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Biomedical subjects

Tatsuya Shibata

Publications and source records attributed to Tatsuya Shibata.

9 recordsLinked to original sources
PubMed2006

Degradation of Escherichia coli RecN aggregates by ClpXP protease and its implications for DNA damage tolerance.

Protein degradation in bacteria plays a dynamic and critical role in the cellular response to environmental stimuli such as heat shock and DNA damage and in removing damaged proteins or protein aggregates. Escherichia coli recN is a member of the structural maintenance of chromosomes family and is required for DNA double strand break (DSB) repair. This study shows that RecN protein has a short half-life and its degradation is dependent on the cytoplasmic protease ClpXP and a degradation signal at the C terminus of RecN. In cells with DNA DSBs, green fluorescent protein-RecN localized in discrete foci on nucleoids and formed visible aggregates in the cytoplasm, both of which disappeared rapidly in wild-type cells when DSBs were repaired. In contrast, in DeltaclpX cells, RecN aggregates persisted in the cytoplasm after release from DNA damage. Furthermore, analysis of cells experiencing chronic DNA damage revealed that proteolytic removal of RecN aggregates by ClpXP was important for cell viability. These data demonstrate that ClpXP is a critical factor in the cellular clearance of cytoplasmic RecN aggregates from the cell and therefore plays an important role in DNA damage tolerance.

Bacterial Proteins↗
PubMed2006

A TNF receptor loop peptide mimic blocks RANK ligand-induced signaling, bone resorption, and bone loss.

Activating receptor activator of NF-kappaB (RANK) and TNF receptor (TNFR) promote osteoclast differentiation. A critical ligand contact site on the TNFR is partly conserved in RANK. Surface plasmon resonance studies showed that a peptide (WP9QY) that mimics this TNFR contact site and inhibits TNF-alpha-induced activity bound to RANK ligand (RANKL). Changing a single residue predicted to play an important role in the interaction reduced the binding significantly. WP9QY, but not the altered control peptide, inhibited the RANKL-induced activation of RANK-dependent signaling in RAW 264.7 cells but had no effect on M-CSF-induced activation of some of the same signaling events. WP9QY but not the control peptide also prevented RANKL-induced bone resorption and osteoclastogenesis, even when TNFRs were absent or blocked. In vivo, where both RANKL and TNF-alpha promote osteoclastogenesis, osteoclast activity, and bone loss, WP9QY prevented the increased osteoclastogenesis and bone loss induced in mice by ovariectomy or low dietary calcium, in the latter case in both wild-type and TNFR double-knockout mice. These results suggest that a peptide that mimics a TNFR ligand contact site blocks bone resorption by interfering with recruitment and activation of osteoclasts by both RANKL and TNF.

Amino Acid Sequence↗
PubMed2006

Effects of an intravenous infusion of Ringer's solution on eruption rates of incisor teeth in anesthetized rats.

OBJECTIVE: The vasculature within the socket is reportedly involved in determining the position of continuously erupting teeth. Thus, loss of body fluid in anesthetized rats, which would affect the vascular physiology, should influence tooth movement. We investigated the effects of an infusion of Ringer's solution on the systemic arterial blood pressure, regional blood flow at the base of the incisor, and axial tooth movement in anesthetized rats to determine the cause of tooth displacement. MATERIAL AND METHODS: In the experimental group, the animals received intravenous infusions of Ringer's solution at 27 microl/min for 13 h. In the control group, the animals did not receive the infusion. RESULTS: The infusion of Ringer's solution suppressed an increase of the mean arterial blood pressure from 86 to 80 mmHg and a decrease of the regional blood flow from 170 to 217 mV, and increased the eruption rate from 267 to 361 microm/13 h during the experimental period. There was a positive correlation between the eruption rate and regional blood flow, and a negative correlation between the blood pressure and regional blood flow. CONCLUSIONS: These results suggest that an infusion of Ringer's solution can cause an increase in the regional blood flow, resulting in increased fluid volume, elevated intra-socket pressure, and increased eruptive movement. It is possible that the regional vascular volume and/or pressure within the socket play an important role in determining the position of the incisor.

Animals↗
PubMed2006

Mechanical behavior of bovine periodontal ligament under tension-compression cyclic displacements.

In the present study, the mechanical response of bovine periodontal ligament (PDL) subjected to displacement-controlled tension-compression harmonic oscillations and subsequent rupture was examined. Specimens including dentine, cementum, PDL, and alveolar bone were extracted from different depths and locations of bovine first molars. They were immersed in a saline solution at room temperature and clamped on their bone and dentine extremities. The samples were tested at +/-35% of the PDL's width, with a frequency of 1 Hz. The mechanical parameters evaluated were hysteresis, phase lag, and the modulus of the stress-stretch ratio curves in tension and compression. The tensile strength and the corresponding stretch ratio were also recorded. Stress-stretch ratio curves indicated a non-linear, time-dependent response with hysteresis and preconditioning effects. The hysteresis and phase lag in compression were much higher than in tension, suggesting that the dissipated energy was higher in compression than in tension. The root depth and location did not play essential roles for the tension or compression data, with the exception of limited statistical differences for tensile strength and corresponding stretch ratio. Thus, biological variability in the specimens, as a result of different bone contours, PDL width, and fiber orientation, did not affect the energy-absorbing capacity of the PDL. The evolution of the stress rate with stress demonstrated a constant increase of stiffness with stress. The stiffness values were twofold higher in tension than in compression. The data also showed that the stiffness of the PDL was comparable with data reported for other soft tissues.

Analysis of Variance↗
PubMed2005

Functional overlap between RecA and MgsA (RarA) in the rescue of stalled replication forks in Escherichia coli.

Escherichia coli RecA protein plays a role in DNA homologous recombination, recombination repair, and the rescue of stalled or collapsed replication forks. The mgsA (rarA) gene encodes a highly conserved DNA-dependent ATPase, whose yeast orthologue, MGS1, plays a role in maintaining genomic stability. In this study, we show a functional relationship between mgsA and recA during DNA replication. The mgsA recA double mutant grows more slowly and has lower viability than a recA single mutant, but they are equally sensitive to UV-induced DNA damage. Mutations in mgsA and recA cause lethality in DNA polymerase I deficient cells, and suppress the temperature-dependent growth defect of dnaE486 (Pol III alpha-catalytic subunit). Moreover, recAS25P, a novel recA allele identified in this work, does not complement the slow growth of DeltamgsA DeltarecA cells or the lethality of polA12 DeltarecA, but is proficient in DNA repair, homologous recombination, SOS mutagenesis and SOS induction. These results suggest that RecA and MgsA are functionally redundant in rescuing stalled replication forks, and that the DNA repair and homologous recombination functions of RecA are separated from its function to maintain progression of replication fork.

Adenosine Triphosphatases↗
PubMed2004

Role of the Escherichia coli RecQ DNA helicase in SOS signaling and genome stabilization at stalled replication forks.

The RecQ protein family is a highly conserved group of DNA helicases that play roles in maintaining genomic stability. In this study, we present biochemical and genetic evidence that Escherichia coli RecQ processes stalled replication forks and participates in SOS signaling. Cells that carry dnaE486, a mutation in the DNA polymerase III alpha-catalytic subunit, induce an RecA-dependent SOS response and become highly filamented at the semirestrictive temperature (38 degrees C). An recQ mutation suppresses the induction of SOS response and the filamentation in the dnaE486 mutant at 38 degrees C, causing appearance of a high proportion of anucleate cells. In vitro, RecQ binds and unwinds forked DNA substrates with a gap on the leading strand more efficiently than those with a gap on the lagging strand or Holliday junction DNA. RecQ unwinds the template duplex ahead of the fork, and then the lagging strand is unwound. Consequently, this process generates a single-stranded DNA (ssDNA) gap on the lagging strand adjacent to a replication fork. These results suggest that RecQ functions to generate an initiating signal that can recruit RecA for SOS induction and recombination at stalled replication forks, which are required for the cell cycle checkpoint and resumption of DNA replication.

Adenosine Triphosphatases↗
PubMed2004

The biomechanical properties of the healing periodontium of replanted rat mandibular incisors.

One of the most important aspects in tooth replantation seems to be restoration of the tooth support function of the healing periodontal ligament (PDL). We examined the support function, as measured by the mechanical properties, of the healing PDL at 7, 14, and 21 days after replantation of the left mandibular incisor in rats. From each dissected left mandible, a transverse section(650 microm in thickness) of the incisor was cut through an axis near the labial alveolar crest. Each section was intrusively loaded at a rate of 5 mm min(-1), and the shear stress-strain curve for the PDL was analyzed. Mechanical measures of the healing PDL showed gradual improvement after replantation. By 21 days, the mechanical strength returned to 53% of the control value; the extensibility, to 85%; the stiffness, to 61%; and the toughness, to 52%. The healing PDL exhibited reattachment of fibers in the middle region of the PDL, and the birefringent collagen fibers appeared to have regained the functional orientation by 14 days. The ratios occupied by the birefringent collagen fibers in the tooth-related, middle, and bone-related areas of the healing PDL gradually improved and returned to 78, 51, and 48% of the respective control values by 21 days. These results suggest that the support function of the healing PDL is gradually restored and that the biomechanical restoration is closely related to the reorganization and reorientation of collagen fiber bundles in replanted rat incisors.

Analysis of Variance↗
PubMed2003

S100A4: a novel negative regulator of mineralization and osteoblast differentiation.

S100A4 is an intracellular calcium-binding protein expressed by osteoblastic cells. However, its roles in bone physiology are unknown. Because before matrix mineralization, its expression is markedly diminished, we hypothesized that S100A4 negatively regulates the mineralization process. In this study, we investigated the effects of the inhibition of S100A4 synthesis on osteoblast differentiation and in vitro mineralized nodule formation. Inhibition of S100A4 synthesis was achieved by an antisense approach in the mouse osteoblastic cell line MC3T3-E1. Cell clones that synthesized low levels of S100A4 (AS clones) produced markedly increased number of mineralized nodules at much earlier stages in comparison with controls as demonstrated by Alizarin red S and von Kossa staining. The expression of type I collagen (COLI) and osteopontin (OPN) increased in AS clones compared with controls. Bone sialoprotein (BSP) and osteocalcin (OCN), molecules associated with mineralization and markers for mature osteoblastic phenotype, were expressed in AS clones before their detection in controls. Because S100A4 was not localized in the nucleus of MC3T3-E1 cells and AS clones, it is unlikely that S100A4 directly regulates the expression of these genes. Moreover, the expression of Cbfal/Osf-2 and Osx, transcription factors necessary for the expression of osteoblast-associated genes, remained unchanged in AS clones, indicating that S100A4 may be downstream to these transcription factors. These findings indicate that S100A4 is a novel negative regulator of matrix mineralization likely by modulating the process of osteoblast differentiation.

3T3 Cells↗