Circularization of the HIV-1 RNA genome

Genomic RNA circularization has been proposed for several RNA viruses. In this study, we examined if the 5′ and 3′ ends of the 9-kb HIV-1 RNA genome can interact. In vitro assays demonstrated a specific interaction between transcripts encompassing the 5′ and 3′ terminal 1 kb, suggesting that the HIV-1 RNA genome can circularize. Truncation of the transcripts indicated that the 5′–3′ interaction is formed by 600–700 nt in the gag open reading frame and the terminal 123 nt of the genomic RNA. Detailed RNA structure probing indicates that sequences flanking the 3′ TAR hairpin interact with complementary sequences in the gag gene. Phylogenetic analysis indicates that all HIV-1 subtypes can form the 5′/3′ interaction despite considerable sequence divergence, suggesting an important role of RNA circularization in the HIV-1 replication cycle

APOBEC3G Polymorphism as a Selective Barrier to Cross-Species Transmission and Emergence of Pathogenic SIV and AIDS in a Primate Host

Cellular restriction factors, which render cells intrinsically resistant to viruses, potentially impose genetic barriers to cross-species transmission and emergence of viral pathogens in nature. One such factor is APOBEC3G. To overcome APOBEC3G-mediated restriction, many lentiviruses encode Vif, a protein that targets APOBEC3G for degradation. As with many restriction factor genes, primate APOBEC3G displays strong signatures of positive selection. This is interpreted as evidence that the primate APOBEC3G locus reflects a long-term evolutionary “arms-race” between retroviruses and their primate hosts. Here, we provide direct evidence that APOBEC3G has functioned as a barrier to cross-species transmission, selecting for viral resistance during emergence of the AIDS-causing pathogen SIVmac in captive colonies of Asian macaques in the 1970s. Specifically, we found that rhesus macaques have multiple, functionally distinct APOBEC3G alleles, and that emergence of SIVmac and simian AIDS required adaptation of the virus to evade APOBEC3G-mediated restriction. Our evidence includes the first comparative analysis of APOBEC3G polymorphism and function in both a reservoir and recipient host species (sooty mangabeys and rhesus macaques, respectively), and identification of adaptations unique to Vif proteins of the SIVmac lineage that specifically antagonize rhesus APOBEC3G alleles. By demonstrating that interspecies variation in a known restriction factor selected for viral counter-adaptations in the context of a documented case of cross-species transmission, our results lend strong support to the evolutionary “arms-race” hypothesis. Importantly, our study confirms that APOBEC3G divergence can be a critical determinant of interspecies transmission and emergence of primate lentiviruses, including viruses with the potential to infect and spread in human populations

Measurement of overall quality of life in nursing homes through self-report: the role of cognitive impairment

Measuring quality of life is a necessity for adequate interventions. This paper concerns the usefulness of six self-report measures for overall quality of life for nursing home residents with various levels of cognitive impairment. It was investigated which proportion of residents from four cognition groups could complete a scale, and internal consistency and construct validity of the scales were studied. Data collection took place in ten Dutch nursing homes (N = 227). The proportion of residents that could complete each scale varied. The Depression List could be administered most often to the cognitively most impaired group (43%; Mini Mental State Examination-scores 0–4). In the three cognition groups with MMSE-score >5, internal consistency of the Depression List, Geriatric Depression Scale and Negative Affect Scale was adequate in all three groups (alpha ≥.68). Intercorrelation was highest for the Philadelphia Geriatric Center Morale Scale, the Depression List, and the Geriatric Depression Scale (rho ≥.65). Nonetheless, self-report scales were not strongly correlated with two observational scales for depression, especially in cognitively severely impaired residents (rho ≤.30). In conclusion, it may not be possible to measure overall quality of life through self-report, and possibly also through observation, in many nursing home residents

Predicted survival vs. actual survival in terminally ill noncancer patients in Dutch nursing homes

Studies on the prediction of survival have mainly focused on hospital and hospice patients suffering from cancer. The aim of this study was to describe the predicted vs. the actual survival in terminally ill, mainly noncancer patients in Dutch nursing homes (NHs). A prospective cohort study was conducted in 16 NHs representative for The Netherlands. A total of 515 NH patients with a maximum life expectancy of 6 weeks, as assessed by an NH physician, were included. NH physicians were accurate in more than 90% of their prognoses for terminally ill-mainly noncancer-NH patients, when death occurred within 7 days. Fora longer period of time, their predictions became inaccurate. In the category of patients who were expected to die within 8-21 days, predictions were accurate in 16.0%, and in, the category of patients expected to die within 22-42 days, this was 13.0%. Predictions in these categories were mainly optimistic (patient died earlier) in 68.6% and 52.2%, respectively. The findings of this study suggest that accurate prediction of survival of (mainly) noncancer patients in NHs is only possible when death is imminent and seems to be dependent on an intimate knowledge of patients. Prognostication over a longer period of time tends to be less accurate, and, therefore, continues to be a challenging task for NH physicians

Improvements in the quality of co-ordination of nursing care following implementation of the Resident Assessment Instrument in Dutch nursing homes

Aim. To study the effect of implementation of the Resident Assessment Instrument (RAI) on the quality of co-ordination of nursing care in Dutch nursing homes. Background. The Resident Assessment Instrument (RAI) was designed to improve the quality of care and quality of life in nursing homes. Until now, only noncontrolled studies on the effects of implementation of the RAI have been carried out. Design/methods. Quasi-experimental; intervention wards with RAI compared with wards with no intervention. We used the co-ordination of nursing care instrument, which includes measures for case history, care plan, end of shift report, communication, patient allocation and patient report. The scores on these scales represent the quality of nursing procedures on a ward. The measurements were done 1 month before and 8 months after RAI-implementation in 18 wards in 10 nursing homes in the Netherlands. Results. Out of 348 somatic patients on the participating wards who met the inclusion criteria and signed an informed consent, 278 could be measured at the first and 218 at the second data collection. 175 residents could participate twice. We used a meta-analysis technique to study the mean differences between eight couples of RAI/control wards before and after the intervention. The mean difference scores showed significant positive improvement in the RAI group for case history, there were minor (not statistically significant) improvements for all other scores and the total score. These results are encouraging especially in light of the fact that RAI-implementation in all the experimental wards did not proceed according to plan, owing to staffing and software problems. Conclusions. We conclude that the RAI has the potential to improve the quality of co-ordination of care in nursing homes

Reverse transcription assays with transcribed transcripts and vRNA–tRNA complexes isolated from virions

<p><b>Copyright information:</b></p><p>Taken from "The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation"</p><p></p><p>Nucleic Acids Research 2007;35(5):1649-1659.</p><p>Published online 18 Feb 2007</p><p>PMCID:PMC1865047.</p><p>© 2007 The Author(s).</p> () The differences in the anti-PBS and anti-PAS sequences between tRNA and tRNA are boxed in the latter molecule. The anti-PAS and anti-PBS motifs are boxed in gray. The HIV-1 PAS and PBS motifs were mutated to complement the tRNA primer in the mutant PAS/PBS-lys1,2 (M). Long-term culturing of the mutant virus resulted in a revertant virus that gained replication capacity by a point mutation in the PAS motif (R). The U to C mutation stabilizes the interaction of the anti-PAS with the PAS motif. () Reverse transcription initiation of HIV-1 leader RNA transcripts. tRNA primers were annealed to the transcribed wt, mutant (M) and revertant (R) transcripts or the vRNA–tRNA complexes were isolated from the corresponding virions. Primers were extended by addition of HIV-1 RT enzyme and P-dCTP for the extension assay or dTTP, dGTP and P-dCTP for extension. This results in the extension of the tRNA primer with 1 and 5 nt, respectively. The extended primers were separated on a denaturing polyacrylamide gel. The tRNA product runs at a higher position in the gel than the tRNA product due to different base modification