Sequence diversity of South Pacific isolates of Taro bacilliform virus and the development of a PCR-based diagnostic test.

We have analysed the sequence variability in the putative reverse transcriptase (RT)/ribonuclease H (RNaseH) and the C-terminal coat protein (CP)-coding regions from Taro bacilliform virus (TaBV) isolates collected throughout the Pacific Islands. When the RT/RNaseH-coding region of 22 TaBV isolates from Fiji, French Polynesia, New Caledonia, Papua New Guinea (PNG), Samoa, Solomon Islands and Vanuatu was examined, maximum variability at the nucleotide and amino acid level was 22.9% and 13.6%, respectively. Within the CP-coding region of 13 TaBV isolates from Fiji, New Caledonia, PNG, Samoa and the Solomon Islands, maximum variability at the nucleotide and amino acid level was 30.7% and 19.5%, respectively. Phylogenetic analysis showed that TaBV isolates from the Solomon Islands showed greatest variability while those from New Caledonia and PNG showed least variability. Based on the sequences of the TaBV RT/RNaseH-coding region, we have developed a PCR-based diagnostic test that specifically detects all known TaBV isolates. Preliminary indexing has revealed that TaBV is widespread throughout Pacific Island countries. A sequence showing approximately 50% nucleotide identity to TaBV in the RT/RNaseH-coding region was also detected in all taro samples tested. The possibility that this may represent either an integrated sequence or the genome of an additional badnavirus infecting taro is discussed.

A promoter derived from taro bacilliform badnavirus drives strong expression in transgenic banana and tobacco plants.

Taro bacilliform virus (TaBV) is a pararetrovirus of the genus Badnavirus which infects the monocotyledonous plant, taro ( Colocasia esculenta). A region of the TaBV genome spanning nucleotides 6,281 to 12 (T1200), including the 3' end of open reading frame 3 (ORF 3) and the intergenic region to the end of the tRNA(met)-binding site, was tested for promoter activity along with four different 5' deletion fragments (T600, T500, T250 and T100). In transient assays, only the T1200, T600, T500 fragments were shown to have promoter activity in taro leaf, banana suspension cells and tobacco callus. When these three promoters were evaluated in stably transformed, in vitro-grown transgenic banana and tobacco plants, all were found to drive near-constitutive expression of either the green fluorescent protein or beta-glucuronidase (GUS) reporter gene in the stem (or pseudostem), leaves and roots, with strongest expression observed in the vascular tissue. In transgenic banana leaves, the T600 promoter directed four-fold greater GUS activity than that of the T1200, T500 and the maize polyubiquitin-1 promoters. In transgenic tobacco leaves, the levels of GUS expression directed by the three promoters was between four- and ten-fold lower than that of the double Cauliflower mosaic virus 35S promoter. These results indicate that the TaBV-derived promoters may be useful for the high-level constitutive expression of transgenes in either monocotyledonous or dicotyledonous species.

Genomic characterisation of taro bacilliform virus.

Taro bacilliform virus (TaBV) has been classified as a putative badnavirus based on its non-enveloped, bacilliform virion morphology and transmission by mealybugs. The complete nucleotide sequence of a Papua New Guinea isolate of TaBV has now been determined and comprises 7458 bp. The genome contains four open reading frames (ORFs) on the plus-strand that potentially encode proteins of 17, 16, 214 and 13 kDa. The size and organisation of TaBV ORFs 1-3 is similar to that of most other badnaviruses, while the location of ORF 4 is similar to that of ORF 4 and ORF X of the atypical badnaviruses Citrus yellow mosaic virus and Cacao swollen shoot virus, respectively. The putative amino acid sequence of TaBV ORF 3 contained motifs that are conserved amongst badnavirus proteins including aspartic protease, reverse transcriptase (RT) and ribonuclease H (RNase H). The highly conserved putative plant tRNA(met)-binding site was also present in the 935 bp intergenic region of TaBV. Phylogenetic analysis using the amino acid sequence of ORF 3 showed that TaBV branched most closely to Dioscorea bacilliform virus. These results confirm that TaBV is a pararetrovirus of the genus Badnavirus, family Caulimoviridae.

Isothermal amplification and multimerization of DNA by Bst DNA polymerase.

We have demonstrated the isothermal in vitro amplification and multimerization of several different linear DNA targets using only two primers and the strongly strand-displacing exonuclease-negative Bst DNA polymerase. This reaction has been termed linear target isothermal multimerization and amplification (LIMA). LIMA has been compared with cascade rolling-circle amplification and has been found to be less sensitive but to yield similar variable-length multimeric dsDNA molecules. Products from several different LIMA reactions were characterized by restriction analysis and partial sequence determination. They were found to be multimers of subsets of the target sequence and were not purely primer derived. The sensitivities with respect to target concentration of several different LIMA reactions were determined, and they varied from 0.01 amol to 1 fmol. The sensitivity and specificity of LIMA were further tested using E. coli genomic DNA, and the selective amplification of a transposon fragment was demonstrated. A successful strategy for reducing LIMA-dependent background DNA synthesis in rolling-circle amplification embodiments was devised. This entailed the affinity purification of circular DNA templates before amplification.

Phase transition of a quasi-one-dimensional system.

The statistical mechanics of the quasi-one-dimensional system of DNA is studied with the Morse and Deng-Fan potentials for the interstrand hydrogen bonds of nucleotide pairs. The intrastrand interactions between nucleotides are characterized by a simple harmonic potential in which the coupling strength has a significant effect on the phase transition of the DNA system.

Probing the interaction between inactivation gating and Dd-sotalol block of HERG.

Potassium channels encoded by HERG underlie I:(Kr), a sensitive target for most class III antiarrhythmic drugs, including methanesulfonanilides such as Dd-sotalol. Recently it was shown that these drugs are trapped in the channel as it closes during hyperpolarization. At the same time, HERG channels rapidly open and inactivate when depolarized, and methanesulfonanilide block is known to develop in a use-dependent manner, suggesting a potential role for inactivation in drug binding. However, the role of HERG inactivation in class III drug action is uncertain: pore mutations that remove inactivation reduce block, yet many of these mutations also modify the channel permeation properties and could alter drug affinity through gating-independent mechanisms. In the present study, we identify a definitive role for inactivation gating in Dd-sotalol block of HERG, using interventions complementary to mutagenesis. These interventions (addition of extracellular Cd(2+), removal of extracellular Na(+)) modify the voltage dependence of inactivation but not activation. In normal extracellular solutions, block of HERG current by 300 micromol/L Dd-sotalol reached 80% after a 10-minute period of repetitive depolarization to +20 mV. Maneuvers that impeded steady-state inactivation also reduced Dd-sotalol block of HERG: 100 micromol/L Cd(2+) reduced steady-state block to 55% at +20 mV (P:<0.05); removing extracellular Na(+) reduced block to 44% (P:<0.05). An inactivation-disabling mutation (G628C-S631C) reduced Dd-sotalol block to only 11% (P:<0.05 versus wild type). However, increasing the rate of channel inactivation by depolarizing to +60 mV reduced Dd-sotalol block to 49% (P:<0.05 versus +20 mV), suggesting that the drug does not primarily bind to the inactivated state. Coexpression of MiRP1 with HERG had no effect on inactivation gating and did not modify Dd-sotalol block. We postulate that Dd-sotalol accesses its receptor in the open pore, and the drug-receptor interaction is then stabilized by inactivation. Whereas deactivation traps the bound methanesulfonanilide during hyperpolarization, we propose that HERG inactivation stabilizes the drug-receptor interaction during membrane depolarization.

De novo methylation at intronic CpG islands of Igf2r is associated with decreased expression of antisense RNA in aged mice.

Changes in cytosine methylation status of several genes have been implicated in the aging process. We have examined methylation status of differentially methylated regions of insulin-like growth factor II receptor gene during mouse senescence. Bisulfite-aided genomic sequencing revealed that methylated CpG residues were extended beyond the 3' boundary of de novo methylation sequence of DMR2 in aged mice. Furthermore, the de novo methylation of DMR2 in aged mice was associated with decreased expression of antisense transcript which recruits DMR2 as a promoter. On the contrary, methylation status of DMR1 was well-maintained during senescence. Accordingly, no significant changes in expression levels of sense transcripts were observed during the course of mouse aging.

Stereoselective interactions of the enantiomers of chromanol 293B with human voltage-gated potassium channels.

Selective inhibitors of the slow component of the cardiac delayed rectifier K(+) current, I(Ks), are of interest as novel class III antiarrhythmic agents and as tools for studying the physiologic roles of the I(Ks) current. Racemic chromanol 293B is an inhibitor of both native I(Ks) and its putative molecular counterpart, the KvLQT1+minK ion channel complex. We synthesized the (+)-[3S,4R] and (-)-[3R,4S] enantiomers of chromanol 293B using chiral intermediates of known absolute configuration and determined their relative potency to block recombinant human K(+) channels that form the basis for the major repolarizing K(+) currents in human heart, including KvLQT1+minK, human ether-a-go-go-related gene product (hERG), Kv1.5, and Kv4.3, corresponding to the slow (I(Ks)), rapid (I(Kr)), and ultrarapid (I(Kur)) delayed rectifier currents and the transient outward current (I(To)), respectively. K(+) channels were expressed in mammalian cells and currents were recorded using the whole-cell patch-clamp technique. We found that the physicochemical properties and relative potency of the enantiomers differed from those reported previously, with (-)-[3R,4S]293B nearly 7-fold more potent in block of KvLQT1+minK than (+)-[3S,4R]293B, indicating that the original stereochemical assignments were reversed. K(+) current inhibition by (-)-293B was selective for KvLQT1+minK over hERG, whereas the stereospecificity of block for KvLQT1+minK and Kv1.5 was preserved, with (-)-293B more potent than (+)-293B for both channel complexes. We conclude that the (-)-[3R,4S] enantiomer of chromanol 293B is a selective inhibitor of KvLQT1+minK and therefore a useful tool for studying I(Ks).

Effects of serotonin depletion by p-chlorophenylalanine, p-chloroamphetamine or 5,7-dihydroxytryptamine on central dopaminergic neurons: focus on tuberoinfundibular dopaminergic neurons and serum prolactin.

Three serotonin (5-HT) neurotoxins, p-chlorophenylalanine (PCPA, 125 and 250 mg/kg, i.p.), p-chloroamphetamine (PCA, 10 mg/kg, i.p.) and 5,7-dihydroxytryptamine (5,7-DHT, 200 microg/rat, i.c.v.) were used to examine whether depletion of central 5-HT has an effect on central dopaminergic (DA) neuronal activities or on prolactin (PRL) secretion. Adult ovariectomized Sprague-Dawley rats primed with estrogen (polyestradiol phosphate, 0.1 mg/rat, s.c.) were treated with one of three neurotoxins and then decapitated in the morning after 3-7 days. Blood sample and brain tissues were collected. The acute effect of PCA (from 30 to 180 min) was also determined. The concentrations of 5-HT, DA and their metabolites, 5-hydroxyindoleacetic acid and 3,4-dihydroxyphenylacetic acid, in the median eminence, striatum and nucleus accumbens were determined by HPLC-electrochemical detection. All three toxins significantly depleted central 5-HT stores by 11-20%. Except for PCPA, neither PCA nor 5,7-DHT had any significant effect on basal DA neuronal activities or PRL secretion. PCA also exhibited an acute effect on the release and reuptake of 5-HT and DA. In summary, depletion of central 5-HT stores to a significant extent for 3-7 days did not seem to affect basal DA neuronal activity and PRL secretion.

Modulation of HERG potassium channels by extracellular magnesium and quinidine.

Torsades de pointes is a polymorphic ventricular arrhythmia resulting from congenital or drug-induced (acquired) QT prolongation. Pharmacologic suppression of repolarizing potassium currents is one mechanism causing the acquired long QT (LQT) syndrome. Recent studies have linked mutations in a gene encoding a potassium channel subunit (HERG) to the LQT syndrome. Clinical experience indicates that intravenous magnesium sulfate is effective in reversing torsades de pointes, but the molecular basis of this effect is not understood. This study was designed to investigate the effects of extracellular magnesium (Mg2+) on HERG potassium currents. HERG potassium channels were expressed in Xenopus oocytes and in a human cell line and were examined by voltage-clamp methods. Extracellular Mg2+ (0.3-10 mM) caused a concentration-dependent shift in the membrane-potential dependence of HERG channel opening, causing a reduction in K+ current. This effect was much greater than that observed in another human delayed rectifier K+ channel, hKv1.5, suggesting a specific interaction with the HERG channel. Quinidine is an antiarrhythmic drug that also causes torsades de pointes under certain conditions. Quinidine (3 microM) inhibited HERG currents expressed in oocytes by 32.1 +/- 3.2% (n = 5), whereas 1 microM quinidine inhibited HERG currents in tsA201 cells by 75.8 +/- 2.4% (n = 12). Increasing extracellular Mg2+ did not relieve the inhibition by quinidine, but caused additional suppression. These results indicate that extracellular Mg2+ exerts a direct action on HERG potassium channels, resulting in suppression of outward repolarizing potassium current. It is concluded that modulation of this important K+ current is not the mechanism by which intravenous magnesium terminates drug-induced LQT and torsades de pointes. Potent suppression of HERG channel current by quinidine, compared with that of I(Ks) and I(Na), is a likely contributor to torsades de pointes arrhythmias.

Actions of genistein on cystic fibrosis transmembrane conductance regulator channel gating. Evidence for two binding sites with opposite effects.

Previous studies have shown that genistein increased cystic fibrosis transmembrane conductance regulator (CFTR) channel activity in the presence of saturating concentrations of forskolin and calyculin A in intact cells. Possible molecular mechanisms for genistein's action include inhibition of tyrosine kinases, inhibition of serine/threonine protein phosphatases, or direct binding of genistein to CFTR. Since genistein inhibits several enzymes that hydrolyze ATP, and ATP hydrolysis is an intrinsic property of CFTR, we examined the effect of genistein on CFTR gating in excised inside-out patches from Hi-5 insect cells and NIH3T3 cells expressing recombinant CFTR. Genistein (50 microM) did not open phosphorylated CFTR channels by itself, but increased the ATP- induced CFTR channel current by approximately twofold. A similar magnitude of enhancement was observed when genistein was applied with PKI, a specific inhibitor of protein kinase A, or vanadate, a tyrosine phosphatase inhibitor, suggesting that inhibition of protein phosphatases or tyrosine kinases does not account for genistein's effects. The enhancement of channel current increased with increasing concentrations of genistein and reached a maximum at 35 microM genistein. At higher concentrations of genistein concentration, CFTR channel current decreased, resulting in a bell-shaped dose-response relationship. In the absence of genistein, both open- and closed-time histograms could be fitted with a single exponential function, yielding a mean open time (tauO) of 0.302 +/- 0.002 s, and a mean closed time (tauC) of 0.406 +/- 0.003 s. In the presence of 50 microM genistein, the open time histogram could be fitted with a double exponential function with tauO1 = 0.429 +/- 0. 003 s and tauO2 = 2.033 +/- 0.173 s. Thus, genistein induced a prolonged open state, an effect that mimics that of nonhydrolyzable ATP analogs. Closed time analysis showed that 50 microM genistein caused a prolonged closed state with a time constant of 2.410 +/- 0.035 s. We thus conclude that (a) the effects of genistein are likely caused by a direct binding of the drug to the CFTR protein, and (b) at least two binding sites are required to explain the effects of genistein: a high affinity site that decreases the closing rate and a low affinity site that reduces the opening rate.

Genomic structure and expression of murine poly(A) binding protein II gene.

The genomic structure and expression of the murine poly(A) binding protein II (mPABII) gene were analyzed by using genomic DNA and cDNA clones. The expression level of the mPABII gene varied among tissues. Besides two transcripts detected in all tissues, an additional transcript was detected in testis. The mPAB gene has pseudogenes or related genes in its genome.

Genistein potentiates wild-type and delta F508-CFTR channel activity.

Effects of genistein on wild-type (wt) and delta F508-cystic fibrosis transmembrane conductance regulator (CFTR) were studied in NIH/3T3 cells stably transfected with wt or mutant CFTR cDNA. As measured by I- efflux, half-maximal concentration of agonist (K1/2) for forskolin-dependent activation was greater for delta F508-CFTR than wt-CFTR. Genistein decreased the K1/2 for both forms of the channel and increased the maximal activity of delta F508-CFTR by 3.7-fold. In cell-attached patches, 10 microM forskolin induced minimal delta F508-CFTR activity with characteristic prolonged closed times (estimated time constant, > 30 s). Genistein increased the forskolin-induced macroscopic currents of wt-CFTR and delta F508-CFTR by 3- and 19-fold, respectively. Variance analysis suggested that in the presence of forskolin and genistein the open probabilities (Po) of wt- and delta F508-CFTR were identical. In single-channel studies, at maximal adenosine 3',5'-cyclic monophosphate (cAMP) stimulation, genistein increased the Po of wt-CFTR by prolonging the open time, but, at submaximal cAMP stimulation, the Po was increased by prolonging the open time and shortening the closed time. In excised patches with CFTR channels preactivated in the cell-attached mode, genistein increased ATP-dependent wt- and delta F508-CFTR current about twofold by prolonging the open time. Our results thus suggest that phosphorylation-dependent activation of delta F508-CFTR is defective and that genistein corrects this defect at least in part by binding to the CFTR protein.

Modulation of CFTR chloride channels by calyculin A and genistein.

Modulation of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel by calyculin A and genistein was studied in Hi-5 insect cells infected with baculovirus containing the wild-type CFTR cDNA. In cell-attached patches, CFTR channel activity was not observed until stimulated by forskolin in 90% of the cells, suggesting a low level of basal adenosine 3',5'-cyclic monophosphate activity. Calyculin A, a specific inhibitor of phosphatases 1 and 2A, increased forskolin-induced CFTR activity by 17.2-fold. CFTR channel currents did not deactivate completely after forskolin was withdrawn in the continued presence of calyculin A. Genistein enhanced forskolin-induced CFTR activity by 44.9-fold but could neither activate the CFTR by itself nor prevent complete deactivation on removal of forskolin. Genistein together with calyculin A could adequately prevent deactivation of CFTR currents. Noise analysis of the macroscopic CFTR currents revealed significant differences in the mean current-variance-relationship and the corner frequency of the noise spectra between currents activated by forskolin plus genistein and those activated by forskolin plus calyculin A. Furthermore, genistein enhanced CFTR activity induced by saturating concentrations of forskolin and calyculin A. Our results suggest that genistein and calyculin A modulate the CFTR by different mechanisms and that genistein might inhibit calyculin A-insensitive dephosphorylation of the CFTR.

Central administration of 8-OH-DPAT and mCPP stimulates prolactin secretion in ovariectomized, estrogen-treated rats: lack of an effect on tuberoinfundibular dopaminergic neuron activity.

The effects of central administration of two serotonin receptor agonists, 8-OH-DPAT and mCPP, on tuberoinfundibular dopaminergic (TIDA) neuron activity and serum prolactin (PRL) levels in ovariectomized, estrogen-treated rats were determined. 8-OH-DPAT dose-dependently (0.1-10 microgram/rat, icv) stimulated serum PRL levels, and depressed serotonergic neuron activity in 30 min. However, the TIDA neuron activity was not affected at all. Similar treatment of mCPP was less effective than 8-OH-DPAT: only the highest dose of mCPP (10 microgram) stimulated PRL secretion and inhibited serotonergic neuron activity. No change in TIDA neuron activity was observed either. We conclude that central serotonin acts on 5-HT1 receptors to stimulate the PRL secretion, which may not involve the TIDA neurons.

Effect of intergranular versus intragranular cornstarch on tablet friability and in vitro dissolution.

The effect of blending dry cornstarch versus wet granulation with the drug and other excipients on friability and in vitro dissolution of a ticlopidine hydrochloride tablet formulation was studied. The friability of the tablets was reduced by wet granulating cornstarch with the drug and other excipients compared with the dry blending. The dissolution rate and the tablet-to-tablet variability was improved by incorporating cornstarch in the wet-granulation stage. The lactose placebo tablets, which were wet granulated with either a binder solution or without a binder, also showed reduced tablet friability due to the incorporation of cornstarch in the wet-granulation step. Examination of the tablet cross sections under the scanning electron microscope indicated clumping of starch grains when starch was blended in the dry form. Starch grains were well embedded in the other materials of the tablet and not readily visible when starch was wet granulated with the other excipients. This results in better bonding, fewer weak points, and better homogeneity of the starch disintegrator within the tablet, which accounts for better friability and improved dissolution.

Effect of moisture and crushing strength on tablet friability and in vitro dissolution.

The friability and dissolution of a formulation of compressed tablets were studied by varying the granulation moisture and tablet crushing strength. A general quadratic response surface model was used to analyze the data. The response surface contour plots of tablet friability consisted of a series of ellipsoidal curves. The optimum friability corresponding to a granulation moisture content and a tablet crushing strength was a simple minimum. The in vitro dissolution contour plots showed a stationary ridge system. Along the ridge, a large number of combinations of tablet crushing strength and granulation moisture represented 100% drug dissolution. The contour overlays of friability and dissolution contour plots showed a region where both the friability and dissolution requirement could be met. The analysis of the data by means of multiple linear regression was helpful in understanding the role of granulation moisture and tablet crushing strength on tablet friability and in vitro dissolution.

Powder flow studies III: tensile strength, consolidation ratio, flow rate, and capsule-filling-weight variation relationships.

The tensile strength of consolidated powder beds was studied by applying a series of loads to the surface of the powder beds in a tensile tester. The results were plotted as tensile strength versus consolidation pressure. The linearity of these plots suggests a direct relationship between tensile strength and consolidation pressure. The following plots gave linear relationships: (1) tensile strength versus consolidation ratio, (b) tensile strength versus coefficient of variation of the filled weight of the capsules, and (c) logarithm of the tensile strength versus logarithm of the flow rate. These results suggest a direct relationship between tensile strength and consolidation ratio and their usefulness in studying powder flow. The physical significance of the empirical equation used in consolidation studies was explored. A comparison of the empirical equation with a theoretically derived equation, under certain assumptions, suggests that the consolidation ratio is a function of the ratio of the initial volume to the net volume and a function of the coefficient of Rankine. The coefficient of Rankine is a function of the angle of internal friction in the static powder bed.

North american glacial history extended to 75,000 years ago.

By concentrating carbon-14 through thermal diffusion, it is possible to extend the range of carbon-14 dating to 75,000 years ago. Samples with very low contamination levels have been encountered, and a reliable chronology appears possible. A Pacific Northwest climatic curve has been derived from palynological studies. The Pacific Northwest curve and the Great Lakes glacial history are age-calibrated by radiocarbon dating. The climatic patterns in the Pacific Northwest and Northwest Europe are similar in the early part of the last glaciation, with interstades near 60,000, 65,000, and 70,000 years ago. An age of 74,700 years for the St. Pierre interstade indicates a possible correlation with the previous interglacial.