Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array

Background  

A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification of SNPs or insertion/deletions (INDELs) for high throughput genotyping and high density mapping. Here we applied SFP markers to a lingering question about the source of salt tolerance in a particular rice recombinant inbred line (RIL) derived from a salt tolerant and salt sensitive parent.     

Juvenile hormone acid and ecdysteroid together induce competence for metamorphosis of the Verson's gland in Manduca sexta

In the last larval instar of Lepidoptera, ecdysteroid in the absence of juvenile hormone (JH) is believed to cause the shift from larval to pupal development. In Manduca sexta, tissues such as the Verson's gland and crochet epidermis become pupally committed before the earliest pulse of ecdysteroid that occurs on day 2. What causes the change in commitment in these tissues? First it was necessary to determine at what stage these tissues become competent to express the pupal program. Last instar larvae of different ages were induced to molt prematurely by feeding the ecdysteroid analog RH5992 and Verson's gland proteins were analyzed by SDS-polyacrylamide gel electrophoresis. Glands became competent to make pupal proteins between 24 and 32 h after the last larval ecdysis. Next, hormonal regulation of competence was examined in ligated abdomens of 12h last instar larvae. Treatment with JH II acid or methoprene acid plus a low dose (1/50th of the molt inducing dose) of RH5992 induced competence, whereas RH5992 alone, methoprene acid alone or methoprene plus RH5992 did not. Verson's glands maintained in vitro produced pupal proteins in response to methoprene acid together with RH5992 but not with RH5992 alone. Likewise, crochet epidermis lost the ability to make crochets (metamorphic change) only in isolated abdomens treated with JH II acid or methoprene acid and low doses of RH5992. In conclusion, JH acid in the presence of basal levels of ecdysteroid induces tissue competence for metamorphosis. Metamorphic competence is followed by commitment, induced by a small pulse of ecdysteroid in the absence of JH, and finally by expression caused by a high titer of ecdysteroid. It is proposed that JH acid is an essential metamorphic hormone.     

Pregnancy diagnosis in zoo animals by estrogen determination in feces

Estrogen concentration in feces was investigated in five different herbivorous species of zoo animals. Using a nonspecific estrogen radioimmunoassay, in four species (red buffalo, yak, Grevy's zebra, and Nubian ibex) pregnancy was revealed by measuring estrogen concentration in feces. In hippopotamus, the levels of fecal estrogens were not different between pregnant and nonpregnant animals.     

Zinc efficiency is correlated with enhanced expression and activity of zinc-requiring enzymes in wheat

Zinc (Zn) is an essential micronutrient for plants. The ability of plants to maintain significant yields under low Zn is termed Zn efficiency (ZE) and its genetic and mechanistic basis is still not well understood. Previously, we showed that root Zn uptake did not play a role in ZE. In the current study, Zn-efficient and -inefficient wheat (Triticum aestivum) genotypes were grown for 13 d in chelate buffer nutrient solutions at low (0.1 pM), sufficient (150 pM), and high (1 microM) Zn(2+) activities and analyzed for root-to-shoot translocation of Zn, subcellular leaf Zn distribution, and activity and expression of the Zn-requiring enzymes in leaves. No correlation between ZE and Zn translocation to the shoot was found. Furthermore, total and water-soluble concentrations of leaf Zn were not associated with ZE, and no differences in subcellular Zn compartmentation were found between Zn-efficient and -inefficient genotypes. However, the expression and activity of the Zn-requiring enzymes copper (Cu)/Zn superoxide dismutase (SOD) and carbonic anhydrase did correlate with differences in ZE. Northern analysis suggested that Cu/ZnSOD gene expression was up-regulated in the Zn-efficient genotype, Kirgiz, but not in inefficient BDME. Under Zn deficiency stress, the very Zn-efficient genotype Kirgiz and moderately Zn-efficient Dagdas exhibited an increased activity of Cu/ZnSOD and carbonic anhydrase when compared with Zn-inefficient BDME. These results suggest that Zn-efficient genotypes may be able to maintain the functioning of Zn-requiring enzymes under low Zn conditions; thus, biochemical Zn utilization may be an important component of ZE in wheat.     

Spectroscopic studies of 9-hydroxyellipticine binding to DNA

The binding of 9-hydroxyellipticine to calf thymus DNA, poly[d(A-T)]₂, and poly-[d(G-C)]₂ has been studied in detail by means of CD, linear dichroism, resonance light scattering, and molecular dynamics. The transition moment polarizations of 9-hydroxyelliptiycine were determined in polyvinyl alcohol stretched film. Spectroscopic solution studies of the DNA/drug complex are combined with theoretical CD calculations using the final 50 ps of a series of molecular dynamics simulations as input. The spectroscopic data shows 9-hydroxyellipticine to adopt two main binding modes, one intercalative and the other a stacked binding mode involving the formation of drug oligomers in the DNA major groove. Analysis of the intercalated binding mode in poly[d(A-T)]₂ suggests the 9-hydroxyellipticine hydroxyl group lies in the minor groove and hydrogen bonds to water with the pyridine ring protruding into the major groove. The stacked binding mode was examined using resonance light scattering and it was concluded that the drug was forming small oligomer stacks rather than extended aggregates. Reduced linear dichroism measurements suggested a binding geometry that precluded a minor groove binding mode where the plane of the drug makes a 45° angle with the plane of the bases. Thus it was concluded that the drug stacks in the major groove. No obvious differences in the mode of binding of 9-hydroxyellipticine were observed between different DNA sequences; however, the stacked binding mode appeared to be more favorable for calf thymus DNA and poly[d(G-C)]₂ than for poly[d(A-T)]₂, an observation that could be explained by the slightly greater steric hindrance of the poly[d(A-T)]₂ major groove. A strong concentration dependence was observed for the two binding modes where intercalation is favored at very low drug load, with stacking interactions becoming more prominent as the drug concentration is increased. Even at DNA : drug mixing ratios of 70:1 the stacked binding mode was still important for GC-rich DNAs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 127–143, 1998     

Modulatory Effect of Lycopene on Deltamethrin-Induced Testicular Injury in Rats

Aim of the current study was to investigate the ability of deltamethrin to induce testicular injury in rats and its possible attenuation with lycopene. Rats were divided into three groups: Group I (DEL) received deltamethrin, 5 mg/kg b.w./day orally, in corn oil. Group II (DEL + Lyc) received oral dose of lycopene (4 mg/kg b.w./day) in corn oil concurrently with deltamethrin following the same regimen as in group I. Group III (Control) received appropriate volume of corn oil. After 4 weeks, deltamethrin-treated rats showed decreased body weight, serum testosterone, luteinizing hormone and follicle-stimulating hormone levels. Testicular total oxidant capacity (TOC), nitrite/nitrate (NOx), poly (ADP-ribose) polymerase (PARP), and DNA damage were significantly increased. RT-PCR demonstrated significant up-regulation in testicular mRNA for glutathione-S-transferase and heat-shock protein-70 (HSP-70), whereas steroidogenic acute regulatory (StAR) protein was down-regulated after deltamethrin exposure. Lycopene was able to restore body weight, serum testosterone, StAR mRNA, TOC, NOx levels, and PARP activity with significant decrease in HSP-70 mRNA, and DNA damage. In conclusion, lycopene was able to counteract the deleterious effect of deltamethrin.     

Effect of Ascorbic Acid on the Degradation of Cyanocobalamin and Hydroxocobalamin in Aqueous Solution: A Kinetic Study

The degradation kinetics of 5 × 10⁻⁵ M cyanocobalamin (B₁₂) and hydroxocobalamin (B_12b) in the presence of ascorbic acid (AH₂) was studied in the pH range of 1.0–8.0. B₁₂ is degraded to B_12b which undergoes oxidation to corrin ring cleavage products. B_12b alone is directly oxidized to the ring cleavage products. B₁₂ and B_12b in degraded solutions were simultaneously assayed by a two-component spectrometric method at 525 and 550 nm without interference from AH₂. Both degrade by first-order kinetics and the values of the rate constants at pH 1.0–8.0 range from 0.08 to 1.05 × 10⁻⁵ s⁻¹ and 0.22–7.62 × 10⁻⁵ s⁻¹, respectively, in the presence of 0.25 × 10⁻³ M AH₂. The t_1/2 values of B₁₂ and B_12b range from 13.7 to 137.5 h and 2.5–87.5 h, respectively. The second-order rate constants for the interaction of AH₂ with B₁₂ and B_12b are 0.05–0.28 × 10⁻² and 1.10–30.08 × 10⁻² M⁻¹ s⁻¹, respectively, indicating a greater effect of AH₂ on B_12b compared to that of B₁₂. The k_obs–pH profiles for both B₁₂ and B_12b show the highest rates of degradation around pH 5. The degradation of B₁₂ and B_12b by AH₂ is affected by the catalytic effect of phosphate ions on the oxidation of AH₂ in the pH range 6.0–8.0.KEY WORDS: ascorbic acid, cyanocobalamin, degradation, hydroxocobalamin, kinetics, two-component spectrometry     

Association of Genetic Variants of MTHFR,ENPP1, and ADIPOQ with Myocardial Infarction in Egyptian Patients

The study aimed to investigate the association between MTHFR C677T, ENPP1 K121Q, and ADIPOQ 45 T/G gene polymorphisms and incidence of myocardial infarction (MI) in Egyptian patients. The study included 60 unrelated patients suffering from their first MI and 60 unrelated controls. Patients were recruited from Kasr-El Eini hospital, Cairo University. The previously mentioned polymorphisms were determined in all participants by PCR–RFLP. There was no significant difference in the distribution of genotypes and alleles of MTHFR C677T between groups. In contrast, significant difference was found in the distributions of genotypes and alleles of ENPP1 K121Q and ADIPOQ 45 T/G between MI patients and controls (P = 0.01, P = 0.004, P = 0.009, P = 0.001, respectively). Univariate analysis revealed that 121Q ENPP1 and 45 G ADIPOQ alleles were associated with the increased risk of MI (OR = 3; 95 % CI = 1.45–6.2; P = 0.004 and OR = 5.8; 95 % CI = 1.92–17.54; P = 0.001, respectively). The mutant homozygous genotypes of MTHFR, ENPP1, and ADIPOQ were more prevalent in diabetic hypertensive MI patients than it was among non-diabetic normotensive MI patients. Regarding the coagulation profile, INR (P = 0.009) and PC % (P = 0.022) were significantly different among the three genotypes of MTHFR C677T. The 677 T, 121 Q, and 45G variants were associated with MI in Egyptian patients; however, more studies are needed to determine the possible protective effect for these polymorphisms in our population.     

Occurrence of two closely related ricefishes, Javanese medaka (Oryzias javanicus) and Indian medaka (O. dancena) at sites with different salinity in Peninsular Malaysia

Among ricefishes of the genus Oryzias, the Javanese medaka (O. javanicus) and the Indian medaka (O. dancena) are highly adaptable to seawater. Although wide distribution of the two species in the brackish waters of South and South-East Asia has been reported, their habitat preference remains unknown. We surveyed 12 sites in five estuarial areas of the west coast of Peninsular Malaysia from Kuala Gula to Tanjung Piai. Both species were found in all five areas, suggesting their distribution throughout the west coast of Peninsular Malaysia. This is the southernmost-recorded appearance of O. dancena, to the best of our knowledge. However, the habitats of the two species were essentially separated: of the 12 surveyed sites, the species were found in co-existence at only two sites, and one or the other species was found alone at the remaining 10 sites. We compared temperature, salinity, pH, and dissolved oxygen (DO) at the sampling sites and found that the habitat of O. javanicus is with higher salinity and DO. The salinity and DO at the sites of co-existence are near the lowest values found at the O. javanicus-only sites, and the highest values at the O. dancena-only sites. These results suggest that O. javanicus and O. dancena habitats are essentially separated; the former prefers hyperosmotic conditions while the latter prefers hypoosmotic conditions, and the latter may be more tolerant of hypoxia. The two sites of co-existence are points of contact between the species’ separate distribution areas.     

Long-term alteration of anxiolytic effects of ovarian hormones in female mice by a peripubertal immune challenge

Recent reports indicate that exposure to some stressors, such as shipping or immune challenge with the bacterial endotoxin, lipopolysaccharide (LPS), during the peripubertal period reduces sexual receptivity in response to ovarian hormones in adulthood. We hypothesized that a peripubertal immune challenge would also disrupt the response of a non-reproductive behavior, anxiety-like behavior, to ovarian hormones in adulthood. Female C57Bl/6 mice were injected with LPS during the peripubertal period and tested for anxiety-like behavior in adulthood, following ovariectomy and ovarian hormone treatment. Treatment with estradiol followed by progesterone reduced anxiety-like behavior in control, but not LPS-treated females. We next determined if the disruptive effect of LPS on adult behavior were limited to the peripubertal period by treating mice with LPS either during this period or in adulthood. LPS treatment during the peripubertal period disrupted the anxiolytic effect of ovarian hormones, whereas treatment in adulthood did not. We further tested if this model of peripubertal immune challenge was applicable to an outbred strain of mice (CD-1). Similar to C57Bl/6 mice, LPS treatment during the peripubertal period, but not later, disrupted the anxiolytic effect of estradiol and progesterone. These data suggest that a peripubertal immune challenge disrupts the regulation of anxiety-like behavior by ovarian hormones in a manner that persists at least for weeks after the termination of the immune challenge.