Publications by authors named "Makiko Shimoji"

A virulence bacterium, , evolved parallel to its host human, therefore, can work as a marker for tracing the human migration. We found . strains indigenous in the southernmost islands of Japanese Archipelago, Okinawa, and defined them as hspOkinawa and hpRyukyu.

View Article and Find Full Text PDF

Loss of pod shattering is one of the most important domestication-related traits in legume crops. The non-shattering phenotypes have been achieved either by disturbed formation of abscission layer between the valves, or by loss of helical tension in sclerenchyma of endocarp, that split open the pods to disperse the seeds. During domestication, azuki bean () and yard-long bean ( cv-gr.

View Article and Find Full Text PDF

Background: is a pathogenic bacterium that causes various gastrointestinal diseases in the human stomach. is well adapted to the human stomach but does not easily infect other animals. As a model animal, Mongolian gerbils are often used, however, the genome of the inoculated may accumulate mutations to adapt to the new host.

View Article and Find Full Text PDF
Article Synopsis
  • Enterococcus gilvus CR1, a bacteria isolated from raw cow's milk, is capable of producing carotenoids.
  • The complete genome sequencing of this strain was conducted using the PacBio RS II technology, resulting in a circular chromosome.
  • The genome assembly consists of 2,863,043 base pairs, has a G+C content of 41.86%, and includes three plasmids containing carotenoid biosynthesis genes.
View Article and Find Full Text PDF

EG9 is a strain isolated from well-ripened cheese and accelerates free amino acid production during cheese ripening. Its complete genome sequence was determined using the PacBio RS II platform, revealing a single circular chromosome of 2,927,257 bp, a G+C content of 46.59%, and three plasmids.

View Article and Find Full Text PDF
Article Synopsis
  • - LQ80 is a bacterial strain found in liquid feed intended for pigs.
  • - The complete genome sequence was obtained using the PacBio RS II sequencing technology.
  • - The genome consists of a single circular chromosome that is 3,230,192 base pairs long, with a G+C content of 44.66%, and includes seven plasmids.
View Article and Find Full Text PDF

The complete genome sequence of sp. strain IBARAKI in a -containing culture was determined using the PacBio RS II platform. The genome is a single circular chromosome of 3,693,233 nucleotides (nt), with a GC content of 44%.

View Article and Find Full Text PDF
Article Synopsis
  • Subsp. G50 is a specific strain that has the ability to stimulate the immune system and was isolated from Napier grass.
  • Researchers sequenced the entire genome of this strain using the advanced PacBio RS II sequencing platform.
  • The genome is made up of a single circular chromosome that is 2,346,663 base pairs long, has a G+C content of 35.03%, and does not contain any plasmids.
View Article and Find Full Text PDF

We have developed and characterized a bacterial consortium that reductively dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S rRNA and reductive dehalogenase genes showed that the consortium is highly enriched with Dehalococcoides spp. that have two vinyl chloride reductive dehalogenase genes, bvcA and vcrA, and a trichloroethene reductive dehalogenase gene, tceA.

View Article and Find Full Text PDF
Article Synopsis
  • PacBio RS II is a groundbreaking third-generation DNA sequencer that can read single molecules of DNA in real-time without needing to amplify them.
  • Its unique technology allows direct observation of DNA synthesis and offers key advantages like long read lengths, high accuracy, low bias, and the ability to analyze epigenetics.
  • PacBio RS II is suitable for various applications including whole genome sequencing, targeted sequencing, and studying complex populations, making it valuable for both research and clinical use.
View Article and Find Full Text PDF

A free-living ciliate, Trimyema compressum, found in anoxic freshwater environments harbors methanogenic archaea and a bacterial symbiont named TC1 in its cytoplasm. Here, we report the complete genome sequence of the TC1 symbiont, consisting of a 1.59-Mb chromosome and a 35.

View Article and Find Full Text PDF
Article Synopsis
  • The complete genome sequence of Lactobacillus curvatus was obtained using the PacBio RS II technology.
  • The genome consists of a single circular chromosome that is 1,848,756 base pairs long and has a G+C content of 42.1%.
  • It contains low G+C regions and features 43 identical sequence pairs that are longer than 1,000 base pairs, with no plasmids found in the genome.
View Article and Find Full Text PDF

Isoprene is the most abundant type of nonmethane, biogenic volatile organic compound in the atmosphere, and it is produced mainly by terrestrial plants. The tropical tree species Ficus septica Burm. F.

View Article and Find Full Text PDF
Article Synopsis
  • Second-generation sequencers (SGS) have made whole genome sequencing affordable for many non-model organisms, but many genomes remain unassembled.
  • Researchers used single molecule real-time (SMRT) sequencing to reconstruct the azuki bean genome, achieving superior contiguity and coverage compared to SGS-based assemblies.
  • The SMRT assembly produced longer contigs with fewer gaps, leading to better gene annotations and covering 86% of the azuki bean genome, demonstrating its effectiveness even when combined with SGS data.
View Article and Find Full Text PDF

Chemosynthetic symbiosis is one of the successful systems for adapting to a wide range of habitats including extreme environments, and the metabolic capabilities of symbionts enable host organisms to expand their habitat ranges. However, our understanding of the adaptive strategies that enable symbiotic organisms to expand their habitats is still fragmentary. Here, we report that a single-ribotype endosymbiont population in an individual of the host vent mussel, Bathymodiolus septemdierum has heterogeneous genomes with regard to the composition of key metabolic gene clusters for hydrogen oxidation and nitrate reduction.

View Article and Find Full Text PDF

The first complete genome sequence of the type strain Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (DSM 50071(T)) was determined in a single contig by PacBio RS II. The genome (6,317,050 bp, G+C content of 66.52%) contained 10 sets of >1,000-bp identical sequence pairs and 183 tandem repeats.

View Article and Find Full Text PDF

Here, we report the complete genome sequences of low-passage virulent and high-passage avirulent variants of pathogenic Leptospira interrogans serovar Manilae strain UP-MMC-NIID, a major causative agent of leptospirosis. While there were no major differences between the genome sequences, the levels of base modifications were higher in the avirulent variant.

View Article and Find Full Text PDF

The first complete genome sequence of Clostridium sporogenes DSM 795(T), a nontoxigenic surrogate for Clostridium botulinum, was determined in a single contig using the PacBio single-molecule real-time technology. The genome (4,142,990 bp; G+C content, 27.98%) included 86 sets of >1,000-bp identical sequence pairs and 380 tandem repeats.

View Article and Find Full Text PDF
Article Synopsis
  • The complete genome sequences of Staphylococcus aureus subsp. aureus Rosenbach 1884 strain DSM 20231(T) were analyzed using the PacBio RS II technology.
  • The genome consists of a chromosome that is 2,755,072 base pairs long with a G+C content of 32.86%.
  • It also includes a plasmid that measures 27,490 base pairs in length, with a G+C content of 30.69%.
View Article and Find Full Text PDF

A Dehalococcoides-containing bacterial consortium that performed dechlorination of 0.20 mM cis-1,2-dichloroethene to ethene in 14 days was obtained from the sediment mud of the lotus field. To obtain detailed information of the consortium, the metagenome was analyzed using the short-read next-generation sequencer SOLiD 3.

View Article and Find Full Text PDF

We report the first complete genomic sequence of Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 13311, the leading food-borne pathogen and a reference strain used in drug resistance studies. De novo assembly with PacBio sequencing completed its chromosome and one plasmid.

View Article and Find Full Text PDF

We report the complete genome sequences of eight Helicobacter pylori strains isolated from patients with gastrointestinal diseases in Okinawa, Japan. Whole-genome sequencing and DNA methylation detection were performed using the PacBio platform. De novo assembly determined a single, complete contig for each strain.

View Article and Find Full Text PDF

Three chitinases, designated gazyumaru latex chitinase (GLx Chi)-A, -B, and -C, were purified from the latex of gazyumaru (Ficus microcarpa). GLx Chi-A,-B, and -C are an acidic class III (33 kDa, pI 4.0), a basic class I (32 kDa, pI 9.

View Article and Find Full Text PDF

A PHP Error was encountered

Severity: Notice

Message: fwrite(): Write of 34 bytes failed with errno=28 No space left on device

Filename: drivers/Session_files_driver.php

Line Number: 272

Backtrace:

A PHP Error was encountered

Severity: Warning

Message: session_write_close(): Failed to write session data using user defined save handler. (session.save_path: /var/lib/php/sessions)

Filename: Unknown

Line Number: 0

Backtrace: