Assessing differential gene expression with small sample sizes in oligonucleotide arrays using a mean-variance model

The identification of the genes that are differentially expressed in two-sample microarray experiments remains a difficult problem when the number of arrays is very small. We discuss the implications of using ordinary t-statistics and examine other commonly used variants. For oligonucleotide arrays with multiple probes per gene, we introduce a simple model relating the mean and variance of expression, possibly with gene-specific random effects. Parameter estimates from the model have natural shrinkage properties that guard against inappropriately small variance estimates, and the model is used to obtain a differential expression statistic. A limiting value to the positive false discovery rate (pFDR) for ordinary t-tests provides motivation for our use of the data structure to improve variance estimates. Our approach performs well compared to other proposed approaches in terms of the false discovery rate.     

Hydroxylated analogues of the orally active broad spectrum antifungal, Sch 51048 (1), and the discovery of posaconazole [Sch 56592; 2 or (S,S)-5

As part of a detailed study, the syntheses, biological activities, and pharmacokinetic properties of hydroxylated analogues of the previously described broad spectrum antifungal agents, Sch 51048 (1), Sch 50001 (3), and Sch 50002 (4), are described. Based on an overall superior profile, one of the alcohols, Sch 56592 (2), was selected for clinical studies.     

Mass-spectrometric characterization of cisplatin binding sites on native and denatured ubiquitin

Because interactions between cisplatin and plasma proteins contribute to drug efficacy and side effects, it is important to understand both the binding sites of cisplatin on the proteins and the formation of protein–cisplatin adducts. Previous results suggest that cisplatin preferentially binds to residues on the protein surface. The present work employed electrospray ionization mass spectrometry (MS) to identify such sites on both native and denatured ubiquitin (Ub). Fourier transform (FT) MS and tandem MS (MS/MS and MS³) enable analysis of Ub–cisplatin adduct digests to locate specific cisplatin binding sites. Results indicate that there are three such binding sites, i.e., M1, T12 and T14, and D32, on native Ub. The intensity of the relevant peaks in the FT-MS spectrum of the native Ub adduct digest demonstrates that residues T12 and T14 comprise the primary cisplatin binding site under the native conditions rather than residue M1 as reported in previous research studies. It is found in the present work, however, that M1 is the primary binding site on denatured Ub. Comparison of cisplatin binding sites on native and denatured Ub in this research demonstrates that the conformation of a protein significantly influences the preference of cisplatin for specific binding sites.     

Affinity labeling of spinach phosphoribulokinase subsequent toS-methylation at Cys16

The chloroplast enzyme phosphoribulokinase is reversibly deactivated by oxidation of Cys16 and Cys55 to a disulfide. Although not required for catalysis, Cys16 is an active-site residue positioned at the nucleotide-binding domain (Porter and Hartman, 1988). The hyperreactivity of Cys16 has heretofore limited further active-site characterization by chemical modification. To overcome this limitation, the partially active enzyme,S-methylated at Cys16, has been probed with a potential affinity reagent. Treatment of methylated enzyme with bromoacetylethanolamine phosphate results in essentially complete loss of catalytic activity. Inactivation follows pseudo-first-order kinetics and exhibits a rate saturation with an apparentK _d of 3–4 mM. ATP, but not ribulose 5-phosphate, affords substantial protection. Complete inactivation correlates with incorporation of 1 mol of [¹⁴C]reagent per mole of enzyme subunit. Amino acid analysis of the [¹⁴C]-labeled enzyme demonstrates that only cysteine is modified, and mapping of tryptic digests shows that Cys55 is a major site of alkylation. These results indicate that Cys55 is also located in the ATP-binding domain of the active-site.     

Chemosensory stimulation of luteinizing hormone secretion in male Siberian hamsters (Phodopus sungorus)

Male Siberian hamsters (Phodopus sungorus) housed in long days (LD), but not short days (SD) release luteinizing hormone (LH) when exposed to females. This study examined whether this response is specific to a female and identifies the source of a stimulus that induces LH release. Serum concentrations of LH, testosterone (T), follicle stimulating hormone (FSH), and cortisol were examined in all experiments. T concentrations mirrored the LH response; FSH and cortisol were unchanged in response to all stimuli. Exposure to an LD female, irrespective of her reproductive status, but not an SD female, elicited LH release. Exposure to another male did not trigger LH release. Males released LH when allowed physical contact with an anesthetized female, but not when separated from a normally active female, suggesting that tactile or nonvolatile chemosensory stimuli elicit LH release. Urine and secretions collected from the vagina as well as oral, midventral, perineal, and rectal glands, elicited marked behavioral responses in male P. sungorus. Despite these behavioral responses, only feces from females elicited LH release in males. Males released LH in response to feces extracted from the rectum and to cotton swabs that had been rubbed against the rectal mucosa, suggesting that a component of rectal secretions may trigger LH release in male Siberian hamsters. Taken together, these data and previous data from our laboratory indicate that both the production of and the response to a pheromone that triggers the selective release of LH is regulated by day length.     

Molecular epidemiology and novel combinations of auxotype, serovar, and plasmid content in tetracycline-resistant Neisseria gonorrhoeae isolated in Canada

Between October 1987 and June 1989, 84 isolates of Neisseria gonorrhoeae carrying the TetM resistance determinant (TRNG) were received at the Laboratory Centre for Disease Control, Ottawa, from six Canadian provinces and were characterized into classes based on auxotype, serovar and plasmid content. One-fifth (17/84) of the TRNG were also penicillinase producing (PPNG). The PPNG-TRNG isolates comprised six classes based on auxotype, serovar, and plasmid content. Most (16/17) PPNG-TRNG carried 3.2-MDa beta-lactamase plasmids and the 25.2-MDa TetM-containing plasmid. We report, for the first time, the association of a 4.5-MDa beta-lactamase plasmid with the 25.2-MDa plasmid in a clinical TRNG isolate. Non-PPNG TRNG isolates comprised 11 classes based on auxotype, serovar, and plasmid content, including two previously unreported auxotype-serovar classes, P/IB-26 and P/IB-20.     

The composition and function of all‐male herds of Thornicroft's giraffe,Giraffa camelopardalis thornicrofti,in Zambia

Temporary all‐male social groups are formed in a number of animal species. We examined 34 years of data collected from 36 male Thornicroft's giraffe in the Luangwa Valley, Zambia, to test a set of predictions related to five possible functions of all‐male herds (predator protection, practicing aggressive skills, prolonging life, nutritional demands and resource learning). We found that all‐male herds were significantly smaller than mixed‐sex herds, usually contained a mature bull, and were not dependent upon season or habitat. Dyadic associations between males in single sex herds were quite weak, with <25% of potential male dyads sighted together in an all‐male herd. Our data are best explained as a resource learning strategy adopted by males to obtain more extensive knowledge about the habitat, including both food and female distribution. However, other benefits in the form of predator protection, dietary intake and sharpening competitive skills for future contests over estrous females also seem to mediate formation of giraffe all‐male groups. We conclude that the primary advantage of roaming in all‐male herds changes during the life history of males.     

Saccharomyces cerevisiae: Population Divergence and Resistance to Oxidative Stress in Clinical,Domesticated and Wild Isolates

Background

Saccharomyces cerevisiae has been associated with human life for millennia in the brewery and bakery. Recently it has been recognized as an emerging opportunistic pathogen. To study the evolutionary history of S. cerevisiae, the origin of clinical isolates and the importance of a virulence-associated trait, population genetics and phenotypic assays have been applied to an ecologically diverse set of 103 strains isolated from clinics, breweries, vineyards, fruits, soil, commercial supplements and insect guts.

Methodology/Principal Findings

DNA sequence data from five nuclear DNA loci were analyzed for population structure and haplotype distribution. Additionally, all strains were tested for survival of oxidative stress, a trait associated with microbial pathogenicity. DNA sequence analyses identified three genetic subgroups within the recombining S. cerevisiae strains that are associated with ecology, geography and virulence. Shared alleles suggest that the clinical isolates contain genetic contribution from the fruit isolates. Clinical and fruit isolates exhibit high levels of recombination, unlike the genetically homogenous soil isolates in which no recombination was detected. However, clinical and soil isolates were more resistant to oxidative stress than any other population, suggesting a correlation between survival in oxidative stress and yeast pathogenicity.

Conclusions/Significance

Population genetic analyses of S. cerevisiae delineated three distinct groups, comprising primarily the (i) human-associated brewery and vineyard strains, (ii) clinical and fruit isolates (iii) and wild soil isolates from eastern U.S. The interactions between S. cerevisiae and humans potentiate yeast evolution and the development of genetically, ecologically and geographically divergent groups.