A 54 kDa band (P54) was continually detected with the 30 kDa viral capsid protein (CP) on the SDS-PAGE migration profile of purified potato virus Y (PVY). P54 was observed following the use of two different procedures for the purification of the PVY from infected tobacco. It was a constitutively expressed tobacco protein. The analysis of the PVY preparation showed that P54 has aggregation properties and precipitates, thus pulling down the virus. We used an enzyme-linked immunosorbent assay (ELISA) to study the relationship between P54 and the PVY particles. We performed an inhibition test with monoclonal antibodies (mAb) directed against the PVY-CP, to show that these two components interact. This result was confirmed by western blot. The internal sequence of five major peptides, obtained by C-lysine endoprotease digestion of the P54 followed by HPLC separation, showed 100% homology with the large subunit of the ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO-LSU) of tobacco. MAb directed against RubisCO-LSU were produced and used to reveal the RubisCO-LSU/PVY complex in infected tobacco extracts. A phage library displaying random heptapeptides was used to isolate several peptides that specifically bound to the native form of the PVY. The sequences of thirty-three phage-displayed peptides, which bound specifically to this virus, present further discontinuous sequence homologies with the RubisCO-LSU. Five peptides (p1 to p5) corresponding to the RubisCO-LSU homologous regions were used for a bacterial two-hybrid system to confirm in vivo direct interactions between the selected RubisCO-LSU regions and the PVY-CP. We propose that the PVY-CP may be involved in the production of mosaics and yellowing symptoms in tobacco through its interaction with RubisCO-LSU.

No summary available.

Genus Ceratomyxa comprises coelozoic parasites of mainly marine and brackish water fish. This study describes a new Ceratomyxa species, Ceratomyxa schwanefeldii n. sp. which parasitizes the gall bladder of Barbonymus schwanefeldii collected from Sungai Tong in Setiu, Terengganu, Malaysia. The new species was described using morphological characteristics, and on nucleotide sequences of small subunit ribosomal DNA (SSU rDNA) and large subunit ribosomal DNA (LSU rDNA). Ceratomyxa schwanefeldii n. sp. exhibited vermiform shape plasmodia with slow undulatory motility, measuring 151.6 ± 86.0 (43.0–271.0) μm in length and 15.1 ± 4.8 (9.3–22.7) μm in width, with blunt poles at both ends. The mature spores were crescent-shaped, strongly arched in frontal view, with a sutural line between the two valves tapering to blunt ends. Formalin-fixed spores were 3.0 ± 0.4 (2.4–3.9) μm in length, 12.6 ± 1.2 (10.8–15.4) μm in thickness, with a concave posterior angle, 104.8° ± 10.2° (73.4–123.8). Two equal-sized spheroid polar capsules measured 1.5 ± 0.2 (1.2–1.8) μm in length and 1.3 ± 0.2 (0.9–1.7) μm in width. Phylogenetic analyses by Maximum likelihood and Bayesian Inference algorithms positioned C. schwanefeldii n. sp. as a sister species to Unicapsulocaudum mugilum and clustered within the clade of Amazonian freshwater Ceratomyxa species. The LSU rDNA phylogeny revealed that C. schwanefeldii n. sp. clusters within the marine Ceratomyxa clade and forms a sister relationship with C. leatherjacketi. This study represents the first description of a freshwater Ceratomyxa in Malaysia and the fourth recorded detection in the Asian region.

No summary available.

Many rDNA molecular phylogenetic studies result in trees that are incongruent to either alternative gene tree reconstructions and/or morphological assumptions. One reason for this outcome might be the application of suboptimal phylogenetic substitution models. While the most commonly implemented models describe the evolution of independently evolving characters fairly well, they do not account for character dependencies such as rRNA strands that form a helix in the ribosome. Such nonindependent sites require the use of models that take into account the coevolution of the complete nucleotide pair (doublet). We analyzed 28S rDNA (LSU) demosponge phylogenies using a “doublet” model for pairing sites (rRNA-helices) and compared our findings with the results of “standard” approaches using Bayes factors. We demonstrate that paired and unpaired sites of the same gene result in different reconstructions and that usage of a doublet model leads to more reliable demosponge trees. We show the influence of more sophisticated models on phylogenetic reconstructions of early-branching metazoans and the phylogenetic relationships of demosponge orders.

Although the taxonomy of oligotrich ciliates has been widely investigated, yet the species diversity remains poorly known. We newly designed a pair of oligotrich-specific LSU rDNA primers covering the 600-bp D1/D2 region, and it was effective for detecting oligotrich species. Using the primers, we constructed the cloning libraries to investigate the species diversity of oligotrichs in the northern coastal waters of the South China Sea. In total, 165 oligotrich sequences were obtained from five widely separated sampling sites. Sixty operational taxonomic units (OTUs) were obtained at 99% similarity threshold, and low-abundance OTUs with no more than two sequences contributed most of these (about 78%). Our findings are consistent with previous morphological studies, Strombidium was found the most abundant and widely distributed genus in this area. In addition, the BLAST search in the NCBI database resulted in 95% OTUs matching with named oligotrich species in similarity below 99%. Therefore, oligotrich morphospecies diversity has been underestimated as low-abundance species, and the LSU rDNA oligotrich sequence database needs to be better promoted.