Makoto Watanabe

Bio: Makoto Watanabe is an academic researcher from Nara Medical University. The author has contributed to research in topics: Botryococcus braunii & Terahertz radiation. The author has an hindex of 32, co-authored 262 publications receiving 3738 citations. Previous affiliations of Makoto Watanabe include Stanford University & University of Stuttgart.

Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843.

Abstract: The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5 842 795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restrictionmodification systems were notable characteristics of the M. aeruginosa genome.

Thraustochytrid Aurantiochytrium sp. 18W-13a accummulates high amounts of squalene.

Abstract: Here we report on the 18W-13a strain of Aurantiochytrium sp., which accumulates very high amounts of squalene. The squalene contents and production at 4 d of culture were 198 mg/g and 1.29±0.13 g/L, respectively, exceptionally high values compared to previous reports.

Effects of carbon source on growth and morphology of Botryococcus braunii

Abstract: The green colonial alga Botryococcus braunii is characterized by the ability to produce and accumulate large amounts of hydrocarbons. We isolated and established an axenic clonal strain of B. braunii B70 and investigated the effects of organic carbon sources, including glucose, mannose, fructose, galactose, or acetate, on growth under light and dark conditions. This algal strain had the capacity to grow photo-, mixo-, or heterotrophically. Growth was promoted substantially following exposure of the algae to glucose or mannose under light exposure. Cells could grow under continuous darkness with glucose or mannose. In the presence of glucose under light or dark conditions, cell and colony size, and the intracellular granules containing oil, were markedly larger than those cultured without glucose.

Pattern recognition with machine learning on optical microscopy images of typical metallurgical microstructures.

Abstract: For advanced materials characterization, a novel and extremely effective approach of pattern recognition in optical microscopic images of steels is demonstrated. It is based on fast Random Forest statistical algorithm of machine learning for reliable and automated segmentation of typical steel microstructures. Their percentage and location areas excellently agreed between machine learning and manual examination results. The accurate microstructure pattern recognition/segmentation technique in combination with other suitable mathematical methods of image processing and analysis can help to handle the large volumes of image data in a short time for quality control and for the quest of new steels with desirable properties.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Acute Kidney Injury Network: report of an initiative to improve outcomes in acute kidney injury

Abstract: Acute kidney injury (AKI) is a complex disorder for which currently there is no accepted definition. Having a uniform standard for diagnosing and classifying AKI would enhance our ability to manage these patients. Future clinical and translational research in AKI will require collaborative networks of investigators drawn from various disciplines, dissemination of information via multidisciplinary joint conferences and publications, and improved translation of knowledge from pre-clinical research. We describe an initiative to develop uniform standards for defining and classifying AKI and to establish a forum for multidisciplinary interaction to improve care for patients with or at risk for AKI. Members representing key societies in critical care and nephrology along with additional experts in adult and pediatric AKI participated in a two day conference in Amsterdam, The Netherlands, in September 2005 and were assigned to one of three workgroups. Each group's discussions formed the basis for draft recommendations that were later refined and improved during discussion with the larger group. Dissenting opinions were also noted. The final draft recommendations were circulated to all participants and subsequently agreed upon as the consensus recommendations for this report. Participating societies endorsed the recommendations and agreed to help disseminate the results. The term AKI is proposed to represent the entire spectrum of acute renal failure. Diagnostic criteria for AKI are proposed based on acute alterations in serum creatinine or urine output. A staging system for AKI which reflects quantitative changes in serum creatinine and urine output has been developed. We describe the formation of a multidisciplinary collaborative network focused on AKI. We have proposed uniform standards for diagnosing and classifying AKI which will need to be validated in future studies. The Acute Kidney Injury Network offers a mechanism for proceeding with efforts to improve patient outcomes.