Describing the orthology signal in a PPI network at a functional, complex level

In recent work, stable evolutionary signal induced by orthologous proteins has been observed in a Yeast protein-protein interaction (PPI) network. This finding suggests more connected subgraphs of a PPI network to be potential mediators of evolutionary information. Because protein complexes are also likely to be present in such subgraphs, it is interesting to characterize the bias of the orthology signal on the detection of putative protein complexes. To this aim, we propose a novel methodology for quantifying the functionality of the orthology signal in a PPI network at a protein complex level. The methodology performs a differential analysis between the functions of those complexes detected by clustering a PPI network using only proteins with orthologs in another given species, and the functions of complexes detected using the entire network or sub-networks generated by random sampling of proteins. We applied the proposed methodology to a Yeast PPI network using orthology information from a number of different organisms. The results indicated that the proposed method is capable to isolate functional categories that can be clearly attributed to the presence of an evolutionary (orthology) signal and quantify their distribution at a fine-grained protein level

A methodology for detecting the orthology signal in a PPI network at a functional complex level

Contains fulltext : 93730.pdf (preprint version ) (Open Access)13 p

A methodology for detecting the orthology signal in a PPI network at a functional complex level.

\u3cp\u3eStable evolutionary signal has been observed in a yeast protein-protein interaction (PPI) network. These finding suggests more connected regions of a PPI network to be potential mediators of evolutionary information. Because more connected regions of PPI networks contain functional complexes, we are motivated to exploit the orthology relation for identifying complexes that can be clearly attributed to such evolutionary signal. We proposed a computational methodology for detecting the orthology signal present in a PPI network at a functional complex level. Specifically, we examined highly functionally coherent putative protein complexes as detected by a clustering technique in the complete yeast PPI network, in the yeast sub-network which spans only ortholog proteins as determined by a given second organism, and in yeast sub-networks induced by a set of proteins randomly selected. We proposed a filtering technique for extracting orthology-driven clusters with unique functionalities, that is, neither enriched by clusters identified using the complete yeast PPI network nor identified using random sampling. Moreover, we extracted functional categories that can be clearly attributed to the presence of evolutionary signal as described by these clusters. Application of the proposed methodology to the yeast PPI network indicated that evolutionary information at a functional complex level can be retrieved from the structure of the network. In particular, we detected protein complexes whose functionality could be uniquely attributed to the evolutionary signal. Moreover, we identified functions that are over-represented in these complexes due the evolutionary signal.\u3c/p\u3

Efficacy of Posaconazole against Three Clinical Aspergillus fumigatus Isolates with Mutations in the cyp51A Gene▿

The in vivo efficacy of posaconazole against 4 clinical Aspergillus fumigatus isolates with posaconazole MICs ranging from 0.03 to 16 mg/liter, as determined by CLSI method M38A, was assessed in a nonneutropenic murine model of disseminated aspergillosis. The underlying resistance mechanisms of the isolates included substitutions in the cyp51A gene at codon 220 (M220I), codon 54 (G54W), and codon 98 (L98H). The latter was combined with a 34-bp tandem repeat in the gene promoter region (TR L98H). The control isolate exhibited a wild-type phenotype without any known resistance mechanism. Oral posaconazole therapy was started 24 h after infection and was given once daily for 14 consecutive days. Mice were treated with four different doses (1 to 64 mg/kg of body weight), and survival was used as the end point. Survival was dependent both on the dose and on the MIC. The Hill equation with a variable slope fitted the relationship between the dose/MIC ratio and 14-day survival well (R2, 0.92), with a 50% effective dose (ED50) of 29.0 mg/kg (95% confidence interval [CI], 15.6 to 53.6 mg/kg). This also applied to the relationship between the area under the plasma concentration-time curve (AUC)/MIC ratio and 14-day survival (50% effective pharmacodynamic index [EI50], 321.3 [95% CI, 222.7 to 463.4]). Near-maximum survival was reached at an AUC/MIC ratio of nearly 1,000. These results indicate that treatment of infections with A. fumigatus strains for which MICs are 0.5 mg/liter requires doses exceeding the present licensed doses. Increasing the standard dosing regimen may have some effect and may be clinically useful if no alternatives are available

Development of azole resistance in Aspergillus fumigatus during azole therapy associated with change in virulence

Contains fulltext : 88544.pdf (publisher's version ) (Open Access)Four sequential Aspergillus fumigatus isolates from a patient with chronic granulomatous disease (CGD) eventually failing azole-echinocandin combination therapy were investigated. The first two isolates (1 and 2) were susceptible to antifungal azoles, but increased itraconazole, voriconazole and posaconazole MICs were found for the last two isolates (3 and 4). Microsatellite typing showed that the 4 isolates were isogenic, suggesting that resistance had been acquired during azole treatment of the patient. An immunocompromised mouse model confirmed that the in vitro resistance corresponded with treatment failure. Mice challenged with the resistant isolate 4 failed to respond to posaconazole therapy, while those infected by susceptible isolate 2 responded. Posaconazole-anidulafungin combination therapy was effective in mice challenged with isolate 4. No mutations were found in the Cyp51A gene of the four isolates. However, expression experiments of the Cyp51A showed that the expression was increased in the resistant isolates, compared to the azole-susceptible isolates. The microscopic morphology of the four isolates was similar, but a clear alteration in radial growth and a significantly reduced growth rate of the resistant isolates on solid and in broth medium was observed compared to isolates 1 and 2 and to unrelated wild-type controls. In the mouse model the virulence of isolates 3 and 4 was reduced compared to the susceptible ones and to wild-type controls. For the first time, the acquisition of azole resistance despite azole-echinocandin combination therapy is described in a CGD patient and the resistance demonstrated to be directly associated with significant change of virulence

Pharmacodynamics of ceftolozane combined with tazobactam against Enterobacteriaceae in a neutropenic mouse thigh model

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Impact of cyp51A Mutations on the Pharmacokinetic and Pharmacodynamic Properties of Voriconazole in a Murine Model of Disseminated Aspergillosis ▿

The in vivo efficacy of voriconazole against 4 clinical Aspergillus fumigatus isolates with MICs ranging from 0.125 to 2 mg/liter (CLSI document M38A) was assessed in a nonneutropenic murine model of disseminated aspergillosis. The study involved TR/L98H, M220I, and G54W mutants and a wild-type control isolate. Oral voriconazole therapy was started 24 h after intravenous infection of mice and was given once daily for 14 consecutive days, with doses ranging from 10 to 80 mg/kg of body weight, using survival as the endpoint. Survival for all isolates was dependent on the voriconazole dose level (R2 value of 0.5 to 0.6), but a better relationship existed for the area under the concentration-time curve over 24 h in the steady state divided by the MIC (AUC/MIC ratio) or the AUC for the free, unbound fraction of the drug divided by the MIC (fAUC/MIC ratio) (R2 value of 0.95 to 0.98). The 24-h fAUC/MIC ratio showed a clear relationship to effect, with an exposure index for amount of free drug required for 50% of maximum effectiveness (fEI50) of 11.17 at day 7. Maximum effect was reached at values of around 80 to 100, comparable to that observed for posaconazole and A. fumigatus. Mice infected with an isolate having a MIC of 2 mg/liter required an exposure that was inversely correlated with the increase in MIC compared to that of the wild-type control, but due to nonlinear pharmacokinetics, this required only doubling of the voriconazole dose. The efficacy of voriconazole for isolates with high MICs for other triazoles but voriconazole MICs within the wild-type population range was comparable to that for the wild-type control. Finally, we used a grapefruit juice-free murine model of aspergillosis and concluded that this model is appropriate to study pharmacokinetic/pharmacodynamic relationships of voriconazole