ICAAC eyes PIs, NNRTIs, and STIs.
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Animals↗
SEARCH · PubMed Health
Results for “mutation load”
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HIV resistance: the new enemy.
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Anti-HIV Agents↗
Neurology update.
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AIDS Dementia Complex↗
Virological response in multidrug-experienced HIV-1-infected subjects failing highly active combination regimens after shifting from lamivudine to didanosine.
The aim of this study (the RESCUE trial) was to verify the effect of a shift from a lamivudine-containing to a didanosine-containing regimen on viral replication in HIV-1-infected subjects who had experienced prior treatment failure. Sixteen patients (didanosine-experienced in 14/16 cases) were consecutively enrolled: eight patients shifted from lamivudine to didanosine without other changes in their drug regimen. The other eight shifted from lamivudine to didanosine and changed one or more of their other drugs according to their physician's judgement. At the time of the regimen shift, all the subjects exhibited a high-level phenotypic resistance to both zidovudine and lamivudine with changes at codons 70-219 in 100% of cases, at codon 215 in 13 of 16 patients, and the M184V substitution in 13/16 patients. Phenotypic susceptibility to didanosine was maintained in the majority of cases (14/16) despite the high prevalence of changes at codon 184. A statistically significant decrease in viral load (P<0.005) without a significant increase in CD4 lymphocytes (P=0.514) was observed after 3 and 6 months from the introduction of the didanosine-containing regimen. These findings suggest the possibility of achieving a viral load response to didanosine-containing regimens in patients with reverse transcriptase (RT) M184V mutations who were previously treated with this drug and its possible use in salvage combinations.
Acquired Immunodeficiency Syndrome↗
Protease inhibitor-sparing regimens: new evidence strengthens position.
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Alkynes↗
Analysis of a long-term discrepancy in drug-targeted genes in plasma HIV-1 RNA and PBMC HIV-1 DNA in the same patient.
Drug-resistance genotypes were investigated in a patient under treatment with anti-HIV drugs. Since the drug resistance-associated mutations in plasma HIV-1 RNA and proviral DNA in peripheral blood mononuclear cells (PBMCs) were inconsistent, changes were followed over time, and the discrepancy was shown to persist for a long period. In plasma HIV-1 RNA, D67N, K70R, T215Y, and Y188L were present in the reverse transcriptase (RT) region, and two primary mutations, I84V and L90M, were noted in the protease (Pro) region. In contrast, in proviral DNA, no drug resistance-associated mutations were found in the RT region, and mutations such as L90L/M were only infrequently present in the Pro region. This situation persisted for more than 3 years. In addition, sequencing analysis of the V3 loop in the envelope gene showed that non-syncytium-inducing/macrophage-tropic viruses contribute to acquisition of drug resistance. In this study, drug-resistant viruses were produced primarily at macrophages, and drug-sensitive viruses were maintained in PBMCs as a reservoir.
Amino Acid Sequence↗
Proliferative characteristics of chronic crypt cells in C57BL/6J and A/J mice as predictors of subsequent tumor formation.
It has been proposed that the number and extent of tumors formed after chronic exposure to dimethylhydrazine (DMH) can be predicted by the indigenous number and distribution of DNA-synthesizing cells in the murine colonic mucosa, and that this sensitivity to DMH is genetically determined. In order to test this hypothesis we studied two genetically distinct inbred strains of mice; the DMH-sensitive A/J (A) mouse, and the relatively DMH-resistant C57BL/6J (B) mouse before and after a single exposure to DMH. The untreated A strain had the longer crypt column [33.2 +/- 0.8 (SD) cells versus 28.8 +/- 0.9 cells], a higher absolute number of labeled cells per crypt column (4.4 +/- 0.6 versus 2.6 +/- 0.9), a greater labeling index (13.4 +/- 1.6% versus 9.1 +/- 2.9%), a wider proliferative compartment, and a greater number and percentage of labeled cells in the middle and upper thirds of the crypt than the untreated B strain. After acute exposure to DMH the A strain lost 14 +/- 3% of their total body weight, while the B strain lost 0.5 +/- 2% total body weight 48 h post-DMH. There was an initial loss of cryptal cells, a drop in the labeling index, and a subsequent increase and overshoot in the number of labeled cells and the labeling index. This pattern of cell loss and recovery over time was parallel in both strains, and thus cannot explain the differences in ultimate tumor formation after chronic exposure to the carcinogen. The data are consistent with the theory that the susceptibility to DMH carcinogenesis can be predicted by the indigenous proliferative characteristics of the murine colonic mucosa. The acute proliferative response to DMH in these strains is similar and parallel; thus ultimate tumor load may depend on long term effects such as the establishment of stable transmissible mutations.
1,2-Dimethylhydrazine↗
[Generalized epilepsy disclosing medium-chain-acyl-CoA dehydrogenase deficiency].
BACKGROUND: Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is the most common inherited defect of fatty acid beta-oxidation. As it causes life-threatening symptoms, it is mandatory to diagnose deficiencies of this enzyme in families. CASE REPORT: A boy was admitted at the age of 3 months because of a recent attack of generalized seizures. His parents were second cousins and one of his 2 sisters, 6 years old, suffered from epilepsy. At admission, the patient had moderate hepatomegaly; he was given clonazepam and phenytoin because of persistent status epilepticus. He developed a fever (temp.: 39 degrees) and a rash 24 hours later. A viral etiology was suggested by CSF contents of 104 cells/mm3 and 1 g/l protein. The patient was given aciclovir. Blood glucose, transaminases, ammonia, lactate, pyruvate and amino acids levels were normal. Analysis of urine by GC-MS revealed a large lactate peak and dicarboxylic acids, unsaturated dicarboxylic acids, hydroxyhexanoate, 7-hydroxyoctanoate, hexanoylglycine and suberylglycine. This profile indicated a MCAD deficiency. The plasma contained partially oxidized medium-chain fatty acids, such as octanoic acid and especially 4-decenoic acid. the diagnosis was confirmed by a phenylpropionate loading test and specific enzyme assay in fibroblasts. Molecular studies identified a G 985 mutation in the patient and revealed that the parents were heterozygotes for the mutation. The condition of the patient at the age of 18 months is excellent; he has a regular, adequate caloric intake and avoids fasting. He has not taken anti-epileptic drugs for the past 6 months. CONCLUSION: There is no typical clinical presentation of MCAD-deficiency; the most frequent features are vomiting and lethargy. Episodic hypoglycemia has been reported, but hypoglycemia was not found in our patient. Molecular studies will allow neonatal diagnosis of the next affected siblings.
Acyl-CoA Dehydrogenase↗
Interferon resistance of hepatitis C virus genotype 1b: relationship to nonstructural 5A gene quasispecies mutations.
A 40-amino-acid sequence located in the nonstructural 5A (NS5A) protein of hepatitis C virus genotype 1b (HCV-1b) was recently suggested to be the interferon sensitivity-determining region (ISDR), because HCV-1b strains with an ISDR amino acid sequence identical to that of the prototype strain HCV-J were found to be resistant to alpha interferon (IFN-alpha) whereas strains with amino acid substitutions were found to be sensitive (N. Enomoto, I. Sakuma, Y. Asahina, M. Kurosaki, T. Murakami, C. Yamamoto, N. Izumi, F. Marumo, and C. Sato, J. Clin. Invest. 96:224-230, 1995; N. Enomoto, I. Sakuma, Y. Asahina, M. Kurosaki, T. Murakami, C. Yamamoto, Y. Ogura, N. Izumi, F. Marumo, and C. Sato, N. Engl. J. Med. 334:77-81, 1996). We used single-strand conformation polymorphism (SSCP) analysis, combined with cloning and sequencing strategies, to characterize NS5A quasispecies in HCV-1b-infected patients and determine the relationships between pre- and posttreatment NS5A quasispecies mutations and the IFN-alpha sensitivity of HCV-1b. The serine residues involved in phosphorylation of NS5A protein were highly conserved both in the various patients and in quasispecies in a given patient, suggesting that phosphorylation is important in NS5A protein function. A hot spot for amino acid substitutions was found at positions 2217 to 2218; it could be the result of either strong selection pressure or tolerance to these amino acid replacements. The proportion of synonymous mutations was significantly higher than the proportion of nonsynonymous mutations, suggesting that genetic variability in the region studied was the result of high mutation rates and viral replication kinetics rather than of positive selection. Sustained HCV RNA clearance was associated with low viral load and low nucleotide sequence entropy, suggesting (i) that the replication kinetics when treatment is started plays a critical role in HCV-1b sensitivity to IFN-alpha and (ii) that HCV-1b resistance to IFN-alpha could be conferred by numerous and/or related mutations that could be patient specific and located at different positions throughout the viral genome and could allow escape variants to be selected by IFN-alpha-stimulated immune responses. No NS5A sequence appeared to be intrinsically resistant or sensitive to IFN-alpha, but the HCV-J sequence was significantly more frequent in nonresponder quasispecies than in sustained virological responder quasispecies, suggesting that the balance between NS5A quasispecies sequences in infected patients could have a subtle regulatory influence on HCV replication.
Amino Acid Sequence↗
Mutations in the interferon-sensitivity determining region of hepatitis C virus and transcriptional activity of the nonstructural region 5A protein.
Amino acid (aa) mutations in the interferon-sensitivity determining region (ISDR) (aa position 237-276 of the nonstructural region 5A [NS5A] protein consisting of 447 amino acids) of hepatitis C virus (HCV) are related to increased interferon sensitivity and low viral load, but its mechanism has not been clarified. Recently, the NS5A protein has been reported to have a transcriptional activation function, like other viral transactivator proteins known to repress interferon-induced gene expression, and the ISDR overlaps one of the acidic amino acid regions, putative domains conferring this activity. In the present study, we investigated the transcriptional activation function of the ISDR itself and the effect of amino acid mutations in the ISDR on this activity. The full-length or truncated NS5A cDNA with different ISDR sequences was cloned into a yeast or mammalian expression vector to form a fusion protein consisting of the GAL4 DNA-binding domain (GAL4-DBD) and NS5A protein. Following transfection, the transcriptional activities of these constructs were determined using beta-galactosidase (yeast) or chloramphenicol acetyltransferase (CAT) (mammalian cell) reporter gene expression under the control of GAL4 binding sites. In yeast, both the full-length sequence of NS5A-R (a clone with one aa mutation in the ISDR) and NS5A-S (a derivative of NS5A-R with six aa mutations in the ISDR) had no distinguishable transcriptional activity, whereas an amino-terminal deletion construct of NS5A-R (aa position 228-447) lacking 227 aa, showed remarkable activity with the relative value of 117.0 over that of the backbone vector. The same deletion mutant of NS5A-S produced five times higher activity with the relative value of 575.0, indicating that aa mutations in the ISDR profoundly affect this transcriptional activity. In a hepatoma cell line, HuH-7, the transcriptional activity was more prominent with a construct consisting of only the ISDR and short flanking sequences (aa 228-284) than larger deletion constructs of NS5A-R. Analysis using six different ISDR clones revealed that different mutations enhanced this activity to various extent compared with the wild-type ISDR. In particular, site-directed mutagenesis targeted to the aa position 252 showed that this aa residue had profound influence on the activity. These results suggest that the ISDR has a transcriptional activity, and it is enhanced by aa mutations that are also related to decreased viral load and increased interferon sensitivity. The possible association between transcriptional activation and interferon sensitivity or viral replication should be studied further.
Amino Acid Sequence↗
Deleterious mutation and the evolution of eusociality.
Certain arguments concerning the evolution of eusociality form a classic example of the application of the principles of kin selection. These arguments center on the different degrees of relatedness of potential beneficiaries of an individual's efforts, for example a female's higher relatedness to her sisters than to her daughters in a haplodiploid system. This type of reasoning is insufficicnt to account for the evolution and maintainence of sexual reproduction, because parthenogenic females produce offspring that are more closely related to them than are offspring produced sexually. Among the forces invoked to explain sexual reproduction is deleterious mutation. This factor can be shown to favor eusociality as well, because siblings produced by helping carry fewer deleterious alleles on average than would offspring. The strength of this effect depends on the genomewide deleterious mutation rate, U, and on the selection coefficient, s, associated with deleterious alleles. For small s, the effect depends approximately on the product Us. This phenomenon illustrates that an assumption implicit in some analyses-that the relatedness of an individual to an actor is all that matters to its value to that actor-can fail for the evolution of eusociality as it does for the evolution of sex.
Animals↗
Frequent human leukocyte antigen class I alleles are associated with higher viral load among HIV type 1 seroconverters in Thailand.
The loss of viral control by the host may be due to the evolution of viruses with mutations that limit presentation by human leukocyte antigen (HLA) to cytotoxic T cells. The authors hypothesized that the consequence of such evolution might be that persons with common HLA class I alleles would be less able to control viremia, on average, than would those with rare alleles. HLA class I typing was completed for 128 injection drug users who seroconverted in a prospective cohort study in Bangkok, Thailand. Logistic regression was used to model viral load (greater than or equal to the median) at 9 and 12 months after seroconversion with an HLA score that profiled the relative prevalence of each individual's alleles. At 12 months after seroconversion, injection drug users with the most common HLA alleles (highest quartile HLA score) had an almost 4-fold increased risk for higher viral load (> or = 32,055 copies/mL) than injection drug users with less common HLA alleles (adjusted odds ratio, 3.92; 95% confidence interval, 1.3-11.8). These findings support the importance of frequency-dependent effects of host genes on HIV type 1 evolution in different populations and suggest that HLA-driven viral evolution critically influences control of viremia in early HIV type 1 infection.
Alleles↗
Paralysis periodica paramyotonica caused by SCN4A Arg1448Cys mutation.
Paralysis periodica paramyotonica is an overlapping disease that shares the features of paramyotonia characteristic of paramyotonia congenita (PC) and periodic paralysis characteristic of hyperkalemic periodic paralysis. We report the case of a 23-year-old man with paralysis periodica paramyotonica. His father and a younger brother also exhibited a similar phenotype. A SCN4A Arg1448Cys mutation was detected in this family. The affected family members exhibited marked shifts in compound muscle action potential amplitudes on exercise test, and muscle weakness could be induced by potassium loading and cold exposure. This case demonstrates that SCN4A Arg1448Cys can produce paralysis periodica paramyotonica. Other genetic or environmental factors may modulate the manifestation of SCN4A Arg1448Cys mutation.
Adult↗
The effect of the acrodermatitis enteropathica mutation on zinc uptake in human fibroblasts.
The acrodermatitis enteropathica (AE) mutation affects intestinal zinc absorption. Our goal was to determine whether the AE mutation affects zinc uptake in human fibroblasts. Zinc uptake was determined during initial rates of uptake (10 min) following incubation in HEPES/saline buffer. Zinc uptake (from 0.25 to 1 microM) into normal fibroblasts was significantly greater than into the AE fibroblasts (p < 0.05). In order to identify factors that may alter cellular zinc uptake and be affected by the AE mutation, zinc uptake in the presence of albumin or bicarbonate was measured. Albumin restricted zinc uptake in both normal and AE fibroblasts, whereas bicarbonate stimulated zinc uptake in the normal fibroblasts. The effect of bicarbonate on zinc uptake in the AE fibroblasts was significantly reduced in both the Pronase-sensitive and Pronase-resistant compartments. Following loading of the fibroblasts with 1 microM zinc for 60 min, zinc efflux and retention were measured. The AE mutation did not affect zinc retention compared to normal fibroblasts. We conclude that the AE mutation affects both zinc binding to the cell surface and its translocation across the plasma membrane into the cell, possibly mediated through a defective anionic exchange mechanism.
Acrodermatitis↗
A sensitive in-house RT-PCR genotyping system for combined detection of plasma HIV-1 and assessment of drug resistance.
Quantification of the viral burden and identification of drug resistant mutations are important laboratory tools in the management of HIV-1 infected patients. However, widespread use of assays for viral load determination and genotyping is still hampered by the high cost. Here, an in-house RT-PCR-sequencing assay for HIV-1 drug resistance monitoring with the potential to be used both as a qualitative assay to detect the virus in plasma and as a genotyping system is described. A total of 377 clinical samples, collected from 374 HIV-infected patients of diverse geographic origin, were tested. The nested RT-PCR for amplification of the protease reverse transcriptase gene was found positive for 350 (92.8%) and 346 (91.8%) of 377 samples, respectively. All amplification-failures were due to viral loads of below 500 copies/ml. However, low viral load does not exclude amplification since 80.2 and 76% of 121 samples with viral loads of less than 500 copies/ml were amplified successfully for protease and reverse transcriptase, respectively. The high sensitivity of the assay was independent of the HIV-subtype, with a broad range of different HIV-1 subtypes tested. In conclusion the RT-PCR-direct sequencing method is convenient for the sensitive detection and subsequent genotyping of plasma RNA from a broad range of different HIV-1 subtypes. The assay enables the accurate follow-up of patients under treatment at a significantly reduced cost compared to the currently available commercial assays for viral load assessment and genotyping.
Anti-HIV Agents↗
Conformation-sensitive gel electrophoresis as an ideal high-throughput strategy for accurate detection of sequence variations in DNA: screening hTomm and hTimm genes.
Conformation-sensitive gel electrophoresis is a heteroduplex-based method that is particularly well suited to high-throughput analyses. Its simplicity makes it amenable to various adaptations and modifications to enhance its applicability to genome-wide mutation scans. Technical aspects that markedly improve the conformation-sensitive gel electrophoresis performance by combining high throughput and high resolution of the bands facilitating the interpretation of the results are described here. The authors report some of the results they have obtained in the screening of the exon 1 of human Timm8A gene as an example of the suitability of the conformation-sensitive gel electrophoresis-based protocol that has been adapted to optimize its throughput, speed, and simplicity in the recognition of both heterozygous and homozygous DNA mutations. The higher throughput is achieved by using 12 batches per gel. The length of the gel is sufficient for an adequate well-to-read distance for each batch that allows a clear distinction and resolution of the conformation-sensitive gel electrophoresis bands. Standardization of the procedure using multichannel pipettes reduces the preparation time of the 96-well PCRs to 10 min and also accelerates the gel loading. The resulting bands give high-quality images, allowing easy detection of known as well as novel mutations.
DNA↗
The relationship between HBV-DNA levels and cirrhosis-related complications in Chinese with chronic hepatitis B.
We studied the hepatitis B virus (HBV)-DNA levels below which the development of cirrhosis-related complications became unlikely in chronic hepatitis B (CHB). Seventy-nine Chinese CHB patients with cirrhosis-related complications and 158 age-, sex- and HBeAg status-matched patients without complications were enrolled. The precore and core promoter mutations were detected by the Line Probe assay (LiPA). HBVDNA levels were determined by Digene assay and Cobas Amplicor Monitor test. Patients with complications had higher HBVDNA levels than those without complications (P = 0.02). HBeAg-positive patients with complications had similar alanine transferase (ALT) and HBVDNA levels and frequency of precore mutations, but higher frequency of core promoter mutations (P = 0.003), compared with those without complications. Anti-HBe-positive patients with complications had higher ALT and HBVDNA levels (P < 0.01) but similar frequency of precore and core promoter mutations, compared with those without complications. Anti-HBe patients (24.5%) with complications had HBVDNA levels <10(4) copies/mL. The major factor for the development of cirrhotic complications was viral loads but cirrhotic complications continued to develop in patients with HBVDNA levels below 10(4) copies/mL.
Adult↗
New insights into the spring-loaded conformational change of influenza virus hemagglutinin.
Influenza virus hemagglutinin undergoes a conformational change in which a loop-to-helix "spring-loaded" conformational change forms a coiled coil that positions the fusion peptide for interaction with the target bilayer. Previous work has shown that two proline mutations designed to disrupt this change disrupt fusion but did not determine the basis for the fusion defect. In this work, we made six additional mutants with single proline substitutions in the region that undergoes the spring-loaded conformational change and two additional mutants with double proline substitutions in this region. All double mutants were fusion inactive. We analyzed one double mutant, F63P/F70P, as an example. We observed that F63P/F70P undergoes key low-pH-induced conformational changes and binds tightly to target membranes. However, limited proteolysis and electron microscopy observations showed that the mutant forms a coiled coil that is only approximately 50% the length of the wild type, suggesting that it is splayed in its N-terminal half. This work further supports the hypothesis that the spring-loaded conformational change is necessary for fusion. Our data also indicate that the spring-loaded conformational change has another role beyond presenting the fusion peptide to the target membrane.
3T3 Cells↗