Sub-GOFA: A tool for Sub-Gene Ontology function analysis in clonal mosaicism using semantic (logical) similarity

Clonal mosaicism (a detectable post-zygotic mutational event in cellular subpopulations) is common in cancer patients. Detected segments of clonal mosaicism are usually bundled into large-locus regions for statistical analysis. However, low-frequency genes are overlooked and are not sufficient to elucidate qualitative differences between cancer patients and non-patients. Therefore, it is of interest to develop and describe a tool named Sub-GOFA for Sub-Gene Ontology function analysis in clonal mosaicism using semantic similarity. Sub-GOFA measures the semantic (logical) similarity among patients using the sub-GO network structures of various sizes segmented from the gene ontology (GO) for clustering analysis. The sub-GO''s root-terms with significant differences are extracted as disease-associated genetic functions. Sub-GOFA selected a high ratio of cancer-associated genes under validation with acceptable threshold.     

Inhibition of veratridine-induced delayed inactivation of the voltage-sensitive sodium channel by synthetic analogs of crambescin B

Crambescin B carboxylic acid, a synthetic analog of crambescin B, was recently found to inhibit the voltage-sensitive sodium channels (VSSC) in a cell-based assay using neuroblastoma Neuro 2A cells. In the present study, whole-cell patch-clamp recordings were conducted with three heterologously expressed VSSC subtypes, Na_v1.2, Na_v1.6 and Na_v1.7, in a human embryonic kidney cell line HEK293T to further characterize the inhibition of VSSC by crambescin B carboxylic acid. Contrary to the previous observation, crambescin B carboxylic acid did not inhibit peak current evoked by depolarization from the holding potential of ?100 mV to the test potential of ?10 mV in the absence or presence of veratridine (VTD). In the presence of VTD, however, crambescin B carboxylic acid diminished VTD-induced sustained and tail currents through the three VSSC subtypes in a dose-dependent manner, whereas TTX inhibited both the peak current and the VTD-induced sustained and tail currents through all subtypes of VSSC tested. We thus concluded that crambescin B carboxylic acid does not block VSSC in a similar manner to TTX but modulate the action of VTD, thereby causing an apparent block of VSSC in the cell-based assay.     

Activation of Glyoxylate Cycle Enzymes in Cucumber Fruits Exposed to CO2

Cucumber fruits exposed to a 60% CO₂ environment for 3 d at20°C showed a higher respiration rate, a lower respiratoryquotient, and lower levels of malate, citrate + isocitrate,and glyoxylate than did control fruits. Moreover, in the CO₂treatment, fumarate and succinate increased dramatically onthe first day and after the second day, respectively, while2-oxoglutarate showed a temporary increase on the first dayand a subsequent decrease. Isocitrate lyase and malate synthaseactivity tended to increase throughout the experimental periodof the CO₂ treatment. These results appear to point to a rapidoperation of glyoxylate cycle due to high CO₂. (Received November 14, 1997; Accepted March 2, 1998)     

Photochemical Isomerization of Leaf Aldehyde

Isopimpinellin, bergapten, xanthotoxin, kokusagine, evoxine and japonin were isolated and identified in the leaves of Orixa japonica (Rutaceae) as feeding inhibitors against Spodoptera litura F. (Noctuidae). Isopimpinellin exhibited the most potent activity among above substances at the feeding inhibitory test. The isolated evoxine was the optical antipode of the previously reported one.     

Evidence that three histidine residues of a base non-specific and adenylic acid preferential ribonuclease from Rhizopus niveus are involved in the catalytic function.

In order to study the structure-function relationship of an RNase T2 family enzyme, RNase Rh, from Rhizopus niveus, we investigated the roles of three histidine residues by means of site-specific mutagenesis. One of the three histidine residues of RNase RNAP Rh produced in Saccharomyces cerevisiae by recombinant DNA technology was substituted to a phenylalanine or alanine residue. A Phe or Ala mutant enzyme at His46 or His109 showed less than 0.03%, but a mutant enzyme at His104 showed 0.54% of the enzymatic activity of the wild-type enzyme with RNA as a substrate. Similar results were obtained, when ApU was used as a substrate. The binding constant of a Phe mutant enzyme at His46 or His109 towards 2'-AMP decreased twofold, but that at His104 decreased more markedly. Therefore, we assumed that these three histidine residues are components of the active site of RNase Rh, that His104 contributes to some extent to the binding and less to the catalysis, and that the other two histidine residues and one carboxyl group not yet identified are probably involved in the catalysis. We assigned the C-2 proton resonances of His46, His104, and His109 by comparison of the 1H-NMR spectra of the three mutant enzymes containing Phe in place of His with that of the native enzyme, and also determined the individual pKa values for His46 and His104 to be 6.70 and 5.94. His109 was not titrated in a regular way, but the apparent pKa value was estimated to be around 6.3. The fact that addition of 2'-AMP caused a greater effect on the chemical shift of His104 in the 1NMR spectra as compared with those of the other histidine residues, may support the idea described above on the role of His104.     

The role of fibroblast growth factors on the differentiation of vaginal epithelium of neonatal mice

The uterus and upper 3/5 of the vagina originate from the Müllerian duct; however, these organs show quite distinct characteristics in morphology and function. To investigate factors controlling vaginal epithelial cell differentiation from a single layer of pseudostratified epithelium to a multi-layered stratified epithelium with keratin, we focused on fibroblast growth factors (Fgfs). Transformation related protein 63 (Trp63) expression, a marker of stratified epithelium, increased in the Müllerian vaginal epithelial cells from days 0 to 5, and keratin 14 (Krt14) was expressed from day 5, suggesting that Trp63-negative vaginal epithelial cells can differentiate into Trp63-positive cells after birth. Fgf7 and Fgf10 were localized in the vaginal stroma but their receptor, Fgf receptor 2IIIb (Fgfr2IIIb), was localized in the vaginal epithelium. Both Fgf9 and its receptor, Fgfr2IIIc, were localized in the vaginal epithelium. Vaginae cultured with FGF10 or anti-FGF9 antibody showed stratified epithelium with an intense Krt14 expression; however, an inhibitor of phosphorylation of mitogen-activated protein kinase 1/3 (MAPK1/3) canceled the effect of FGF10 and anti-FGF9 antibody. Thus, Fgf10 stimulates the differentiation of pseudostratified epithelial cells into stratified cells via MAPK1/3 pathway, and Fgf9 inhibits this differentiation in the neonatal mouse vagina.     

Computational investigation of the substrate recognition mechanism of protein D-aspartyl (L-isoaspartyl) O-methyltransferase by docking and molecular dynamics simulation studies and application to interpret size exclusion chromatography data

Unusual amino acid residues such as L-β-aspartyl (Asp), D-α-Asp, and D-β-Asp have been detected in proteins and peptides such as α-crystallin in the lens and β-amyloid in the brain. These residues increase with age, and hence they are associated with age-related diseases. The enzyme protein D-aspartyl (L-isoaspartyl) O-methyltransferase (PIMT) can revert these residues back to the normal L-α-Asp residue. PIMT catalyzes transmethylation of S-adenosylmethionine to L-β-Asp and D-α-Asp residues in proteins and peptides. In this work, the substrate recognition mechanism of PIMT was investigated using docking and molecular dynamics simulation studies. It was shown that the hydrogen bonds of Ser60 and Val214 to the carboxyl group of Asp are important components during substrate recognition by PIMT. In addition, specific hydrogen bonds were observed between the main chains of the substrates and those of Ala61 and Ile212 of PIMT when PIMT recognized L-β-Asp. Hydrophobic interactions between the (n-1) residue of the substrates and Ile212 and Val214 of PIMT may also have an important effect on substrate binding. Volume changes upon substrate binding were also evaluated in the context of possible application to interpretation of size exclusion chromatography data.     

A dynamical system analysis of the development of spontaneous lower extremity movements in newborn and young infants

This study's aim was to evaluate the characteristics of newborn and young infants' spontaneous lower extremity movements by using dynamical systems analysis. Participants were 8 healthy full-term newborn infants (3 boys, 5 girls, mean birth weight and gestational age were 3070.6 g and 39 weeks). A tri-axial accelerometer measured limb movement acceleration in 3-dimensional space. Movement acceleration signals were recorded during 200 s from just below the ankle when the infant was in an active alert state and lying supine (sampling rate 200 Hz). Data were analyzed linearly and nonlinearly. As a result, the optimal embedding dimension showed more than 5 at all times. Time dependent changes started at 6 or 7, and over the next four months decreased to 5 and from 6 months old, increased. The maximal Lyapnov exponent was positive for all segments. The mutual information is at its greatest range at 0 months. Between 3 and 4 months the range in results is narrowest and lowest in value. The mean coefficient of correlation for the x-axis component was negative and y-axis component changed to a positive value between 1 month old and 4 months old. Nonlinear time series analysis suggested that newborn and young infants' spontaneous lower extremity movements are characterized by a nonlinear chaotic dynamics with 5 to 7 embedding dimensions. Developmental changes of an optimal embedding dimension showed a U-shaped phenomenon. In addition, the maximal Lyapnov exponents were positive for all segments (0.79-2.99). Infants' spontaneous movement involves chaotic dynamic systems that are capable of generating voluntary skill movements.