Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples

BACKGROUND: Gene expression microarray technology continues to evolve and its use has expanded into all areas of biology. However, the high dimensionality of the data makes analysis a difficult challenge. Evaluating measurements and estimating the significance of the observed differences among samples remain important issues that must be addressed for each technology platform. In this work we use a consecutive sampling method to characterize the dispersion patterns of data generated from Illumina fiberoptic bead-based oligonucleotide arrays. RESULTS: To describe general properties of the dispersion we used a linear function SD = a + bY(mean), approximating the standard deviation across arrays (Y(mean )is the mean expression of a given consecutive sample). First we examined three levels of variability: 1) same cell culture, same reverse transcription, duplicate hybridizations; 2) same cell culture, reverse transcription replicates; 3) parallel cultures. Each higher level is expected to introduce a new source of variability. We observed minor differences in the constant term: the mean values are 3.5, 3.1 and 3.5, respectively. However, the mean coefficient b increased from 0.045 to 0.147 and 0.133. We compared the coefficients derived from the consecutive sampling to those obtained from the standard deviation of individual gene expressions and found them in good agreement. In the second experiment samples we detected 11 genes with systematically different expressions between the experiment samples treated with glucose oxidase and controls and corroborated the selection using the Mann-Whitney and other tests. We also compared the consecutive sampling and coincidence method to t-test: the average percentage of consistency was above 80 for the former and below 50 for the latter. CONCLUSION: Our results indicate that the consecutive sampling method and standard deviation function provide a convenient description of the overall dispersion of Illumina arrays. We observed that the constant term of the standard deviation function is at average approximately the same for duplicate hybridization as for the assays with additional sources of variability. Furthermore, among the genes affected by glucose oxidase treatment we identified 6 genes in oxidative stress pathways and 5 genes involved in DNA repair. Finally, we noted that the consecutive sampling and coincidence test provide, under given conditions, more consistent results than the t-test. REVIEWERS: This article was reviewed by Alexander Karpikov (nominated by MarkGerstein), Jordan King and Eugene V. Koonin

Antineoplastic and Cytotoxic Activities of Nickel(II) Complexes of Thiosemicarbazones

Nickel(II) complexes of thiosemicarbazons were observed to be potent cytotoxic agents in human and rodent tissue cultured tumor cells. Each compound demonstrated a slightly different profile in the various histological types of tumors. The nickel complex of Appip demonstrated the most potent in vivo activity in the Ehrlich ascites carcinoma. This agent selectively inhibited L1210 DNA and purine syntheses, and DNA polymerase α, PRPP-amido transferase, IMP-dehydrogenase, dihydrofolate reductase, TMP-kinase and thymidylate synthetase activities. L1210 DNA strand scission was evident and DNA viscosity was reduced after 24 hr incubation. The nickel complexes were not L1210 DNA topoisomerase II inhibitors

Physical Activity and Hippocampal Sub-Region Structure in Older Adults with Memory Complaints.

BackgroundPhysical activity (PA) plays a major role in maintaining cognition in older adults. PA has been shown to be correlated with total hippocampal volume, a memory-critical region within the medial temporal lobe (MTL). However, research on associations between PA and MTL sub-region integrity is limited.ObjectiveTo examine the relationship between PA, MTL thickness, and its sub-regions, and cognitive function in non-demented older adults with memory complaints.MethodsTwenty-nine subjects aged ≥60 years, with memory complaints were recruited for this cross-sectional study. PA was tracked for 7 days using accelerometers, and average number of steps/day determined. Subjects were categorized into two groups: those who walked ≤4000 steps/day (lower PA) and those with >4000 steps/day (higher PA). Subjects received neuropsychological testing and 3T MRI scans. Nonparametric ANCOVAs controlling for age examined differences between the two groups.ResultsTwenty-six subjects aged 72.7(8.1) years completed the study. The higher PA group (n = 13) had thicker fusiform gyrus (median difference = 0.11 mm, effect size (ES) = 1.43, p = 0.001) and parahippocampal cortex (median difference = 0.12 mm, ES = 0.93, p = 0.04) compared to the lower PA group. The higher PA group also exhibited superior performance in attention and information-processing speed (median difference = 0.90, ES = 1.61, p = 0.003) and executive functioning (median difference = 0.97, ES = 1.24, p = 0.05). Memory recall was not significantly different between the two groups.ConclusionOlder non-demented individuals complaining of memory loss who walked >4000 steps each day had thicker MTL sub-regions and better cognitive functioning than those who walked ≤4000 steps. Future studies should include longitudinal analyses and explore mechanisms mediating hippocampal related atrophy

The Hypolipidemic and Anti-Inflammatory Activity of Boronated Aromatic Amino Acids in CF1 Male Mice

The boronated aromatic amino acids were shown to be potent hypolipidemic agents in mice lowering both serum cholesterol and triglycerides after 16 days. Selective compounds were as effective as the clinical standards. Furthermore, the compounds were effective anti-inflammatory agents reducing local and central pain as well as suppressing LPS induced endotoxic shock in mice. These agents inhibited lysosomal and proteolytic enzymes of the liver and macrophages as a part of their mechanism of action

Cytotoxic Action of Carboxyborane Heterocyclic Amine Adducts

The heterocyclic carboxyborane amines were found to be potent cytotoxic agents in the murine L1210 lymphoid leukemia and human HeLa suspended carcinoma cells. These agents were observed to inhibit HeLa DNA topoisomerase II activity ~ 200 μM and L1210 topoisomerase II activity ≥ 100 μM. These agents did not cause DNA protein linked breaks themselves, but upon incubation for 14-24 hr did enhance the ability of VP-16 to cause cleavable complexes. The heterocyclic amineboranes inhibited DNA synthesis and caused DNA strand scission. They were additive with VP-16 in affording these results as well as inhibiting colony growth of L1210 cells after co-incubation for 1 hr. The agents inhibited in vitro PKC phosphorylation of both L1210 lymphoid leukemia and human topoisomerase II enzyme

Transepithelial Transport and Metabolism of Boronated Dipeptides Across Caco-2 and HCT-8 Cell Monolayers

Oral delivery of proteins and peptides as therapeutic agents is problematic due to their low bioavailability. This study examined the effect of boronation on the transepithelial transport and metabolism of three glycine-phenylalanine dipeptides in Caco-2 and HCT-8 cell monolayers. The three dipeptides exhibited passive transport characteristics in the monolayer systems. However, metabolism of the boronated dipeptides did occur, but to a lesser extent than the non-boronated glycine-phenylalanine dipeptide. The same metabolic scheme was seen in both cell monolayer system, but greater metabolism was seen in the HCT-8 cell monolayers

Neurology

Contains reports on six research projects.United States Public Health Service (B-3055-4, B-3090-4, MH-06175-02)United States Navy, Office of Naval Research (Contract Nonr-1841(70))United States Air Force (AF49(638)-1313), administered by the Electronic Systems Laboratory, M. I. T

Neurology

Contains reports on eight research projects.U.S. Navy (Office of Naval Research (Nonr-1841(70))U. S. Public Health Service (MH-06175-02)U. S. Air Force (AF49(638)-1313)U. S. Public Health Service (B-3055-4)U. S. Public Health Service (B-3090-4

Neurology

Contains reports on nineteen research projects.United States Public Health Service (B-3055-3, B-3090-3, 38101-22)United States Navy, Office of Naval Research (Contract Nonr-1841(70))Unites States Air Force (AF33(616)-7588, AFAOSR 155-63)United States Army Chemical Corps (DA-18-108-405-Cml-942)National Institutes of Health (Grant MH-04734-03)National Aeronautics and Space Administration (Grant NsG-496

Do brief motivational interventions reduce drinking game frequency in mandated students? An analysis of data from two randomized controlled trials.

PURPOSE: College students frequently engage in drinking games (DG) and experience a variety of consequences as a result. It is currently unknown whether brief motivational interventions (BMI) that provide feedback on DG participation can reduce this high risk behavior. This study examined outcome data from two randomized clinical trials to examine whether BMIs facilitate change in DG frequency and how these changes may occur. METHODS: Mandated college students (Trial 1, N = 198, 46% female; Trial 2, N = 412; 32% female) were randomized to BMI or comparison control conditions. Hierarchical linear modeling (HLM) was used to compare the BMI and comparison groups to determine whether the BMI reduced DG participation over time. Percent change talk (PCT) during the discussion of DG during the session was examined as a predictor of change in DG frequency, and gender was examined as a moderator of treatment effects. RESULTS: Controlling for regular drinking frequency, participants who received a BMI did not significantly reduce their DG frequency relative to the comparison group in either sample, and the BMI was equally ineffective at reducing DG behavior for men and women. DG-related PCT during the BMI was associated with lower DG frequency at the second follow-up in both Trials. In Trial 1, PCT during the BMI was associated with less steep increases in DG frequency across the course of all follow-ups. Effects of PCT on DG behavior were not moderated by gender. CONCLUSIONS: Findings did not support hypothesized reductions in DG participation following a BMI. Future research should explore whether targeted DG-specific interventions could reduce DG participation and the role of in-session client language in facilitating such change