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Yutaka Kikuchi

Publications and source records attributed to Yutaka Kikuchi.

At least 19 recordsLinked to original sources
PubMed2025

Extrinsic heterogeneity: Collectivity in isotropic conformational fluctuations of chromosomes.

Eukaryotic interphase chromosomes maintain a three-dimensional conformation within the nucleus and undergo fluctuations. However, the analysis of chromosome conformational fluctuations has been mainly limited to chromosome conformation capture data that record the contact frequencies between chromosomal regions. Herein, we investigated chromosome fluctuations as polymers based on experimental data from sequential fluorescence in situ hybridization using a multiomics methodology. To describe the principal modes of chromosome fluctuations, we applied principal-component analysis to the three-dimensional conformation information of single chromosomes in 446 mouse embryonic stem cells obtained from sequential fluorescence in situ hybridization data analysis for spatial genomics and signals of nuclear factors (histone marks, repeat DNAs, and proteins in interchromosomal nuclear compartments). We found that chromosome fluctuations exhibit both isotropic and anisotropic modes. The isotropic conformational fluctuations of all chromosome types tended to synchronize each other, reflecting extrinsic heterogeneity in chromosome conformation that is independent of the cell cycle. In contrast, anisotropic conformational fluctuations, occurring in a spindle-like shape, were associated with the interactions between repeat DNAs and nuclear factors. These results highlight the importance of dissecting cell-cycle-independent nuclear organization based on the conformational folding of chromosomes and the interactions between genomic regions and nuclear factors.

Animals↗
PubMed2007

Initial specification of the epibranchial placode in zebrafish embryos depends on the fibroblast growth factor signal.

In vertebrates, cranial sensory ganglia are mainly derived from ectodermal placodes, which are focal thickenings at characteristic positions in the embryonic head. Here, we provide the first description of the early development of the epibranchial placode in zebrafish embryos using sox3 as a molecular marker. By the one-somite stage, we saw a pair of single sox3-expressing domains appear lateral to the future hindbrain. The sox3 domain, which is referred to here as the early lateral placode, is segregated during the early phase of segmentation to form a pax2a-positive medial area and a pax2a-negative lateral area. The medial area subsequently developed to form the otic placode, while the lateral area was further segregated along the anteroposterior axis, giving rise to four sox3-positive subdomains by 26 hr postfertilization. Given their spatial relationship with the expression of the markers for the epibranchial ganglion, as well as their positions and temporal changes, we propose that these four domains correspond to the facial, glossopharyngeal, vagal, and posterior lateral line placodes in an anterior-to-posterior order. The expression of sox3 in the early lateral placode was absent in mutants lacking functional fgf8, while implantation of fibroblast growth factor (FGF) beads restored the sox3 expression. Using SU5402, which inhibits the FGF signal, we were able to demonstrate that formation of both the early lateral domains and later epibranchial placodes depends on the FGF signal operating at the beginning of somitogenesis. Together, these data provide evidence for the essential role of FGF signals in the development of the epibranchial placodes.

Animals↗
PubMed2006

Fgf signaling negatively regulates Nodal-dependent endoderm induction in zebrafish.

In zebrafish development, Nodal signaling is critical for the induction of endoderm and mesoderm. Three transcription factors downstream of Nodal, Bonnie and Clyde (Bon), Faust (Fau)/Gata5 and Casanova (Cas), are required for endoderm induction. However, it is not yet fully understood how the Nodal signaling pathway regulates the decision process of endoderm and mesoderm induction. In this study, we focused on Fgf signaling, downstream of Nodal signaling, during endoderm induction. We found that activation of Fgf signaling decreases the number of cas-expressing endodermal cells. Conversely, inhibition of this signaling increases the number of endodermal cells without affecting the expression of Nodal, Nodal antagonists, bon or fau/gata5. Inhibition of Fgf signaling in endoderm mutants suggests that this signaling negatively regulates cas expression by a pathway parallel to Bon and Fau/Gata5 in the molecular cascade leading to endoderm. Furthermore, activation of Fgf signaling can overcome Cas-mediated abrogation of mesodermal gene expression. Altogether, these results suggest that Fgf signaling negatively regulates endoderm induction, possibly through repression of cas expression and down-regulation of Cas function.

Animals↗
PubMed2006

The yolk syncytial layer regulates myocardial migration by influencing extracellular matrix assembly in zebrafish.

The roles of extra-embryonic tissues in early vertebrate body patterning have been extensively studied, yet we know little about their function during later developmental events. Here, we analyze the function of the zebrafish extra-embryonic yolk syncytial layer (YSL) specific transcription factor, Mtx1, and find that it plays an essential role in myocardial migration. Downregulating the function of Mtx1 in the YSL leads to cardia bifida, a phenotype in which the myocardial cells fail to migrate to the midline. Mtx1 in the extra-embryonic YSL appears to regulate the embryonic expression of fibronectin, a gene previously implicated in myocardial migration. We further show dosage-sensitive genetic interactions between mtx1 and fibronectin. Based on these data, we propose that the extra-embryonic YSL regulates myocardial migration, at least in part by influencing fibronectin expression and subsequent assembly of the extracellular matrix in embryonic tissues.

Animals↗
PubMed2006

[Identification of fungi using DNA sequences: an approach to identify Fusarium species isolated from domestic unpolished rice].

Molecular approaches are being developed to provide for the rapid and objective identification of fungi. We attempted the identification of Fusarium species by a genetic analysis to validate practically the utility of a molecular approach for fungal identification and to reveal its limitations, and sequenced three regions, the 5' end of the 28S rRNA gene (D2 region) and the internal transcribed spacer 1 and 2 (ITS1 and ITS2) regions, in the rRNA genes. The DNA sequences of 38 Fusarium strains isolated from domestic unpolished rice were compared for similarity with entries in the GenBank. Based on this comparison, it was estimated that all these three regions, as a minimum, must be compared with the database to identify Fusaria at the species level. According to the combinations of sequences in the three regions, the 38 isolates were classified into 13 groups. Out of the 13 groups, 6 groups (20 isolates in total) could be identified as definite species based only on the sequence data. For the other 6 groups (17 isolates in total), candidate species were limited on the basis of the sequence similarity, and then the isolates were identified at the species level with the aid of morphology. Only one isolate could not be identified. These results verified that DNA sequence comparison with the GenBank database is useful for the identification of Fusarium species.

DNA↗
PubMed2005

Eomesodermin is a localized maternal determinant required for endoderm induction in zebrafish.

In zebrafish, endoderm induction occurs in marginal blastomeres and requires Casanova (Cas), the first endoderm-specific factor expressed in the embryo. Whereas the transcription factors Gata5 and Bon are necessary and sufficient for cas expression in marginal blastomeres, Bon and Gata5 are unable to induce cas in animal pole cells, suggesting that cas expression requires an additional, unidentified factor(s). Here, we show that cas expression depends upon the T box transcription factor Eomesodermin (Eomes), a maternal determinant that is localized to marginal blastomeres. Eomes synergizes potently with Bon and Gata5 to induce cas, even in animal pole blastomeres. We show that Eomes is required for endogenous endoderm induction, acting via an essential binding site in the cas promoter. Direct physical interactions between Eomes, Bon, and Gata5 suggest that Eomes promotes endoderm induction in marginal blastomeres by facilitating the assembly of a transcriptional activating complex on the cas promoter.

Animals↗
PubMed2005

Endoderm development in vertebrates: fate mapping, induction and regional specification.

The formation of the vertebrate body plan begins with the differentiation of cells into three germ layers: ectoderm, mesoderm and endoderm. Cells in the endoderm give rise to the epithelial lining of the digestive tract, associated glands and respiratory system. One of the fundamental problems in developmental biology is to elucidate how these three primary germ layers are established from the homologous population of cells in the early blastomere. To address this question, ectoderm and mesoderm development have been extensively analyzed, but study of endoderm development has only begun relatively recently. In this review, we focus on the 'where', 'when' and 'how' of endoderm development in four vertebrate model organisms: the zebrafish, Xenopus, chick and mouse. We discuss the classical fate mapping of the endoderm and the more recent progress in characterizing its induction, segregation and regional specification.

Animals↗
PubMed2004

Notch signaling can regulate endoderm formation in zebrafish.

Early in vertebrate development, the processes of gastrulation lead to the formation of the three germ layers: ectoderm, mesoderm, and endoderm. The mechanisms leading to the segregation of the endoderm and mesoderm are not well understood. In mid-blastula stage zebrafish embryos, single marginal cells can give rise to both endoderm and mesoderm (reviewed by Warga and Stainier [2002] The guts of endoderm formation. In: Solnica-Krezel L, editor. Pattern formation in zebrafish. Berlin: Springer-Verlag. p 28-47). By the late blastula stage, however, single marginal cells generally give rise to either endoderm or mesoderm. To investigate this segregation of the blastoderm into cells with either endodermal or mesodermal fates, we analyzed the role of Notch signaling in this process. We show that deltaC, deltaD, and notch1 are expressed in the marginal domain of blastula stage embryos and that this expression is dependent on Nodal signaling. Activation of Notch signaling from an early stage leads to a reduction of endodermal cells, as assessed by sox17 and foxA2 expression. We further find that this reduction in endoderm formation by the activation of Notch signaling is preceded by a reduction in the expression of bonnie and clyde (bon) and faust/gata5, two genes necessary for endoderm formation (Reiter et al. [1999] Genes Dev 13:2983-2995; Reiter et al. [2001] Development 128:125-135; Kikuchi et al. [2001] Genes Dev 14:1279-1289). However, activation of Notch signaling in bon mutant embryos leads to a further reduction in endodermal cells, also arguing for a bon-independent role for Notch signaling in endoderm formation. Altogether, these results suggest that Notch signaling plays a role in the formation of the endoderm, possibly in its segregation from the mesoderm.

Animals↗
PubMed2004

The POU domain protein spg (pou2/Oct4) is essential for endoderm formation in cooperation with the HMG domain protein casanova.

The gastrulating vertebrate embryo develops three germlayers: ectoderm, mesoderm, and endoderm. Zebrafish endoderm differentiation starts with the activation of sox17 by casanova (cas). We report that spg (pou2/Oct4) is essential for endoderm formation. Embryos devoid of maternal and zygotic spg function (MZspg) lack endodermal precursors. Cell transplantations show that spg acts in early endodermal precursors, and cas mRNA-injection into MZspg embryos does not restore endoderm development. spg and cas together are both necessary and sufficient to activate endoderm development, and stimulate expression of a sox17 promoter-luciferase reporter. Endoderm and mesoderm derive from a common origin, mesendoderm. We propose that Spg and Cas commit mesendodermal precursors to an endodermal fate. The joint control of endoderm formation by spg and cas suggests that the endodermal germlayer may be a tissue unit with distinct genetic control, thus adding genetic support to the germlayer concept in metazoan development.

Animals↗
PubMed2004

Postprandial increase in plasma concentrations of remnant-like particles: an independent risk factor for restenosis after percutaneous coronary intervention.

Postprandial increase in remnant lipoprotein concentrations has been suggested as an important atherogenic factor. However, the influence of these remnants on the development of restenosis after percutaneous coronary intervention (PCI) remains to be examined. The present study was designed to address this point. In 60 consecutive patients with successful PCI, the influences of possible risk factors on the development of restenosis, including remnant-like particles (RLP) cholesterol (RLP-C) and triglyceride (RLP-TG), were examined. While mean concentrations of RLP-C and RLP-TG were normal in fasting state, postprandial change in RLP-C concentrations was a significant and independent risk factor for restenosis after PCI. The calculated cut-off index (COI) for the change was +64%. When the patients were divided into 2 groups according to this COI, minimal lumen diameter (MLD) and reference coronary diameter were comparable before and immediately after PCI between the high- (COI < 64%) and the low- (COI < 64%) responders. However, follow-up coronary angiography 3 to 6 months after PCI demonstrated that MLD, late loss, and loss index were all worse in the high responders compared with the low responders. These results indicate that post-prandial increase in RLP-C concentrations is an independent risk factor for restenosis after successful PCI, even in patients with normal fasting RLP-C levels.

Aged↗
PubMed2004

Propagation of a protease-resistant form of prion protein in long-term cultured human glioblastoma cell line T98G.

Human prion diseases, such as Creutzfeldt-Jakob disease (CJD), a lethal, neurodegenerative condition, occur in sporadic, genetic and transmitted forms. CJD is associated with the conversion of normal cellular prion protein (PrP(C)) into a protease-resistant isoform (PrP(res)). The mechanism of the conversion has not been studied in human cell cultures, due to the lack of a model system. In this study, such a system has been developed by culturing cell lines. Human glioblastoma cell line T98G had no coding-region mutations of the prion protein gene, which was of the 129 M/V genotype, and expressed endogenous PrP(C) constitutively. T98G cells produced a form of proteinase K (PK)-resistant prion protein fragment following long-term culture and high passage number; its deglycosylated form was approximately 18 kDa. The PK-treated PrP(res) was detected by immunoblotting with the mAb 6H4, which recognizes residues 144-152, and a polyclonal anti-C-terminal antibody, but not by the mAb 3F4, which recognizes residues 109-112, or the anti-N-terminal mAb HUC2-13. These results suggest that PrP(C) was converted into a proteinase-resistant form of PrP(res) in T98G cells.

Cell Line, Tumor↗
PubMed2004

Tropane alkaloid production and shoot regeneration in hairy and adventitious root cultures of Duboisia myoporoides-D. leichhardtii hybrid.

Co-culture conditions for Duboisia myoporoides-D. leichhardtii hybrid hairy root induction were investigated using leaf explants and Agrobacterium rhizogenes ATCC 15834. The bacteria density and duration of co-culture greatly affected the induction rate; the highest rate of 50% was obtained when the leaf explants were co-cultured for 2 d with 10(6) bacteria. One hairy root clone that showed the fastest root growth was selected and used for comparison study with adventitious roots cultured with 0.5 mg/l indole-3-acetic acid (IAA). The hairy roots cultured in Murashige and Skoog (MS) liquid medium grew well and yielded much more tropane alkaloids (35 mg/l scopolamine and 17 mg/l hyoscyamine) than adventitious roots cultured in 0.5 mg/l IAA after 6 weeks of culture at 25 degrees C in the dark. The hairy and adventitious roots (2.5 cm) grown in liquid media were divided into 5 parts (each 0.5 cm) along the root axis. Distribution of scopolamine and IAA was then determined by enzyme-linked immunosorbent assay (ELISA). Inverse relationship between contents of scopolamine and IAA was observed in the hairy roots; increase of scopolamine and decrease of IAA were proportional to the distance from the root meristem. In contrast, the contents of scopolamine and IAA were relatively constant in the adventitious roots. In shoot regeneration experiments, the hairy and adventitious root segments (1 cm) were placed onto 1/2 MS solid medium containing various concentrations of IAA and BA cultured at 25 degrees C under 16 h light. In adventitious roots, the shoots regenerated on media containing 6-benzyladenine (BA) (0.5 to 5 mg/l), and 100% regeneration was observed in medium with 0.1 mg/l IAA and 2 mg/l BA. On the other hand, shoot regeneration was only observed in 33% of hairy roots cultured on medium containing 5 mg/l BA.

Alkaloids↗
PubMed2003

Functional analysis of three genetic polymorphisms in the glucocorticoid receptor gene.

Glucocorticoids are widely used as potent anti-inflammatory drugs. Glucocorticoids exert their pharmacological effects by binding to a glucocorticoid receptor (GR), which promotes expression of its target genes or suppresses transcription mediated by other transcriptional factors, such as nuclear factor-kappaB (NF-kappaB). To identify genetic polymorphisms affecting glucocorticoid responses, the GR gene was sequenced, and two novel single nucleotide alterations, 1510A>T (T504S) and 1952C>T (S651F), were identified in addition to an adenine base insertion at nucleotide 2314 (2314insA). mRNA expression levels of T504S and S651F were comparable with that of the wild type (WT), whereas the mRNA level of 2314insA was reduced to approximately 36% of the WT level. Protein expression was reduced to approximately 66% of WT levels in S651F and to approximately 6% in 2314insA. No significant change was seen in the T504S variant levels. The instability of the 2314insA mRNA, S651F protein, and 2314insA protein was confirmed by time course experiments. The transcriptional activity of S651F and 2314insA was also reduced to approximately 63 and 2% of the WT levels, respectively, in the luciferase reporter assay. Moreover, the inhibitory effect of GR on NF-kappaB transactivation was reduced to approximately 81 and 12% of the WT levels for S651F and 2314insA, respectively. These results indicated that the overall transcriptional activity and inhibitory effect on NF-kappaB transactivation of S651F and 2314insA have partially reduced and almost abrogated, respectively, almost paralleling their reduced protein expression levels caused by mRNA and/or protein instabilities. Thus, these two variations were suggested to influence the response to glucocorticoid treatment.

Animals↗
PubMed2003

Autonomic function in Kawasaki disease with myocardial infarction: usefulness of monitoring heart rate variability.

BACKGROUND: Despite anticoagulant therapy, many patients with Kawasaki disease and giant coronary artery aneurysm develop myocardial infarction. These patients have a high risk of sudden death, but the etiology is not clear. We studied autonomic function and the possibility of malignant ventricular arrhythmia through heart rate variability. METHODS: We studied six Kawasaki disease patients with myocardial infarction and 16 normal controls. Heart rate variability was investigated using a 24 h electrocardiogram. We assessed the standard deviation from the mean of the normal R-R intervals (SDNN), the proportion of adjacent R-R intervals with a difference greater than 50 msec (pNN50) and the root-mean square of successive R-R differences as time-domain analysis (rMSSD). We assessed very low-frequency power, low-frequency power (LF), high-frequency power (HF) and the LF/HF ratio in frequency-domain analysis. RESULTS: There was no significant difference in SDNN, but there was a significant difference in pNN50 and rMSSD. Patients with Kawasaki disease showed lower HF and higher LF/HF than normal controls. CONCLUSION: Our findings suggest that patients with Kawasaki disease and myocardial infarction show decreased vagal activity, which could cause malignant arrhythmia.

Adolescent↗
PubMed2003

Overexpression of NP95 mRNA by tumor promoters in the promotion phase of a two-stage BALB/3T3 cell transformation assay.

We studied altered gene expressions in BALB/3T3 cells treated by different tumor promoters in the promotion phase of a transformation assay, an in vitro model of a two-stage carcinogenicity test, using fluorescent mRNA differential display analysis. Expression of the NP95 gene, which was previously found to be the gene of a murine nuclear protein associated with cell proliferation, was increased in the cultures treated by 12-O-tetradecanoylphorbol-13-acetate (TPA), okadaic acid, and orthovanadate. The upregulation of NP95 mRNA was confirmed by reverse transcription-PCR, and Northern blot. TPA, okadaic acid, and orthovanadate enhanced cell proliferation as measured by a 5-bromo-2'-deoxyuridine incorporation assay. The expression level of NP95 mRNA was not affected by the treatment with typical carcinogens benzo[a]pyrene and 3-methylcholanthrene at concentrations at which they act as initiators of cell transformation. These facts may imply that the enhancement of cell transformation by these tumor promoters is due, at least in part, to the acceleration of cell proliferation. NP95 mRNA was also increased in the transformed BALB/3T3 cells. Overexpression of NP95 may also participate in the maintenance of the transformed phenotype.

Animals↗
PubMed2003

Efficacy of iodine-123-15-(p-iodophenyl)-3-R, S-methylpentadecanoic acid single photon emission computed tomography imaging in detecting myocardial ischemia in children with Kawasaki disease.

To evaluate its efficacy in detecting myocardial ischemia in children, iodine-123-labeled 15-(p-iodophenyl)-3-R, S-methylpentadecanoic acid (BMIPP) myocardial single photon emission computed tomography (SPECT) imaging was performed in 16 pediatric patients with Kawasaki disease (KD, 11 male, 5 female; mean age and range: 13 years 8 months and 8 years 11 months to 17 years 7 months). Five children with chest pain and no cardiac disease were studied as controls (2 male, 3 female; mean age and range: 13 years 4 months and 9 years 4 months to 17 years 11 months). Selective coronary angiography was also performed in the 16 patients to evaluate the location of coronary stenosis and coronary aneurysms. The SPECT images were expressed as polar maps (Bull's eye maps) and the 'defect' area was defined as where the uptake of BMIPP was less than the standardized BMIPP images of the 5 control children. In the 16 patients, 33 segments had coronary aneurysms and 10 (10/33: 30.3%) had significant coronary stenosis on selective coronary angiography. Nine of the 10 (90%) segments with significant coronary stenosis showed a defect on the BMIPP image whereas only 6 of the 23 (26.1%) segments without coronary stenosis showed a defect on BMIPP imaging. The sensitivity of BMIPP SPECT imaging for detection of coronary stenosis was 90% (9/10) and its specificity was 73.9% (17/23), whereas the sensitivity of (201)Tl SPECT imaging was 80% (8/10) and its specificity was 60% (14/23). There was no significant difference between the BMIPP and 201Tl SPECT images in either the sensitivity or specificity for the detection of coronary stenosis. In the present series, only one case had discordant BMIPP uptake (BMIPP uptake < (201)Tl uptake) in which there was a large coronary aneurysm and re-canalization after complete obstruction at segment 1 of the right coronary artery. This discordant BMIPP uptake reflects the possibility of ischemic but viable myocardium after re-canalization of a large aneurysm in KD. In conclusion, BMIPP SPECT imaging is useful for detecting the areas of ischemic myocardium caused by coronary artery stenosis in children with KD.

Adolescent↗
PubMed2002

Left atrial tachyarrhythmia in fetal lambs.

To evaluate the hemodynamic effect of rapid left atrial pacing on fetal circulation, a fetal supraventricular tachyarrhythmia model was made and the aortic pressure, central venous pressure, and left and right ventricular outputs were measured in ten fetal lambs. Under maternal anesthesia, the uterus was opened, and under local anesthesia, catheters were inserted into thefetal superior vena cava and ascending aorta through a neck incision. Pacing leads were then sutured onto the fetal left atrial appendage via left thoracotomy. Ventricular output was estimated using echocardiography by a transuterine approach. Fetal hemodynamics were observed without pacing (control), and at the pacing rates of 200, 300, 350, and 400/min. The aortic pressure decreased when the left atrium was paced at 300/min or more and the central venous pressure increased when the left atrium was paced at 350/min or more. The left and right ventricular outputs decreased when the left atrium was paced at 350/min or more. The left ventricular output was 215+/-54 mL/kg per minute at control, 205+/-60 mL/kg minute when paced at 200/min, 178+/-58 mL/kg per minute when paced at 300/min, but decreased to 164+/-44 mL/kg per minute when paced at 350/min and to 149+/-57 mL/kg per minute when paced at 400/min. The right ventricular output was 338+/-66 mL/kg per minute at control, 336+/-95 mL/kg per minute when paced at 200/min, 273+/-91 mL/kg per minute when paced at 300/min, but decreased to 256+/-80 mL/kg per minute when paced at 350/min and to 202+/-76 mL/kg per minute when paced at 400/min. Fetal circulatory failure was initially confirmed when the left atrium was paced at 300/min in this left atrial tachyarrhythmia model.

Animals↗