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.     

Phylogeography of the leaf beetle Chrysolina virgata in wetlands of Japan inferred from the distribution of mitochondrial haplotypes

The genetic differentiation among populations of the leaf beetle Chrysolina virgata living in wetlands of Japan was studied based on the sequence data of the mitochondrial cytochrome oxidase subunit I gene region (750 bp). Two distinct lineages of mitochondrial haplotypes were found: one (clade A) consisted of 26 haplotypes distributed over the distribution range of C. virgata between north‐east Honshu and Kyushu, whereas the other (clade B) was monotypic and confined to a small region in north‐east Honshu where it coexisted with clade A. Nested clade analysis for these haplotypes suggested that range expansion and following differentiation due to isolation by distance might have resulted in the present distribution pattern of the haplotypes in clade A. We discuss the evolutionary process leading to the occurrence of two distinct haplotype clades in Japan in terms of repeated colonization from the continent and range expansion and contraction during climatic changes.     

Regional excitatory and inhibitory amino acid levels in epileptic El mouse brain

Inbred mutant El mice are highly susceptible to convulsive seizures upon tossing stimulation. The levels of excitatory (e.g. glutamate and aspartate) and inhibitory amino acids [e.g. -aminobutyrate (GABA)] were examined in discrete regions of stimulated El mice [El(+)] non-stimulated El mice [El(-)] and ddY mice, which do not have convulsive disposition. In comparison with ddY, a general increased levels of aspartate, glutamate, glutamine, and taurine were detected in brain regions of El(-). The levels of GABA and glycine were almost the same in ddY and El(-). Compared to El(+), the levels of aspartate, glutamate, glutamine, and GABA in El(-) were either the same or higher. In the case of taurine and glycine, the levels in El(-) were either the same or lower than El(+). Alanine is special in that El(-) have a higher level than El(+) in hippocampus but lower in cerebellum. Furthermore, while marked changes were registered in several brain regions, none of the amino acids investigated showed any significant differences in the hypothalamus of three different groups of mice.     

Adherence of streptococci to surface-modified glass

Four types of surface-modified glass were prepared. Aminopropyl glass was prepared by alkylsilylation of glass slides with gamma-aminopropyltriethoxysilane. This glass carries primary amino groups which may be protonated at pH 7.2. Owing to the presence of both positively charged ions and hydrophobic ethoxyl groups, the glass is considered to be amphipathic. Three other types of surface-modified glass slides were prepared from aminopropyl glass by forming Schiff's bases with three aldehydes: glucose, glyoxylic acid and hexanal. The aldehyde-treated slides were subsequently reduced using sodium borohydride. Thus, the surface of the glass was rendered hydrophilic, ampholytic or hydrophobic, respectively. The adherence of two Streptococcus sanguis strains and two Streptococcus mutans strains to the surface-modified glass slides was studied. Different strains showed differences in adherence to these slides depending on their physico-chemical surface properties. For S. sanguis ATCC 10556, hydrophobic bonds seemed to be most important, while in S. mutans OMZ 176, ionic interactions made the highest contribution to adhesion. Hydrogen bonds seemed to contribute least to adherence.     

Diagnosis of a case of pulmonary carcinosarcoma by detection of rhabdomyosarcoma cells in sputum

Cytologic examination of sputum samples from an elderly patient revealed the presence of two cell populations: squamous cell carcinoma cells and rhabdomyosarcoma cells. The abnormal squamous cells showed both keratinizing and nonkeratinizing forms while some of the rhabdomyosarcoma cells showed cross striations. Sputum cytology was thus able to suggest a diagnosis of pulmonary carcinosarcoma. Histologically, the tumor was composed mainly of sarcomatous tissue showing various kinds of cells: fusiform or fibrous cells, round anaplastic cells, spindled cells with typical cross striations and myoblastic cells. A partially myxomatous degeneration was present. In addition, squamous cell carcinoma proliferated along the bronchi and formed small invasive cell nests in the sarcomatous tissue. No transition between the two components was noted. Both cellular constituents had metastasized to an interlobar lymph node.     

Concentrations of essential elements after repeated administrations of tin and selenium

To study effects of simultaneous administration of tin (Sn) and selenium (Se) on concentrations of several essential elements, mice were injected with either SnCl2 (ip) or Na2SeO3 (sc), alone or both compounds at a daily dose of 5 mumol/kg each for 12 consecutive days. Mice were sacrificed at 20 h after the last injection and concentrations of Sn, Se, Na, Ca, Zn, P, Fe, K, and Mg in the liver, kidney, spleen, pancreas, testis, seminal vesicle, lung, femoral muscle, and femoral bone were determined. In the control mice, Sn and Se concentrations were the highest in bone (0.69 micrograms Sn and 6.93 micrograms Se/g dry wt). Administered Sn was found to accumulate in all organs except the testis. Among the essential elements determined, Na was the most affected in terms of concentration in the organs and Mg was the least affected element in these organs. Among the organs tested, each elemental concentration in the pancreas was most affected. Simultaneous injections of Sn and Se appeared to keep the correlation coefficients between elements similar to those found in the control mice.     

Contagious egg-distribution on host pods and avoidance of pods received eggs in a wild bruchidKytorhinus sharpianus

The present study investigated the way a wild bruchid, Kytorhinus sharpianus, distributes its eggs on host pods. First, we counted the number of eggs per pod on the host plant (Sophola flavescens) in the field. The egg-distributions by the overwintered-generation adults in July and by the second-generation adults in mid October did not deviate from Poisson distribution because of small numbers of eggs laid. However, the egg-distribution in late August when many first-generation adults emerged was significantly contagious. The deposition of eggs was determined for three types of pods: (A) clean pods, (B) pods with eggs, and (C) those which eggs had been laid on but were removed from later. The numbers of eggs laid newly on three types of pods were significantly different; A>C>B, suggesting that an oviposition marker pheromone (O.M.P.) caused females to avoid pods on which eggs were deposited. Egg-shells reinforced that response. Monte Carlo simulations for the egg-distribution on pods predicted that even if females avoid pods with heavy egg-load through O.M.P., the egg-distribution becomes contagious when there is a large heterogeneity in quality of the pods.     

Bi- and trivoltine complex life cycles in a Kanto (Japan) population of a wild bruchid Kytorhinus sharpianus

The partial trivoltinism and overwintering of Kytorhinus sharpianus Bridwell (Coleoptera: Bruchidae) was studied in the Kanto district, Japan. The later in the summer eggs were laid by the first-generation adults, the higher was the incidence of larval diapause in the second generation. The incidence of diapause also fluctuated between years, influencing the abundance of third-generation larvae. A relatively large proportion of third-generation larvae did not attain the diapause stage by the beginning of winter. The diapause development of larvae in diapause was completed by mid-January. Immature larvae of the third generation also overwintered and emerged as adults in the spring.     

Herpes Simplex Virus-Induced Expression of 70 kDa Heat Shock Protein (HSP70) Requires Early Protein Synthesis But Not Viral DNA Replication

The major 70 kDa heat shock protein (HSP70), which is scarcely expressed in unstressed rodent cells, was apparently induced by infection with herpes simplex virus (HSV). Infection with HSV types 1 and 2 elevated HSP70 mRNA levels within 4 hr post-infection. HSP70 synthesis and accumulation increased in HSV-infected cells. Irradiation of HSV with UV-light abolished the ability to induce HSP70 mRNA. Inhibitors of viral DNA synthesis did not affect the induction of HSP70 in infected cells. Protein synthesis within 2 hr after infection was necessary for HSP70 induction.