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PubMed2005

Optimality of codon usage in Escherichia coli due to load minimization.

The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslational errors and point mutations, an ability which in term is designated "load minimization". One parameter involved in calculating the load minimizing property of the genetic code is codon usage. In most bacteria, synonymous codons are not used with equal frequencies. Different factors have been proposed to contribute to codon usage preference. It has been shown that the codon preference is correlated with the composition of the tRNA pool. Selection for translational efficiency and translational accuracy both result in such a correlation. In this work, it is shown that codon usage bias in Escherichia coli works so as to minimize the consequences of translational errors, i.e. optimized for load minimization.

Codon↗

PubMed2003

Impact of highly active antiretroviral therapy and immunologic status on hepatitis C virus quasispecies diversity in human immunodeficiency virus/hepatitis C virus-coinfected patients.

This study analyzes the effect of highly active antiretroviral therapy (HAART), and thus immunologic status, on hepatitis C virus (HCV) load and quasispecies diversity in patients coinfected with the human immunodeficiency virus (HIV) and HCV. Three cohorts of coinfected patients were analyzed retrospectively over a period of 7 to 10 months: group A was antiretroviral drug naïve at baseline and then on HAART for the remainder of the study, group B did not receive antiretroviral therapy at any point, and group C was on HAART for the entire study. HCV quasispecies diversity was analyzed by sequencing hypervariable region 1. In a longitudinal analysis, there was no significant change from baseline in any immunologic, virologic, or quasispecies parameter in any of the three groups. However, in comparison to groups A and B, group C had significantly higher CD4+- and CD8+-cell counts, a trend toward a higher HCV load, and significantly increased number of HCV clones, entropy, genetic distance, and ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (Ka/Ks). In addition, CD4+-cell count was positively correlated with HCV load, genetic distance, and Ka. Interestingly, patients infected with HCV genotype 2 or 3 had a significantly higher CD4+-cell count, HCV load, genetic distance, and Ka/Ks than those infected with genotype 1. These results suggest that there is no immediate effect of HAART on HCV but that, with prolonged HAART, immune restoration results in an increase in HCV load and quasispecies diversity.

Adult↗

PubMed1995

Supply and transport of peptides presented by class I MHC molecules.

Three observations suggest that the proteasome, transporter associated with antigen processing (TAP) and class I MHC molecules are co-adapted for the generation, transport and loading of specific peptides. Firstly, TAP preferentially transports peptides close in length to the optimum for class I loading; secondly, genetic variation in TAP specificity focusing in the carboxy-terminal of the peptide correlates with preferences among class I molecules for different peptide carboxy-termini; thirdly, TAP associates directly with empty class I molecules and is released by successful peptide loading. This conclusion puts in question the significance for class I loading of proteolytic processing and peptide generation in the endoplasmic reticulum.

Animals↗

PubMed1998

Cytomegalovirus polymerase chain reaction viraemia in patients receiving ganciclovir maintenance therapy for retinitis.

OBJECTIVES: To determine whether recurrence of polymerase chain reaction (PCR) viraemia during maintenance ganciclovir for cytomegalovirus (CMV) retinitis correlates with (i) CMV disease at a new anatomical site, (ii) progression of the presenting retinitis, or (iii) acquisition of genetic changes in gene UL97 associated with resistance to ganciclovir. DESIGN: A previously described cohort of 45 patients presenting with first episode retinitis was followed clinically using ophthalmoscopy and serial tests for PCR viraemia for a median of 7 months. CMV viral load and genetic markers of ganciclovir resistance were measured in PCR-positive samples. METHODS: PCR amplification of the glycoprotein B region of CMV and quantitative competitive PCR assays were employed. Genetic changes in UL97 were identified by sequencing/point mutation assay. RESULTS: PCR viraemia correlated significantly with new episodes of CMV disease (P=0.011) and a trend was seen for the association with progression of retinitis (P=0.07). Amongst the 14 patients PCR-positive during maintenance ganciclovir, 10 (71%) had genetic markers of resistance. None of these patients became PCR-negative in blood after reinduction ganciclovir therapy compared with three out of four without markers of resistance (P=0.022). CONCLUSIONS: CMV PCR viraemia correlated strongly with the development of new episodes of CMV disease. Most patients with progression of retinitis remained PCR-negative in blood, consistent with therapeutic failure due to poor intraocular penetration of ganciclovir. However, the minority who were PCR-positive in blood may have reinfected their eye, and frequently had markers of ganciclovir resistance. The implications of these findings for the management of patients with CMV disease are discussed.

Antiviral Agents↗

PubMed2001

Genetically modified tumour vaccines: an obstacle race to break host tolerance to cancer.

The development of genetically modified tumour vaccines (GMTV) has been prompted by a better understanding of antitumour immune responses and genetic engineering technologies, as well as the identification of numerous tumour antigens (TA) in several malignancies which occasionally induce spontaneous tumour regressions. Cellular vaccines are based on autologous or allogeneic tumour cells genetically engineered to secrete different cytokines, co-stimulatory molecules, or allogeneic HLA molecules in order to provide a strong stimulatory signal together with the presented TA. Another promising approach that is targeted towards breaking immune tolerance to TA, exploits dendritic cells (DC) loaded or genetically modified with TA (and sometimes cytokines). Effective nonviral and viral gene delivery systems have been constructed including a third generation of adenoviral, lentiviral and hybrid vectors. Studies in mice demonstrated that therapeutic, curative immune responses might be elicited by GMTV. Promising results from animal studies are rarely seen in human trials. Several reasons, such as numerous escape mechanisms of slowly evolving spontaneous tumours and immune incompetence of advanced patients, are major concerns. Improved monitoring of immune responses to GMTV is essential to distinguish between responders and non-responders in order to tailor immune therapy strategy to the individual patient.

Animals↗

PubMed2003

CHIP: Defining a dimension of the vulnerability to attention deficit hyperactivity disorder (ADHD) using sibling and individual data of children in a community-based sample.

We are taking a quantitative trait approach to the molecular genetic study of attention deficit hyperactivity disorder (ADHD) using a truncated case-control association design. An epidemiological sample of children aged 5 to 15 years was evaluated for symptoms of ADHD using a parent rating scale. Individuals scoring high or low on this scale were selected for further investigation with additional questionnaires and DNA analysis. Data in studies like this are typically complicated. In the study reported on here, individuals have from 1 to 4 questionnaires completed on them and the sample is composed of a mixture of singletons and siblings. In this paper, we describe how we used a genetic hierarchical model to fit our data, together with a twin dataset, in order to estimate genetic factor loadings. Correlation matrices were estimated for our data using a maximum likelihood approach to account for missing data. We describe how we used these results to create a composite score, the heritability of which was estimated to be acceptably high using the twin dataset. This score measures a quantitative dimension onto which molecular genetic data will be mapped.

Adolescent↗

PubMed1993

Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site.

From genetic and biochemical evidence, we previously proposed 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. Here, we use "toeprint" experiments with Moloney murine leukemia virus reverse transcriptase to analyze the effect of S15 on the formation of the ternary mRNA-30S-tRNA(fMet) complex. We show that the binding of the 30S subunit on the mRNA stops reverse transcriptase near position +10, corresponding to the 3' terminus of the pseudoknot, most likely by stabilizing the pseudoknot conformation. Furthermore, S15 is found to stabilize the binary 30S-mRNA complex. When the ternary 30S-mRNA-tRNA(fMet) complex is formed, a toeprint is observed at position +17. This toeprint progressively disappears when the ternary complex is formed in the presence of increasing concentrations of S15, while a shift from position +17 to position +10 is observed. Beside, RNase T1 footprinting experiments reveal the simultaneous binding of S15 and 30S subunit on the mRNA. Otherwise, we show by filter binding assays that initiator tRNA remains bound to the 30S subunit even in the presence of S15. Our results indicate that S15 prevents the formation of a functional ternary 30S-mRNA-tRNA(fMet) complex, the ribosome being trapped in a preternary 30S-mRNA-tRNA(fMet) complex.

Base Sequence↗

PubMed2003

TT virus in the nasal secretions of children with acute respiratory diseases: relations to viremia and disease severity.

The natural history and pathogenic potential of the recently identified TT virus (TTV) are currently a matter of intensive investigation. In an attempt to shed some light on these issues, nasal and blood specimens of 1- to 24-month-old children hospitalized with a clinical diagnosis of acute respiratory disease (ARD) were examined for the presence, load, and genetic characteristics of TTV. The results have indicated that at least in young children, the respiratory tract not only represents a route by which abundant TTV can be shed into the environment but also may be a site of primary infection and continual replication. Although we found no compelling evidence that TTV was the direct cause of ARD in some of the children studied, the average loads of TTV were considerably higher in patients with bronchopneumonia (BP) than in those with milder ARD, raising interesting questions about the pathophysiological significance of TTV at this site. Furthermore, group 4 TTV was detected almost exclusively in children with BP.

Acute Disease↗

PubMed2004

Inflammatory gene load is associated with enhanced inflammation and early carotid atherosclerosis in smokers.

BACKGROUND AND PURPOSE: Smoking acts as a pro-inflammatory stimulus. Inflammation may provide a key mechanism by which smoking causes atherosclerosis. If so, then the degree to which an individual mounts an inflammatory response is likely to influence atherosclerosis severity. This study examined the impact of inflammatory gene polymorphisms and gene-smoking interactions on common carotid artery intima-media thickness (IMT), a measure of early atherosclerosis. METHODS: In a community population (n=1000), mean IMT was determined using ultrasound. This population was genotyped for 6 polymorphisms in 4 inflammatory genes: IL-6-174, IL-6-572, and IL-6-597; IL-1-beta-31; IL-1 receptor antagonist VNTR and CD14-159. Serum IL-6 levels were measured in the first 500 subjects. Genotypes/haplotypes associated with higher IL-6 levels were designated "inflammatory haplotypes." A gene load score was calculated, in which 2 represented individuals homozygous for > or =2 inflammatory genotypes/haplotypes and 0 was homozygous for none. RESULTS: Increasing gene load of inflammatory genotypes was associated with a linear increase in serum IL-6 levels (P=0.018) and increased carotid artery IMT (P=0.003). There was a significant interaction between gene load and smoking status on carotid IMT (P for interaction=0.002). Specifically, in smokers, carriers of inflammatory haplotypes had significantly increased age- and sex-adjusted IMT (IL-6-174C/IL-6-572G/IL-6-597A, P=0.005; IL-1-beta-31T/IL-1RN*2,P=0.04; CD14-159CC, P=0.028). CONCLUSIONS: These findings support the hypothesis that inflammation and cytokine responses provide a key mechanism by which smoking causes atherogenesis. Secondly, they highlight the importance of gene-environment, and gene-gene-environment interactions in the pathogenesis of atherosclerosis.

Aged↗

PubMedDate not supplied

Relationships between TT virus infection and hepatitis C virus response to interferon therapy in doubly infected patients.

A group of 24 well-characterized patients doubly infected with hepatitis C virus (HCV) and TT virus (TTV) were studied to evaluate whether the loads and number or identity of the genogroups of TTV they carried could affect the response of HCV infection to interferon-alpha (IFN) treatment. The features of HCV infection in the study patients provided a fair representation of the variables that are usually found in considering patients for IFN treatment. The same was true for the features of TTV infection. In particular, plasma loads of TTV varied over a wide range in individual patients, and infection with multiple TTV genogroups was extremely frequent. TTV genogroups 1 and 3 were the most prevalent, followed by genogroups 4 and 5. The HCV response to IFN was evaluated by measuring plasma viraemia at 24 hours and 30 days after initiation of treatment. The results showed that the TTV parameters investigated had little or no impact on the response of HCV to therapy. Due to study design, these results do not exclude that the presence of a concomitant TTV infection can affect how HCV infection responds to treatment. However, they indicate that, should such effects exist, they would be independent on load and genetic features of the infecting TTV.

Adult↗

PubMed1986

Catecholamines in kidneys of normotensive and genetically hypertensive rats. Effects of salt load.

The tissue content of norepinephrine, dopamine, and epinephrine was determined in different zones of the kidney in normotensive Sprague-Dawley and Otago Wistar rats and in genetically hypertensive Otago Wistar rats. One kidney in each animal was chronically denervated to allow estimation of the neuronal contribution to renal catecholamine content. In all strains, the renal cortex contained negligible amounts of nonneuronal norepinephrine and dopamine, while outer and inner medullary layers contained progressively larger amounts. Nonneuronal epinephrine was distributed fairly evenly through cortex and medulla. Neuronal norepinephrine content was similar in inner and outer cortex, substantially less in outer medulla, and not discernible in inner medulla. The amounts of neuronal dopamine were consistent with its localization predominantly in noradrenergic nerves. The renal cortices of normotensive Wistar rats contained more neuronal norepinephrine and less neuronal dopamine than those of Sprague-Dawley rats, and the cortices of hypertensive Wistar rats contained slightly more norepinephrine than those of normotensive Wistar rats. In both normotensive strains, long-term salt loading decreased selectively the neuronal norepinephrine in renal cortex. By contrast, in hypertensive animals, cortical norepinephrine was not reduced by salt loading. These results indicate that the genetically hypertensive rat may have an abnormal sympathetic reflex response to increased blood volume.

Animals↗

PubMed2003

Associations between back pain history and lumbar MRI findings.

STUDY DESIGN: Retrospective monozygotic twin cohort study. OBJECTIVES: Our goal was to investigate the associations between different spinal MRI findings and current, past year, and lifetime low back pain after adjusting for occupational physical loading, smoking, genetics, and early family influences. SUMMARY OF BACKGROUND DATA: The role of spinal pathology in back symptoms continues to be controversial. METHODS: The study participants consisted of 115 monozygotic male twin pairs 35 to 69 years of age. The qualitatively assessed MRI parameters were as follows: disc height, bulging, herniations, anular tears, osteophytes, spinal stenosis, and endplate changes. Signal intensity was measured quantitatively. RESULTS: After controlling for age, disc height was associated with all back pain variables studied and anular tears with LBP frequency and intensity during the 12 months before imaging. Both were associated with lifetime frequency of low back pain interfering with daily activities, disability, and intensity of the worst lifetime pain episode. Other MRI findings did not explain the various symptom histories. Adjusting for physical loading in the past 12 months increased the associations of anular tears and "low back pain today" and 12-month low back pain parameters. After controlling for genotype and other familial influences, the within-pair differences in disc height and anular tears accounted for 6% to 12% of the total variance in the within-pair differences of low back pain variables. CONCLUSION: These findings raise new questions about the underlying mechanisms of LBP. The sensitivities of the only significant MRI parameters, disc height narrowing and anular tears, are poor, and these findings alone are of limited clinical importance.

Adult↗

PubMed1976

Evaluation and re-evaluation of genetic radiation hazards in man. III. Other relevant data and risk assessment.

Some of the advances in mammalian radiation genetics, human genetics and cytogenetics that were made during the last 2-3 years and that have either a direct bearing on, or that may be potentially useful in, the evaluation of genetic radiation hazards in man have been examined. Among these are (1) the new data on the incidence of genetic diseases in man; (2) the latest results of the study of mortality rates among children born to survivors of the atomic bombings of Hiroshima and Nagasaki; (3) new data on the radiation-induction of reciprocal translocations in human spermatogonia; (4) new results from radiation studies with mice on skeletal mutations, autosomal recessive lethals, sex-chromosome losses, translocation induction and recovery etc., and (5) a re-analysis of the earlier data on dose-rate effects for the induction of specific locus mutations in mouse spermatogonia. Using the pertinent new information as a basis, quantitative estimates are presented employing both a direct method of expressing risks in terms of effects per unit dose of irradiation and the indirect doubling-dose method of expressing these as increments over the load of genetic disorders occurring spontaneously in man.

Chromosome Aberrations↗

PubMed2006

Assessment of simple movements reflects impairment in Huntington's disease.

Clinical rating, caudate atrophy, disturbed movement performance, neuropsychological testing, and age-related genetic disease load (CAG index) are tools that reflect impairment after onset of Huntington's disease (HD). Objectives were to compare scored HD symptoms, results of neuropsychological testing and of instrumental measurement of simple motion sequences, assess caudate atrophy and CAG index, and investigate their relation to each other in 131 subjects of various HD stages. Caudate atrophy and CAG index significantly increased in advanced HD patients. Motor test results significantly differed between HD patients and 49 controls, but not between HD gene carriers and controls. Instrumental test outcomes, scored HD intensity, caudate atrophy, and CAG index significantly correlated to each other. Neuropsychological testing, which we only performed in the HD gene carriers and the previously untreated HD patients, reflected the early appearance of HD symptoms and correlated with the motor test results. Results of our applied instrumental tool measure impaired movement performance, which is not specific for HD, but reflects the various methods assessed and the slowly evolving symptoms of the degenerative process in HD.

Adult↗

PubMed2005

A threefold genetic allee effect: population size affects cross-compatibility, inbreeding depression and drift load in the self-incompatible Ranunculus reptans.

A decline in population size can lead to the loss of allelic variation, increased inbreeding, and the accumulation of genetic load through drift. We estimated the fitness consequences of these processes in offspring of controlled within-population crosses from 13 populations of the self-incompatible, clonal plant Ranunculus reptans. We used allozyme allelic richness as a proxy for long-term population size, which was positively correlated with current population size. Crosses between plants of smaller populations were less likely to be compatible. Inbreeding load, assessed as the slope of the relationship between offspring performance and parental kinship coefficients, was not related to population size, suggesting that deleterious mutations had not been purged from small populations. Offspring from smaller populations were on average more inbred, so inbreeding depression in clonal fitness was higher in small populations. We estimated variation in drift load from the mean fitness of outbred offspring and found enhanced drift load affecting female fertility within small populations. We conclude that self-incompatibility systems do not necessarily prevent small populations from suffering from inbreeding depression and drift load and may exacerbate the challenge of finding suitable mates.

Alleles↗

PubMed2003

Assessment of complex movements reflects dysfunction in Huntington's disease.

Results of various complex instrumental tools, rating scales, caudate atrophy and CAG repeat length may reflect the severity of Huntington's disease (HD). A simple assessment task for dysfunction due to disease is the standardized, computer based performance of peg insertion. The objectives of our study were to compare scored HD symptoms, computed bicaudate diameter ratio (BDR), age related genetic disease load (CAG index = [CAG-35.5 x age]) and peg insertion scores between asymptomatic 34 HD gene carriers, 89 previously untreated HD patients with psychiatric or motor symptoms, or both, and 51 treated HD patients. We measured the period of the total time taken to insert 25 pegs from a rack into a series of appropriate holes, calculated the CAG index, estimated the bicaudate diameter ratio (BDR) of a current brain CT and scored the HD patients under blind conditions. Times for the peg insertion task significantly differed between HD patients and controls, but not between HD gene carriers and controls. BDR and CAG index reflected the increase of symptoms in HD. Peg insertion results and scored severity of HD, BDR and CAG index significantly correlated with each other. Peg insertion scores are not specific diagnostic markers for HD, but they reflect clinical symptoms of neurodegeneration. The performance of peg insertion involves visuospatial cognition, self-elaboration of internal strategies, sorting and planning of movement. Therefore peg insertion particularly reflects executive dysfunction in early HD and additionally motor impairment in advanced HD.

Adult↗

PubMed1992

Gene mutations in myelodysplasia.

The myelodysplastic syndrome is a paradigm of human preleukaemia. Normal haemopoiesis is progressively displaced by an abnormal clone derived from a mutated stem cell. The initial mutation is unknown but its occurrence may be related to the overall load of random mutations which are a consequence of both intrinsic DNA defects and external mutagens. Evolution of the pathological population is marked by an increasing load of genetic lesions at the molecular and cytogenetic levels. Ras mutations can be detected in the blood of about 50% of MDS patients. Fms mutations are less common but these lesions can be found both in patients and in haematologically normal subjects who have previously received cytotoxic therapy suggesting that they can occur early in the preleukaemic process. Clonal haemopoiesis in the absence of either ras or fms mutations can occur in these subjects. The data suggest the inability of mutant ras or fms genes alone to produce observable preleukaemic changes but that subjects with these mutations may be predisposed to future MDS. Ras mutations are a common accompaniment of a wide variety of malignancies and experimental transfection of the mutant gene can induce a malignant phenotype in cultured cells. There are many possible mechanisms for this transformation which may be relevant in a clinical context. Experimentally observed effects include a direct influence on the cell cycle, the induction of drug resistance and the stimulation of autocrine growth factor production. It may eventually be possible to define which gene mutations are important in conferring a malignant state, which determine phenotype and which are of incidental significance.

Genes, fms↗

PubMed2004

The epidemic of obesity and changes in food intake: the Fluoride Hypothesis.

The epidemic of obesity is worldwide. It will be followed by an epidemic of diabetes. Although there is a genetic basis for obesity and diabetes, the current epidemic reflects the failure of our ancient genes to cope with a modern toxic environment. To put it another way, the genetic background loads the gun, but the environment pulls the trigger. Diet, lifestyle and exercise are the cornerstones of current approaches to treating obesity. However, these approaches that depend on individuals making lifestyle changes have been ineffective in preventing the epidemic. An alternative model views obesity as an epidemiological disease with food(s) and other environmental agents acting on the host to produce disease. The consumption patterns for many foods have changed over the past 30 years, but the increase in the consumption of high-fructose corn syrup (HFCS) for soft drinks is far and away the largest. Moreover, the rise in HFCS intake is an environmental insult that has occurred at exactly the same time as obesity began to increase in prevalence. Rising soft drink consumption is associated with a decrease in milk consumption and a decrease in calcium intake, which has an inverse relationship to body mass index (BMI). To combat the epidemic of obesity, we need new strategies that flow from the epidemiological model. The Fluoride Hypothesis for obesity proposes that we can make environmental changes that when made, will reduce the epidemic of obesity, in much the same way as fluoride reduced the incidence of dental disease. Fluoride-like strategies can work without the personal effort required by changes in lifestyle. In this context, fluoride is also an acronym for treatment and prevention of obesity: For Lowering Universal Obesity Rates are Implement ideas that Don't demand Effort (FLUORIDE).

Animals↗