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.     

Spacing and kinship in the Formosan squirrel living in different habitats

Summary Spacing and kinship of the Formosan squirrel, Callosciurus erythraeus thaiwanensis, were studied in two different habitats. One, native habitat in the woods of Kenting, southern Formosa, was rich in available food throughout the year and had several species of predators. The other, a site in Kamakura, central Japan where squirrels had been introduced, had relatively scanty food and few potential predators. 1. Home ranges among males and between sexes overlapped extensively in both habitats. 2. Females occupied exclusive home ranges in Kamakura but had small overlapping home ranges in Ken-ting. 3. Most males disappeared from their natal areas at 1 year old in both habitats (86% in Kamakura and 93% in Ken-ting), but less females disappeared (36% in Kamakura and 35% in Ken-ting). 4. In Kamakura, daughters settled adjacent to the mother or inherited the home range of the mother, but never shared the mother's home range. In Ken-ting, 35% of daughters shared the home range with their mothers. 5. Tolerance among female kin in Ken-ting was probably facilitated by the richness of available food throughout the year, and functioned to reduce predation risk via alarm calling and mobbing.     

Prostacyclin stimulation of adenylate cyclase activity in human thyroid membranes

Effect of prostacyclin (PGI2) on adenylate cyclase activity in human thyroid membranes was examined. PGI2 caused a dose- and time-dependent production of cyclic AMP (cAMP) with high potency. When GTP was added in concentrations up to 100 uM, the activation of adenylate cyclase by PGI2 was increased. In the assay medium containing 3 mM ATP, 10 uM GTP and nucleotide regenerating system, the replacement of Mg2+ by increasing concentrations of Mn2+ caused a progressive loss of PGI2 as well as TSH-stimulated adenylate cyclase activities, while high concentrations of Mg2+ (12 or 18 mM) slightly suppressed the activity stimulated by either PGI2 or TSH. Both agents had an additive effect on the stimulation of adenylate cyclase activity in the presence of either 6 mM Mg2+ or 6 mM Mn2+. Gamma-globulin fraction containing non-stimulatory TSH receptor antibody which was prepared from a patient with chronic thyroiditis, suppressed only TSH- but not PGI2-stimulation of the adenylate cyclase activity. These results suggest that PGI2 can stimulate the adenylate cyclase activity in human thyroid tissue, and that PGI2-stimulation may be mediated by the different system from TSH-dependent one.     

Hepatic lesions in experimental Campylobacter jejuni infection of mice

Mice orally infected with Campylobacter jejuni developed focal infiltrative necrotic lesions in the liver, as determined by both histology and liver function tests. The initial histopathological feature was a focal infiltrative lesion in the parenchyma and portal triads. Foci of infiltrative lesions became necrotic between days 30 and 60 post-inoculation (p.i.). During this period, portal infiltrates increased in severity. From month 4 p.i., focal areas of infiltrative necrosis in the liver parenchyma became extensive. Study of liver function demonstrated mild elevations of transaminases, alkaline phosphatase and lactic dehydrogenase, and also the presence of hypoalbuminaemia. Although histopathological changes of the liver became gradually more marked after day 30 p.i., liver functions of infected mice were most affected at 2 months p.i. The capacity of C. jejuni to induce hepatic lesions seemed to be related to that of organisms to persist in the gall bladder; there was no correlation between biliary carriage in infected mice and positive faecal culture.     

Diurnal changes in the vertical distribution of phytoplankton in hypertrophic Lake Kasumigaura,Japan

The daily vertical migration of five species;Microcystis aeruginosa (Kütz.) Trevis,Anabaena spiroides Klebahn f.crassa (L.) Elenkin,Aphanizomenon flos-aquae (L.) Ralfs,Melosira granulata (E). Ralfs, andCoscinodiscus lacustris Grun. was studied using a close-interval water sampler on a calm summer day in Lake Kasumigaura. Many colonies ofMicrocystis were observed at the middle of the water column (approx. 1.5 m depth) in the afternoon, and at the surface in the early morning.Anabaena occurred mostly in the upper layer whileAphanizomenon tended to be uniformly distributed. The difference in migration patterns suggests thatMicrocystis is superior toAnabaena andAphanizomenon in obtaining both light and nutrients from this lake. Among diatoms,Melosira remained at the bottom of the water column throughout day and night, but Coscinodiscus was uniformly distributed.