Genetic code correlations: Differential rates of non-enzymatic activation of hydrophobic amino acids by ATP

The relative rates of non-enzymatic activation of several hydrophobic amino acids by ATP have been found to bear an interesting relationship to the ordering of these amino acids in the genetic anticode. All of these hydrophobic amino acids (phe, leu, val, ile and met) have adenylic acid, the most hydrophobic nucleotide, as the central and most important member of their anticodons, and the ordering of their relative rates of nonenzymatic activation by ATP has been found not to correlate with the ordering of the hydrophobicities of the amino acids themselves, but rather with the ordering of the average estimates of the hydrophobicities of their respective anticodonic dinucleotides. These data suggest that the genetic code is based not just on hydrophobic relationships or affinities between amino acids and nucleotides, but perhaps more importantly, on the total reaction chemistry between amino acids and nucleotides.     

A freeze-fracture study of hormone-induced branching in the fungus Achlya.

The induction of the male sexual organ primordia (antheridial hyphae) by the steriod hormone antheridiol in the water mold Achlya ambisexualis Raper requires the production and secretion of the enzyme cellulase. It is postulated that a localized secretion of cellulase produces a limited area of wall hydrolysis that is blown out into a lateral bleb by turgor pressure. Freeze-etch preparations show membrane profiles similar to those seen in other systems where exocytosis is occurring. Such a mechanism would provide the required localized secretion of cellulase. Water stress, imposed by polyethylene glycol, prevents the formation of antheridial hyphae, the secretion of cellulase and the expected membrane profiles. After a period of recovery from water stress antheridial hyphae are formed, cellulase secretion occurs and the expected membrane profiles are restored.     

Satellite Ic: a possible link between the satellite DNAs of D. virilis and D. melanogaster.

In this study, we isolated and characterized a previously undetected cryptic satellite DNA comprising 0.1% of the total nuclear genome of D. virilis. This satellite is hidden from detection in neutral CsCl by satellite I and is therefore designated cryptic satellite I or Ic. Sequence analysis reveals that Ic is the repeating heptanucleotide [poly d(AATATAG): d(CTATATT)]. It is more closely related to the three simple sequence satellite DNAs of D. melanogaster, a distantly related species, than it is to any of the major D. virilis satellite DNA sequences. Ic may therefore be a link between the simple sequence satellites of D. virilis and D. melanogaster. As an extension of this theory, we have constructed a "family tree" linking the satellites of D. virilis and D. melanogaster by a series of "simple" operations. Only one intermediate required by this evolutionary scheme has not yet been identified.     

Quantitative high-performance thin-layer chromatography of dansyl derivatives of biogenic amines

A procedure for the separation, detection, and quantification of picomole levels of dansyl derivatives of the biogenic amines, dopamine, norepinephrine, octopamine, and serotonin, has been developed using high-performance thin-layer chromatography. The detection limit is 1 to 2 pmol. Each of the amine derivatives has been detected in insect brain tissue and a solvent system has been developed for the separation and quantification of octopamine in insect tissue samples.     

Monitoring oak processionary moth Thaumetopoea processionea L. using pheromone traps: the influence of pheromone lure source,trap design and height above the ground on capture rates

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Improved Detection of Rare HIV-1 Variants using 454 Pyrosequencing

454 pyrosequencing, a massively parallel sequencing (MPS) technology, is often used to study HIV genetic variation. However, the substantial mismatch error rate of the PCR required to prepare HIV-containing samples for pyrosequencing has limited the detection of rare variants within viral populations to those present above ~1%. To improve detection of rare variants, we varied PCR enzymes and conditions to identify those that combined high sensitivity with a low error rate. Substitution errors were found to vary up to 3-fold between the different enzymes tested. The sensitivity of each enzyme, which impacts the number of templates amplified for pyrosequencing, was shown to vary, although not consistently across genes and different samples. We also describe an amplicon-based method to improve the consistency of read coverage over stretches of the HIV-1 genome. Twenty-two primers were designed to amplify 11 overlapping amplicons in the HIV-1 clade B gag-pol and env gp120 coding regions to encompass 4.7 kb of the viral genome per sample at sensitivities as low as 0.01-0.2%.