Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets

This paper first presents basic Petri net components representing molecular interactions and mechanisms of signalling pathways, and introduces a method to construct a Petri net model of a signalling pathway with these components. Then a simulation method of determining the delay time of transitions, by using timed Petri nets — i.e. the time taken in firing of each transition — is proposed based on some simple principles that the number of tokens flowed into a place is equivalent to the number of tokens flowed out. Finally, the availability of proposed method is confirmed by observing signalling transductions in biological pathways through simulation experiments of the apoptosis signalling pathways as an example.     

Mitochondrial genome structure of a cytoplasmic hybrid between tomato and wild potato

A physical map of the mitochondrial genome was constructed for a male-sterile tomato, MSA1, which had been generated by an asymmetric cell fusion between tomato (Lycopersicon esculentum) and wild potato (Solanum acaule). The entire genomic sequence of the MSA1 mitochondria (450 kb) was represented by five maps. Even if sequence duplications were taken into consideration, at least two linkage groups (maps 1–4 and map 5) were necessary to show the overall genome. The mitochondrial genome structure of MSA1 was also analyzed by comparing the Southern hybridization patterns of MSA1 and its parents (tomato and wild potato). The mitochondrial genome of MSA1 consists of a complex mixture of the parental genomes with at least 11 molecular recombination events. Received: 23 February 1998 / Revision received: 2 March 1998 / Accepted: 14 March 1998     

PPARG Genotype Accounts for Part of Individual Variation in Body Weight Reduction in Response to Calorie Restriction

Several studies indicate that expression of the peroxisome proliferator–activated receptor γ (PPARG) gene is influenced by calorie restriction. The aim of this study was to investigate whether PPARG gene variations are associated with weight reduction and changes in coronary heart disease (CHD) risk factors in response to a 14‐week calorie restriction. In total, 95 middle‐aged, Japanese women (BMI ≥25 kg/m²) enrolled as subjects for 14 weeks and attended weekly dietary lectures instructing them on how to consume a nutritionally balanced diet of 1,200 kcal/day. Eight single‐nucleotide polymorphisms (SNPs) in the PPARG gene (rs1801282 (Pro/Ala), rs2292101, rs2959272, rs1386835, rs709158, rs1175540, rs1175544, and rs1797912) were analyzed. Body weight decreased significantly (?7.7 ± 3.1 kg; ?11.3 ± 4.4%) during the intervention. Six PPARG SNPs (rs2959272, rs1386835, rs709158, rs1175540, rs1175544, and rs1797912) were significantly associated with the weight reduction, with rs1175544 having the strongest association (P = 0.004). No differences across the rs1175544 genotypes were observed in any of the blood analyses or in blood pressure. In a multiple regression analysis, the rs1175544 genotypes accounted for 7% of the total weight reduction variance. These data suggest that one SNP of the PPARG genotype accounted for a significant portion of the total body weight reduction variance in response to a short‐term intervention consisting of calorie restriction; however, no relationship was found between these SNPs and the changes in CHD risk factors which accompanied weight loss.     

T134, a Small-Molecule CXCR4 Inhibitor, Has No Cross-Drug Resistance with AMD3100, a CXCR4 Antagonist with a Different Structure

T22, an analog of polyphemusin II (18 amino acid residues), was found to block T-tropic human immunodeficiency virus type 1 (HIV-1) entry into target cells as a CXCR4 inhibitor. We synthesized T134, a small analog (14 amino acid residues) of T22 with reduced positive charges. T134 exhibited highly potent activity and significantly less cytotoxicity in comparison to that of T22. T134 prevents the anti-CXCR4 monoclonal antibody from binding to peripheral blood mononuclear cells but has no effect on the binding of anti-CCR5 monoclonal antibodies. Since T134 inhibits the binding of stromal cell-derived factor-1 (SDF-1) to MT-4 cells, it seems that T134 prevents HIV-1 entry by binding to CXCR4. The bicyclam AMD3100 has also been shown to block HIV-1 entry via CXCR4 but not via CCR5. Both T134 and AMD3100 are CXCR4 antagonists and low-molecular-weight compounds but have different structures. Our results indicate that T134 is active against wild-type T-tropic HIV-1 strains and against AMD3100-resistant strains.     

Expression of chemically synthesized alpha-neo-endorphin gene fused to E. coli alkaline phosphatase.

An alpha-neo-endorphin (alpha NE) gene, which we previously synthesized chemically and inserted into E. coli beta-galactosidase gene of pK013 plasmid, has been excised and fused to E. coli alkaline phosphatase (APase) gene. One of the transformants was named E15/pA alpha NE1. Under the APase gene regulation, APase-alpha NE chimeric protein was expressed at 1.3 X 10(6) molecules per cell, and accounted for about 60% of total cellular proteins. The HPLC pattern of CNBr treated E15/pA alpha NE1 was very simple reflecting the high content of the chimeric protein and low numbers of methionine residues in it. A series of genes encoding APase-alpha NE chimeric proteins in which 30 to 94 C-terminal amino acid residues were replaced by (met)-alpha NE, was cloned in E. coli. Transportation of the chimeric proteins to periplasmic space was studied. All chimeric proteins were apparently processed by signal peptidase but few, if any, was transported to the periplasmic space.     

Purification and Properties of a Lectin from the Fruitbodies of Flammulina velutipes

A lectin was purified to homogeneity from the fruitbodies of Flammulina velutipes by conventional purification procedures. The purified lectin was demonstrated to be a dimeric protein consisting of two identical subunits with an apparent molecular mass of 11 kDa. The lectin was an acidic protein with a pI value of 5.4, and devoid of cysteine, methionine, and histidine as amino acid constituents. Its hemagglutinating activity was totally unaffected by mono- and oligosaccharides and glycosides, but inhibited by some desialylated glycoproteins. Immunological assays revealed that no protein cross-reacting with rabbit anti-i⁷. velutipes lectin antibody was apparently present in vegetatively growing mycelia but was distributed throughout the fruitbody at different concentrations.     

Lipids of Algae

The carotenoid pigments prepared from acetone extracts of chlorella were separated into epiphasic and hypophasic fractions by partition between petroleum ether and 90% methanol. Each fraction was subjected to column chromatography, using aluminium oxide, magnesium oxide, calcium hydroxide or calcium carbonate as adsorbent. The absorption maxima of the separated pigments in hexane and in carbon disulfide were compared with those of the known pigments. Some of the separated pigments were identified as those previously known which follow: α-carotene, β-carotene, rhodoxanthin, sarcinaxanthin, lutein and neoxanthin. Two unknown pigments with absorption maxima not yet reported were separated. The first showed absorption maxima at 478 m_μ in hexane and 518 m_μ in carbon disulfide, and the second at 383, 402 and 425 m_μ in hexane and 428 and 450 m_μ in carbon disulfide.     

Editor's choice: Large,Male Germ Cell-Specific Hypomethylated DNA Domains With Unique Genomic and Epigenomic Features on the Mouse X Chromosome

To understand the epigenetic regulation required for germ cell-specific gene expression in the mouse, we analysed DNA methylation profiles of developing germ cells using a microarray-based assay adapted for a small number of cells. The analysis revealed differentially methylated sites between cell types tested. Here, we focused on a group of genomic sequences hypomethylated specifically in germline cells as candidate regions involved in the epigenetic regulation of germline gene expression. These hypomethylated sequences tend to be clustered, forming large (10 kb to ∼9 Mb) genomic domains, particularly on the X chromosome of male germ cells. Most of these regions, designated here as large hypomethylated domains (LoDs), correspond to segmentally duplicated regions that contain gene families showing germ cell- or testis-specific expression, including cancer testis antigen genes. We found an inverse correlation between DNA methylation level and expression of genes in these domains. Most LoDs appear to be enriched with H3 lysine 9 dimethylation, usually regarded as a repressive histone modification, although some LoD genes can be expressed in male germ cells. It thus appears that such a unique epigenomic state associated with the LoDs may constitute a basis for the specific expression of genes contained in these genomic domains.     

Effect of Ethanol and Theophylline on Circadian Rhythm of Rat Locomotion

The effect of ethanol and theophylline on the circadian rhythm of rat locomotion was investigated. Male Wistar rats synchronized to 12: 12 h light-dark cycles were divided into four groups for treatment with saline, ethanol, theophylline, and ethanol plus theophylline. Animals in each group were orally administered saline, ethanol (2.0 g/kg body wt), theophylline (10 mg/kg body wt), and ethanol plus theophylline, respectively, six times every 2 h during the 12-h light span. Spontaneous loco-motor activity was continuously monitored by an animal activity recorder at 15-min intervals. Total activity count, circadian rhythm characteristics of activity (amplitude, acrophase, and mesor), power spectral patterns, and slope of fluctuation (a measurement of ultradian periodicity) were calculated. Ethanol administration decreased the total activity count by 60% and phase-delayed the onset of activity rhythm by 9.5 h on the day after treatment. The absolute value of the slope of fluctuation was increased by ethanol administration. The mean recovery time evaluated by rhythm detection was 3.8 days. Theophylline administration increased the light phase activity, but caused no phase delay of the onset time of the locomotor activity rhythm. The decrease in total activity count and phase delay of onset of the activity rhythm caused by ethanol were partially antagonized by theophylline. However, the prolonged effects of ethanol, represented by a late recovery time and an increase in the slope of fluctuation, were not influenced by theophylline.