Biomedical subjects

Henrik Andersson

Publications and source records attributed to Henrik Andersson.

5 recordsLinked to original sources

PubMed2006

Evaluation of microarray data normalization procedures using spike-in experiments.

BACKGROUND: Recently, a large number of methods for the analysis of microarray data have been proposed but there are few comparisons of their relative performances. By using so-called spike-in experiments, it is possible to characterize the analyzed data and thereby enable comparisons of different analysis methods. RESULTS: A spike-in experiment using eight in-house produced arrays was used to evaluate established and novel methods for filtration, background adjustment, scanning, channel adjustment, and censoring. The S-plus package EDMA, a stand-alone tool providing characterization of analyzed cDNA-microarray data obtained from spike-in experiments, was developed and used to evaluate 252 normalization methods. For all analyses, the sensitivities at low false positive rates were observed together with estimates of the overall bias and the standard deviation. In general, there was a trade-off between the ability of the analyses to identify differentially expressed genes (i.e. the analyses' sensitivities) and their ability to provide unbiased estimators of the desired ratios. Virtually all analysis underestimated the magnitude of the regulations; often less than 50% of the true regulations were observed. Moreover, the bias depended on the underlying mRNA-concentration; low concentration resulted in high bias. Many of the analyses had relatively low sensitivities, but analyses that used either the constrained model (i.e. a procedure that combines data from several scans) or partial filtration (a novel method for treating data from so-called not-found spots) had with few exceptions high sensitivities. These methods gave considerable higher sensitivities than some commonly used analysis methods. CONCLUSION: The use of spike-in experiments is a powerful approach for evaluating microarray preprocessing procedures. Analyzed data are characterized by properties of the observed log-ratios and the analysis' ability to detect differentially expressed genes. If bias is not a major problem; we recommend the use of either the CM-procedure or partial filtration.

Computational Biology↗

PubMed2006

Transcriptional profiling of host responses in mouse lungs following aerosol infection with type A Francisella tularensis.

Tularaemia caused by inhalation of type A Francisella tularensis bacteria is one of the most aggressive infectious diseases known, but the reasons for the very rapid spread of the organism from the lungs to internal organs and the ensuing mortality are unknown. The present study used the mouse model to examine in detail the host immune response in the lung. After an aerosol challenge with 20 c.f.u. of the type A strain FSC033, all mice developed clinical signs of severe disease, showed weight loss by day 4 of infection and died the next day. Histopathological findings in the lung revealed acute inflammation and intense vasculitis and perivasculitis on day 4. Gene transcriptional changes in the mouse lung samples were examined on days 1, 2 and 4 of infection using a cDNA microarray with 20,600 mouse clones representing 18,500 genes. In total, 424 genes were found to be differentially expressed, some of which were both up- and downregulated at different time points, 192 of which were upregulated and 234 of which were downregulated for at least one time point. A high percentage of selected genes identified by the microarray analysis were confirmed to be differentially regulated by quantitative real-time PCR. Categorization of the differentially expressed genes showed that those preferentially involved in host immune responses were activated extensively on day 4 but hardly or not at all on days 1 and 2. Further analysis revealed that several of the genes upregulated on day 4 are known to depend on gamma interferon or tumour necrosis factor alpha for their regulation. In keeping with this finding, tumour necrosis factor alpha and gamma interferon levels were found to be increased significantly in bronchoalveolar lavage on day 4.

Aerosols↗

PubMed2006

A microarray analysis of the murine macrophage response to infection with Francisella tularensis LVS.

The response of cells of the mouse macrophage cell line J774 to infection with Francisella tularensis LVS was analysed by means of a DNA microarray representing approximately 18,500 genes (20,600 clones). The adaptive response was modest at all time points, and at most, 81 clones were differentially regulated from the time point of uptake of bacteria (0 min) up to 240 min later. For all five time points, 229 clones fulfilled the criteria of being differentially regulated, i.e. the ratio between infected versus non-infected cells was at least 1.7-fold up- or down-regulated and P <0.05. It was found that many of the differentially regulated genes are known to respond to stress in general and to oxidative stress specifically. However, at 120 min it was observed that genes that lead to depletion of glutathione were upregulated. Possibly, this was a result of mechanisms induced by F. tularensis. Generally, there was a conspicuous lack of inflammatory responses and, for example, although tumour necrosis factor alpha (TNF-alpha) was upregulated at 0 min, a significant down-regulation was noted at all subsequent time points. When cells were treated with an inhibitor of inducible nitric oxide synthase (iNOS) or the antioxidant N-acetylcysteine (NAC), the infection-induced cytopathogenic effect was significantly inhibited. Together, the results suggest that F. tularensis LVS infection confers an oxidative stress upon the target cells and that many of the host-defence mechanisms appear to be intended to counteract this stress. The infection is characterized by a very modest inflammatory response.

Acetylcysteine↗

PubMed2002

Effects of high-resistant-starch banana flour (RS(2)) on in vitro fermentation and the small-bowel excretion of energy, nutrients, and sterols: an ileostomy study.

BACKGROUND: Resistant starch (RS) has attracted interest because of its effects in the colon and implications for health. Knowledge of how RS influences small-intestinal absorption of nutrients, sterol metabolism, and colonic fermentation is sparse. OBJECTIVES: The objectives of this study were to measure the effect of RS(2), a type of RS in banana flour, on the ileal excretion of energy, nutrients, and sterols, and to compare in vivo measurement of RS in the ileostomy model with previously published intubation data. In addition, we sought to estimate a fermentation pattern by using ileal effluents for in vitro fermentation. DESIGN: The present study was divided into 2 parts. Study A involved 10 ileostomy subjects who were given a controlled diet with the addition of 30 g raw green banana flour (RBF)/d, which contains RS(2), or cooked green banana flour (CBF)/d in random order. Study B involved 7 ileostomy subjects who were given a plant-polysaccharide-free diet with the addition of 30 g RBF/d. RESULTS: In study A, the dry weight of the ileostomy effluents and the ileal excretion of energy, iron, and chenodeoxycholic acid, but not total sterols, were higher after the addition of RBF than of CBF to the diet. In vitro fermentation of the ileal effluents obtained after the addition of RBF to the diet showed higher concentrations of acetate and butyrate. In study B, the ileal excretion of starch was lower than the amount calculated from earlier studies by use of the intubation technique. CONCLUSIONS: The addition of RBF containing RS(2) to the diet of ileostomy subjects did not interfere with small-bowel absorption of nutrients or total sterols, except for a small increase in iron excretion. The ileostomy model seems to give reliable results for in vivo measurement of RS.

Adult↗

PubMed2002

Oat bran stimulates bile acid synthesis within 8 h as measured by 7alpha-hydroxy-4-cholesten-3-one.

BACKGROUND: Oat bran contains soluble fibers, such as beta-glucan, that increase bile acid excretion and thus decrease serum cholesterol. Bile acid synthesis correlates with serum concentrations of the metabolite 7alpha-hydroxy-4-cholesten-3-one (alpha-HC). OBJECTIVE: The objective was to investigate whether consumption of beta-glucan from oat bran increases bile acid synthesis, as measured by the serum alpha-HC concentration, within hours after consumption in response to the loss of bile acids from the liver. DESIGN: In a randomized, single-blind, wheat bran-controlled study with crossover design, 8 subjects were served a controlled diet during 2 periods of 3 d each, with an 11-d washout between the periods. Breakfast included either 75 g extruded oat bran, of which 11 g was beta-glucan, or 75 g wheat bran, of which 1 g was beta-glucan. Alpha-HC was measured by HPLC on each day at 0, 12, and 24 h after breakfast and also at 8 h after breakfast on the first day. RESULTS: After 8 and 12 h of the oat bran diet period, the serum alpha-HC concentration was 84% (P = 0.012) and 92% (P = 0.017) higher, respectively, than that before breakfast. Serum concentrations returned to the baseline value after 24 h. Wheat bran did not influence serum alpha-HC concentrations. CONCLUSIONS: Consumption of beta-glucan from oat bran nearly doubled the serum alpha-HC concentration within 8 h, indicating increased bile acid synthesis. alpha-HC in serum could be used as a marker of increased bile acid excretion induced by the diet.

Adult↗