Publications by authors named "Takashi Aoki"

277 Publications

Information Retrieval on Oncology Knowledge Base using Recursive Paraphrase Lattice.

J Biomed Inform 2021 Feb 11:103705. Epub 2021 Feb 11.

Xcoo, Inc., Mitsuyama Bldg., 4F, 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan. Electronic address:

For annotation in cancer genomic medicine, oncologists have to refer to various knowledge bases worldwide and retrieve all information (e.g., drugs, clinical trials, and academic papers) related to a gene variant. However, oncologists find it difficult to search these knowledge bases comprehensively because there are multiple paraphrases containing abbreviations and foreign languages in their terminologies including diseases, drugs, and genes. In this paper, we propose a novel search method considering deep paraphrases, which helps oncologists retrieve essential annotation resources swiftly and effortlessly. Our method recursively finds paraphrases based on paraphrase corpora, expands a source document, and finally generates a paraphrase lattice. The proposed method also feedbacks beneficial information regarding the paraphrases applied for a search, which is useful for selecting search results and considering a query for the succeeding search. The results of an experiment demonstrated that our method could retrieve important annotation information that could not be retrieved using a conventional search system and simple paraphrasing. Additionally, annotation experts evaluated our method and found it to be practical.
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http://dx.doi.org/10.1016/j.jbi.2021.103705DOI Listing
February 2021

A Case of Prolonged Catatonia Caused by Sjögren's Syndrome.

Case Reports Immunol 2020 3;2020:8881503. Epub 2020 Nov 3.

Department of Psychiatry, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan.

Sjögren's syndrome (SS) is a chronic autoimmune disorder, often associated with some neuropsychiatric symptoms as well as systemic lupus erythematosus. Although catatonia is frequently reported in patients with systemic lupus erythematosus, it has been rarely reported in patients with SS. Herein, we present a case of SS with catatonia effectively and safely treated with modified electroconvulsive therapy (ECT). A 58-year-old woman showed prolonged catatonia and depressive mood along with pathologically dried eye and mouth. Based on physical findings and blood tests, she was diagnosed with SS. Because of the presence of pressure sores, we were unable to perform lumbar puncture for the diagnosis of abacterial encephalitis. Alternatively, single-photon emission computed tomography of her brain revealed multifocal hypoperfused areas in the parietotemporal region. Consequently, we performed ECT for the treatment of catatonia comorbid with SS. Following 20 sessions of ECT, the catatonia was improved without obvious adverse effects. One week after the last ECT, elevated levels of interleukin-6 were identified in the cerebral fluid. After receiving steroid pulse therapy, she has not experienced catatonia for more than 5 years. SS can cause catatonia, and ECT is a safe and effective option for the treatment of catatonia with SS.
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http://dx.doi.org/10.1155/2020/8881503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655257PMC
November 2020

ASC-deficiency impairs host defense against Aeromonas hydrophila infection in Japanese medaka, Oryzias latipes.

Fish Shellfish Immunol 2020 Oct 23;105:427-437. Epub 2020 Jul 23.

Department of Biochemistry and Applied Bioscience, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan. Electronic address:

Apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) is a component of inflammasome, which plays crucial roles in the inflammatory response. In mammals, ASC regulates caspase-1 activation, thereby inducing pyroptosis and producing activated inflammatory cytokines. In addition, ASC also interacts with receptor-interacting protein kinase 2 (RIPK2) and induces nuclear factor-κB (NF-κB) activation. However, the role of ASC remains poorly understood in fish. In this study, we focused on elucidating the role of ASC in fish that were infected with Aeromonas hydrophila using Japanese medaka (Oryzias latipes) as fish model, and ASC-knockout (KO) medaka was established using CRISPR-Cas9 system. ASC-KO and wild type (WT) medakas were infected with A. hydrophila, and mortality was observed. ASC-KO medaka demonstrated higher mortality than WT. Moreover, the expression of immune-related genes in the kidney and intestine of the ASC-KO and WT medakas challenged with A. hydrophila were analyzed. Following A. hydrophila infection, the kidney of ASC-KO medaka exhibited significantly lower expression of NF-κB regulated genes (e.g., IL-1β, IL-6, IL-8 and TNF-α) and RIPK2 gene than in WT kidney. Moreover, to investigate the immune response against A. hydrophila via ASC in the medaka, bacterial burden, superoxide anion production, and lactate dehydrogenase release in the kidney cells of ASC-KO medaka were measured. After infection, these responses in ASC-KO medaka were significantly decreased compared to those in WT. These results suggest that the medaka ASC plays a critical role against A. hydrophila infection by inducing inflammatory responses and cell death for bacterial clearance.
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http://dx.doi.org/10.1016/j.fsi.2020.07.027DOI Listing
October 2020

Structure of water and polymer at the buried polymer/water interface unveiled using heterodyne-detected vibrational sum frequency generation.

Phys Chem Chem Phys 2020 Aug 17;22(29):16527-16531. Epub 2020 Jul 17.

Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

The structure of the prototypical acrylic polymer (poly(methyl methacrylate): PMMA)/water interface is elucidated at the molecular level using heterodyne-detected sum-frequency generation. Two distinct OH groups of interfacial water are found at the interface: one forms hydrogen bonds with the carbonyl group and the other weakly interacts with the ester methyl group of the polymer surface.
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http://dx.doi.org/10.1039/d0cp02618bDOI Listing
August 2020

Biobased Poly(itaconic Acid--10-Hydroxyhexylitaconic Acid)s: Synthesis and Thermal Characterization.

Materials (Basel) 2020 Jun 14;13(12). Epub 2020 Jun 14.

Corporate Research & Business Division, Kaneka Corporation, 2-3-18 Nakanoshima, Kita-ku, Osaka 530-8288, Japan.

Renewable vinyl compounds itaconic acid (IA) and its derivative 10-hydroxyhexylitaconic acid (10-HHIA) are naturally produced by fungi from biomass. This provides the opportunity to develop new biobased polyvinyls from IA and 10-HHIA monomers. In this study, we copolymerized these monomers at different ratios through free radical aqueous polymerization with potassium peroxodisulfate as an initiator, resulting in poly(IA--10-HHIA)s with different monomer compositions. We characterized the thermal properties of the polymers by thermogravimetric analysis (TGA) and Fourier-transform infrared spectroscopy (FT-IR). The nuclear magnetic resonance analysis and the gel permeation chromatography showed that the polymerization conversion, yield, and the molecular weights (weight-averaged w and number-averaged n) of the synthesized poly(IA--10-HHIA)s decreased with increasing 10-HHIA content. It is suggested that the hydroxyhexyl group of 10-HHIA inhibited the polymerization. The TGA results indicated that the poly(IA--10-HHIA)s continuously decomposed as temperature increased. The FT-IR analysis suggested that the formation of the hydrogen bonds between the carboxyl groups of IA and 10-HHIA in the polymer chains was promoted by heating and consequently the polymer dehydration occurred. To the best of our knowledge, this is the first time that biobased polyvinyls were synthesized using naturally occurring IA derivatives.
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http://dx.doi.org/10.3390/ma13122707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7345788PMC
June 2020

Interleukin-17A/F1 from Japanese pufferfish (Takifugu rubripes) stimulates the immune response in head kidney and intestinal cells.

Fish Shellfish Immunol 2020 Aug 11;103:143-149. Epub 2020 May 11.

Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-kibanadai-nishi, Miyazaki, 889-2192, Japan. Electronic address:

In mammals, interleukin (IL)-17A and IL-17F, mainly produced by Th17 cells, are hallmark inflammatory cytokines that play important roles in the intestinal mucosal immune response. In contrast, three mammalian IL-17A and IL-17F counterparts (IL-17A/F1-3) have been identified in teleosts, and most of their functions have been described in the lymphoid organs. However, their function in the intestinal mucosal immune response is poorly understood. In this study, a recombinant (r) tiger puffer fish fugu (Takifugu rubripes) IL-17A/F1 was produced and purified using a mammalian expression system, and was used to stimulate cells isolated from fugu head kidney and intestines. The gene expression levels of TNF-α, IL-1β, IL-6, and β-defensin-like protein-1 (BD-1) genes were evaluated at 0, 3, 6 and 12 h post-stimulation (hps). Phagocytic activity and superoxide anion production were evaluated at the same time points using an NBT assay. The rIL-17A/F1 protein was shown to induce the expression of pro-inflammatory cytokines and antimicrobial peptides in both head kidney and intestinal cells. Expression levels for IL-1β, TNF-α, and IL-6 were all up-regulated between 3 and 12 hps. In addition, stimulation with rIL-17A/F1 enhanced phagocytic activity at 24 hps. Superoxide anion production was increased at 48 hps in the head kidney cells and moderately increased at 48 hps in intestinal cells. This study suggests that fugu IL-17A/F1 plays an important role in promoting the innate immune response and may act as a bridge between innate and adaptive immunity in the head kidney and intestine.
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http://dx.doi.org/10.1016/j.fsi.2020.05.016DOI Listing
August 2020

Interleukin-17A/F1 Deficiency Reduces Antimicrobial Gene Expression and Contributes to Microbiome Alterations in Intestines of Japanese medaka ().

Front Immunol 2020 17;11:425. Epub 2020 Mar 17.

Department of Biochemistry and Applied Bioscience, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.

In mammals, interleukin (IL)-17A and F are hallmark inflammatory cytokines that play key roles in protection against infection and intestinal mucosal immunity. In the gastrointestinal tract (GI), the induction of antimicrobial peptide (AMP) production via Paneth cells is a fundamental role of IL-17A and F in maintaining homeostasis of the GI microbiome and health. Although mammalian IL-17A and F homologs (referred to as IL-17A/F1-3) have been identified in several fish species, their function in the intestine is poorly understood. Additionally, the fish intestine lacks Paneth cells, and its GI structure is very different from that of mammals. Therefore, the GI microbiome modulatory mechanism via IL-17A/F genes has not been fully elucidated. In this study, Japanese medaka () were used as a teleost model, and IL-17A/F1-knockout (IL-17A/F1-KO) medaka were established using the CRISPR/Cas9 genome editing technique. Furthermore, two IL-17A/F1-deficient medaka strains were generated, including one strain containing a 7-bp deletion (-7) and another with an 11-bp addition (+11). After establishing F2 homozygous KO medaka, transcriptome analysis (RNA-seq) was conducted to elucidate IL-17A/F1-dependent gene induction in the intestine. Results of RNA-seq and real-time PCR (qPCR) demonstrated down-regulation of immune-related genes, including interleukin-1β (β), complement 1q subunit C (), transferrin a (), and G-type lysozyme (), in IL-17A/F1-KO medaka. Interestingly, protein and lipid digestive enzyme genes, including phospholipase A2, group IB (), and elastase-1-like (), were also downregulated in the intestines of IL-17A/F1-KO medaka. Furthermore, to reveal the influence of these downregulated genes on the gut microbiome in IL-17A/F1-KO, 16S rRNA-based metagenomic sequencing analysis was conducted to analyze the microbiome constitution. Under a non-exposed state, the intestinal microbiome of IL-17A/F1-KO medaka differed at the phylum level from wild-type, with significantly higher levels of Verrucomicrobia and Planctomycetes. Additionally, at the operational taxonomic unit (OTU) level of the human and fish pathogens, the Enterobacteriaceae was the dominant species in IL-17A/F1-KO medaka. These findings suggest that IL-17A/F1 is involved in the maintenance of a healthy gut microbiome.
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http://dx.doi.org/10.3389/fimmu.2020.00425DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092794PMC
March 2020

Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase of .

FASEB J 2019 11 16;33(11):13002-13013. Epub 2019 Sep 16.

Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

African trypanosomiasis, sleeping sickness in humans or nagana in animals, is a potentially fatal neglected tropical disease and a threat to 65 million human lives and 100 million small and large livestock animals in sub-Saharan Africa. Available treatments for this devastating disease are few and have limited efficacy, prompting the search for new drug candidates. Simultaneous inhibition of the trypanosomal glycerol kinase (TGK) and trypanosomal alternative oxidase (TAO) is considered a validated strategy toward the development of new drugs. Our goal is to develop a TGK-specific inhibitor for coadministration with ascofuranone (AF), the most potent TAO inhibitor. Here, we report on the identification of novel compounds with inhibitory potency against TGK. Importantly, one of these compounds (compound 17) and its derivatives (17a and 17b) killed trypanosomes even in the absence of AF. Inhibition kinetics revealed that derivative 17b is a mixed-type and competitive inhibitor for TGK and TAO, respectively. Structural data revealed the molecular basis of this dual inhibitory action, which, in our opinion, will aid in the successful development of a promising drug to treat trypanosomiasis. Although the EC of compound 17b against trypanosome cells was 1.77 µM, it had no effect on cultured human cells, even at 50 µM.-Balogun, E. O., Inaoka, D. K., Shiba, T., Tsuge, C., May, B., Sato, T., Kido, Y., Nara, T., Aoki, T., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Michels, P. A. M., Watanabe, Y.-I., Moore, A. L., Harada, S., Kita, K. Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase of
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http://dx.doi.org/10.1096/fj.201901342RDOI Listing
November 2019

Effect of sequential C-terminal tryptophans on green fluorescent protein fluorescence.

FEBS Open Bio 2018 Jul 29;8(7):1176-1183. Epub 2018 May 29.

Department of Molecular Biosciences School of Pharmaceutical Sciences Health Sciences University of Hokkaido Ishikari-Tobetsu Japan.

The effect of the addition of sequential C-terminal tryptophan residues on the fluorescence intensity of GFP was investigated. Tandem repeats of six tryptophan residues markedly decreased fluorescence intensity. This phenomenon is likely to occur because of the inhibition of GFP folding, resulting in insolubility. Exploiting this phenomenon, we constructed a cloning vector that facilitates the identification of recombinant colonies of by the activation of GFP.
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http://dx.doi.org/10.1002/2211-5463.12445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026694PMC
July 2018

Transcriptome analysis of immune response against Vibrio harveyi infection in orange-spotted grouper (Epinephelus coioides).

Fish Shellfish Immunol 2017 Nov 20;70:628-637. Epub 2017 Sep 20.

Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan; International Degree Program of Ornamental Fish Science and Technology, International College, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan. Electronic address:

Vibrio harveyi is a gram-negative bacterium reported as found in many aquaculture species. To increase knowledge of the immune response against V. harveyi, in this study we performed transcriptome analysis of head kidney and spleen in orange-spotted grouper (Epinephelus coioides) at 1 and 2 days post-infection (dpi), using the Illumina sequencing platform. After de novo assembly, a total of 79,128 unigenes was detected with an N50 of 2511 bp. After alignments with sequences recorded in the major databases (NT, NR, Swiss-Prot COG, KEGG, Interpro and GO), based on sequence similarity, 61,208 (77.4%) of the unigene total could be annotated using at least one database. Comparison of gene expression levels between V. harveyi and a control group at each time point revealed differentially expressed genes (DEGs) (P < 0.05): a total of 7918 (5536 upregulated and 2282 downregulated genes) from head kidney at 1 day post infection (dpi), 4260 (1444 upregulated and 2816 downregulated genes) from head kidney at 2 dpi, 7887 (4892 upregulated and 2995 downregulated genes) from spleen at 1 dpi, and 8952 (7388 upregulated and 1564 downregulated genes) from spleen at 2 dpi. The DEGs were mainly annotated into signal transduction and immune system categories, based on the KEGG database. The DEGs were enriched in immune-related pathway functions, NOD-like receptor signaling pathways, Toll-like receptor signaling pathways, NF-κB signaling pathways, and Jak-STAT signaling pathways. Additionally, we selected several DEGs and validated their expression level by RT-qPCR. The data generated in this study may provide a valuable resource for further immune response research and offer improved strategies against V. harveyi infection in teleost fishes.
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http://dx.doi.org/10.1016/j.fsi.2017.09.052DOI Listing
November 2017

Using CRISPR/Cas9-mediated gene editing to further explore growth and trade-off effects in myostatin-mutated F4 medaka (Oryzias latipes).

Sci Rep 2017 09 12;7(1):11435. Epub 2017 Sep 12.

Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan.

Myostatin (MSTN) suppresses skeletal muscle development and growth in mammals, but its role in fish is less well understood. Here we used CRISPR/Cas9 to mutate the MSTN gene in medaka (Oryzias latipes) and evaluate subsequent growth performance. We produced mutant F0 fish that carried different frameshifts in the OlMSTN coding sequence and confirmed the heritability of the mutant genotypes to the F1 generation. Two F1 fish with the same heterozygous frame-shifted genomic mutations (a 22 bp insertion in one allele; a 32 bp insertion in the other) were then crossbred to produce subsequent generations (F2~F5). Body length and weight of the MSTN F4 medaka were significantly higher than in the wild type fish, and muscle fiber density in the inner and outer compartments of the epaxial muscles was decreased, suggesting that MSTN null mutation induces muscle hypertrophy. From 3~4 weeks post hatching (wph), the expression of three major myogenic related factors (MRFs), MyoD, Myf5 and Myogenin, was also significantly upregulated. Some medaka had a spinal deformity, and we also observed a trade-off between growth and immunity in MSTN F4 medaka. Reproduction was unimpaired in the fast-growth phenotypes.
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http://dx.doi.org/10.1038/s41598-017-09966-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5595883PMC
September 2017

Whole-Genome Sequence of subsp. Strain 91-197, Isolated from Hybrid Striped Bass ( sp.) in the United States.

Genome Announc 2017 Jul 20;5(29). Epub 2017 Jul 20.

Integrated Institute for Regulatory Science, Research Organization for Nao and Life Innovation, Waseda University, Waseda Tsurumaki-cho, Shinjuku-ku, Tokyo, Japan

subsp. is a causative bacterium of fish pasteurellosis, which has caused serious economic damage to aquaculture farms worldwide. Here, the whole-genome sequence of subsp. 91-197, isolated in the United States, suggests that this genome consists of two chromosomes and two plasmids.
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http://dx.doi.org/10.1128/genomeA.00600-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522928PMC
July 2017

[Aortic Stenosis Combined with Cold Agglutinin Disease].

Kyobu Geka 2017 Jul;70(7):490-492

Department of Thoracic and Cardiovascular Surgery, Hirosaki University Graduate School of Medicine, Hirosaki, Japan.

Cardiac surgery on a patient with cold agglutinin disease is high risk for thromboembolism due to hypothermia perioperative. A 75-year-old woman with cold agglutinin disease underwent aortic valve replacement for severe aortic stenosis. Cold antibody was detected by preoperative screening test for blood transfusion. In order to prevent thromboembolic event during the operation, we maintained rectal temperature at around 36 degrees centigrade during the cardiopulmonary bypass by warming blood in the bypass circuit. Furthermore, antegrade warm blood cardioplegia was injected intermittently for keeping cardiac arrest. There was no thromboembolic event perioperatively.
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July 2017

Synthesis and Detection by HPLC of 3-Oxohexadecanoyl-CoA for the Study of Peroxisomal Bifunctional Proteins.

J Oleo Sci 2017 Jul 13;66(7):745-751. Epub 2017 Jun 13.

Department of Molecular Biosciences, School of Pharmaceutical Sciences, Health Sciences University of Hokkaido.

3-oxohexadecanoyl-CoA was synthesized for the study of D-bifunctional protein (EC 4. 2. 1. 107, EC 4. 2. 1. 119, EC 1. 1. 1. n12) and L-bifunctional protein (EC 4. 2. 1. 17, EC 5. 3. 3. 8, EC 1. 1. 1. 35). First, tetradecanal was subjected to the Reformatsky reaction with ethyl bromoacetate, and the product was then converted into ethyl 3-oxohexadecanoate. After acetalization of the 3-oxo ester with ethylene glycol, 3,3-ethlenedioxyhexadecanoic acid was obtained by alkaline hydrolysis. The acid was condensed with coenzyme A (CoA) by the mixed anhydride method, and the resulting CoA ester was deprotected with 4 M HCl to obtain 3-oxohexadecanoyl-CoA. In addition, the behavior of the CoA ester under several conditions of high-performance liquid chromatography (HPLC) was also investigated. We established separation detection of (R)-3-hydroxyhexadecanoyl-CoA, (S)-3-hydroxyhexadecaboyl-CoA, 3-oxohexadecanoyl-CoA, and trans-2-hexadecenoyl-CoA.
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http://dx.doi.org/10.5650/jos.ess16239DOI Listing
July 2017

Complete Genome Sequence of subsp. Strain OT-51443 Isolated from Yellowtail () in Japan.

Genome Announc 2017 May 25;5(21). Epub 2017 May 25.

Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan

Pseudotuberculosis caused by infection of subsp. has caused serious economic damages to aquaculture farms worldwide. Here, the whole-genome sequence of subsp. strain OT-51443, isolated in Japan, was determined and suggests that this genome consists of two chromosomes and five plasmids.
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http://dx.doi.org/10.1128/genomeA.00404-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5477405PMC
May 2017

On-site Direct Detection of Astaxanthin from Salmon Fillet Using Raman Spectroscopy.

Mar Biotechnol (NY) 2017 Apr 4;19(2):157-163. Epub 2017 Apr 4.

Integrated Institute for Regulatory Science, Research Organization for Nano and Life Innovation, Waseda University, 513 Tsurumaki-cho, Sbinjuku-ku, Tokyo, 162-0041, Japan.

A new technology employing Raman spectroscopy is attracting attention as a powerful biochemical technique for the detection of beneficial and functional food nutrients, such as carotenoids and unsaturated fatty acids. This technique allows for the dynamic characterization of food nutrient substances for the rapid determination of food quality. In this study, we attempt to detect and measure astaxanthin from salmon fillets using this technology. The Raman spectra showed specific bands corresponding to the astaxanthin present in salmon and the value of astaxanthin (Raman band, 1518 cm) relative to those of protein/lipid (Raman band, 1446 cm) in the spectra increased in a dose-dependent manner. A standard curve was constructed by the standard addition method using astaxanthin as the reference standard for its quantification by Raman spectroscopy. The calculation formula was established using the Raman bands typically observed for astaxanthin (i.e., 1518 cm). In addition, we examined salmon fillets of different species (Atlantic salmon, coho salmon, and sockeye salmon) and five fillets obtained from the locations (from the head to tail) of an entire Atlantic salmon. Moreover, the sockeye salmon fillet exhibited the highest astaxanthin concentration (14.2 mg/kg), while coho salmon exhibited an intermediate concentration of 7.0 mg/kg. The Raman-based astaxanthin concentration in the five locations of Atlantic salmon was more strongly detected from the fillet closer to the tail. From the results, a rapid, convenient Raman spectroscopic method was developed for the detection of astaxanthin in salmon fillets.
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http://dx.doi.org/10.1007/s10126-017-9739-7DOI Listing
April 2017

Segmentation of human upper body movement using multiple IMU sensors.

Annu Int Conf IEEE Eng Med Biol Soc 2016 Aug;2016:3163-3166

This paper proposes an approach for the segmentation of human body movements measured by inertial measurement unit sensors. Using the angular velocity and linear acceleration measurements directly, without converting to joint angles, we perform segmentation by formulating the problem as a classification problem, and training a classifier to differentiate between motion end-point and within-motion points. The proposed approach is validated with experiments measuring the upper body movement during reaching tasks, demonstrating classification accuracy of over 85.8%.
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http://dx.doi.org/10.1109/EMBC.2016.7591400DOI Listing
August 2016

Characterization of a specific monoclonal antibody against immunoglobulin light kappa/L1 chain in olive flounder (Paralichthys olivaceus).

Fish Shellfish Immunol 2017 Jan 11;60:88-96. Epub 2016 Nov 11.

Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, South Korea. Electronic address:

Immunoglobulins (Ig) are heterodimeric proteins that play critical roles in the adaptive immune system of vertebrates. Because of their plasticity, teleostean Igs are more diverse, and thus do not conform to mammalian classifications. Because of this, mammalian-based Ig cell markers cannot be used successfully to study immune responses in fish. There is therefore a need to produce Ig-specific cell markers for fish. Here, we attempted to identify the specific isotype detected by an Ig light chain-specific monoclonal antibody (anti-olive flounder IgL-mAb: M7C3-4) that we had previously produced [11]. Three newly identified sequences of the Ig light chain from olive flounder were classified according to their isotypes. Subsequent analyses revealed that M7C3-4 was able to specifically detect lymphocytes expressing one of the κ chains (Igκ-a) in olive flounder. Interestingly, Igκ-a B cells were more abundant in spleen and trunk-kidney than in peripheral blood, indicating a distribution different from that of IgM B cells. Our work reveals interesting aspects of B cell distribution and differentiation, and may aid in the production of suitable and effective cell markers for olive flounder.
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http://dx.doi.org/10.1016/j.fsi.2016.11.023DOI Listing
January 2017

Constitutive overexpressed type I interferon induced downregulation of antiviral activity in medaka fish (Oryzias latipes).

Dev Comp Immunol 2017 03 5;68:12-20. Epub 2016 Nov 5.

Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan, ROC; Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan, ROC. Electronic address:

In fish, as well as vertebrates, type I interferons (IFNs) are important cytokines that help to provide innate, antiviral immunity. Although low amounts of IFN are constitutively secreted under normal physiological conditions, long-term and excessive IFN stimulation leads to reduced sensitivity to the IFN signal. This provides a negative feedback mechanism that prevents inappropriate responses and autoimmunity. At present, however, neither IFN desensitization nor the normal physiological role of constitutive IFN are well characterized in fish. The objective here was therefore to produce and characterize a transgenic medaka fish (Oryzias latipes), designated IFNd-Tg, that constitutively overexpressed the IFNd gene. A dual promoter expression vector was constructed for overexpression of IFNd under an EF1α promoter and a DsRed reporter gene under control of a γF-crystaline promoter. The phenotype of the IFNd-Tg fish had a lower response to poly(I:C) and increased susceptibility to nervous necrosis virus (NNV) infection compared to wild-type (WT). Furthermore, transduction of IFN signals for STAT1b, STAT2 and IRF9 were down-regulated in the IFNd-Tg fish, and expression levels of RLR signal molecules (MDA5, MITA, IRF1 and IRF3) were lower than in WT. The constitutive overexpression of IFNd resulted in desensitization of IFN-stimulation, apparently due to downregulation of IFN signal transduction, and this caused increased susceptibility to NNV.
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http://dx.doi.org/10.1016/j.dci.2016.11.003DOI Listing
March 2017

A member of the immunoglobulin superfamily, orange-spotted grouper novel immune gene EcVig, is induced by immune stimulants and type I interferon.

Fish Shellfish Immunol 2016 Nov 22;58:415-422. Epub 2016 Sep 22.

Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan. Electronic address:

A novel grouper immune gene, EcVig was identified in orange-spotted grouper (Epinephelus coioides). We recently determined that EcVig expression can be induced by infection with nervous necrosis virus (NNV, an RNA virus), whereas NNV replication may be suppressed when EcVig was overexpressed. Although EcVig appeared to be involved in grouper antiviral activity, its immune effects have not been well characterized. In the present study, two PAMPs (pathogen-associated molecular patterns; lipopolysaccharides [LPS] and synthetic double-stranded RNA polyriboinosinic-polyribocytidylic acid [poly(I:C)]), as well as fish DNA virus (red sea bream iridovirus, RSIV; grouper iridovirus, GIV), were used to study EcVig responses in orange-spotted grouper. In addition, groupers were given recombinant type I interferon to determine whether EcVig expression was induced. Poly(I:C) rapidly induced substantial expression of EcVig, whereas LPS stimulation did not appear to have any effect in grouper intestine. Expression levels of total EcVig and other IFN-stimulated genes (ISGs) were all significantly increased after RSIV and GIV infection. Furthermore, stimulation of recombinant type I IFN also increased EcVig expression. We conclude that EcVig may be a novel IFN-stimulated gene that demonstrates an antiviral immune response.
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http://dx.doi.org/10.1016/j.fsi.2016.09.039DOI Listing
November 2016

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

Source Code Biol Med 2016 17;11:12. Epub 2016 Aug 17.

Xcoo, Inc., 4-2-5, Hongo, Bunkyo-ku, Tokyo, Japan.

Background: Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required.

Results: We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure.

Conclusions: Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.
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http://dx.doi.org/10.1186/s13029-016-0058-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987990PMC
August 2016

Nonvortical Rashba Spin Structure on a Surface with C_{1h} Symmetry.

Phys Rev Lett 2016 Jul 30;117(1):016803. Epub 2016 Jun 30.

Department of Nanomaterials Science, Chiba University, Chiba 263-8522, Japan.

A totally anisotropic peculiar Rashba-Bychkov (RB) splitting of electronic bands was found on the Tl/Si(110)-(1×1) surface with C_{1h} symmetry by angle- and spin-resolved photoelectron spectroscopy and first-principles theoretical calculation. The constant energy contour of the upper branch of the RB split band has a warped elliptical shape centered at a k point located between Γ[over ¯] and the edge of the surface Brillouin zone, i.e., at a point without time-reversal symmetry. The spin-polarization vector of this state is in-plane and points almost the same direction along the whole elliptic contour. This novel nonvortical RB spin structure is confirmed as a general phenomenon originating from the C_{1h} symmetry of the surface.
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http://dx.doi.org/10.1103/PhysRevLett.117.016803DOI Listing
July 2016

Draft Genome Sequence of the Fish Pathogen Mycobacterium pseudoshottsii Strain JCM15466, a Species Closely Related to M. marinum.

Genome Announc 2016 Feb 11;4(1). Epub 2016 Feb 11.

Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.

Mycobacterium pseudoshottsii is a slowly growing photochromogenic mycobacterium and fish pathogen isolated from wild marine fishes. M. pseudoshottsii closely resembles M. marinum, which is a human and animal pathogen. Here, we report the draft genome sequence of M. pseudoshottsii strain JCM15466, originally isolated from striped bass, Morone saxatilis.
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http://dx.doi.org/10.1128/genomeA.01630-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751307PMC
February 2016

Expression of immunogenic structural proteins of cyprinid herpesvirus 3 in vitro assessed using immunofluorescence.

Vet Res 2016 Jan 8;47. Epub 2016 Jan 8.

Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.

Cyprinid herpesvirus 3 (CyHV-3), also called koi herpesvirus (KHV), is the aetiological agent of a fatal disease in carp and koi (Cyprinus carpio L.), referred to as koi herpesvirus disease. The virus contains at least 40 structural proteins, of which few have been characterised with respect to their immunogenicity. Indirect immunofluorescence assays (IFAs) using two epitope-specific monoclonal antibodies (MAbs) were used to examine the expression kinetics of two potentially immunogenic and diagnostically relevant viral antigens, an envelope glycoprotein and a capsid-associated protein. The rate of expression of these antigens was determined following a time-course of infection in two CyHV-3 susceptible cell lines. The results were quantified using an IFA, performed in microtitre plates, and image analysis was used to analyse confocal micrographs, enabling measurement of differential virus-associated fluorescence and nucleus-associated fluorescence from stacks of captured scans. An 8-tenfold increase in capsid-associated protein expression was observed during the first 5 days post-infection compared to a ≤ 2-fold increase in glycoprotein expression. A dominant protein of ~100 kDa reacted with the capsid-associated MAb (20F10) in western blot analysis. This band was also recognised by sera obtained from carp infected with CyHV-3, indicating that this capsid-associated protein is produced in abundance during infection in vitro and is immunogenic to carp. Mass spectrometry carried out on this protein identified it as a previously uncharacterised product of open reading frame 84. This abundantly expressed and immunogenic capsid-associated antigen may be a useful candidate for KHV serological diagnostics.
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http://dx.doi.org/10.1186/s13567-015-0297-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705813PMC
January 2016

Expression and biological activity of two types of interferon genes in medaka (Oryzias latipes).

Fish Shellfish Immunol 2016 Jan 30;48:20-9. Epub 2015 Nov 30.

Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan. Electronic address:

Type I interferon (IFN) is one of most important cytokines for antiviral responses in fish innate immunity, after the induction pathway following pattern recognition. In this study, 2 types of type I IFN mRNA from a medaka (Japanese rice fish; Oryzias latipes) were identified and classified (phylogenetic analysis) into subgroup-a and -d by (designated olIFNa and olIFNd, respectively). Both olIFNa and olIFNd (encoding 197 and 187 amino acid residues, respectively) contained 2 cysteines. Gene expression pattern of olIFNa, olIFNd and IFN-stimulated genes (ISGs) was assessed (quantitative real-time reverse transcriptase PCR, qRT-PCR) in various organs (i.e., whole kidney, liver and spleen) of medaka stimulated by polyI:C or infected with nervous necrosis virus (NNV). Expression of olIFNa, olIFNd and ISGs, especially the ISG15 gene, were significantly upregulated after NNV-infection. Furthermore, olIFNa, olIFNd and ISGs mRNAs were sufficiently induced in DIT cells (i.e., medaka hepatoma cell line) transfected with polyI:C or infected with NNV. In addition, in vitro biological activities of recombinant olIFNa and olIFNd (rolIFNa and rolIFNd) produced by mammalian cell line HEK293T were also characterized. Expression of GIG1a and ISG15 genes in kidney cells of adult medaka were induced by rolIFNa or rolIFNd. The olIFNs-overexpressing DIT cells had reduced viral titers following NNV infection. Therefore, we inferred that 2 type I IFNs were involved in innate immunity (antiviral response) in medaka fish.
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http://dx.doi.org/10.1016/j.fsi.2015.11.036DOI Listing
January 2016

TALENs-mediated gene disruption of myostatin produces a larger phenotype of medaka with an apparently compromised immune system.

Fish Shellfish Immunol 2016 Jan 11;48:212-20. Epub 2015 Nov 11.

Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan. Electronic address:

Although myostatin, a suppressor of skeletal muscle development and growth, has been well studied in mammals, its function in fish remains unclear. In this study, we used a popular genome editing tool with high efficiency and target specificity (TALENs; transcription activator-like effector nucleases) to mutate the genome sequence of myostatin (MSTN) in medaka (Oryzias latipes). After the TALEN pair targeting OlMyostatin was injected into fertilized medaka eggs, mutant G0 fish carrying different TALENs-induced frameshifts in the OlMSTN coding sequence were mated together in order to transmit the mutant sequences to the F1 generation. Two F1 mutants with frameshifted myostatin alleles were then mated to produce the F2 generation, and these F2 OlMSTN null (MSTN(-/-)) medaka were evaluated for growth performance. The F2 fish showed significantly increased body length and weight compared to the wild type fish at the juvenile and post-juvenile stages. At the post-juvenile stage, the average body weight of the MSTN(-/-) medaka was ∼25% greater than the wild type. However, we also found that when the F3 generation were challenged with red spotted grouper nervous necrosis virus (RGNNV), the expression levels of the interferon-stimulated genes were lower than in the wild type, and the virus copy number was maintained at a high level. We therefore conclude that although the MSTN(-/-) medaka had a larger phenotype, their immune system appeared to be at least partially suppressed or undeveloped.
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http://dx.doi.org/10.1016/j.fsi.2015.11.016DOI Listing
January 2016

Pathogenesis of acute hepatopancreatic necrosis disease (AHPND) in shrimp.

Fish Shellfish Immunol 2015 Dec 6;47(2):1006-14. Epub 2015 Nov 6.

Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC. Electronic address:

Acute hepatopancreatic necrosis disease (AHPND), also called early mortality syndrome (EMS), is a recently emergent shrimp bacterial disease that has resulted in substantial economic losses since 2009. AHPND is known to be caused by strains of Vibrio parahaemolyticus that contain a unique virulence plasmid, but the pathology of the disease is still unclear. In this study, we show that AHPND-causing strains of V. parahaemolyticus secrete the plasmid-encoded binary toxin PirAB(vp) into the culture medium. We further determined that, after shrimp were challenged with AHPND-causing bacteria, the bacteria initially colonized the stomach, where they started to produce PirAB(vp) toxin. At the same early time point (6 hpi), PirB(vp) toxin, but not PirA(vp) toxin, was detected in the hepatopancreas, and the characteristic histopathological signs of AHPND, including sloughing of the epithelial cells of the hepatopancreatic tubules, were also seen. Although some previous studies have found that both components of the binary PirAB(vp) toxin are necessary to induce a toxic effect, our present results are consistent with other studies which have suggested that PirB(vp) alone may be sufficient to cause cellular damage. At later time points, the bacteria and PirA(vp) and PirB(vp) toxins were all detected in the hepatopancreas. We also show that Raman spectroscopy "Whole organism fingerprints" were unable to distinguish between AHPND-causing and non-AHPND causing strains. Lastly, by using minimum inhibitory concentrations, we found that both virulent and non-virulent V. parahaemolyticus strains were resistant to several antibiotics, suggesting that the use of antibiotics in shrimp culture should be more strictly regulated.
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http://dx.doi.org/10.1016/j.fsi.2015.11.008DOI Listing
December 2015

To complete its replication cycle, a shrimp virus changes the population of long chain fatty acids during infection via the PI3K-Akt-mTOR-HIF1α pathway.

Dev Comp Immunol 2015 Nov 23;53(1):85-95. Epub 2015 Jun 23.

Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan. Electronic address:

White spot syndrome virus (WSSV), the causative agent of white spot disease (WSD), is a serious and aggressive shrimp viral pathogen with a worldwide distribution. At the genome replication stage (12 hpi), WSSV induces a metabolic rerouting known as the invertebrate Warburg effect, which boosts the availability of energy and biosynthetic building blocks in the host cell. Here we show that unlike the lipogenesis that is seen in cancer cells that are undergoing the Warburg effect, at 12 hpi, all of the long chain fatty acids (LCFAs) were significantly decreased in the stomach cells of WSSV-infected shrimp. By means of this non-selective WSSV-induced lipolysis, the LCFAs were apparently diverted into β-oxidation and used to replenish the TCA cycle. Conversely, at 24 hpi, when the Warburg effect had ceased, most of the LCFAs were significantly up-regulated and the composition was also significantly altered. In crayfish these changes were in a direction that appeared to favor the formation of WSSV virion particles. We also found that, at 24 hpi, but not at 12 hpi, the PI3K-Akt-mTOR-HIF1α pathway induced the expression of fatty acid synthase (FAS), an enzyme which catalyzes the conversion of acetyl-CoA into LCFAs. WSSV virion formation was impaired in the presence of the FAS inhibitor C75, although viral gene and viral DNA levels were unaffected. WSSV therefore appears to use the PI3K-Akt-mTOR pathway to induce lipid biosynthesis at 24 hpi in order to support viral morphogenesis.
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http://dx.doi.org/10.1016/j.dci.2015.06.001DOI Listing
November 2015

The cytosolic sensor, DDX41, activates antiviral and inflammatory immunity in response to stimulation with double-stranded DNA adherent cells of the olive flounder, Paralichthys olivaceus.

Fish Shellfish Immunol 2015 Jun 14;44(2):576-83. Epub 2015 Mar 14.

Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju, 660-701, Republic of Korea. Electronic address:

DDX41, a receptor belonging to the DExD family, functions as a DNA sensor in the mammalian cytoplasm and mediates the antiviral response in host cells. Here, the olive flounder DDX41 was found to have 2267-bp long and encodes a putative protein of 614 amino acid residues. The olive flounder DDX41 mRNA was presented in all tested tissues, and was distinctly expressed in fish naturally infected with LCDV. High expression levels were observed in the heart, liver, kidney and stomach. Furthermore, the olive flounder DDX41 mRNA expression increased significantly in adherent (monocyte-like) cells following stimulation with a DNA virus. Reporter assays showed that the transcriptional activity of the IFN-I promoter was enhanced in DDX41-overexpressing HINAE cells treated with C-di-GMP (dinucleotides). Overexpression of DDX41 also induced the antiviral and inflammatory cytokine gene expression through cytoplasmic C-di-GMP treatment. These results suggest that DDX41 functions as a cytosolic DNA sensor that is capable of inducing antiviral activity and inflammatory responses in the olive flounder.
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http://dx.doi.org/10.1016/j.fsi.2015.03.008DOI Listing
June 2015