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Alessandra Riva

Publications and source records attributed to Alessandra Riva.

12 recordsLinked to original sources
PubMed2024

Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease.

Exclusive enteral nutrition (EEN) is a first-line therapy for pediatric Crohn's disease (CD), but protective mechanisms remain unknown. We established a prospective pediatric cohort to characterize the function of fecal microbiota and metabolite changes of treatment-naive CD patients in response to EEN (German Clinical Trials DRKS00013306). Integrated multi-omics analysis identified network clusters from individually variable microbiome profiles, with Lachnospiraceae and medium-chain fatty acids as protective features. Bioorthogonal non-canonical amino acid tagging selectively identified bacterial species in response to medium-chain fatty acids. Metagenomic analysis identified high strain-level dynamics in response to EEN. Functional changes in diet-exposed fecal microbiota were further validated using gut chemostat cultures and microbiota transfer into germ-free Il10-deficient mice. Dietary model conditions induced individual patient-specific strain signatures to prevent or cause inflammatory bowel disease (IBD)-like inflammation in gnotobiotic mice. Hence, we provide evidence that EEN therapy operates through explicit functional changes of temporally and individually variable microbiome profiles.

Crohn Disease↗
PubMed2006

In vitro activities of tritrpticin alone and in combination with other antimicrobial agents against Pseudomonas aeruginosa.

The in vitro activity of the cathelicidin tritrpticin was investigated against multidrug-resistant Pseudomonas aeruginosa. The isolates were susceptible to the peptide at concentrations of 0.50 to 8 mg/liter. Tritrpticin completely inhibits lipopolysaccharide procoagulant activity at a 10 microM concentration. Fractionary inhibitory concentration indexes (0.385, 0.312, and 0.458) demonstrated synergy between the peptide and beta-lactams.

Anti-Bacterial Agents↗
PubMed2005

Comments on selected fundamental aspects of microarray analysis.

Microarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses. In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone.

Computational Biology↗
PubMed2005

In vitro activity of MSI-78 alone and in combination with antibiotics against bacteria responsible for bloodstream infections in neutropenic patients.

MSI-78 is a 22 amino acid amphipathic peptide with potent antimicrobial activity against Gram-positive and Gram-negative organisms, including antibiotic-resistant strains. In this study, we assessed the in vitro activity of MSI-78 alone and in combination with eight clinically used antimicrobial agents against several strains of Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis and Escherichia coli isolated from blood of neutropenic febrile patients. Antimicrobial activity of MSI-78 was measured by minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), time-kill studies and checkerboard titration method. The Gram-negative isolates were susceptible to the peptide at concentrations in the range 0.50-16 mg/L, while staphylococci showed lower susceptibility. MSI-78 demonstrated a higher antimicrobial activity than colistin against Gram-negative organisms. The checkerboard titration method demonstrated synergy when the peptide was combined with beta-lactams. These results provide evidence for the potential use of MSI-78 in the management of severe infections in neutropenic patients.

Anti-Bacterial Agents↗
PubMed2005

Prevalence of atrial fibrillation and associated factors in a population of long-term hemodialysis patients.

BACKGROUND: Hemodialysis (HD) is associated with cardiovascular structural modifications; moreover, during HD, rapid electrolytic changes occur. Both factors may favor the onset of atrial fibrillation. METHODS: To define the prevalence of atrial fibrillation and identify associated factors, 488 patients on long-term HD therapy (age, 66.6 +/- 13.4 years; men, 58.0%; duration of HD, 76.5 +/- 84.3 months) were studied. RESULTS: Atrial fibrillation was reported in 27.0% of patients; paroxysmal in 3.5%, persistent in 9.6%, and permanent in 13.9%. Clinical and echocardiographic variables were considered: patients with atrial fibrillation were older (71.8 +/- 9.3 versus 64.7 +/- 14.2 years; P < 0.01), and its prevalence increased with age. Patients with arrhythmia had a longer duration of dialysis therapy (93.2 +/- 100.5 versus 70.2 +/- 76.7 months; P = 0.02). Atrial fibrillation was associated significantly with ischemic heart disease (P < 0.01), dilated cardiomyopathy (P < 0.01), acute pulmonary edema (P < 0.05), valvular disease (P < 0.05), cerebrovascular accidents (P < 0.05), and predialytic hyperkalemia (P < 0.05). Patients with atrial fibrillation more frequently showed left atrial dilatation (59.8% versus 34.5%; P < 0.0001), and in these subjects, left ventricular ejection fraction was significantly lower (53.9% versus 57.4%; P = 0.029). No association was found between arrhythmia and hypertension or diabetes. Multivariate analysis confirmed that patient age (P < 0.001), duration of HD therapy (P = 0.001), and left atrial dilatation (P < 0.001) were associated with atrial fibrillation. CONCLUSION: Atrial fibrillation is much more frequent in HD patients than in the general population; age, duration of HD history, presence of some heart diseases, and left atrial dilatation are associated with the arrhythmia.

Adult↗
PubMed2005

In vitro activity of the histatin derivative P-113 against multidrug-resistant pathogens responsible for pneumonia in immunocompromised patients.

The in vitro activity of the histatin derivative P-113, alone or combined with eight antibiotics, was investigated against multidrug-resistant strains isolated from clinical specimens of immunocompromised patients with pneumonia. The gram-negative isolates were susceptible to P-113. S. aureus showed less susceptibility. Synergy was demonstrated when P-113 was combined with beta-lactams against gram-negative organisms.

Drug Resistance, Multiple, Bacterial↗
PubMed2005

In vitro activity and killing effect of uperin 3.6 against gram-positive cocci isolated from immunocompromised patients.

The in vitro activity of uperin 3.6, alone or combined with six antibiotics, against gram-positive cocci, including Rhodococcus equi, methicillin-resistant staphylococci, and vancomycin-resistant enterococci, was investigated. All isolates were inhibited at concentrations of 1 to 16 mg/liter. Synergy was demonstrated when uperin 3.6 was combined with clarithromycin and doxycycline.

Amphibian Proteins↗
PubMed2004

Characterization of the GATC regulatory network in E. coli.

BACKGROUND: The tetranucleotide GATC is methylated in Escherichia. coli by the DNA methyltransferase (Dam) and is known to be implicated in numerous cellular processes. Mutants lacking Dam are characterized by a pleiotropic phenotype. The existence of a GATC regulated network, thought to be involved in cold and oxygen shift, had been proposed and its existence has recently been confirmed. The aim of this article is to describe the components of the GATC regulated network of E. coli in detail and propose a role of this network in the light of an evolutionary advantage for the organism. RESULTS: We have classified the genes of the GATC network according to the EcoCyc functional classes. Comparisons with all of E. coli's genes and the genes involved in the SOS and stress response show that the GATC network forms a group apart. The functional classes that characterize the network are the Energy metabolism (in particular respiration), Fatty acid/ Phospholipid metabolism and Nucleotide metabolism. CONCLUSIONS: The network is thought to come into play when the cell undergoes coldshock and is likely to enter stationary phase.The respiration is almost completely under GATC control and according to our hypothesis it will be blocked at the moment of coldshock; this might give the cell a selective advantage as it increases its chances for survival when entering stationary phase under coldshock. We predict the accumulation of formate and possibly succinate, which might increase the cell's resistance, in this case to antimicrobial agents, when entering stationary phase.

Biological Evolution↗
PubMed2004

The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA.

The number of statistical tools used to analyze transcriptome data is continuously increasing and no one, definitive method has so far emerged. There is a need for comparison and a number of different approaches has been taken to evaluate the effectiveness of the different statistical tools available for microarray analyses. In this paper, we describe a simple and efficient protocol to compare the reliability of different statistical tools available for microarray analyses. It exploits the fact that genes within an operon exhibit the same expression patterns. In order to compare the tools, the genes are ranked according to the most relevant criterion for each tool; for each tool we look at the number of different operons represented within the first twenty genes detected. We then look at the size of the interval within which we find the most significant genes belonging to each operon in question. This allows us to define and estimate the sensitivity and accuracy of each statistical tool. We have compared four statistical tools using Bacillus subtilis expression data: the analysis of variance (ANOVA), the principal component analysis (PCA), the independent component analysis (ICA) and the partial least square regression (PLS). Our results show ICA to be the most sensitive and accurate of the tools tested. In this article, we have used the protocol to compare statistical tools applied to the analysis of differential gene expression. However, it can also be applied without modification to compare the statistical tools developed for other types of transcriptome analyses, like the study of gene co-expression.

Bacillus subtilis↗
PubMed2004

The difficult interpretation of transcriptome data: the case of the GATC regulatory network.

Genomic analyses on part of Escherichia coli's chromosome had suggested the existence of a GATC regulated network. This has recently been confirmed through a transcriptome analysis. Two hypotheses about the molecular control mechanism have been proposed-(i) the GATC network regulation is caused by the presence of GATC clusters within the coding sequences; the regulation is the direct consequence of the clusters' hemi-methylation and therefore their elevated melting temperature, (ii) the regulation is caused by the presence of GATCs in the non-coding 500 bp upstream regions of the affected genes; it is the consequence of an interaction with a regulatory protein like Fnr or CAP. An analysis of the transcriptome data has not allowed us to decide between the two hypotheses. We have therefore taken a classic genomic approach, analyzing the statistical distribution of GATC along the chromosome, using a realistic model of the chromosome as theoretical reference. We observe no particular distribution of GATC in the non-coding upstream regions; however, we confirm the presence of GATC clusters within the genes. In order to verify that the particular distribution observed in E. coli is not a statistical artefact, but has a physiological role, we have carried out the same analysis on Salmonella, making the hypothesis that the genes containing a GATC clusters should be largely the same in the two bacteria. This has been indeed observed, showing that the genes containing a GATC cluster are part of a regulation network. The present is a case study, which demonstrates that the analysis of transcriptome data does not always permit to identify the primary cause of a phenomenon observed; on the other hand, a classic genomic approach linked with a comparative study of related genomes may allow this identification.

Computational Biology↗
PubMed2002

Efficacy of quinupristin-dalfopristin in preventing vascular graft infection due to Staphylococcus epidermidis with intermediate resistance to glycopeptides.

A rat model was used to investigate the efficacy of quinupristin-dalfopristin (Q-D) in the prevention of vascular prosthetic graft infection due to methicillin-resistant Staphylococcus epidermidis with intermediate resistance to glycopeptides. The in vitro activity of the compound was compared to that of vancomycin by MIC determination and time-kill study. Moreover, the efficacy of collagen-sealed Q-D-soaked Dacron was evaluated in a rat model of graft infection. Graft infections were established in the subcutaneous tissue of the backs of 120 adult male Wistar rats. The in vivo study included a control group, one contaminated group that did not receive any antibiotic prophylaxis, two contaminated groups that received grafts soaked with 10 and 100 micro g of Q-D per ml, respectively, and two contaminated groups that received grafts soaked with 10 and 100 micro g of vancomycin per ml, respectively. Rats that received Dacron grafts soaked with 100 micro g of Q-D per ml showed no evidence of infection (<10 CFU/ml). In contrast, for rats that received Dacron grafts soaked with 10 micro g of Q-D per ml and Dacron grafts soaked with 10 or 100 micro g of vancomycin per ml, the quantitative graft cultures demonstrated 2.2 x 10(2) +/- 1.3 x 10(2), 2.2 x 10(6) +/- 1.9 x 10(5), and 5.6 x 10(2) +/- 0.3 x 10(2) CFU/ml, respectively. Taken together the results of the study demonstrate that the use of Dacron grafts soaked with Q-D can result in significant bacterial growth inhibition and show that this compound is potentially valuable for prevention of vascular prosthetic graft infection.

Animals↗