Protein S3 fragments neighboring mRNA during elongation and termination of translation on the human ribosome

Protein S3 fragments were determined that crosslink to modified mRNA analogues in positions +5 to +12 relative to the first nucleotide in the P-site bound codon in model complexes mimicking states of ribosomes at the elongation and translation termination steps. The mRNA analogues contained a Phe codon UUU/UUC at the 5′-termini that could predetermine the position of the tRNA^Phe on the ribosome by the P-site binding and perfluorophenylazidobenzoyl group at a nucleotide in various positions 3′ of the UUU/UUC codon. The crosslinked S3 protein was isolated from 80S ribosomal complexes irradiated with mild UV light and subjected to cyanogen bromide—induced cleavage at methionine residues with subsequent identification of the crosslinked oligopeptides. An analysis of the positions of modified oligopeptides resulting from the cleavage showed that, in dependence on the positions of modified nucleotides in the mRNA analogue, the crosslinking sites were found in the N-terminal half of the protein (fragment 2–217) and/or in the C-terminal fragment 190–236; the latter reflects a new peculiarity in the structure of the mRNA binding center in the ribosome, unknown to date. The results of crosslinking did not depend on the type of A-site codon or on the presence of translation termination factor eRF1.     

MPDA: Microarray pooled DNA analyzer

Background  

Microarray-based pooled DNA experiments that combine the merits of DNA pooling and gene chip technology constitute a pivotal advance in biotechnology. This new technique uses pooled DNA, thereby reducing costs associated with the typing of DNA from numerous individuals. Moreover, use of an oligonucleotide gene chip reduces costs related to processing various DNA segments (e.g., primers, reagents). Thus, the technique provides an overall cost-effective solution for large-scale genomic/genetic research. However, few publicly shared tools are available to systematically analyze the rapidly accumulating volume of whole-genome pooled DNA data.     

Development of respiratory trees in the holothurian <Emphasis Type="Italic">Apostichopus japonicus</Emphasis> (Aspidochirotida: Holothuroidea)

The development of respiratory trees in the holothurian Apostichopus japonicus has been studied using light and electron microscopy. Primordial respiratory trees emerge in 2–3-mm-long animals (2 months after fertilization). They arise as two independent outgrowths from the dorsal wall of the anterior part of the cloaca. Upon first emerging and throughout the course of development, the left respiratory tree is longer than the right one. A common base develops in 4-mm-long animals (2–3 months after fertilization). In yearlings, the left respiratory tree grows into gaps between the loops of the intestinal tube interlaced with intestinal hemal vessels. The developing coelomic and luminal epithelia have ultrastructural peculiarities. The luminal epithelium of respiratory trees has been shown for the first time to comprise nerve cells and their processes. Characteristic structural features of the epithelia are shown to begin developing as early as in 4-mm-long animals (2–3 months after fertilization). In yearlings, the respiratory trees demonstrate definitive structural patterns and are entirely functional.     

Translation termination factor eRF1 of the ciliate <Emphasis Type="Italic">Blepharisma japonicum</Emphasis> recognizes all three stop codons

In species with variant genetic codes, one or two stop codons encode amino acid residues and are not recognized by the intrinsic class I translation termination factor (eRF1). Ciliata include a large number of species with variant genetic codes. The stop codon specificity of the Blepharisma japonicum translation termination factor eRF1 was determined in an in vitro eukaryotic translation system and in an in vivo assay (a dual reporter system). It was shown that eRF1 of B. japonicum retained specificity to all three stop codons, although the efficiency of peptydyl-tRNA hydrolysis in the presence of UGA was reduced in the in vitro assay. Since Heterotrichea (including B. japonicum) are the earliest diverged lineage in the phylogenetic tree of ciliates, B. japonicum probably possesses a universal genetic code similar to the putative ciliate ancestor group.     

Translation termination factor of eRFI of the ciliate Blepharisma japonicum recognizes all three stop codons

We have determined the type of stop codon specificity of Blepharisma japonicum translation termination factor eRF1 in an in vitro reconstituted eukaryotic translation system and in in vivo assay (the dual reporter system). We have shown that B. japonicum eRF1 retained specificity towards all three stop codons although efficiency of peptydyl-tRNA hydrolysis in the presence of UGA is reduced in an in vitro assay. We suggest that since the heterotrich B. japonicum represents the earliest diverged lineage on phylogenetic tree of ciliates, B. japonicum has the universal genetic code as ancestor group for all ciliates.     

Neoplasia in the connective tissue of the musselMytilus trossulus from polluted areas of Nakhodka Bay, Sea of Japan

A tumor was found for the first time in a musselMytilus trossulus from aheavily polluted area of Nakhodka Bay, Sea of Japan. Tumor cells were found in the connective tissue of different organs and also in gill vessels and hemal sinuses of the visceral mass. They were both attached and diffuse. The tumor was at an advanced stage, replacing the normal connective tissue cells, and formed nodes. The tumor cells were polymorphic, with a high nucleocytoplasmic ratio, and had a prominent nucleolus. The size of their nuclei was three to five times that of the nuclei of agranular hemocytes. The mitotic activity of the tumor cells was more than an order of magnitude higher than in the normal cells: The mean mitotic index was 1.4±0.5%, ranging from 0.97 to 2.3% in different organs. The mitotic indices in the connective tissue cells of three normal mussels were 0, 0, and 0.12%. A significant proportion (up to 78%) of the mitotic cells were at metaphase. The frequency of abnormal mitoses was 17%. Metaphases with displaced (often multiple) chromosomes constituted 71% of abnormal mitoses; anaphases, 8%; and tri- and tetrapolar mitoses, 11%. The tumor described is similar to diffuse sarcomatoid diseases of mussels from other geographical regions.