Biomedical subjects

Annamaria Ricciardi

Publications and source records attributed to Annamaria Ricciardi.

6 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↗

PubMed2006

Enzymatic activities of lactic acid bacteria isolated from Cornetto di Matera sourdoughs.

Forty-one strains of lactic acid bacteria (LAB) isolated from Cornetto di Matera sourdoughs were screened for their enzymatic activities, to elucidate their possible roles during the fermentation process. Urease, peptidase, phytase, phosphatase and beta-glucosidase activities were measured spectrophotometrically using synthetic substrates. Proteolytic activities were examined in model doughs, using neutral and acidified sterile doughs as controls. All strains had low urease, glutamyl aminopeptidase and iminopeptidase activities, whereas differences within species were observed for the other enzymatic activities. Leuconostoc mesenteroides and Lactobacillus curvatus strains generally showed high aminopeptidase, X-prolyl dipeptidyl aminopeptidase, beta-glucosidase and phytase activities, while the enzymatic activities of Lactobacillus plantarum, Lactobacillus pentosus and Weissella cibaria varied between strains. In order to classify the strains on the basis of similar enzymatic profiles, a hierarchical cluster analysis was carried out. Several strains of L. plantarum, L. curvatus and Leuc. mesenteroides showed an interesting combination of proteolytic, peptidase, beta-glucosidase and phytase activities, suggesting their possible usefulness as a mixed starter culture in bread-making processes.

6-Phytase↗

PubMed2006

Proteolysis in model sourdough fermentations.

Model wheat doughs started with six different lactic acid bacteria (LAB), with or without a commercial baker's yeast culture, were used to study proteolysis in sourdough fermentations. Cell counts, pH, and free amino acid concentration were measured. Sequential extraction of dough samples was performed to separate wheat proteins. The salt-soluble protein fraction (albumins and globulins) was analyzed by RP-HPLC and SDS-PAGE, whereas propanol-soluble (gliadins) and insoluble (glutenins) protein fractions were analyzed by SDS-PAGE only. Multivariate statistical methods were used for the analysis of results. The presence of yeasts and LAB affected RP-HPLC and SDS-PAGE patterns of the salt-soluble fraction in a complex way. The only changes in the gluten proteins that could be related to the presence of LAB were the appearance of new protein fragments (20 and 27 kDa) from gliadins and the degradation of high molecular weight glutenin subunits.

Analysis of Variance↗

PubMed2005

Phenotypic characterization of lactic acid bacteria from sourdoughs for Altamura bread produced in Apulia (Southern Italy).

In order to study the composition of the lactic acid bacteria (LAB) community of sourdoughs used for the manufacture of Altamura bread, a traditional durum wheat bread produced in Apulia (Southern Italy), 111 strains of LAB were isolated and characterized. The phenotypic characterization of the isolates, carried out using a set of 29 tests, allowed the identification of 15 clusters at the 80% similarity level by hierarchical cluster analysis. Of the isolates, 88% were identified as facultatively heterofermentative LAB (Lactobacillus plantarum, Lb. paracasei, Lb. casei) and 12% as heterofermentative LAB (Lb. brevis, Leuconostoc mesenteroides). SDS-PAGE profiles of whole cell proteins of 68 strains confirmed the identification. Both the diversity and structure of the lactic microflora for sourdoughs for Altamura bread varied among samples.

Bread↗

PubMed2004

Generation of cytomegalovirus (CMV)-specific CD4 T cell lines devoid of alloreactivity, by use of a mixture of CMV-phosphoprotein 65 peptides for reconstitution of the T helper repertoire.

BACKGROUND: CD8 cells specific for cytomegalovirus (CMV) provide valuable support in immunocompromised patients. Recent studies have focused on the generation of cytotoxic T lymphocyte (CTL) lines by use of new biotechnological techniques. Yet CD4 cells have been neglected, even though they contribute to the persistence of adoptively transferred CTLs. METHODS: We identified novel T helper (Th) peptides recognized by CD4 cells on the immunodominant protein pp65. These peptides were used as a mixture to generate CD4 cell lines. RESULTS: The peptide library, which, theoretically, is recognized by 85% of white individuals on the basis of the frequency of the relevant human leukocyte antigen class II alleles, was stimulatory for 82% of pp65 responders. T cell lines generated by use of the pool recognized protein antigens. Selection for CMV-specific cells resulted in rapid depletion of allospecific T cells. Selection with individual peptides allowed further selection against potential cross-alloreactivity. Cultured CD4 cells showed no signs of functional senescence. CD4 cells activated by use of a Th peptide helped expand CMV-specific CTLs. CONCLUSIONS: By use of a simple procedure, an immunodominant peptide library can generate T cell lines from allodonors, for the perspective reconstitution of the Th repertoire in immunocompromised hemopoietic stem-cell transplant recipients.

Adoptive Transfer↗

PubMed2002

A statistical procedure for the analysis of microbial communities based on phenotypic properties of isolates.

A novel statistical procedure for the analysis of microbial communities based on phenotypic properties of randomly collected isolates is presented and discussed. The procedure allows the representation of the microbial communities as a set of ellipses in a bidimensional graph. This representation is obtained by the following steps: (a) measurement of a set of binary phenotypic properties for n isolates belonging to k samples, each representing a different community; (b) repeated sampling by bootstrapping of the m samples, thus obtaining, for each community, i subsamples of j isolates; (c) calculation of the frequency of positive results for each test for each subsample; (d) calculation of the matrix of Euclidean distances between the k x i frequency vectors; (e) use of multidimensional scaling (MDS) to obtain a representation in two dimensions of the distance relationships between the frequency vectors; (f) plotting of the 95% confidence ellipses for the i frequency vectors of each of the k communities. By using both simple, synthetic microbial communities, and samples of lactic acid bacteria isolated from natural microbial communities (sourdoughs, compressed yeast, fermented sausages), it was demonstrated that the position and shape of the ellipses are clearly related to the composition of the community, while the relationship between the size of the ellipses and the phenotypical diversity of the community is less straightforward: while communities with very different diversity (measured with the Functional Evenness index and the mean taxonomic distance) had ellipses that were very different in size, there was no strict proportionality between the size of the ellipse and the diversity of the community. Nevertheless, the representation of microbial communities obtained by bootstrapping and multidimensional scaling appears to be superior to the more usual representation based on tabulation of the frequencies of isolates belonging to different clusters.

Animals↗