Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data

<p>Abstract</p> <p>Background</p> <p><it>Bacillus subtilis </it>natto is closely related to the laboratory standard strain <it>B. subtilis </it>Marburg 168, and functions as a starter for the production of the traditional Japanese food "natto" made from soybeans. Although re-sequencing whole genomes of several laboratory domesticated <it>B. subtilis </it>168 derivatives has already been attempted using short read sequencing data, the assembly of the whole genome sequence of a closely related strain, <it>B. subtilis </it>natto, from very short read data is more challenging, particularly with our aim to assemble one fully connected scaffold from short reads around 35 bp in length.</p> <p>Results</p> <p>We applied a comparative genome assembly method, which combines <it>de novo </it>assembly and reference guided assembly, to one of the <it>B. subtilis </it>natto strains. We successfully assembled 28 scaffolds and managed to avoid substantial fragmentation. Completion of the assembly through long PCR experiments resulted in one connected scaffold for <it>B. subtilis </it>natto. Based on the assembled genome sequence, our orthologous gene analysis between natto BEST195 and Marburg 168 revealed that 82.4% of 4375 predicted genes in BEST195 are one-to-one orthologous to genes in 168, with two genes in-paralog, 3.2% are deleted in 168, 14.3% are inserted in BEST195, and 5.9% of genes present in 168 are deleted in BEST195. The natto genome contains the same alleles in the promoter region of <it>degQ </it>and the coding region of <it>swrAA </it>as the wild strain, RO-FF-1.</p> <p>These are specific for γ-PGA production ability, which is related to natto production. Further, the <it>B. subtilis </it>natto strain completely lacked a polyketide synthesis operon, disrupted the plipastatin production operon, and possesses previously unidentified transposases.</p> <p>Conclusions</p> <p>The determination of the whole genome sequence of <it>Bacillus subtilis </it>natto provided detailed analyses of a set of genes related to natto production, demonstrating the number and locations of insertion sequences that <it>B. subtilis </it>natto harbors but <it>B. subtilis </it>168 lacks. Multiple genome-level comparisons among five closely related <it>Bacillus </it>species were also carried out. The determined genome sequence of <it>B. subtilis </it>natto and gene annotations are available from the Natto genome browser <url>http://natto-genome.org/</url>.</p

Two-photon excitable boron complex based on tridentate imidazo[1,5-a]pyridine ligand for heavy-atom-free mitochondria-targeted photodynamic therapy

We have synthesized a cyan fluorescent boron complex based on a tridentate imidazo[1,5-a]pyridine ligand. The boron complex was found to have potential applications as not only a chiroptical material but also a heavy-atom-free mitochondria-targeted photosensitizer for cancer treatment

情報リテラシー教育におけるプレゼンテーションのピアレビュー分析 : 医療福祉系短期大学における事例

　「情報科学実習」科目で実施した「総合演習課題」において学生が回答したピアレビューの内容を分析し，学生のプレゼンテーションにおける相互評価の基準の明確化を試みた。ピアレビューで回答のあったコメントを元にKJ法(蓄積された情報から関連するものを整理し統合する手法)による分類を行った結果，17の小カテゴリーが判明し，それらは大きく「発表内容に関する」「発表態度に関する」「スライドの出来に関する」「質疑応答・その他」の，４つのカテゴリーにまとめられた。最も多くのコメントが「発表内容に関する」カテゴリーであったが，グループごとの成績とカテゴリーを比較した場合，「スライドの出来に関する」カテゴリーが上位グループに集中していた。学生間の相互評価で高評価を得るためには，発表内容の精査はもちろん，ある程度のスライドのデザイン性が必要になることが分かった。To enhance students’ communication ability and learning effects, we introduced collaborativelearning into the class of ‘Practice of Information Literacy,’ and let students do group presentations and peer reviews. We analyzed the peer review comments posted by students, and tried to clarify evaluation standard of the student presentation. The comments responded were classified into 17 small groups by KJ method, and furthermore, they were categorized into four major groups; comments about “content of the presentation,” “announcement attitude,” “quality of the slides”, and “questions and answers and others”. More than half of the comments belonged to the category of “content of the presentation,” while much more comments on “quality of slides” seen in the highly rated groups. We confirmed that in mutual evaluation, students focus attention on not only the content of the presentation but slide design

Non-Fermi-liquid behavior of the organic superconductor κ-(BEDT-TTF)4Hg2.89Br8 probed by 13C NMR

An organic salt, κ-(BEDT-TTF)4Hg2.89Br8 exhibits superconductivity at 4.3 K under ambient pressure suggesting non-Fermi-liquid (NFL) behavior just above Tc. Whereas most organic superconductors are controlled by the bandwidth in the half-filled electron system, this salt realizes a carrier doping away from the half-filled electron system as well as high-Tc cuprates. In order to investigate the origin of NFL behavior, we assessed 13C-NMR measurements in this salt and observed the antiferromagnetic fluctuation as same as in an organic antiferromagnet κ-(BEDT-TTF)2Cu[N(CN)2]Cl with the gap structure. Application of pressure suppresses (T1T)^[-1] and shifts its maximum to lower temperatures with (T1T)^[-1] becoming constant above 2 GPa. These results suggest that applying pressure alters the electron system from NFL to FL state and that antiferromagnetic fluctuations contribute to the origin of NFL behavior

Low-frequency dynamics of κ-(BEDT-TTF)2Cu(NCS)2 observed by 13C NMR

κ-(BEDT-TTF)2Cu(NCS)2 [BEDT-TTF: bis-(ethylenedithio)-tetrathiafulvalene] behaves as a semiconductor at high temperatures, whereas it behaves as a Fermi liquid just above the superconducting transition temperature. To reveal the cause of this behavior, we experimented on κ-(BEDT-TTF)2Cu(NCS)2, in which one side of the central C=C in the BEDT-TTF molecules is substituted with 13C nuclei. We perfomed 13C-nuclear magnetic resonance (NMR) spectroscopy on this salt and measured the temperature dependence of its spectral linewidths and its spin-spin relaxation time T2. We found anomalies in its linewidths and T2, which we connected to the ethylene motion within the salt. Compared with the 13C-NMR measurements of κ-(BEDT-TTF-d8)2Cu(NCS)2, we obtained the experimental evidence of the connection between the ethylene motion and the conduction electrons. Considering this connection, we examined the semiconductive behavior of κ-(BEDT-TTF)2Cu(NCS)2 at high temperatures. The contribution of ethylene motion to the electronic state is thought to be a common feature of BEDT-TTF salts