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.     

Purification and characterization of α-glucosidases produced by Saccharomyces in response to three distinct maltose genes

α-Glucosidases or maltases (EC 3.2.1.20) were purified to electrophoretic homogeneity from a respective strain of Sacchromyces cerevisiae which carries a single MAL gene, either MALα, MALβ or MALγ, using gluconate-Sepharose affinity chromography and isoelectrofocusing. Of these maltases, two types of maltase were obtained from the MALγ strain, the pI values of which were 5.6 and 5.9. From the MALα and MALβ strain was obtained only one type of maltase with the pI at 5.6 which was identical to one of the maltases from the MALγ strain. These four maltases possessed the same properties, except for pI. They were monomers with molecular weights of between 66 000 and 67 000. With regard to the substrate specificity, they hydrolyzed maltose and sucrose exclusively but not α-methulglucoside nor maltooligosaccharide. They did not differ in immunological properties.     

Nonlethal G0-ts mutant tsJT60 becomes lethal at the nonpermissive temperature after transformation: a hint for new cancer chemotherapeutics

tsJT60 is a nonlethal temperature-sensitive (ts) mutant of a Fischer rat cell line (3Y1) classified as a G0 mutant; i.e., the ts defect is not expressed within the cell growth cycle but is expressed only between the G0 and S phase. tsJT60 clones transformed with oncogenes such as adenovirus E1A, polyoma large T, polyoma middle T, v-Ki-ras, and LTR activated c-myc, or with a chemical carcinogen N-methyl-N'-nitro-N-nitrosoguanidine, grew well at 34 degrees C. However, most of these clones grew slowly at 40 degrees C, producing many floating dead cells, and some clones were killed at 40 degrees C. When they were cultured under conditions inadequate for growth of untransformed cells, such as high cell density or serum restriction, they were killed at 40 degrees C. These and previous results from SV40- and adenovirus-transformed tsJT60 clones favour the idea that transformed tsJT60 cells occasionally enter the G0 phase and are metabolically imbalanced at 40 degrees C during self-stimulation from the G0 to S phase. We propose that a drug which exclusively block, G0-G1 transition would be cytocidal to transformed cells but cytostatic to normal cells.     

Oxidation and esterification of cis- and trans-isomers of octadecenoic and octadecadienoic acids in isolated rat liver

The metabolism of 9-octadecenoic and 9,12-octadecadienoic acids with different geometrical configurations was compared in isolated perfused rat liver. More ketone bodies were produced when the trans-isomers were infused. In contrast, only the cis-isomer augmented the triacylglycerol secretion almost entirely as very-low-density lipoprotein (VLDL). Although these responses were independent of the difference in the degree of unsaturation in both the cis- and trans-isomers, the trans-monoenic acid compared to the trans-dienic acid was incorporated more readily into perfusate and hepatic lipids. Quantitative information was obtained with radioactive tracer experiments. The hepatic uptakes of 9-[10-14C]octadecenoic acids were comparable in the cis- and trans-isomers. The trans-octadecenoic acid compared to the cis counterpart was oxidized more readily and incorporated more into liver phospholipid but less into perfusate and liver triacylglycerol. These reciprocal responses counterbalanced each other. The lower rates of triacylglycerol synthesis and secretion in the liver perfused with the trans-octadecenoic acid was confirmed using [2- 3H]glycerol as a tracer. The marked difference in the channelling of cis- and trans-fatty acids in the pathways of oxidation and esterification seems to modify the VLDL secretion in perfused rat liver. Present observations indicate a considerable difference in the fate of unsaturated fatty acids with different configurations. trans-Fatty acids are expected to be an efficient energy source in animal tissues and may not be hyperlipidemic.     

Healing modes correlate with visuotectal pattern formation in regenerating embryonic Xenopus retina

After removal of the nasal or the temporal two-thirds of the embryonic (stage 32) eye, the remaining one-third sized fragment undergoes wound healing and then, in most cases, regenerates to form a new eye. Using gross anatomy and histology techniques, we categorized eye fragments into three healing mode categories over the first 24 hr after surgery (stage 37-38). Representative animals were reared through metamorphosis and their visuotectal projections were assayed using standard electrophysiology techniques. In the "rounded-up" healing mode, the cut edges of the fragment pinch to close the wound; retinal cell type layers (pigmented retinal epithelium (pre), photoreceptors, interneurons, ganglion cells) and a lens are present by 24 hr postsurgery. No extraneous or disorganized cells are present either internal or external to the fragments. These fragments regenerated to form normal projections 83% of the time and pattern duplicated projections only 17% of the time. In the "intermediate" healing mode, wound closure is not complete by 24 hr post surgery and groups of disorganized cells are present in the fragment and amassed between the healing cut edges. These fragments formed pattern duplicated projections 72% of the time. In the tongue healing mode, an ectopic mass of cells, contiguous with the main body of the fragment, forms a supernumerary retina in the region of the ablation. At 24 hr post surgery, the cells of the main body fragment form retinal layers; the cells of the tongue, excluding the presence of differentiated pre cells, remain undifferentiated, resembling ciliary margin. The cut edges of the main body fragment eventually fuse with the tongue to form a single eyeball. Tongue fragments formed pattern duplicated projections 100% of the time. In addition, pattern duplicated points derived from nasal fragments appeared most often in the posterior region of the tectum, the normal site of innervation of the nasal retina. This differed significantly from temporal fragment derived duplicated points which appeared more often in the front of the tectum, the normal site of innervation by temporal retina. Thus, the specificity of pattern duplicated innervation is related to the positional values remaining in the fragment after partial retinal ablation. The data indicate that cell movements during healing, whether overt as in the tongue healing mode, or remaining internal to the fragment as in the intermediate healing mode, are intimately correlated with pattern forming mechanisms which underlie pathological visuotectal duplication.     

Positional heterogeneity of interaction between fragments of avian limb bud in organ culture

We have previously succeeded in culturing whole leg bud from stage 21-23 chick embryos and observed a leg structure with typical cartilage pattern in vitro. In the present study, we have attempted the organ culture of the fragmented leg bud and investigated its capacity to form cartilage. Leg buds from stages 17-21 chick embryos were dissected into four pieces in the anteroposterior sequence (named 1, 2, 3, and 4, respectively) and cultured on a membrane filter in a medium consisting of Ham's F-12, chick serum, and chick embryo extract. After 6 days in culture, two central fragments (2 and 3) developed into large cartilaginous masses, while anterior (1) and posterior (4) fragments formed few or small cartilaginous masses. In addition, when these less chondrogenic fragments were combined, pinned together, and cultured, large cartilaginous masses were formed from 1 + 4 combinations but not from 1 + 1 or 4 + 4 combinations. These observations were analyzed quantitatively by measurement of 35SO4 incorporation into the sulfated glycosaminoglycan (S-GAG) and of final DNA content per explant, and by histological reconstruction of the chick-quail chimera explant. The results showed that (a) the 1 + 4 combination resulted in higher S-GAG synthesis and final DNA content than the 1 + 1 or 4 + 4 combinations in stage 18 and 21 leg buds (P less than 5%); (b) removal of ectoderm from the leg bud inhibited the increase observed for the 1 + 4 combination; c) in chick-quail chimera explants the cartilage formed from the 1 + 4 combination was largely of fragment 1 origin. These results demonstrate, first, the presence of a difference in chondrogenic capacity along the anteroposterior axis in the leg bud and, second, the occurrence of an interaction between anterior and posterior fragments which mimics the effects of grafting a zone of polarizing activity (ZPA). The mechanism of ZPA function is still unknown but the ectoderm may play some role. Some roles for ectoderm in ZPA function and differences in mesodermal responsiveness to ZPA factor(s) are suggested.     

Colchicine activates cell cycle-dependent genes in growth-arrested rat 3Y1 cells

When growth-arrested 3Y1 cells (Fischer rat fibroblasts) were exposed to 3 X 10(-5) M colchicine, they entered S phase after a 12-h lag period which is the same as that in serum-stimulated cells. The expression of genes such as c-fos, c-myc, JE, KC, ornithine decarboxylase, and histone H3, analyzed by Northern blotting, increased in a cell-cycle dependent manner after colchicine treatment. The increased level of mRNAs was much smaller in colchicine-stimulated cells than in serum-stimulated cells, corresponding to the lower frequency of the former cells entering S phase. The course of the prereplicative phase seems to be similar in terms of the expression of cell cycle-dependent genes in cells stimulated with colchicine and in those stimulated with serum.     

Synthesis of dihydrothymidine and thymidine glycol 5'-triphosphates and their ability to serve as substrates for Escherichia coli DNA polymerase I

5,6-Dihydrothymidine 5'-triphosphate (DHdTTP) was synthesized by catalytic hydrogenation of thymidine 5'-triphosphate (dTTP). Thymidine glycol 5'-triphosphate (dTTP-GLY) was prepared by bromination of dTTP followed by treatment with Ag2O. The modified nucleotides were extensively purified by anion-exchange high-performance liquid chromatography (HPLC). Alkaline phosphatase digestion of DHdTTP and dTTP-GLY gave the expected products (5,6-dihydrothymidine and cis-thymidine glycol), the identities of which were confirmed by reverse-phase HPLC using authentic markers. HPLC analysis of the alkaline phosphatase digested DHdTTP revealed that DHdTTP was a mixture of C5 diastereoisomers [(5S)- and (5R)-DHdTTP]. Despite the significant distortion of the pyrimidine ring in DHdTTP, it was incorporated in place of dTTP during primer elongation catalyzed by Escherichia coli DNA polymerase I Klenow fragment. The rate of incorporation of DHdTTP was about 10-25-fold lower than that of dTTP. On the other hand, dTTP-GLY, which also has a distorted pyrimidine ring, did not replace dTTP, and no elongation of the primer was observed. In order to study the preference of incorporation of the diastereoisomers of DHdTTP into DNA, salmon testes DNA, activated by exonuclease III, was used as a template for DNA polymerase I Klenow fragment in the presence of [3H]DHdTTP (S and R mixture) and normal nucleotides. After enzymatic digestion of the DNA to nucleosides, the products were analyzed by HPLC. The ratio of the isomers incorporated into DNA (S:R = 73.27) was virtually the same as that of the [3H]DHdTTP substrates (S:R = 79.21).(ABSTRACT TRUNCATED AT 250 WORDS)