Biomedical subjects

Tomoko Yamada

Publications and source records attributed to Tomoko Yamada.

At least 19 recordsLinked to original sources

PubMed2026

Mega-enhancers compartmentalize transcriptionally active long genes in the brain.

Exceptionally long genes and cis-regulatory enhancers are selectively activated in mammalian brain neurons, and these loci are mutation hotspots in neurological disorders. However, the organization of these large genomic elements at the level of chromosome folding, beyond local enhancer-promoter interactions, remains poorly understood. Here we report the discovery of a genomic subcompartment in the mouse cerebellum formed by near-megabase-long enhancers and their associated long genes encoding synaptic or signalling proteins. Genomic regions within this subcompartment are enriched in the outer half of the nucleus, whereas other transcriptionally active structures are enriched in the nuclear interior. Using an in vivo CRISPR genetic mini screen, we uncover a specific role for the transcription factor Etv1 in coupling the compartmentalization of neuronal long genes with their expression. Together, our study defines mechanisms that organize transcriptionally active genes across chromosomes in the mammalian brain.

Animals↗

PubMed2023

Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum.

Dynamic regulation of gene expression plays a key role in establishing the diverse neuronal cell types in the brain. Recent findings in genome biology suggest that three-dimensional (3D) genome organization has important, but mechanistically poorly understood functions in gene transcription. Beyond local genomic interactions between promoters and enhancers, we find that cerebellar granule neurons undergoing differentiation in vivo exhibit striking increases in long-distance genomic interactions between transcriptionally active genomic loci, which are separated by tens of megabases within a chromosome or located on different chromosomes. Among these interactions, we identify a nuclear subcompartment enriched for near-megabase long enhancers and their associated neuronal long genes encoding synaptic or signaling proteins. Neuronal long genes are differentially recruited to this enhancer-dense subcompartment to help shape the transcriptional identities of granule neuron subtypes in the cerebellum. SPRITE analyses of higher-order genomic interactions, together with IGM-based 3D genome modeling and imaging approaches, reveal that the enhancer-dense subcompartment forms prominent nuclear structures, which we term mega-enhancer bodies. These novel nuclear bodies reside in the nuclear periphery, away from other transcriptionally active structures, including nuclear speckles located in the nuclear interior. Together, our findings define additional layers of higher-order 3D genome organization closely linked to neuronal maturation and identity in the brain.

Journal Article↗

PubMed2006

Caffeic acid attenuates the decrease in cortical BDNF mRNA expression induced by exposure to forced swimming stress in mice.

We previously reported that caffeic acid produces antidepressive-like effects in the forced swimming test in mice, an animal model of depression. Increased evidence suggests that brain-derived neurotrophic factor (BDNF), a member of the neurotrophin family that has high affinity for the tyrosine kinase receptor B (TrkB), plays an important role in the pathophysiology and treatment of depression. The present study examined whether caffeic acid affects the expression levels of BDNF and TrkB mRNA in brain regions of mice subjected to a forced swimming test. Caffeic acid (4 mg/kg, i.p.) reduced the duration of immobility of mice in the forced swimming test. The levels of BDNF mRNA in the frontal cortex as well as TrkB mRNA in the amygdala were significantly decreased after the forced swimming test, and the former reduction was significantly inhibited by caffeic acid (4 mg/kg, i.p.). Caffeic acid (4 mg/kg, i.p.) did not modify the levels of BDNF and TrkB mRNA in brain regions of naive mice. These results suggest that caffeic acid can attenuate the down-regulation of BDNF transcription that results from stressful conditions.

Animals↗

PubMed2006

P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation.

Human DSIF, a heterodimer composed of hSpt4 and hSpt5, plays opposing roles in transcription elongation by RNA polymerase II (RNA Pol II). Here, we describe an evolutionarily conserved repetitive heptapeptide motif (consensus = G-S-R/Q-T-P) in the C-terminal region (CTR) of hSpt5, which, like the C-terminal domain (CTD) of RNA Pol II, is highly phosphorylated by P-TEFb. Thr-4 residues of the CTR repeats are functionally important phosphorylation sites. In vitro, Thr-4 phosphorylation is critical for the elongation activation activity of DSIF, but not to its elongation repression activity. In vivo, Thr-4 phosphorylation is critical for epidermal growth factor (EGF)-inducible transcription of c-fos and for efficient progression of RNA Pol II along the gene. We consider this phosphorylation to be a switch that converts DSIF from a repressor to an activator. We propose the "mini-CTD" hypothesis, in which phosphorylated CTR is thought to function in a manner analogous to phosphorylated CTD, serving as an additional code for active elongation complexes.

Amino Acid Sequence↗

PubMed2006

Memory, attention, and executive functions before and after sine and pulse wave electroconvulsive therapies for treatment-resistant major depression.

OBJECTIVE: Studies of the cognitive effects of electroconvulsive therapy (ECT) have resulted in controversial findings up to now, partly because researchers and reviewers have not always made a clear distinction among various aspects of cognition and because there are many parameters involved in the administration of ECT that have a potential impact on cognition. The present study focused on the impact of sine and pulse waveforms on anterograde memory and nonmemory cognitive functions. METHODS: We assigned 18 patients with unipolar major depression or bipolar I or II disorder, most recent episode depressed, to receive sine wave or pulse wave ECT and assessed their cognitive function before and after ECT, using a neuropsychologic test battery that measured anterograde memory, attention, and executive functions. Outcomes were measured, on average, 8.2 days after the last ECT session. RESULTS: Both waveforms were equally effective in alleviating depression. Those who received sine wave ECT showed statistically significant deterioration in attention and executive tasks, such as the Stroop test, which measures selective attention (P = 0.02), and the dual task, which taps divided attention (P = 0.01). On the other hand, those who received pulse wave ECT improved to a significant degree in certain memory tasks, such as visual memory (P = 0.01) and general memory (P = 0.01) of the Wechsler Memory Scale-Revised (WMS-R), as well as in the dual task (P = 0.01). The between-group comparison revealed robust superiority of the pulse wave over the sine wave in terms of the dual task (P = 0.004). CONCLUSIONS: Anterograde memory improved to a statistically significant or nonsignificant degree at 1 week post-ECT in comparison with pre-ECT regardless of waveforms. Attention/executive functions tended to deteriorate with sine wave ECT but improved with pulse wave ECT.

Attention↗

PubMed2006

Paraneoplastic pemphigus mimicking erosive mucosal lichen planus associated with primary hepatocellular carcinoma.

A 58-year-old Japanese male visited us with painful lesions on the lower lip, oral mucosa and genital region of an 8-month duration. Histological features of the genital lesion were almost consistent with lichenoid tissue reaction. A few intraepidermal acantholytic keratinocytes were also seen in the suprabasal clefts. Direct immunofluorescence exhibited cell surface immunoglobulin (Ig)G deposition and linear deposition of fibrinogen at the dermoepidermal junction. IgG anti-desmoglein (Dsg)3 antibody, but not anti-Dsg1 antibody, was detected in the patient's serum by enzyme-linked immunosorbent assay. Immunoblotting using normal human epidermal extract detected the 210-kD envoplakin, 190-kD periplakin and 130-kD Dsg3. The diagnosis of paraneoplastic pemphigus (PNP) was made. Subsequent investigation revealed a large space-occupying lesion in the liver. Histological findings from liver biopsy specimen were consistent with hepatocellular carcinoma. The patient has been alive 38 months after the diagnosis of PNP was made, although the liver mass has slowly enlarged. Our case is clinically and histologically similar to erosive mucosal lichen planus. Immunological studies confirmed the diagnosis of PNP. The results of negative Dsg1 and positive Dsg3 were consistent with clinical features showing severe mucosal involvement without cutaneous erosion. In PNP, the association with non-hematological solid tumor is extremely rare.

Biomarkers, Tumor↗

PubMed2006

A case of epidermolysis bullosa acquisita with autoantibody to anti-p200 pemphigoid antigen and exfoliative esophagitis.

BACKGROUND: Some cases of a subepidermal blistering disease associated with autoantibodies to more than two antigens have been reported. OBSERVATION: A 52-year-old Japanese woman had pruritic blisters on almost the whole body as well as erosive lesions in the oral cavity and esophagus. A histological finding was subepidermal bullae. Direct immunofluorescence (IF) revealed a linear deposition of IgG, IgM and C3 at the epidermal basement membrane zone (BMZ). Indirect IF using human skin split by 1 M NaCl as a substrate showed IgG antibody reactive with the dermal side. By immunoblot analysis using normal human dermal extract, the 200-kDa and 290-kDa bands were detected. Indirect IF did not show any anti-BMZ antibody activity, when using the skin of the patient with recessive dystrophic epidermolysis bullosa as a substrate. CONCLUSION: We regarded our case as epidermolysis bullosa acquisita with autoantibody to anti-p200 pemphigoid antigen. This is the second case in the literature associated with autoantibodies to these two antigens.

Autoantibodies↗

PubMed2005

Leukotoxin family genes in Staphylococcus aureus isolated from domestic animals and prevalence of lukM-lukF-PV genes by bacteriophages in bovine isolates.

Leukotoxin family genes in Staphylococcus aureus isolated from domestic animals were examined by polymerase chain reaction. LukS and lukF genes were detected in all 48 avian and 72 porcine isolates of S. aureus. LukE and lukD genes, located in a putative staphylococcal pathogenicity island (Sapln3/Saplm3), were recognized in 44 (91.7%) of 48 avian isolates, but these genes were not detected in porcine isolates. In 297 bovine isolates collected from mastitic cow's milk and bulk milk from dairy farms in two regions, lukM and lukF-PV(P83) genes in addition to lukS-lukF and lukE-lukD genes were detected in 100 (62.5%) of the 160 isolates from Ishikawa and in118 (86.1%) of the 137 isolates from Hokkaido. When the lysogeny of S. aureus bovine isolates was examined by treatment with mitomycin C, clearing of the culture due to cell lysis was observed in 34 (91.9%) of 37 lukM-lukF-PV(P83) genes--positive isolates. In addition, we isolated a novel lukM-lukF-PV(P83)-carrying (designated phiLukM), and revealed that the lukM-lukF-PV(P83) genes were located very close to an amidase gene on the temperate phage genomes. These results suggest horizontal transmission of lukM-lukF-PV(P83) genes by temperate bacteriophages in S. aureus of bovine origin.

Animal Diseases↗

PubMed2005

Effects of a 5-HT7 receptor antagonist DR4004 on the exploratory behavior in a novel environment and on brain monoamine dynamics in mice.

The present study examined whether serotonin (5-hydroxytryptamine; 5-HT)7 receptors play a role in the modulation of emotionality in mice using the selective 5-HT7 receptor antagonist 2a-[4-(4-phenyl-1,2,3,6-tetrahydropyridyl)butyl]-2a,3,4,5-tetrahydrobenzo (c,d)indol-2-(1H)-one (DR4004). The emotionality of mice was evaluated in terms of exploratory activity in the hole-board test. The mice treated with DR4004 (2.5-10 mg/kg, i.p.) displayed a dose-dependent decrease in locomotor activity by moving less distance in the hole-board, and statistically significant decreases were observed at 5 and 10 mg/kg. On the other hand, DR4004 (10 mg/kg, i.p.) did not affect spontaneous motor activity. In a neurochemical study, decreases in amygdaloid dopamine and 5-HT turnover were observed in mice in which locomotor activity in the hole-board test was attenuated following the administration of DR4004 (10 mg/kg, i.p.). Also, a simple linear regression analysis revealed that locomotor activity on the hole-board was significantly correlated with dopamine and 5-HT turnover in amygdala. Furthermore, co-injection of the selective dopamine reuptake inhibitor 1-(2-[bis(4-fluorophenyl)methoxy]ethyl)-4-(3-phenylpropyl)piperazine (GBR12909; 1.25-5 mg/kg, i.p.) or the selective 5-HT reuptake inhibitor fluvoxamine (20 mg/kg, i.p.) significantly reversed the DR4004 (10 mg/kg, i.p.)-induced decrease in locomotor activity in the hole-board test. These findings constitute the behavioral evidence that 5-HT7 receptors may play a role in the modulation of emotionality. Furthermore, it is also suggested that amygdaloid dopamine and 5-HT neuronal systems may be involved in this modulation.

Amygdala↗

PubMed2005

General anesthesia for patient with type III homocystinuria (tetrahydrofolate reductase deficiency).

Homocystinuria, a rare autosomal recessive genetic disease, is generally classified into 3 types (types I-III). Extremely rare type III is from a defect of the enzyme tetrahydrofolate reductase which converts homocysteine to methionine. The anesthetic problem of type III homocystinuria is the elevation of serum homocysteine and the deficiency of essential amino acid methionine, which result in the perioperative thromboembolic events and nitrous oxide-induced neurological impairment. We provided successful anesthetic management for a patient with type III homocystinuria, during which we were careful to take measures against perioperative thromboembolism and did not use nitrous oxide.

Adult↗

PubMed2005

High frequency of Hermansky-Pudlak syndrome type 1 (HPS1) among Japanese albinism patients and functional analysis of HPS1 mutant protein.

Hermansky-Pudlak syndrome (HPS) is an autosomal recessive disorder characterized by oculocutaneous albinism (OCA), bleeding tendency, and lysosomal accumulation of ceroid-like material. Seven genetically distinct subtypes of HPS are known in humans; most are rare outside of Puerto Rico. Here, we describe the analysis of the HPS1 gene in 24 Japanese OCA patients who lacked mutations in the four genes known to cause OCA (TYR/OCA1, P/OCA2, TYRP1/OCA3, and MATP/OCA4), and the identification of eight different HPS1 mutations in ten of these patients, four of which were novel (W583X, L668P, 532insC, 1691delA). An IVS5+5G --> A splice consensus mutation was particularly frequent, the result of a founder effect for this allele in Japanese patients. Functional analysis by transfection of the L668P variant into Hps1-mutant melan-ep mouse melanocytes showed that this missense substitution is pathologic, resulting in an Hps-1 protein that is unable to assemble into the biogenesis of lysosome-related organelles complex-3.

Albinism↗

PubMed2005

A case of mixed bullous disease of epidermolysis bullosa acquisita and linear IgA bullous dermatosis.

A 75-year-old Japanese male visited us with bullous eruptions on the extremities. Physical examination revealed large bullae on the hands, lower legs and feet. The oral mucosa was also involved. Histology disclosed subepidermal blister with inflammatory cell infiltrates in the dermis. Direct immunofluorescence showed deposits of IgG and IgA at the cutaneous basement membrane zone. Indirect immunofluorescence on 1 M NaCl-split human skin sections demonstrated that the patient's IgG antibodies reacted with the dermal side of the split, while IgA antibodies reacted with the epidermal side. Immunoblotting showed that the patient's serum reacted with the NC1 domain of type VII collagen (290-kDa epidermolysis bullosa acquisita antigen) as well as the 120-kDa linear IgA bullous dermatosis antigen, LAD-1. Systemic prednisolone resulted in a favorable response. From the clinicopathological findings, the present case is not consistent with either epidermolysis bullosa acquisita or IgA bullous dermatosis. Therefore, we regarded the case as mixed bullous disease of epidermolysis bullosa acquisita and linear IgA bullous dermatosis. Such a case has not been previously reported.

Administration, Oral↗

PubMed2004

Biological activity of barbados cherry (acerola fruits, fruit of Malpighia emarginata DC) extracts and fractions.

Fractionation of barbados cherry (acerola fruit, a fruit of Malpighia emarginata DC.) extracts were performed by organic solvent extractions and column chromatographies, using two extraction methods. Higher cytotoxic activity was concentrated in fractions A4 and A6 (acetone extract), and H3 and HE3 (hexane extract). These four fractions showed higher cytotoxic activity against tumor cell lines such as human oral squamous cell carcinoma (HSC-2) and human submandibular gland carcinoma (HSG), when compared with that against normal cells such as human periodontal ligament fibroblasts (HPLF) and human gingival fibroblasts (HGF). HE2 (hexane extract), AE2 (ethyl acetate extract), AE3, AE4, AE5, A8, A9 and A10 showed some relatively higher anti-bacterial activity on the Gram-positive Staphylococcus epidermidis ATCC 1228 but were ineffective on the representative Gram-negative species E. coli and Ps. aeruginosa. The fractions were inactive against Helicobacter pylori, two representative Candida species, and human immunodeficiency virus (HIV). H3, H4 and HE3, which displayed higher tumor-specific cytotoxicity also showed higher multidrug resistance (MDR) reversal activity, than (+/-)-verapamil as positive control. ESR spectroscopy shows that the radical-mediated oxidation is not involved in the induction of tumor-specific cytotoxic activity. The tumor specific cytotoxic activity and MDR reversal activity of barbados cherry may suggest its possible application for cancer therapy.

Anti-Infective Agents↗

PubMed2004

Purification and characterization of paralytic shellfish toxin transforming enzyme from Mactra chinensis.

A carbamoylase, which catalyzes hydrolysis of the carbamoyl (or N-sulfocarbamoyl) moiety of paralytic shellfish toxins, was purified from the digestive glands of the Japanese clam Mactra chinensis. Using five steps of column chromatography, 290 microg of Carbamoylase I showing homogeneity on SDS-PAGE was obtained. Carbamoylase I was revealed to be a glycoprotein, having estimated molecular weight of 190 kDa. Observation of single band equivalent to 94 kDa on SDS-PAGE under reducing conditions suggested it to be a homodimer. The optimal temperature and pH were 20 degrees C and 7.0. Carbamoylase I did not require a divalent cation and its activity was inhibited by the serine proteinase inhibitors, benzenesulfonyl fluoride and 4-(2-aminoethyl)-benzenesulfonyl fluoride. Carbamoylase I hydrolyzed both carbamate and N-sulfocarbamate toxins. The presence or absence of a hydroxyl moiety at the N-1 position of the substrate toxins did not significantly alter the reaction rate, but the stereochemistry of sulfate esters at C-11 greatly affected it. The K(m) was 3.02 microM for saxitoxin as a substrate. Nineteen amino acids of the N-terminal sequence were identified by the Edman method. MALDI-TOF-MS/MS spectra of (18)O-labeled tryptic peptides indicated the possible internal amino acid sequences of five peptides.

Amino Acid Sequence↗

PubMed2004

Human Spt6 stimulates transcription elongation by RNA polymerase II in vitro.

Recent studies have suggested that Spt6 participates in the regulation of transcription by RNA polymerase II (RNAPII). However, its underlying mechanism remains largely unknown. One possibility, which is supported by genetic and biochemical studies of Saccharomyces cerevisiae, is that Spt6 affects chromatin structure. Alternatively, Spt6 directly controls transcription by binding to the transcription machinery. In this study, we establish that human Spt6 (hSpt6) is a classic transcription elongation factor that enhances the rate of RNAPII elongation. hSpt6 is capable of stimulating transcription elongation both individually and in concert with DRB sensitivity-inducing factor (DSIF), comprising human Spt5 and human Spt4. We also provide evidence showing that hSpt6 interacts with RNAPII and DSIF in human cells. Thus, in vivo, hSpt6 may regulate multiple steps of mRNA synthesis through its interaction with histones, elongating RNAPII, and possibly other components of the transcription machinery.

Animals↗

PubMed2003

A novel hydrogen peroxide-induced phosphorylation and ubiquitination pathway leading to RNA polymerase II proteolysis.

DNA damage-induced ubiquitination of the largest subunit of RNA polymerase II, Rpb1, has been implicated in transcription-coupled repair for years. The studies so far, however, have been limited to the use of bulky helix-distorting DNA damages caused by UV light and cisplatin, which are corrected by the nucleotide excision repair pathway. Non-bulky, non-helix-distorting damages are caused at high frequency by reactive oxygen species in cells and corrected by the base excision repair pathway. Contrary to a classic view, we recently found that the second type of DNA lesions also causes RNA polymerase II stalling in vitro. In this paper, we show that hydrogen peroxide (H(2)O(2)) causes significant ubiquitination and proteasomal degradation of Rpb1 by mechanisms that are distinct from those employed after UV irradiation. UV irradiation and H(2)O(2) treatment cause characteristic changes in protein kinases phosphorylating the carboxyl-terminal domain at Ser-2 and -5. The H(2)O(2)-induced ubiquitination is likely dependent on unusual Ser-5 phosphorylation by ERK1/2. Moreover, the H(2)O(2)-induced ubiquitination occurs on transcriptionally engaged polymerases without the help of Cockayne syndrome A and B proteins and von Hippel-Lindau tumor suppressor proteins, which are all required for the UV-induced ubiquitination. These results suggest that stalled polymerases are recognized and ubiquitinated differentially depending on the types of DNA lesions. Our findings may have general implications in the basic mechanism of transcription-coupled nucleotide excision repair and base excision repair.

Cell Death↗

PubMed2003

Phage conversion of exfoliative toxin A in Staphylococcus aureus isolated from cows with mastitis.

An exfoliative toxin produced by Staphylococcus aureus is the causative agent of staphylococcal scalded-skin syndrome (SSSS) in young children. Recently, we reported that only few isolates of S. aureus from bovine mastitis contained the eta gene encoding exfoliative toxin A (ETA) and produced ETA in vitro. In this study, we isolated temperate phages from two ETA-positive bovine isolates of S. aureus by treatment with mitomycin C. Polymerase chain reaction (PCR) assay of the phage genomes suggested that the temperate phages carried the structural gene for ETA. Moreover, the nucleotide sequence analysis of the PCR products revealed that the eta gene was located very close to an amidase gene on the phage genomes. The nucleotide sequence for the amidase gene of the bovine phage (bovine phi ETA) differed at nine positions from that of the amidase gene of phi ETA from a human isolate reported by Yamaguchi et al. [Mol. Microbiol. 38 (2000) 694], suggesting that eta-converting phages are heterogeneous. Bovine phi ETA had a head with a hexagonal outline and a non-contractile and flexible tail. Bovine phi ETA was able to lysogenize ETA-negative bovine isolates of S. aureus, and the lysogenized S. aureus isolates had the ability to produce ETA. These results suggest the possibility of horizontal transmission of the eta gene by temperate bacteriophages among bovine isolates of S. aureus.

Amidohydrolases↗

PubMed2003

Taurine transporter in primary cultured neonatal rat heart cells: a comparison between cardiac myocytes and nonmyocytes.

In the present study, we examined the characteristics of the taurine transporter and the intracellular taurine content in cultured neonatal heart cells. Primary cultures of cardiac myocytes and cardiac fibroblasts (nonmyocytes) were prepared from 1-day-old Wistar rats. The parameters examined were: (a) intracellular taurine content by the HPLC method, (b) the expression levels of taurine transporter mRNA and protein using northern and western blot analysis, and (c) transporter activity determined by the uptake of 3H-labeled taurine. The taurine content of myocytes was significantly higher (3-fold) than that of nonmyocytes. Taurine transporter mRNA was strongly expressed in both myocytes and nonmyocytes, whereas the magnitude [normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene expression] of the transporter mRNA expressed in myocytes was lower than that in nonmyocytes. The expression level of transporter protein in myocytes was also lower than that of nonmyocytes. Uptake of radiolabeled taurine into monolayer cultures of heart cells was stimulated markedly by the presence of Na+ in the medium, whereas this uptake was almost abolished in the absence of Na+. The Na+/taurine stoichiometry was 2:1 for both myocytes and nonmyocytes. Kinetic analysis showed that a single saturable system was involved in taurine uptake into both cell types. In myocytes, the apparent K(m) and V(max) values for the transporter were 20.7+/-0.5 microM and 1.07+/-0.01 nmol/10(6)cells/30 min, respectively. Similarly, those of nonmyocytes were 20.3+/-0.7 microM and 0.42+/-0.01 nmol/10(6)cells/30 min. These findings indicated that both myocytes and nonmyocytes expressed an identical taurine transporter with a Michaelis-Menten constant of 20-21 microM and that a higher taurine content in myocytes may be associated with a higher V(max).

Animals↗