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PubMed2002

In vivo HIV-1 compartmentalisation: drug resistance-associated mutation distribution.

Four patients who had received highly active antiretroviral therapy (HAART), and had postmortem samples stored, were tested for genotypic resistance using consensus sequencing. One patient was further investigated using single-copy sequencing. Patients 1, 3, and 4 showed a relatively uniform distribution of resistance-associated mutations, with only a small number (one to three) of protease mutations detectable. Patient 2 had a number of detectable mutations (four to eight, depending on the tissue) with similar distributions between the tissues. The exception was viruses detected in the esophagus, which were more diverse. Plasma was a moderately representative tissue of the viruses circulating in these individuals. However, some mutations detectable in some tissues were not seen in plasma (e.g., M46I and D30N in the protease). Single-copy sequencing revealed a wide distribution of quasi-species and a number of defective viruses in the proviral DNA and RNA. This study supports the concept that a wide variety of quasi-species circulate in each individual and that there may be viruses evolving independently in different body compartments.

Adult↗
PubMed2004

Ecologically relevant stress resistance: from microarrays and quantitative trait loci to candidate genes - a research plan and preliminary results using Drosophila as a model organism and climatic and genetic stress as model stresses.

We aim at studying adaptation to genetic and environmental stress and its evolutionary implications at different levels of biological organization. Stress influences cellular processes, individual physiology, genetic variation at the population level, and the process of natural selection. To investigate these highly connected levels of stress effects, it is advisable - if not critical - to integrate approaches from ecology, evolution, physiology, molecular biology and genetics. To investigate the mechanisms of stress resistance, how resistance evolves, and what factors contribute to and constrain its evolution, we use the well-defined model systems of Drosophila species, representing both cosmopolitan species such as D. melanogaster with a known genome map, and more specialized and ecologically well described species such as the cactophilic D. buzzatii. Various climate-related stresses are used as model stresses including desiccation, starvation, cold and heat. Genetic stress or genetic load is modelled by studying the consequences of inbreeding, the accumulation of (slightly) deleterious mutations, hybridization or the loss of genetic variability. We present here a research plan and preliminary results combining various approaches: molecular techniques such as microarrays, quantitative trait loci (QTL) analyses, quantitative PCR, ELISA or Western blotting are combined with population studies of resistance to climatic and genetic stress in natural populations collected across climatic gradients as well as in selection lines maintained in the laboratory.

Adaptation, Physiological↗
PubMed2005

Quantification of the newly detected lamivudine resistant YSDD variants of Hepatitis B virus using molecular beacons.

A real-time based amplification assay with molecular beacons was used to detect and quantify PCR amplicons to discriminate between the newly described Lamivudine-resistant YSDD variant, a known YIDD variant and wild-type Hepatitis B virus (HBV) DNA in the YMDD region of the polymerase gene. Using this assay, we retrospectively analysed samples from two HBV chronically infected Asian twin sisters, starting 9 weeks before therapy, during and between two periods of treatment with Lamivudine. In order to analyse more accurately the dynamics of variant DNA loads during and after therapy, this real time assay was compared to three other mutation analysis techniques, restriction fragment length polymorphism (RFLP), InnoLipa HBV-DR assay and direct sequence analysis. With this technique, new information on the dynamics of variants during and after therapy was obtained.

Amino Acid Motifs↗
PubMed2005

Amino acid mutations of the infectious clone from Chinese EIAV attenuated vaccine resulted in reversion of virulence.

The Chinese equine infectious anemia virus (EIAV) donkey-leukocyte attenuated vaccine (DLV) provides a unique natural model system by which attenuated mechanism and immunological control of lentivirus replication may be studied. We analyzed the critical consensus mutations that occurred during the viral passages in vitro and in vivo for vaccine's preparation. Based on the full-length infectious clone pLGFD3 (EIAV vaccine background) and according to mutations displayed during viral attenuation, we successfully constructed an infectious clones pLG5-3-l in which gag and env genes were point-mutated by overlap PCR mutagenesis strategy. pLG5-3-l was proved to have the ability of effective replication in vitro cells culture systems by Reverse Transcriptase Assay and virion observation under electron microscopy. Results of the in vivo experiments indicated that marked differences occurred between the mutated virus and their parental virus in clinical manifestation and plasma viral replication during 6-month observation period. In contrast to asymptom of animals infected with pLGFD3-V, the mutated virus (pLG5-3-l-V) developed typical clinical progression in the corresponding experimentally infected animals. The results of the distinct differences in clinical profiles and viral dynamics before and after mutation of EIAV infectious clone will help to understand the protective mechanism of Chinese EIAV vaccine and shed light on novel HIV vaccine design.

Amino Acid Substitution↗
PubMed2004

Chicken anemia virus induced apoptosis: underlying molecular mechanisms.

In 1990, the chicken anemia virus (CAV) genome was cloned by us and proven to be representative for CAV isolates worldwide. This genome contains unique promoter/enhancer replication elements and genes. Upon infection of its target cells, CAV replicates via a double-stranded (ds) DNA intermediate. From this ds CAV molecule, a single mRNA is transcribed, which encodes for three distinct proteins VP1, VP2, and VP3 or apoptin. Its capsid contains only the VP1 protein. However, for the production of the neutralizing epitope, co-synthesis of VP1 and VP2 are needed. CAV genomes with mutations in the 12 bp insert of the promoter/enhancer region were shown to produce immunogenic functional CAV particles. Mutations in these and other regulatory elements of CAV might also decrease its virus load resulting in a reduced pathogenic effect. CAV causes fatal cytopathogenic effects in e.g. chicken thymocytes via apoptosis. Under in vitro conditions, CAV replicates only in transformed chicken cell lines, which indicates that at least a part of the CAV life-cycle requires transformed-like cellular events. In these transformed cell lines, the synthesis of the apoptin protein alone mimics the CAV-induced apoptosis, whereas the VP2 protein also harbors some apoptotic activity. Extensive studies on apoptin resulted in the characterization of domains essential for its apoptotic activity and nuclear localization, which seems to be related with its ability to induce apoptosis. Therefore, both VP2 and apoptin are of interest in reducing the pathogenicity of CAV infections. A series of biomedical studies on apoptin have been carried out in human cell systems, which are informative about the mechanism of CAV-induced apoptosis in chicken (transformed) cells. Synthesis of apoptin alone induces apoptosis in various human transformed and/or tumorigenic cell lines, but not in normal human diploid cells. A striking difference in the cellular localization of apoptin was observed in human normal diploid cells versus tumor cells. In all tumor cells, apoptin is located mainly in the heterochromatic regions of the nucleus, whereas in normal cells it is present in peri-nuclear structures. Apoptin contains a bipartite nuclear localization signal, and one domain that resemble a nuclear export signal. Elucidation of parts of the apoptin-induced apoptotic pathway revealed unique characteristics: apoptin-induced apoptosis is independent of the tumor suppressor p53. The anti-apoptotic protein Bcl-2 does not inhibit but even accelerates apoptin-induced apoptosis in tumor cells, whereas over expression of Bcl-2 in normal cells has no effect on the apoptin activity. Upstream caspases are not involved, whereas downstream caspase 3 is, but seems not to be essential. A number of novel proteins were shown to interact with apoptin in transformed cells. Future studies of apoptin, VP2 and related cellular proteins in chicken cells will unravel the regulatory aspects of CAV-induced apoptosis.

Animals↗
PubMed1996

H2-M mutant mice are defective in the peptide loading of class II molecules, antigen presentation, and T cell repertoire selection.

H2-M is a nonconventional major histocompatibility complex (MHC) class II molecule that has been implicated in the loading of peptides onto conventional class II molecules. We generated mice with a targeted mutation in the H2-Ma gene, which encodes a subunit for H2-M. Although the mutant mice express normal class II cell surface levels, these are structurally distinct from the compact SDS-resistant complexes expressed by wild-type cells and are predominantly bound by class II-associated invariant chain peptides (CLIPs). Cells from these animals are unable to present intact protein antigens to class II-restricted T cells and show reduced capacity to present exogenous peptides. Numbers of mature CD4+ T lymphocytes in mutant mice are reduced 3- to 4-fold and exhibit altered reactivities. Overall, this phenotype establishes an important role for H2-M in regulating MHC class II function in vivo and supports the notion that self-peptides contribute to the specificity of T cell positive selection.

Animals↗
PubMed2002

Raised serum ferritin predicts non-response to interferon and ribavirin treatment in patients with chronic hepatitis C infection.

BACKGROUND/AIM: Previous studies have indicated that response to interferon therapy is inversely proportional to the amount of body iron stores. We have studied the relationship between serum ferritin, transferrin saturation, liver iron, presence of HFE-C282Y gene mutation and response to treatment in patients with chronic hepatitis C infection. METHODS: Two hundred and fifty-six naive, HCV-RNA positive patients (60% males, median age 38 years, range 21-70) were treated with interferon and ribavirin for 6 months. Iron indices and the presence of the C282Y mutation were measured. In 242 (94%) patients iron deposition were determined by Perls staining method. Patients with negative HCV-RNA at 6 months after the end of treatment were defined as sustained viral responders. RESULTS: Non-responders (n = 127) had significantly higher median s-ferritin values compared with sustained viral responders (130 microg/L vs. 75 microg/L P < 0.001). There was no difference in transferrin saturation among the two response groups. Only 23% (4/7) of patients with Perls grade 1 in liver biopsies responded to treatment vs. 54% (122/225) patients without iron deposition (P = 0.02), however, 10/13-non-responders had HCV genotype one. Two patients (0.8%) were homozygous for the C282Y mutation, 36 patients were heterozygous (14%). Among mutation carriers 26/38 achieved sustained response compared with 102/216 non-carriers (68% vs. 48%, P = 0.02). In a multivariate analysis s-ferritin (P = 0.030) and C282Y carrier status (P = 0.012) remained independent predict of sustained response. CONCLUSIONS: Raised s-ferritin values predicate non-response to interferon-ribavirin therapy in hepatitis C patients. Response rate in C282Y mutation carriers seems greater than in non-carriers.

Adult↗
PubMed1997

Review article: the screening, diagnosis and optimal management of haemochromatosis.

Haemochromatosis was first recognized as a disease entity over a century ago and its hereditary nature recognized over 60 years ago. However it was only in late 1996 that the haemochromatosis gene was cloned and a single C282Y mutation confirmed as being the cause of all HLA-linked iron overload in Caucasian populations. Haemochromatosis is common, occurring in approximately 1 in 300 people in Caucasian populations, and untreated can cause serious morbidity and early death. However, the disease remains much underdiagnosed for reasons such as lack of awareness of the disease, the presence of normal liver function tests and the lack or non-specific nature of symptoms. A commercially available DNA-based test for the haemochromatosis gene is likely to be available in the near future but its place in the diagnosis and management of the disorder is not yet clear. Assessment of body iron stores by measurement of serum ferritin and transferrin saturation, hepatic iron stores and hepatic architecture by liver biopsy will remain important in the future. The haemochromatosis mutation itself has as yet no known influence on morbidity other than via iron loading and organ failure, in particular, hepatic cirrhosis. Thus, diagnosing patients before the development of hepatic cirrhosis is crucial because iron depletion by venesection treatment before the development of cirrhosis results in a normal life expectancy.

Genetic Testing↗
PubMed2002

The impact of the M184V substitution in HIV-1 reverse transcriptase on treatment response.

The M184V mutation in the HIV-1 reverse transcriptase gene is primarily associated with rapid, high-level lamivudine (3TC) resistance. It has also been observed to arise under selective pressure by abacavir, to which it confers low-level resistance. Although the development of viral drug resistance remains a major concern in antiretroviral therapy, it is known that some immunological and clinical benefit can still be derived from highly active antiretroviral therapy (HAART) regimens despite resistance-associated virological failure. This residual benefit on a failing regimen is commonly attributed to the preservation of fitness-reducing protease inhibitor (PI) resistance mutations under continued drug pressure. However, fitness-reducing nucleoside reverse transcriptase inhibitor (NRTI) mutations may also contribute to the effect. M184V is both common in the treated population and fitness-reducing. A number of studies, both of dual nucleoside therapy and HAART, have noted a residual treatment effect for 3TC despite the assumed or observed presence of M184V and high-level phenotypic resistance. The speed and consistency with which this mutation is selected by 3TC under suboptimal viral suppression therefore makes M184V a particularly interesting model for further clinical studies on the association of drug resistance with ongoing treatment benefit. While fitness considerations are likely to be a major contributor to the clinical observations noted, there are a number of other potential mechanisms that may contribute to a continuing response to 3TC in the presence of M184V. These include the delay and reversal of zidovudine (ZDV) resistance, hypersensitization to other NRTIs, reduced reverse transcriptase (RT) processivity and a possible reduction in RT pyrophosphorolysis. The full impact of M184V on therapeutic prospects will require further elucidation; ideally, the risk/benefit of preserving this substitution would be investigated in randomized trials. However, existing data suggest that the presence of this mutation may preserve some benefit in spite of the loss of 3TC susceptibility which, with further study, may prove valuable.

Antiretroviral Therapy, Highly Active↗
PubMed1999

Mechanism of recruitment of DnaB helicase to the replication origin of the plasmid pSC101.

Although many bacterial chromosomes require only one replication initiator protein, e.g., DnaA, most plasmid replicons depend on dual initiators: host-encoded DnaA and plasmid-encoded Rep initiator protein for replication initiation. Using the plasmid pSC101 as a model system, this work investigates the biological rationale for the requirement for dual initiators and shows that the plasmid-encoded RepA specifically interacts with the replicative helicase DnaB. Mutations in DnaB or RepA that disrupt RepA-DnaB interaction cause failure to load DnaB to the plasmid ori in vitro and to replicate the plasmid in vivo. Although, interaction of DnaA with DnaB could not substitute for RepA-DnaB interaction for helicase loading, DnaA along with integration host factor, DnaC, and RepA was essential for helicase loading. Therefore, DnaA is indirectly needed for helicase loading. Instead of a common surface of interaction with initiator proteins, interestingly, DnaB helicase appears to have at least a limited number of nonoverlapping surfaces, each of which interacts specifically with a different initiator protein.

Bacterial Proteins↗
PubMed2003

Prevalence of drug resistance mutations and non-B subtypes in newly diagnosed HIV-1 patients in Denmark.

The aim of this study was to monitor the prevalence of drug resistance mutations in newly diagnosed HIV-1 positive individuals in Denmark. In addition we assessed the prevalence of non-B subtypes based on phylogenetic analysis of the pol gene. Plasma samples from 104 newly diagnosed HIV-1 positive patients were obtained in the year 2000. The entire protease gene and 320 amino acids of the reverse transcriptase gene were genotyped. Sequences were obtained from 97 patients. No subjects displayed primary resistance mutations in the protease gene, whereas all carried 1 or more secondary mutations. Resistance mutations in the RT-gene associated with NRTI-resistance were found in 1 patient, who was infected with zidovudine resistant HIV-1 harbouring the M41L mutation in combination with T215S and L210S. The T215S mutation has been showed to be associated with reversion of zidovudine resistance. The T215S mutation was found in 1 additional patient. The subtype distribution was subtype B 59%, C 18%, A 8%, CRF02_AG 5%, CRF01_AE 4%, D 3% and G 2%. We found 2 patients (2%) with mutations associated with resistance in the RT-gene and none in the protease gene indicating a low prevalence of resistant HIV-1 in Denmark in the year 2000.

Adolescent↗
PubMed2004

Long-term virological effect of highly active antiretroviral therapy on cerebrospinal fluid and relationship with genotypic resistance.

The objective of this study was to assess the long-term virological response in cerebrospinal fluid (CSF) in patients treated with highly active antiretroviral therapy (HAART) and to compare this response to CSF and plasma human immunodeficiency virus (HIV) drug resistance profiles. Paired CSF and plasma specimens were drawn from 18 patients receiving HAART at baseline and after 9 to 70 months of therapy. At baseline, median HIV-1 RNA concentrations were 4.13 log10 copies/ml in CSF and 5.31 log10 copies/ml in plasma. At the time of on-therapy CSF sampling, HIV-1 RNA was undetectable in CSF from 13/18 patients (72%), and in plasma from 9/18 patients (50%). The genotypic analysis at baseline revealed reverse transcriptase (RT) resistance mutations in 7 of 11 (64%) CSF samples and in 8 of 11 (73%) plasma samples. No patient had protease resistance mutations, except for secondary mutations. At the time of virological failure in CSF, new RT and protease resistance mutations were found in both CSF and plasma of the two patients with both baseline and on-treatment paired evaluations. At long-term follow-up, the proportion of patients failing to respond virologically was lower in CSF than in plasma. Virological failure in CSF was associated with failure to respond in plasma and onset of new drug resistance mutations in both compartments.

AIDS Dementia Complex↗
PubMed2004

Quantitative effects of palivizumab and donor-derived T cells on chronic respiratory syncytial virus infection, lung disease, and fusion glycoprotein amino acid sequences in a patient before and after bone marrow transplantation.

A patient with respiratory syncytial virus (RSV) infection and severe combined immunodeficiency was studied during a 3-month period of bone marrow transplantation and palivizumab infusion. No RSV isolates with palivizumab escape mutations were identified. Donor lymphocytes, including CD8 cells, appeared to markedly reduce the RSV load but increased the pulmonary symptoms. Immunosuppressive therapy ameliorated lung disease but allowed the RSV load to rebound.

Amino Acid Sequence↗
PubMed2006

Identification of HIV type 1 group N infections in a husband and wife in Cameroon: viral genome sequences provide evidence for horizontal transmission.

HIV-1 is classified into three groups, M (major), N (non-M non-O), and O (outlier); each group arose from a separate transmission of SIVcpz into humans. HIV-1 group N was recently discovered and infections with this virus are rare with only eight documented cases. All group N infections have been found in Cameroon and there is no evidence of direct linkage between the infected patients. We report here the identification of HIV-1 group N infections in a husband and wife. The group N infection in the husband, 1131-03, was identified first based on seroreactivity in peptide EIAs and confirmed by PCR amplification of group N viral sequences. Subsequently the wife, 1015-04, was evaluated and confirmed to also be infected with a group N virus. Near full-length viral genomes were amplified and sequenced from each patient's specimen. The low level of diversity between the two viral sequences provides evidence of horizontal transmission of group N from one spouse to the other. Patient 1131-03 was receiving antiviral therapy consisting of reverse transcriptase inhibitors; the treatment appears effective for suppression of group N viral replication based on apparently low viral load in plasma specimens collected from the patient and the absence of drug resistance mutations in RT sequences amplified from 1131-03. This report brings to 10 the number of group N infections identified and to 5 the number of group N genomes sequenced. Although group N infections continue to be rare, group N is a pathogenic virus and its prevalence needs to be monitored.

Adult↗
PubMed2006

Successful treatment with atazanavir and lopinavir/ritonavir combination therapy in protease inhibitor-susceptible and protease inhibitor-resistant HIV-infected patients.

The combination of atazanavir (ATV) plus lopinavir/ritonavir (LPV/r) has been used in practice. However, clinical data supporting its use are limited. The objective of this study was to evaluate the efficacy and tolerability of regimens with ATV + LPV/r in protease inhibitor (PI)-susceptible and PI-resistant patients. A retrospective review of 2703 charts was performed to identify all patients who received ATV + LPV/r. From June 2003 to January 2005, 33 patients received ATV + LPV/r with nucleoside reverse transcriptase inhibitors (NRTIs) for 3 months or more. Virologic success (HIV-RNA < 400 copies per milliliter) was achieved in 30 patients (91%) in a median of 10 weeks (range, 2-68). Nineteen of the 23 patients (83%) who had ultrasensitive viral load (VL) assays were nondetectable. Among patients with 6 or more protease resistance (PR) mutations (PI-resistant), 11 of 14 (79%) achieved virologic success. Eleven of those received phenotypic testing (10 Virtual Phenotype, VircoLab, Baltimore, MD). Despite predicted phenotypic resistance to ATV (6 patients) and LPV/r (7 patients), virologic success was achieved in 4 of 6 (67%) and 4 of 7 (57%), respectively. The 3 PI-resistant patients who were virologic failures had extensive prior LPV/r use, 8-11 PR mutations, and predicted phenotypic resistance to LPV/r, but 2 of 3 had CD4 increases with ATV + LPV/r. Overall, 28 patients (85%) continue to tolerate ATV + LPV/r for a median of 32 weeks follow-up (range, 12-76). Combination ATV + LPV/r with NRTIs appears safe, tolerable, and efficacious in PI-resistant patients (>/=6 PR mutations) and predicted phenotypic resistance to ATV and LPV/r. Further studies of ATV + LPV/r in HIV-treatment are warranted.

Adult↗
PubMed1994

Structural elements of rps0 mRNA involved in the modulation of translational initiation and regulation of E. coli ribosomal protein S15.

Previous experiments showed that S15 inhibits its own translation by binding to its mRNA in a region overlapping the ribosome loading site. This binding was postulated to stabilize a pseudoknot structure that exists in equilibrium with two stem-loops and to trap the ribosome on its mRNA loading site in a transitory state. In this study, we investigated the effect of mutations in the translational operator on: the binding of protein S15, the formation of the 30S/mRNA/tRNA(fMet) ternary initiation complex, the ability of S15 to inhibit the formation of this ternary complex. The results were compared to in vivo expression and repression rates. The results show that (1) the pseudoknot is required for S15 recognition and translational control; (2) mRNA and 16S rRNA efficiently compete for S15 binding and 16S rRNA suppresses the ability of S15 to inhibit the formation of the active ternary complex; (3) the ribosome binds more efficiently to the pseudoknot than to the stem-loop; (4) sequences located between nucleotides 12 to 47 of the S15 coding phase enhances the efficiency of ribosome binding in vitro; this is correlated with enhanced in vivo expression and regulation rates.

Base Sequence↗
PubMed1994

Polynucleotide phosphorylase of Escherichia coli induces the degradation of its RNase III processed messenger by preventing its translation.

Polynucleotide phosphorylase, a 3' to 5' processive exoribonuclease is post-transcriptionally autocontrolled and it was previously shown that this control is dependent on a 5' processing by RNase III. In this paper, the mechanism of regulation is analyzed by studying the properties of a pnp-lacZ translational gene fusion. It is shown that this message is stable, even when processed by RNase III, and that the degradation rate is directly linked to the intracellular concentration of polynucleotide phosphorylase or to the pnp-lacZ messenger translation rate. Mutations able to decrease the level of repression are all located in the ribosome loading site. Taken together, these results suggest that polynucleotide phosphorylase is able to recognize specifically the processed messenger and to prevent its translation, thus allowing degradation of the message.

Base Sequence↗