Three phases in the evolution of the standard genetic code: how translation could get started

A primordial genetic code is proposed, having only four codons assigned, GGC meaning glycine, GAC meaning aspartate/glutamate, GCC meaning alanine-like and GUC meaning valine-like. Pathways of ambiguity reduction enlarged the codon repertoire with CUC meaning leucine, AUC meaning isoleucine, ACC meaning threonine-like and GAG meaning glutamate. Introduction of UNN anticodons, in a next episode of code evolution in which nonsense elimination was the leading theme, introduced a family box structure superposed on the original mirror structure. Finally, growth rate was the leading theme during the remaining repertoire expansion, explaining the ordered phylogenetic pattern of aminoacyl-tRNA synthetases. The special role of natural aptamers in the process is high-lighted, and the error robustness characteristics of the code are shown to have evolved by way of a stepwise, restricted enlargement of the tRNA repertoire, instead of by an exhaustive selection process testing myriads of codes

Some aspects on the biology of Deroceras panormitanum and Derocerus reticulatum with special emphasis on effects caused by some agricultural chemicals : a thesis presented in partial fulfilment of the requirements for the degree of Masterate of Science in Zoology at Massey University

Two species of slugs Deroceras panormitanum ( Lessona & Pollonera, 1882 ).and Deroceras reticulatum ( Muller, 1774). were chosen as a subject for investigation. In part 'A' the fecundity and longevity of D. panormitanum was observed at four different locations, three at constant temperatures, and the fourth in Shade-house, which was the control site. A seasonal effect was evident in Shade-house, more eggs being oviposited in Spring and Autumn than in Winter. No such effect was observed with the constant temperatures. The number of eggs per cluster was 22.5 in Shade-house, 23.2 at 16 °C, 22.9 at 24 °C, and 18.5 at 5 °C. The average number of clusters oviposited per slug was 1.3 in Shade-house, 1.4 at 16 °C, 1.1 at 24 °C and 0.4 at 5 °C. The average number of eggs laid by each slug in this part of the experiment was 28.7 in Shade-house, 31.8 at 16 °C, 25.2 at 24 °C, and 7.7 at 5 °C. The optimal condition for slugs to oviposit was at 16 °C. Thirteen D.panormitanum and fifteen D. reticulatum that hatched on the same day were kept in the laboratory till natural death ensued. The average number of eggs per cluster for D. panormitanum was 15.6, and for D. reticulatum 15.4 . The number of clusters per slug was 3.8 for D. panormitanum and 3.5 for D. reticulatum, and the average number of eggs oviposited per slug was 59.8 for D. panormitanum, and 53.4 for D. reticulatum. The effects of Temperature, Humidity, and Evaporation-rate, was correlated with oviposition rate. An increase in temperature and evaporation-rate showed a positive correlation, with an increase in oviposition rate. Humidity has a negative correlation with oviposition rate. Significantly more eggs hatched from D. panormitanum 59.9 %, than of D. reticulatum 53.0 % , under laboratory conditions. The time taken for eggs to hatch is temperature dependent, taking for D. panormitanum an average of 33.7 days for Shade-house, 20.9 days at 16 °C, 16.5 days at 24 °C, and 103.4 days at 5 °C. The average number of eggs hatched for D. panormitanum in Shade-house was 38.3 % , at 16 °C 37.0 %, at 24 °C 32.1 % , and at 5 °C 25.4 %. In the laboratory D. panormitanum's average life-span was 171 days, and D. reticulatum 151 days. At the four temperatures D. panormitanum survived for an average of 32.7 days in Shade-house, 23.2 days at 16 °C, 16.8 days at 24 °C, and at 5°C for 63.1 days. In part 'B' eightythree biocides were tested against the slug species D. panormitanum and D. reticulatum. These included 16 fungicides, 16 insecticides, 26 herbicides, and 2 molluscicides, at the maximum rates as specified by the manufacturer. Five fungicides, two insecticides, five herbicides, one molluscicide, and seven of the combinations showed high ovicidal activity. Five insecticides, one molluscicide, and ten of the combinations showed high toxicity when ingested, and two insecticides,one molluscicide, and six of the combinations were highly effective when used as a surface spray. Metaldehyde and methiocarb were effective in all three treatments,and phorate was a good bait and contact molluscicide. Dazomet caused a reluctance by slugs to cross the treated area to obtain food, and as a result died of starvation in the refuge area. The effects of all two possible combinations of three herbicides and three insecticides could not be determined from a knowledge of their individual properties. Each reacted in an undetermined manner according to their combined properties

TripleSent: a triple store of events associated with their prototypical sentiment

The current generation of sentiment analysis systems is limited in their real-world applicability because they cannot detect utterances that implicitly carry positive or negative sentiment. We present early stage research ideas to address this inability with the development of a dynamic triple store of events associated with their prototypical sentiment

The first peptides: the evolutionary transition between prebiotic amino acids and early proteins

The issues we attempt to tackle here are what the first peptides did look like when they emerged on the primitive earth, and what simple catalytic activities they fulfilled. We conjecture that the early functional peptides were short (3 to 8 amino acids long), were made of those amino acids, Gly, Ala, Val and Asp, that are abundantly produced in many prebiotic synthesis experiments and observed in meteorites, and that the neutralization of Asp's negative charge is achieved by metal ions. We further assume that some traces of these prebiotic peptides still exist, in the form of active sites in present-day proteins. Searching these proteins for prebiotic peptide candidates led us to identify three main classes of motifs, bound mainly to Mg^{2+} ions: D(F/Y)DGD corresponding to the active site in RNA polymerases, DGD(G/A)D present in some kinds of mutases, and DAKVGDGD in dihydroxyacetone kinase. All three motifs contain a DGD submotif, which is suggested to be the common ancestor of all active peptides. Moreover, all three manipulate phosphate groups, which was probably a very important biological function in the very first stages of life. The statistical significance of our results is supported by the frequency of these motifs in today's proteins, which is three times higher than expected by chance, with a P-value of 3 10^{-2}. The implications of our findings in the context of the appearance of life and the possibility of an experimental validation are discussed.Comment: 22 pages, 2 figures, J. Theor. Biol. (2009) in pres