Directional evolution of size coupled with ascertainment bias for variation in Drosophila microsatellites

Species-specific differences in microsatellite locus length and ascertainment bias have both been proposed to explain differences in microsatellite variability and length usually observed when loci isolated in one species are used to survey variation in a related species. Here we provide a simple algebraic approach to independently estimate the contributions of true species-specific length differences and ascertainment bias. We apply this approach to a reciprocal-isolation microsatellite study and show contributions of both ascertainment bias and a true longer average microsatellite length in Drosophila melanogaster compared with D. simulans.     

Nucleic acid amplification strategies for DNA microarray-based pathogen detection

DNA microarray-based screening and diagnostic technologies have long promised comprehensive testing capabilities. However, the potential of these powerful tools has been limited by front-end target-specific nucleic acid amplification. Despite the sensitivity and specificity associated with PCR amplification, the inherent bias and limited throughput of this approach constrain the principal benefits of downstream microarray-based applications, especially for pathogen detection. To begin addressing alternative approaches, we investigated four front-end amplification strategies: random primed, isothermal Klenow fragment-based, phi29 DNA polymerase-based, and multiplex PCR. The utility of each amplification strategy was assessed by hybridizing amplicons to microarrays consisting of 70-mer oligonucleotide probes specific for enterohemorrhagic Escherichia coli O157:H7 and by quantitating their sensitivities for the detection of O157:H7 in laboratory and environmental samples. Although nearly identical levels of hybridization specificity were achieved for each method, multiplex PCR was at least 3 orders of magnitude more sensitive than any individual random amplification approach. However, the use of Klenow-plus-Klenow and phi29 polymerase-plus-Klenow tandem random amplification strategies provided better sensitivities than multiplex PCR. In addition, amplification biases among the five genetic loci tested were 2- to 20-fold for the random approaches, in contrast to >4 orders of magnitude for multiplex PCR. The same random amplification strategies were also able to detect all five diagnostic targets in a spiked environmental water sample that contained a 63-fold excess of contaminating DNA. The results presented here underscore the feasibility of using random amplification approaches and begin to systematically address the versatility of these approaches for unbiased pathogen detection from environmental sources.     

Chromium is the proximate clastogenic species for lead chromate-induced clastogenicity in human bronchial cells

Hexavalent chromium (Cr(VI)) is a well-established human lung carcinogen with potentially widespread exposure. Solubility is a key factor in the carcinogenicity of Cr(VI), with the water-insoluble or 'particulate' compounds being the more potent carcinogens. Studies have indicated that the component ions are responsible for their clastogenicity, but it is uncertain whether chromium (Cr), lead (Pb) or some combination of the two is responsible for the clastogenic effects. Accordingly, we compared the clastogenicity of lead chromate (LC) with soluble sodium chromate (SC) and lead glutamate (LG) in WTHBF-6 human lung cells. We found that 1436microM was the maximal intracellular level of Pb after exposure to clastogenic concentrations of LC. However, clastogenesis was not observed after exposure to LG, even when intracellular Pb concentrations reached 13,347microM, indicating that intracellular Pb levels did not reach clastogenic levels in WTHBF-6 cells after LC treatment. By contrast, SC was clastogenic damaging 16 and 44% of metaphase cells at intracellular Cr doses of 312 and 1262microM respectively, which was comparable to the clastogenesis observed after LC treatment. LC damaged 10, 27 and 37% of metaphases at intracellular Cr doses of 288, 926 and 1644microM, respectively. These data indicate that with respect to LC-induced clastogenicity, Cr and not Pb is the proximate clastogenic species in human lung cells.     

Improved quantitative detection of 11 urinary phthalate metabolites in humans using liquid chromatography-atmospheric pressure chemical ionization tandem mass spectrometry

Phthalates are widely used as industrial solvents and plasticizers, with global use exceeding four million tons per year. We improved our previously developed high-performance liquid chromatography-atmospheric pressure chemical ionization-tandem mass spectrometric (HPLC-APCI-MS/MS) method to measure urinary phthalate metabolites by increasing the selectivity and the sensitivity by better resolving them from the solvent front, adding three more phthalate metabolites, monomethyl phthalate (mMP), mono-(2-ethyl-5-oxohexyl)phthalate (mEOHP) and mono-(2-ethyl-5-hydroxyhexyl)phthalate (mEHHP); increasing the sample throughput; and reducing the solvent usage. Furthermore, this improved method enabled us to analyze free un-conjugated mono-2-ethylhexyl phthalate (mEHP) by eliminating interferences derived from coelution of the glucuronide-bound, or conjugated form, of the mEHP on measurements of the free mEHP. This method for measuring phthalate metabolites in urine involves solid-phase extraction followed by reversed-phase HPLC-APCI-MS/MS using isotope dilution with (13)C(4) internal standards. We further evaluated the ruggedness and the reliability of the method by comparing measurements made by multiple analysts at different extraction settings on multiple instruments. We observed mMP, monoethyl phthalate (mEP), mono-n-butyl phthalate (mBP), monobenzyl phthalate (mBzP), mEHP, mEHHP and mEOHP in the majority of urine specimens analyzed with DEHP-metabolites mEHHP and mEOHP present in significantly higher amounts than mEHP.     

Metabolic oligosaccharide engineering as a tool for glycobiology

Oligosaccharides transact information exchange at the cell surface and modulate the activities and distribution of proteins within cells. Recently, the ability to modify monosaccharide structures within cellular glycans through metabolic processes has offered a new avenue for biological studies. The technique of metabolic oligosaccharide engineering has been used to disrupt glycan biosynthesis, chemically modify cell surfaces, probe metabolic flux inside cells, and to identify specific glycoprotein subtypes from the proteome.     

Estimating the accuracy of psychological scales using longitudinal data

This article presents a method for estimating the accuracy of psychological screening scales using receiver operating characteristic curves and associated statistics. Screening scales are typically semicontinuous within a known range with distributions that are nearly symmetric when the target condition is present and highly skewed when the condition is absent. We model screening scale outcomes using truncated normal distributions that accommodate these different distributional shapes and use subject-specific random effects to adjust for multiple assessments within individuals. Using the proposed model, we estimate the accuracy of the Symptom Checklist as a measure of major depression from a repeatedly screened sample of patients.     

Mantled howler population of Hacienda La Pacifica, Costa Rica, between 1991 and 1998: effects of deforestation

A survey of the mantled howler (Alouatta palliata) population on Hacienda La Pacifica, Guanacaste, Costa Rica, was done in July and August of 1998 to determine population parameters following deforestation due to major canal construction between 1990 and 1994. The survey was carried out in a manner identical to our 1991 survey and consisted of a single pass and two re-surveys of all forested areas of the farm. As canal construction effectively increased fragmentation of the habitat, we predicted decreased population and group size over this time. Results indicated that between the 1991 and 1998 survey, group size decreased but not significantly, and there were significantly fewer adult males and adult females per group. Population size, however, remained unchanged as there was an increase in animals in the immature age classes. An increase in the infant to adult female ratio suggests a stable or even expanding population, which could represent recovery from the initial disturbance of deforestation. Thus, despite changes in the forest and land use patterns, the area now appears to support the same number of howlers as found in previous surveys.     

Stalk segment 5 of the yeast plasma membrane H(+)-ATPase. Labeling with a fluorescent maleimide reveals a conformational change during glucose activation

Glucose is well known to cause a rapid, reversible activation of the yeast plasma membrane H(+)-ATPase, very likely mediated by phosphorylation of two or more Ser/Thr residues near the C terminus. Recent mutagenesis studies have shown that glucose-dependent activation can be mimicked constitutively by amino acid substitutions in stalk segment 5 (S5), an alpha-helical stretch connecting the catalytic part of the ATPase with transmembrane segment 5 (Miranda, M., Allen, K. E., Pardo, J. P., and Slayman, C. W. (2001) J. Biol. Chem. 276, 22485-22490). In the present work, the fluorescent maleimide Alexa-488 has served as a probe for glucose-dependent changes in the conformation of S5. Experiments were carried out in a "3C" version of the ATPase, from which six of nine native cysteines had been removed by site-directed mutagenesis to eliminate background labeling by Alexa-488. In this construct, three of twelve cysteines introduced at various positions along S5 (A668C, S672C, and D676C) reacted with the Alexa dye in a glucose-independent manner, as shown by fluorescent labeling of the 100 kDa Pma1 polypeptide and by isolation and identification of the corresponding tryptic peptides. Especially significant was the fact that three additional cysteines reacted with Alexa-488 more rapidly (Y689C) or only (V665C and L678C) in plasma membranes from glucose-metabolizing cells. The results support a model in which the S5 alpha-helix undergoes a significant change in conformation to expose positions 665, 678, and 689 during glucose-dependent activation of the ATPase.     

Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein

Histidine pK(a) values were measured in charge-reversal (K78E, K97E, K127E, and K97E/K127E) and charge-neutralization (E10A, E101A, and R35A) mutants of staphylococcal nuclease (SNase) by (1)H-NMR spectroscopy. Energies of interaction between pairs of charges (DeltaG(ij)) were obtained from the shifts in pK(a) values relative to wild-type values. The data describe the distance dependence and salt sensitivity of pairwise coulombic interactions. Calculations with a continuum electrostatics method captured the experimental DeltaG(ij) when static structures were used and when the protein interior was treated empirically with a dielectric constant of 20. The DeltaG(ij) when r(ij) < or = 10 A were exaggerated slightly in the calculations. Coulomb's law with a dielectric constant near 80 and a Debye-Hückel term to account for screening by the ionic strength reproduced the salt sensitivity and distance dependence of DeltaG(ij) as well as the structure-based method. In their interactions with each other, surface charges behave as if immersed in water; the Debye length describes realistically the distance where interactions become negligible at a given ionic strength. On average, charges separated by distances (r(ij)) approximately 5 A interacted with DeltaG(ij) approximately 0.6 kcal/mole in 0.01 M KCl, but DeltaG(ij) decayed to < or =0.10 kcal/mole when r(ij) = 20 A. In 0.10 M KCl, DeltaG(ij) approximately 0.10 kcal/mole when r(ij) = 10 A. In 1.5 M KCl, only short-range interactions with r(ij) < or = 5 A persisted. Although at physiological ionic strengths the interactions between charges separated by more than 10 A are extremely weak, in situations where charge imbalance exists many weak interactions can cumulatively produce substantial effects.