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Marcel Ooms

Publications and source records attributed to Marcel Ooms.

10 recordsLinked to original sources
PubMed2005

The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation.

The untranslated leader RNA is the most conserved part of the human immunodeficiency virus type I (HIV-1) genome. It contains many regulatory motifs that mediate a variety of steps in the viral life cycle. Previous work showed that the full-length leader RNA can adopt two alternative structures: a long distance interaction (LDI) and a branched multiple-hairpin (BMH) structure. The BMH structure exposes the dimer initiation site (DIS) hairpin, whereas this motif is occluded in the LDI structure. Consequently, these structures differ in their capacity to form RNA dimers in vitro. The BMH structure is dimerization-competent, due to DIS hairpin formation, but also presents the splice donor (SD) and RNA packaging (Psi) hairpins. In the LDI structure, an extended RNA packaging (Psi(E)) hairpin is folded, which includes the splice donor site and gag coding sequences. The gag initiation codon is engaged in a long distance base pairing interaction with sequences in the upstream U5 region in the BMH structure, thus forming the evolutionarily conserved U5-AUG duplex. Therefore, the LDI-BMH equilibrium may affect not only the process of RNA dimer formation but also translation initiation. In this study, we designed mutations in the 3'-terminal region of the leader RNA that alter the equilibrium of the LDI-BMH structures. The mutant leader RNAs are affected in RNA dimer formation, but not in their translation efficiency. These results indicate that the LDI-BMH status does not regulate HIV-1 RNA translation, despite the differential presentation of the gag initiation codon in both leader RNA structures.

Base Sequence↗
PubMed2005

HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome.

HIV-1 replication can be efficiently inhibited by intracellular expression of an siRNA targeting the viral RNA. However, HIV-1 escape variants emerged after prolonged culturing. These RNAi-resistant viruses contain nucleotide substitutions or deletions in or near the targeted sequence. We observed an inverse correlation between the level of resistance and the stability of the siRNA/target-RNA duplex. However, two escape variants showed a higher level of resistance than expected based on the duplex stability. We demonstrate that these mutations induce alternative folding of the RNA such that the target sequence is occluded from binding to the siRNA, resulting in reduced RNAi efficiency. HIV-1 can thus escape from RNAi-mediated inhibition not only through nucleotide substitutions or deletions in the siRNA target sequence, but also through mutations that alter the local RNA secondary structure. The results highlight the enormous genetic flexibility of HIV-1 and provide detailed molecular insight into the sequence specificity of RNAi and the impact of target RNA secondary structure.

Anti-HIV Agents↗
PubMed2005

The effect of integrated emotion-oriented care versus usual care on elderly persons with dementia in the nursing home and on nursing assistants: a randomized clinical trial.

OBJECTIVES: To examine the effect of integrated emotion-oriented care on nursing home residents with dementia and nursing assistants. DESIGN: A multi-site randomized clinical trial with matched groups, and measurements at baseline and after seven months. SETTING: Sixteen psychogeriatric wards in fourteen nursing homes in the Netherlands. PARTICIPANTS: One hundred and forty-six elderly residents with the diagnosis dementia of the Alzheimer (DAT) type, mixed DAT and vascular dementia, and dementia syndrome (NAO) and 99 nursing assistants. INTERVENTIONS: Integrated emotion-oriented care and usual care. MESUREMENTS: Demented elderly: Behaviour and mood related to adaptation to the illness and the institutionalization. Nursing assistants: General health as measured by feelings of stress, stress reactions, feeling of competence and illness. RESULTS: Positive effects in favour of the integrated emotion-oriented care were found in mild to moderately demented residents on two adaptive tasks: maintaining an emotional balance (less anxiety) and preserving a positive self-image (less dissatisfaction). In the trained group of nursing assistants fewer stress reactions were found only in those who perceived improvement in their emotion-oriented care skills after training. CONCLUSION: Emotion-oriented care is more effective with regard to the emotional adaptation in nursing homes of persons with a mild to moderate dementia. For the severely demented elderly we did not find this surplus value. This outcome is of clinical importance for elderly persons with dementia who are cared for in nursing homes. With respect to the nursing assistants it is concluded that emotion-oriented care has a positive influence on stress reactions in some of them.

Absenteeism↗
PubMed2004

Probing alternative foldings of the HIV-1 leader RNA by antisense oligonucleotide scanning arrays.

Scanning arrays of antisense DNA oligonucleotides provide a novel and systematic means to study structural features within an RNA molecule. We used this approach to probe the structure of the untranslated leader of the human immunodeficiency virus type 1 (HIV-1) RNA genome. This 335 nt RNA encodes multiple important replication signals and adopts two mutually exclusive conformations. The poly(A) and the dimer initiation signal (DIS) sequences of the leader RNA are base-paired in the long-distance interaction (LDI) conformation, but both domains form distinct hairpins in the branched multiple hairpins (BMH) conformation. An RNA switch mechanism has been proposed to regulate the activity of the DIS dimerization signal that is masked in one, yet exposed in the other conformation. The two RNA conformations demonstrate discrete differences in the array-based hybridization patterns. LDI shows increased hybridization in the poly(A) region and decreased hybridization in the DIS region when compared with BMH. These results provide additional evidence for the structure models of the two alternative leader RNA conformations. We also found a correlation between the efficiency of oligonucleotide hybridization and the accessibility of the RNA structure as determined by chemical and enzymatic probing in previous studies. The array approach therefore provides a very sensitive method to detect structural differences in related transcripts.

Base Pairing↗
PubMed2004

A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions.

The genome of retroviruses, including human immunodeficiency virus type 1 (HIV-1), consists of two identical RNA strands that are packaged as noncovalently linked dimers. The core packaging and dimerization signals are located in the downstream part of the untranslated leader of HIV-1 RNA-the Psi and the dimerization initiation site (DIS) hairpins. The HIV-1 leader can adopt two alternative conformations that differ in the presentation of the DIS hairpin and consequently in their ability to dimerize in vitro. The branched multiple-hairpin (BMH) structure folds the poly(A) and DIS hairpins, but these domains are base paired in a long distance interaction (LDI) in the most stable LDI conformation. This LDI-BMH riboswitch regulates RNA dimerization in vitro. It was recently shown that the Psi hairpin structure is also presented differently in the LDI and BMH structures. Several detailed in vivo studies have indicated that sequences throughout the leader RNA contribute to RNA packaging, but how these diverse mutations affect the packaging mechanism is not known. We reasoned that these effects may be due to a change in the LDI-BMH equilibrium, and we therefore reanalyzed the structural effects of a large set of leader RNA mutations that were presented in three previous studies (J. L. Clever, D. Mirandar, Jr., and T. G. Parslow, J. Virol. 76:12381-12387, 2002; C. Helga-Maria, M. L. Hammarskjold, and D. Rekosh, J. Virol. 73:4127-4135, 1999; R. S. Russell, J. Hu, V. Beriault, A. J. Mouland, M. Laughrea, L. Kleiman, M. A. Wainberg, and C. Liang, J. Virol. 77:84-96, 2003). This analysis revealed a strict correlation between the status of the LDI-BMH equilibrium and RNA packaging. Furthermore, a correlation is apparent between RNA dimerization and RNA packaging, and these processes may be coordinated by the same LDI-BMH riboswitch mechanism.

5' Untranslated Regions↗
PubMed2004

[Three new observational scales for use in Dutch nursing homes: scales from the Resident Assessment Instrument for Activities of Daily Living, cognition and depression].

The reliability and validity of three MDS scales for ADL, cognition and depression are described. The scales consist of items of the Minimum Data Set of the Resident Assessment Instrument and are available just after an MDS assessment. Data collection took place in nine Dutch nursing homes (N = 227) and consisted of three MDS assessments within one month to determine reliability. Several criterion measures were assessed in order to determine convergent validity. Intra- and inter-rater reliability and internal consistency were determined as well as correlation coefficients of the criterion measures and the MDS scales. All three MDS scales appear reliable, especially the ADL-Hierarchy has very good psychometric properties (intra- and inter-rater Intra Class Correlation were 0.81 and 0.83, respectively). Convergent validity of the ADL-Hierarchy and the Cognitive Performance Scale is good, the Depression Rating Scale appears valid in residents with moderate cognitive disorders at the most, but the results are more difficult to interpret in residents with severe cognitive disorders. The MDS scales appear useful in clinical practice and for research purposes in the Dutch nursing homes.

Activities of Daily Living↗
PubMed2003

The effect of depression on social engagement in newly admitted Dutch nursing home residents.

PURPOSE: To study the effect of depression (high levels of depressive symptoms) on social engagement. DESIGN AND METHODS: In 65 nursing homes in the Netherlands, 562 newly admitted residents were assessed at admission. Social engagement was measured with the MDS Index of Social Engagement. A multivariate logistic regression model was used to study the effect of depression, measured according to the MDS-depression rating scale and controlled for confounders, on social engagement. RESULTS: Fifty-one percent of the newly admitted residents had a low level of social engagement; twenty seven percent were depressed (high levels of depressive symptoms). Residents with a depression were significantly more often found to have low social engagement (OR 3.3), and confounders did not influence the strength of this relationship. Low social engagement on admission is predicted by depression and low cognitive performance, and to a lesser extent by impairments in vision and ADL. IMPLICATIONS: Low social engagement is very common in newly admitted nursing home residents, and depression is an important independent risk factor.

Aged↗
PubMed2002

In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes.

The HIV-1 RNA genome forms dimers through base pairing of a palindromic 6-mer sequence that is exposed in the loop of the dimer initiation signal (DIS) hairpin structure (loop-loop kissing). The HIV-1 leader RNA can adopt a secondary structure conformation that is not able to dimerize because the DIS hairpin is not folded. Instead, this DIS motif is base-paired in a long distance interaction (LDI) that extends the stem of the primer-binding site domain. In this study, we show that targeting of the LDI by either antisense oligonucleotides or specific mutations can induce the conformational switch to a branched multiple hairpin (BMH) structure, and this LDI-to-BMH switch coincides with increased RNA dimerization. Another interesting finding is that the extended LDI stem can resist a certain level of destabilization, indicating that a buffer is created to prevent a premature conformational switch and early dimerization. Because the tRNA(Lys3) primer for reverse transcription anneals to multiple sequence elements of the HIV-1 leader RNA, including sequences in the LDI stem, we tested whether tRNA-annealing can destabilize the LDI stem such that RNA dimerization is triggered. Using a combination of stem-destabilizing approaches, we indeed measured a small but significant effect of tRNA-annealing on the ability of the RNA template to form dimers. This observation suggests that HIV-1 RNA can act as a checkpoint to control and coordinate different leader functions through conformational switches. This in vitro result should be verified in subsequent in vivo studies with HIV-infected cells.

5' Untranslated Regions↗
PubMed2002

[Whether or not to treat pneumonia curatively in (demented) psychogeriatric patients: evaluation of a guideline for nursing home physicians].

A guideline was developed to support decision-making about whether or not to treat pneumonia curatively in psychogeriatric (demented) nursing home patients. This guideline was developed as a 'checklist of considerations', primarily of the ethical and legal aspects of decision-making. Nursing home physicians used and evaluated the list. The list's acceptance was assessed by measuring the frequency of the list's use, and judgements of the list's contents and 'usefulness'. The list was used in 50 out of 58 participating nursing homes, in 47% of the 489 psychogeriatric patients in whom pneumonia occurred. The list was found somewhat to very useful to support decision-making in 47% of 107 individual patients. For the targeted patient category as a whole, 85% of 48 physicians who were asked retrospectively (one physician per home) found the list somewhat to very useful. The content of the list was judged favourably. In conclusion, the nursing home physicians accepted the considerations of the checklist as a basis for decision-making on whether or not to treat pneumonia curatively in psychogeriatric patients. In the future, the format of the list can be adapted for use in diverse clinical situations. Suggestions are provided to increase user friendliness and usefulness.

Aged↗