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PubMed2000

Expression of the wax-specific condensing enzyme CUT1 in Arabidopsis.

The Arabidopsis thaliana gene CUT1 encodes a very-long-chain fatty acid-condensing enzyme required for the production of epicuticular wax in bolting stems. We have examined the expression pattern of CUT1 in Arabidopsis at different developmental stages and under different environmental conditions. RNA blot analysis showed that CUT1 was highly expressed in shoots, but not in roots. CUT1 expression was detectable throughout development. Light was required for CUT1 expression, and expression was increased by salt and drought treatments. The promoter region of the CUT1 gene was cloned, and 1.2 kb of the sequence 5' to the translation start codon was used to direct beta-glucuronidase (GUS) expression in transgenic plants. Histochemical and fluorometric (quantitative) GUS assays confirmed that the CUT1 promoter directed epidermal-specific expression and was highly active in Arabidopsis and in tobacco. A construct using the CUT1 promoter to drive CUT1 expression (CUT1p-CUT1) was used to transform Arabidopsis. Transgenic plants which had somewhat increased (overexpression) or greatly reduced (co-suppression) wax loads were recovered. Thus, the CUT1 promoter should be useful for genetic engineering applications that require epidermis-specific expression of genes.

Acyltransferases↗
PubMedDate not supplied

[The non-conventional transmissible agents at the origin of transmissible subacute spongiform encephalopathies].

The transmissible subacute spongiform human encephalopathies are neurological diseases, always fatal and with a prolonged incubation time. In infected patients, an accumulation of a host protein from the genes, the prion protein, is observed in proportionality to the infectious load. The prion protein gene is the major determinant of the genetic susceptibility in relation to subacute spongiform encephalopathies. On neuropathological examination, patients have a characteristic triad: neuronal vacuolisation, neuronal death and glial reaction. The nature of agents involved in these subacute spongiform encephalopathies is not known. Most authors think that the causal agent is a pathological form of the PrP protein partially resistant to proteinase K (the prion). For others, it is a more classical structure including an independent genome for which the prion protein will be either the receptor or the virulent factor. The apparition of bovine spongiform encephalopathy in the United Kingdom and of the new variant of Creutzfelt-Jakob disease brings into question the discovery of new subacute spongiform diseases and involves the proposition of efficacious protective measures for public and animal health.

Animals↗
PubMed2002

[Do polymorphisms of the SDF1 and CCR2b genes modify the course of hepatitis C or HIV/HCV co-infection?].

BACKGROUND AND OBJECTIVE: Complementary to the CCR5-Delta32 mutation polymorphisms in the genes of CCR2b (CCR2b-V64 I) and stromal derived factor (SDF)-1 (SDF-1 3'A) affect the course of the human immunodeficiency virus (HIV) infection. While the CCR5-Delta32 mutation is also increased in chronic hepatitis C virus (HCV) infection it is unclear, whether the CCR2b-V64 I and the SDF-1 3'A polymorphisms also are associated with chronic HCV infection. METHODS: We analyzed the frequencies of the CCR2b-V64I and SDF1 - 3'A mutation in patients with HIV/HCV coinfection (n = 130), HIV infection (n = 105), HCV infection (n = 153) and 112 healthy blood donors. We stratified each group into homozygous mutations, heterozygous mutations and homozygous wild types, respectively. The resulting subsets were compared with respect to HIV and HCV loads, CD4 and CD8 cell counts. RESULTS: The mutant SDF1 - 3'A allele was found at 20.3 % frequency in patients with HCV infection and at 20.4 % frequency in patients with HIV/HCV coinfection, respectively. It was present in 27.1 % of the patients with HIV infection and 27.9 % of the healthy controls (not significant). The number of SDF-1 3) A homozygous patients was highest in patients with HIV/HCV coinfection and significantly different compared to the Hardy-Weinberg equilibrium (p = 0.010, chi (2) = 9.15). However, CD4- and CD8-cell counts or viral loads were not affected by this mutation. The frequency of the CCR2b-V64 I allele was similar in all patient groups. However, CCR2b-V64 I heterozygous patients showed HIV loads that were threefold lower than in CCR2b wildtype patients (22.9 x 103 vs. 6.4 x 103 copies/ml, not significant). Furthermore, hepatitis C viral loads were reduced roughly by 30 %. CONCLUSION: These results suggest that the SDF1 - 3'A and CCR2b-V64I mutations do not affect the course of HCV and HIV/HCV infection in the same manner as does the CCR5-Delta32 mutation.

Adolescent↗
PubMed1976

Primary angle-closure glaucoma. Oculometry, epidemiology, and genetics in a high risk population.

The ocular dimensions in patients suffering from primary angle-closure glaucoma (a.c.g.) have been studied in several clinical series, chiefly in Caucasians. The epidemiology and aetiology of a.c.g. are less well known although genetic factors seem to be involved. Eskimos have recently been shown to constitute a high risk population with respect to a.c.g. Consequently, a series of oculometric, epidemiologic, and genetic studies among Greenland Eskimos was undertaken. Besides the immediate purpose, prevention of blindness in this population, the survey had important general aspects and the following main results were obtained: 1a) Ocular dimensions, as well as clinical symptoms, in Eskimo a.c.g. patients correspond closely to those of a.c.g. reports from other ethnic groups and 1b) ocular dimensions of the anterior segment in the general Eskimo population deviate conspicuously towards the low level characteristic of all samples of a.c.g. patients. 2) A.c.g. prevalence rates were estimated at 1.6% in males and 5.1% in females of the general population aged 40 years or more. The epidemiology of a.c.g. seems to reflect closely the variations of axial anterior chamber depth (ACD) according to race (Eskimo, Caucasian), sex and age. Empirical a.c.g. risk estimates, depending on the ACD value, were obtained in elderly females. 3) A relatively shallow chamber was found in 1st and 2nd degree relatives of a.c.g. patients, in close agreement with an earlier study in Caucasians (Törnquist 1953). However, also in the general Eskimo population a pronounced familial resemblance with respect to ACD and corneal diameter was found. Thus the family studies indicate that the size of the anterior chamber shows a mainly genetic determination, which probably constitutes the genetic basis of a.c.g. as well. With this background a hypothesis is discussed, which interprets the small anterior chambers in Eskimos as a result of genetic adaptation to arctic environment. Corneal protection may have been the significant advantage and the a.c.g. load in elderly persons a relatively less important cost.

Adolescent↗
PubMed2026

The genetic code at the balance point of error and demand.

The origin and organizing principles of the genetic code remain central problems in molecular evolution. The low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure is optimized for robustness to mutations and translational errors. For the construction of effective molecular machines, the repertoire of encoded amino acids must also be diverse enough in physicochemical features. Here, we examine whether the standard genetic code can be understood as a near-optimal solution balancing these two objectives: minimizing error load and aligning codon assignments with the naturally occurring amino acid composition. Using simulated annealing, we explore this trade-off across a broad range of parameters. We find that the standard genetic code resides near an optimum in the fitness landscape of possible genetic codes. The degeneracy of the code plays a dual role, minimizing mistranslation errors while matching codon multiplicity to amino acid usage frequencies. As a result, uniform codon usage alone is sufficient to recover the empirical amino acid composition, without any additional bias. It is a highly effective solution that balances fidelity against resource availability constraints. A comparative analysis of natural variants also reveals a functional decoupling: error robustness acts as a rigid global constraint determined by code topology, whereas compositional alignment serves as a more flexible variable that adapts to lineage-specific demands. These results support a multi-objective optimization framework in which the genetic code reflects a balance between translational fidelity and proteomic demand.

Genetic Code↗
PubMed1999

Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community.

We used a culture-independent approach, namely, thermal gradient gel electrophoresis (TGGE) analysis of ribosomal sequences amplified directly from community DNA, to determine changes in the structure of the microbial community following phenol shocks in the highly complex activated sludge ecosystem. Parallel experimental model sewage plants were given shock loads of chlorinated and methylated phenols and simultaneously were inoculated (i) with a genetically engineered microorganism (GEM) able to degrade the added substituted phenols or (ii) with the nonengineered parental strain. The sludge community DNA was extracted, and 16S rDNA was amplified and analyzed by TGGE. To allow quantitative analysis of TGGE banding patterns, they were normalized to an external standard. The samples were then compared with each other for similarity by using the coefficient of Dice. The Shannon index of diversity, H, was calculated for each sludge sample, which made it possible to determine changes in community diversity. We observed a breakdown in community structure following shock loads of phenols by a decrease in the Shannon index of diversity from 1.13 to 0.22 in the noninoculated system. Inoculation with the GEM (Pseudomonas sp. strain B13 SN45RE) effectively protected the microbial community, as indicated by the maintenance of a high diversity throughout the shock load experiment (H decreased from 1.03 to only 0.82). Inoculation with the nonengineered parental strain, Pseudomonas sp. strain B13, did not protect the microbial community from being severely disturbed; H decreased from 1.22 to 0.46 for a 3-chlorophenol-4-methylphenol shock and from 1.03 to 0.70 for a 4-chlorophenol-4-methylphenol shock. The catabolic trait present in the GEM allowed for bioprotection of the activated sludge community from breakdown caused by toxic shock loading. In-depth TGGE analysis with similarity and diversity algorithms proved to be a very sensitive tool to monitor changes in the structure of the activated sludge microbial community, ranging from subtle shifts during adaptation to laboratory conditions to complete collapse following pollutant shocks.

Bacteria↗
PubMed2006

High stability of yellow fever 17D-204 vaccine: a 12-year restrospective analysis of large-scale production.

We have retrospectively analyzed 12 bulk lots of yellow fever vaccine Stamaril, produced between 1990 and 2002 and prepared from the same seed lot that has been in continuous use since 1990. All vaccine batches displayed identical genome sequence. Only four nucleotide substitutions were observed, compared to previously published sequence, with no incidence at amino-acid level. Fine analysis of viral plaque size distribution was used as an additional marker for genetic stability and demonstrated a remarkable homogeneity of the viral population. The total virus load, measured by qRT-PCR, was also homogeneous pointing out reproducibility of the vaccine production process. Mice inoculated intracerebrally with the different bulks exhibited a similar average survival time, and ratio between in vitro potency and mouse LD(50) titers remained constant from batch-to-batch. Taken together, these data demonstrate the genetic stability of the strain at mass production level over a period of 12 years and reinforce the generally admitted idea of the safety of YF17D-based vaccines.

Animals↗
PubMed2003

Genetic basis for hypertrophic cardiomyopathy: implications for diagnosis and treatment.

Familial hypertrophic cardiomyopathy is a genetic disease defined by cardiac hypertrophy in the absence of an increased external load. It is the most common inherited cardiac disorder occurring in 1 in 500 individuals. Ten genes exhibiting over 200 mutations have been identified. However, about 75% are due to mutations in just three genes: e-myosin heavy chain, cardiac troponin T, and myosin binding protein-C. Certain phenotypes are more common with certain genes, such as the myosin binding protein-C gene, which induces the disease predominantly in the fifth or sixth decade of life. Genetic animal models in the mouse and rabbit have helped to elucidate the pathophysiology. The primary defect imparted by the specific mutation alters contractile function, which stimulates release of various growth factors that induce secondary cardiac hypertrophy and fibrosis. Placebo single-blinded studies in the mouse indicate that losartan reverses the phenotype; in the rabbit, simvastatin essentially reversed the phenotype after 12 weeks of therapy. Clinical trials are ongoing in human familial hypertrophic cardiomyopathy.

Animals↗
PubMed2005

Quasispecies heterogeneity within the E1/E2 region as a pretreatment variable during pegylated interferon therapy of chronic hepatitis C virus infection.

A series of 29 patients undergoing treatment for chronic hepatitis C virus (HCV) genotype 1 infection with pegylated alpha-2a interferon plus ribavirin were studied for patterns of response to antiviral therapy and viral quasispecies evolution. All patients were treatment naive and had chronic inflammation and fibrosis on biopsy. As part of an analysis of pretreatment variables that might affect the outcome of treatment, genetic heterogeneity within the viral E1-E2 glycoprotein region (nucleotides 851 to 2280) was assessed by sequencing 10 to 15 quasispecies clones per patient from serum-derived PCR products. Genetic parameters were examined with respect to response to therapy based on serum viral RNA loads at 12 weeks (early viral response) and at 24 weeks posttreatment (sustained viral response). Nucleotide and amino acid quasispecies complexities of the hypervariable region 1 (HVR-1) were less in the responder group in comparison to the nonresponder group at 12 weeks, and genetic diversity was also less both within and outside of the HVR-1, with the difference being most pronounced for the non-HVR-1 region of E2. However, these genetic parameters did not distinguish responders from nonresponders for sustained viral responses. Follow-up studies of genetic heterogeneity based on the HVR-1 in selected responders and nonresponders while on therapy revealed greater evolutionary drift in the responder subgroup. The pretreatment population sequences for the NS5A interferon sensitivity determinant region were also analyzed for all patients, but no correlations were found between treatment response and any distinct genetic markers. These findings support previous studies indicating a high level of genetic heterogeneity among chronically infected HCV patients. One interpretation of these data is that early viral responses are governed to some extent by viral factors, whereas sustained responses may be more influenced by host factors, in addition to effects of viral complexity and diversity.

Adolescent↗
PubMed2003

In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading.

In vivo characterization of regulatory polymorphisms is a key requirement for next-generation human genetic analysis. Here we describe haploChIP, a method that uses chromatin immunoprecipitation (ChIP) and mass spectrometry to identify differential protein-DNA binding in vivo associated with allelic variants of a gene. We demonstrate this approach with the imprinted gene SNRPN. HaploChIP showed close correlation between the level of bound phosphorylated RNA polymerase II at the SNRPN locus and allele-specific expression. Application of the approach to the TNF/LTA locus identified functionally important haplotypes that correlate with allele-specific transcription of LTA. The haploChIP method may be useful in high-throughput screening for common DNA polymorphisms that affect gene regulation in vivo.

Alleles↗
PubMed1976

[The radiation load of the Swiss population due to radiodiagnosis].

It is recommended that the so-called "genetically significant dose" (GSD) be applied as a quantitative index of the radiation exposure of the genetic material of a population, i.e. the dose which, if received by every member of the population, would be expected to produce the same total genetic injury to the population as do the actual doses received by the various individuals. The GSD of the Swiss population for the year 1971 was calculated on the basis of information received from physicians concerning approximately 60 000 patients. Exeripmental determination of the gonad dose was done in various hospitals with the aid of TLD dosimeter, and sensitive high-pressure and normal-pressure ionization chambers. The results show that the annual rate of increase of X-ray diagnostic examinations is 3-4% in Switzrland as elsewhere. The GSD for Switzerland amounted in 1971 to 42-43 mrad per person as compared with 22 mrad in 1957. The "annual mean marrow dose of a population" can be calculated from the single doses received from each part of active bone marrow irradiated in the course of an X-ray examination and, as in the case of the genetically significant dose, from the demographic figures mentioned. The annual mean marrow dose (1971) for the Swiss population was tentatively calculated using the values of the mean marrow dose per examination of the UK survey of 1957/58 and amounts to about 121 mrad. Barium meal contributes about 30% of the total, while intravenous pyelography, carium enema, lumbar spine and mass miniature radiographies each account for about 10%.

Bone Marrow↗
PubMed2025

High-affinity CD16A polymorphism associated with reduced risk ofsevere COVID-19.

CD16A is an activating Fc receptor on NK cells that mediates antibody-dependent cellular cytotoxicity (ADCC), a key mechanism in antiviral immunity. However, the role of NK cell-mediated ADCC in SARS-CoV-2 infection remains unclear, particularly whether it limits viral spread and disease severity or contributes to the immunopathogenesis of COVID-19. We hypothesized that the high-affinity CD16AV176 polymorphism influences these outcomes. Using an in vitro reporter system, we demonstrated that CD16AV176 is a more potent and sensitive activator than the common CD16AF176 allele. To assess its clinical relevance, we analyzed 1,027 patients hospitalized with COVID-19 from the Immunophenotyping Assessment in a COVID-19 cohort (IMPACC), a comprehensive longitudinal dataset with extensive transcriptomic, proteomic, and clinical data. The high-affinity CD16AV176 allele was associated with a significantly reduced risk of ICU admission, mechanical ventilation, and severe disease trajectories. Lower anti-SARS-CoV-2 IgG titers were correlated to CD16AV176; however, there was no difference in viral load across CD16A genotypes. Proteomic analysis revealed that participants homozygous for CD16AV176 had lower levels of inflammatory mediators. These findings suggest that CD16AV176 enhances early NK cell-mediated immune responses, limiting severe respiratory complications in COVID-19. This study identifies a protective genetic factor against severe COVID-19, informing future host-directed therapeutic strategies.

Humans↗
PubMed2001

CCR5 promoter polymorphisms in a Kenyan perinatal human immunodeficiency virus type 1 cohort: association with increased 2-year maternal mortality.

The CCR5 chemokine receptor acts as a coreceptor with CD4 to permit infection by primary macrophage-tropic human immunodeficiency virus type 1 (HIV-1) strains. The CCR5Delta32 mutation, which is associated with resistance to infection in homozygous individuals and delayed disease progression in heterozygous individuals, is rare in Africa, where the HIV-1 epidemic is growing rapidly. Several polymorphisms in the promoter region of CCR5 have been identified, the clinical and functional relevance of which remain poorly defined. We evaluated the effect of 4 CCR5 promoter mutations on systemic and mucosal HIV-1 replication, disease progression, and perinatal transmission in a cohort of 276 HIV-1-seropositive women in Nairobi, Kenya. Mutations at positions 59353, 59402, and 59029 were not associated with effects on mortality, virus load, genital shedding, or transmission in this cohort. However, women with the 59356 C/T genotype had a 3.1-fold increased risk of death during the 2-year follow-up period (95% confidence interval [CI], 1.0-9.5) and a significant increase in vaginal shedding of HIV-1-infected cells (odds ratio, 2.1; 95% CI, 1.0-4.3), compared with women with the 59356 C/C genotype.

Adult↗
PubMed2007

Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution.

Populations of RNA viruses are often characterized by abundant genetic variation. However, the relative fitness of these mutations is largely unknown, although this information is central to our understanding of viral emergence, immune evasion, and drug resistance. Here we develop a phylogenetic method, based on the distribution of nonsynonymous and synonymous changes, to assess the relative fitness of polymorphisms in the structural genes of 143 RNA viruses. This reveals that a substantial proportion of the amino acid variation observed in natural populations of RNA viruses comprises transient deleterious mutations that are later purged by purifying selection, potentially limiting virus adaptability. We also demonstrate, for the first time, the existence of a relationship between amino acid variability and the phylogenetic distribution of polymorphisms. From this relationship, we propose an empirical threshold for the maximum viable deleterious mutation load in RNA viruses.

Amino Acid Sequence↗
PubMed1996

Homocysteine response to methionine challenge in four obligate heterozygotes for homocystinuria and relationship with cystathionine beta-synthase mutations.

Fasting and post-methionine load plasma total homocysteine concentrations were investigated in the parents of two homocystinuric patients. Three genetic mutations in the cystathionine beta-synthase gene were found. In the patient of family 1, a frequent Caucasian mutation. T833C, was found on one allele, while the mutation on the other allele has not yet been defined. In the patient of family 2, a mutation C569T, recently described by Sperandeo and colleagues, was found on one allele, while a novel mutation, G346A, was characterized on the other allele. The frequent gene mutation T833C was detected in a heterozygous mother who, surprisingly, exhibited strictly normal fasting and post-methionine load homocysteinaemia. In contrast, in the other family, we found a novel mutation (G346A) in the mother located near Lys 119, the putative binding site of phosphopyridoxal phosphate. This mother exhibited increased fasting and post-methionine load homocysteinaemia. These observations could explain the conflicting results reported for vascular pathologies in parents of homocystinuric patients and direct the search for genetic mutations in these vascular pathologies.

Adolescent↗
PubMed1996

The Genetic Variance Maintained by Pleiotropic Mutation

The equilibrium genetic variance of a quantitative trait under mutation-selection balance is analysed using a population genetic model. I assume that mutations have both phenotypic effects on a quantitative trait and deleterious effects on fitness itself. Hence, genetic variance is generated by pleiotropic effects of such deleterious mutations. If the deleterious effect is large, the predicted genetic variance is notably smaller than the equilibrium genetic variance predicted by the mutation-selection balance model with the rare-alleles approximation. The model further suggests that the ratio of the equilibrium genetic variance to the variance of allelic effects of new mutations is proportional to the ratio of total mutation load to the net selection coefficient on new mutations. It is also suggested that the net selection coefficient is equal to the per-generation proportional increment of genetic variance by new mutations.

Journal Article↗
PubMed2000

The spectrum of hearing loss due to mitochondrial DNA defects.

Heteroplasmic mitochondrial DNA (mtDNA) defects are an important cause of neurological disease. Although hearing impairment is common in patients with mtDNA defects, the spectrum and pathophysiology of the hearing loss is not well characterized. We therefore studied the relationship between cochlear and brainstem auditory function in 23 patients harbouring a range of different mtDNA mutations. Based upon the pure tone audiogram, patients fell into three distinct groups: (i) normal hearing, (ii) mild to moderate predominantly high frequency hearing loss, and (iii) severe or profound hearing loss at all frequencies. Within this study group only certain genetic defects were associated with hearing loss, and for individuals harbouring the A3243G point mutation, the severity of the hearing loss correlated with the percentage level of mutated mtDNA (mutation load) in skeletal muscle. The 10 patients who had a moderate hearing loss or less had normal brainstem auditory evoked responses and MRI, but it was not possible to interpret the brainstem auditory evoked responses in 13 patients with severe hearing loss. Otoacoustic emissions were absent in patients with a moderate or more severe hearing loss. These findings are consistent with a predominantly cochlear origin for the hearing deficit, which is determined by the precise genetic defect and the percentage mutation load.

Adult↗
PubMed1993

[Molecular medicine].

The introduction of new methods into medicine, such as recombinant DNA, production of monoclonal antibodies, and particularly polymerase chain reactions, yielded much knowledge and information in fields like preventive medicine (prenatal screening), reproduction strategies (preimplantation diagnosis of genetic defects), molecular diagnosis (oncological and infectious diseases), gene therapy, etc. In many areas the practical use of these sophisticated approaches has become technically feasible yet due to the high cost involved it is still limited. The introduction of some screening programs will be associated with ethical problems of serious impact. To date we can already establish presymptomatic diagnosis of some progressive diseases for which however no therapy is available. Potential abuse of confidential genetic information as well as the possibilities of using gene therapy for "corrective eugenics" are loaded with serious ethical problems. Prospective doctors have to be prepared for this situation in the course of undergraduate studies of medicine. (Ref. 11.)

Abortion, Eugenic↗