by a number of vegetative shoots, which may be deformed but are very elastic and resistent. The number of shoots in a polycormon varies from 3–5 below, and up to 40–50 at and above the timberline. They are formed by shoots of a number of filial successions. The decay of a polycormon results from decreasing vitality of single shoots or, very often, it is caused by the impact of snow and ice. Considering, however, the fact that single shoots have a sufficient adventitious root system and are thus physiologically independent, the dying of the other shoots does not mean a danger for the existence of the remaining part of the polycormon. The age of a polycormon as a whole is difficult to determine. Fagus polycormons can be considered as a typical growthform of the highest sites of the association Aceri-Fagetum. No other tree species is able to form close stands under these conditions. This phenomenon is of primary importance for the existence of this plant community. The unusual character of the structure and dynamics of the highest Aceri-Fagetum stands gives rise to a special type of the alpine timberline which should be understood not as a ‘line’ but as a transitional zone between the closed stands and the hon-wooded plant communities of the subalpine vegetation zone. The dynamic succession of the Fagus polycormons guarantees the stability of the Fagus stands forming the alpine timberline.
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  • 9
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    Plant ecology 48 (1982), S. 123-131 
    ISSN: 1573-5052
    Keywords: Ecology ; Fringe communities ; Numerical classification ; Ostrya carpinifolia woods ; Phytogeographic elements ; Phytosociology ; Southern Alps (N-Italy) ; Vegetation dynamics ; Wood edge communities
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Forest regeneration in the vegetation complex of the submontane belt in the Southern Alps involves the active participation ofOstrya carpinifolia woods and their wood edge communities. The corresponding syndynamical processes are described by employing phytosociological, phytogeographical and ecological methods. It is concluded that: (i) The communities of the grassland-wood transition are of major importance in the successional developments in this man-made vegetation complex. (ii) Many species occurring in the region of the deciduous forests of Eurasia find their refuge in such transitional communities and are supposed to play an important part in the succession. (iii) Ostrya carpinifolia is considered as an early successional tree species.
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  • 10
    ISSN: 1573-5052
    Keywords: Alyssum serpyllifolium subspecies ; Nickel accumulation ; Nickel tolerance ; Ecology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Experiments were carried out on the tolerance to, and uptake of, nickel by three iberian subspecies of Alyssum serpylliforium Desf. Two of these subspecies, the serpentine-endemic ssp. lusitanicum from Bragança, Portugal and ssp. malacitanum from Málaga, Spain, are hyperaccumulators (〉 1000 μg/g in dried material) of nickel. Their possible ancestor, ssp. serpyllifolium (from Granada, Spain) was a non-accumulator of this element. Seeds of the two serpentine-endemics germinated extensively in nickel concentrations up to 12 000 μg/g (1.2%) whereas ssp. serpyllifolium only germinated in nickel concentrations below 60 μg/ml. Tolerance tests involving measurement of new root lengths of excised seedlings placed in varying nickel concentrations, again showed much greater tolerance of the two serpentinophytes. In both series of experiments, the order of tolerance was: ssp. lusitanicum 〉 ssp. malacitanum 〉 ssp. serpyllifolium. In pot trials involving seedlings of ssp. malacitanum grown in mixtures containing varying amounts of calcium, magnesium, and nickel, the most important finding was that plants will tolerate higher nickel contents in the soil when excess calcium is added. This is achieved by lowering the uptake of nickel. There appeared to be some concomitant reduction in calcium uptake in the presence of nickel, and some increase in uptake of magnesium. The resultant lower calcium/magnesium ratio in the plant, though not symptomatic of a favourable condition for colonization of serpentine soils, probably results from a mechanism which renders nickel innocuous to the plant at the expense of calcium uptake. It is suggested that the physiological characters of ssp. lusitanicum and ssp malacitanum are sufficiently different to support arguments for promoting the latter to full specific rank as has now been done for ssp. lusitanicum.
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  • 11
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    Plant ecology 55 (1984), S. 57-64 
    ISSN: 1573-5052
    Keywords: Ecology ; Hepaticae ; Pioneer vegetation ; Resurrection (poikilohydric) plants ; Riccia ; South West Africa
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Three associations of the Nanocyperion teneriffae Lebrun 1947 (Sporoboletalia festivi Lebrun 1947) are described. They are physiognomically and ecologically similar to associations of the Mediterranean Isoeto-Nanojuncetea Br.-Bl. et Tx. 1943 and Helianthemetalia guttati Br.-Bl. 1940. They are rich in very specialized therophytes and resurrection plants.
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  • 12
    ISSN: 1573-5036
    Keywords: Actinorhizas ; Ecology ; Gamma irradiation ; Hippophaë rhamnoides ; Longidorus ; Nematode ; Nodulation ; Root nodules ; Soil sterilization ; Succession
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary To explain the decline of Hippophaë scrub in the vegetation succession in the dunes of The Netherlands, the growth and nodulation of Hippophaë plants grown in pots, using soil from an early stage (site AH) and a post-optimum stage (site HP), were investigated. In HP-soil nodulation, yield, and the nitrogen and phosphorus content of test plants were always lower and the number of necrotic nodules and the dry matter content were always higher than in AH-soil, even after inoculation with crushed nodules and the addition of a nutrient solution. Plants in HP-soil also had darker roots, less root hairs, a higher number of short lateral roots and a higher percentage of dead roots than those in AH-soil. These characteristics of adverse growth conditions disappeared upon ignition or gamma-irradiation of HP-soil. Possible explanations of these results are discussed. The degeneration of Hippophaë scrub cannot be ascribed to the age of the plants, the absence of sufficient infective endophyte particles or to abiotic factors such as unfavourable physical (particle size) or chemical soil conditions but is caused by biotic factors. No indications were obtained that plant-pathogenic fungi and bacteria are involved. HP-soil in contrast to AH-soil, however, contained large numbers of the nematodeLongidorus sp., a species known to cause root deformations. The conclusion was that this nematode is one of the biotic factors involved in the degeneration of the Hippophaë scrub. This degeneration is due to a restriction of the root system resulting in a low phosphate uptake, a low nodulation capacity and, as a consequence, a low nitrogen content. The results demonstrate that biotic soil factors are important in influencing succession in higher plant communities.
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  • 13
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    Plant and soil 69 (1982), S. 293-297 
    ISSN: 1573-5036
    Keywords: Ecology ; Frankia ; Nitrogen fixation ; Water potential
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Growth responses of Frankia isolates to decreasing water potential were monitored in systems where potentials were controlled by KCl, NaCl and Polyethylene glycol. The highest potential tested was −2 bar (basal medium). The general pattern emerging was that isolates fromAlnus glutinosa, A. viridis andComptonia peregrina showed declining growth at potentials below −2 to −5 bar. AMyrica gale isolate showed declining growth with decreasing potential. All isolates were more sensitive to decreases in potential in a matric controlled than an osmotic controlled system. They all showed approximately 50 percent growth reduction at −5 to −8 bar, and meagre growth at −16 bar after 35 days. The Comptonia isolate was the most vigorous at low potentials. Nitrogen fixation ability was monitored for two isolates. Highest specific activities were observed between −3 and −5 bar for the Myrica isolate and between −5 and −7.5 bar for theA. glutinosa isolate.
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  • 14
    ISSN: 1573-5036
    Keywords: Actinorhizas ; (Actinomycetes) ; Ecology ; Hippophaë ; (Mystiflora: Elaeagnaceae) ; Longidorus ; (Nematoda: Longidoridae) ; Nodulation ; Soil ; sterization ; Vegetational succession ; Tylenchorhynchus (Nematoda: Tylenchrohynchidae)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Hippophaë rhamnoides seedlings were grown in sterilized and unsterilized soil from a decliningH. rhamnoides scrub, to which different numbers ofLongidorus sp. andTylenchorhynchus microphasmis were added. In sterilized and unsterilized soil, retardation of growth, content of dry matter in the shoots, and incidence of deformed short lateral roots of test plants were positively correlated with counts of both nematode species. Nitrogen content in the shoots, nodulation on the roots of test plants and increase increase in nematodes were negatively correlated with the initial number of both nematode species in sterilized soil. In unsterilized soil, an unknown biotic factor was present that reduces growth ofH. rhamnoides, nodulation and multiplication of the nematodes. This factor seems to interact with the nematodes in reducing growth ofH. rhamnoides.
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  • 15
    ISSN: 1573-5036
    Keywords: Catalase ; Ecology ; Fertilizers ; H2O2∶H2O2 oxidoreductase ; Rhizosphere effects ; Soil enzymes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Catalase activity of a loamy sand under a 3-year crop rotation in the southeastern U.S.A. was monitored. Corn (Zea mays L.), cotton (Gossypium hirsutum L.), and soybean [Glycine max (L.) Merr.] were the summer crops in the rotation. Winter wheat (Triticum aestivum L.) was planted after corn, and soybean was followed by a winter fallow period. Cotton was followed by a mixture of common vetch (Vicia sativa L.) and crimson clover (Trifolium incarnatum Gibelli & Belli) which was eventually plow-incorporated as a green manure. Highest mean catalase activities were recorded in soil under the wheat, soybean, and winter legume crops; lowest activities were found in soil bearing corn and cotton, and during the winter fallow period. The fertilization regime influenced soil catalase activity independently of the crop. Soil deficient in any of the major elements showed low enzyme activity. Highest activity was found in soil fertilized with P and K, and with N supplied by a winter legume crop. Addition of supplementary mineral nitrogen to this regime reduced catalase activity. Elimination of the winter legume crop from an otherwise complete fertilization regime resulted in a drastic reduction in enzyme activity. In soil receiving a complete fertilization regime there was a close correlation between soil catalase and xylanase activities. A similar correlation between these two enzymes was not found in soil receiving incomplete fertilization.
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  • 16
    ISSN: 1573-5036
    Keywords: Chitin ; Chitinase ; Chitinglycanohydrolase ; E. C. 3.2.1.14 ; Ecology ; Fertilizers ; Rhizosphere effects ; Soil enzymes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Chitinase activity was determined by incubating a mixture of toluene-treated soil with 1% (w/w) colloidal chitin suspension for 18 h at 37°C and then, after dilution, assaying the amount of N-acetyl-glucosamine released. Maximal chitinase activity was observed at 45°C and optimal pH for enzymatic reaction was 5.0–5.5. Soil chitinase activity decreased with increasing soil depth and was significantly affected by crop cover and fertilization regime. Chitin added to soil stimulated chitinase activity. Enzyme activity was correlated with the soil fungal population but not with numbers of actinomycetes or bacteria. A specialized mycoflora was associated with chitin decomposition.
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  • 17
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    Hydrobiologia 76 (1981), S. 87-96 
    ISSN: 1573-5117
    Keywords: Ecology ; production ; Gulf of Bothnia ; pelagial ; benthos
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Production biology in the Bothnian Bay is discussed and compared to that of the southern parts of the Baltic. Severe ice-conditions, low water temperatures in spring and early summer and a pronounced water-colouring cause a delay of the spring development of phytoplankton and a low annual production in the Bothnian Bay. This delay makes possible a higher efficiency of the pelagic system as the zooplankton fauna can develop in harmony with the food resources. The downward transport of energy and matter to the bottom communities from an efficient pelagial should be small and temporally unpredictable, which is thought to be an adequate explanation of the observed very low benthic fauna biomasses in the Bothnian Bay.
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  • 18
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    Hydrobiologia 73 (1980), S. 181-193 
    ISSN: 1573-5117
    Keywords: Ecology ; feeding ; invertebrate behavior ; larval biology ; Rotifer ; sessile rotifer ; substrate-dependent survivorship ; substrate selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
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  • 19
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    Environmental biology of fishes 5 (1980), S. 27-32 
    ISSN: 1573-5133
    Keywords: Salvelinus fontinalis ; Salmo salar (ouananiche) ; Ecology ; Salmonids ; Atlantic salmon
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis The age structures of brook charr (Salvelinus fontinalis) and ouananiche (Salmo salar) stocks inhabiting a large rapid the river Méo, tributary to the Caniapiscau River were used to compare population stability and production of these species in north central Quebec. The brook chart stock was stable whereas ouananiche showed considerable variation in year class strength. Stock estimates were not significantly different for the two species although the brook charr estimate was 1.5 that of the ouananiche. Production estimates differed by a greater margin because of different growth patterns. Brook chair production was estimated at 19.4 kg ha−1 yr−1. Above age 2+ it was 11.4 kg ha−1 yr−1 which compares with 4.8 kg ha−1 yr−1 for the same age groups of ouananiche.
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  • 20
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    Environmental biology of fishes 5 (1980), S. 117-133 
    ISSN: 1573-5133
    Keywords: Cycles ; Communities ; Diversity ; Ecology ; Estuary ; Multiple regressions ; Oceanography ; Salinity ; Seasons ; Time-series analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis From November 1975 to April 1977 nocturnal dermersal fish were sampled fortnightly at ten sites in Serpentine Creek using a three meter beam trawl with a 3.2 cm mesh net. Forty-five species from thirty-four families were obtained totalling 14 518 individuals with the six most abundant species comprising approximately 72% of the catch. Using multiple regression techniques with Fourier transformations, the mean number of species (S) and abundance (N) of all fish were found to conform to a regular annual cyclical pattern with maxima in April and May. A trend toward declining abundances of individuals and species was present. Shannon (H′) and Gleason (G) diversity indices showed no regular seasonal trends and are considered poor indicators of pollution. In comparison with other estuarine studies at different latitudes Serpentine Creek conforms to the theory that more tropical waters have the greatest faunal diversity. Seventeen of the 22 most abundant species demonstrated a regular annual cycle of abundance. The number of species, abundance and diversity measures were greatest about 1 km from the mouth of the creek and gradually declined upstream. This was the region with highest macrobenthos diversity and with the most stable abiotic values. Temperature and/or salinity were positively correlated with the abundance of eleven species. The species were placed in five groups according to their periodic characteristics. The proportion of ‘resident’ species was low and this is consistent with Tyler's (1971) theory of temperature stabilized fish assemblages. The known biology of six species is related to their occurrence. Salinity and temperature values in the creek exhibit an annual cycle which preceeds that of Bramble Bay by approximately one month. Rainfall in the watershed was correlated with observed salinity values. It is postulated that salinity is the common feature between temperate and tropical estuaries in the maintenance of community cycles.
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  • 21
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    Environmental biology of fishes 6 (1981), S. 95-103 
    ISSN: 1573-5133
    Keywords: Behavior ; Ecology ; Parental care ; Reproductive cycles ; Colonial nesting ; Etroplus maculatus ; Etroplus suratensis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis The Asian cichlids,Etroplus maculatus (the orange chromide) and E. suratensis (the green chromide) in Sri Lanka reproduce twice during the year when water conditions are favorable for nest construction and maintaining visual contact with offspring. These are the drier premonsoonal and monsoonal seasons when water turbidity decreased and salinity increased. When breeding in isolation orange chromide pairs selected dense vegetation where nests were camouflaged. During the peak breeding cycle (July) orange chromide pairs selected sparse vegetation for nesting as a compromise between survival of young and availability of adult food. These areas were also occupied by foraging non-breeding conspecifics which increased the threat of cannibalism of offspring. Under these pressures most orange chromides nested in colonies which helped decrease both actual and attempted cannibalism. The sympatric green chromide does not forage during nesting and nest site selection was determined mainly by factors favoring offspring survival. Biparental care is exhibited by both species. One member of an orange chromide pair stands guard over offspring while the other leaves the territory to forage — their roles are reversed every few minutes. The total parental investment is equivalent to the full investment of a single parent. Monogamy appears to be maintained by their metabolic constraints. In the green chromide both parents are vigilant over offspring and neither forages thus spending twice as much time in parental investment.
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    Environmental biology of fishes 6 (1981), S. 207-211 
    ISSN: 1573-5133
    Keywords: Fish ; Ecology ; Population density ; Exploitation ; Tagging ; Catch per effort
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Population and exploitation estimates were made from angler recaptures of Chautauqua Lake muskellunge,Esox masquinongy Mitchill. Fish were tagged during Conservation Department studies in 1941–1946, 1961–1965 and 1976–1978. Population estimates of adult fish ranged from one to seven fish per hectare and angler exploitation rates of tagged fish fluctuated from 3.8% to 14.1%. Relative catch indicators suggest a major decline in the lake's muskellunge population during the last decade. Overexploitation, habitat alteration and interspecific competition with recently introduced fish species were cited as probable causes of the decline.
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    Environmental biology of fishes 6 (1981), S. 213-218 
    ISSN: 1573-5133
    Keywords: Australia ; Communities ; Cycles ; Diversity ; Ecology ; Estuary ; Lunar periodicity ; Migration ; Sub-tropics ; Tides
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis A series of 10 sites were sampled at new and full moon phases in a vertically homogenous estuary, Serpentine Creek, Queensland, Australia. Forty-five species (14,518 individuals) were caught and analysed using standardized Shannon & Gleason diversity indices, and total number of species and individuals. The coefficients of variation for these values were greater for times than for sites. There were no significant differences between 14 pairs of new and full moon phases fort,t,t, andt, or between mean number of individuals for the 16 most abundant species. If significant variations do exist within months, then experiments should be done between spring and neap tides as this study found no differences between the spring tides associated with new and full moon phases.
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    Environmental biology of fishes 6 (1981), S. 371-375 
    ISSN: 1573-5133
    Keywords: Anguilliformes ; Anguillidae ; Leptocephalus ; Fish larvae ; Horizontal distribution ; Vertical distribution ; Spawning area ; Migration ; Ultrasonic tracking ; Hydrography ; Ecology ; North Atlantic ; Anguilla anguilla ; A. rostrata
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis This report presents preliminary results of the 1979 Sargasso Sea expedition from February to May 1979. Information is given on horizontal and vertical distribution of eel larvae and adults, adult eel tracking and pelagic trawling. Related matters such as electrophoretic studies on anguilliform larvae, feeding of eel larvae, predation on leptocephali, occurrence of other anguilliform larvae and hydrography are mentioned.
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    Environmental biology of fishes 7 (1982), S. 177-180 
    ISSN: 1573-5133
    Keywords: Temperature ; Behavior ; Ecology ; Fisheries ; Fish ; Marine juveniles
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Sixteen yearling winter flounder, tested individually for 3-day periods in electronic shuttleboxes, voluntarily occupied an 8–27°C range of temperature, with a modal final thermal preferendum of 18.5°C (mean 18.7°C, median 19°C, midpoint 17.5°C, s.d. 1.9°C, S k + 0.33). The locomotor activity pattern of the yearling fish in the laboratory was markedly nocturnal, with mean hourly nocturnal activity exceeding mean hourly diurnal activity by a factor of 3.4. Maximum activity occurred at 0300 EST, minimum activity at 1400 EST. While activity generally increased with temperature, a local activity minimum occurred at 18.7°C, coinciding with the 24-hour mean final thermal preferendum. Comparison of these laboratory data with previously published field data suggest that behavioral responses to temperature and light play significant roles in determining age- and size-specific differences in seasonal depth stratification and onshore-offshore distributions in this species.
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    Environmental biology of fishes 5 (1980), S. 109-116 
    ISSN: 1573-5133
    Keywords: Bay ; Dispersal ; Ecology ; Egg type ; Fish larvae ; Islands ; Points ; Rocky habitats ; Species turnover
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Reef fish community composition in three segments of a peninsular rocky shoreline in the Gulf of California was estimated over four periods by visual observation. ‘Point’ and ‘bay’ segments had regular and distinct species compositions over most periods while a ‘middle’ segment was least distinct but consistently had the greatest number of species. Compositional change along the peninsula was least regular during the coldest sea temperature period (April). Mean species turnover between segments was highest between point and bay. Within segments, the point had greater compositional predictable composition (lowest species turnover). When species with regular frequency of encounter were classified into ‘point’, ‘middle’, ‘bay’, and ‘no trend’ groups it was found that comparatively more ‘point’ species had pelagic eggs and comparatively more ‘bay’ species had demersal eggs. Beta diversity of rocky-shore fishes along the physical gradient of the Punta Doble peninsula reflects a transition between exposed and protected rocky shoreline communities. The correlated physical environmental characteristics associated with exposed and protected habitats are discussed in relation to diversity regulation and dispersal strategies in reef fishes.
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    Environmental biology of fishes 6 (1981), S. 361-365 
    ISSN: 1573-5133
    Keywords: Mimicry ; Shamming death ; Africa ; Fish ; Chafing ; Predation ; Ecology ; Cyrtocara
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Haplochromis (=Cyrtocara) livingstoni, one of the predatory cichlids of the sand community of Lake Malawi, Africa, occurs at a density of 1.3 individuals per hectare. They are territorial, defending areas 15 m wide by 40 m long along the interface of sand andVallisneria weed beds. Individuals use a ‘death feigning’ hunting pattern to capture prey. From a position of lying on their sides semiburied in the sand, these fish attack small cichlids. During four hours of SCUBA observations three successful attacks from this position were seen. After an attack the small cichlids scatter and the predator moves on toward a new aggregation of fish where it again plays dead. Individuals feign death an average of seven times per thirty minutes watch. Death feigning behavior is initiated in two ways. The fish either 1) is stationary with its ventral surface on or close to the sand, and then falls onto its side, or 2) drops from the water colum into `lying on side' position. The initial behavioral actions of the latter method are similar to chafing behavior. But instead of chafing the sand and rising again off the bottom, the fish plows into the sand and remains immobile. These data further add to the evidence that cichlids are remarkably flexible in their feeding behavior.
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    Environmental biology of fishes 7 (1982), S. 121-136 
    ISSN: 1573-5133
    Keywords: Seasonality ; Predator-prey ; Predator interference ; Turnoverrate ; Diversity ; Ecology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Development of the fish community on a submerged 16 m barge and variation in fish abundance on nearby transects were surveyed twice monthly for twenty months. A steady increase in abundance was observed for certain fishes on the barge, whereas a few species exhibited distinct seasonal variation on both the barge and transects. Most of the seasonal species settled between March and May. Some seasonal species appeared to be site selective in their settlement and consequently settled juveniles were clumped in their distribution. An abundance of preferred topographical features may be why settlement was relatively high at the study site and indirectly why predators became significantly (r3 = 7.67***, N = 37) more abundant at the study area during the months of maximum prey settlement. Concurrent settlement of several species during the same few months may be important because juveniles become an abundant food source to predators during those few months only. Periodic swamping of predators by abundant juvenile prey may improve the chances for individuals of rarer prey species to be overlooked and therefore be succesfully recruited.
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    Environmental biology of fishes 9 (1983), S. 41-53 
    ISSN: 1573-5133
    Keywords: Artificial reefs ; Competition ; Intermediate disturbance ; Ecology ; Mortality ; Predation ; Recruitment ; Stability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis In January 1977, a record breaking cold spell caused fish kills at Big Pine Key, Florida. Census data collected before and after the cold spell from a series of model reefs constructed in 1975 showed a significant drop in mean number of reef fish species and individuals. Following this disturbance, high recruitment of juveniles occurred, presumably due to reduced competition, predation, or a combination of these. Model and natural patch reef communities examined the summer following the cold spell (1977) were significantly different from those examined the summer before (1976) and the second summer following the cold spell (1978). During the summer of 1977, a significantly smaller mean fish size and a significantly greater mean number of species and individuals were observed. Increased species richness following the cold spell is consistent with the intermediate disturbance hypothesis. Contrary to some theoretical predictions, results suggest reef fish communities are highly resilient to some regional disturbance.
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    Plant and soil 56 (1980), S. 123-139 
    ISSN: 1573-5036
    Keywords: Actinorhizas ; Ecology ; Endophyte distribution ; Hippophaë rhamnoides ; Infective potential ; Nodulation ; Root nodules
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The infective potential (IP) of nodule homogenates from field-grownHippophaë rhamnoides L. ssp.rhamnoides was determined by counting the number of nodules formed on test plants after inoculation with various dilutions of the homogenates. The IP was almost constant,i.e. 105 to 106 per gram of fresh nodule material. Methods to store nodule material without loss of IP were tested. The IP of air-dried nodule powders stored at 6°C hardly decreased during a period of more than a year. Data are presented on the IP of soil samples from sites representing various stages of dune formation. BeforeH. rhamnoides appeared, the IP was low: 1 to 36 nodules were formed on test plants per kg of soil. This low IP was due to low numbers of infective endophyte particles in these soils. During the succession of theH. rhamnoides scrub, the IP of the soil increased, due to the increase in the number of endophyte particles in the soil. Gradually, however, nodulation was limited by other environmental factors. The nature of these factors is discussed.
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    Plant and soil 61 (1981), S. 71-80 
    ISSN: 1573-5036
    Keywords: Ecology ; Fluorescent antibody ; Immunofluorescence ; Rhizobium japonicum ; Rhizosphere ; Root surfaces ; Soybean
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Populations of nativeRhizobium japonicum 123 in the rhizospheres of field and pot grown plants as determined by immunofluorescence were calculated on the basis of root surface area. The density ofR. japonicum 123 on the root fluctuated between a few hundred to over a thousand per square centimeter of root surface. As root volume expanded rapidly, the Rhizobium density fell to less than one hundred per unit area. There was no appreciable effect due to different plant, nitrogen amendment, or addition of another strain ofR. japonicum, on the surface density of the nativeR. japonicum population on roots. Nor did the native population influence the added strain. Direct examination of root surface segments revealed that naturalized rhizobia existed sparsely on root surfaces in the form of short rods. They were observed to be attached sideways or in a polar manner on root hairs, epidermal cells, and at junctions of tap and lateral roots. There was no evidence of specific stimulation of the homologous Rhizobium by the host plant as a prelude to nodulation.
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    Environmental biology of fishes 11 (1984), S. 121-130 
    ISSN: 1573-5133
    Keywords: Ecology ; Habitat ; Feeding ; Age ; Growth ; Reproduction ; Mississippi
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Etheostoma swaini, the gulf darter, was collected from the Black Creek drainage in southern Mississippi (February 1978 – April 1979). The gulf darter generally inhabits small- to moderate-size creeks and occurs over a sand or sandy mud bottom, often in association with aquatic vegetation or a layer of organic debris. Larval dipterans were the most important food items, both numerically and volumetrically. Chironomids were found in 71–100% of the stomachs in all except the unusual March 16 collection. The length frequency distribution and the scale annuli analysis indicated there were three year-classes present in the population at any one time. Fifty-one percent of the specimens taken were less than 12 months old. During the mid-February to late March spawning season gulf darters were most often collected over clean gravel or gravelsand substrates. Laboratory observations suggest that the female burrows into the gravel where the demersal, adhesive eggs are deposited. Female gulf darters significantly outnumbered males at a ratio of 59:41.
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    Environmental biology of fishes 11 (1984), S. 173-190 
    ISSN: 1573-5133
    Keywords: Percidae ; Etheostomatini ; Darters ; Ecomorphology ; Embryology ; Ecology ; Early life history
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis The early development of northern logperch, Percina caprodes semifasciata, was examined from an ecological perspective and in relation to the theory of saltatory ontogeny. Steps, the intervals of relative homeostasis, separated by thresholds, rapid switches to new form and function resulting from canalization of changes in the preceeding step, are described and related to environmental factors. Adaptive shifts in growth allometries provided further evidence of the saltatory nature of ontogeny. Logperch eggs are small (1.2 mm diameter), demersal, and adhesive. The simple embryonic respiratory system reflects high oxygen availability on the lotic spawning grounds. Hatching occurs early, relative to other darters, and free embryos are pelagic. The small free embryos presumably drift downstream to lentic areas, where small planktonic food is more abundant. Logperch are therefore nonguarding, open substrate spawning lithopelagophils and, along with other Percina species, have not advanced from ancestral percid reproductive styles. Percina species have generally remained in ancestral habitats-rivers and lakes. The close correlation between developmental patterns of logperch and environmental factors is therefore interpreted as a restriction based on retention of ancestral characteristics, not as evidence of novel adaptations to new habitats.
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    Environmental biology of fishes 11 (1984), S. 277-299 
    ISSN: 1573-5133
    Keywords: Percidae ; Etheostomatini ; Ecomorphology ; Embryology ; Ecology ; Early life history ; Heterochrony
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis The early development of rainbow darter, Etheostoma caeruleum, was examined from an ecological perspective. Steps and thresholds of ontogeny to completion of body squammation are defined, and related to environmental factors. Rainbow darter eggs are about 2 mm diameter, considerably larger than those of related logperch (Percina caprodes). The embryonic vitelline respiratory plexus is much more extensive. The pelagic interval characteristic of logperch and ancestral percids is eliminated and onset of exogenous feeding is delayed. The larger larvae of the rainbow darter can begin feeding directly on aquatic insects, and complete their life cycle in streams. Therefore, shifts in the timing of important thresholds (e.g. exogenous feeding) are ecologically important. Furthermore, early maturation and/or delayed bone and scale formation may be responsible for reductions in the lateralis system and scalation in this and other darter species.
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  • 35
    ISSN: 1573-5133
    Keywords: Cichlid ; Ecology ; Behavior ; Evolution ; Tropics ; Polymorphism ; Central America ; Lake Malawi ; Africa
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Cichlasoma citrinellum is a polymorphic species whose individual coloration varies from the dark grey markings typical of the species to yellow, orange, and red. In Lake Jiloá, Nicaragua the depth distribution of these latter, nongrey, golden morphs shows dramatic seasonal variation. In the height of the dry season in February over 50% of the gold morphs occur above 9 m, but as the breeding season approaches they migrate deeper such that less than 7% of the gold population occurs above 9 m at the onset of the breeding season. During the rainy season when breeding occurs most of the gold morphs occur below 15 m. It appears that gold morphs ‘voluntarily’ move into deeper water to breed rather than being aggressively forced deeper by larger, territorial grey morphs as was implied in an earlier paper (McKaye & Barlow 1976). Since the morphs of this species assortatively mate and select different habitats in which to breed, future sympatric splitting of this species is possible. Likely examples of sympatric speciation and of incipient speciation in the family Cichlidae are discussed.
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  • 36
    ISSN: 1573-5133
    Keywords: Fish ; Nematode ; Populations ; Life cycle ; Host factors ; Ecology ; Parasites
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis A total of 314 white suckers (Catostomus commersoni) taken monthly during May to December 1975 and in April and May 1976 from southern Lake Huron, Ontario, Canada, were examined forCapillaria catostomi. Prevalence determined from fresh white suckers (66%) was significantly lower than from frozen white suckers (81%). However, there was no significant difference in prevalence ofC. catostomi in samples taken at monthly intervals; in male and female white suckers; or in the age categories. Mean intensity of infection was not significantly different in fresh (9.6 [± 13.41]) or frozen (10.4 [± 13.11]) white suckers. There was no significant difference in intensities between monthly samples in male and female white suckers or in the age categories. Suckers were infected with 1–172 worms. The percentage of male, female and immature worms did not change with sex or age of host or by month. The frequency distribution showed the parasites were overdispersed. A possible life cycle forC. catostomi involving an oligochaete intermediate host is discussed and an attempt made to explain the almost constant levels of prevalence and intensity.
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    Biopolymers 19 (1980), S. 823-831 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of the DNA-binding oligopeptide distamycin A on the B to A transition of DNA in ethanol/water solutions has been studied by means of CD. (The overbars indicate that it does not matter which particular form of the corresponding families is considered.) The results show that increasing the concentration of distamycin A reverses the A conformation (in 82% ethanol) to the B conformation due to its strong binding and stabilization of the latter. In accordance with previous data for pure aqueous solutions, a site size of 3.5 base pairs is obtained from the studies in water/ethanolic solutions. From the data on the B to A transition in the presence of distamycin A, we estimated the length of the cooperativity ν0 = 10 base pairs.The results demonstrate that the oligopeptide systems of distamycin, as well as those of netropsin, are effective stabilizers of the DNA B-conformation.
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Tetrapeptides with proline in position 2, asparagine or leucine in position 3, and glycine in positions 1 and 4, with end groups free or blocked on the N-terminal side, were studied in their various ionic states in 2H2O and in Me2SO-d6 by 1H- and 13C-nmr. In order to clarify or refine some details, successive substitutions of the residues in these peptides with amino acids enriched to 85% in 13C, or to 85% 13C plus 97% 2H were carried out. The 1H and 13C chemical shifts as well as the 1H-1H, 13C-13C, and 13C-1H coupling constants and the signal intensities show strong similarity of behavior between the tetrapeptides of asparagine and leucine. The main conformational characteristics are (1) the almost total stabilization of the trans conformer in the type I β-turn structure when the peptide is in the zwitterion state dissolved in Me2SO. This is deduced from the 3JC3αH-N3H and the 3JC2′-H3α coupling constants, which both furnish a dihedral angle of φ3 = -90°, and from the positive value of the temperature coefficient of the glycine-4 amide protons, which suggests a type 4 → 1 hydrogen bond; (2) the evolution of cis and trans isomer fractions which change with the ionic state of the peptides in Me2SO, whereas they remain constant in aqueous solution; and (3) the conformation of the pyrrolidine ring as it follows the variations in cis:trans isomer populations together with the side-chain rotamer fractions of the residue in position 3. In the β-turn conformation the isomer cis is less abundant and the pyrrolidine ring is more flexible; this explains the perfect accommodation of the proline residue in position 2 of a bend. The interdependence of these phenomena where interactive forces play a predominant role underlines the importance of cooperative effects in the molecule. The results also suggest that the cis isomer of proline can adapt itself just as well as the trans isomer to position 2 of a type I β-turn.
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An algorithm is presented for the Monte Carlo simulation of the decay of fluorescence polarization from segmentally flexible molecules. Based on the random walk model of Brownian motion, the treatment explicitly follows the stochastic changes in the diffusion coefficients as the molecule bends. It includes the effects of a linear restoring force opposing the bending and the effects of hydrodynamic coupling between the translational, rotational, and bending motions. One application is presented: the simulation of anisotropy decay curves for hinged rods. A variety of decay curves are obtained, including single- and multiexponential behavior, and the following conclusions are reached: (1) increasing the flexibility is usually, but not always, accompanied by a more rapid rate of depolarization; (2) reducing the size of the fluorescent subunit will usually, but not always, increase the rate of depolarization; and (3) the complex interplay between the effects of molecular shape, relative sizes of the subunits, restoring force, and orientation of the transition dipoles renders it unlikely that any simple method can be used to interpret anisotrophy data without simulation. In particular, it is not possible to determine the extent of bending by fitting the data with the two-exponential approximation used by some investigators in the past.
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    Biopolymers 19 (1980), S. 977-990 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C-nmr spectra of red seaweed galactans, belonging to the agar and carrageenan groups or having the “intermediate” type of structure, were interpreted on the basis of 13C-nmr spectra of model compounds. Signal assignments have been made for most of the known extreme structures of such galactans. 13C-nmr spectroscopy was shown to be a rapid and convenient method of structural analysis, which permits one to determine the type of galactan structure, the absolute configurations of its constituents (galactose and 3,6-anhydrogalactose), and the positions of the sulfate and O-methyl groups in a polysaccharide molecule.
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric response of human umbilical cord hyaluronic acid in various environments has been studied at microwave frquencies using a resonant microwave cavity as a probe. Both the real and imaginary parts of complex dielectric constant and the loss tangent for hyaluronate solutions are obtained by utilizing equations for perturbation of a resonant cavity. Dielectric changes at room temperature have been observed in aqueous solutions of hyaluronic acid as a function of concentration ranging from 0 to 350 mg/ml. The data indicate the existence of ordered phases in hyaluronate solutions at selective concentrations, that is, exhibiting lyotropic-type transitions. Hyaluronate solutions at 1.5 and 3 mg/ml concentrations have been studied at various pH in the range of 6-8 and at constant ionic strength 0.1. A temperature-dependent transition in hyaluronate solution of 120 mg/ml concentration has been observed at physiological temperature. It is shown that this temperature-dependent behavior can be related to the orientational polarizability term in the Debye theory of polar molecules in liquids.
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    Biopolymers 19 (1980), S. 945-964 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In 1974, Zimm described a theory which predicts that the sedimentation coefficient of high-molecular-weight DNA will decrease as the rotor speed of measurement increases. In 1979, this theory was revised, and the new formula predicts speed-dependence effects that are substantially smaller than the predictions of the original version. This report describes the results of subjecting both the original and the revised versions of the theory to quantitative tests using a well-defined sucrose-gradient system and a DNA of known molecular weight (T4c DNA). T4c bacteriophage is a mutant, whose DNA contains the unmodified base cytosine, instead of the glucosylated hydroxymethylcytosine characteristic of the T-even bacteriophages, and has a molecular weight of 115 ± 3 × 106. The DNA of the wild-type phage (T4D+) was also used in some experiments.In addition to the quantitative tests, the experiments test for an effect first observed by Rubenstein and Leighton, which showed that the sedimentation coefficient measured for T2 DNA depended on the composition of the centrifuge tube used for the measurement (tube composition effect). It can be inferred from this observation that an interaction occurs between particle and tube wall during sedimentation, and this leads to a reduction in sedimentation velocity independent of the reduction in S described by Zimm's theory.The results show that in the range of 25,000-50,000 rpm, the original but theoretically incorrect form of the theory quite accurately describes the sedimentation behavior of both T4c and T4D+ DNA, although T4D+ was a special case in some respects. The revised (corrected) form of the theory predicts much less of a speed-dependence effect than that actually observed. The discrepancy between corrected theory and observation suggests that other factors (perhaps arising from the use of the swinging bucket rotor geometry) are causing the additional observed reduction in S20,w. However, the experiments show that the tube composition effect does not seem to be one of these.
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The fixation of cis (NH3)2Cl2Pt(II) to poly(I)·poly(C) leads to the formation of two complexed species. One involves coordination to a single base (accounting for about 70% of the total platinum bound over the rb range 0.07-0.25) and the other to two bases which are not adjacent to each other but may be on the same strand and separated by a loop. Reaction of the platinum compound with poly(I) gives in addition to the above two species a minor one (about 15%, independent of rb over the range 0.05-0.30) in which the platinum is bound to two adjacent bases. The availability of such coordination reduces the dominance of the 1:1 species, which, however, remains the major one (ca. 55%).
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    Biopolymers 19 (1980), S. 1329-1344 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The complex of CH3Hg(II) with the accessible cysteines of glyceraldehyde-3-phosphate dehydrogenase (GAPD, EC 1.2.1.12) from rabbit muscle has been studied by phosphorescence and optically detected magnetic resonance (ODMR) spectroscopy. The wavelength dependence of the phosphorescence decay kinetics has also been measured. Comparison of CH3Hg(II)-GAPD with GAPD by these methods shows that a specific optically resolved tryptophan site of GAPD is perturbed by the interaction with a nearby mercury atom. The perturbation on the luminescence and ODMR properties is typical of an external heavy-atom effect. Based on the x-ray diffraction structure of the lobster enzyme, it is proposed that the heavy-atom effect results from the interaction of tryptophan-310 with CH3Hg(II) bound to cysteine-281 in the rabbit muscle enzyme.
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  • 45
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    Biopolymers 19 (1980), S. 1415-1434 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The energy of interaction of a spermine molecule with the A- and B-forms of DNA has been calculated, assuming that the molecule of spermine is fixed in the narrow groove of the DNA helix with the formation of hydrogen bonds between the amino groups of spermine and the phosphate groups of DNA. The atom-atom potentials method was used. Optimal structures for the A-DNA-spermine and B-DNA-spermine complexes are suggested. It is shown that, in agreement with the experimental data, the interaction of the spermine molecule with the A-DNA is energetically more favorable than that with the B-DNA. Two main factors are responsible for this: (1) the distance between neighboring phosphates of the chain in A-DNA (which is about 1 Å less than that in B-DNA) corresponds better to the distance between the amino groups of the propyl part of spermine; and (2) the orientation of phosphate groups in A-DNA inside the groove is preferable for complex formation with spermine to the outside groove arrangement of the phosphates in B-DNA. These conclusions are further confirmed by the calculations for DNA-propane diamine complexes.
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  • 46
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of a synthetic analog of valinomycin, cyclo[-(D-Ile-Lac-Ile-D-Hyi)3-] (C60H102N6O18), has been determined by x-ray diffraction procedures. The crystals are orthorhombic, space group P212121, with cell parameters a = 11.516, b = 15.705, c = 39.310 Å, and Z = 4. The atomic coordinates for the C, N, O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation. Values of standard (R) and weighted (Rw) reliability factors after refinement are 0.073 and 0.056, respectively. The structure is completely asymmetric. The cyclic molecular backbone is stabilized by six intramolecular hydrogen bonds N—H…O=C, five bonds being of the 4→1 type and one being of the 5→1 type. The side chains are located on the molecular periphery. The conformational state of isoleucinomycin in the crystal is intermediate between the corresponding crystalline states of valinomycin and meso-valinomycin. The observed conformation suggests that complexation could proceed via entry of the ion at the face possessing the L-Lac residues, the less crowded face.
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  • 47
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    Biopolymers 19 (1980), S. 1555-1566 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Possible conformations of lacto-N-tetraose, lacto-N-neotetraose, related disaccharides, and other milk oligosaccharides have been studied by an energy-minimization procedure using empirical potential functions. Lacto-N-tetraose favors a “curved” conformation, while lacto-N-neotetraose favors an approximately “straight” conformation. These two conformations differ mainly in the position of the terminal galactose residue with respect to the rest of the molecule. This difference explains the greater strength of lacto-N-neotetraose compared with lacto-N-tetraose in its ability to inhibit the cross-reaction of blood group P1 fractions with Type XIV pneumococcal antipolysaccharide. Although the favored conformation of lacto-N-tetraose (inactive) agrees with the model proposed by the earlier workers, that for lacto-N-neotetraose (active) differs. The favored conformations for the disaccharides galactose-β(1-4)-N-acetylglucosamine, galactose-β(1-3)-N-acetylglucosamine, and lactose are similar in overall shape, differing only in the nature and orientation of the side groups. This explains their nearly equal inhibitory activity. These theoretical models also explain the increased activity of lacto-N-fucopentaose I over that of lacto-N-tetraose and the relative activities of the substituted lactoses. The present studies suggest that it is the overall shape of the molecule which is important for activity, rather than the terminal β(1-4)-linked galactose residue alone.
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  • 48
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    Biopolymers 19 (1980), S. 1571-1585 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C spin-lattice relaxation times of poly(L-lysine) have been obtained at 67.9 MHz in aqueous solution and in a mixed solvent (40% methanol/60% water). A concomitant determination of the conformation by CD permits the correlation of conformation and rotational diffusion of the polymer. The dependence on pH of the spin-lattice relaxation times of the 13Cα and the side-chain carbon resonances reflects the diffusional motion in the random-coil conformation, in the helix-coil transition, and in the conformation of the α-helix. In the mixed solvent the reorientational correlation time of the Cα-Hα vector increases from τ = 0.37 nsec (random coil) to τ = 12.0 nsec (α-helix). In aqueous solution the correlation time of this vector increases from τ = 0.33 nsec (random coil) to τ ≫ 11 nsec. The reorientation rates of the side-chain methylene groups in the two solvents are markedly different. The reorientation of all methylene groups is reduced in the mixed solvent.
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  • 49
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solid-state conformation of copolymers of β-benzyl-L-aspartate [L-Asp(OBzl)] with L-leucine (L-Leu), L-alanine (L-Ala), L-valine (L-Val), γ-benzyl-L-glutamate [L-Glu(OBzl)], or ∊-carbobenzoxy-L-lysine (Cbz-L-Lys) has been studied by ir spectroscopy and circular dichroism (CD). The ir spectra in the region of the amide I and II bands and in the region of 700-250 cm-1 have been determined. The results from the ir studies are in good agreement with data obtained by CD experiments. Incorporation of the amino acid residues mentioned above into poly[L-Asp(OBzl)] induces a change from the left-handed into the right-handed α-helix. This conformational change for the poly[L-Asp(OBzl)] copolymers was observed in the following composition ranges: L-Leu, 0-15 mol %; L-Ala, 0-32 mol %; L-Val, 0-8 mol %; L-Glu(OBzl), 3-10 mol %; and Cbz-L-Lys, 0-9 mol %.
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  • 50
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    Biopolymers 19 (1980), S. 1667-1673 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dry purified ligamentum nuchae elastin has been investigated for physical aging. The samples were quenched from a temperature (197°C) close to the softening point to a number of measuring temperatures ranging from -20 to +180°C. At each temperature, the small-strain torsional creep properties were determined at a number of elapsed intervals after the quench. Aging effects were found over the whole temperature range, and the creep and aging behavior of elastin turned out to be very similar to that of synthetic polymers.
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  • 51
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 52
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    Biopolymers 19 (1980), S. 1705-1713 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Covalently closed circular DNA can exist in different configurations known as circular, toroidal, and interwound. Changes among these forms can be made in several ways, including the insertion of dye molecules between adjacent base pairs, which tends to untwist the double-helical structure. The aim of this paper is to discuss these configurations, and the changes among them, in the context of classical elastomechanics. The concepts of twisting, linkage and writhing are explained. Simple experiments on a twisted linear-elastic rod are described, and it is shown that although the circular and interwound forms may be modeled in this way, the toroidal form does not occur, being mechanically unstable. Theoretical energy calculations by Levitt on bent and twisted DNA show that DNA exhibits a particular kind of nonlinear elasticity in which there is an unusual coupling between bending and twisting. The aim of the paper is to show qualitatively that this special kind of elasticity can stabilize the toroidal form of closed circular DNA.
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  • 53
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    Biopolymers 19 (1980), S. 1357-1374 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Light-scattering, viscosity, and sedimentation experiments on aqueous solutions of k-carrageenan show that this sulfated polygalactose is an expanded flexible random coil. This expansion is due to long-range interactions that are predominantly electrostatic. Extrapolation of viscosity data to infinite ionic strength provided values for the intrinsic viscosity which were subjected to the Stockmayer-Fixman analysis, giving a value for the Mark-Houwink coefficient under theta-conditions, Kθ, of 0.27. The characteristic ratio, C∞, under these conditions is 7.8, and the conformation factor σ is 2. In a solution of 0.118 ionic strength, where a Mark-Houwink exponent aη of 0.86 is found, the radii of gyration calculated from viscosity data are lower than those found from the angular dependence of scattered light. On the other hand, the radius of gyration found from the sedimentation rate agrees well with the light-scattering radius. The relations between molecular parameters are corrected for the poly-dispersity of the sample.
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    Biopolymers 19 (1980), S. 1407-1414 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 19 (1980) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 56
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    Biopolymers 19 (1980), S. 1475-1489 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An approximate analytic expression for the translational friction coefficient of a toroid modeled as a continuous shell of frictional elements is derived using the Kirkwood approximation. The accuracy of this expression was determined by comparing the friction coefficients predicted by it to those predicted by extrapolated shell-model calculations using the modified Oseen tensor. To show that these calculations do indeed yield the correct friction coefficients, actual translational friction coefficients were determined by observing settling rates of macroscopic model rings or toroids in a high-viscosity silicone fluid. Our conclusion is that the approximate expression yields friction coefficients that are about 1.5-3% low for finite rings. For thin rings, a comparison is also made with the exact result of Yamakawa and Yamaki [J. Chem. Phys. 57, 1572 (1972); 58, 2049 (1973)] for the translational friction of plane polygonal rings. This comparison shows that the approximate expression yields results which are low by 2-3% unless the rings are extremely thin, in which case the error is larger. In the limit of an infinitely thin ring the approximate expression reduces to the Kirkwood result [J. Polym. Sci. 12, 1 (1954)], which is low by 8.3%. We discuss briefly how this work may be useful in determining the structure of DNA compacted by various solvent-electrolyte systems and polyamines.
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    Biopolymers 19 (1980), S. 1451-1474 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Internal Brownian motions of clean φ29 and λ-DNAs have been studied using photon-correlation techniques at both visible (λ0 = 632.8 nm) and uv (λ0 = 363.8 nm) wavelengths. The present dynamic light scattering data, which extend to K2 = 19 × 1010 cm-2, can in every case be satisfactorily simulated by a Rouse-Zimm model polymer with an appropriate choice of the three model parameters. The effects of pH, salt concentration, single-strand breaks, and molecular weight on those model parameters have also been investigated. Intact clean DNAs exhibit surprisingly little variation with pH from 7.85 to 10.25, with salt concentration from 0.01 NaCl to 5.4M NH4Cl, or with molecular weight or GC content. The single-strand breaks have no effect at pH 9.46, but produce dramatic changes in the model parameters at pH 10.0 and 10.25, indicating the introduction of titratable joints at those pHs. The failure of either single-strand breaks or a large change in GC content to alter the model parameters in the neutral pH range is a strong indication that local denaturation is not required for those flexions and torsions that dominate the relaxation of fluctuations in the scattered light. The Langevin relaxation time for the slowest internal mode of a particular Rouse-Zimm model derived from the dynamic light scattering data is compared with pertinent literature data extrapolated to the same molecular weight. The present algorithm for determining model parameters from the light-scattering Dapp vs K2 curve actually yields a Langevin time in fairly good agreement with the literature value. For unknown reasons the light-scattering D0 values generally exceed those obtained from the molecular weight and sedimentation coefficient by about 20%.
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  • 58
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    Biopolymers 19 (1980), S. 1507-1515 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Raman spectra of polyribouridylic acid excited in the uv region, from 363 to 290 nm, are reported. The conformational changes of the polymer from random coil to ordered structure with stacked bases at high and low temperature, respectively, are reflected by important changes in the Raman line intensities; this Raman hypochromism is itself a function of the excitation wavelength - its profile has been determined and shows negative values in the region of 290 nm (near resonance), i.e., hypochromism becomes hyperchromism. Thus the knowledge of the hypochromism excitation profile is important in following order-disorder transition of a polymer using resonance Raman spectroscopy. Theoretical attempts are proposed for explanation, involving not only the relative variations of the molar extinction coefficient on the order-disorder transition of the polymer, but also the damping factors of the vibronic levels. The theoretical curve is found to fit adequately the experimental data over the excitation range, using only the frequency of the O-O transition of uracil and a vibronic linewidth of 2200 cm-1.
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  • 59
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    Biopolymers 19 (1980), S. 2177-2190 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The preferential interaction of sodium poly(α-L-glutamate) and poly(α-L-glutamic acid) with the solvent components in water/2-chloroethanol mixtures has been determined using density-increment measurements. The degree of preferential interaction was deduced from the density increments at constant molality of 2-chloroethanol and at constant chemical potential of 2-chloroethanol. Sodium poly(α-L-glutamate) and poly(α-L-glutamic acid) are both preferentially hydrated in the whole range of solvent composition. A dehydration process occurs during the 2-chloroethanol-induced coil-to-helix transition of sodium poly(α-L-glutamate). This dehydration process was attributed to the release of some moles of water from the neighborhood of the peptide bond during the nucleation of the helix. After the conformational transition, sodium poly(α-L-glutamate) is solvated by one 2-chloroethanol molecule. The location of water and 2-chloroethanol molecules in the different parts of the residue (more polar and less polar portions) is also discussed.
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    Biopolymers 19 (1980), S. 2223-2245 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Complex formation between tryptamine and mononucleotides and dinucleoside phosphates containing adenine and/or cytosine has been studied at five pD's ranging from 1.1 to 7.4 by proton magnetic resonance spectroscopy. Chemical shifts of base ring protons and the ribose anomeric proton in the nucleotides and indole ring protons in tryptamine were monitored and their changes with pD and intermolecular interactions interpreted qualitatively. Stacked complexes were found to exist at all pD's in the range studied. Complex geometries differ depending on pD. An electrostatic interaction between the tryptamine amino group and the nucleotide phosphate group contributes to complex formation above pD 4 but is not strong enough to shift the dinucleoside phosphate equilibrium towards the unstacked conformer.
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  • 61
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    Biopolymers 20 (1981), S. 169-185 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The IR data for the R1 CO-O-CHR2-CO-NHR3 derivatives are interpreted in terms of a H…π interaction involving the N—H bond and the π orbitals of the ester function and giving rise to a high ν(C=O) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values φ # -90°, ψ # 0°. The H…π interaction in MeCO-L-Lac-NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(C=O) ester or amide frequency of the middle function in β-folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.
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    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 20 (1981), S. 251-268 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double-strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.
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  • 64
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The crystal structures of L-3,4-dehydroproline, t-butoxycarbonyl-L-3,4-dehydroproline amide, and acetyl-L-3,4-dehydroproline amide have been determined. L-3,4-Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t-butoxycarbonyl-L-3,4-dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl-L-3,4-dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L-3,4-dehydroproline is 0.046 based on 529 reflections; for t-butoxycarbonyl-L-3,4-dehydroproline amide, 0.050 based on 792 reflections; and for acetyl-L-3,4-dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t-Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl-L-3,4-dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present φ and ψ values corresponding to those of a right-handed α-helical conformation (conformation A), the t-Boc and acetyl derivatives both have φ and ψ values corresponding to a collagenlike conformation (conformation F).
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    Biopolymers 20 (1981), S. 359-371 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α-chains and β- and γ-components are 1.550 ± 0.08 × 10-7, 1.000 ± 0.05 × 10-7, and 0.835 ± 0.04 × 10-7 cm2/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α-chain), 21.5 nm (β-component), and 25.7 nm (γ-component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α-chains and β-and γ-components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.
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    Biopolymers 20 (1981), S. 387-397 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichroic spectra and oscillator strengths of the π-π transition near 190 nm are calculated for helical (Gly)6 and (Ala)6 at 30° intervals of the backbone torsion angles (φ,ψ) over the range -180° ≤ φ ≤ -60°, -60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)6 at (φ,ψ) angles corresponding to the α-helix, the poly(Pro) II helix, a collagen single helix, a poly-(MeAla) helix, and single β-helices are found to agree well with most of the available experimental data.
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  • 67
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the fluorinated antimalarial drug fluoroquine [7-fluoro-4-(diethyl-amino-1-methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and 19F-nmr chemical-shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well-known analog chloroquine. At low drug-to-base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (Tm) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the 19F-nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D2O vs H2O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. 19F-nmr relaxation experiments were carried out to measure the spin-lattice relaxation time (T1), 19F{1H} nuclear Overhauser effect (NOE), off-resonance intensity ratio (R), off-resonance rotating-frame spin-lattice relaxation time (T1ρoff), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton-fluorine dipolar and chemical-shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine-DNA complex can be well described by a motional model incorporating long-range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Empirical conformational energy calculations have been carried out for N-methyl derivatives of alanine and phenylalanine dipeptide models and N-methyl-substituted active analogs of three biologically active peptides, namely thyrotropin-releasing hormone (TRH), enkephalin (ENK), and luteinizing hormone-releasing hormone (LHRH). The isoenergetic contour maps and the local dipeptide minima obtained, when the peptide bond (ω) preceding the N-methylated residue is in the trans configuration show that (1) N-methylation constricts the conformational freedom of both the ith and (i + 1)th residues; (2), the lowest energy position for both residues occurs around φ = -135° ± 5° and ψ = 75° ± 5°, and (3) the αL conformational state is the second lowest energy state for the (i + 1)th residue, whereas for the ith residue the C5 (extended) conformation is second lowest in energy. When the peptide bond (ωi) is in the cis configuration the ith residue is energetically forbidden in the range φ = 0° to 180° and ψ = -180° to +180°. Conformations of low energy for ωi = 0° are found to be similar to those obtained for the trans peptide bond. In all the model systems (irrespective of cis or trans), the αR conformational state is energetically very high. Significant deviations from planarity are found for the peptide bond when the amide hydrogen is replaced by a methyl group. Two low-energy conformers are found for [(N-Me)His2]TRH. These conformers differ only in the φ and ψ values at the (N-Me)His2 residue. Among the different low-energy conformers found for each of the ENK analogs [D-Ala2,(N-Me)Phe4, Met5]ENK amide and [D-Ala2,(N-Me)Met5]ENK amide, one low-energy conformer was found to be common for both analogs with respect to the side-chain orientations. The stability of the low-energy structures is discussed in the light of the activity of other analogs. Two low-energy conformers were found for [(N-Me)Leu7]LHRH. These conformations differ in the types of bend around the positions 6 and 7 of LHRH. One bend type is eliminated when the active analog [D-Ala6,(M-Me)Leu7]LHRH is considered.
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  • 69
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Based on steric and electrostatic considerations, the prerequisites for binding to DNA via the intercalation mechanism are proposed. Steric contour energy curves are presented to demonstrate the region inaccessible to an intercalant. They are calculated with a 6-n (n = 14) potential. This method is a soft potential analog of an excluded-volume approach. Electrostatic contours on the steric surface illustrate the relatively positive and negative regions of the binding site. The principal intercalation sites, predicted to fit into B-DNA via a tetramer-duplex unit, and the unconstrained dimer-duplex units, obtained in crystal structures, are examined. These contours illustrate the requirements of size, conformation, and net atomic charges necessary for intercalation and optimum binding. Based on the limited space available for intercalation by the presence of the backbone and the maximum base-pair separation of 8.25 Å, an Essential Metabolite Exclusion Hypothesis is presented.
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  • 70
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    Biopolymers 20 (1981), S. 345-357 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In carbonate buffer at pH 10.5, a transparent solution of poly(L-lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β-structure and α-helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α-helix and β-structure was observed as a function of either poly(L-lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.
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  • 71
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    Biopolymers 20 (1981), S. 707-718 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Observations of induced circular dichroism (CD) bands in chloroform solution demonstrate the formation of specific, asymmetric complexes of the aromatic ligands 2-pyridone and 2,6-dichlorobenzoic acid with cyclic dipeptides of the general formula cyclo(L-Pro-X). The induced CD changes sign with the configuration of X due to subtle influences of the side chain on the geometry of the complex. Computations of interaction energies suggest that a plausible model for the complex of an aromatic ligand with the -CONH- of the cis secondary amide is a nearly planar arrangement of six heavy atoms in a ring containing two hydrogen bonds. The observed CD is matched by that computed for a tilt of the aromatic ligand toward the side chain of X. Binding constants were determined from the induced CD as a function of ligand concentration. For dichlorobenzoic acid these are about 450m-1 for the secondary amide and 50m-1 for the tertiary amide. For pyridone the binding constant is about 45m-1 for either the secondary or tertiary amide. For comparison self-dimerization constants determined by vapor-pressure osmometry in chloroform solution at 25°C are 870, 350, 50, and 20m-1 for pyridone, benzoic acid, dichlorobenzoic acid, and cyclo(L-Pro-Gly), respectively.
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  • 72
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    Biopolymers 20 (1981), S. 803-816 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton and phosphorus nmr have been used to investigate the double-helical structures of polyriboadenylic acid [poly(A)] formed in acidic solutions (pH 〈 6). The results obtained at low pH (∼4.5) are consistent with the model for the acid poly(A) double helix proposed by Rich [Rich, A., Davies, D. R., Crick, F. H. C. & Watson, J. D. (1961) J. Mol. Biol. 3, 71-86]. Other models that have been proposed are inconsistent with the nmr data. The nmr measurements have also been used to examine the conformation of poly(A) helix in the half-protonated state. Although the base-stacking arrangement of this state is similar to that observed in the more extensively protonated low-pH state, the phosphate backbone conformation is different from that found in either the neutral or low-pH structures.
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  • 73
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A study of the near-uv CD spectrum of lysozyme was carried out in the presence and absence of the inhibitor tri-N-acetylglucosamine, and theoretical chiroptical calculations based on the tetragonal crystal structure of the enzyme and the enzyme-inhibitor complex were performed. The results of these calculations indicate that the near-uv CD spectrum of lysozyme can be adequately explained in terms of negative rotatory strengths arising from the tryptophan 1La (293-300 nm) and the disulfide n-σ* bands (250 rm), and positive rotatory strength contributions from the tryptophan 1Lb bands (291 nm) and the tyrosine 1Lb bands (275 nm). Contributions to the rotatory strength of each band were approximated in terms of specific interactions between chromophores. It was found that the rotatory strength of most of the near-uv transitions arises primarily from coupling interactions involving other side-chain chromophores and amide groups which are in close proximity. Changes which are observed in the lysozyme CD spectrum on binding of tri-N-acetylglucosamine may be explained in terms of changes in the rotatory strength which result from interactions of the 1La transitions of the active-site tryptophans with the acetamide groups of the inhibitor. The reasonable agreement which is found between the experimental and calculated rotatory strengths implies that the crystal conformation of lysozyme must resemble the solution conformation.
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  • 74
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    Biopolymers 20 (1981) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 75
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    Biopolymers 20 (1981), S. 39-51 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod-Wyman-Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this constant.
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  • 76
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    Biopolymers 20 (1981), S. 65-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200-320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first-approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in solution.
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  • 77
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Photon-correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA2Glu and yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 105M-1 in the absence of magnesium to 1.5 × 106M-1 in 10 mM Mg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.
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  • 78
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    Biopolymers 20 (1981), S. 231-235 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 79
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    Biopolymers 20 (1981), S. 237-240 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 80
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    Biopolymers 20 (1981), S. 243-247 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 81
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A conformational quantum-mechanical study of (Gly-Phe-Pro) and (Gly-Pro-Phe) repeating tripeptide sequences has been carried out with the PCILO method. Using appropriate molecules as a model, we investigated the conformational possibilities of each in situ residue. Computations have been done taking into account the two typical pyrrolidine ring puckering and the most favorable orientations of the phenylalanyl side chain. Major conclusions drawn from this study are that the phenylalanyl can be accommodated at both second and third positions in the sequence without preventing the formation of triple-helix conformation. However, the analogy observed between the rotational possibilities around the second residue of Gly-Pro-Pro and Gly-Phe-Pro indicates that phenylalanyl in the second position favors the triple-helix formation.
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  • 82
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    Biopolymers 20 (1981), S. 327-343 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the nucleosome core particle in solution has been studied by neutron scattering using the full-contrast variation technique, which reduces the experimental spectra to three fundamental scatter functions holding information on shape and structure. Systematic calculations of the fundamental scatter functions expected from proposed core-particle models have been compared with the observed functions and show that the neutron-scattering criteria severely restrict the number of models which can be valid for the structure in solution. The best model for the core particle in solution has a hydrophobic histone core about which 1.7 ± 0.1 turns of DNA are wrapped at a pitch between 3.0 and 3.5 nm. This core contains most of the histone and has an average thickness of 4 nm and diameter 6.4-7.5 nm. While solution scattering is not able to specify uniquely the actual shape of the core to high resolution, all models which are possible for the shape of the core to a resolution justified by the data have been considered. It is clear that cylindrical or wedge shapes compatible with the above dimensions are valid structures. A hole probably penetrates the histone core, but the data do not allow a diameter greater than 1 nm. Available evidence suggests that about a quarter of the total histone is outside the core.
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  • 83
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between published vicinal proton-proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L-proline, 4-hydroxy-L-proline, 4-fluoro-L-proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated: (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substitutents on 3JHH; (2) an empirical correlation between proton-proton torsion angles and the pseudorotational parameters P and τm is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least-squares procedure. Two pseudorotation ranges were considered, classified as type N (χ2 positive sign) and type S (χ2 negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, τN, PS, τS) and the equilibrium constant K. The present results indicate that, in general, the geometrical properties found in x-ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:1 conformational equilibrium between well-defined N- and S-type forms. Introduction of an amide group at the C-terminal end has no observable effect on this equilibrium, but the formation of a peptide bond at the imino nitrogen site results in a pronounced, but not exclusive, preference for an S-type form which is roughly 1.1 kcal/mol more stable than its N-type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N-type state, but N-acetylation results in the appearance of a minor (S-type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77-88%) corresponds to the N-type conformer observed in the solid state; the minor S-form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4°-8° in most cases. In all, the proline ring is far less “floppy” than hitherto assumed.
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  • 84
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard-core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.
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  • 85
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    Biopolymers 20 (1981), S. 2121-2136 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This report presents a quantitative test of the ability of the counterion condensation theory to describe the proton-induced lowering of DNA melting temperature. From a general approach of Record et al. [Record, M. T., Anderson, C. F. & Lohman, T. H. (1978) Q. Rev. Biophys. 11, 103-178], we have obtained an expression that may be computer-fitted to the experimental data by numerical minimization of χ2. To do this, in addition to the assumptions made by Record et al., it was necessary to suppose that the interchange between protons and sodium is independent of pH and, due to the absence of data, take the enthalpies of protonation as thermally independent over the experimental temperature range. The dependences of the enthalpy of denaturation at neutral pH on sodium concentration and on G + C content were taken from literature. In the fitting process we have used 250 melting temperatures obtained at different pH and sodium concentrations for various natural DNAs. The theoretical expression gives a good quantitative description of the G + C and sodium concentration influences on the phenomenon but is only qualitative with respect to the dependence of dT/d log[Na+] on the pH. The adjusted pK values for the bases in denatured DNA agree with those for isolated deoxynucleosides. Interchange between sodium and protons is found to be less than 1:1. Calculated protonation enthalpies are ill-defined because of their low numerical influence. In short, it appears that the theory gives a good description of most of the aspects of the phenomenon even if it has some shortcomings, perhaps due to the great number of assumptions.
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  • 86
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    Biopolymers 20 (1981), S. 2137-2142 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the kinetics of replacement of O2 by CO in hemoglobin in the presence and absence of organic cosolvents (methanol, ethanol, iso-propanol, n-propanol, formamide, acetamide, N-methyl-formamide) and at 10 and 25°C. Quantitative analysis of the results indicates that these cosolvents do not affect the intrinsic binding constants of ligands to the heme when hemoglobin is in the R conformation. The present results confirm the previously reported suggestion that the effects of the above cosolvents on the oxygen affinity of hemoglobin are related to effects on the T ⇄ R conformational equilibrium.
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  • 87
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    Biopolymers 20 (1981), S. 2195-2202 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Preparations have been made of acid-soluble collagens whose telopeptides have suffered different levels of proteolytic attack. The collagens with more intact telopeptides form fibrils more rapidly than those with degraded telopeptides. In addition, we have shown that a high molecular weight aggregate rich in the carboxyterminal CNBr peptide, α1CB6, can be found in cyanogen bromide digests of fibrils formed from intact collagen. A similar aggregate is found in CNBr digests of native tendons. The aggregate formed in fibrils assembled in vitro can be stabilized by reduction, and its generation is strongly dependent on the presence of intact telopeptides. The latter point is the most objective evidence that to reproduce the characteristics of native fibrils in vitro, the collagen telopeptides must be preserved from proteolysis.
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  • 88
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    Biopolymers 20 (1981), S. 2225-2241 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present an alternative to the common lattice model for nonspecific DNA-protein interactions by using ligands that translate freely along the polynucleotide instead of binding to distinct lattice sites along the polynucleotide chain. The general model we present corresponds to a one-dimensional continuum gas and is referred to as the “continuum model” to distinguish it from the general lattice model. Explicit expressions are obtained for the binding isotherm equation for two version of the continuum model, including the effects of binding-site exclusion and attractions between bound ligands. Theoretical results are compared to those obtained from the McGhee-von Hippel (1974) analysis of the lattice model with cooperative interactions between ligands occupying more than one lattice site. Practical applications of the continuum model are illustrated by analyzing (i) the noncooperative binding to single-stranded DNA by RNase (Jensen and von Hippel, 1976), and (ii) the highly cooperative binding to poly(rA) by a proteolyzed fragment of the gene 32 protein of phage T4 (Lonberg et al., 1981).
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  • 89
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The structure of water and its interaction energy with a fragment of B-DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen-bonded filaments of water are reported and discussed. The stabilization of the B-conformation induced by the solvent with counterion (“ion-induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x-ray and neutron beam) data on DNA insolution.
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  • 90
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational response of calf thymus DNA to solvent conditions altered by varying amounts of ethanol and NaCl has been monitored by circular dichroism (CD). These measurements, which extend over a much greater range of conditions than previously examined, reveal (above critical concentrations of ethanol and salt) a condensed form of the macro-molecule with unusually large positive ellipticity in the 250-300-nm region [the Ψ(+) state]. Mere increase in NaCl concentration at constant 35% (v/v) concentration of ethanol suffices to convert such Ψ(+) samples - via a series of intermediate forms with CD spectra resembling those of A-DNA, then B-DNA - into Ψ(-) states having anomalously large negative ellipticity similar to the well-known Ψ(-) forms produced by above-critical concentrations of poly-(ethylene oxide) and salt. These ethanol/salt-induced transitions are all completely reversible and can occur without formation of any visible precipitates. We suggest that they represent predominantly tertiary structural changes of B-form DNA molecules analogous to the changes which occur in several other systems where Ψ(+) ⇌ Ψ(-) interconversion has been reported. A “skein-of-yarn” model for the condensed tertiary (and quaternary, i.e., aggregated) state of the DNA affords one possible explanation for the inversions of ellipticity in all these cases. Such a model accords well with the accepted description of cholesteric liquid crystals.
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  • 91
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    Biopolymers 21 (1982), S. 17-24 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Computer simulation shows that the time required to attain near sedimentation equilbrium is dramatically reduced by a two-step initial loading in which a macromolecular solution at low or zero concentration is layered above one at a higher concentration. To achieve the minimum time requires a good estimate of the molecular weight, but at least a 50% reduction in time can be achieved if the molecular weight of the macromolecule is known only within a factor of 2. Numerical solutions to the differential equation of the ultracentrifuge are calculated using the finite element method. An efficient Gaussian elimination algorithm can be used to minimize calculation time and computer storage requirements.
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    Biopolymers 21 (1982), S. 79-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aldehydes present in acid-soluble type I collagen react with pyrenebutyrylhydrazine to form various types of complexes under different reaction conditions. These complexes exhibit one or more of three different pyrene fluorescence bands: monomer, excimer, and aggregate fluorescence. Collagen, whose aldehydes have been reduced with NaBH4, does not react with this fluorescent hydrazine, confirming that the hydrazine reacts specifically with aldehyde groups to form hydrazones. The absence of a reaction with pepsin-treated collagen also shows that the fluorescent labels are primarily in the nonhelical terminal telopeptides. Upon dialysis, the pyrene label bound to a saturated aldehyde in an α-chain is lost; whereas that bound to an unsaturated aldehyde remains on the protein. The pyrene monomer fluorescence in the β-chain of old collagen is stronger than that of young collagen. The formation of the pyrene excimer fluorescence implies the proximity of two pyrene molecules, probably attached to two adjacent aldehydes. Upon changing from acidic to neutral pH, both excimer and aggregate fluorescence bands disappear within a few seconds, revealing a very rapid alteration at the telopeptides.
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  • 93
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    Biopolymers 21 (1982), S. 147-157 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe conditions which lead to complete helix formation of poly(I) in the presence of NH4+. Binding of NH4+ is shown to be specific in the presence of Li+, which does not by itself support helix formation under these conditions. The NH4+-poly(I) complex is characterized by uv, CD, and ir spectroscopy. The CD spectrum is strikingly different from those of the Na+ or K+ complexes, the first extremum being changed from negative for the metal ions to positive for NH4+. A stereospecific model is proposed for the NH4+-poly(I) helix in which the N of NH4+ is located on the axis of the four-stranded helix, midway between planar tetramers formed by the bases. The model is consistent with the tetrahedral symmetry of NH4+, the requirement for four acceptable hydrogen bonds, the observed stability of the helix, and the accepted geometry of the backbone.
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  • 94
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    Biopolymers 21 (1982), S. 159-167 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It has recently been proven that the counterion condensate around an isolated line charge in an electrolyte, as characterized by nonlinear Poisson-Boltzmann theory, is an encapsulating δ-function. Here the identical result is shown to hold in the framework of the polyelectrolyte theory of Fuoss, Katchalsky, and Lifson. The proof fully exploits analytic solutions to the differential equation which are not available for the nonlinear, cylindrical Poisson-Boltzmann equation.
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  • 95
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    Biopolymers 21 (1982), S. 203-218 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The extent and modes of binding of the divalent metal ions Mn2+ and Co2+ to DNA and the effects of salt on the binding have been studied by measurements of the effects of these paramagnetic metal ions on the longitudinal and transverse relaxation rates of the protons of the solvent water molecules, a technique that is sensitive to overall binding. The number of water molecules coordinated to the DNA-bound Mn2+ and Co2+ is found to be between five and six, and the electron spin relaxation times and the electron-nuclear hyperfine constants associated with Mn2+ and Co2+ are little or not affected by the binding. These observations indicate little disturbance of the hydration sphere of Mn2+ and Co2+ upon binding to DNA. An average 2-3-fold reduction in the exchange rate of the water of hydration of the bound metal ions and an order-of-magnitude increase in their rotational correlation time are attributed to hydrogen-bond formation with the DNA. The binding constants of Mn2+ to DNA, at metal concentrations approaching zero, are found to be inversely proportional to the second power of the salt concentration, in agreement with the predictions of Manning's polyelectrolyte theory. A remarkable quantitative agreement with the polyelectrolyte theory is also obtained for the anticooperativity in the binding of Mn2+ to DNA, although the experimental results can be well accounted for by another simple electrostatic model. The various modes of binding of divalent metal ions to DNA are discussed.
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  • 96
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    Biopolymers 21 (1982), S. 265-275 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dc electrical conductivity of films of the polyelectrolyte complexes of glycol chitosan (GlChi) with the sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) was measured at temperatures above and below room temperature. The maximum field strength in the thinnest film used amounted to 3 × 104 V/cm. A plot of normalized current against the reciprocal of the absolute temperature revealed two regions with different slopes, and activation energies in these two regions have been obtained for all the complexes. The activation energies in the high-temperature region vary from 0.85 to 1.18 eV and in the low-temperature region from 0 to 0.22 eV. Reasons are given to show that the conductivity is probably ionic. Near room temperature, the current-voltage relation is almost linear in the GlChi-DS complex, while in the other three complexes the current varies as a power n of the voltage with the value of n ranging from 1.7 to 2.5. A rise in temperatures causes an increase in the slope of the log I vs log V plot in GlChi-DS and GlChi-CMC complexes. The nonlinear current-voltage relation is ascribed to a space-charge-limited conductivity.
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  • 97
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    Biopolymers 21 (1982), S. 301-319 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Five different glucomannan samples were recrystallized from dilute solution. Depending on the experimental conditions, the crystals obtained could be identified as corresponding to the mannan I (anhydrous precipitate of more or less regular lozenge-shaped crystals) or mannan II (hydrated gel-forming pseudo-fibrillar precipitate). High-molecular-weight material, low temperature of crystallization, or a polar crystallization medium favored the mannan II polymorph, whereas a low-molecular weight, a high temperature of crystallization, and a crystallization medium of low polarity yielded the mannan I polymorph. Since the base-plane unit-cell dimensions are fairly constant with respect to variation of glucose, it is likely that isomorphous replacement of mannose by glucose occurs in glucomannan crystallization; the data also indicate that perfection of the glucomannan crystals was reduced in specimens having a high glucose:mannose ratio. The oriented crystallization of glucomannan on cellulose microfibrils was also studied under conditions where the mannan I polymorph was obtained. This gave shish-kebab structures that were characterized.
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  • 98
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The primary hydration process of native biopolymers is analyzed in a brief review of the literature, pertaining to various aspects of biopolymer-water systems. Based on this analysis, a hydration model is proposed that implies that the solution conformation of native biopolymers is stable at and above a critical degree of hydration (hp′ = 0.06-0.1 g H2O/g polymer). This water content corresponds to the fraction of strongly bound water, and amounts to ∼20% of the primary hydration sphere. In order to test this model, detailed sorption-desorption scanning experiments were performed on a globular protein (α-chymotrypsin). The results obtained are consistent with the proposed hydration model. They show that under certain experimental conditions, sorption isotherms can be obtained that do not exhibit hysteresis. These data represent equilibrium conditions and are thus accessible to thermodynamic treatment. Valid thermodynamic functions, pertinent to the interaction of water with biopolymers in their solution state, can be obtained from these sorption experiments.
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  • 99
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    Biopolymers 21 (1982), S. 451-458 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The light scattering of bovine serum albumin (BSA) has been measured at protein concentration up to 90 g/L and at pH values between 4.4 and 7.6. The dependence of scattering on both protein concentration and pH may be quantitatively accounted for by a simple extension of the hard-sphere model for protein solutions [Ross, P. D. & Minton, A. P. (1977) J. Mol. Biol. 112, 437-452] allowing for electrostatic repulsions between molecules. According to the extended model, the radius of the effective hard spherical particle representing BSA varies with the net electrical charge of the BSA molecule in a manner which may be calculated from electrostatic theory.
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  • 100
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    Biopolymers 21 (1982), S. 475-497 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A complete analysis of all possible conformations with correct hydrogen bonds of the collagen II type was performed on the basis of developed simultaneous equations. Using a unimodal search (by varying Ψ3), the energetically favorable structure was obtained. No other energetically satisfactory structural solutions are possible. The next aim was to obtain a precise model of the molecule. The program used includes a subroutine for continual deformation of the pyrrolidine rings. The set of parameters determining the structure consists of 14 independent variables (8 dihedral and 6 bond angles). As starting points for the energy optimization, conformations produced by scanning and some structures from previous work were used. The final structures (practically the same for both polymers) have helix parameters h = 0.285 nm and t = 52°, which are in excellent agreement with the 7/2 symmetry of diffraction data. The conformations of the pyrrolidine rings are of the B type, i.e., C2-Cβ-exo-Cγ-endo. For both polypeptides, the conformations of imino acids in position 3 of the triplet are the same; in position 2, however, they are slightly different. The difference in diffraction patterns for the 7/2 and 10/3 helices is discussed.
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