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  • 1
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    Entomologia experimentalis et applicata 86 (1998), S. 175-182 
    ISSN: 1570-7458
    Keywords: Aleyrodidae ; greenhouse whitefly ; nitrogen ; host selection ; oviposition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Tomato plants, Lycopersicon esculentum Miller cv 'Tres Cantos', were supplied with high (308 ppm), medium (140 ppm) and low (84 ppm) nitrogen doses in order to determine the influence of nitrogen fertilization on feeding and oviposition site selection by greenhouse whitefly adults, T. vaporariorum (Westwood). The nitrogen and water content was higher in plants supplied with 308 N ppm than in plants with medium or low nitrogen doses and no differences were found in soluble sugar content. The leaves of the upper plant stratum (leaves 1–5) had the greatest nitrogen and water content, independent of the nitrogen dose applied. The plants were exposed to T. vaporariorum adults into a greenhouse under two current (late autumn-winter and spring-early summer) situations of the tomato crop in the Mediterranean area. The distribution of whitefly adults on the plants was affected by the nitrogen dose in both experimental conditions, the number of adults was higher on the plants supplied with high nitrogen dose. Within plants, adult distribution was affected by leaf position, the upper plant stratum being preferred for feeding. Whitefly females selected for oviposition and laid more eggs on plants and leaves of plants with higher nitrogen and water contents. We conclude that whitefly host selection for feeding and ovipositing are related to differences in nitrogen and water content of the host plant.
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  • 2
    ISSN: 1570-7458
    Keywords: fecundity ; host plant quality ; Pistia stratiotes ; Spodoptera pectinicornis ; nitrogen ; trichomes ; oviposition ; biological control of weeds
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We determined the influence of larval host quality of the floating aquatic weed Pistia stratiotes L. (Araceae) on the fecundity and egg distribution of the biological control agent Spodoptera pectinicornis (Hampson) (Lepidoptera: Noctuidae). Different nutritional levels were produced by growing plants with relatively low and high levels of nitrogen, phosphorus and potassium fertilizer. Female and male pupal biomass were significantly greater when the larvae were fed leaves from the high fertilizer plants. Although the fertilizer treatments did not significantly influence total fecundity, there was an indirect effect as adults from larger pupae were more fecund. Regardless of treatment, ovipositing females formed a depression in the leaf surface by removing trichomes into which they deposited the egg masses. Most of the egg masses were laid on the lower leaf surface, on leaf positions 5–8 (counting from the young inner to the outer leaves) and during days 1–2 post-eclosion. Most of the eggs were laid in masses but about 12% were solitary. Females fed the low fertilizer treatment laid a greater proportion (mean ± s.e.) of their eggs as solitary eggs (17.3 ± 3.4% of total eggs) than did females fed the high fertilizer treatment (8.3 ± 2.3% of total eggs). The increased percentage of solitary eggs laid by the females from the low quality larval diet may be an adaptive response to decrease competition among the progeny.
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  • 3
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    Acta biotheoretica 33 (1984), S. 35-50 
    ISSN: 1572-8358
    Keywords: Evolution ; falsification ; Darwinism ; philosophy of science
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called “the theory of common descent”), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.
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  • 4
    ISSN: 1570-7458
    Keywords: Bemisia argentifolii ; Encarsia formosa ; poinsettia ; parasitoids ; nitrogen ; tri-trophic level interactions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract More wasps of Encarsia formosa Gahan (Hymenoptera: Aphelinidae) were found on fertilized poinsettias, Euphorbia pulcherrima (Willd.) (Euphorbiaceae), than on non-fertilized plants. Parasitization of Bemisia argentifolii Bellows & Perring (Homoptera: Aleyrodidae) by E. formosa was higher on plants treated with calcium nitrate than with ammonium nitrate or on control plants. In a no-choice test, host feeding by E. formosa was higher when hosts were on fertilized plants than when hosts were on control plants. The nitrogen content of whitefly pupae reared on plants treated with ammonium nitrate was higher than those on calcium nitrate-treated plants. Variability in the parasitization of B. argentifolii by E. formosa appears to be due to host plant-mediated differences in the whiteflies. E. formosa may be influenced by the nutritional suitability of the host, which influences whether wasps continue to oviposit, feed, or disperse.
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  • 5
    ISSN: 1570-7458
    Keywords: Brassica rapa ; B. juncea ; consumption rate ; glucosinolates ; growth rate ; indolyl ; isothiocyanate ; Mamestra configurata ; nitrogen
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Mamestra configurata (Walker) (Lep., Noctuidae) larvae were fed excisedBrassica juncea (commercial brown mustard) orB. rapa cv. Tobin (Canola) foliage of three plant growth stages-rosette (stage 2), stem elongation (stage 3) and flowering (stage 4). Relative consumption rates (RCRi) were not significantly different between the plant species. Within theB. juncea treatments, there were no significant growth stage differences in RCRi. However, withinB. rapa, RCRi increased with advancing plant growth stage. Larvae fedB. juncea foliage had significantly reduced relative growth rates (RGRi) compared to larvae fedB. rapa foliage. Within theB. juncea treatments, RGRi decreased with advancing plant growth stage. There were no significant growth stage differences in RGRi in theB. rapa treatments. RGRi was inversely proportional to the levels of isothiocyanate-releasing glucosinolates in theB. juncea treatments. RCRi was inversely proportional to the levels of indolyl glucosinolates in theB. rapa treatments. Levels of total phenols and catechols inB. juncea did not show any trend which could be related to growth stage effects in the insect nutritional indices. InB. rapa, levels of phenols and catechols in stage 3 and 4 foliage were lower than that of stage 2 foliage. Analyses of total nitrogen in field-grown plants showed reductions in percent nitrogen from rosette to flowering stage foliage. The response ofM. configurata to different growth stages of its host plants are discussed in relation to changing levels of allelochemicals and nitrogen.
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  • 6
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    Entomologia experimentalis et applicata 92 (1999), S. 205-216 
    ISSN: 1570-7458
    Keywords: Samea multiplicalis ; Spodoptera pectinicornis ; Pistia stratiotes ; waterlettuce ; nitrogen utilization efficiency ; compensatory feeding ; nitrogen ; biological control of weeds
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Compensatory responses of caterpillars fed low quality food include increased consumption and utilization of essential nutrients. Information about an insect's responses to nutritional challenges from their host plants could benefit weed biological control efforts in the selection and establishment of new agents. The target weed, Pistia stratiotes L. (Araceae) is a floating aquatic plant that has relatively low nitrogen levels which are further diluted with high water content. Efforts to establish the insect Spodoptera pectinicornis (Hampson) (Lepidoptera: Noctuidae) for biological control of P. stratiotes could benefit by examining the nutritional responses of a similar widely established lepidopteran species, Samea multiplicalis (Guenèe) (Lepidoptera: Pyralidae). Larvae of this species were fed leaves of P. stratiotes plants that had been fertilized (NPK) at high and low rates. The leaves of the fertilized plants had a 4.3-fold increase in nitrogen (dry weight) and a 1.6-fold increase in water content. The results suggest that no compensatory increases occurred in larvae fed leaves from the low fertilized plants as no changes were found in fresh mass consumption or nitrogen utilization efficiency. Consequently, development time from second-third instars to pupation was delayed about 3 days compared with larvae fed the high nitrogen leaves. Furthermore, consumption of nitrogen was only 30% and its accumulation into larval tissues was only 60% compared with the larvae fed the high fertilized leaves. The resulting larvae had both a final biomass and a growth rate that were reduced by 40%. Regardless of plant fertilizer level, the larvae fed at a rate 5–10 times greater than that of similar lepidopteran species consuming either low or high quality diets, suggesting that the S. multiplicalis larvae may be functioning at their biological limit for ingesting food.
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  • 7
    ISSN: 1572-8358
    Keywords: Animal cognition ; Evolution ; Representation ; Computation ; Significance ; Phenomenology ; Autonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A distinction is made between two definitions of animal cognition: the one most frequently employed in cognitive sciences considers cognition as extracting and processing information; a more phenomenologically inspired model considers it as attributing to a form of the outside world a significance, linked to the state of the animal. The respective fields of validity of these two models are discussed along with the limitations they entail, and the questions they pose to evolutionary biologists are emphasized. This is followed by a presentation of a general overview of what might be the study of the evolution of knowledge in animals.
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  • 8
    ISSN: 1570-7458
    Keywords: Coleoptera ; bruchidae ; anesthesia ; carbon dioxide ; nitrogen ; cold ; oviposition and mating
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The effect of anesthetizing with carbon dioxide, nitrogen, or low temperature on the reproductive behavior and fecundity of Callosobruchus subinnotatus was investigated. Males and females anesthetized with N2 as virgins had shorter recovery time, copulated earlier, and had shorter mating time than those subjected to CO2 or low temperature. Exposure of males and females to 2.0±0.5 °C for 10 min had the most profound effect on the recovery periods, copulation time, and duration of mating. Adults anesthetized with CO2 and low temperature laid fewer eggs than those anesthetized with N2. Females were more affected than males by the treatments, except when males were chilled for 10 min, and this prolonged the time for commencement of mating. The mode of anesthesia could affect egg production because vitellogenesis and choriogenesis take place in the imago stage of bruchids.
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  • 9
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    Entomologia experimentalis et applicata 64 (1992), S. 225-238 
    ISSN: 1570-7458
    Keywords: Lymantria dispar (L.) ; diet switching ; nitrogen ; specialization ; plant-animal interactions ; insect behavior
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Gypsy moth (Lymantria dispar (L.) (Lepidoptera: Lymantriidae)) larvae were reared from hatch on 1.25% N or 3.5% N artificial diet (previous diet) and switched reciprocally to the other diet (current diet) after molting into the second, third, fourth, or fifth instar. The nitrogen concentration of food consumed during previous instars had a strong residual effect on the growth rate in subsequent instars when a diet switch was made during instars two through four, but did not affect growth rate of fifth-instar larvae despite effects on food consumption and utilization. In early instars, larvae reared on 1.25% N artificial diet and then switched to 3.75% N diet had lower mass-adjusted growth rates than larvae continuously reared on 3.75% N diet. Conversely, larvae reared on 3.75% N diet and switched to 1.25% N had higher mass-adjusted growth rates than larvae reared continuously on 1.25% N diet. Relative to larvae previously reared on 1.25% N diet, fifth-instar male larvae previously reared on 3.75% N diet had slightly lower consumption rates, higher net growth efficiency (ECD), and higher gross growth efficiency (ECI). Larvae previously reared on 3.75% N diet tended to have lower food assimilation efficiency (AD) and lower nitrogen assimilation efficiency (AD(N)). Although both previous and current diet nitrogen concentration strongly affected larval growth and food utilization, the interaction term between these was not significant for any response variables except ECD and ECI. Because the interaction term reflects the effect of switching per se, the results indicate that there was a metabolic cost associated with switching, but no inherent net cost or benefit of diet-switching to growth.
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  • 10
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    Entomologia experimentalis et applicata 61 (1991), S. 7-16 
    ISSN: 1570-7458
    Keywords: Plutella xylostella ; Trichoplusia ni ; Hellula phidilealis ; Artogeia rapae ; nitrogen ; population growth ; cabbage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The effects of different nitrogen (N) fertilization rates (0, 45, 90, and 168 kg N/ha), plant nitrogen concentration, and plant biomass on abundance and population growth of diamondback moth, Plutella xylostella (L.), cabbage looper, Trichoplusia ni (Hübner), cabbage budworm, Hellula phidilealis (Walker), imported cabbageworm, Artogeia rapae (L.), and cross-striped cabbageworm, Evergestis rimosalis (Guenée), were investigated in Homestead and Sanford, Florida in 1987. The effects of these factors on the parasitization of P. xylostella were also examined. In Homestead, abundance of most insect pests and parasitized P. xylostella increased with an increase in the level of N applied and with an increase in plant biomass. Similar results were found in Sanford, although results were not consistently significant. Abundance of most insect pests was significantly positively correlated with plant N concentration. Multiple regression analyses indicated that foliar biomass was significantly more important than N fertilization rate and subsequent plant N concentration at predicting abundance of insect pests and parasitized P. xylostella on cabbage.
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  • 11
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    Entomologia experimentalis et applicata 77 (1995), S. 205-210 
    ISSN: 1570-7458
    Keywords: nitrogen ; maize ; lepidopterous stem and cob borers ; Sesamia calamistis ; Eldana saccharina ; Mussidia nigrivenella ; Cryptophlebia leucotreta ; dead hearts ; stem tunneling ; yields
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The influence of four nitrogen levels (0, 60, 90 and 120 kg N/ha) on growth of maize and development of lepidopterous pests was investigatdd in a field trial. Nitrogen had a positive effect on both plant growth variables (plant height, stem diameter and yield), and development and survival ofSesamia calamistis andEldana saccharina, and thereby increased the incidence of dead hearts and stem tunneling. However, the percent yield loss due to artificial infestation decreased with increasing N application rate from 20% to 11% in the in the 0kg/ha and 120kg/ha treatment, respectively. Using a multiple regression analysis, plant height, plant diameter and stem tunneling were found to be the most important variables explaining the variability in maize yield.
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  • 12
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    Entomologia experimentalis et applicata 92 (1999), S. 165-177 
    ISSN: 1570-7458
    Keywords: Chrysomelidae ; herbivory ; Asteraceae ; life history ; nitrogen ; plant quality ; season
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phytophagous insects which feed on the leaves of herbaceous host plants have to adapt their life histories to the fact that protein nitrogen is usually highest in growing tissues in spring. We monitored field populations of larvae and adults of three chrysomelid species (Galeruca tanaceti (L.) (main host Achillea millefolium (L.) Yarrow), Cassida rubiginosa (Mueller) (main host Cirsium arvense (L.) Scop.) and Oreina luctuosa (Suffrian) (host Centaurea scabiosa (L.)) together with the amount of protein nitrogen of their food resources and host plant biomass. As expected, the development of host quality, measured as concentration of protein nitrogen, and host plant biomass showed inverse trends during the season. The euryphagous G. tanaceti attacks Achillea early and profits from high nitrogen concentrations in the leaves. Occasional overexploitations of local populations of Achillea are compensated by the capacity to move to other host species. In C. rubiginosa, a species with a host range restricted to the Cardueae, the main larval feeding activity is postponed to a period when the nitrogen content of the host leaves had dropped to 50% of its initial value, but when host plant biomass had increased by 30%. In the monophagous O. luctuosa the larval development is synchronized with a still later phase of host phenology, at which the nitrogen content is below 50% but plant biomass has reached its maximum. There seem to be selection factors, which oppose the use of high quality food in spring and which force the latter two species to postpone their larval development to a later time in the year. This could be caused by numerous factors like, for example, mean daytime temperature. Later in the season the larvae have to cope with the low quality of their host plants. They have, however, the advantage of large quantities of food available. A laboratory study with adults and mature larvae of O. luctuosa shows that this species can overcome low levels of protein nitrogen either by selecting younger leaves with higher nitrogen concentrations or by increasing the daily food consumption rate (RCR) on leaves with a low level of nitrogen and by a prolongation of the feeding period. In this way the larvae compensate the effect of lower daily growth rates (RGR) and a lower food conversion index (ECI) on poor food quality: Regardless of the level of protein nitrogen there was no statistically significant difference in total gain of weight during the third-instar feeding period and in the weight at the end of the third larval stage. The three investigated chrysomelids show that there exists a broad spectrum of adaptations to overcome the dilemma of variable food quality.
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  • 13
    ISSN: 1572-8927
    Keywords: Supersaturation ; nitrogen ; cosolvent ; cetyltrimethylammonium bromide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The decomposition of ammonium nitrite in water creates a supersaturated solution of nitrogen. The same process occurs in water-organic solvent mixtures. Acetone, dioxane, dimethylsulfoxide (DMSO) and dimethylformamide (DMF) are the cosolvents used in this study. The limits of supersaturation of nitrogen (C SL /mol L−1) were determined in all of these solvent mixtures by releasing the dissolved gas sonicationally and measuring the volume of released gas. C SL was generally increased in the presence of cosolvents. The effectiveness sequence of organic solvents was found to be as DMF〈DMSO〈Dioxanet≅Acetone. Transportation period of small bubbles formed during sonication is changed by compositions of solvent mixtures. These periods may depend on the viscosity of the solution. Effects of the presence of cetyltrimethylammonium bromide were also studied. It was concluded that there may be a relation between the strength of the watercosolvent H-bonds and C SL and all of the measured quantities of this study were generally affected by micelle formation.
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  • 14
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    Journal of insect behavior 11 (1998), S. 179-189 
    ISSN: 1572-8889
    Keywords: open-air foraging ; caste ; polyethism ; litter feeder ; nitrogen ; termite
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Southeast Asian nasute termite Longipeditermes longipes forages on the open ground on leaf litter. Its monomorphic workers carry back food balls in their mandibles while dimorphic soldiers defensively surround the marching columns and the foraging patches. When mechanically disturbed, workers hide under the litter, whereas antennating soldiers face as closely as possible the source of disturbance. Foragers prefer the lower, nitrogen-rich layer of the litter. Soldier behavior and column organization (returning workers in the center lanes, outgoing workers in the two flanking lanes) are similar to those in the related genera Hospitalitermes and Lacessititermes, which, however, tend to forage above ground.
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  • 15
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    Journal of solution chemistry 13 (1984), S. 335-348 
    ISSN: 1572-8927
    Keywords: Solubility ; Henry's law coefficients ; Ostwald coefficients ; aqueous solutions ; nitrogen
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The solubility of nitrogen in pure liquid water was measured in the pressure range 45 to 115 kPa and in the temperature range 5 to 50°C. These data are used to obtain Henry coefficients H 2,1 (T,P s,1 ) at the vapor pressure P s,1 of water. The temperature dependence of H 2,1 (T,P s,1 ) is accounted for by both a Clarke-Glew (CG) type fitting equation, and a power series in T−1, as suggested by Benson and Krause (BK). The imprecision of our measurements is characterized by an average deviation of ±0.038% from a four-term CG equation, and by an average deviation of ±0.042% from a three-term BK equation. From the temperature variation of H 2,1 (T,P s,1 ) partial molar quantities referring to the solution process, such as enthalpies and heat capacities of solution, are obtained. They are given in tabular form, together with H 2,1 (T,P s,1 ) and derived Ostwald coefficients L∞, at rounded temperatures. Finally, experimental results are compared with values calculated via scaled particle theory.
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  • 16
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    Catalysis letters 13 (1992), S. 45-53 
    ISSN: 1572-879X
    Keywords: Ammonia ; synthesis ; nitrogen ; rate-determining step ; potassium promotion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The simple concept of a single rate-determining step, the dissociation of N2(a), in ammonia synthesis is inconsistent with experimental results. It is proposed that three reaction steps, N2(a) → 2N(a) (1) N(a) + H(a)→NH(a) (2) NH3(a)→NH3(g) (3) are dominant in determining the rate of synthesis. Under industrial conditions reactions (2) and (3) are more important than (1). The role of K+ as promoter in these reactions is discussed, especially as an “anchor” for adsorbed oxygen.
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  • 17
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    Catalysis letters 16 (1992), S. 159-164 
    ISSN: 1572-879X
    Keywords: Chemisorption ; nitrogen ; carbon dioxide ; platinum ; water gas shift reaction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The relationship between sites responsible for nitrogen chemisorption and sites responsible for stronger adsorption of carbon dioxide on platinum black is reported. A 2 to 1 ratio has been found between molecules of more strongly adsorbed carbon dioxide and molecules of nitrogen chemisorbed on individual samples. This relationship has allowed us to deduce the structure of chemisorbed carbon dioxide. Carbon dioxide is relatively weakly chemisorbed on platinum. Reasons for the weakness of this chemisorption are discussed.
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  • 18
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    Catalysis letters 37 (1996), S. 163-165 
    ISSN: 1572-879X
    Keywords: nitrogen ; Rh(111) ; thermal desorption ; Arrhenius parameters ; lateral interactions ; NO decomposition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Associative desorption of N atoms from the Rh(111) surface is simulated in the framework of the lattice-gas model. The Arrhenius parameters and nearest-neighbour lateral interaction employed to describe the measured thermal desorption spectra are as follows:v=1013 s−1,E d=40 kcal/mol, and ε1=1.7 kcal/mol. The results obtained are used to clarify the role of nitrogen desorption in the NO + CO reaction on Rh(111) atT=400–700 K andP NO≈P CO≈0.01 atm.
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  • 19
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    Monatshefte für Chemie 125 (1994), S. 1033-1039 
    ISSN: 1434-4475
    Keywords: Prebiotic peptide formation ; Evolution ; Clay catalysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Die Fähigkeit von Tonmineralien der Montmorillonitklasse zur Katalyse von Peptidbildungsreaktionen aus Aminosäuren in wäßriger Lösung wurde am Beispiel von Glyzin und Kupfer sowie Kalzium und Morillonit untersucht. Experimente mit Verdampfungszyklen haben gezeigt, daß kleinere Mengen von Di- und Tripeptiden aus der Aminosäure gebildet werden. Die weitere Polymerisation von Dipeptiden hingegen scheint wesentlich leichter in diesem Reaktionssystem zu verlaufen als der Anfangsschritt der Bildung des Dipeptides. Eine mögliche Rolle von Tonmineralien in der präbiotischen Peptidevolution kann daher in der Verlängerung von Peptidketten gesehen werden. Kupferionen in der Tonmatrix zeigen keinerlei Vorteile gegenüber den üblichen Kalziumionen, die in natürlichem Montmorillonit vorkommen.
    Notes: Summary The ability of montmorillonite clay minerals for catalyzing peptide formation from amino acids in aqueous solution has been investigated using glycine and Cu2+ and Ca2+ containing montmorillonites as reaction systems. Evaporation cycle experiments showed that minor amounts of di- and tripeptide are formed from the amino acid. Further polymerization of dipeptide, however, seems to be more favoured by this reaction system than the initial step of dipeptide formation, and a possible role of clays in prebiotic peptide evolution could be seen therefore in the prolongation of peptide chains. Cu2+ ions in the clay matrix did not show any advantage over the usual Ca2+ ions embedded in natural montmorillonite.
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  • 20
    ISSN: 1433-4909
    Keywords: Key words Thermococcus ; Pyrococcus ; Thermophilic ; Phosphofructokinase ; Evolution ; ADP ; Glycolysis ; ATP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The ADP-dependent phosphofructokinase (PFK) from Thermococcus zilligii has been purified 950 fold; it had a specific activity of 190 U mg−1. The enzyme required Mg2+ ions for optimal activity and was specific for ADP. The forward reaction kinetics were hyperbolic for both cosubstrates (pH optimum of 6.4), and the apparent K m values for ADP and fructose-6-phosphate were 0.6 mM (apparent V max of 243 U mg−1) and 1.47 mM (apparent V max of 197 U mg−1), respectively. Significantly, the enzyme is indicated to be nonallosteric but was slightly activated by some monovalent cations including Na+ and K+. The protein had a subunit size of 42.2 kDa and an estimated native molecular weight of 66 kDa (gel filtration). Maximal reaction rates for the reverse reaction were attained at pH 7.5–8.0, and the apparent K m values for fructose-1,6-bisphosphate and AMP were 0.56 mM (apparent V max of 2.9 U mg−1) and 12.5 mM, respectively. The biochemical characteristics of this unique ADP-dependent enzymatic activity are compared to ATP and pyrophosphate-dependent phosphofructokinases.
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  • 21
    ISSN: 1433-4909
    Keywords: Key wordsNatronomonas pharaonis ; Natronobacteria ; Archaea ; Serine protease ; Chymotrypsinogen ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A protease of a molecular mass of approximately 30 kDa was isolated and purified from the haloalkaliphilic archaeon Natronomonas (formerly Natronobacterium) pharaonis. The enzyme hydrolyzed synthetic peptides, preferentially at the carboxyl terminus of phenylalanine or leucine, as well as large proteins. Hydrolysis occurred over the range of pH from 6 to 12, with an optimum at pH 10. The temperature optimum was 61°C. The enzyme was nearly equally active over the range of salt concentration from 0.5 to 4 M (NaCl or KCl). A strong cross-reaction with a polyclonal antiserum against human chymotrypsin was observed. Enzymatic activity was inhibited by typical serine protease inhibitors. There was significant homology between N-terminal and internal sequences from autolytic fragments and the sequence of bovine chymotrypsinogen B; the overall amino acid composition was similar to that of vertebrate chymotrypsinogens. Evidence for a zymogen-like processing of the protease was obtained. Cell extracts from other halobacteria exhibited similar proteolytic activity and immunoreactivity. The data suggested a widespread distribution of a chymotrypsinogen B-like protease among halo- and haloalkaliphilic Archaea.
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  • 22
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    Aquatic sciences 53 (1991), S. 263-272 
    ISSN: 1420-9055
    Keywords: Lake ecosystem ; chl-a ; phosphorus ; nitrogen ; river flow ; thermocline ; simulation model ; multiple regression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The management variables which primarily affect phytoplankton biomass (as chl-a) in Lake Mjøsa, Norway, are total phosphorus loading (TP) and the timing and volume of water through flow (by active storage reservoirs). The response of the lake to changes in these factors is studied using a simulation model of the lake ecosystem. Chl-a responses from both observed data and the simulated results are extracted by multiple regression. Results show that decreasing TP load decreases chl-a, but less at low TP levels (〈 10 mg TP · m−3). There is also a certain time period for peak river flow which gives the least yield of chl-a per unit TP. This time period occurs in early summer (i.e., around June 10) if the total phosphorus load is low, and later if the load is high. Both observations and simulation results show that a high water flow increases chl-a at low epilimnion depths (〈 15 m), but that the same high water flow decreases chl-a when epilmnion is deep.
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  • 23
    ISSN: 1570-7458
    Keywords: Alsophila pometaria ; Geometridae ; Anisota senatoria ; Citheroniidae ; Quercus ; nutritional ecology ; herbivory ; nutritional indices ; consumption ; growth ; utilization efficiency ; nitrogen ; water ; tannins ; phenols ; gut pH ; digestive enzymes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Description / Table of Contents: Résumé Alimentées sur feuillage jeune de chêne, les chenilles d'Alsophila pometaria avaient un taux relatif de croissance (RGR) et un taux relatif d'accumulation d'azote (RNAR) plus élevés que les chenilles d'Anisota senatoria alimentées sur feuillage mûr de chêne. Bien que le jeune feuillage soit plus efficacement digéré par A. pometaria (AD plus élevé), il n'est pas assimilé et utilisé pour la croissance avec de meilleurs rendements (les ECI ne sont pas différents). Ainsi le taux de croissance plus élevé d'A. pometaria est dû entièrement à un taux de consommation plus important (RCR et RNCR). Le feuillage jeune est significativement plus riche en azote et en eau que le feuillage mûr, mais les niveaux de phénol et de tanins sont les mêmes. A pometaria consomme les feuilles de différentes espèces de chênes au même taux, indépendamment de la teneur en azote, tandis que A. senatoria accroît sa consommation en réponse à une diminution de la teneur en azote. Il en résulte que le taux de croissance d'A. pometaria dépend directement de la teneur en azote des feuilles, tandis que celui d'A. senatoria en est indépendant. Les systèmes digestifs des deux insectes sont biochimiquement semblables et sont efficaces pour la digestion des protéines. Les tanins et les phénols n'influent pas sur les indices nutritionnels de ces deux espèces. Nous estimons que le principal intérêt de l'alimentation printanière est la disponibilité en feuillage succulent, riche en azote, et non l'absence de feuilles à haute teneur en tanin. L'alimentation printanière semble correspondre à une strategie alimentaire qui favorise la croissance aux dépens de l'efficacité tandis que l'alimentation en fin d'été est une stratégie qui favorise l'efficacité sur la rapidité.
    Notes: Abstract The larvae of Alsophila pometaria (Harr.), feeding on the young foliage of oak, has a higher relative growth rate (RGR) and relative nitrogen accumulation rate (RNAR) than the larvae of Anisota senatoria (J. E. Smith), feeding on the mature foliage of oak. Although the young oak foliage is more efficiently digested by A. pometaria (higher AD's), it is not more efficiently assimilated and used for growth (no difference in ECI's). Thus, the higher growth rate of A. pometaria is due entirely to a higher consumption rate (RCR and RNCR). Young foliage is significantly higher in nitrogen and water than mature foliage, but phenol and tannin levels are comparable in young and old foliage. A. pometaria consumes the foliage of different oak species at the same rate, independent of nitrogen content, while A. senatoria increases its consumption rate in response to decreased nitrogen levels. As a result, the growth rate of A. pometaria is directly related to leaf nitrogen content, while the growth rate of A. senatoria is independent of leaf nitrogen. The two species of insects have digestive systems that are very similar biochemically, and that are well-designed for effective protein digestion. Tannins and phenols do not influence the nutrional indices of either species. We suggest that the major benefit of spring feeding is the availability of succulent, high-nitrogen foliage, and not the avoidance of high-tannin foliage. The spring feeder appears to have a feeding strategy that favors rapid growth at the expense of efficiency, while the late summer feeder has a strategy that favors efficiency over rate.
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    Entomologia experimentalis et applicata 36 (1984), S. 293-295 
    ISSN: 1570-7458
    Keywords: ryegrass ; Oscinella frit ; Geomyza tripunctata ; nitrogen
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  • 25
    ISSN: 1572-879X
    Keywords: adsorption ; adsorption isotherms ; dinitrogen ; FTIR spectroscopy ; geminal species ; NaY ; nitrogen ; zeolites
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Adsorption of N2 on NaY zeolites at 85 K and equilibrium pressures higher than 1 kPa results in the formation of geminal dinitrogen complexes characterized by an IR band at 2333.5 cm−1 (2255.4 cm−1 after adsorption of 15N2). With decreasing equilibrium pressure the complexes tend to loose one N2 ligand, thus forming linear species characterized by an IR band at 2336.8 cm−1 (2258.7 cm−1 after adsorption of 15N2). All species disappear completely after evacuation. Co-adsorption of N2 and CO revealed that the dinitrogen complexes are formed on Na+ cations. The changes in the concentrations of the linear and geminal N2 species with the changes in the equilibrium pressure are excellently described by equations of adsorption isotherms proposed earlier for mono- and di-carbonyls.
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  • 26
    ISSN: 1572-8757
    Keywords: kinetics ; isotope-exchange ; nitrogen ; adsorption ; methane ; zeolite ; equilibria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Physics , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The Isotope Exchange Technique (IET) was used to simultaneously measure pure and binary gas adsorption equilibria and kinetics (self-diffusivities) of CH4 and N2 on pelletized 4A zeolite. The experiment was carried out isothermally without disturbing the adsorbed phase. CH4 was selectively adsorbed over N2 by the zeolite because of its higher polarizability. The multi-site Langmuir model described the pure gas and binary adsorption equilibria fairly well at three different temperatures. The selectivity of adsorption of CH4 over N2 increased with increasing pressure at constant gas phase composition and temperature. This curious behavior was caused by the differences in the sizes of the adsorbates. The diffusion of CH4 and N2 into the zeolite was an activated process and the Fickian diffusion model described the uptake of both pure gases and their mixtures. The self-diffusivity of N2 was an order of magnitude larger than that for CH4. The pure gas self-diffusivities for both components were constants over a large range of surface coverages (0 〈 θ 〈 0.5). The self-diffusivities of CH4 and N2 from their binary mixtures were not affected by the presence of each other, compared to their pure gas self-diffusivities at identical surface coverages.
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  • 27
    ISSN: 1572-879X
    Keywords: platinum ; rhodium ; alloy ; surface composition ; nitrogen ; oxygen
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    Topics: Chemistry and Pharmacology
    Notes: Abstract Two kinds of adsorbed N atoms exist on a Pt0.25Rh0.75(100) surface. One desorbs at 490 K and the other desorbs at 650 K. The former reacts with H2 at 400 K, but the latter does not. It is supposed that the adsorption of these two N atoms is responsible of the surface composition, ratio of Pt and Rh.
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  • 28
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    Journal for general philosophy of science 21 (1990), S. 309-328 
    ISSN: 1572-8587
    Keywords: Evolution ; evolutionäre Erkenntnistheorie ; Organismus ; Autonomie ; Abbildungskritik
    Source: Springer Online Journal Archives 1860-2000
    Topics: Philosophy , Nature of Science, Research, Systems of Higher Education, Museum Science
    Notes: Summary The concept of evolutionary epistemology has been critically discussed by philosophers who have mainly pointed to unacceptable philosophical tenets (cf. Vittorio Hösle, this Journal, Vol. 19 (1988), pp. 348–377). However, as most philosophers are extremely reluctant to critically treat the biological theories on which the ideas of evolutionary epistemology are based, the invalid concepts of adaption escaped their critical scrutiny. Therefore the influence of preconceived biological theories on the biological basis of evolutionary epistemology and the distorting consequences on the philosophical level could not be elaborated. The following context sketches a new view of organismic reasoning and its impact on evolutionary aspects of epistemology. The basic theorem of adaptation is shown to be unacceptable and invalid if organisms are conceived as autonomous entities which can only evolve according to their specific internal organismic properties.
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  • 29
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    Entomologia experimentalis et applicata 62 (1992), S. 29-36 
    ISSN: 1570-7458
    Keywords: Alkaloids ; cinnabar moth ; insect genetics ; larval performance ; Lepidoptera ; nutritional ecology ; nitrogen ; sugar ; Tyria jacobaeae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In a laboratory experiment using full-sibs, 60% of the variation in pupal weight of the monophage Tyria jacobaeae L. (Lepidoptera, Arctiidae) could be explained by variation in the nitrogen concentration of the food plant, Senecio jacobaea L. and only 4% by variation in sugar concentration. Larval weight and growth rates of young and old larvae were also positively correlated with nitrogen and sugar concentration. Developmental time was negatively correlated with nitrogen concentration. In a second experiment full-sib families differed significantly in larval weight at day 7, mortality, growth rate and developmental time. Pupal weight did not differ significantly among families, but was positively correlated with nitrogen concentration of Senecio. Larval performance was not significantly influenced by concentrations of sugars or alkaloids. We conclude that larval performance of Tyria during most of the larval period is mainly determined by genetic factors, but pupal weights are primarily determined by nitrogen concentration of the food plant.
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  • 30
    ISSN: 1432-1211
    Keywords: Key words Antigen processing ; Evolution ; Cell surface molecules ; Mhc ; Class I antigens
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  • 31
    ISSN: 1432-1211
    Keywords: Key words NRAMP ; Fish ; Carp ; Evolution ; Expression
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    Topics: Biology , Medicine
    Notes: Abstract  The mouse Lsh/Ity/Bcg locus regulates natural resistance to intracellular pathogens, and the Nramp1 gene was isolated as its candidate. Nramp is part of a small family of at least two genes, Nramp1 and Nramp2. In the present study, a full-length cDNA for carp NRAMP has been isolated and characterized. Nucleotide and predicted amino acid sequence analysis indicate that the carp NRAMP encodes a 548 amino acid membrane protein with 12 putative transmembrane domains, two N-linked glycosylation sites, and an evolutionarily conserved consensus transport motif. The peptide sequence identity among carp and human NRAMP2 is 78%, and 65% with human NRAMP1. Reverse transcription-polymerase chain reaction revealed that carp NRAMP is ubiquitously expressed. Phylogenetic analysis, using neigbor-joining, showed that the carp NRAMP protein clustered together with mammalian NRAMP2 proteins.
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  • 32
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    Immunogenetics 50 (1999), S. 301-308 
    ISSN: 1432-1211
    Keywords: Key words T-cell receptors ; Variable region genes ; Evolution ; Phylogeny ; Diversity
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    Topics: Biology , Medicine
    Notes: Abstract  The receptor of a T lymphocyte (TCR) recognizes nonself antigens in the company of major histocompatibility complex (MHC) molecules presented to it by the antigen-presenting cell. The variable region of TCR is encoded by either a concatenation of variable region (TCR-V), diversity region (TCR-D), and joining region (TCR-J) genes, or a concatenation of TCR-V and TCR-J genes. The TCR-V genes exist as a multigene family in vertebrate species. Here we study the evolutionary relationships of TCR-V genes from humans, sheep, cattle, rabbits, mice, and chicken. These six species can be classified into two groups according to the frequency of γδ T-cells in their peripheral T-cell populations. The "γδ low" group of species includes humans and mice, in which γδ T-cells constitute very limited portion of the T-cell population. The "γδ high" group includes sheep, cattle, rabbits, and chicken, in which γδ T-cells comprise up to 60% of the T-cell population. Here, we compiled TCR-V sequences from the six species and conducted a phylogenetic analysis. We identified various TCR-V gene subgroups based on the analysis. We found that humans and mice have representatives from nearly all of the subgroups identified, while other species have lost subgroups to different extent. Therefore, the γδ low species have a high degree of diversity of TCR-V genes, while γδ high species all have limited diversity of TCR-V genes. This pattern is similar to that found for immunoglobulin variable region (IGV) genes.
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  • 33
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    Immunogenetics 50 (1999), S. 329-335 
    ISSN: 1432-1211
    Keywords: Key words Marsupials ; Light chains ; Variable regions ; IGK ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  A full-length and several partial cDNAs encoding IGK light chains from the marsupial South American opossum, Monodelphis domestica, were isolated and characterized. Using these clones as a starting point, the expressed IGKV repertoire was sampled by anchored polymerase chain reaction using an IGKC-specific primer. Based on nucleotide sequences of twenty unique, expressed IGKV-J combinations, there are at least four IGKV families and two J segments. Southern blot analysis revealed each IGK-V family contains multiple gene segments totaling at least thirty-five IGKV in the opossum genome. No evidence for particular, recurrent IGKV-J combinations in the opossum IGK repertoire was seen, rather the V-J combinations appeared random and diverse. Each of the four IGKV families appear more closely related to V segments from placental mammals than to each other, suggesting the duplication of the IGKV families prior to the separation of marsupials and placental mammals more than one-hundred-million years ago. Overall, the complexity of opossum light chain V segments appears greater than that found in the heavy chain, and light chains are likely to contribute significantly to Ig diversity in this species.With this report, the homologues encoding all three classes of eutherian Ig chains, IGH, IGL, and IGK, have been described in a non-placental mammal.
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  • 34
    ISSN: 1432-1211
    Keywords: Key words MHC ; MIC ; Nonhuman primates ; Evolution
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    Immunogenetics 49 (1999), S. 295-302 
    ISSN: 1432-1211
    Keywords: Key words Major histocompatibility complex ; Class II ; Antigen processing ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Proper peptide presentation by major histocompatibility complex (MHC)-encoded class II antigens is dependent on the products of the MHC DM loci. We identified the rabbit orthologues (RLA-DMA and -DMB) of human HLA-DMA and -DMB and found that they have 76.9% and 78.8% identity with HLA-DMA and -DMB, respectively. Like classical class II MHC genes, RLA-DM genes are more closely related to human HLA-DM genes than to mouse H2-DM. Among the DM family, there is a high degree of variability at the amino terminus of the DMa chains, and length variability in the cytoplasmic tails of both DMα and DMβ. The rabbit DM genes are coexpressed with class II genes in lymphoid tissues, as are the DM genes of other mammals. The RLA-DM locus maps to the class II region of the rabbit MHC, and is flanked by the DP and DOB loci. Despite having some similarities to class II genes of bony fishes, the DM family represents a separate branch of the MHC class II family.
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  • 36
    ISSN: 1432-1211
    Keywords: Key words Mhc ; Class II A ; Cichlid ; Fish ; Evolution
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  • 37
    ISSN: 1432-1211
    Keywords: Key words Beta2-microglobulin ; Evolution ; Sturgeon ; cDNA ; Genomic
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  • 38
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    Mycorrhiza 4 (1993), S. 1-4 
    ISSN: 1432-1890
    Keywords: Tropics ; Mycotrophy ; Spore dispersal ; Community composition ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This article introduces reports concerning the occurrence of mycorrhizae on epiphytes in Costa Rica, Ethiopia, Venezuela, Malaysia, and Mexico. Association of vesicular-arbuscular mycorrhizal fungi with the roots of epiphytes is not well known. Vesicular-arbuscular mycorrhizal fungi (VAM) do occur in the canopy, but are uncommon except in certain sites and host taxa. Occurrence of VAM on epiphytes may be constrained by mineral nutrient availability and spatial heterogeneity in the canopy. Nevertheless, epiphytes present unique opportunities to study influences of mycorrhizae on vascular plant community composition and on the evolution of mycorrhizal associations.
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  • 39
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    Biology and fertility of soils 9 (1990), S. 110-118 
    ISSN: 1432-0789
    Keywords: Kuehneltiella terricola gen. nov., sp. nov. ; Soil ciliates ; Colpodidae ; Systematics ; Evolution ; Australia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The morphology and biology of the colpodid ciliate Kuehneltiella terricola gen. nov., sp. nov. has been investigated using living organisms, various silver impregnation methods, and scanning electron microscopy. The new species has been isolated in soil from central Australia and might be endemic to this continent. The new genus Kuehneltiella differs from its nearest relative, Bresslaua, in having a right oral polykinetid composed of a single row of dikinetids. A reinvestigation of Lynn's slides of Bresslaua insidiatrix showed that, contrary to the statement of Lynn (1979), this species has a typic colpodid right oral polykinetid, i.e., composed of many short, disordered kineties. A brief review of the literature suggests that simple, single-rowed, right oral polykinetids are apomorphic in the colpodids s. str. Further, this special character has obviously evolved independently several times within the class Colpodea and even within the colpodids s. str. An illustrated key to the genera of the family Colpodidae is provided.
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    Biology and fertility of soils 9 (1990), S. 101-109 
    ISSN: 1432-0789
    Keywords: Phryganella acropodia ; Testate amoeba ; Growth rate ; Rhizopoda ; Feeding ; Fungal species ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Clones of Phryganella acropodia were cultivated under different trophic conditions with bacteria as the food source. The doubling time was estimated to be 3 days. The edibility of four species of fungi, Aspergillus niger, Cunninghamella echinulata, Penicillium echinulatum and Stilbella bulbicola, was tested, but only Penicillium enchinulatum and Stilbella bulbicola were eaten and digested by the amoeba. An ultrastructure examination showed that there are two contractile vacuoles, many dictyosomes, a single nucleus with several nucleoli, and peroxisomes. The pseudopodia are filiform when attached to the substrate but change to lobose when the animal is floating. A thin organic membrane covers the aperture of resting forms.
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  • 41
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    Biology and fertility of soils 9 (1990), S. 95-100 
    ISSN: 1432-0789
    Keywords: Assulina-Valkanovia ; Testacea ; Polymorphism ; Genotypes ; Evolution ; Spruce forest ; Sphagnum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The taxonomy and evolution of the Assulina-Valkanovia complex were investigated in a spruce forest soil which included a Sphagnum plot (GDR, Thuringia). In both habitats Assulina muscorum occurred in two colour forms (brown and colourless) and four shapes. A quantified phenospectrum from Assulina muscorum was obtained. The four shapes were distributed differently between the brown and the colourless forms in Sphagnum and soil. The shell measurements showed statistically significant differences between the brown and the colourless forms. Even between the two brown populations there were some significant differences. Each of the four shape types of brown and of colourless Assulina can be kept in clonal cultures for some time. However, without selection, single cultures eventually revert to mixed types. The four shape types show different degrees of stability. These colour and shape forms are genotypes, which can also occur for short periods in the natural habitats. The brown populations in Sphagnum and in the soil were dominated by different shape types during the period of investigation. Valkanovia elegans cannot be distinguished from Assulina muscorum type 4, but Valkanovia can inhabit both upper and lower soil horizons, whereas Assulina and its forms lives exclusively in the upper horizon (litter). Valkanovia from the lower horizon is constant in clonal culture. The conclusion of the present investigation is that there are stable and unstable constellations within a changeable genome, which give asexual groups both a taxonomic structure and a continuum of forms. Selection can increase stability, by polygenic control of features.
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  • 42
    ISSN: 1432-0789
    Keywords: Key words Microbial biomass C ; Water-soluble organic carbon ; Light fraction organic carbon ; Fertilizer ; nitrogen ; 13C nuclear magnetic resonance ; Infrared spectrophotometry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Soil samples taken from four experimental sites that had been cropped to continuous corn for 3–11 years in Ontario and Quebec were analyzed to evaluate changes in quantity and quality of labile soil organic carbon under different nitrogen (N) fertility and tillage treatments. Addition of fertilizer N above soil test recommendations tended to decrease amounts of water-soluble organic carbon (WSOC) and microbial biomass carbon (MBC). The quality of the WSOC was characterized by 13C nuclear magnetic resonance and infrared spectrophotometry and the results indicated that carbohydrates, long-chain aliphatics and proteins were the major components of all extracts. Similar types of C were present in all of the soils, but an influence of management was evident. The quantity of soil MBC was positively related to the quantities of WSOC, carbohydrate C, and organic C, and negatively related to quantities of long-chain aliphatic C in the soil. The quantity of WSOC was positively related to the quantities of protein C, carbohydrate C, and negatively related to the quantity of carboxylic C. The quantity of soil MBC was not only related to quantities of soil WSOC but also to the quality of soil WSOC.
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    Biology and fertility of soils 26 (1998), S. 169-172 
    ISSN: 1432-0789
    Keywords: Key words Urea ; Coated fertilizers ; Ammonium ; nitrogen ; Nitrate nitrogen ; Nitrogen uptake
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Understanding the fate of different forms of nitrogen (N) fertilizers applied to soils is an important step in enhancing N use efficiency and minimizing N losses. The growth and N uptake of two citrus rootstocks, Swingle citrumelo (SC), and Cleopatra mandarin (CM), seedlings were evaluated in a pot experiment using a Candler fine sand (hyperthermic, uncoated, Typic Quartzipsamments) without N application or with 400 mg N kg–1 applied as urea or controlled-release fertilizers (CRF; either as Meister, Osmocote, or Poly-S). Meister and Osmocote are polyolefin resin-coated urea with longevity of N release for 270 days (at 25°C). Poly-S is a polymer and sulfur-coated urea with release duration considerably shorter than that of either Meister or Osmocote. The concentrations of 2 M KCl extractable nitrate nitrogen (NO3 –-N) and ammonium nitrogen (NH4 +-N) in the soil sampled 180 days and 300 days after planting were greater in the soil with SC than with CM rootstock seedlings. In most cases, the extractable NH4 + and NO3 – concentrations were greater for the Osmocote treatment compared to the other N sources. For the SC rootstock seedlings, dry weight was greater with Meister or Poly-S compared with either Osmocote or urea. At the end of the experiment, ranking of the various N sources, with respect to total N uptake by the seedlings, was: Meister = Osmocote 〉 Poly-S 〉 Urea 〉 no N for CM rootstock, and Meister = Poly-S = Osmocote 〉 Urea 〉 no N for SC rootstock. The study demonstrated that for a given rate of N application the total N uptake by seedlings was greater for the CRF compared to urea treatment. This suggests that various N losses were lower from the CRF source as compared to those from soluble fertilizers.
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    Biology and fertility of soils 26 (1997), S. 31-34 
    ISSN: 1432-0789
    Keywords: Key words Microbial biomass ; Air-drying ; Extractable ; nitrogen ; Extractable phosphorus ; Tropical soil
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The microbial contribution to extractable N and P after the air-drying of eight Indian dry tropical Ultisols was quantified. Air-drying of the soils decreased microbial biomass C by 25–53% but increased extractable N and P by 14–34% and 24–121%, respectively. This increase in the extractable N and P was accounted for, to some extent, by microbial biomass killed due to air-drying. Microbial biomass contributes 17–36% and 19–82% to the extractable N and P, respectively, possibly due to air-drying of the soils. I conclude that due to contamination of microbial biomass with the available nutrients in air-dried soils, measurements of extractable nutrients should be made on field-moist soils.
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  • 45
    ISSN: 1432-0819
    Keywords: Key wordsZoned magma body ; Chemical variation ; ash-flow sheets ; Tephra sequence ; Differentiation ; time constraints ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract The Rainier Mesa ash-flow is a large (1200 km3), 11.6 My old, chemically zoned unit that ranges in composition from 55 to 76% SiO2– one of the largest chemical ranges ever observed in a large volume ash-flow sheet. Two chemical trends occur in this sheet, a low silica (55–66% SiO2) and a high silica (〉66% SiO2) trend. Ninety per cent of the Rainier Mesa sheet occurs in the high silica trend. Immediately beneath the Rainier Mesa sheet is a thick tephra sequence. The chemical variation of this sequence is nearly equivalent to the high silica portion of the Rainier Mesa ash-flow sheet (about 66–78% SiO2). Throughout the tephra sequence numerous small ash-flow layers occur, and each ash-flow layer is chemically zoned from more evolved at the base to less evolved at the top. This is consistent with having been erupted from a zoned magma body. The lowest silica tephra units are at the base of the sequence and the highest silica units are at the top – that is, the large-scale chemical trend of the entire sequence is opposite to that of the individual ash-flow layers. These ash-flow layers are of very small volume. The tephra sequence provides a unique record of the incremental development of the zoned, high silica portion of the Rainier Mesa magma body.
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  • 46
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    Calcified tissue international 33 (1981), S. 603-618 
    ISSN: 1432-0827
    Keywords: Preameloblasts ; Tooth germs ; Monkey ; Enamel ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Summary Cytodifferentiation of inner enamel epithelium and the adjacent connective tissue from the tip of the cervical loop to the initiation of enamel elaboration in twoMacaca species was examined. Ten- to twelve-month-old specimens were fixed by perfusion and the permanent tooth buds were prepared for transmission electron microscopy. At the cervical loop proper, inner enamel epithelium cells have lobed nuclei, a paucity of cytoplasm, and wide extracellular spaces; the basal lamina facing the dental papilla is straight. With increasing distance from the tip of the cervical loop, the following changes occur gradually: (a) preameloblasts elongate from 15 to 45 µm, and their organelles, particularly mitochondria and profiles of rough endoplasmic reticulum, become more numerous; (b) extracellular spaces decrease between preameloblasts starting at the basal (infranuclear) end; (c) the basement membrane becomes convoluted and associated with aperiodic fibers; (d) preodontoblast projections penetrate the aperiodic fibers; (e) collagen fibers subjacent to the basement membrane increase in density, with particularly thick fibers paralleling the aperiodic fibers. These modifications occur within three-fourths of the distance from the tip of the cervical loop to the mineralization front. The condensation of preodontoblasts is followed immediately by predentin synthesis. Concomitantly, the basement membrane breaks down and the aperiodic fibers are engulfed by preameloblasts. Preameloblast projections penetrate junctional predentin, contact mineralized dentin, and enamel synthesis ensues. At this stage the ameloblast is 45 µm long, the nucleus is central or basal, the Golgi apparatus has migrated apically, but the Tomes' process has not yet formed. The results indicate that odontogenesis inMacaca monkeys more closely resembles human odontogenesis than does that in the murine rodents.
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  • 47
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    Bulletin of volcanology 59 (1997), S. 161-170 
    ISSN: 1432-0819
    Keywords: Key words Structure ; Evolution ; Uplift ; Geodetic modeling ; Alban Hills
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract  The Alban Hills, a Quaternary volcanic center lying west of the central Apennines, 15–25 km southeast of Rome, last erupted 19 ka and has produced approximately 290 km3 of eruptive deposits since the inception of volcanism at 580 ka. Earthquakes of moderate intensity have been generated there at least since the Roman age. Modern observations show that intermittent periods of swarm activity originate primarily beneath the youngest features, the phreatomagmatic craters on the west side of the volcano. Results from seismic tomography allow identification of a low-velocity region, perhaps still hot or partially molten, more than 6 km beneath the youngest craters and a high-velocity region, probably a solidified magma body, beneath the older central volcanic construct. Thirty centimeters of uplift measured by releveling supports the contention that high levels of seismicity during the 1980s and 1990s resulted from accumulation of magma beneath these craters. The volume of magma accumulation and the amount of maximum uplift was probably at least 40×106 m3 and 40 cm, respectively. Comparison of newer levelings with those completed in 1891 and 1927 suggests earlier episodes of uplift. The magma chamber beneath the western Alban Hills is probably responsible for much of the past 200 ka of eruptive activity, is still receiving intermittent batches of magma, and is, therefore, continuing to generate modest levels of volcanic unrest. Bending of overburden is the most likely cause of the persistent earthquakes, which generally have hypocenters above the 6-km-deep top of the magma reservoir. In this view, the most recent uplift and seismicity are probably characteristic and not precursors of more intense activity.
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  • 48
    ISSN: 1432-0827
    Keywords: Periodontal ligament fibroblast ; Mineralized nodule ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Summary The purposes of this study were to determine whether periodontal ligament (PDL) cells are capable of producing mineralized nodules in vitro and to analyze ultrastructural features of the nodules. Rat PDL cells were obtained from coagulum in the socket at 2 days after tooth extraction and cultured at confluence in standard medium containing Dulbecco's Modified Eagle's Medium supplemented with 10% FBS and antibiotics. To test mineralized nodule formation, cells were further cultured for an additional 3 weeks in the standard medium containing (1) ascorbic acid (50 μg/ml) and sodium β-glycerophosphate (10 mM), (2) ascorbic acid, sodium β-glycerophosphate, and dexamethasone (5 μM), or (3) ascorbic acid alone. Cells were then fixed in 2.5% glutaraldehyde, postfixed in 1% OsO4, and prepared for light and electron microscopy. Threedimensional nodules containing mineralized matrices were formed only when the cells were cultured in the presence of ascorbic acid and dexamethasone. They were composed of multilayered fibroblasts (up to 13 layers), and highly organized collagen fibrils with 64 nm cross-banding patterns between the cell layers. The fibroblasts in the nodules exhibited an elongated shape with a high degree of cytoplasmic polarity throughout the nodule, and have the morphological features of PDL fibroblasts as seen in vivo. Mineral deposition with needle-like crystals was initiated on collagen fibrils located in intercellular spaces of the upper cell layers and became increasingly heavier towards the bottom half of the nodules. X-ray microanalysis and electron diffraction analysis confirmed that mineral deposition contained calcium and phosphate in the form of immature hydroxyapatite. These nodules contained neither osteoblasts nor osteocytes, and have their own morphological organization and characteristics which differ from those formed by bone cells in culture. Therefore, these data suggest that PDL cells are capable of forming mineralized tissue in vitro with the morphological characteristics different from bone mineralized nodules.
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  • 49
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    Current genetics 17 (1990), S. 223-227 
    ISSN: 1432-0983
    Keywords: Orotidine-5′-phosphate decarboxylase ; Cephalosporium acremonium ; Recombinant DNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned the Cephalosporium acremonium pyr4 gene by cross-hybridization with the equivalent gene from Neurospora crassa, the closest relative from which this gene is available. The C. acremonium pyr4 gene complements an E. coli pyrF mutant lacking orotidine-5′-phosphate decarboxylase (OMPdecase), and most probably does not contain introns. Maxicell analysis in E. coli shows that it encodes a 46 kDa polypeptide. The C. acremonium OMPdecase contains a highly conserved pentadecapeptide characteristic for this category of enzyme. Extensive sequence comparison suggests an important role of this region in enzymatic activity.
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  • 50
    ISSN: 1432-0983
    Keywords: Trypanosomes ; RNA polymerase ; Transcription ; Evolution ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have sequenced the genes encoding te largest subunits of the three classes of DNA-dependent RNA polymerases of Trypanosoma brucei. The nucleotide and deduced amino acid sequences were compared and aligned with the corresponding sequences of other eukaryotes. Phylogenetic relationships were subsequently calculated with a distant matrix, a bootstrapped parsimony and a maximum-likelihood method. These independent calculations resulted in trees with very similar topologies. The analyses show that all the largest subunits of T. brucei are evolutionarily distant members within each of the three RNA polymerase classes. An early separation of the trypanosomal subunits from the eukaryotic lineage might from the fundamental basis for the unusual transcription process of this species. Finally, all dendrograms show a separate ramification for the largest subunit of RNA polymerase I, II and III. RNA polymerase II and/or III form a bifurcation with the archaebacterial lineage. RNA polymerase I, however, arises separately from the eubacterial β′ lineage. This suggests that the three eukaryotic RNA polymerase classes are not simply derived by two gene duplications of an ancestral gene with subsequent differentiation.
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  • 51
    ISSN: 1432-0983
    Keywords: Cyanophora paradoxa ; Ferredoxin-NADP+-oxidoreductase ; Protein-import ; Evolution
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    Topics: Biology
    Notes: Summary Cyanophora paradoxa is an important model organism for the study of the transition from endocytobiontic cyanobacteria to factual eukaryotic cell organelles. The cyanelles of these organisms possess cyanobacterial, as well as plastidic, characteristics. Although the transfer of cyanellar proteins from cytosolic into cyanellar space has been shown, the process of translocation of a known protein across the peptidoglycan layer and the envelope membranes has not been characterized. In this study we demonstrate that a specific and obligate cyanelle protein —Ferredoxin-NADP+-oxidoreductase (FNR) — is coded on the nuclear genome, synthesized on 80S ribosomes and transported from the eukaryotic cell compartment into the cyanelles of Cyanophora paradoxa, an original intracellular host-guest relation. These results indicate a gene transfer from guest to host genome and support the view that, in spite of their cyanobacterial origin, cyanelles have been evolved to cell organelles comparable to plastids.
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  • 52
    ISSN: 1432-1432
    Keywords: Evolution ; κ-Casein ; Cytochrome b ; Artiodactyla ; Ruminantia ; Caprinae ; Capricornis
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    Topics: Biology
    Notes: Abstract Nucleotide sequences for the κ-casein precursor proteins have been determined from the genomic DNAs or hair roots of the Ruminantia. The coding regions, exons 2, 3, and 4, were amplified separately via the three kinds of PCRs and then directly sequenced. The primers were designed from the sequence of bovine κ-casein gene; they were applicable for the amplification of the κ-casein genes from the 13 species in the Ruminantia except exon 2 of the lesser mouse deer. These results permitted an easy phylogenetic analysis based on the sequences of an autosomal gene. A phylogenetic tree was constructed from the mature K-casein sequences and compared with the tree of the cytochrome b genes which were sequenced from the same individuals. The Cervidae (sika deer, Cervus nippon) were separated from the branch of the Bovidae on the tree of κ-casein genes with a relatively high confidence level of the bootstrap analysis, but included in the branch of the Bovidae on the tree of cytochrome b genes. The κ-casein tree indicated a monophyly of the subfamily Caprinae, although the internal branches were uncertain in the Caprinae. The tree based on the nucleotide sequences of cytochrome b genes clearly showed the relationships of the closely related species in the genus Capricornis consisting of serow (C. smatorensis), Japanese serow (C. crispus), and Formosan serow (C. swinhoei). These results would be explained by the difference of resolving power between the κ-casein and the cytochrome b sequences.
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  • 53
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    Journal of molecular evolution 43 (1996), S. 399-404 
    ISSN: 1432-1432
    Keywords: Asarum ; Dioscorea ; Angiosperms ; Evolution ; Legumins ; Seed proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Analysis of legumin-encoding cDNAs fromDioscorea caucasica Lipsky (Dioscoreaceae) and fromAsarum europaeum L. (Aristolochiaceae) shows that there is an especially methionine-rich legumin subfamily present in the lower angiosperm clades including the Monocotyledoneae. It is characterized by a methionine content of 3–4 mol% which is roughly triple the methionine proportion of most other legumins. These “MetR” legumins, if present, still have to be detected in the higher angiosperms including the important seed crops. Evolutionary analysis suggests that the MetR legumins are the result of a gene duplication allowing the differentiation of legumin genes according to their sulfur content. The duplication event must have taken place before the split into mono- and dicotyledonous plants but probably after the separation of angiosperms and gymnosperms.
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  • 54
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    Journal of molecular evolution 43 (1996), S. 685-689 
    ISSN: 1432-1432
    Keywords: Retroposons ; Integration targets ; Evolution
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    Topics: Biology
    Notes: Abstract Genomic DNA fragments generated by the reverse transcription of cellular RNA are called retroposons. Because they are flanked by short repeats, mammalian retroposons are believed to integrate at staggered chromosomal breaks. Recently, a significant sequence pattern associated with the integration of Alu and ID repeats was identified (Jurka 1996). It is represented by the 5′ TTAAAA consensus sequence around the 5′ ends of flanking repeats of Alu, ID, as well as, of B1 and B2 retroposed elements as shown in this paper. This consensus is a potential target for enzymatic nicking which probably occurs in the complementary strand between 3′ AA and the following 3′ TTTT bases. The first four bases of the flanking repeats corresponding to the 3′ TTTT consensus sequence show some sequence variations that may be affected by complementary base pairing between the A-rich RNA tails and the DNA target sequences prior to nicking and reverse transcription. We discuss potential evidence for such base pairing based on correlated variations in nucleotide composition of different tail and target regions.
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  • 55
    ISSN: 1432-1432
    Keywords: Alleles ; Evolution ; Gene conversion ; Introns ; Nematode
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    Topics: Biology
    Notes: Abstract Globin genes from theCaenorhabditis speciesbriggsae andremanei were identified and compared with a previously describedC. elegans globin gene. The encoded globins share between 86% and 93% amino acid identity, with most of the changes in or just before the putative B helix.C. remanei was found to have two globin alleles,Crg1-1 andCrgl-2. The coding sequence for each is interrupted by a single intron in the same position. The exons of the two genes are only 1 % divergent at the nucleotide level and encode identical polypeptides. In contrast, intron sequence divergence is 16% and numerous insertions and deletions have significantly altered the size and content of both introns. Genetic crosses show thatCrg1-1 andCrgl-2 segregate as alleles. Homozygous lines for each allele were constructed and northern analysis confirmed the expression of both alleles. These data reveal an unusual situation wherein two alleles encoding identical proteins have diverged much more rapidly in their introns than the silent sites of their coding sequences, suggesting multiple gene conversion events.
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  • 56
    ISSN: 1432-1432
    Keywords: Evolution ; Expression patterns ; α-Amylase ; Glucose repression ; Starch induction ; Intra- and interspecific variation ; Drosophila ; Gene expression ; Regulatory genes
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    Topics: Biology
    Notes: Abstract Intraspecific variation of α-amylase activity in D. melanogaster and D. immigrans, which is distantly related to D. melanogaster, and interspecific variation of α-amylase activity in 18 Drosophila species were examined. The amount of intraspecific variation of α-amylase activities measured in terms of coefficient of variation in D. melanogaster and D. immigrans was one-half and one-tenth or less, respectively, of the interspecific variation in 18 Drosophila species. We also surveyed the response patterns of α-amylase activity to dietary carbohydrates at the larval and adult stages. The levels of α-amylase activity depended on both repression by dietary glucose (glucose repression) and induction by dietary starch (starch induction). In general, our data suggest that glucose repression was conserved among species at both stages while starch induction was mainly observed in larvae, although the degree of the response depended on species. In D. lebanonensis lebanonensis and D. serrata, larvae expressed electrophoretically different α-amylase variants (isozymes) from those of adult flies. These results may suggest that the regulatory systems responsible both for the response to environment and developmental expression are different among species in Drosophila.
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  • 57
    ISSN: 1432-1432
    Keywords: Soybean ; Ferritin ; Plant-animal ; Monocotyledons ; Dicotyledons ; Plastid ; Gene organization ; Evolution ; Intron
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Ferritin, a protein widespread in nature, concentrates iron −1011−1012-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor (based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization in plants and animals, made possible by the cloning of a dicot (soy-bean) ferritin gene presented here and the recent cloning of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In plant ferritin genes, the number of introns (n = 7) is higher than in animals (n = 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding sequences and the high conservation of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid, the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.
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  • 58
    ISSN: 1432-1432
    Keywords: Evolution ; Multigene family ; Recombination ; Trypanosome ; Variant surface glycoprotein
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    Topics: Biology
    Notes: Abstract The surface of the parasitic protozoanTrypanosoma brucei spp. is covered with a dense coat consisting of a single type of glycoprotein molecule, the variant surface glycoprotein (VSG). There may be as many as 1,000 genes for VSG within the genome ofT. brucei, and the switch of expression from one to another is the phenomenon of antigenic variation. As an approach to understanding the evolution of VSG genes we have determined the genomic DNA sequences of the eight genes encoding the variant surface glycoprotein 117 (VSG) family. From these data we have observed a number of features concerning the relationships between these genes: (1) there is a region of high variability confined to the N-terminus of the coding sequence, and comparison of the sequences with the available X-ray diffraction crystal structures suggests that two of the most variable stretches within the N-terminal domain are present on surface-exposed loops, indicating a role for epitope selection in evolution of these genes; (2) the 29 nucleotides surrounding the splice acceptor site are absolutely conserved in all eight 117 VSG genes; (3) numerous insertion/deletion mutations are located within or immediately downstream of the C-terminal protein-coding sequences: (4) within 500 by downstream of the insertion/deletion mutations are one or two copies of a repeat motif highly homologous to the recombinogenic 76-bp repeat sequences present upstream of many VSG basic copy genes and the expression-linked copy.
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  • 59
    ISSN: 1432-1432
    Keywords: Metalloproteinase ; Disintegrin ; Evolution ; Venom ; Phylogeny ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolution of the Metalloproteinase Disintegrin Cysteine-rich (MDC) gene family and that of the mammalian Matrix-degrading Metalloproteinases (MMPs) are compared. The alignment of snake venom and mammalian MDC and MMP precursor sequences generated a phylogenetic tree that grouped these proteins mainly according to their function. Based on this observation, a common ancestry is suggested for mammalian and snake venom MDCs; it is also possible that gene duplication of the already-assembled domain structure, followed by divergence of the copies, may have significantly contributed to the evolution of the functionally diverse MDC proteins. The data also suggest that the structural resemblance of the zinc-binding motif of venom MDCs and MMPs may best be explained by common ancestry and conservation of the proteolytic motifs during the divergence of the proteins rather than through convergent evolution.
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  • 60
    ISSN: 1432-1432
    Keywords: Krebs cycle ; Evolution ; Metabolism ; Citric acid cycle ; Chemical design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into asingle-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.
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  • 61
    ISSN: 1432-1432
    Keywords: Histone H1° ; 3′ untranslated region ; Slippage ; Sequence simplicity ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The H1° gene has a long 3′ untranslated region (3′UTR) of 1,125 nucleotides in the rat and 1,310 in humans. Analysis of the sequences shows that they have features of simple DNA that suggest involvement of replication slippage in their evolution. These features include the length imbalance between the rat and human sequences; the abundance of single-base repeats, two-base runs and other simple motifs clustered along the sequence; and the presence of single-base repeat length polymorphisms in the rat and mouse sequences. Pairwise comparisons show numerous short insertions/deletions, often flanked by direct repeats. In addition, a proportion of short insertions/deletions results from length differences in conserved single-base repeats. Quantification of the sequence simplicity shows that simple sequences have been more actively incorporated in the human lineage than in the rodent lineage. The combination of insertions/deletions and nucleotide substitutions along the sequence gives rise to three main regions of homology: a highly variable central region flanked by more conserved regions nearest the coding region and the polyA addition site.
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  • 62
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    Journal of molecular evolution 16 (1980), S. 149-150 
    ISSN: 1432-1432
    Keywords: Exons ; Evolution ; Heme-binding proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary It is known that globin genes contain three exons with the middle exon coding for a four-helical supersecondary structure responsible for heme binding. Since this portion of the globin peptide chain can be structurally superimposed onto the cytochromec and cytochromeb 5 chains (Argos and Rossmann 1979), it can be inferred that the cytochromec gene will contain only one coding sequence while the cytochromeb 5 gene will be composed of three exons as found in the globin gene.
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  • 63
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    Journal of molecular evolution 16 (1980), S. 211-267 
    ISSN: 1432-1432
    Keywords: Nucleic acids ; Proteins ; Natural selection ; Genetics ; Nonrandom molecular divergence ; Nonrandom REH theory ; Evolution ; mRNA ; DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary REH theory is extended by deriving the theoretical equations that permit one to analyze the nonrandom molecular divergence of homologous genes and proteins. The nonrandomicities considered are amino acid and base composition, the frequencies with which each of the four nucleotides is replaced by one of the other three, unequal usage of degenerate codons, distribution of fixed base replacements at the three nucleotide positions within codons, and distributions of fixed base replacements among codons. The latter two distributions turn out to dominate the accuracy of genetic distance estimates. The negative binomial density is used to allow for the unequal mutability of different codon sites, and the implications of its two limiting forms, the Poisson and geometric distributions, are considered. It is shown that the fixation intensity — the average number of base replacements per variable codon - is expressible as the simple product of two factors, the first describing the asymmetry of the distribution of base replacements over the gene and the second defining the ratio of the average probability that a codon will fix a mutation to the probability that it will not. Tables are given relating these features to experimentally observable quantities inα hemoglobin,β hemoglobin, myoglobin, cytochromec, and the parvalbumin group of proteins and to the structure of their corre-sponding genes or mRNAs. The principal results are (1) more accurate methods of estimating parameters of evolutionary interest from experimental gene and protein sequence data, and (2) the fact that change in gene and protein structure has been a much less efficient process than previously believed in the sense of requiring many more base replacements to effect a given structural change than earlier estimation procedures had indicated. This inefficiency is directly traceable to Darwinian selection for the nonrandom gene or protein structures necessary for biological function. The application of these methods is illustrated by detailed consideration of the rabbitα -andβ hemoglobin mRNAs and the proteins for which they code. It is found that these two genes are separated by about 425 fixed base replacements, which is a factor of two greater than earlier estimates. The replacements are distributed over approximately 114 codon sites that were free to accept base mutations during the divergence of these two genes.
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  • 64
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    Journal of molecular evolution 17 (1981), S. 31-42 
    ISSN: 1432-1432
    Keywords: Pea ; Mung bean ; Genome organization ; Evolution ; Amplification ; Repetitive DNA ; Single copy DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Essentially all of the sequences in the pea (Pisum sativum) genome which reassociate with single copy kinetics at standard (Tm -25°C) criterion follow repetitive kinetics at lower temperatures (about Tm-35°C). Analysis of thermal stability profiles for presumptive single copy duplexes show that they contain substantial mismatch even when formed at standard criterion. Thus most of the sequences in the pea genome which are conventionally defined as “single copy” are actually “fossil repeats” — that is, they are members of extensively diverged (mutuated) and thus presumably ancient families of repeated sequences. Coding sequences as represented by a cDNA probe prepared from poly-somal poly(A) + mRNA reassociate with single copy kinetics regardless of criterion and do not form mismatched duplexes. The coding regions thus appear to be composed of true single copy sequences but they cannot represent more than a few percent of the pea genome. Ancient diverged repeats are present, but not a prominent feature of the smaller mung bean (Vigna radiata) genome. An extension of a simple evolutionary model is proposed in which these and other differences in genome organization are considered to reflect different rates of sequence amplification or genome turnover during evolution. The model accounts for some of the differences between typical plant and animal genomes.
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  • 65
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    Journal of molecular evolution 17 (1981), S. 368-376 
    ISSN: 1432-1432
    Keywords: Evolution ; Phylogeny ; Maximum likelihood ; Parsimony ; Estimation ; DNA sequences
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.
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  • 66
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    Journal of molecular evolution 18 (1981), S. 15-17 
    ISSN: 1432-1432
    Keywords: Amino acid code ; Evolution ; Primitive codes ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Differences between mitochondrial codes and the universal code indicate that an evolutionary simplification has taken place, rather than a return to a more primitive code. However, these differences make it evident that the universal code is not the only code possible, and therefore earlier codes may have differed markedly from the previous code. The present universal code is probably a “frozen accident.” The change in CUN codons from leucine to threonine (Neurospora vs. yeast mitochondria) indicates that neutral or near-neutral changes occurred in the corresponding proteins when this code change took place, caused presumably by a mutation in a tRNA gene.
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  • 67
    ISSN: 1432-1432
    Keywords: Monomeric hemoglobins ; Dimeric hemoglobins ; Chironomus ; Antibodies ; Evolution ; Gene duplication
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    Topics: Biology
    Notes: Summary The monomeric hemoglobins ofChironomus tentans andC. pallidivittatus have been isolated and separated into their respective components by gel chromatography on Sephadex G-75 and ion-exchange chromatography on DEAE-Sephacel. The amino acid compositions of the purified components are given. The sequence of the 30 N-terminal amino acid residues of one of the monomeric components (Hb I fromC. pallidivittatus) was determined and found to be identical in almost all of its parts with the monomeric hemoglobins ofC. thummi (CTT III and CTT IV). Antibodies against the monomeric hemoglobins Hb I and Hb IIc and the dimeric fraction were highly specific and no cross reaction between dimeric and monomeric hemoglobins could be demonstrated. The antibodies against the monomers crossreact with the monomeric hemoglobins CTT III and CTT IV ofC. thummi. Taken together with genetic data, the immunological results indicate that divergence of monomeric from dimeric forms was an early event in the evolution of the various hemoglobins inChironomus.
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    Journal of molecular evolution 30 (1990), S. 489-492 
    ISSN: 1432-1432
    Keywords: Actinomyces ; Phosphotransferase ; Aminoglycoside ; Phylogenetic tree ; Evolution
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    Topics: Biology
    Notes: Summary The protein sequences of seven 3′-aminoglycoside phosphotransferases falling into the six identified types and three 6′-aminoglycoside phosphotransferases were analyzed to give a rooted phylogenetic tree. This tree supports the origin of these groups of enzymes in an ancestor closely related to the actinomycetes, and that horizontal transfer of the resistance genes occurred, possibly via transposons. The implications for genetic engineering of a novel antibiotic are discussed.
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  • 69
    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Evolution ; Echinoderms ; Sea stars ; DNA sequence ; Mitochondrial proteins ; Mitochondrial tRNA genes
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    Notes: Summary We have cloned and sequenced over 9 kb of the mitochondrial genome from the sea starPisaster ochraceus. Within a continuous 8.0-kb fragment are located the genes for NADH dehydrogenase subunits 1, 2, 3, and 4L (ND1, ND2, ND3, and ND4L), cytochrome oxidase subunits I, II, and III (COI, COII, and COIII), and adenosine triphosphatase subunits 6 and 8 (ATPase 6 and ATPase 8). This large fragment also contains a cluster of 13 tRNA genes between ND1 and COI as well as the genes for isoleucine tRNA between ND1 and ND2, arginine tRNA between COI and ND4L, lysine tRNA between COII and ATPase 8, and the serine (UCN) tRNA between COIII and ND3. The genes for the other five tRNAs lie outside this fragment. The gene for phenylalanine tRNA is located between cytochrome b and the 12S ribosomal genes. The genes for tRNAglu and tRNAthr are 3′ to the 12S ribosomal gene. The tRNAs for histidine and serine (AGN) are adjacent to each other and lie between ND4 and ND5. These data confirm the novel gene order in mitochondrial DNA (mtDNA) of sea stars and delineate additional distinctions between the sea star and other mtDNA molecules.
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  • 70
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    Journal of molecular evolution 19 (1982), S. 20-27 
    ISSN: 1432-1432
    Keywords: GU base pairing ; RNA replication ; Globular proteins ; Genetic code ; Evolution
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    Notes: Summary It has previously been shown that the formation of GU base pairs in RNA copying processes leads to an accumulation of G and U in both strands of the replicating RNA, which results in a non-random distribution of base triplets. In the present paper, this distribution is calculated, and, using the χ2-test, a correlation between the distribution of triplets and the amino acid composition of the evolutionarily conservative interior regions of selected globular proteins is established. It is suggested that GU wobbling in early replication of RNA could have led to the observed amino acid composition of present-day protein interiors. If this hypothesis is correct, the GU wobbling must have been very extensive in the imprecisely replicating RNA, even reaching values close to the critical for stability of its double-helical structure. Implications of the hypothesis both for the evolution of the genetic code and of proteins are discussed.
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  • 71
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    Journal of molecular evolution 19 (1983), S. 203-213 
    ISSN: 1432-1432
    Keywords: Evolution ; Phylogenetic distribution ; Repetitive-dispersed DNAs ; Speciation ; Transposons
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    Notes: Summary We have examined the phylogenetic distribution of a spectrum ofDrosophila repetitive-dispersed DNAs ranging from structurally complex transposable elements to scrambled middle repetitive sequences. Our data suggest that unlike typical “genes” these DNAs are unstable components of the drosophilid genome. The unusual behavior of these repetitive-dispersed DNAs raises the possibility that this type of sequence may have an important role in the evolution of the family Drosophilidae.
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  • 72
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    Journal of molecular evolution 33 (1991), S. 68-75 
    ISSN: 1432-1432
    Keywords: DNA ; Genome size ; Repetitive DNA ; Amphibians ; Reptiles ; Evolution
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    Notes: Summary Many characters differentiate amphibian from reptilian genomes. The former have, on the average, larger and more variable genome sizes, a greater repetitive DNA percentage, and a higher interspersion level among DNAs with different degrees of repetitivity. Reptiles have more reduced and uniform genome sizes, a repetitive DNA percentage generally lower than 50%, and a lower interspersion level. Other differences can be observed in the chromosome banding and in the correlations between genome size and other morphometric and functional parameters of the cell. The differences found in amphibians and reptiles seem to indicate that in these two vertebrate classes there is a different tendency toward or tolerance of the accumulation and preservation of genetically dispensable DNA fractions. This might depend either on a different propensity toward genic amplification or on the appearance, in reptiles, of stricter and more efficient constraints regulating genome size.
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  • 73
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    Journal of molecular evolution 33 (1991), S. 133-141 
    ISSN: 1432-1432
    Keywords: Y-chromosome ; DNA ; Human ; Primate ; Evolution ; PUPPY sequence ; Alu element
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    Notes: Summary A Y-chromosomal DNA fragment has been isolated from a human Y-Charon 21A recombinant library. Evolutionary analysis of 1F5 indicates that the size and sequence of this fragment have been conserved in higher primates. Deletion mapping and in situ hybridization analysis have localized 1F5 to the middle euchromatic portion of the long arm of the human Y chromosome at Yq11.2. Sequence analysis revealed the presence of an atypical Alu element and two regions rich in polypyrimidine-polypurine residues.
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  • 74
    ISSN: 1432-1432
    Keywords: Bacteria ; Sugars ; Phosphotransferase system ; Transport proteins ; Evolution ; Sequence comparisons ; NADH dehydrogenase ; Mitochondria
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    Notes: Summary The amino acid sequences of 15 sugar permeases of the bacterial phosphoenolpyruvatedependent phosphotransferase system (PTS) were divided into four homologous segments, and these segments were analyzed to give phylogenetic trees. The permease segments fell into four clusters: the lactose-cellobiose cluster, the fructose-mannitol cluster, the glucose-N-acetylglucosamine cluster, and the sucrose-β-glucoside cluster. Sequences of the glucitol and mannose permeases (clusters 5 and 6, respectively) were too dissimilar to establish homology with the other permeases, but short regions of statistically significant sequence similarities were noted. The functional and structural relationships of these permease segments are discussed. Some of the homologous PTS permeases were found to exhibit sufficient sequence similarity to subunits 4 and 5 of the eukaryotic mitochondrial NADH dehydrogenase complex to suggest homology. Moreover, subunits 4 and 5 of this complex appeared to be homologous to each other, suggesting that these PTS and mitochondrial proteins comprise a superfamily. The integral membrane subunits of the evolutionarily divergent mannose PTS permease, the P and M subunits, exhibited limited sequence similarity to subunit 6 of the mitochondrial F1F0-ATPase and subunit 5b of cytochrome oxidase, respectively. These results suggest that PTS sugar permeases and mitochondrial proton-translocating proteins may be related, although the possibility of convergent evolution cannot be ruled out.
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    Journal of molecular evolution 15 (1980), S. 149-159 
    ISSN: 1432-1432
    Keywords: Genes ; REH theory ; Genetic distance ; Evolution ; mRNA ; Nucleic acids
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    Notes: Summary It is shown how REH theory in conjunction with mRNA or gene sequence data can be used to obtain estimates of the fixation intensity, the number of varions, and the total mutations fixed between homologous pairs of nucleic acids. These estimates are more accurate than those that can be derived from amino acid sequence data. The method is illustrated forα andβ hemoglobin genes and these improved estimates are compared with those made from the amino acid sequences for which those genes code. Significant differences are found between the estimates made by these two methods. For theβ hemoglobin gene sequences examined here, the fixation intensity is some-what less than the protein data had suggested, and the number of rations is considerably greater. Depending on the gene sequences examined, between 62 and 83% of the codons appear able to fix mutations during the divergences considered. This reflects the constraints of natural selection on acceptable mutations. The total number of base replacements separating the genes for human, mouse, and rabbitβ hemoglobin varies from 61 to 105 depending on the pair examined. Rabbitα andβ hemoglobin are separated by at least 290 fixed mutations. For such distantly related sequences estimates made from protein and mRNA data differ less, reflecting the higher quality of information from the many observed changes in primary structure. The effects of nonrandom gene structure on these evolutionary estimates and the fact that various genetic events are not equiprobable are discussed.
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    Journal of molecular evolution 21 (1984), S. 54-57 
    ISSN: 1432-1432
    Keywords: Mitochondrion ; Cytochrome C ; Rhodospirillaceae ; Endosymbiosis ; rRNA ; Evolution
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    Notes: Summary The comparative morphology and pigmentation of protists suggest that those with tubular mitochondrial cristae belong to a different lineage than those with lamellar cristae and that the evolutionary divergence might have been very early. We propose that the difference in cristal morphology is the result of separate origins of the mitochondria from endosymbionts related to the Rhodospirillaceae (purple nonsulfur bacteria) but differing in the morphology of their internal membranes. Comparisons of the cytochromes c of protists and the Rhodospirillaceae and of 16s rRNA T1 oligonucleotide catalogs in the Rhodospirillaceae do not contradict, and in fact provide support for, the idea. More extensive evidence may be lacking simply because cytochromes c have been studied in very few protists with tubular mitochondrial cristae.
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    Journal of molecular evolution 21 (1984), S. 72-75 
    ISSN: 1432-1432
    Keywords: Heat ; Rates of copy error ; Evolution
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    Notes: Summary Heat induces a number of premutational lesions (for example, the deamination of cytosine to uracil) in DNA and RNA. These kinds of errors occur in resting as well as replicating polynucleotides. However, an increase in temperature also raises the probability of copying error occurring in nucleic acids because of increased thermal noise in the replicative machinery. In most modern genetic systems, the majority of heat-induced lesions are efficiently repaired. It follows that the importance of heat-induced error increases as the effectiveness of repair declines. We show in this paper that the error rate of enzymatic polynucleotide copying is expected to increase monotonically with temperature. We also explore the effects of temperature variations on the early evolution of biological information transmission mechanisms.
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    Journal of molecular evolution 30 (1990), S. 60-71 
    ISSN: 1432-1432
    Keywords: Cysteine endopeptidase ; Cysteine proteinase ; Inhibitor ; Cystatin ; Kininogen ; Evolution ; Amino acid sequence
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    Notes: Summary We have examined the amino acid sequences of a number of proteins that have been suggested to be related to chicken cystatin, a protein from chicken egg white that inhibits cysteine proteinases. On the basis of statistical analysis, the following proteins were found to be members of the cystatin superfamily: human cystatin A, rat cystatin A(α), human cystatin B, rat cystatin B(β), rice cystatin, human cystatin C, ox colostrum cystatin, human cystatin S, human cystatin SA, human cystatin SN, chicken cystatin, puff adder cystatin, human kininogen, ox kininogen, rat kininogen, rat T-kininogens 1 and 2, human α2HS-glycoprotein, and human histidine-rich glycoprotein. Fibronectin is shown not to be a member of this superfamily, and the c-Ha-ras oncogene protein p21(Val-12) probably is not a member also. It was convenient to divide members of the superfamily into four types on the basis of the presence of one, two, or three copies of cystatin-like segments and the presence or absence of disulfide bonds. Evolutionary dendrograms were calculated by three methods, and from these we have constructed a scheme depicting the sequence of events in the evolution of these proteins. We suggest that about 1000 million years ago a precursor containing disulfide loops appeared, and that all disulfide-containing cystatins are derived from this. We follow the evolution of the proteins of the superfamily along four main lineages, with special attention to the part that duplication of segments has played in the development of the more complex molecules.
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    Journal of molecular evolution 37 (1993), S. 426-434 
    ISSN: 1432-1432
    Keywords: Primate ; Evolution ; Protamine ; Polymerase chain reaction ; Sperm proteins
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    Notes: Abstract Protamine P1 genes have been sequenced by PCR amplification and direct DNA sequencing from 9 primates representing 5 major families, Cebidae (new world monkeys), Cercopithecidae (old world monkeys), Hylobatidae (gibbons), Pongidae (gorilla, orangutan, and chimpanzee), and Hominidae (human). In this recently diverged group of primates these genes are clearly orthologous but very variable, both at the DNA level and in their expressed amino acid sequences. The rate of variation amongst the protamine Pls indicates that they are amongst the most rapidly diverging polypeptides studied. However, some regions are conserved both in primates and generally in other placental mammals. These are the 13 N-terminal residues (including a region of alternating serine and arginine residues (the motif SRSR, res. 10–13) susceptible to Ser phosphorylation), a tract of six Arg residues (res. 24–29) in the center of the molecule, and a six-residue region (RCCRRR, res. 39–44), consisting of a pair of cysteines flanked by arginines. Detailed consideration of nearest neighbor matrices and trees based on maximum parsimony indicates that PI genes from humans, gorillas, and chimpanzees are very similar. The amino acid and nucleotide differences between humans and gorillas. are fewer than those between humans and chimpanzees. This finding is at variance with data from DNA-DNA hybridization and extensive globin and mitochondrial DNA sequences which place human and chimpanzee as closest relatives in the super family, Hominoidea. This may be related to the fact that protamine Pls are expressed in germ line rather than somatic cells. In contrast to the variability of the exon regions of the protamine P1 genes, the sequence of the single intron is highly conserved.
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    Journal of molecular evolution 38 (1994), S. 1-17 
    ISSN: 1432-1432
    Keywords: HSP70 ; Heat shock ; Evolution ; Phylogeny ; Yeast ; Multigene family ; Subcellular compartmentalization
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    Notes: Abstract Eukaryotic genomes encode multiple 70-kDa heat-shock proteins (HSP70s). The Saccharomyces cerevisiae HSP70 family is comprised of eight members. Here we present the nucleotide sequence of the SSA3 and SSB2 genes, completing the nucleotide sequence data for the yeast HSP70 family. We have analyzed these yeast sequences as well as 29 HSP70s from 24 additional eukaryotic and prokaryotic species. Comparison of the sequences demonstrates the extreme conservation of HSP70s; proteins from the most distantly related species share at least 45% identity and more than one-sixth of the amino acids are identical in the aligned region (567 amino acids) among all proteins analyzed. Phylogenetic trees constructed by two independent methods indicate that ancient molecular and cellular events have given rise to at least four monophyletic groups of eukaryotic HSP70 proteins. Each group of evolutionarily similar HSP70s shares a common intracellular localization and is presumed to be comprised of functional homologues; these include heat-shock proteins of the cytoplasm, endoplasmic reticulum, mitochondria, and chloroplasts. HSP70s localized in mitochondria and plastids are most similar to the DnaK HSP70 homologues in purple bacteria and cyanobacteria, respectively, which is consistent with the proposed prokaryotic origin of these organelles. The analyses indicate that the major eukaryotic HSP70 groups arose prior to the divergence of the earliest eukaryotes, roughly 2 billion years ago. In some cases, as exemplified by the SSA genes encoding the cytoplasmic HSP70s of S. cerevisiae, more recent duplication events have given rise to subfamilies within the major groups. The S. cerevisiae SSB proteins comprise a unique subfamily not identified in other species to date. This subfamily appears to have resulted from an ancient gene duplication that occurred at approximately the same time as the origin of the major eukaryotic HSP70 groups.
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  • 81
    ISSN: 1432-1432
    Keywords: Drosophila melanogaster ; Evolution ; Hybrid dysgenesis ; I elements ; Transposons
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    Notes: Summary There are two categories of strains inDrosophila melanogaster with respect to the I-R system of hybrid dysgenesis. The inducer strains contain particular transposable elements named I factors. They are not present in the strains of the other category called reactive (R) strains. Defective I elements are present in the pericentromeric regions of both categories of strains. This last subfamily of I sequences has not yet been described in detail and little is known about its origin. In this paper, we report that the defective I elements display an average of 94% of sequence identity with each other and with the transposable I factor. The results suggest that they cannot be the progenitors of the present day I factors, but that each of these two subfamilies started to evolve independently several million years ago. Furthermore, the sequence comparison of these I elements with an active I factor fromDrosophila teissieri provides useful information about when the deleted I elements became immobilized.
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  • 82
    ISSN: 1432-1432
    Keywords: Repetitive DNA ; Tandem repeats ; Sequence analysis ; Recombination ; Isolated populations ; Evolution
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    Notes: Abstract The satellite DNA family pDoP102 is species specific for the cave cricket Dolichopoda schiavazzii, an endemic species of mainland and insular Tuscany. It consists of numerous tandemly arranged repeats, 102 bp in length, and evolved most probably after cladogenesis of D. schiavazzii from the D. baccettii-aegilion group within the last 2.3 ± 0.8 million years. A sequence comparison of 31 clones (53 repetition units) from three isolated populations reveals a very high degree of sequence homogeneity within the species with no evidence for any specific population features. This appears to be in contrast to the results of allozyme analyses which account for a relatively old evolutionary divergence of the Elba island population from the mainland ones. Since the assumption of actual gene flow and recent colonization is rejected, the observed sequence homogeneity is hypothesized to be maintained by recombination processes preventing fixation of newly introduced mutations on pDoP102 sequence clusters.
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    Journal of molecular evolution 32 (1991), S. 296-303 
    ISSN: 1432-1432
    Keywords: Prebiotic chemistry ; Primordial soup ; Oparin hypothesis ; Evolution ; Impact catastrophism
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    Notes: Summary In the traditional concept for the origin of life as proposed by Oparin and Haldane in the 1920s, prebiotic reactants became slowly concentrated in the primordial oceans and life evolved slowly from a series of highly protracted chemical reactions during the first billion years of Earth's history. However, chemical evolution may not have occurred continuously because planetesimals and asterioids impacted the Earth many times during the first billion years, may have sterilized the Earth, and required the process to start over. A rapid process of chemical evolution may have been required in order that life appeared at or before 3.5 billion years ago. Thus, a setting favoring rapid chemical evolution may be required. A chemical evolution hypothesis set forth by Woese in 1979 accomplished prebiotic reactions rapidly in droplets in giant atmospheric reflux columns. However, in 1985 Scherer raised a number of objections to Woese's hypothesis and concluded that it was not valid. We propose a mechanism for prebiotic chemistry in clouds that satisfies Scherer's concerns regarding the Woese hypothesis and includes advantageous droplet chemistry. Prebiotic reactants were supplied to the atmosphere by comets, meteorites, and interplanetary dust or synthesized in the atmosphere from simple compounds using energy sources such as ultraviolet light, corona discharge, or lightning. These prebiotic monomers would have first encountered moisture in cloud drops and precipitation. We propose that rapid prebiotic chemical evolution was facilitated on the primordial Earth by cycles of condensation and evaporation of cloud drops containing clay condensation nuclei and nonvolatile monomers. For example, amino acids supplied by, or synthesized during entry of, meteorites, comets, and interplanetary dust would have been scavenged by cloud drops containing clay condensation nuclei. Polymerization would have occurred within cloud systems during cycles of condensation, freezing, melting, and evaporation of cloud drops. We suggest that polymerization reactions occurred in the atmosphere as in the Woese hypothesis, but life originated in the ocean as in the Oparin-Haldane hypothesis. The rapidity with which chemical evolution could have occurred within clouds accommodates the time constraints suggested by recent astrophysical theories.
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    Journal of molecular evolution 32 (1991), S. 415-420 
    ISSN: 1432-1432
    Keywords: Drosophila melanogaster ; Drosophila virilis ; mastermind ; Gene comparison ; Repetitive sequences ; Homopolymers ; Evolution
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    Notes: Summary Themastermind gene ofDrosophila melanogaster encodes a novel, highly repetitive nuclear protein required for neural development. To identify functionally important regions we have initiated an interspecific comparison of the gene inDrosophila virilis. Mastermind transcription and genomic organization are similar in both species and sequence analysis reveals significant conservation in a major cluster of charged amino acids. In contrast, extensive variation is noted in homopolymer domains that immediately flank the acidic cluster. Distinct patterns of evolutionary change can be identified: the major difference between unique regions are occasional amino acid substitutions whereas the repetitive areas are characterized by numerous large in-frame insertions/deletions and a nearly threefold higher rate of amino acid replacement. Conservation of the acidic domain suggests that it has an important functional role whereas the hypervariable homopolymer regions appear to be under less selective constraints than adjacent unique areas.
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    Journal of molecular evolution 36 (1993), S. 448-457 
    ISSN: 1432-1432
    Keywords: Retrovirus ; HIV ; CD4 ; Minus strand ; Alternate reading frame ; Frameshift ; Divergence ; Evolution
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    Topics: Biology
    Notes: Summary A local sequence similarity of HIV envelope proteins (gp120 and gp41) to immunoglobulins suggests that a mimicry phenomenon may form the basis of the HIV-cell membrane interaction and of HIV-induced autoimmune reaction. We explored the hypothesis of any deeper relationship between HIV env proteins and immunoglobulin family members. An overall DNA sequence similarity between gp41 coding region of env gene and the HIV-receptor CD4 gene was observed and a 14-base-long oligonucleotide, almost unique in the GenBank, was found in gp41 and CD4 genes. The alignment of env gene to CD4 gene and to 84 different sequences showed a significantly higher homology score and a nonrandom similarity in the CD4-env alignment. A significant similarity was also found between the env protein and the sequence encoded by an alternate reading frame of CD4 gene. Our observations suggest that gp41 coding region might have a different origin than the gp120 coding region of the env gene, and that a divergent evolution might link gp41 to CD4 or immunoglobulin family members. In this study the analysis of alternate-reading-frame products is also proposed as a novel approach to investigate evolutionary links and structure-function relationships.
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    Journal of molecular evolution 35 (1992), S. 156-180 
    ISSN: 1432-1432
    Keywords: DNA damage ; DNA repair ; Chromatin ; Evolution ; Nucleosomes ; Nuclear matrix ; Active genes ; Z-DNA ; Sperm ; Mutation ; Molecular clock
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    Topics: Biology
    Notes: Summary Some evolutionary consequences of different rates and trends in DNA damage and repair are explained. Different types of DNA damaging agents cause nonrandom lesions along the DNA. The type of DNA sequence motifs to be preferentially attacked depends upon the chemical or physical nature of the assaulting agent and the DNA base composition. Higher-order chromatin structure, the nonrandom nucleosome positioning along the DNA, the absence of nucleosomes from the promoter regions of active genes, curved DNA, the presence of sequence-specific binding proteins, and the torsional strain on the DNA induced by an increased transcriptional activity all are expected to affect rates of damage of individual genes. Furthermore, potential Z-DNA, H-DNA, slippage, and cruciform structures in the regulatory region of some genes or in other genomic loci induced by torsional strain on the DNA are more prone to modification by genotoxic agents. A specific actively transcribed gene may be preferentially damaged over nontranscribed genes only in specific cell types that maintain this gene in active chromatin fractions because of (1) its decondensed chromatin structure, (2) torsional strain in its DNA, (3) absence of nucleosomes from its regulatory region, and (4) altered nucleosome structure in its coding sequence due to the presence of modified histones and HMG proteins. The situation in this regard of germ cell lineages is, of course, the only one to intervene in evolution. Most lesions in DNA such as those caused by UV or DNA alkylating agents tend to diminish the GC content of genomes. Thus, DNA sequences not bound by selective constraints, such as pseudogenes, will show an increase in their AT content during evolution as evidenced by experimental observations. On the other hand, transcriptionally active parts may be repaired at rates higher than inactive parts of the genome, and proliferating cells may display higher repair activities than quiescent cells. This might arise from a tight coupling of the repair process with both transcription and replication, all these processes taking place on the nuclear matrix. Repair activities differ greatly among species, and there is a good correlation between life span and repair among mammals. It is predicted that genes that are transcriptionally active in germ-cell lineages have a lower mutation rate than bulk DNA, a circumstance that is expected to be reflected in evolution. Exception to this rule might be genes containing potential Z-DNA, H-DNA, or cruciform structures in their coding or regulatory regions that appear to be refractory to repair. This study supports the molecular clock hypothesis when applied to one gene within a group of related species and contends that evolutionary rates might vary between genes and gene segments not only as a result of differences in selective constraints but also as a result of differences in the rate of damage minus rate of repair among different segments of chromatin DNA.
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    Journal of molecular evolution 40 (1995), S. 570-577 
    ISSN: 1432-1432
    Keywords: Alternate reading frames ; Evolution ; Overlapping frames ; Homology search ; Primary sequence analysis ; Polycistronic genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Hypothetical Products from Noncoding Frames (i.e., HyPNoFs) are hypothetical, not-coded proteins, translated from alternate reading frames (i.e., coding+1 and coding+2) of cDNAs. HyPNoFs of CD4, PKC, oncostatin, bcl-2 proto-oncogene, tumor suppressor p53, cystic fibrosis transmembrane regulator (CFTR), and tumor necrosis factors a and β were searched as query sequences vs the SWISS-PROT data bank. Homology searches carried out revealed that hypothetical products (i.e., HyPNoFs) may share high similarity with real protein products actually coded. Sequence similarity of hypothetical products to real proteins is sometimes very high, suggesting common conformational features, according to the Sander and Schneider cutoff value. This finding supports the hypothesis that eukaryotic DNA, currently considered to be monocistronic, might occasionally have polycistronic regions, carrying different protein messages on overlapping frames. As yet, polycistronic genes have been observed in viral genomes only. The presence of polycistronic regions in eukaryotic genes is likely reminiscent of an ancient strategy, rather than a present feature of the genome in eukaryotes. These data suggest that thorough investigation of HyPNoFs is likely to improve our ability to trace genes' evolution and to investigate structure-function relationships of protein and DNA sequences.
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    Journal of molecular evolution 40 (1995), S. 601-607 
    ISSN: 1432-1432
    Keywords: Prolamine ; Sperm proteins ; Evolution ; Mammals
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    Topics: Biology
    Notes: Abstract Prolamine P1 genes have been sequenced following PCR amplification from 11 mammals representing five major mammalian orders: Rodentia (rat and guinea pig), Carnivora (cat and bear), Proboscidea (elephant), Perissodactyla (horse), and Artiodactyla (camel, deer, elk, moose, and gazelle). The predicted amino acid sequence for these genes together with previously reported sequences results in a data set of 25 different P1 genes and 30 different P1 amino acid sequences. The alignment of all these sequences reveals that prolamines are amongst the most rapidly diverging proteins studied. In spite of the large number of differences there are conserved motifs that are also common to birds such as the N-terminal ARYR followed by the triple alternating SRSRSR phosphorylation site. The central region contains 3 arginine clusters consisting of 5–6 arginines each. The C-terminus appears to be the most variable region of the protamines. Overall the molecular evolution of P1 genes is in agreement with the expected species evolution supporting that these genes have evolved vertically.
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    Journal of molecular evolution 36 (1993), S. 545-554 
    ISSN: 1432-1432
    Keywords: Echinoderms ; Evolution ; Phylogeny ; mtDNA ; Mitochondrial gene arrangements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Previous analyses have demonstrated that, among the echinoderms, the sea star (class: Asteroidea) mitochondrial genome contains a large inversion in comparison to the mitochondrial DNA of sea urchins (class: Echinoidea). Polymerase chain reaction amplification, DNA cloning, and sequencing have been used to examine the relationships of the brittle stars (class: Ophiuroidea) and sea cucumbers (class: Holothuroidea) to the sea stars and sea urchins. The DNA sequence of the regions spanning potential inversion junctions in both brittle stars and sea cucumbers has been determined. This study has also revealed a highly modified tRNA cluster in the ophiuroid mitochondrial genome. Our data indicate mitochondrial gene arrangement patterns that group the sea cucumbers with sea urchins and sea stars with brittle stars. This use of molecular characters clarifies the relationships among these classes.
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  • 90
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    Journal of molecular evolution 39 (1994), S. 489-495 
    ISSN: 1432-1432
    Keywords: Repetitive sequences ; Sequence variability ; Evolution ; Heterochromatin ; DNA curvature
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two highly abundant satellite DNAs comprise 36% of the Tenebrio obscurus (Tenebrionidae, Coleoptera) genome. They are designated as satellite I and satellite II with the monomer length of 344 and 142 base pairs (bp), respectively. Both satellites differ in their nucleotide (nt) sequences, but the frequency of point mutations, well-conserved length of monomer variants, stretches of shared mutations characteristic for the process of gene conversion, and distribution of both satellites in regions of centromeric heterochromatin of all chromosomes indicate that the same evolutionary processes act on both of them with the same, or similar, rate. While satellite I shares no sequence similarity with any other known nt sequence, satellite II is 79.7% homologous with the highly abundant satellite from closely related Tenebrio molitor. Difference in the frequency of point mutations and absence of shared mutations indicating gene conversion strongly suggest that in these two closely related species mutational processes affecting satellite DNAs seem to be changed. Retarded electrophoretic mobility, due to sequence-induced curvature of DNA helix axis, was observed for T. obscurus satellite II, but not for satellite I. Although evolutionary processes act with different rates in T. obscurus and T. molitor satellites the monomer length and sequence-induced curvature are well preserved in both 142-bp satellites, as well as in, at the nt sequence level completely divergent, Palorus ratzeburgii (Tenebrionidae) satellite, indicating potential importance of these parameters in their evolution.
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  • 91
    ISSN: 1432-1432
    Keywords: Snake venom ; Bothrops ; Phospholipase ; Myotoxin ; Evolution ; cDNA ; Gene duplication ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The sequence coding for a snake venom phospholipase A2 (PLA2), BJUPLA2, has been cloned from a Bothrops jararacussu venom gland cDNA library. The cDNA sequence predicts a precursor containing a 16-residue signal peptide followed by a molecule of 122 amino acid residues with a strong sequence similarity to group II snake venom PLA2's. A striking feature of the cDNA is the high sequence conservation of the 5′ and 3′ untranslated regions in cDNAs coding for PLA2's from a number of viper species. The greatest sequence variation was observed between the regions coding for the mature proteins, with most substitutions occurring in nonsynonymous sites. The phylogenetic tree constructed by alignment of the amino acid sequence of BJUPLA2 with group II PLA2's in general groups them according to current taxonomical divisions and/or functional activity. It also suggests that gene duplications may have occurred at a number of different points during the evolution of snake venom group II PLA2's.
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  • 92
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    Journal of molecular evolution 41 (1995), S. 238-246 
    ISSN: 1432-1432
    Keywords: Cellular slime molds ; Animals ; Fungi ; Plantae ; Maximum-likelihood method ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phylogenetic position of Dictyostelium inferred from 18S rRNA data contradicts that from protein data. Protein trees always show the close affinity of Dictyostelium with animals, fungi, and plants, whereas in 18S rRNA trees the branching of Dictyostelium is placed at a position before the massive radiation of protist groups including the divergence of the three kingdoms. To settle this controversial issue and to determine the correct position of Dictyostelium, we inferred the phylogenetic relationship among Dictyostelium and the three kingdoms Animalia, Fungi, and Plantae by a maximum-likelihood method using 19 different protein data sets. It was shown at the significance level of 1 SE that the branching of Dictyostelium antedates the divergence of Animalia and Fungi, and Plantae is an outgroup of the Animalia-Fungi-Dictyostelium clade.
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  • 93
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    Journal of molecular evolution 41 (1995), S. 293-298 
    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to theDrosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in themontium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling speciesD. auraria, D. triauraria, andD. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental speciesD. bicomuta, D. serrata, andD. birchii, as well as in the Afrotropical speciesD. diplacantha andD. seguyi. The complete separation of the genes is observed in the Indian speciesD. kikkawai andD. jambulina and in the Afrotropical speciesD. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among themontium species are discussed.
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  • 94
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    Journal of molecular evolution 41 (1995), S. 293-298 
    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to the Drosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in the montium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling species D. auraria, D. triauraria, and D. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental species D. bicomuta, D. serrata, and D. birchii, as well as in the Afrotropical species D. diplacantha and D. seguyi. The complete separation of the genes is observed in the Indian species D. kikkawai and D. jambulina and in the Afrotropical species D. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among the montium species are discussed.
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  • 95
    ISSN: 1432-1432
    Keywords: Giardia ; Trichomonas ; CDK ; CDC ; Unicellular ; Metazoa ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cyclin-dependent kinase (CDK) and cell division control (CDC2) sequences are strongly conserved among eukaryotes and may complement the use of other sequence families in eukaryotic phylogenetic inference. We synthesized degenerate PCR primers to amplify the catalytic region of CDK homologs in representatives of the earliest available lineages of eukaryotes. CDK family sequence-based, maximum-likelihood distance measurements with neighbor joining, and Fitch-Margoliash least-squares analyses produced unrooted dendrograms that included protists, yeasts, and higher eukaryotes. Bootstrap confidence estimates supported CDK-based phylogenetic groupings among the protists, fungi, and vertebrates although resolution within these groups was often insignificant. However, Trichomonas vaginalis and Giardia lamblia exhibited two of the most divergent CDK-like sequences consistent with rRNA-phylogenetic inference of early divergence of these eukaryotic lineages. In the evolution from unicellular to multicellular organisms, a constellation of amino acid residues aligning with the human, CDK N-terminal β sheet may have undergone abrupt replacement.
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  • 96
    ISSN: 1432-1432
    Keywords: Lens ; Crystallin ; Squid ; Chicken ; Gene ; Regulation ; AP-1 ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previous experiments have shown that the minimal promoters required for function of the squid SL20-1 and SL11 crystallin genes in transfected rabbit lens epithelial cells contain an overlapping AP-1/antioxidant responsive element (ARE) upstream of the TATA box. This region resembles the PL-1 and PL-2 elements of the chicken βB 1-cry stallin promoter which are essential for promoter function in transfected primary chicken lens epithelial cells. Here we demonstrate by site-directed mutagenesis that the AP-1/ARE sequence is essential for activity of the squid SL20-1 and SL11 promoters in transfected embryonic chicken lens cells and fibroblasts. Promoter activity was higher in transfected lens cells than in fibroblasts. Electrophoretic mobility shift and DNase protection experiments demonstrated the formation of numerous complexes between nuclear proteins of the embryonic chicken lens and the AP-1/ARE sequences of the squid SL20-1 and SL11 crystallin promoters. One of these complexes comigrated and cross-competed with that formed with the PL-1 element of the chicken βB1-crystallin promoter. This complex formed with nuclear extracts from the lens, heart, brain, and skeletal muscle of embryonic chickens and was eliminated by competition with a consensus AP-1 sequence. The nonfunctional mutant AP-1/ ARE sequences did not compete for complex formation. These data raise the intriguing possibility that entirely different, nonhomologous crystallin genes of the chicken and squid have convergently evolved a similar cis-acting regulatory element (AP-1/ARE) for high expression in the lens.
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  • 97
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    Journal of molecular evolution 41 (1995), S. 813-832 
    ISSN: 1432-1432
    Keywords: Phylogeny ; Evolution ; Carbamoylphosphate synthetase ; Dihydroorotase ; Aspartate transcarbamoylase ; Intron ; Exon ; Arginine biosynthesis ; Pyrimidine biosynthesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Carbamoylphosphate is a common intermediate in the metabolic pathways leading to the biosynthesis of arginine and pyrimidines. The amino acid sequences of all available proteins that catalyze the formation of carbamoylphosphate were retrieved from Genbank and aligned to estimate their mutual phylogenetic relations. In gram-negative bacteria carbamoylphosphate is synthesized by a two-subunit enzyme with glutamiriase and carbamoylphosphate synthetase (CPS) activity, respectively. In gram-positive bacteria and lower eukaryotes this two-subunit CPS has become dedicated to arginine biosynthesis, while in higher eukaryotes the two subunits fused and subsequently lost the glutaminase activity. The CPS dedicated to pyrimidine synthesis is part of a multifunctional enzyme (CPS II), encoding in addition dihydroorotase and aspartate transcarbamoylase. Evidence is presented to strengthen the hypothesis that the two “kinas” subdomains of all CPS isozymes arose from a duplication of an ancestral gene in the progenote. A further duplication of the entire CPS gene occurred after the divergence of the plants and before the divergence of the fungi from the eukaryotec root, generating the two isoenzymes involved in either the synthesis of arginine or that of pyrimidines. The mutation rate was found to be five- to tenfold higher after the duplication than before, probably reflecting optimization of the enzymes for their newly acquired specialized function. We hypothesize that this duplication arose from a need for metabolic channeling for pyrimidine biosynthesis as it was accompanied by the tagging of the CPS gene with the genes for dihydroorotase and aspartate transcarbamoylase, and as the duplication occurred independently also in gram-positive bacteria. Analysis of the exon-intron organization of the two “kinase” subdomains in CPS I and II suggests that ancient exons may have comprised approx. 19 amino acids, in accordance with the prediction of the “intron-early” theory.
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  • 98
    ISSN: 1432-1432
    Keywords: Ribonuclease ; Gene duplication ; Evolution ; Ruminants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic analysis, based on the primary structures of mammalian pancreatic-type ribonucleases, indicated that gene duplication events, which occurred during the evolution of ancestral ruminants, gave rise to the three paralogous enzymes present in the bovine species. Herein we report data that demonstrate the existence of the orthologues of the bovine pancreatic, seminal, and cerebral ribonucleases coding sequences in the genomes of giraffe and sheep. The “seminal” sequence is a pseudogene in both species. We also report an analysis of the transcriptional expression of ribonuclease genes in sheep tissues. The data presented support a model for positive selection acting on the molecular evolution of ruminant ribonuclease genes.
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  • 99
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    Journal of molecular evolution 17 (1981), S. 167-181 
    ISSN: 1432-1432
    Keywords: Evolution ; Genetics ; REH theory ; Mutations ; Natural selection ; Nucleic acids ; Proteins ; Paleogenetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have independently repeated the computer simulations on which Nei and Tateno (1978) base their criticism of REH theory and have extended the analysis to include mRNAs as well as proteins. The simulation data confirm the correctness of the REH method. The high average value of the fixation intensity μ2 found by Nei and Tateno is due to two factors: 1) they reported only the five replications in which μ2 was high, excluding the forty-five replications containing the more representative data;and 2) the lack of information, inherent to protein sequence data, about fixed mutations at the third nucleotide position within codons, as the values are lower when the estimate is made from the mRNAs that code for the proteins. REH values calculated from protein or nucleic acid data on the basis of the equiprobability of genetic events underestimate, not overestimate, the total fixed mutations. In REH theory the experimental data determine the estimate T2 of the time average number of codons that have been free to fix mutations during a given period of divergence. In the method of Nei and Tateno it is assumed, despite evidence to the contrary, that every amino acid position may fix a mutation. Under the latter assumption, the measure X2 of genetic divergence suggested by Nei and Tateno is not tenable: values of X2 for theα hemoglobin divergences are less than the minimum number of fixed substitutions known to have occurred. Within the context of REH theory, a paradox, first posed by Zuckerkandl, with respect to the high rate of covarion turnover and the nature of general function sites in proteins is resolved.
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  • 100
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    Journal of molecular evolution 30 (1990), S. 333-346 
    ISSN: 1432-1432
    Keywords: Protamine ; Evolution ; Nuclear protein ; DNA condensation ; Sperm proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The availability of the amino acid sequence for nine different mammalian P1 family protamines and the revised amino acid sequence of the chicken protamine galline (Oliva and Dixon 1989) reveals a much close relationship between mammalian and avian protamines than was previously thought (Nakano et al. 1976). Dot matrix analysis of all protamine genes for which genomic DNA or cDNA sequence is available reveals both marked sequence similarities in the mammalian protamine gene family and internal repeated sequences in the chicken protamine gene. The detailed alignments of the cis-acting regulatory DNA sequences shows several consensus sequence patterns, particularly the conservation of a cAMP response element (CRE) in all the protamine genes and of the regions flanking the TATA box, CAP site, N-terminal coding region, and polyadenylation signal. In addition we have found a high frequency of the CA dinucleotide immediately adjacent to the CRE element of both the protamine genes and the testis transition proteins, a feature not present in other genes, which suggests the existence of an extended CRE motif involved in the coordinate expression of protamine and transition protein genes during spermatogenesis. Overall these findings suggest the existence of an avian-mammalian P1 protamine gene line and are discussed in the context of different hypotheses for protamine gene evolution and regulation.
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