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Muhammad Azman Zakaria, Mohd Zulkhairi Mohd Yusoff, Mohd Rafein Zakaria, Mohd Ali Hassan, Thomas K Wood, Toshinari Maeda
Pseudogenes in the Escherichia coli genome are assumed to be non-functional. In this study, Keio collection BW25113∆ yqiG and YqiG-producing strain (BW25113/pCA24N-YqiG) were used to evaluate the importance of pseudogene yqiG in hydrogen metabolism. Our results show pseudogene protein YqiG was identified as an essential protein in the production of biohydrogen from glucose. The mutant yqiG decreased biohydrogen production from 37 µmol mg-1 protein to 6 µmol mg-1 protein compared to the wild-type strain, and glucose consumption was reduced by 80%...
October 2018: 3 Biotech
Katsuyoshi Matsuoka, Shunsuke Hamada, Mikiko Shimizu, Kosaku Nanki, Shinta Mizuno, Hiroki Kiyohara, Mari Arai, Shinya Sugimoto, Yasushi Iwao, Haruhiko Ogata, Tadakazu Hisamatsu, Makoto Naganuma, Takanori Kanai, Mayumi Mochizuki, Masayuki Hashiguchi
Since anti-tumor necrosis factor (TNF)-α agents (TNF-α inhibitors) induce both clinical response and remission in patients with moderate to severe inflammatory bowel disease (IBD), the use of anti-TNF therapies has fundamentally changed the approach to treatment for patients with IBD. Infliximab (IFX) is a TNF-α inhibitor approved for the induction and remission of Crohn's disease (CD). However, even among patients who initially demonstrate a clinical response to IFX therapy, secondary loss of response occurs, although the reason remains unknown...
2018: PloS One
Enrique Martínez-Carranza, Luis Servín-González, Miguel Cocotl-Yañez, Gloria Soberón-Chávez
The understanding of why a gene is essential for a bacterium has implications in different research areas, such as bacterial evolution, synthetic biology, and biotechnology, making the identification of essential genes a very active research field. Bacterial essential genes have been defined, among other criteria, by the inability to obtain viable mutants in such genes. In the case of Escherichia coli this approach led to the construction of the Keio collection of single-gene knockout mutants that contains deletions of all the open reading frames present in the genome with the exception of 303 genes that were found to be essential for the growth of this bacterium...
September 24, 2018: FEMS Microbiology Letters
Tokunori Kanazawa, Yasuhiro Minami, Masahiro Jinzaki, Masahiro Toda, Kazunari Yoshida, Hikaru Sasaki
BACKGROUND: and purpose: Solitary fibrous tumor (SFT)/hemangiopericytoma (HPC) is radiologically difficult to distinguish from meningioma, especially angiomatous meningioma. This study aimed to detect texture parameters to distinguish SFT/HPC from angiomatous meningioma using magnetic resonance imaging texture analysis (MRTA) with commercially available software. MATERIALS AND METHODS: We retrospectively investigated textural parameters in 43 newly diagnosed SFTs/HPCs, angiomatous meningiomas, and other WHO grade Ⅰ meningiomas treated at Keio University Hospital...
September 18, 2018: World Neurosurgery
Masahiro Toda, Kenzo Kosugi, Hiroyuki Ozawa, Kaoru Ogawa, Kazunari Yoshida
Objective  The main purpose of this article is to assess the effectiveness and safety of surgery via the endoscopic endonasal approach (EEA) for cavernous sinus (CS) lesion in patients with nonfunctioning pituitary adenomas (NFPA). Design  Retrospective study. Setting  Keio University Hospital. Participants  Thirty patients who underwent CS surgery via the EEA between 2009 and 2017 for Knosp grade 4 NFPA with pre- and postoperative magnetic resonance imaging available for volumetric analysis. Main Outcome Measures  Clinical presentation, extent of resection, and surgical complications...
October 2018: Journal of Neurological Surgery. Part B, Skull Base
Masayoshi Shinjoh, Norio Sugaya, Yoshio Yamaguchi, Noriko Iibuchi, Isamu Kamimaki, Anna Goto, Hisato Kobayashi, Yasuaki Kobayashi, Meiwa Shibata, Satoshi Tamaoka, Yuji Nakata, Atsushi Narabayashi, Mitsuhiro Nishida, Yasuhiro Hirano, Takeshi Munenaga, Kumiko Morita, Keiko Mitamura, Takao Takahashi
OBJECTIVES: We assessed the vaccine effectiveness (VE) of inactivated influenza vaccine (IIV) in children 6 months to 15 years of age during the 2016/17 season. In addition, we estimated the impact of repeated vaccination in children on VE. METHODS: Our study for VEs in preventing influenza and admission due to influenza were conducted according to a test-negative case-control design (TNCC) based on influenza rapid diagnostic test results. We also analyzed the VE by vaccine status in the current and previous seasons for the impact of repeated vaccination...
September 5, 2018: Vaccine
Takahito Suto, Yukio Yonemoto, Koichi Okamura, Hideo Sakane, Kimihiko Takeuchi, Yasuyuki Tamura, Tetsuya Kaneko, Keio Ayabe, Hirotaka Chikuda
OBJECTIVES: To assess the middle-term outcome of iguratimod (IGU) in rheumatoid arthritis (RA) patients. METHODS: Sixty-nine RA patients (14 males and 55 females, mean age of 64.0 years) receiving IGU-containing therapies were enrolled. We divided these patients into three groups based on the treatment at the baseline: an IGU group, a Methotrexate (MTX) plus IGU group, and a biologics plus IGU group. The baseline characteristics and clinical course were evaluated over three years...
August 10, 2018: Modern Rheumatology
Diego E Egoburo, Rocío Diaz Peña, Daniela S Alvarez, Manuel S Godoy, Mariela P Mezzina, M Julia Pettinari
Manipulation of global regulators is one of the strategies used for the construction of bacterial strains suitable for the synthesis of bioproducts. However, the pleiotropic effects of these regulators can vary in different conditions and are often strain dependent. This study analyzed the effects of ArcA, CreC, Cra and Rob using single deletion mutants of the well characterized and completely sequenced Escherichia coli strain BW25113. Comparison of the effects of each regulator on the synthesis of major extracellular metabolites, tolerance to several compounds and synthesis of native and non-native bioproducts in different growth conditions allowed the discrimination of the particular phenotypes that can be attributed to the individual mutants, and singled out Cra and ArcA as the regulators with the most important effects on bacterial metabolism...
July 20, 2018: Applied and Environmental Microbiology
Kazuma Yagi, Takanori Asakura, Ho Namkoong, Shoji Suzuki, Takahiro Asami, Satoshi Okamori, Tatsuya Kusumoto, Yohei Funatsu, Hirofumi Kamata, Tomoyasu Nishimura, Makoto Ishii, Tomoko Betsuyaku, Naoki Hasegawa
BACKGROUND: Pulmonary Mycobacterium avium complex (pMAC) disease is a chronic, slowly progressive disease. The aim of the present study was to determine the association of six-minute walk test (6MWT) parameters with pulmonary function and the health-related quality of life (HRQL) in patients with pMAC disease. METHODS: This cross-sectional study included adult patients with pMAC and was conducted at Keio University Hospital. We investigated the relationship of 6MWT parameters with clinical parameters, including pulmonary function, and HRQL, which was assessed using the 36-Item Short Form Health Survey (SF-36) and St...
July 13, 2018: BMC Pulmonary Medicine
Natalie Gugala, Joe Lemire, Kate Chatfield-Reed, Ying Yan, Gordon Chua, Raymond J Turner
It is essential to understand the mechanisms by which a toxicant is capable of poisoning the bacterial cell. The mechanism of action of many biocides and toxins, including numerous ubiquitous compounds, is not fully understood. For example, despite the widespread clinical and commercial use of silver (Ag), the mechanisms describing how this metal poisons bacterial cells remains incomplete. To advance our understanding surrounding the antimicrobial action of Ag, we performed a chemical genetic screen of a mutant library of Escherichia coli —the Keio collection, in order to identify Ag sensitive or resistant deletion strains...
July 6, 2018: Genes
Genta Aoki, Yasubumi Sakakibara
Motivation: The convolutional neural network (CNN) has been applied to the classification problem of DNA sequences, with the additional purpose of motif discovery. The training of CNNs with distributed representations of four nucleotides has successfully derived position weight matrices on the learned kernels that corresponded to sequence motifs such as protein-binding sites. Results: We propose a novel application of CNNs to classification of pairwise alignments of sequences for accurate clustering of sequences and show the benefits of the CNN method of inputting pairwise alignments for clustering of non-coding RNA (ncRNA) sequences and for motif discovery...
July 1, 2018: Bioinformatics
Claudia Hahn, Michael Hans, Christina Hein, Anne Dennstedt, Frank Mücklich, Petra Rettberg, Christine Elisabeth Hellweg, Lars Ingo Leichert, Christopher Rensing, Ralf Moeller
Several Escherichia coli deletion mutants of the Keio collection were selected for analysis to better understand which genes may play a key role in copper or silver homeostasis. Each of the selected E. coli mutants had a deletion of a single gene predicted to encode proteins for homologous recombination or contained functions directly linked to copper or silver transport or transformation. The survival of these strains on pure copper surfaces, stainless steel, and alloys of aluminum, copper and/or silver was investigated...
October 2018: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
Rubén Monárrez, Yin Wang, Yingmei Fu, Chun-Hsing Liao, Ryo Okumura, Molly R Braun, George A Jacoby, David C Hooper
Expression of the quinolone resistance gene qnrS1 is increased by quinolones, but unlike induction of some other qnr genes, the bacterial SOS system is not involved and no lexA box is found upstream. Nonetheless, at least 205 bp of upstream sequence is required for induction to take place. An upstream sequence bound to beads trapped potential binding proteins from cell extracts that were identified by mass spectrometry as Dps, Fis, Ihf, Lrp, CysB, and YjhU. To further elucidate their role, a reporter plasmid linking the qnrS1 upstream sequence to lacZ was introduced into cells of the Keio collection with single-gene deletions and screened for lacZ expression...
September 2018: Antimicrobial Agents and Chemotherapy
T Asakura, M Ishii, K Ishii, S Suzuki, H Namkoong, S Okamori, H Kamata, K Yagi, Y Funatsu, T Betsuyaku, N Hasegawa
BACKGROUND: Little is known about the clinical characteristics and health-related quality of life (HQOL) of elderly patients with pulmonary Mycobacterium avium complex (pMAC) disease. OBJECTIVES: To evaluate HQOL using the 36-Item Short-Form Health Survey and St George's Respiratory Questionnaire (SGRQ) and to investigate the predictors of HQOL changes among elderly patients with pMAC disease. METHODS: This prospective cohort registry was conducted at Keio University Hospital, Tokyo, Japan, between May 2012 and July 2015 and included 84 patients with pMAC disease aged 75 years who had completed the HQOL questionnaire and 48 patients with pMAC disease who had been followed up and completed the HQOL questionnaire in cross-sectional and longitudinal analyses, respectively...
June 1, 2018: International Journal of Tuberculosis and Lung Disease
Giacomo Savini, Kazuno Negishi, Kenneth J Hoffer, Domenico Schiano Lomoriello
PURPOSE: To evaluate the results of intraocular lens (IOL) power calculation using different corneal power measurements provided by an optical biometer combined with a dual Scheimpflug analyzer and a Placido disk topographer (Galilei G6). SETTING: G.B. Bietti Foundation, Rome, Italy, and Keio University Hospital, Tokyo, Japan. DESIGN: Evaluation of diagnostic technology. METHODS: Consecutive patients having cataract surgery were enrolled...
June 2018: Journal of Cataract and Refractive Surgery
Hideki Mori, Hidekazu Suzuki, Juntaro Matsuzaki, Tatsuhiro Masaoka, Takanori Kanai
Background and aim: Although sitafloxacin (STFX)-containing regimens are effective rescue treatments for Helicobacter pylori infection, prevalence of fluoroquinolone resistance in H. pylori has increased rapidly worldwide. The change in resistance levels and gyrA mutations, a major cause of fluoroquinolone resistance, after unsuccessful STFX-containing treatment has not been investigated. Methods: We conducted a retrospective, non-randomized study to compare the minimum inhibitory concentrations (MICs) of STFX and the location of gyrA mutations in H...
April 2018: United European Gastroenterology Journal
Kaori Sakurai, Shotaro Chubachi, Hidehiro Irie, Akihiro Tsutsumi, Naofumi Kameyama, Takashi Kamatani, Hidefumi Koh, Takeshi Terashima, Hidetoshi Nakamura, Koichiro Asano, Tomoko Betsuyaku
BACKGROUND: Neutrophil-to-lymphocyte ratio (NLR) is a biomarker of inflammation in chronic obstructive pulmonary disease (COPD) patients. But, a meaningful threshold and the longitudinal changes are unknown. We aimed to investigate the association between NLR and the clinical characteristics of COPD patients and to determine a meaningful threshold and the longitudinal changes for NLR. METHODS: Keio University and its affiliate hospitals conducted an observational COPD cohort study over 3 years...
May 2, 2018: BMC Pulmonary Medicine
Takeshi Murata, Hiromitsu Jinno, Maiko Takahashi, Masayuki Shimoda, Tetsu Hayashida, Kaori Kameyama, Yuko Kitagawa
The number of long-term breast cancer survivors with a risk of late recurrence is increasing. Hormone-receptor-positive patients have greater risks of late recurrence. Although several studies demonstrated that extended adjuvant endocrine therapy reduces the incidence of late recurrence, it remains unclear which hormone-receptor-positive patients have greater risks of late recurrence. Hormone-receptor-positive breast cancer patients were retrospectively selected from the prospective database of primary breast cancer patients treated at Keio University Hospital from January 1989 to December 2003...
April 23, 2018: Breast Journal
Motoaki Sano, Masaru Suzuki, Koichiro Homma, Kei Hayashida, Tomoyoshi Tamura, Tadashi Matsuoka, Yoshinori Katsumata, Shuko Onuki, Junichi Sasaki
It has been reported that hydrogen gas exerts a therapeutic effect in a wide range of disease conditions, from acute illness such as ischemia-reperfusion injury, shock, and damage healing to chronic illness such as metabolic syndrome, rheumatoid arthritis, and neurodegenerative diseases. Antioxidant and anti-inflammatory properties of hydrogen gas have been proposed, but the molecular target of hydrogen gas has not been identified. We established the Center for Molecular Hydrogen Medicine to promote non-clinical and clinical research on the medical use of hydrogen gas through industry-university collaboration and to obtain regulatory approval of hydrogen gas and hydrogen medical devices (http://www...
April 2018: Acute Medicine & Surgery
Takeo Kosaka, Toshiaki Shinojima, Shinya Morita, Mototsugu Oya
The present study aimed to evaluate the efficacy of cabazitaxel in Japanese patients affected by metastatic castration-resistant prostate cancer (mCRPC) previously treated with a docetaxel-containing regimen. In this retrospective study, 41 patients with mCRPC treated with cabazitaxel at Keio University Hospital were retrospectively reviewed. Cabazitaxel at a dose of 20-25 mg/m² was administered every 3 or 4 weeks. Clinicopathological factors and laboratory data were collected to assess the prognostic factors for overall survival (OS) and progression-free survival (PFS)...
May 2018: Cancer Science
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