The effect of hybrid transgression on environmental tolerance in experimental yeast crosses.

Evidence is rapidly accumulating that hybridization generates adaptive variation. Transgressive segregation in hybrids could promote the colonization of new environments. Here, we use an assay to select hybrid genotypes that can proliferate in environmental conditions beyond the conditions tolerated by their parents, and we directly compete them against parental genotypes in habitats across environmental clines. We made 45 different hybrid swarms by crossing yeast strains (both Saccharomyces cerevisiae and S. paradoxus) with different genetic and phenotypic divergence. We compared the ability of hybrids and parents to colonize seven types of increasingly extreme environmental clines, representing both natural and novel challenges (mimicking pollution events). We found that a significant majority of hybrids had greater environmental ranges compared to the average of both their parents' ranges (mid-parent transgression), but only a minority of hybrids had ranges exceeding their best parent (best-parent transgression). Transgression was affected by the specific strains involved in the cross and by the test environment. Genetic and phenotypic crossing distance predicted the extent of transgression in only two of the seven environments. We isolated a set of potentially transgressive hybrids selected at the extreme ends of the clines and found that many could directly outcompete their parents across whole clines and were between 1.5- and 3-fold fitter on average. Saccharomyces yeast is a good model for quantitative and replicable experimental speciation studies, which may be useful in a world where hybridization is becoming increasingly common due to the relocation of plants and animals by humans.

Understanding the clinical pharmacokinetics of a GABAA partial agonist by application of in vitro tools.

1. 4-Oxo-4,5,6,7-tetrahydro-1H-indole-3-carboxylic acid (4-methylaminomethyl-phenyl)-amide (1), developed for general anxiety disorder, was discontinued from clinical development due to unsuitable oral pharmacokinetics. 2. In humans, (1) demonstrated an unacceptable high apparent oral clearance (Cl(p)/F) that also demonstrated a supraproportional dose-exposure relationship. Secondary peaks in the plasma concentration-time profile suggested possible enterohepatic recirculation of (1). A combination of in vitro mechanistic tools was applied to better understand the processes underlying these complex clinical pharmacokinetic profiles of (1). 3. In metabolism experiments, (1) was shown to be a substrate of monoamine oxidase A (MAO-A) as well as being metabolized by cytochrome P450. The former appeared to be a high K(M) process with a high capacity, while the latter showed saturation between 1 and 10 microM, consistent with the supraproportional dose-exposure relationship. 4. In a sandwich-cultured hepatocyte model, (1) was shown to be a substrate for both uptake and efflux into the canicular space, which is consistent with the observation of pharmacokinetics suggestive of enterohepatic recirculation. Finally, in human epithelial colon adenocarcinoma cell line (Caco-2) and Madin-Darby canine kidney cells transwell flux experiments, (1) was shown to have relatively low permeability and a basolateral-to-apical flux ratio consistent with the activity of P-glycoprotein. 5. In combination, a compounding of the contributions of MAO-A, hepatic uptake and efflux transporters, and P-glycoprotein to the disposition of (1) may underlie the low oral exposure, saturable clearance, and aberrant concentration versus time profiles observed for this compound in humans.

Protein variation in Adh and Adh-related in Drosophila pseudoobscura. Linkage disequilibrium between single nucleotide polymorphisms and protein alleles.

A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

An efficient region of interest acquisition method for dynamic magnetic resonance imaging.

Motivated by work in the area of dynamic magnetic resonance imaging (MRI), we develop a new approach to the problem of reduced-order MRI acquisition. Efforts in this field have concentrated on the use of Fourier and singular value decomposition (SVD) methods to obtain low-order representations of an entire image plane. We augment this work to the case of imaging an arbitrarily-shaped region of interest (ROI) embedded within the full image. After developing a natural error metric for this problem, we show that determining the minimal order required to meet a prescribed error level is in general intractable, but can be solved under certain assumptions. We then develop an optimization approach to the related problem of minimizing the error for a given order. Finally, we demonstrate the utility of this approach and its advantages over existing Fourier and SVD methods on a number of MRI images.

A comparison study of linear reconstruction techniques for diffuse optical tomographic imaging of absorption coefficient.

We compare, through simulations, the performance of four linear algorithms for diffuse optical tomographic reconstruction of the three-dimensional distribution of absorption coefficient within a highly scattering medium using the diffuse photon density wave approximation. The simulation geometry consisted of a coplanar array of sources and detectors at the boundary of a half-space medium. The forward solution matrix is both underdetermined, because we estimate many more absorption coefficient voxels than we have measurements, and ill-conditioned, due to the ill-posedness of the inverse problem. We compare two algebraic techniques, ART and SIRT, and two subspace techniques, the truncated SVD and CG algorithms. We compare three-dimensional reconstructions with two-dimensional reconstructions which assume all inhomogeneities are confined to a known horizontal slab, and we consider two 'object-based' error metrics in addition to mean square reconstruction error. We include a comparison using simulated data generated using a different FDFD method with the same inversion algorithms to indicate how our conclusions are affected in a somewhat more realistic scenario. Our results show that the subspace techniques are superior to the algebraic techniques in localization of inhomogeneities and estimation of their amplitude, that two-dimensional reconstructions are sensitive to underestimation of the object depth, and that an error measure based on a location parameter can be a useful complement to mean squared error.

Linkage analysis of 150 high-risk prostate cancer families at 1q24-25.

Confirmation of linkage and estimation of the proportion of families who are linked in large independent datasets is essential to understanding the significance of cancer susceptibility genes. We report here on an analysis of 150 high-risk prostate cancer families (2,176 individuals) for potential linkage to the HPC1 prostate cancer susceptibility locus at 1q24-25. This dataset includes 640 affected men with an average age at prostate cancer diagnosis of 66. 8 years (range, 39-94), representing the largest collection of high-risk families analyzed for linkage in this region to date. Linkage to multiple 1q24-25 markers was strongly rejected for the sample as a whole (lod scores at theta = 0 ranged from -30.83 to -18. 42). Assuming heterogeneity, the estimated proportion of families linked (alpha) at HPC1 in the entire dataset was 2.6%, using multipoint analysis. Because locus heterogeneity may lead to false rejection of linkage, data were stratified based on homogeneous subsets. When restricted to 21 Caucasian families with five or more affected family members and mean age at diagnosis < = 65 years, the lod scores at theta = 0 remained less than -4.0. These results indicate that the overall portion of hereditary prostate cancer families whose disease is due to inherited variation in HPC1 may be less than originally estimated.

Wavelet domain image restoration with adaptive edge-preserving regularization.

In this paper, we consider a wavelet based edge-preserving regularization scheme for use in linear image restoration problems. Our efforts build on a collection of mathematical results indicating that wavelets are especially useful for representing functions that contain discontinuities (i.e., edges in two dimensions or jumps in one dimension). We interpret the resulting theory in a statistical signal processing framework and obtain a highly flexible framework for adapting the degree of regularization to the local structure of the underlying image. In particular, we are able to adapt quite easily to scale-varying and orientation-varying features in the image while simultaneously retaining the edge preservation properties of the regularizer. We demonstrate a half-quadratic algorithm for obtaining the restorations from observed data.

Major histocompatibility complex variation in the endangered Przewalski's horse.

The major histocompatibility complex (MHC) is a fundamental part of the vertebrate immune system, and the high variability in many MHC genes is thought to play an essential role in recognition of parasites. The Przewalski's horse is extinct in the wild and all the living individuals descend from 13 founders, most of whom were captured around the turn of the century. One of the primary genetic concerns in endangered species is whether they have ample adaptive variation to respond to novel selective factors. In examining 14 Przewalski's horses that are broadly representative of the living animals, we found six different class II DRB major histocompatibility sequences. The sequences showed extensive nonsynonymous variation, concentrated in the putative antigen-binding sites, and little synonymous variation. Individuals had from two to four sequences as determined by single-stranded conformation polymorphism (SSCP) analysis. On the basis of the SSCP data, phylogenetic analysis of the nucleotide sequences, and segregation in a family group, we conclude that four of these sequences are from one gene (although one sequence codes for a nonfunctional allele because it contains a stop codon) and two other sequences are from another gene. The position of the stop codon is at the same amino-acid position as in a closely related sequence from the domestic horse. Because other organisms have extensive variation at homologous loci, the Przewalski's horse may have quite low variation in this important adaptive region.

Evidence for a rare prostate cancer-susceptibility locus at chromosome 1p36.

Combining data from a genomic screen in 70 families with a high risk for prostate cancer (PC) with data from candidate-region mapping in these families and an additional 71 families, we have localized a potential hereditary PC-susceptibility locus to chromosome 1p36. Because an excess of cases of primary brain cancer (BC) have been observed in some studies of families with a high risk for PC, and because loss of heterozygosity at 1p36 is frequently observed in BC, we further evaluated 12 families with both a history of PC and a blood relative with primary BC. The overall LOD score in these 12 families was 3.22 at a recombination fraction (theta) of .06, with marker D1S507. On the basis of an a priori hypothesis, this group was stratified by age at diagnosis of PC. In the younger age group (mean age at diagnosis <66 years), a maximum two-point LOD score of 3.65 at straight theta = .0 was observed, with D1S407. This linkage was rejected in both early- and late-onset families without a history of BC (LOD scores -7.12 and -6.03, respectively, at straight theta = .0). After exclusion of 3 of the 12 families that had better evidence of linkage to previously described PC-susceptibility loci, linkage to the 1p36 region was suggested by a two-point LOD score of 4.74 at straight theta = .0, with marker D1S407. We conclude that a significant proportion of these families with both a high risk for PC and a family member with BC show linkage to the 1p36 region.

Effect of supplementing a fibre basal diet with different nitrogen forms on ruminal fermentation and microbial growth in an in vitro semi-continuous culture system (RUSITEC)

Incubation trials were carried out with the rumen simulation technique (RUSITEC) to study the effects of four forms of N on the growth of ruminal micro-organisms and the fermentation variables when an all-fibre basal diet was incubated. The basal diet consisted of 10 g neutral-detergent fibre (NDF) from grass hay plus 2 g NDF from sugarbeet pulp. N forms were isolated soyabean protein, soyabean peptides, amino acids blended to profile soyabean protein and NH3 as NH4Cl. Half of the daily N supply was infused as NH4Cl and the other half was infused as each of the four treatments described. Non-NH3 N (NAN) forms increased NDF (P = 0.006), acid-detergent fibre (P = 0.003) and cellulose (P = 0.015) disappearance after 48 h incubation, CO2 (P < 0.001), CH4 (P = 0.002) and total volatile fatty acids production (P < 0.001), as well as the molar percentages of isobutyrate, isovalerate and valerate, which reflected the fermentation of amino acid C skeletons. NAN treatments also increased microbial N flow (P < 0.001) compared with NH3, with peptides and protein supporting more (P = 0.036) than amino acids. The proportion of microbial N derived from NH3 decreased successively (P < 0.05) with NH3 > amino acids > peptides > protein treatments, indicating preferential uptake of peptides without passage through the NH3 pool. Microbial efficiency (g microbial N/kg organic matter apparent disappearance) was greater (P = 0.002) for the NAN forms than for the NH3 treatment, with peptides and protein treatments supporting higher (P = 0.009) values than amino acid treatment. These results indicate that N forms other than NH3 are required for optimal fibre digestion and microbial growth.

Statistically based methods for anomaly characterization in images from observations of scattered radiation.

In this paper, we present an algorithm for the detection, localization, and characterization of anomalous structures in an overall region of interest given observations of scattered electromagnetic fields obtained along the boundary of the region. Such anomaly detection problems are encountered in applications including medical imaging, radar signal processing, and geophysical exploration. The techniques developed in this work are based on a nonlinear scattering model relating the anomalous structures to the observed data. A sequence of M-ary hypothesis tests are employed first to localize anomalous behavior to large areas and then to refine these initial estimates to better characterize the true target structures. We introduce a method for the incorporation of prior information into the processing which reflects constraints relevant directly to the anomaly detection problem such as the number, shapes, and sizes of anomalies present in the region. The algorithm is demonstrated using a low-frequency, inverse conductivity problem found in geophysical applications.

Outcomes of treatment of socially rehabilitated methadone maintenance patients in physicians' offices (medical maintenance): follow-up at three and a half to nine and a fourth years.

OBJECTIVE: To determine whether selected socially rehabilitated former heroin addicts maintained on methadone can continue successful rehabilitation while maintained on methadone by primary care physicians rather than licensed clinics. This procedure has been termed "medical maintenance." DESIGN: Cohort study with 42-111 months of follow-up. SETTING: Offices of hospital staff physicians (internists or family practitioners). PATIENTS: The 100 patients met extensive entry criteria, including five or more years in conventional methadone maintenance treatment; stable employment or other productive activity; verifiable financial support; and no criminal involvement, use of illegal drugs, or excessive alcohol use within three or more years. MEASUREMENTS AND MAIN RESULTS: Outcome measures used were retention in treatment, discharge for one of several reasons, lost medication incidents, and substance abuse. At one, two, and three years of treatment, 98, 95, and 85 patients, respectively, remained in medical maintenance. Cumulative proportional survival in treatment was 0.735 +/- 0.048 at five years and 0.562 +/- 0.084 at nine years. After 42-111 months, 72 patients remained in good standing; 15 patients had unfavorable discharges (11 for cocaine use, three for misuse of medication, and one for administrative violations); seven voluntarily withdrew from methadone in good standing (after receiving it for 9.1-24.4 years); four died; one transferred to a chronic care facility; and one voluntarily left the program. CONCLUSIONS: Carefully selected methadone maintenance patients in medical maintenance have a high retention rate and a low incidence of substance abuse and lost medication. Voluntary withdrawal from methadone maintenance after one or two decades is possible. The authors believe that medical maintenance should be made available to appropriate patients in other localities.

Nonphysician placement of arterial catheters. Experience with 500 insertions.

To improve availability of arterial line placement, we developed a nonphysician protocol for respiratory therapists to insert arterial catheters. In our experience with more than 500 catheter insertions, in which placement lasted from 1 to 20 days, superficial infection occurred in 5 percent of patients and a major complication occurred in only 1 patient. These results show that specially trained nonphysician personnel can insert arterial catheters safely when following a protocol. Similar reallocation of existing resources should increase patient care while decreasing patient care cost in most settings.

Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura.

The alcohol dehydrogenase (Adh) region of Drosophila pseudoobscura, which includes the two genes Adh and Adh-Dup, was used to examine the pattern and organization of linkage disequilibrium among pairs of segregating nucleotide sites. A collection of 99 strains from the geographic range of D. pseudoobscura were nucleotide-sequenced with polymerase chain reaction-mediated techniques. All pairs of the 359 polymorphic sites in the 3.5-kb Adh region were tested for significant linkage disequilibrium with Fisher's exact test. Of the 74,278 pairwise comparisons of segregating sites, 127 were in significant linkage disequilibrium at the 5% level. The distribution of five linkage disequilibrium estimators D(ij), D2, r(ij), r2 and D(ij) were compared to theoretical distributions. The observed distributions of D(ij), D2, r(ij) and r2 were consistent with the theoretical distribution given an infinite sites model. The observed distribution of D(ij) differed from the theoretical distribution because of an excess of values at -1 and 1. No spatial pattern was observed in the linkage disequilibrium pattern in the Adh region except for two clusters of sites nonrandomly associated in the adult intron and intron 2 of Adh. The magnitude of linkage disequilibrium decreases significantly as nucleotide distance increases, or a distance effect. Adh-Dup had a larger estimate of the recombination parameter, 4Nc, than Adh, where N is the effective population size and c is the recombination rate. A comparison of the mutation and recombination parameters shows that 7-17 recombination events occur for each mutation event. The heterogeneous estimates of the recombination parameter and the inverse relationship between linkage disequilibrium and nucleotide distance are no longer significant when the two clusters of Adh intron sites are excluded from analyses. The most likely explanation for the two clusters of linkage disequilibria is epistatic selection between sites in the cluster to maintain pre-mRNA secondary structure.

Estimates of gene flow in Drosophila pseudoobscura determined from nucleotide sequence analysis of the alcohol dehydrogenase region.

The genetic structure of Drosophila pseudoobscura populations was inferred from a nucleotide sequence analysis of a 3.4-kb segment of the alcohol dehydrogenase (Adh) region. A total of 99 isochromosomal strains collected from 13 populations in North and South America were used to determine if any population departed from a neutral model and to estimate levels of gene flow between populations. This study also included the nucleotide sequences from two sibling species, D. persimilis and D. miranda. We estimated the neutral mutation parameter, 4N mu, in synonymous and noncoding sites for 17 subregions of Adh in each of nine populations with sample sizes greater than three. The nucleotide diversity data in the nine populations was tested for departures from an equilibrium neutral model with two statistical tests. The Tajima and the Hudson, Kreitman, Aguade tests showed that each population fails to reject a neutral model. Tests for genetic differentiation between populations fail to show any population substructure among the North American populations of D. pseudoobscura. The nucleotide diversity data is consistent with direct and indirect measures of gene flow that show extensive dispersal between populations of D. pseudoobscura.

Molecular population genetics of an electrophoretically monomorphic protein in the alcohol dehydrogenase region of Drosophila pseudoobscura.

Nucleotide sequence data from the alcohol dehydrogenase (Adh) region of 18 isochromosomal strains of Drosophila pseudoobscura were used to determine whether the lack of amino acid polymorphism in ADH results from a low neutral mutation rate or a recent directional selection event. We estimated the neutral mutation parameter, 4Nmu, in synonymous sites for 17 subregions of Adh. The nucleotide diversity data were tested for departures from an equilibrium neutral model with two statistical tests. The Tajima test and the Hudson, Kreitman and Aguade test each failed to reject a neutral model. These results suggest that the ADH enzyme of D. pseudoobscura lacks amino acid polymorphisms because the neutral mutation rate of nonsynonymous sites is low. The neutral mutation parameter for synonymous sites is heterogeneous between domains of the Adh region. These data indicate that selective constrains on synonymous sites can vary between functional domains.

Nucleotide sequence analysis of Adh genes estimates the time of geographic isolation of the Bogota population of Drosophila pseudoobscura.

The population of Drosophila pseudoobscura at Bogota, Columbia, is geographically and partially reproductively isolated from populations in the main body of the species in North America. The degree of genetic differentiation and time of divergence between populations at Bogota and Apple Hill, CA, were estimated by comparison of 3388 nucleotides in the alcohol dehydrogenase region (Adh and Adh-Dup genes) of 18 strains. Of the 146 polymorphic nucleotide sites detected, 68 and 31 were unique to the Apple Hill and Bogota samples, respectively, and 53 were shared. On the basis of an observed net divergence per nucleotide site of 0.264% between the two samples, the Bogota and North American populations were estimated to have been separated for at least 155,000 years. This divergence time suggests that D. pseudoobscura extended its range from North America to South America in a period of Pleistocene glaciation, when habitat suitable for the species presumably existed in lowland Central America.