Biomedical subjects

Barbara Biasotti

Publications and source records attributed to Barbara Biasotti.

4 recordsLinked to original sources

PubMed2007

Normalization of low-density microarray using external spike-in controls: analysis of macrophage cell lines expression profile.

BACKGROUND: The normalization of DNA microarrays allows comparison among samples by adjusting for individual hybridization intensities. The approaches most commonly used are global normalization methods that are based on the expression of all genes on the slide and on the modulation of a small proportion of genes. Alternative approaches must be developed for microarrays where the proportion of modulated genes and their distribution are unknown and they may be biased towards up- or down-modulated trends. RESULTS: The aim of the work is to study the use of spike-in controls to normalize low-density microarrays. Our test-array was designed to analyze gene modulation in response to hypoxia (a condition of low oxygen tension) in a macrophage cell line. RNA was extracted from controls and cells exposed to hypoxia, mixed with spike RNA, labeled and hybridized to our test-array. We used eight bacterial RNAs as source of spikes. The test-array contained the oligonucleotides specific for 178 mouse genes and those specific for the eight spikes. We assessed the quality of the spike signals, the reproducibility of the results and, in general, the nature of the variability. The small values of the coefficients of variation revealed high reproducibility of our platform either in replicated spots or in technical replicates. We demonstrated that the spike-in system was suitable for normalizing our platform and determining the threshold for discriminating the hypoxia modulated genes. We assessed the application of the spike-in normalization method to microarrays in which the distribution of the expression values was symmetric or asymmetric. We found that this system is accurate, reproducible and comparable to other normalization methods when the distribution of the expression values is symmetric. In contrast, we found that the use of the spike-in normalization method is superior and necessary when the distribution of the gene expression is asymmetric and biased towards up-regulated genes. CONCLUSION: We demonstrate that spike-in controls based normalization is a reliable and reproducible method that has the major advantage to be applicable also to biased platform where the distribution of the up- and down-regulated genes is asymmetric as it may occur in diagnostic chips.

Action Potentials↗

PubMed2004

Chlorination by-products (CBPs) in drinking water and adverse pregnancy outcomes in Italy.

Chlorination by-products (CBPs) in drinking water have been associated with an increased risk of adverse pregnancy outcomes, including small for gestational age at term (term-SGA) and preterm delivery. Epidemiological evidence is weakened by a generally inaccurate exposure assessment, often at an ecological level. A case control study with incident cases was performed in nine Italian towns between October 1999 and September 2000. A total of 1,194 subjects were enrolled: 343 preterm births (26th-37th not completed week of pregnancy), 239 term-SGA (from 37th completed week, and weight less than the lowest 10th percentile) and 612 controls. Exposure was assessed both by applying a questionnaire on mothers' personal habits during pregnancy and by water sampling directly at mothers' homes. Levels of trihalomethanes (THMs) were low (median: 1.10 microg l(-1)), while chlorite and chlorate concentrations were relatively high (median: 216.5 microg l(-1) for chlorites and 76.5 microg l(-1) for chlorates). Preterm birth showed no association with CBPs, while term-SGA, when chlorite levels > or =200 microg l(-1) combined with low and high levels of inhalation exposure are considered, suggested a dose-response relationship (adjusted-Odds Ratios (ORs): 1.52, 95%CI: 0.91-2.54 and 1.70, 95%CI: 0.97-3.0, respectively). A weak association with high exposure levels of either THMs (> or =30 microg l(-1)), or chlorite or chlorate (> or =200 microg l(-1)) was also found (adjusted-OR: 1.38, 95%CI: 0.92-2.07). Chlorine dioxide treatment is widespread in Italy; therefore, chlorite levels should be regularly and carefully monitored and their potential effects on pregnancy further evaluated and better understood.

Adult↗

PubMed2003

Synthesis of photoactivable inhibitors of osteoclast vacuolar ATPase.

Amides of (2Z,4E)-5-[(5,6-dichloroindol-2-yl)]-2-methoxy-N-[3-[4-[3-(carboxymethoxy)phenyl)] piperazin-1-yl]propyl]-2,4-pentadienamide (1) and of 5-(5,6-dichloro-2-indolyl)-2-methoxy-2,4-pentadienoic acid (2) are strong inhibitors of the vacuolar ATPase located on the plasma membrane of osteoclasts. In order to understand which V-ATPase subunit is involved in the interaction with these novel inhibitors, analogues containing a photoactivable group and an iodine atom were designed. A series of alcohols or amines containing the photoactivable trifluoroaziridinophenyl or benzophenone moiety and an iodine atom were linked to the above acids via an ester or amide group. These compounds could be thereafter used as a radioactive photoprobe to label the protein. Whereas the compounds containing the photoactivable groups maintained good inhibitory activity, the introduction of the bulky iodine atom was generally detrimental, decreasing potency significantly. Better results were obtained by linking 3-(4-aminopiperidinomethyl)-3'-iodobenzophenone to 3-ethoxy-4-(2-(5,6-dichlorobenzimidazolyl))benzoic acid to give the corresponding amide 27, that inhibited vacuolar ATP-ase with a IC(50)=140 nM. The feasibility of introducing a radioactive 125I atom was ascertained by exchanging the iodine with a tributylstannyl group, that was again substituted by iodine.

Amides↗

PubMedDate not supplied

[Laparoscopic versus mini-cholecystectomy: analysis of hospital costs and social costs in a prospective randomized study].

The aim of the study was to calculate the hospital and social costs in relation to efficacy of clinical outcome, hospital stay and time off work in two groups of patients randomly treated with laparoscopic or mini-cholecystectomy. One hundred and eighty-one patients with simple, symptomatic gallstone disease were included in the study; of these, 9 cases were excluded because of conversion to conventional cholecystectomy. Eighty-six cases underwent laparoscopic cholecystectomy and 86 mini-cholecystectomy. Operative time (median time: 35 minutes) and hospital stay (median stay: 3 days) were the same for both surgical procedures. The median time off work was 10 days for laparoscopic cholecystectomy and 20 days for mini-cholecystectomy (P = 0.007). Hospital expenses showed a saving of 820.48 euros for each patient undergoing mini-cholecystectomy. Since laparoscopic cholecystectomy is associated with a shorter period off work, it seems to be cheaper with a daily saving of 164.96 and 146.51 Euros per patient, according to cost/effectiveness and cost/utility analyses, respectively. Consequently, although laparoscopic cholecystectomy shows a better outcome in terms of socioeconomic aspects and patient compliance, in an attempt to rationalize hospital expenditure, we would advocate mini-cholecystectomy for those patients who do not need to return to work early.

Adult↗