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.     

Development of social grooming between mother and offspring in wild chimpanzees

Grooming between female chimpanzees and their offspring was studied in the Mahale Mountains, Tanzania. Infants under 2 years of age rarely groomed their mothers, and mostly groomed accessible parts of their mother's bodies, if they did so. Most older adolescents reciprocated grooming with their mothers almost equally. Daughters appeared to mature socially earlier than sons, judging from the earlier ages at which a female infant began to groom her mother, groom mutually with her, and groom others. Weaning infants groomed their mothers more when they were in oestrus than when they were not. Development of the use of grooming as a means of social manoeuvring is discussed.     

Distribution of Clostridium botulinum type C in Ishikawa prefecture, and applicability of agglutination to identification of nontoxigenic isolates of C. botulinum type C.

Since deaths of waterfowls have frequently been observed in Lake Kahoku near Kanazawa city, Japan, we attempted an ecological study on Clostridium botulinum type C in four other lakes as well as Lake Kahoku. One hundred and twenty-nine (56%) of 230 soil samples collected gave rise to lethal toxicity in mice with the characteristic “wasp-waist” symptom. All of the 51 samples arbitrarily selected were neutralized by C. botulinum type C antitoxic serum. A further seasonal study throughout the year at a given shore area of Lake Kahoku disclosed that nearly all samples gave rise to toxicity due to C. botulinum type C during the autumn season when the most waterfowls congregate. Toxigenic strains of C. botulinum type C were isolated together with nontoxigenic strains that were culturally and biochemically similar to the toxigenic strains. Both the toxigenic and nontoxigenic strains were equally agglutinable by an antiserum prepared against one of the nontoxigenic strains. Further extensive studies on the specificity of the agglutination method for identification were performed with 112 strains of 46 clostridial species. None of the strains used except some strains of C. novyi type A and a strain of C. botulinum type D was agglutinable. Based on the findings for cultural, biochemical, and agglutinable properties, the nontoxigenic strains were identified as C. botulinum type C. Also, C. novyi type A isolates showing colonies covered with a small pearly layer zone but surrounded by an aberrantly wide lecithinase zone are discussed.     

Purification of a fibrolast-inhibitory factor from Actinobacillus actinomycetemcomitans Y4

Abstract A factor showing inhibitory activity against human gingival fibrolasts was extracted from the cytosol fraction of Actinobacillus actinomycetemcomitans Y4. The activity markedly inhibited the proliferation of human gingival fibrolasts, but had no effect on cell viability or gross morphology. No such activity was found in cytosol fractions from either Porphyromonas gingivalis 381 or Escherichia coli HB101. The extract from A. actinomycetemcomitans Y4 was then purified by anion-exchange chromatography, hydroxyapatite chromatography and gel-filtration chromatography to give a single band on SDS-PAGE with an apparent molecular mass of 65 kDa. The purification ratio was 183-fold with a recovery rate of 5% compared with the crude extract (starting material) when the activity was assessed by direct cell counts.     

Use of an activated carbon column for the synthesis of disaccharides by use of a reversed hydrolysis activity of β-galactosidase

Summary An activated carbon column was utilized for the synthesis of disaccharides by use of a reversed hydrolysis activity of an immobilized -galactosidase column in order to shift the equilibrium to the direction of condensation. The yields of lactulose and allo-lactulose from galactose and fructose, and N-acetyl lactosamine and N-acetyl allolactosamine from galactose and N-acetyl glucosamine, were 11.3% and 10.0%, respectively.     

Effect of Exogenous Gangliosides on Amino Acid Uptake and Na+,K+-ATPase Activity in Superior Cervical and Nodose Ganglia of Rats

The effects of some gangliosides on active uptake of nonmetabolizable alpha-aminoisobutyric acid (AIB) and Na+, K+-ATPase and Ca2+, Mg2+-ATPase activities in superior cervical ganglia (SCG) and nodose ganglia (NG) excised from adult rats were examined during aerobic incubation at 37 degrees C for 2 h. In NG, amino acid uptake was greatly accelerated with the addition of galactosyl-N-acetylgalactosaminyl-[N-acetylneuraminyl]-galactosylgluc osyl ceramide (GM1) (85%) and also with N-acetylgalactosaminyl-[N-acetylneuraminyl]-galactosylglucosyl ceramide (GM2) or [N-acetylneuraminyl]-galactosyl-N-acetylgalactosaminyl-[N-acetyl- neuraminyl]-galactosylglucosyl ceramide (GD1a) (43% each) compared with a nonaddition control at a 5 nM concentration. Under identical conditions, Na+, K+-ATPase activity was strongly stimulated with GM1 (180%) and GD1a (93%), whereas Ca2+, Mg2+-ATPase activity showed no change. In SCG, on the other hand, AIB uptake was apparently inhibited (-27%) by addition of GM1, with a slight decrease in Na+, K+-ATPase but no change in Ca2+, Mg2+-ATPase activity in the tissue. Both asialo-GM1, in which N-acetylneuraminic acid is deficient, and Forssman glycolipid, which is not present in nervous tissue, failed to produce any significant increase in both SCG and NG not only in amino acid uptake, but also in Na+, K+-ATPase activity. A kinetic study of active AIB uptake showed that GM1 ganglioside produced an increase in Km with no change in Vmax in SCG, whereas it caused a decrease in Km with a slight increase in Vmax in NG. Treatment of NG and SCG with neuraminidase from Vibrio cholerae, an enzyme that split off sialic acid from polysialoganglioside, leaving GM1 intact, caused little inhibition of the amino acid uptake.(ABSTRACT TRUNCATED AT 250 WORDS)