Statistical implications of pooling RNA samples for microarray experiments

BACKGROUND: Microarray technology has become a very important tool for studying gene expression profiles under various conditions. Biologists often pool RNA samples extracted from different subjects onto a single microarray chip to help defray the cost of microarray experiments as well as to correct for the technical difficulty in getting sufficient RNA from a single subject. However, the statistical, technical and financial implications of pooling have not been explicitly investigated. RESULTS: Modeling the resulting gene expression from sample pooling as a mixture of individual responses, we derived expressions for the experimental error and provided both upper and lower bounds for its value in terms of the variability among individuals and the number of RNA samples pooled. Using virtual pooling of data from real experiments and computer simulations, we investigated the statistical properties of RNA sample pooling. Our study reveals that pooling biological samples appropriately is statistically valid and efficient for microarray experiments. Furthermore, optimal pooling design(s) can be found to meet statistical requirements while minimizing total cost. CONCLUSIONS: Appropriate RNA pooling can provide equivalent power and improve efficiency and cost-effectiveness for microarray experiments with a modest increase in total number of subjects. Pooling schemes in terms of replicates of subjects and arrays can be compared before experiments are conducted

Effects of Long-Term Pioglitazone Treatment on Peripheral and Central Markers of Aging

BACKGROUND: Thiazolidinediones (TZDs) activate peroxisome proliferator-activated receptor gamma (PPARgamma) and are used clinically to help restore peripheral insulin sensitivity in Type 2 diabetes (T2DM). Interestingly, long-term treatment of mouse models of Alzheimer\u27s disease (AD) with TZDs also has been shown to reduce several well-established brain biomarkers of AD including inflammation, oxidative stress and Abeta accumulation. While TZD\u27s actions in AD models help to elucidate the mechanisms underlying their potentially beneficial effects in AD patients, little is known about the functional consequences of TZDs in animal models of normal aging. Because aging is a common risk factor for both AD and T2DM, we investigated whether the TZD, pioglitazone could alter brain aging under non-pathological conditions. METHODS AND FINDINGS: We used the F344 rat model of aging, and monitored behavioral, electrophysiological, and molecular variables to assess the effects of pioglitazone (PIO-Actos® a TZD) on several peripheral (blood and liver) and central (hippocampal) biomarkers of aging. Starting at 3 months or 17 months of age, male rats were treated for 4-5 months with either a control or a PIO-containing diet (final dose approximately 2.3 mg/kg body weight/day). A significant reduction in the Ca2+-dependent afterhyperpolarization was seen in the aged animals, with no significant change in long-term potentiation maintenance or learning and memory performance. Blood insulin levels were unchanged with age, but significantly reduced by PIO. Finally, a combination of microarray analyses on hippocampal tissue and serum-based multiplex cytokine assays revealed that age-dependent inflammatory increases were not reversed by PIO. CONCLUSIONS: While current research efforts continue to identify the underlying processes responsible for the progressive decline in cognitive function seen during normal aging, available medical treatments are still very limited. Because TZDs have been shown to have benefits in age-related conditions such as T2DM and AD, our study was aimed at elucidating PIO\u27s potentially beneficial actions in normal aging. Using a clinically-relevant dose and delivery method, long-term PIO treatment was able to blunt several indices of aging but apparently affected neither age-related cognitive decline nor peripheral/central age-related increases in inflammatory signaling

permanent pacemakers

Implantation of a permanent pacemaker requires a psychological effort on the patient's part for adaptation in the acute term, and chronically, it restricts activities of the patient and may cause some psychiatric disturbances. To investigate psychiatric morbidity and depressive symptomatology of the patients with permanent pacemakers, 84 pacemaker patients were diagnosed using the DSM-III-R criteria and depressive symptoms were determined by modified Hamilton Depression Rating Scale (mHDRS). Sixteen (19.1%) patients had been given a psychiatric diagnosis. The most frequent diagnoses were adjustment disorder (5.9%) and major depressive episode (4.7%). Nine patients (10.7%) were diagnosed as having clinical depression (mHDRS greater than or equal to 17). The mean score of mHDRS was 7.57 +/- 7.46, and the severity of depression was significantly higher in females. The most frequent symptoms are difficulties in work and activities (53.6%), psychic anxiety (48.8%), loss of energy (42.9%), and hypochondriasis and insomnia (39.3%). Depressed mood, psychic anxiety, loss of energy, loss of interest, insomnia, and hypochondriasis were significantly more frequent in females. Uneducated patients had a more significant loss of energy than educated patients. Depressed mood, psychic anxiety, and somatic concerns and symptoms were more frequent in patients with permanent pacemakers than in the general population. These symptoms, resembling mixed anxiety-depression disorder, were related to fears of having a permanent pacemaker, since our series were composed of uneducated patients who did not have enough knowledge about the device