A leaderless mRNA can bind to mammalian 80S ribosomes and direct polypeptide synthesis in the absence of translation initiation factors

Translation initiation in eukaryotic cells is known to be a complex multistep process which involves numerous protein factors. Here we demonstrate that leaderless mRNAs with initiator Met-tRNA can bind directly to 80S mammalian ribosomes in the absence of initiation factors and that the complexes thus formed are fully competent for the subsequent steps of polypeptide synthesis. We show that the canonical 48S pathway of eukaryotic translation initiation has no obvious advantage over the 80S pathway of translation initiation on leaderless mRNAs and suggest that, in the presence of competing mRNAs containing a leader, the latter mechanism will be preferred. The direct binding of the leaderless mRNA to the 80S ribosome was precluded when such an mRNA was supplied with a 5' leader, irrespective of whether it was in a totally single-stranded conformation or was prone to base pairing. The striking similarity between the mechanisms of binding of leaderless mRNAs with mammalian 80S or bacterial 70S ribosomes gives support to the idea that the alternative mode of translation initiation used by leaderless mRNAs represents a relic from early steps in the evolution of the translation apparatus.     

Methods of selecting informative variables

We propose a new method for selection of the most informative variables from the set of variables which can be measured directly. The information is measured by metrics similar to those used in experimental design theory, such as determinant of the dispersion matrix of prediction or various functions of its eigenvalues. The basic model admits both population variability and observational errors, which allows us to introduce algorithms based on ideas of optimal experimental design. Moreover, we can take into account cost of measuring various variables which makes the approach more practical. It is shown that the selection of optimal subsets of variables is invariant to scale transformations unlike other methods of dimension reduction, such as principal components analysis or methods based on direct selection of variables, for instance principal variables and battery reduction. The performance of different approaches is compared using the clinical data.     

Maintenance of plastid RNA editing activities independently of their target sites

RNA editing in plant organelles is mediated by site-specific, nuclear-encoded factors. Previous data suggested that the maintenance of these factors depends on the presence of their rapidly evolving cognate sites. The surprising ability of allotetraploid Nicotiana tabacum (tobacco) to edit a foreign site in the chloroplast ndhA messenger RNA was thought to be inherited from its diploid male ancestor, Nicotiana tomentosiformis. Here, we show that the same ndhA editing activity is also present in Nicotiana sylvestris, which is the female diploid progenitor of tobacco and which lacks the ndhA site. Hence, heterologous editing is not simply a result of tobacco's allopolyploid genome organization. Analyses of other editing sites after sexual or somatic transfer between land plants showed that heterologous editing occurs at a surprisingly high frequency. This suggests that the corresponding editing activities are conserved despite the absence of their target sites, potentially because they serve other functions in the plant cell.     

Qualitative and quantitative characteristics of the extracellular DNA delivered to the nucleus of a living cell

Background  

The blood plasma and other intertissue fluids usually contain a certain amount of DNA, getting there due to a natural cell death in the organism. Cells of this organism can capture the extracellular DNA, whereupon it is delivered to various cell compartments. It is hypothesized that the extracellular DNA is involved in the transfer of genetic information and its fixation in the genome of recipient cell.     

Origin of the genetic code: first aminoacyl-tRNA synthetases could replace isofunctional ribozymes when only the second base of codons was established

Analysis of the updated compilation of more than 8,000 tRNA gene sequences confirmed our previously reported finding that in pairs of consensus tRNAs with complementary anticodons, their second bases in the acceptor stems are also complementary. This dual complementarity points to the following: (1) the operational code embodied in the acceptor stem, and the classic genetic code embodied in the anticodon could have had the same common ancestor; (2) new tRNAs most likely entered primitive translation in pairs with complementary anticodons; and (3) this process of code expansion was directed by the primordial double-strand coding. However, we did not find the dual complementarity when testing all tRNA pairs in which anticodons were complementary only at the central position, but not complementary at least at one of the flanking two positions. This observation, together with certain additional evidence, suggests that both codes were still being shaped (with only the second base established at the time) when the first protein aminoacyl-tRNA synthetases could have already started replacing their ribozymic precursors.     

Selective neutrality of mitochondrial ND2 sequences, phylogeography and species limits in Sitta europaea

Variation and geographic differentiation in mitochondrial DNA (mtDNA) was studied in the widespread and phenotypically variable Eurasian nuthatch (Sitta europaea). To assess whether sequences were evolving in a selectively neutral fashion, we used McDonald–Kreitman [Nature 351 (1991) 652] tests and a tree-based method, which suggested that although ND2 sequences are affected by natural selection against slightly deleterious alleles, the effects do not compromise phylogeographic inferences. Three phylogenetic species-level clades of nuthatches were discovered, corresponding to the Caucasus, southern Europe, and northern Europe plus Asia. Unimodal mismatch distributions within each clade suggest that populations have undergone recent growth. A westward range expansion was inferred from the geographic pattern in nucleotide diversity. Although samples were insufficient, it is possible that nuthatches in England and Japan are recently differentiated. Two specimens of the subspecies S. e. arctica formed a sister group to all other S. europaea, differing by ca. 10% uncorrected sequence divergence, pointing the need for additional study of this phenotypically distinct taxon. As with other species, mtDNA data support major phenotypic distinctions, but not subspecies.     

Screening for caspase-3 inhibitors: effect of a reducing agent on identified hit chemotypes

When studying cysteinyl proteases in general and caspases in particular, it is generally accepted that a reaction buffer must contain a reducing agent to prevent essential cysteinyl groups from spontaneous oxidation. Dithiothreitol (DTT) and beta-mercaptoethanol (beta-MCE) are 2 of the most broadly used reducing agents. While screening a library of small molecules against caspase-3, the authors have found that the nature of the reducing agent used, DTT or beta-MCE, dramatically affects screening results and leads to identification of nonoverlapping hits. Screening in DTT-containing buffer revealed few novel classes of small molecules that selectively and reversibly inhibit caspase-3 but failed to identify isatin sulfonamides recently found to be potent and selective caspase-3 inhibitors (false negatives). On the other hand, screening in the presence of beta-MCE failed to identify a series of hit compounds, 1,3-dioxo-2,3-dichloro-1H-pyrrolo[3,4-c]quinolines, discovered with DTT, whereas isatin sulphonamides in these conditions exhibited strong caspase-3 inhibition. In this work, the authors show that thiol-containing reducing agents can affect catalytic activity of caspase-3 and modify its thermostability in a redox-potential-independent manner. The authors speculate that the differential structural modifications of caspase-3 seen with different reducing agents represent structurally different caspase-3 conformations and are responsible for its differential sensitivity to small molecules of different chemotypes. Hence, selection of the reducing agent may dramatically affect the quality of high-throughput screening campaigns.     

Remarkable ophidiid larva (Neobythitinae) from New Guinean waters

A new type of ophidiid larva referred to the Neobythitinae is described on the basis of one specimen (22.5 mm in standard length: SL) found in the “Dana” flatfish larval collection from New Guinean waters. It is characterized by a very high body (ca. 48% SL), with a single elongate first dorsal-fin ray and protruding abdominal cavity with a long fleshy appendage at its posteroventral end. Generic and specific affinities of the larva are discussed. It is supposed that the larva belongs to one of the Pycnocraspedum species, probably to P. squamipinne.