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Article ; Online: The Spleen Is an Ideal Site for Inducing Transplanted Islet Graft Expansion in Mice.

Takeshi Itoh / Hitomi Nishinakamura / Kenjiro Kumano / Hiroyuki Takahashi / Shohta Kodama

PLoS ONE, Vol 12, Iss 1, p e

2017 Volume 0170899

Abstract: Alternative islet transplantation sites have the potential to reduce the marginal number of islets required to ameliorate hyperglycemia in recipients with diabetes. Previously, we reported that T cell leukemia homeobox 1 (Tlx1)+ stem cells in the spleen ... ...

Abstract	Alternative islet transplantation sites have the potential to reduce the marginal number of islets required to ameliorate hyperglycemia in recipients with diabetes. Previously, we reported that T cell leukemia homeobox 1 (Tlx1)+ stem cells in the spleen effectively regenerated into insulin-producing cells in the pancreas of non-obese diabetic mice with end-stage disease. Thus, we investigated the spleen as a potential alternative islet transplantation site. Streptozotocin-induced diabetic C57BL/6 mice received syngeneic islets into the portal vein (PV), beneath the kidney capsule (KC), or into the spleen (SP). The marginal number of islets by PV, KC, or SP was 200, 100, and 50, respectively. Some plasma inflammatory cytokine levels in the SP group were significantly lower than those of the PV group after receiving a marginal number of islets, indicating reduced inflammation in the SP group. Insulin contents were increased 280 days after islet transplantation compared with those immediately following transplantation (p<0.05). Additionally, Tlx1-related genes, including Rrm2b and Pla2g2d, were up-regulated, which indicates that islet grafts expanded in the spleen. The spleen is an ideal candidate for an alternative islet transplantation site because of the resulting reduced inflammation and expansion of the islet graft.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: MEGANTE: A Web-Based System for Integrated Plant Genome Annotation

Numa, Hisataka / Takeshi Itoh

Plant & cell physiology. 2014 Jan., v. 55, no. 1

2014

Abstract: The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this ... ...

Abstract	The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exonâintron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data from virtually anywhere on the web. The current release of MEGANTE targets 24 plant species from the Brassicaceae , Fabaceae , Musaceae , Poaceae , Salicaceae , Solanaceae , Rosaceae and Vitaceae families, and it allows users to submit a sequence up to 10 Mb in length and to save up to 100 sequences with the annotation information on the server. The MEGANTE web service is available at https://megante.dna.affrc.go.jp/ .
Keywords	bioinformatics ; Brassicaceae ; computer software ; Fabaceae ; genome ; high-throughput nucleotide sequencing ; Internet ; loci ; Musaceae ; open reading frames ; Poaceae ; proteins ; Rosaceae ; Salicaceae ; Solanaceae ; Vitaceae
Language	English
Dates of publication	2014-01
Size	p. e2.
Publishing place	Japanese Society of Plant Physiologists.
Document type	Article
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pct157
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.

Yoshihiro Kawahara / Youko Oono / Hiroyuki Kanamori / Takashi Matsumoto / Takeshi Itoh / Eiichi Minami

PLoS ONE, Vol 7, Iss 11, p e

2012 Volume 49423

Abstract: A filamentous fungus, Magnaporthe oryzae, is a causal agent of rice blast disease, which is one of the most serious diseases affecting cultivated rice, Oryza sativa. However, the molecular mechanisms underlying both rice defense and fungal attack are not ...

Abstract	A filamentous fungus, Magnaporthe oryzae, is a causal agent of rice blast disease, which is one of the most serious diseases affecting cultivated rice, Oryza sativa. However, the molecular mechanisms underlying both rice defense and fungal attack are not yet fully understood. Extensive past studies have characterized many infection-responsive genes in the pathogen and host plant, separately. To understand the plant-pathogen interaction comprehensively, it is valuable to monitor the gene expression profiles of both interacting organisms simultaneously in the same infected plant tissue. Although the host-pathogen interaction during the initial infection stage is important for the establishment of infection, the detection of fungal gene expression in infected leaves at the stage has been difficult because very few numbers of fungal cells are present. Using the emerging RNA-Seq technique, which has a wide dynamic range for expression analyses, we analyzed the mixed transcriptome of rice and blast fungus in infected leaves at 24 hours post-inoculation, which is the point when the primary infection hyphae penetrate leaf epidermal cells. We demonstrated that our method detected the gene expression of both the host plant and pathogen simultaneously in the same infected leaf blades in natural infection conditions without any artificial treatments. The upregulation of 240 fungal transcripts encoding putative secreted proteins was observed, suggesting that these candidates of fungal effector genes may play important roles in initial infection processes. The upregulation of transcripts encoding glycosyl hydrolases, cutinases and LysM domain-containing proteins were observed in the blast fungus, whereas pathogenesis-related and phytoalexin biosynthetic genes were upregulated in rice. Furthermore, more drastic changes in expression were observed in the incompatible interactions compared with the compatible ones in both rice and blast fungus at this stage. Our mixed transcriptome analysis is useful for the simultaneous ...
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Whole-Genome Analysis of Herbicide-Tolerant Mutant Rice Generated by Agrobacterium-Mediated Gene Targeting

Endo, Masaki / Harumi Sasaki-Yamagata / Hiroyuki Kanamori / Masahiko Kumagai / Masao Hamada / Ritsuko Motoyama / Satomi Mori-Hosokawa / Seiichi Toki / Takeshi Itoh / Yoshiaki Nagamura / Yuichi Katayose

Plant & cell physiology. 2015 Jan., v. 56, no. 1

2015

Abstract: Gene targeting (GT) is a technique used to modify endogenous genes in target genomes precisely via homologous recombination (HR). Although GT plants are produced using genetic transformation techniques, if the difference between the endogenous and the ... ...

Abstract	Gene targeting (GT) is a technique used to modify endogenous genes in target genomes precisely via homologous recombination (HR). Although GT plants are produced using genetic transformation techniques, if the difference between the endogenous and the modified gene is limited to point mutations, GT crops can be considered equivalent to non-genetically modified mutant crops generated by conventional mutagenesis techniques. However, it is difficult to guarantee the non-incorporation of DNA fragments from Agrobacterium in GT plants created by Agrobacterium -mediated GT despite screening with conventional Southern blot and/or PCR techniques. Here, we report a comprehensive analysis of herbicide-tolerant rice plants generated by inducing point mutations in the rice ALS gene via Agrobacterium -mediated GT. We performed genome comparative genomic hybridization (CGH) array analysis and whole-genome sequencing to evaluate the molecular composition of GT rice plants. Thus far, no integration of Agrobacterium -derived DNA fragments has been detected in GT rice plants. However, >1,000 single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels) were found in GT plants. Among these mutations, 20â100 variants might have some effect on expression levels and/or protein function. Information about additive mutations should be useful in clearing out unwanted mutations by backcrossing.
Keywords	Agrobacterium ; backcrossing ; comparative genomic hybridization ; crops ; DNA fragmentation ; gene targeting ; genes ; genetic transformation ; herbicide resistance ; homologous recombination ; mutagenesis ; mutants ; point mutation ; polymerase chain reaction ; rice ; screening ; sequence analysis ; single nucleotide polymorphism ; Southern blotting
Language	English
Dates of publication	2015-01
Size	p. 116-125.
Publishing place	Japanese Society of Plant Physiologists.
Document type	Article
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pcu153
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice.

Youko Oono / Takayuki Yazawa / Yoshihiro Kawahara / Hiroyuki Kanamori / Fuminori Kobayashi / Harumi Sasaki / Satomi Mori / Jianzhong Wu / Hirokazu Handa / Takeshi Itoh / Takashi Matsumoto

PLoS ONE, Vol 9, Iss 5, p e

2014 Volume 96946

Abstract: Plant growth is severely affected by toxic concentrations of the non-essential heavy metal cadmium (Cd). Comprehensive transcriptome analysis by RNA-Seq following cadmium exposure is required to further understand plant responses to Cd and facilitate ... ...

Abstract	Plant growth is severely affected by toxic concentrations of the non-essential heavy metal cadmium (Cd). Comprehensive transcriptome analysis by RNA-Seq following cadmium exposure is required to further understand plant responses to Cd and facilitate future systems-based analyses of the underlying regulatory networks. In this study, rice plants were hydroponically treated with 50 µM Cd for 24 hours and ∼60,000 expressed transcripts, including transcripts that could not be characterized by microarray-based approaches, were evaluated. Upregulation of various ROS-scavenging enzymes, chelators and metal transporters demonstrated the appropriate expression profiles to Cd exposure. Gene Ontology enrichment analysis of the responsive transcripts indicated the upregulation of many drought stress-related genes under Cd exposure. Further investigation into the expression of drought stress marker genes such as DREB suggested that expression of genes in several drought stress signal pathways was activated under Cd exposure. Furthermore, qRT-PCR analyses of randomly selected Cd-responsive metal transporter transcripts under various metal ion stresses suggested that the expression of Cd-responsive transcripts might be easily affected by other ions. Our transcriptome analysis demonstrated a new transcriptional network linking Cd and drought stresses in rice. Considering our data and that Cd is a non-essential metal, the network underlying Cd stress responses and tolerance, which plants have developed to adapt to other stresses, could help to acclimate to Cd exposure. Our examination of this transcriptional network provides useful information for further studies of the molecular mechanisms of plant adaptation to Cd exposure and the improvement of tolerance in crop species.
Keywords	Medicine ; R ; Science ; Q
Subject code	572 ; 580
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A Novel Rice Cytochrome P450 Gene, CYP72A31, Confers Tolerance to Acetolactate Synthase-Inhibiting Herbicides in Rice and Arabidopsis

Saika, Hiroaki / Ayako Nishizawa-Yokoi / Fumio Taguchi-Shiobara / Junko Horita / Kiyosumi Hori / Koichiro Kaku / Masahiro Yano / Satoko Nonaka / Satoshi Iwakami / Seiichi Toki / Takashi Matsumoto / Takeshi Itoh / Tsutomu Shimizu / Tsuyoshi Tanaka

Plant physiology. 2014 Nov., v. 166, no. 3

2014

Abstract: A novel cytochrome P450 monooxygenase is involved in multiple-herbicide detoxification and could be useful in herbicide development and molecular breeding in crops . ... Target-site and non-target-site herbicide tolerance are caused by the prevention of ... ...

Abstract	A novel cytochrome P450 monooxygenase is involved in multiple-herbicide detoxification and could be useful in herbicide development and molecular breeding in crops . Target-site and non-target-site herbicide tolerance are caused by the prevention of herbicide binding to the target enzyme and the reduction to a nonlethal dose of herbicide reaching the target enzyme, respectively. There is little information on the molecular mechanisms involved in non-target-site herbicide tolerance, although it poses the greater threat in the evolution of herbicide-resistant weeds and could potentially be useful for the production of herbicide-tolerant crops because it is often involved in tolerance to multiherbicides. Bispyribac sodium (BS) is an herbicide that inhibits the activity of acetolactate synthase. Rice ( Oryza sativa ) of the indica variety show BS tolerance, while japonica rice varieties are BS sensitive. Map-based cloning and complementation tests revealed that a novel cytochrome P450 monooxygenase, CYP72A31, is involved in BS tolerance. Interestingly, BS tolerance was correlated with CYP72A31 messenger RNA levels in transgenic plants of rice and Arabidopsis ( Arabidopsis thaliana ). Moreover, Arabidopsis overexpressing CYP72A31 showed tolerance to bensulfuron-methyl (BSM), which belongs to a different class of acetolactate synthase-inhibiting herbicides, suggesting that CYP72A31 can metabolize BS and BSM to a compound with reduced phytotoxicity. On the other hand, we showed that the cytochrome P450 monooxygenase CYP81A6, which has been reported to confer BSM tolerance, is barely involved, if at all, in BS tolerance, suggesting that the CYP72A31 enzyme has different herbicide specificities compared with CYP81A6. Thus, the CYP72A31 gene is a potentially useful genetic resource in the fields of weed control, herbicide development, and molecular breeding in a broad range of crop species.
Keywords	Arabidopsis ; breeding ; crops ; cytochrome P-450 ; genes ; herbicides
Language	English
Dates of publication	2014-11
Size	p. 1232-1240.
Publishing place	American Society of Plant Biologists
Document type	Article
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1104/pp.113.231266
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Secretory Unit of Islet Transplant Objects (SUITO) Index Can Predict Severity of Hypoglycemic Episodes in Clinical Islet Cell Transplantation

Morihito Takita M.D. / Shinichi Matsumoto M.D., Ph.D. / Huanying Qin / Hirofumi Noguchi / Masayuki Shimoda / Daisuke Chujo / Takeshi Itoh / Koji Sugimoto / Nicholas Onaca / Bashoo Naziruddin / Marlon F. Levy

Cell Transplantation, Vol

2012 Volume 21

Abstract: One endpoint of clinical islet cell transplantation for type 1 diabetic patients is the elimination or reduction of hypoglycemia. We previously developed a simple tool to evaluate islet graft function: the secretory unit of islet transplant objects ( ... ...

Abstract	One endpoint of clinical islet cell transplantation for type 1 diabetic patients is the elimination or reduction of hypoglycemia. We previously developed a simple tool to evaluate islet graft function: the secretory unit of islet transplant objects (SUITO) index. The aim of this study is to clarify the association between the SUITO index and hypoglycemic episodes. Data from 310 clinical evaluations of 11 islet recipients were included in this study. Fasting plasma C-peptide and glucose levels were measured at every evaluation. The SUITO index was calculated according to the following formula: 1500 × C-peptide level (ng/ml)/[blood glucose level (mg/dl) – 63]. The number of hypoglycemic events (<3.8 mmol/L) and severe hypoglycemic events (<2.2 mmol/L or hypoglycemic unawareness) was assessed on the basis of interviews and self-monitoring of blood glucose (SMBG). Receiver operating characteristic (ROC) analysis was performed to determine the cut-off values of the SUITO index for hypoglycemic events. Based on the ROC study, follow-up data after transplantations were divided into the following three groups: low-SUITO (SUITO index <10, n = 91), middle-SUITO (10 ≤SUITO index <26, n = 83), high-SUITO (SUITO index ≤26, n = 125). The frequency of total hypoglycemia in the high-SUITO group was significantly decreased when compared to the other groups (value with Kruskal-Wallis test p < 0.001). The frequency of total severe hypoglycemia was significantly decreased in the low-SUITO group compared to pretransplant status and further decreased in the middle- and high-SUITO group. Spearman correlation coefficients were −0.663 ( p < 0.001) between the number of total hypoglycemic events per one month and the SUITO index and −0.521 ( p < 0.001) between that of severe events and the SUITO index. The SUITO index could predict the severity of hypoglycemic episodes in type 1 diabetic patients who received islet cell transplantations.
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2012-02-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Low Temperature Condition Prevents Hypoxia-Induced Islet Cell Damage and HMGB1 Release in a Mouse Model

Takeshi Itoh / Koji Sugimoto / Morihito Takita / Masayuki Shimoda / Daisuke Chujo / Jeff A. Sorelle / Bashoo Naziruddin Ph.D. / Marlon F. Levy / Shinichi Matsumoto

Cell Transplantation, Vol

2012 Volume 21

Abstract: One of the major issues in clinical islet transplantation is the poor efficacy of islet isolation. During pancreas preservation and islet isolation, islets suffer from hypoxia as islets are highly sensitive to hypoxic conditions. Cold preservation has ... ...

Abstract	One of the major issues in clinical islet transplantation is the poor efficacy of islet isolation. During pancreas preservation and islet isolation, islets suffer from hypoxia as islets are highly sensitive to hypoxic conditions. Cold preservation has been applied to minimize hypoxia-induced cell damage during organ preservation. However, the studies related to hypoxia-induced islet cell damage during islet isolation are limited. Recently, we demonstrated that mouse islets contain high levels of high-mobility group box 1 protein (HMGB1), and during proinflammatory cytokine-induced damage, islets release HMGB1 outside the cell. The released HMGB1 is involved in the initial events of early islet loss. In the present study, we hypothesize that low temperature conditions could prevent both hypoxia induced islet cell damage and HMGB1 release from islets in a mouse model. Isolated mouse islets underwent normoxic condition (95% air and 5% CO 2 ) at 37°C or hypoxic conditions (1% O 2 , 5% CO 2 , and 94% N 2 ) at 37°C (hypoxia-37°C islets), 22°C (hypoxia-22°C islets), or 4°C (hypoxia-4°C islets) for 12 h. In vitro and in vivo viability and functionality tests were performed. HMGB1, IL-6, G-CSF, KC, RANTES, MCP-1, and MIP-1 α levels in the medium were measured. Low temperature conditions substantially reduced hypoxia-induced necrosis ( p < 0.05) and apoptosis ( p < 0.05). In addition, low temperature islet culture significantly increased the insulin secretion from islets by high glucose stimulation ( p < 0.05). All of the recipient mice reversed diabetes after receiving the hypoxia-4°C islets but not after receipt of hypoxia-37°C or 22°C islets. The amounts of released HMGB1, IL-6, G-CSF, KC, RANTES, MCP-1, and MIP-1 α were significantly reduced in the hypoxia-4°C islets compared to those of the hypoxia-37°C islets ( p <0.05). In conclusion, low temperature conditions could prevent hypoxia-induced islet cell damage, inflammatory reactions in islets, and HMGB1 release and expression. Low temperature conditions ...
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2012-07-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evaluation of Osmolality of Density Gradient for Human Islet Purification

Hirofumi Noguchi M.D., Ph.D. / Bashoo Naziruddin / Masayuki Shimoda / Yasutaka Fujita / Daisuke Chujo / Morihito Takita / Han Peng / Koji Sugimoto / Takeshi Itoh / Naoya Kobayashi / Nicholas Onaca / Marlon F. Levy / Shinichi Matsumoto

Cell Transplantation, Vol

2012 Volume 21

Abstract: For pancreatic islet transplantation, the most common method of islet purification is density gradient centrifugation because of the differences in density between islets and acinar tissue. The density of islets/acinar tissue depends on several ... ...

Abstract	For pancreatic islet transplantation, the most common method of islet purification is density gradient centrifugation because of the differences in density between islets and acinar tissue. The density of islets/acinar tissue depends on several conditions, such as osmolality of purification solution. In this study, we evaluated the osmolality of iodixanol-controlled density gradients (400, 450, and 500 mOsm/kg) on the islet purification step. The density of the purification solutions was controlled by changing the volumetric ratio of iodixanol and the purification solutions (iodixanol-Kyoto solutions; IK solutions). The osmolality of density gradients was controlled by addition of 10x Hanks balanced salt solution (HBSS) solution. Density of both islets and acinar tissue increased relative to increase of the osmolality of purification solutions. There were no significant differences among the three groups on islet yield after density-adjusted purification and the rate of postpurification recovery. In vitro and in vivo assays suggest that the quality of islets was similar among the three groups. Our data suggest that efficacy of purification and quality of isolated islets is similar when the osmolality of purification solutions is between 400 and 500 mOsm/kg and density adjustment is applied. Since the density of islet and acinar tissue is changed according to osmolality, the density adjustment is important when using several osmolality solutions.
Keywords	Medicine ; R
Subject code	541
Language	English
Publishing date	2012-03-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correlation of Released HMGB1 Levels with the Degree of Islet Damage in Mice and Humans and with the Outcomes of Islet Transplantation in Mice

Takeshi Itoh / Morihito Takita / Jeffrey A. Sorelle / Masayuki Shimoda / Koji Sugimoto / Daisuke Chujo / Huanying Qin / Bashoo Naziruddin / Marlon F. Levy M.D., F.A.C.S. / Shinichi Matsumoto

Cell Transplantation, Vol

2012 Volume 21

Abstract: Establishing reliable islet potency assay is a critical and unmet issue for clinical islet transplantation. Recently, we reported that islets contained high levels of high mobility group box 1 (HMGB1) and damaged islets released HMGB1 in a mouse model. ... ...

Abstract	Establishing reliable islet potency assay is a critical and unmet issue for clinical islet transplantation. Recently, we reported that islets contained high levels of high mobility group box 1 (HMGB1) and damaged islets released HMGB1 in a mouse model. In this study, we hypothesized that the amount of released HMGB1 could reflect the degree of islet damage, and could predict the outcome of islet transplantation. Four groups of damaged mouse islets and three groups of damaged human islets were generated by hypoxic conditions. These islets were assessed by in vivo (transplantation) and in vitro (released HMGB1 levels, released C-peptide levels, PI staining, TUNEL staining, ATP/DNA, and glucose-stimulated insulin release test) assays. In addition, the ability of each assay to distinguish between noncured ( n = 13) and cured ( n = 7) mice was assessed. The curative rates of STZ-diabetic mice after receiving control, hypoxia-3h, hypoxia-6h, and hypoxia-24h mouse islets were 100%, 40%, 0%, and 0%, respectively. Only amounts of released HMGB1 and ratio of PI staining significant increased according to the degree of damages in both human and mouse islets. In terms of predictability of curing diabetic mice, amounts of released HMGB1 showed the best sensitivity (100%), specificity (100%), positive (100%), and negative predictive values (100%) among all the assays. The amount of released HMGB1 reflected the degree of islet damage and correlated with the outcome of islet transplantation in mice. Hence, released HMGB1 levels from islets should be a useful marker to evaluate the potency of isolated islets.
Keywords	Medicine ; R
Language	English
Publishing date	2012-07-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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