Complete genome sequence of strain m318 isolated from rhizosphere of in high-arsenic-content soil.

strain m318 is an arsenite-oxidizing rhizobacterium isolated from the rhizosphere of an arsenic hyperaccumulator plant, beneficial for arsenic phytoremediation. Here, we report the complete genome sequence of this strain, which consists of a circular chromosome assembled using long reads sequenced on Nanopore and polished with Illumina paired-end reads.

Streptomyces yaizuensis sp. nov., a berninamycin C-producing actinomycete isolated from sponge.

While screening for antibiotics in a marine sample, we discovered a berninamycin C-producing actinomycete, designated YSPA8, isolated from a sponge. A polyphasic approach was used to determine the taxonomic position of the strain. Strain YSPA8 formed sympodially branched aerial mycelia that ultimately segment into chains of spores.

Cloning of three type III polyketide synthases and formation of polyketides in recombinant using cinnamic acid analogs as substrates.

is an actinorhizal plant that coexists with the nitrogen-fixing actinomycete via nodules. It produces a variety of polyketides, including flavonoids, stilbenoids, and diarylheptanoids. These compounds have beneficial biological activities.

Complete genome sequence of sp. strain 22B1P capable of utilizing 3-chlorobenzoate as a carbon source.

sp. strain 22B1P utilizes 3-chlorobenzoate as a carbon source. Complete genome sequencing of strain 22B1P revealed two chromosomes and two plasmids.

External quality assessment survey for SARS-CoV-2 nucleic acid amplification tests in clinical laboratories in Tokyo, 2021.

Introduction: Nucleic acid amplification tests (NAATs) play a pivotal role in clinical laboratories for diagnosing COVID-19. This study aimed to elucidate the accuracy of these tests.

Methods: In 2021, an external quality assessment of NAATs for SARS-CoV-2 was conducted in 47 laboratories in Tokyo, Japan.

Cloning and characterization of NADPH-dependent double-bond reductases from Alnus sieboldiana that recognize linear diarylheptanoids as substrates.

Diarylheptanoids are secondary metabolites of plants that comprise a C-C-C scaffold. They can be broadly classified into linear-type and cyclic-type diarylheptanoids based on their chemical structures. Actinorhizal trees, such as Casuarina, Alnus, and Myrica, which form nodule symbiosis with actinomycetes Frankia, produce cyclic diarylheptanoids (CDHs); in Alnus sieboldiana Matsum.

Isolation and Genomic Analysis of 3-Chlorobenzoate-Degrading Bacteria from Soil.

The compound 3-chlorobenzoate (3-CBA) is a hazardous industrial waste product that can harm human health and the environment. This study investigates the physiological and genetic potential for 3-chlorobenzoate (3-CBA) degradation. Six 3-CBA Gram-negative degraders with different degradation properties belonging to the genera , and were isolated from the soil.

Physiological and genomic analyses of cobalamin (vitamin B)-auxotrophy of sp. nov., a methionine-auxotrophic chitinolytic bacterium isolated from chitin-treated soil.

A novel bacterium designated 5-21a, isolated from chitin-treated upland soil, exhibits methionine (Met) auxotrophy and chitinolytic activity. A physiological experiment revealed the cobalamin (synonym, vitamin B)(Cbl)-auxotrophic property of strain 5-21a. The newly determined complete genomic sequence indicated that strain 5-21a possesses only the putative gene for Cbl-dependent Met synthase (MetH) and lacks that for the Cbl-independent one (MetE), which implies the requirement of Cbl for Met-synthesis in strain 5-21a.

Proportion of Neutrophils in White Blood Cells as a Useful Marker for Predicting Bacteremic Acute Cholangitis.

Objective A positive hemoculture in acute cholangitis is serious, but a blood culture result cannot be obtained at the initial diagnosis and so cannot be used for the severity assessment and decision-making concerning urgent/early biliary drainage. Accordingly, a predictor for bacteremia at the initial diagnosis of acute cholangitis would be particularly useful. We investigated the association between neutrophil proportions in white blood cell counts (%Neutro) and bacteremic acute cholangitis.

Complete Genome Sequence of Rhodococcus qingshengii N9T-4.

Rhodococcus qingshengii N9T-4 can grow on media without added carbon sources. Here, we report the complete nucleotide sequence of the N9T-4 genome, consisting of a chromosome (6,439,972 bp), a linear plasmid (pN9T4-1 [565,206 bp]), and two circular plasmids (pN9T-4-2 [99,662 bp] and pN9T-4-3 [30,419 bp]).

Hitherto-Unnoticed Self-Transmissible Plasmids Widely Distributed among Different Environments in Japan.

Various conjugative plasmids were obtained by exogenous plasmid capture, biparental mating, and/or triparental mating methods from different environmental samples in Japan. Based on phylogenetic analyses of their whole-nucleotide sequences, new IncP/P-1 plasmids that could be classified into novel subgroups were obtained. Mini-replicons of the plasmids were constructed, and each of them was incompatible with at least one of the IncP/P-1 plasmids, although they showed diverse iteron sequences in their regions.

Advanced gallbladder cancer accompanied with cancer-associated dermatomyositis: A case report and literature review.

Rationale: Muscle weakness due to cancer-associated dermatomyositis (CADM) can be misdiagnosed as cancer cachexia and disuse atrophy.

Patient Concerns: A 75-year-old female was admitted to our institute with muscle weakness, dysphagia, and suspected gallbladder cancer. Computed tomography and cytopathological examinations of the liver biopsy and fine-needle aspiration from swollen lymph nodes using endoscopic ultrasonography revealed cancer in the gallbladder body and metastasis to the lymph nodes around the abdominal aorta.

The Deployment of a Newly Developed Proximal Release-Type Colonic Stent Is Feasible for Malignant Colorectal Obstruction near the Anal Verge: A Single-Center Preliminary Study.

Introduction: Colonic self-expandable metallic stents are widely used to treat malignant colorectal obstructions. Stent placement in lesions near the dentate line causes problems, including severe pain due to difficulty in positioning the stent accurately. Therefore, a proximal release-type stent was developed to overcome this issue, and this preliminary study aimed to investigate its efficacy and safety.

Draft Genome Sequence of Lactiplantibacillus plantarum NMZ-1139, Isolated from Whisky Mash.

Lactiplantibacillus plantarum NMZ-1139 was isolated from whisky mash and applied to sour beer production. Here, we report the draft genome sequence of L. plantarum NMZ-1139, which contains 3,117 protein-coding sequences, including genes associated with hop resistance, such as and .

A study of quality assessment in SARS-CoV-2 pathogen nucleic acid amplification tests performance; from the results of external quality assessment survey of clinical laboratories in the Tokyo Metropolitan Government external quality assessment program in 2020.

Introduction: The Tokyo Metropolitan Government (TMG) conducted an external quality assessment (EQA) survey of pathogen nucleic acid amplification tests (NAATs) as a TMG EQA program for SARS-CoV-2 for clinical laboratories in Tokyo.

Methods: We diluted and prepared a standard product manufactured by Company A to about 2,500 copies/mL to make a positive control and distribute it with a negative control. The participants reported the use of the NAATs methods for SARS-CoV-2, the name of the real-time RT-PCR kit, the name of the detection device, the target gene(s), nucleic acid extraction kit, Threshold Cycle value in the case of RT-PCR and the Threshold time value and Differential calculation value in the case of Loop-Mediated Isothermal Amplification (LAMP) method.

Complete Genome Sequence of sp. Strain NK8 (MAFF311271), a Chlorobenzoate-Degrading Bacterium.

sp. strain NK8 grows on 3-chlorobenzoate and shows chemotaxis toward 3-chlorobenzoate and its degradation products, such as chlorocatechols. Complete genome sequencing revealed a 9.

Fluviispira sanaruensis sp., nov., Isolated from a Brackish Lake in Hamamatsu, Japan.

Strain RF1110005, which was isolated from brackish lake water sampled at Lake Sanaru in Japan as a "filterable" bacterial strain, was characterized as a novel species in the genus Fluviispira, family Silvanigrellaceae, order Silvanigrellales, the class Oligoflexia and the phylum Bdellovibrionota. Cells of RF1110005 were aerobic, Gram stain negative, and show a pleomorphic morphology of spiral, filamentous and rod shapes. Catalase reaction was positive.

Complete Genome Sequence of Buttiauxella agrestis DSM 9389.

We report here the complete genome sequence of DSM 9389, which harbors eight 16S rRNA genes classified into three types. The genome sequence of this strain showed a high average nucleotide identity (97.3%) with that of the highly membrane vesicle-producing strain ATCC 33320.

A case of intraductal tubulopapillary neoplasm of the pancreas in a branch duct: a rare case report and literature review.

Background: Intraductal tubulopapillary neoplasm (ITPN) of the pancreas is a new disease concept defined by the World Health Organization in 2010. ITPN progresses with tubulopapillary growth in the pancreatic duct and is known to have a fair prognosis. Localization in the main pancreatic duct (MPD) is one characteristic.

Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate.

RNA-seq analysis of Cupriavidus necator NH9, a 3-chlorobenzoate degradative bacterium, cultured with 3-chlorobenzaote and benzoate, revealed strong induction of genes encoding enzymes in degradation pathways of the respective compound, including the genes to convert 3-chlorobenzaote and benzoate to chlorocatechol and catechol, respectively, and the genes of chlorocatechol ortho-cleavage pathway for conversion to central metabolites. The genes encoding transporters, components of the stress response, flagellar proteins, and chemotaxis proteins showed altered expression patterns between 3-chlorobenzoate and benzoate. Gene Ontology enrichment analysis revealed that chemotaxis-related terms were significantly upregulated by benzoate compared with 3-chlorobenzoate.

16S rRNA Gene Amplicon Sequencing of Gut Microbiota in Three Species of Deep-Sea Fish in Suruga Bay, Japan.

We report here 16S rRNA gene amplicon sequence analysis of the gut microbiota in three species of deep-sea fish collected from Suruga Bay, Japan. Of the three species, two were dominated by the phylum (genus ), while one was dominated by the phyla (genus ) and (unclassified ).