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.     

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.     

A deductive database system PACADE for analyzing 3-D and secondary structures of protein

We have developed a deductive database system PACADE for analyzing3-D and secondary structures of protein. The PA CADE systemconsists of a relational database created from Protein DataBank and a deductive engine DEE based on logic programming.It has the following features: (1) The system has an inferencemechanism. This means by which users can easily write and checkbiological hypotheses using logical and declarative rules insteadof procedural programs. (2) The relational database of the PACADE system stores data on bath 3-D and secondwy structuresof protein. The integration of this two level structure makesfeasible an abstract representation of the protein structure.We describe herein the design, functions, and implementationof this PACADE system.     

Burr marigold (Bidens tripartita L.) roots directly and immediately scavenge rhizosphere methane with highly exuded hydrogen peroxide via a rhizosphere Fenton reaction

Plant and Soil - The major factors controlling the soil methane (CH4) concentration and CH4 emissions of various plant (mainly wetland) species were identified. Five plant species (Oryza sativa,...     

DNA-Binding Properties of the Antibody Specific for the Dewar Photoproduct of Thymidylyl-(3′′-5′′)-Thymidine

A monoclonal antibody (DEM-1) specific for the Dewar photoproduct is used for detection and quantification of photolesions in DNA. To help understand the molecular recognition of damaged DNA by the antibody protein, we have cloned and sequenced the variable region genes of DEM-1. We have also prepared Fab fragments of DEM-1 (DEM1Fab), and synthesized two kinds of 3′-biotinylated oligonucleotides of different lengths containing a central Dewar photoproduct of TpT to analyze the effects of the antigen size on the binding rates by means of surface plasmon resonance (SPR). Results obtained from SPR analyses suggest that DEM1Fab may recognize tetranucleotide unit as the epitope.     

The genetic program to specify ectodermal cells in ascidian embryos

The ascidian belongs to the sister group of vertebrates and shares many features with them. The gene regulatory network (GRN) controlling gene expression in ascidian embryonic development leading to the tadpole larva has revealed evolutionarily conserved gene circuits between ascidians and vertebrates. These conserved mechanisms are indeed useful to infer the original developmental programs of the ancestral chordates. Simultaneously, these studies have revealed which gene circuits are missing in the ascidian GRN; these gene circuits may have been acquired in the vertebrate lineage. In particular, the GRN responsible for gene expression in ectodermal cells of ascidian embryos has revealed the genetic programs that regulate the regionalization of the brain, formation of palps derived from placode-like cells, and differentiation of sensory neurons derived from neural crest-like cells. We here discuss how these studies have given insights into the evolution of these traits.     

Bacterial Contribution to Dissolved Organic Matter in Eutrophic Lake Kasumigaura,Japan

Incubation experiments using filtered waters from Lake Kasumigaura were conducted to examine bacterial contribution to a dissolved organic carbon (DOC) pool. Bacterial abundance, bacterial production, concentrations of DOC, total dissolved amino acids (TDAA), and total dissolved neutral sugars (TDNS) were monitored during the experiments. Bacterial production during the first few days was very high (20 to 35 μg C liter⁻¹ day⁻¹), accounting for 40 to 70% of primary production. The total bacterial production accounted for 34 to 55% of the DOC loss during the experiment, indicating high bacterial activities in Lake Kasumigaura. The DOC degradation was only 12 to 15%, whereas the degradation of TDAA and TDNS ranged from 30 to 50%, suggesting the preferential usage of TDAA and TDNS. The contribution of bacterially derived carbon to a DOC pool in Lake Kasumigaura was estimated using d-amino acids as bacterial biomarkers and accounted for 30 to 50% of the lake DOC. These values were much higher than those estimated for the open ocean (20 to 30%). The ratio of bacterially derived carbon to bulk carbon increased slightly with time, suggesting that the bacterially derived carbon is more resistant to microbial degradation than bulk carbon. This is the first study to estimate the bacterial contribution to a DOC pool in freshwater environments. These results indicate that bacteria play even more important roles in carbon cycles in freshwater environments than in open oceans and also suggests that recent increases in recalcitrant DOC in various lakes could be attributed to bacterially derived carbon. The potential differences in bacterial contributions to dissolved organic matter (DOM) between freshwater and marine environments are discussed.