Normalization for triple-target microarray experiments

<p>Abstract</p> <p>Background</p> <p>Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are <it>Cy</it>3 and <it>Cy</it>5. Recent improvements in the technology (dye-labelling, scanner and, image analysis) allow hybridization up to four samples simultaneously. The two additional dyes are <it>Alexa</it>488 and <it>Alexa</it>494. The triple-target or four-target technology is very promising, since it allows more flexibility in the design of experiments, an increase in the statistical power when comparing gene expressions induced by different conditions and a scaled down number of slides. However, there have been few methods proposed for statistical analysis of such data. Moreover the lowess correction of the global dye effect is available for only two-color experiments, and even if its application can be derived, it does not allow simultaneous correction of the raw data.</p> <p>Results</p> <p>We propose a two-step normalization procedure for triple-target experiments. First the dye bleeding is evaluated and corrected if necessary. Then the signal in each channel is normalized using a generalized lowess procedure to correct a global dye bias. The normalization procedure is validated using triple-self experiments and by comparing the results of triple-target and two-color experiments. Although the focus is on triple-target microarrays, the proposed method can be used to normalize <it>p </it>differently labelled targets co-hybridized on a same array, for any value of <it>p </it>greater than 2.</p> <p>Conclusion</p> <p>The proposed normalization procedure is effective: the technical biases are reduced, the number of false positives is under control in the analysis of differentially expressed genes, and the triple-target experiments are more powerful than the corresponding two-color experiments. There is room for improving the microarray experiments by simultaneously hybridizing more than two samples.</p

Food allergy enhances allergic asthma in mice

BackgroundAtopic march refers to the typical transition from a food allergy in early childhood to allergic asthma in older children and adults. However the precise interplay of events involving gut, skin and pulmonary inflammation in this process is not completely understood.ObjectivesTo develop a mouse model of mixed food and respiratory allergy mimicking the atopic march and better understand the impact of food allergies on asthma.MethodsFood allergy to ovalbumin (OVA) was induced through intra-peritoneal sensitization and intra-gastric challenge, and/or a respiratory allergy to house dust mite (HDM) was obtained through percutaneous sensitization and intra-nasal challenges with dermatophagoides farinae (Der f) extract. Digestive, respiratory and systemic parameters were analyzed.ResultsOVA-mediated gut allergy was associated with an increase in jejunum permeability, and a worsening of Der f-induced asthma with stronger airway hyperresponsiveness and pulmonary cell infiltration, notably eosinophils. There was overproduction of the pro-eosinophil chemokine RANTES in broncho-alveolar lavages associated with an enhanced Th2 cytokine secretion and increased total and Der f-specific IgE when the two allergies were present. Both AHR and lung inflammation increased after a second pulmonary challenge.ConclusionGut sensitization to OVA amplifies Der f-induced asthma in mice

Determinants of Adherence to Diabetes Medications: Findings From a Large Pharmacy Claims Database

Adults with diabetes typically take multiple medications for hyperglycemia, diabetes-associated conditions, and other comorbidities. Medication adherence is associated with improved outcomes, including reduced health care costs, hospitalization, and mortality. We conducted a retrospective analysis of a large pharmacy claims database to examine patient, medication, and prescriber factors associated with adherence to antidiabetic medications

Statistical methodology for the analysis of dye-switch microarray experiments

<p>Abstract</p> <p>Background</p> <p>In individually dye-balanced microarray designs, each biological sample is hybridized on two different slides, once with <it>Cy3 </it>and once with <it>Cy5</it>. While this strategy ensures an automatic correction of the gene-specific labelling bias, it also induces dependencies between log-ratio measurements that must be taken into account in the statistical analysis.</p> <p>Results</p> <p>We present two original statistical procedures for the statistical analysis of individually balanced designs. These procedures are compared with the usual ML and REML mixed model procedures proposed in most statistical toolboxes, on both simulated and real data.</p> <p>Conclusion</p> <p>The UP procedure we propose as an alternative to usual mixed model procedures is more efficient and significantly faster to compute. This result provides some useful guidelines for the analysis of complex designs.</p

SUR QUELQUES CURIOSITÉS D'HISTOIRE NATURELLE DANS LES PERTUIS CHARENTAIS : FAUNE DES INVERTÉBRÉS MARINS

Eight invertebrate species, rediscovered, demographically expanding or newly observed are reported from the Pertuis Charentais Sea. They were sampled from intertidal rocky shores (Alpheus macrocheles, Aslia lefevrei, Epitonium clathrulatum and Haliotis tuberculata), intertidal sand flats (Africorchestia spinifera and Arcuatula senhousia) and subtidal bottoms (Aslia lefevrei and Rapana venosa). One species is pelagic (Lepas anatifera). Most of them are within their natural range. However, R. venosa, native to Southeast Asia, has been introduced in the Pertuis Charentais since the 2010s and its populations are currently expanding. The new northern limit of Africorchestia spinifera along the Atlantic coast is defined as the Ré Island. Phoresis of Crepidula fornicata on Carcinus maenas is noted but was already described in European waters whereas it is a hitherto undescribed and unexpected association with the gastropod R. venosa.Eight invertebrate species, rediscovered, demographically expanding or newly observed are reported from the Pertuis Charentais Sea. They were sampled from intertidal rocky shores (Alpheus macrocheles, Aslia lefevrei, Epitonium clathrulatum and Haliotis tuberculata), intertidal sand flats (Africorchestia spinifera and Arcuatula senhousia) and subtidal bottoms (Aslia lefevrei and Rapana venosa). One species is pelagic (Lepas anatifera). Most of them are within their natural range. However, R. venosa, native to Southeast Asia, has been introduced in the Pertuis Charentais since the 2010s and its populations are currently expanding. The new northern limit of Africorchestia spinifera along the Atlantic coast is defined as the Ré Island. Phoresis of Crepidula fornicata on Carcinus maenas is noted but was already described in European waters whereas it is a hitherto undescribed and unexpected association with the gastropod R. venosa

Subclinical endometritis in dairy cattle is associated with distinct mRNA expression patterns in blood and endometrium

Cattle with subclinical endometritis (SCE) are sub-fertile and diagnosing subclinical uterine disease remains a challenge. The hypothesis for this study was that endometrial inflammation is reflected in mRNA expression patterns of peripheral blood leucocytes. Transcriptome profiles were evaluated in healthy cows and in cows with SCE using circulating white blood cells (WBC) and endometrial biopsy samples collected from the same animals at 45–55 days postpartum. Bioinformatic analyses of microarray-based transcriptional data identified gene profiles associated with distinct biological functions in circulating WBC and endometrium. In circulating WBC, SCE promotes a pro-inflammatory environment, whereas functions related to tissue remodeling are also affected in the endometrium. Nineteen differentially expressed genes associated with SCE were common to both circulating WBC and the endometrium. Among these genes, transcript abundance of immune factors C3, C2, LTF, PF4 and TRAPPC13 were up-regulated in SCE cows at 45–55 days postpartum. Moreover, mRNA expression of C3, CXCL8, LTF, TLR2 and TRAPPC13 was temporally regulated during the postpartum period in circulating WBC of healthy cows compared with SCE cows. This observation might indicate an advantageous modulation of the immune system in healthy animals. The transcript abundance of these genes represents a potential source of indicators for postpartum uterine health

A Temporal -omic Study of Propionibacterium freudenreichii CIRM-BIA1T Adaptation Strategies in Conditions Mimicking Cheese Ripening in the Cold

Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It grows when cheeses are ripened in a warm room (about 24°C). Cheeses with an acceptable eye formation level are transferred to a cold room (about 4°C), inducing a marked slowdown of propionic fermentation, but P. freudenreichii remains active in the cold. To investigate the P. freudenreichii strategies of adaptation and survival in the cold, we performed the first global gene expression profile for this species. The time-course transcriptomic response of P. freudenreichii CIRM-BIA1T strain was analyzed at five times of incubation, during growth at 30°C then for 9 days at 4°C, under conditions preventing nutrient starvation. Gene expression was also confirmed by RT-qPCR for 28 genes. In addition, proteomic experiments were carried out and the main metabolites were quantified. Microarray analysis revealed that 565 genes (25% of the protein-coding sequences of P. freudenreichii genome) were differentially expressed during transition from 30°C to 4°C (P<0.05 and |fold change|>1). At 4°C, a general slowing down was observed for genes implicated in the cell machinery. On the contrary, P. freudenreichii CIRM-BIA1T strain over-expressed genes involved in lactate, alanine and serine conversion to pyruvate, in gluconeogenesis, and in glycogen synthesis. Interestingly, the expression of different genes involved in the formation of important cheese flavor compounds, remained unchanged at 4°C. This could explain the contribution of P. freudenreichii to cheese ripening even in the cold. In conclusion, P. freudenreichii remains metabolically active at 4°C and induces pathways to maintain its long-term survival