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The expression of 1008 open reading frames (OREs) from the yeast Saccharomyces cerevisiae has been examined under eight different physiological conditions, using classical northern analysis. These northern data have been compared with publicly available data from a microarray analysis of the diauxic transition in S.cerevisiae. The results demonstrate the importance of comparing biologically equivalent situations and of the standardization of data normalization procedures. We have also used our northern data to identify co-regulated gene clusters and define the putative target sites of transcriptional activators responsible for their control. Clusters containing genes of known function identify target sites of known activators. In contrast, clusters comprised solely of genes of unknown function usually define novel putative target sites. Finally, we have examined possible global controls on gene expression. It was discovered that OREs that are highly expressed following a nutritional upshift tend to employ favoured codons, whereas those overexpressed in starvation conditions do not. These results are interpreted in terms of a model in which competition between mRNA molecules for translational capacity selects for codons translated by abundant tRNAs. [ABSTRACT FROM AUTHOR]

When antiretroviral treatment suppresses HIV RNA levels to below 50 copies/ml, traces of viremia may still be detected with more sensitive assays. In the ARTEMIS trial, 689 antiretroviral treatment-naive patients were randomized to tenofovir/emtricitabine plus either darunavir/ritonavir (n = 343) or lopinavir/ritonavir (n = 346). HIV-1 RNA was evaluated using the Roche Amplicor® Ultrasensitive assay: plasma samples with HIV RNA < 50 copies/ml were classified as either "No HIV RNA detected" (< 5 HIV RNA copies/ml, optical density = background) or HIV RNA detected (5-50 copies/ml). The percentage of patients in each arm with HIV RNA < 5 copies/ml rose progressively from week 2 to week 192. For patients with baseline HIV RNA ≥ 100,000, the percentage with HIV RNA < 5 copies/ml at week 192 was 66% for darunavir/ritonavir and 63% for lopinavir/ritonavir. For patients with baseline HIV RNA < 100,000 copies/ml, the percentage with HIV RNA < 5 copies/ml at week 192 was 79% for darunavir/ritonavir versus 77% for lopinavir/ritonavir. Of the patients on darunavir/ritonavir with HIV RNA < 50 copies/ml, 63% had levels < 5 copies/ml at week 48, versus 80% at week 192. In summary, HIV-1 RNA suppression to < 5 copies/ml is dependent on baseline HIV RNA levels. The HIV RNA levels can remain under quantification limits but still detectable after 2-4 years of antiretroviral treatment.

There are four key differences between HIV clinical trials in the analysis of HIV drug resistance: (i) baseline resistance testing used versus not used for patient inclusion; (ii) using HIV RNA cutoff levels of ≥ 50 versus ≥ 400 copies/ml to define virologic failure; (iii) testing versus not testing drug resistance in patients who discontinue treatment; (iv) analyzing drug resistance based on intent-to-treat analysis versus the subset of patients with samples genotyped. In this review we illustrate the importance of these issues, using data from 17 clinical trials of first-line nonnucleoside reverse transcriptase inhibitor-based treatment reported in the past 10 years. We also analyzed the data from the efavirenz arm of the SENSE trial, using all the different methods to show the range of results that can be obtained using different methods of analysis. Detection of treatment-emergent nucleoside/nonnucleoside reverse transcriptase inhibitor resistance differs significantly between clinical trials of the same first-line treatment (two nucleoside reverse transcriptase inhibitors/efavirenz), depending on the methods used for testing and analysis. Several clinical trials may have underestimated the prevalence of treatment-emergent drug resistance, by (i) not testing virologic failures with HIV RNA 50-400 copies/ml or (ii) not testing patients after discontinuation of treatment.

The MONET study, comparing darunavir/ritonavir-based triple therapy and monotherapy, has found higher risk of failure in patients with positive HCV serology, but the effects of HCV co-infection on the efficacy of antiretroviral treatment have not been clearly established. A detailed MEDLINE search was conducted to identify cohort studies and clinical trials with published analyses of the efficacy of antiretroviral treatment by HCV co-infection. A meta-analysis of the clinical trials was conducted, with the standardized endpoint of HIV RNA < 50 copies/ml at week 48 (intent to treat, time to loss of virologic response algorithm). Twelve cohort studies, seven clinical trials in antiretroviral-naive patients and three in pretreated patients were identified. In the clinical trials, 637/5,408 (12%) patients had HIV/HCV co-infection by HCV antibody tests; this percentage was in the lower range of the percentage of HIV/HCV co-infected patients reported in cohort studies in North America and Europe (median 37%, range 9-64%). In the meta-analysis of the clinical trials, the mean percentage of patients achieving HIV RNA < 50 copies/ml at week 48 was 68.2% for HIV/HCV co-infected patients versus 80.4% for HIV mono-infected patients. The absolute difference in efficacy was 11.5% (95% CI: 7.7-15.3%; p < 0.001). However, a high proportion of endpoints in the time to loss of virologic response analysis were discontinuations of randomized treatment for adverse events or other reasons. The cause of the lower efficacy of antiretroviral treatment in HIV/HCV co-infected patients is unclear. The low percentage of HIV/HCV co-infected patients in this analysis, compared with published cohort studies, suggests that HCV co-infected patients are underrepresented in HIV clinical trials.