Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II’s sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.     

Trophic associations and specialization of phytophagous beetles (Coleoptera: Chrysomeloidea,Curculionoidea) in the east of the Russian Plain

Data on the trophic associations of beetles with plants in the east of the Russian Plain are summarized and comparative analysis of host specialization of different groups of phytophagous beetles is performed. In terms of the width of the regional trophic spectrum, monophages and narrow oligophages prevail among the Curculionoidea as a whole and in the families Curculionidae and Apionidae in particular, while moderate and broad oligophages prevail in the Chrysomeloidea and in the family Chrysomelidae. Two-thirds of the regional fauna (66%) of Curculionoidea are closely associated with plants of one genus; by contrast, in Chrysomeloidea almost 40% of the species can develop on plants from different genera of one family, the fraction of the narrowly specialized forms comprising only 43%. The higher level of trophic specialization of weevils (Curculionidae, Apionidae) and seed beetles (Bruchidae), as compared to leaf beetles (Chrysomelidae), is probably due to the larval endophagy of most species of these families. Analysis of the distribution of beetles over host plants has shown that the specialized forms are associated with plants of 65 families (about 60% of the regional flora in the east of the Russian Plain). Distribution of beetles over plant families is very non-uniform. Most of the specialized forms (78%) are associated with plants of 15 families, three of which (Asteraceae, Fabaceae, and Brassicaceae) include hosts of more than onethird of the beetle species (37%). Monophages and narrow oligophages are recorded on 201 genera of plants from 59 families. Polyphagous species are recorded on plants of 58 families. The specific features of the distribution of phytophagous beetles over host plants (as compared to other insects) is a high fraction of species developing on coenophobes (particularly those of the family Brassicaceae) typical of the pioneer stages of successions with sparse herbaceous cover, and a small number of species associated with grasses and sedges. These features are most conspicuous in the fauna of Curculionidae.     

Interaction of rabbit skeletal muscle glycogen synthase I with substrate analogs--oxo-UDP hydrazones]

Inhibition of rabbit skeletal muscle glycogen synthase I was studied by using several synthetic substrate analogs: dansylhydrazone of oxo-UDP, 3-hydroxy-2-naphthoylhydrazone of oxo-UDP, salicyloylhydrazone of oxo-UDP, 1-oxyl-2,2,5,5-tetramethylpyrrolidine-3-carbonylhydrazone of oxo-UDP, N'-(dansyl)hydrazinocarbonylhydrazone of oxo-UDP and N'-(fluorenylidene-9)-hydrazinocarbonylhydrazone of oxo-UDP. All these compounds (with the exception of the nitroxyl-containing hydrazone) were characterized by a nonlinear dependence of the reverse reaction rate on the analog concentration in Dixon coordinates. The parabolic type of inhibition was due to the fact that the analogs tested except for the nitroxyl-containing hydrazone were able to interact both with the active center of the enzyme and with the FMN-binding site. The inhibition constants for oxo-UDP hydrazones were calculated for the both centers; their comparison revealed that the affinity of the analogs for the FMN-binding site increased with an increase in the radical hydrophobicity. These data suggest that the site with a high binding affinity for FMN is hydrophobic in nature. Apparently, isoalloxasine-like compounds display the highest affinity for this site.     

Interleukin-4 activates ion channels in B lymphocytes.

The lymphokine interleukin-4 (IL-4) has been shown to induce dramatic changes in the physiology of resting B cells. We have applied the patch clamp technique in the cell attached and inside/out configurations to resting and IL-4-treated B cells to determine whether specific ion conductances result as a consequence of IL-4 action. We report here that two distinct ion channel events occur in B lymphocytes after treatment with IL-4, (i) induction of an inward rectifying K+ channel that is not observed in untreated cells, and (ii) activation of a large conductance anion channel that is normally silent in non-treated cells in the cell attached patch configuration. These data present the first evidence of a direct effect by IL-4 on ion channels and we suggest roles for these two ionic conductances in IL-4-induced B cell activation.     

Essential roles of core starvation-stress response loci in carbon-starvation-inducible cross-resistance and hydrogen peroxide-inducible adaptive resistance to oxidative challenge in Salmonella typhimurium

The starvation-stress response (SSR) of Salmonella typhimurium encompasses the physiological changes that occur upon starvation for an essential nutrient, e.g. C-source. A subset of SSR genes, known as core SSR genes, are required for the long-term starvation survival of the bacteria. Four core SSR loci have been identified in S. typhimuriumrpoSstiAstiB, and stiC. Here we report that in S. typhimurium C-starvation induced a greater and more sustainable cross-resistance to oxidative challenge (15 mM hydrogen peroxide (H₂O₂) for 40 min) than either N- or P-starvation. Of the four core SSR loci, only rpoS and stiC mutants exhibited a defective C-starvation-inducible cross-resistance to H₂O₂ challenge. Interestingly, (unadapted) log-phase S. typhimurium rpoS and stiA mutants were very sensitive to oxidative challenge. Based on this, we determined if these core SSR loci were important for H₂O₂ resistance developed during a 60 min adaptive exposure to 60 μM H₂O₂ (adapted cells). Both unadapted and adapted rpoS and stiA mutants were hypersensitive to a H₂O₂ challenge. In addition, a stiB mutant exhibited normal adaptive resistance for the first 20 mins of H₂O₂ challenge but then rapidly lost viability, declining to a level of about 1.5% of the wild-type strain. The results of these experiments indicate that: (i) the rpoS and stiC loci are essential for the development of C-starvation-inducible cross-resistance to oxidative challenge, and (ii) the rpoSstiA, and, in a delayed effect, stiB loci are needed for H₂O₂-inducible adaptive resistance to oxidative challenge. Moreover, we found that both stiA and stiB are induced by a 60 μM H₂O₂ exposure, but only stiA was regulated (repressed) by (reduced form) OxyR.