Optimization of speed and accuracy of decoding in translation

The speed and accuracy of protein synthesis are fundamental parameters for understanding the fitness of living cells, the quality control of translation, and the evolution of ribosomes. In this study, we analyse the speed and accuracy of the decoding step under conditions reproducing the high speed of translation in vivo. We show that error frequency is close to 10⁻³, consistent with the values measured in vivo. Selectivity is predominantly due to the differences in k_cat values for cognate and near-cognate reactions, whereas the intrinsic affinity differences are not used for tRNA discrimination. Thus, the ribosome seems to be optimized towards high speed of translation at the cost of fidelity. Competition with near- and non-cognate ternary complexes reduces the rate of GTP hydrolysis in the cognate ternary complex, but does not appreciably affect the rate-limiting tRNA accommodation step. The GTP hydrolysis step is crucial for the optimization of both the speed and accuracy, which explains the necessity for the trade-off between the two fundamental parameters of translation.     

Morphological embedding and phonetic reduction: the case of triconstituent compounds

In this paper we propose that the internal bracketing of a word with more than two morphemes is reflected in the phonetic implementation. We hypothesize that embedded forms show more phonetic reduction than forms at higher structural levels (‘Embedded Reduction Hypothesis’). This paper tests the prediction of the Embedded Reduction Hypothesis with triconstituent compounds. The analysis of the durational properties of almost 500 compound tokens shows that there is a lengthening effect on the non-embedded constituent, and a shortening effect on the adjacent embedded constituent. Yet, this predicted effect of embedding interacts with other lexical factors, above all the bigram frequency of the embedded compound. At a theoretical level, these effects mean that the durational properties of the cross-boundary constituents are indicative of the hierarchical structure and of the strength of the internal boundary of triconstituent compounds. Hence, morphological structure is reflected in the speech signal.     

Phytogeography of the bryophyte floras of oak forests and páramo of the Cordillera de Talamanca, Costa Rica

Aim Central America is a biogeographically interesting area because of its location between the rich and very different biota of North and South America. We aim to assess phytogeographical patterns in the bryophyte floras of oak forests and páramo of the Cordillera de Talamanca, Costa Rica. Location Tropical America, in particular the montane area of Cordillera de Talamanca, Costa Rica. Methods The analysis is based on a new critical inventory of the montane bryophyte flora of Cordillera de Talamanca. All species were assigned to phytogeographical elements on the basis of their currently known distribution. Absolute and percentage similarities were employed to evaluate floristic affinities. Results A total of 401 species [191 hepatics (liverworts), one hornwort, 209 mosses] are recorded; of these, 251 species (128 hepatics, one hornwort, 122 mosses) occur in oak forests. Ninety‐three per cent of all oak forest species are tropical in distribution, the remaining 7% are temperate (4%) and cosmopolitan (3%) species. The neotropical element includes almost 74% of the species, the wide tropical element (pantropical, amphi‐atlantic, amphi‐pacific) only 19%. A significant part of the neotropical species from oak forests are species with tropical Andean‐centred ranges (27%). As compared with bryophyte species, vascular plant genera in the study region are represented by fewer neotropical, more temperate and more amphi‐pacific taxa. Bryophyte floras of different microhabitats within the oak forest and epiphytic bryophyte floras on Quercus copeyensis in primary, early secondary and late secondary oak forest show a similar phytogeographical make‐up to the total oak forest bryophyte flora. Comparison of oak forest and páramo reveals a greater affinity of the páramo bryophyte flora to temperate regions and the great importance of the páramo element in páramo. Surprisingly, oak forests have more Central American endemics than páramo. Main conclusions (1) Providing first insights into the phytogeographical patterns of the bryophyte flora of oak forests and páramo, we are able to confirm general phytogeographical trends recorded from vascular plant genera of the study area although the latter were more rich in temperate taxa. (2) Andean‐centred species are a conspicuous element in the bryophyte flora of Cordillera de Talamanca, reflecting the close historical connection between the montane bryophyte floras of Costa Rica and South America. (3) High percentages of Central American endemics in the bryophyte flora of the oak forests suggest the importance of climatic changes associated with Pleistocene glaciations for allopatric speciation.     

Photoinduced Seed Germination of Oenothera biennis L: II. Analysis of the Photoinduction Period

The photoinduction period of Oenothera biennis L. seed germination was analyzed by varying the photoinduction temperature and by substituting red light pulses for continuous red light. At 24°C, seeds require 36 hours of continuous red light for maximal percent germination. The optimal photoinduction temperature is 32°C, with higher and lower temperatures being strongly inhibitory. A 30 minute exposure to far-red light, given immediately after a red light period of 1 to 36 hours, reduces germination by about 25%. Seeds escape from far-red inhibition with a half-time of 5 to 10 hours, depending on the length of the red exposure that precedes the far-red light. Periodic 15 minute pulses of red light can substitute for continuous red light in stimulating germination. Ted red light pulses, with 6 hours of darkness between successive pulses, cause maximal germination. The response to periodic red light is fully reversible by far-red light. Probit analysis of the periodic light response shows that as the length of the dark periods between successive pulses increases, less incident light is needed to induce germination but the population variance in light sensitivity remains constant. Probit analysis of the temperature response shows that as the photoinduction temperature increases from 16 to 32°C, less incident light is needed to induce germination and the population variance in light sensitivity also increases.     

A light and electron microscopic study of the quadriflagellate green algaSpermatozopsis exsultans

The green flagellateSpermatozopsis exsultans Korshikov has been studied in culture by light and electron microscopy. The organism is naked, bears four flagella and is conspicuously spirally twisted. The ultrastructure and location of cell organelles (except the flagellar apparatus) has been investigated in detail using an absolute configuration analysis. With the exception of a doubling of the flagella and of the secondary cytoskeletal microtubule system,S. exsultans has the exact same complement of organelles occupying the same relative positions as has been described forS. similis. The two species are therefore correctly placed in the same genus. The usefulness of absolute orientations of cell organelles for green algal taxonomy and phylogeny is stressed.Dedicated to Prof.M. Mix on the occasion of her 60th birthday.     

Efficient fertile plant regeneration from protoplasts of the Indica rice breeding line IR72 (Oryza sativa L.)

Protoplasts were isolated from embryogenic cell suspensions obtained from mature seed derived embryogenic callus of the advanced Indica type rice breeding line IR72 available from IRRI (International Rice Research Institute), Manila. Culture of protoplasts with the agarose bead type method without nurse culture led to sustained proliferation of protoplast derived clones. A simple culture protocol was developed which stimulated embryogenic development. Germination of somatic embryos has so far produced 277 green plants from 6 independent experiments. 117 plants have been transferred to soil and are growing in the greenhouse. A few of them have already flowered and set seeds.Abbreviations 2,4-D, 2,4 Dichlorophenoxyacetic acid - BAP Benzylaminopurine - CH Casein hydrolysate - ECS Embryogenie cell suspension - Kn Kinetin - NAA Napthaleneacetic acid; Media: - AA Muller and Grafe 1978 - MS Murashige and Skoog 1962 - N6 Chu et al. 1975 - R2 Ohira et al. 1973     

Action Spectrum of the Activity of Acifluorfen-methyl, a Diphenyl Ether Herbicide, in Chlamydomonas eugametos

Light is required for the herbicide activity of diphenyl ether herbicides. An action spectrum of acifluorfen-methyl activity with Chlamydomonas eugametos (Moewus) determined that cell death occurred at two peaks of light; 450 and 670 nanometers. These data indicate both chlorophyll and carotenoids, but not riboflavin, are involved in herbicide toxicity.     

Photosynthesis involvement in the mechanism of action of diphenyl ether herbicides

Photosynthesis is not required for the toxicity of diphenyl ether herbicides, nor are chloroplast thylakoids the primary site of diphenyl ether herbicide activity. Isolated spinach (Spinacia oleracea L.) chloroplast fragments produced malonyl dialdehyde, indicating lipid peroxidation, when paraquat (1,1′-dimethyl-4,4′-bipyridinium ion) or diuron [3-(3,4-dichlorophenyl)-1,1-dimethylurea] were added to the medium, but no malonyl dialdehyde was produced when chloroplast fragments were treated with the methyl ester of acifluorfen (methyl 5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoic acid), oxyfluorfen [2-chloro-1-(3-ethoxy-4-nitrophenoxy)-4-(trifluoromethyl)benzene], or MC15608 (methyl 5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-chlorobenzoate). In most cases the toxicity of acifluorfen-methyl, oxyfluorfen, or MC15608 to the unicellular green alga Chlamydomonas eugametos (Moewus) did not decrease after simultaneous treatment with diuron. However, diuron significantly reduced cell death after paraquat treatment at all but the highest paraquat concentration tested (0.1 millimolar). These data indicate electron transport of photosynthesis is not serving the same function for diphenyl ether herbicides as for paraquat. Additional evidence for differential action of paraquat was obtained from the superoxide scavenger copper penicillamine (copper complex of 2-amino-3-mercapto-3-methylbutanoic acid). Copper penicillamine eliminated paraquat toxicity in cucumber (Cucumis sativus L.) cotyledons but did not reduce diphenyl ether herbicide toxicity.