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PubMed2005

A genetic code Boolean structure. II. The genetic information system as a Boolean information system.

A Boolean structure of the genetic code where Boolean deductions have biological and physicochemical meanings was discussed in a previous paper. Now, from these Boolean deductions we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory. In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96 x 10(25) bits per kg. In addition to this, for the experimental estimations of the minimum energy dissipation in genetic logic operations, we present two postulates: (1) the energy Ei (i=1,2,...,20) of amino acids in the messages conveyed by proteins is proportional to the value of information, and (2) amino acids are distributed according to their energy Ei so the amino acid population in proteins follows a Boltzmann distribution. Specifically, in the genetic message carried by the DNA from the genomes of living organisms, we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.

Algorithms↗

PubMed2005

Ideas about heredity, genetics, and 'medical genetics' in Britain, 1900-1982.

The aim of this paper is to understand how evolving ideas about heredity and genetics influenced new medical interests and practices and, eventually, the formation of 'medical genetics' as a medical specialism in Britain. I begin the paper by highlighting the social and institutional changes through which these ideas passed. I argue that, with time, there was a decisive convergence in thought that combined ideas about the familial aspects of heredity and the health needs of populations with an omnibus 'genetic' approach to health and illness that focused on the structures and activities of chromosomes and genes in individuals. I show how this convergence in thought was spurred on, first, by innovations in genetic science and technology in the years after 1960, and, second, by negotiated protocols and standards of medical practice worked out by bodies such as the relevant royal colleges, the linked associations and societies for medical professionals, affected training and research authorities, and the state. The notion of 'medical genetics' in Britain consequently gained a semblance of unanimity over its basic reference points and arrived at a meaning directly tributary to current acceptance of the term in the context of a medical specialism.

Eugenics↗

PubMed1999

The Emerging Importance of Genetics in Epidemiologic Research III. Bioinformatics and statistical genetic methods.

PURPOSE: To outline potential benefits of integrating recent developments in bioinformatics and statistical genetics with traditional epidemiologic studies to localize genes influencing complex phenotypes and examine genetic effects on disease susceptibility. METHODS: An overview of bioinformatic and statistical approaches for localizing disease-susceptibility genes as well as challenges associated with identifying functional DNA variants and context-dependent genetic effects concludes this three-part series on the importance of genetics in epidemiologic research. RESULTS: Rapidly evolving bioinformatic and statistical methods are providing invaluable information on newly-discovered genes and molecular variation influencing human diseases that is readily available to epidemiologic researchers. CONCLUSIONS: Integrating bioinformatics and molecular biotechnology with epidemiologic methods of assessing disease risk is rapidly expanding our ability to identify genetic influences on complex human diseases. These technological advances are likely to have a profound impact on current knowledge of complex disease etiology, and may reveal novel approaches to disease treatment and prevention.

Data Interpretation, Statistical↗

PubMed2002

Genetic markers in the study of Anisakis typica (Diesing, 1860): larval identification and genetic relationships with other species of Anisakis Dujardin, 1845 (Nematoda: Anisakidae).

Genetic variation at 21 gene-enzyme systems was studied in a sample of an adult population of Anisakis typica (Diesing, 1860) recovered in the dolphin Sotalia fluviatilis from the Atlantic coast of Brazil. The characteristic alleles, detected in this population, made it possible to identify as A. typica, Anisakis larvae with a Type I morphology (sensu Berland, 1961) from various fishes: Thunnus thynnus and Auxis thazard from Brazil waters, Trachurus picturatus and Scomber japonicus from Madeiran waters, Scomberomorus commerson, Euthynnus affinis, Sarda orientalis and Coryphaena hippurus from the Somali coast of the Indian Ocean, and Merluccius merluccius from the Eastern Mediterranean. Characteristic allozymes are given for the identification, at any life-stage and in both sexes, of A. typica and the other Anisakis species so far studied genetically. The distribution of A. typica in warmer temperate and tropical waters is confirmed; the definitive hosts so far identified for this species belong to delphinids, phocoenids and pontoporids. The present findings represent the first established records of intermediate/paratenic hosts of A. typica and extend its range to Somali waters of the Indian Ocean and to the Eastern Mediterranean Sea. A remarkable genetic homogeneity was observed in larval and adult samples of A. typica despite their different geographical origin; interpopulation genetic distances were low, ranging from D(Nei)=0.004 (Eastern Mediterranean versus Somali) to D(Nei)=0.010 (Brazilian versus Somali). Accordingly, indirect estimates of gene flow gave a rather high average value of Nm = 6.00. Genetic divergence of A. typica was, on average, D(Nei)=1.12 from the members of the A. simplex complex (A. simplex s.s, A. pegreffii, A. simplex C) and D(Nei)=1.41 from A. ziphidarum, which all share Type I larvae; higher values were found from both A. physeteris (D(Nei)=2.77)

Alleles↗

PubMed2000

Genetic epidemiologic studies on age-specified traits. NIA Aging and Genetic Epidemiology Working Group.

This commentary calls attention to the value of combining genetic and epidemiologic methods in studies to understand the determinants of two crucial aspects of aging: ages at which certain outcomes (e.g., disease, mortality) occur and rates of change with age of individual's characteristics (e.g., physiologic functions, disease risk factors). Inclusion of age in the specification of traits in genetic epidemiologic studies could lead to improved strategies to increase healthy life expectancy and evaluate individuals' risk for age-related morbidity. Special issues that make genetic epidemiologic approaches important for studies of age-specified phenomena as well as opportunities and challenges for such studies are discussed, including study designs, sampling frames, databases, analytic tools, and related methodological issues. This commentary is based on a report prepared by the Aging and Genetic Epidemiology Working Group, convened by the National Institute on Aging to review opportunities for research on the genetic epidemiology of aging-related outcomes. The report, which contains more extensive discussion, literature review, and references, is available on the World Wide Web at http://www.nih.gov/nia/conferences/GeneticReport111199.htm.

Age Factors↗

PubMed2006

Fine-scale genetic structure among genetic individuals of the clone-forming monotypic genus Echinosophora koreensis (Fabaceae).

BACKGROUND AND AIMS: For rare endemics or endangered plant species that reproduce both sexually and vegetatively it is critical to understand the extent of clonality because assessment of clonal extent and distribution has important ecological and evolutionary consequences with conservation implications. A survey was undertaken to understand clonal effects on fine-scale genetic structure (FSGS) in two populations (one from a disturbed and the other from an undisturbed locality) of Echinosophora koreensis, an endangered small shrub belonging to a monotypic genus in central Korea that reproduces both sexually and vegetatively via rhizomes. METHODS: Using inter-simple sequence repeats (ISSRs) as genetic markers, the spatial distribution of individuals was evaluated using Ripley's L(d)-statistics and quantified the spatial scale of clonal spread and spatial distribution of ISSR genotypes using spatial autocorrelation analysis techniques (join-count statistics and kinship coefficient, F(ij)) for total samples and samples excluding clones. KEY RESULTS: A high degree of differentiation between populations was observed (phi(ST(g)) = 0.184, P < 0.001). Ripley's L(d)-statistics revealed a near random distribution of individuals in a disturbed population, whereas significant aggregation of individuals was found in an undisturbed site. The join-count statistics revealed that most clones significantly aggregate at < or = 6-m interplant distance. The Sp statistic reflecting patterns of correlograms revealed a strong pattern of FSGS for all four data sets (Sp = 0.072-0.154), but these patterns were not significantly different from each other. At small interplant distances (< or = 2 m), however, jackknifed 95% CIs revealed that the total samples exhibited significantly higher F(ij) values than the same samples excluding clones. CONCLUSION: The strong FSGS from genets is consistent with two biological and ecological traits of E. koreensis: bee-pollination and limited seed dispersal. Furthermore, potential clone mates over repeated generations would contribute to the observed high F(ij) values among genets at short distance. To ensure long-term ex situ genetic variability of the endangered E. koreensis, individuals located at distances of 10-12 m should be collected across entire populations of E. koreensis.

Conservation of Natural Resources↗

PubMed2004

Score tests of genetic association in the presence of linkage based on the additive genetic gamma frailty model.

Nuclear families with multiple affected sibs are often collected for genetic linkage analysis of complex diseases. Once linkage evidence is established, dense markers are often typed in the linked region for genetic association analysis based on linkage disequilibrium (LD). Detection of association in the presence of linkage localizes disease genes more accurately than the methods that rely on linkage alone. However, test of association due to LD in the linked region needs to account for dependency of the allele transmissions to different sibs within a family. In this paper, we define a joint model for genetic linkage and association and derive the corresponding joint survival function of age of onset for the sibs within a sibship. The joint survival function is a function of both the inheritance vector and the genotypes at the candidate marker locus. Based on this joint survival function, we derive score tests for genetic association. The proposed methods utilize the phenotype data of all the sibs and have the advantages of family-based designs which can avoid the potential spurious association caused by population admixture. In addition, the methods can account for variable age of onset or age at censoring and possible covariate effects, and therefore provide important tools for modelling disease heterogeneity. Simulation studies and application to the data sets from the 12th Genetic Analysis Workshop indicate that the proposed methods have correct type 1 error rates and increased power over other existing methods for testing allelic association.

Adult↗

PubMedDate not supplied

Genetic variation and genetic load due to the male reproductive component of fitness in Drosophila.

The genetic variation and genetic load due to virility, the male reproductive component of fitness, was measured in Drosophila melanogaster and D. pseudoobscura using males homozygous and heterozygous for the second chromosome of each species. Virility was determined in a female-choice, male mating competition experiment where both mating propensity and fertility were taken into account.--The mean virility of the homozygous D. melanogaster males relative to the heterozygous males was 0.50; the relative mean virility of the quasinormal homozygotes was 0.56. The mean virility of the homozygous D. pseudoobscura males relative to the heterozygous males was 0.70; the relative mean virility of the nonsterile homozygotes was 0.72, and of the quasinormal homozygotes, 0.68.--Depending on the species and chromosome sampled, fertile homozygous males had a mean virility 15 to 50% lower than the mean viability of individuals homozygous for a chromosome with quasinormal viability. The genetic load due to virility was also greater than that due to the female reproductive component. This higher level of hidden genetic variation (or genetic load) indicates that the results of Prout (1971a, b) and Bundgaard and Christian (1972), where the virility component of fitness dominated the dynamics of an artificial polymorphism, may be more general and that virility may dominate the dynamics of natural polymorphisms as well.

Animals↗

PubMedDate not supplied

SGS--Spatial Genetic Software: a computer program for analysis of spatial genetic and phenotypic structures of individuals and populations.

We have developed a program called Spatial Genetic Software (SGS), which provides a user-friendly Windows tool to analyze both local and broad scale genetic and phenotypic structure. It can deal with nearly any type of genetic data, codominant (allozyme, PCR-RFLP, microsatellite) or dominant (RAPD, AFLP) markers, or biparentally (nuclear) or uniparentally (cpDNA and mtDNA) inherited markers. Data based on any of these markers can be analyzed, either as individual genotypes within a single population (local scale) or as allele or haplotype frequencies from different populations (broad scale). We also include a simple approach to analysis of spatial structure for continuous quantitative traits. The program implements various parameters to analyze spatial genetic and phenotypic structure: Moran's index, Geary's index, number of alleles in common, and approaches using genetic distances and F(ST) values. The statistical significance of all measures is verified by the use of a permutation test. The results are assessed by graphics that can be integrated, via the clipboard, to other Windows programs. The details of the computations are given in a table and can be stored as ASCII files.

Demography↗

PubMedDate not supplied

Deficiency of knowledge of genetics and genetic tests among general practitioners, gynecologists, and pediatricians: a global problem.

PURPOSE: The objective of this study was to assess knowledge of genetics and awareness of genetic tests among Dutch general practitioners (GPs), gynecologists (GYNs), and pediatricians (PEDs), as well as factors influencing their knowledge and awareness. METHODS: An anonymous questionnaire inquiry was used, validated with a sample of 52 clinical geneticists (CGs). The study was carried out in primary care (general practice) and secondary care (general and university hospitals) in The Netherlands. A random sample of 200 GPs, 300 GYNs, and 265 PEDs received a questionnaire. In addition, all registered CGs (58) received a questionnaire for validation. In total, 122 GPs, 187 GYNs, 164 PEDs, and 52 CGs returned a completed questionnaire. The main outcome measures were differences in knowledge scores between physicians working in different disciplines and factors influencing these scores. RESULTS: Knowledge scores of GPs (mean 64% correct answers, 61%-66% [95% confidence interval]), GYNs (mean 75% correct answers, 73%-76% [95% confidence interval]), and PEDs (mean 81% correct answers, 79%-82% [95% confidence interval]) were lower than those in the CG validation group (mean 95% correct answers, 94%-96% [95% confidence interval]). The 5th percentile of GPs, GYNs, and PEDs was at approximately 40%, 52% and 62% correct answers, respectively. There was a specific lack of knowledge about DNA testing. In addition to specialty, important factors positively associated with the knowledge scores of nongeneticists are more recent graduation, having taken an elective course in genetics, and providing genetic counseling in their own practice. CONCLUSION: The overall knowledge levels of genetics in many nongeneticist health care providers show clear deficiencies. This is in line with reports from other countries, showing that these deficiencies are a global problem.

Genetic Testing↗

PubMed1982

Estimating genetic and non-genetic components of variance for fasting glucose levels in pedigrees ascertained through non-insulin dependent diabetes.

Fasting glucose levels measured on 337 individuals in 14 pedigrees ascertained through a proband with non-insulin dependent diabetes were used to estimate genetic and non-genetic components of variance under a multifactorial model of inheritance. In this sample genetic factors were important in controlling variation in basal carbohydrate metabolism, as represented by age-adjusted log-fasting glucose. There was no evidence that arbitrary sib common environments or arbitrary parent common environments accounted for significant portions of the variability in fasting glucose in these data. An arbitrary environment shared by parent and offspring, however, had a marginally significant impact on the likelihood. Parameter estimates obtained from multifactorial models analysed in this manner are sensitive to extreme phenotypic values, however, and caution must be exercised in estimating total genetic variation. While additive genetic factors did account for a significant proportion of the total variation in fasting glucose, a large proportion remained unexplained.

Adolescent↗

PubMed2002

Perinuclear neutrophil antibodies are not markers for genetic susceptibility or indicators of genetic heterogeneity in familial ulcerative colitis.

OBJECTIVES: Autoantibodies that bind to the perinuclear region of neutrophils have been suggested to represent subclinical markers of genetic susceptibility and indicators of genetic heterogeneity in ulcerative colitis (UC). However, results from more recent studies have contradicted this statement. To address this discrepancy, we assayed perinuclear neutrophil antibodies in the UC-affected members of 53 families with at least one relative pair affected with UC. METHODS: Perinuclear neutrophil antibodies were detected using an indirect immunofluorescence assay. RESULTS: Perinuclear neutrophil antibodies were present in 53% of the study subjects with ulcerative colitis (UC). In 15 families (28%), all members with UC were positive for perinuclear neutrophil antibodies, whereas in 12 families (23%), none of the UC-affected members were positive. In the remaining 26 families (49%), the results for the UC-affected relatives were discordant. Similar results were found when only sibling pairs were evaluated. Statistical analysis revealed that for all affected relative pairings, observed concordance did not significantly exceed expected concordance. Logistic regression analyses demonstrated that the degree of relationship was not enough to predict concordance for perinuclear neutrophil antibodies, and that these antibodies are not markers of genetic heterogeneity. CONCLUSIONS: Perinuclear neutrophil antibodies are not markers for genetic susceptibility or indicators of genetic heterogeneity in UC.

Adult↗

PubMed1993

Population genetics of a transformable bacterium: the influence of horizontal genetic exchange on the biology of Neisseria meningitidis.

Information of the biochemistry and genetics of bacterial species, usually obtained by the study of single isolates, is enhanced by studies of populations of bacteria. Recent advances in molecular technology, particularly polymerase chain reaction-based nucleotide sequence analysis, provide powerful tools for the study of population genetics. Data obtained by such techniques indicate that, while some bacterial species have a clonal population structure, others are non-clonal or panmictic. Clonal populations are a consequence of asexual reproduction by binary fission; panmictic population structures result from 'horizontal' exchange of genetic material between clones. A consequence of horizontal genetic exchange is mosaic gene structures, recognisable by comparisons of nucleotide sequences. In transformable bacteria, for example the human pathogen Neisseria meningitidis, several different genes, including the gene encoding the class 1 outer membrane protein, a major surface antigen, are mosaics. This genetic process has implications both for vaccine design and in the interpretation of epidemiological data.

Bacterial Outer Membrane Proteins↗

PubMed1988

Genetic analysis of the iron uptake region of the Vibrio anguillarum plasmid pJM1: molecular cloning of genetic determinants encoding a novel trans activator of siderophore biosynthesis.

Clones carrying the iron uptake region of the Vibrio anguillarum plasmid pJM1 were subjected to insertion mutagenesis, using transposon Tn3::HoHo1 which carries a promoterless lacZ gene and can thus generate lacZ transcriptional fusions if inserted downstream from an indigenous promoter. Four classes of insertion mutants were obtained based on the level of expression of components of the iron uptake system, and six genetic units were defined according to the phenotype of the mutants. Five of the six genetic units were crucial for biosynthesis of the siderophore anguibactin. Insertions in the remaining genetic unit led to an iron uptake-deficient phenotype and showed either reduced levels of the outer membrane protein OM2 as well as anguibactin activity or a complet shutoff of both OM2 and anguibactin biosyntheses. Analysis of beta-galactosidase production by cells carrying the lacZ fusion derivatives identified iron-regulated and constitutive transcriptional units as well as their orientation in the genetic units. Molecular cloning of pJM1 plasmid DNA noncontiguous to the iron uptake region also identified genetic determinants for a trans-acting factor required for full expression of anguibactin activity. Evidence obtained from bioassays, spectrophotometric measurements, and the lacZ fusion mutants suggested that the trans-acting factor is a novel activator of siderophore biosynthesis at the transcriptional level.

Cloning, Molecular↗

PubMed2002

Novel design architecture for genetic stability of recombinant poliovirus: the manipulation of G/C contents and their distribution patterns increases the genetic stability of inserts in a poliovirus-based RPS-Vax vector system.

Poliovirus has been studied as a live recombinant vaccine vector because of its attractive characteristics. The genetic instability, however, has hampered recombinant polioviruses (PVs) from being developed as an appropriate vaccine. A variety of different foreign inserts were cloned directly into our poliovirus Sabin 1-based RPS-Vax vector system, resulting in the production of recombinant PVs. The genetic stability of each recombinant PV was examined during 12 rounds of consecutive passage. It was found that the genetic stability of the recombinants was not well correlated with their insert size. Instead, elevated stability was frequently observed in recombinants with inserts of high G/C contents. Furthermore, a comparative study using different constructs of the human immunodeficiency virus env gene revealed that the internal deletion of the unstable insert was seemingly caused by the presence of the adjacent A/T-rich region. The instability of these inserts was completely remedied by (i) increasing the G/C contents and (ii) replacing the local A/T-rich region with the G/C-rich codon without a change of the amino acid. This means that stability is closely associated with the G/C content and the G/C distribution pattern. To see whether these findings can be applied to the design of genetically stable recombinant PV, we have reconstructed the heteromultimeric insert based on our design architecture, including the above-mentioned G/C rules and the template/ligation-free PCR protocol. The heteromultimeric insert was very unstable, as expected, but the manipulated insert with the same amino acid sequence showed complete genetic stability, not only in vitro, but also in vivo. Even though this guideline was established with our RPS-Vax vector system, to some extent, it can also be applied to other live viral vaccine vectors.

Amino Acid Sequence↗

PubMed2005

Finding associations in dense genetic maps: a genetic algorithm approach.

Large-scale association studies hold promise for discovering the genetic basis of common human disease. These studies will consist of a large number of individuals, as well as large number of genetic markers, such as single nucleotide polymorphisms (SNPs). The potential size of the data and the resulting model space require the development of efficient methodology to unravel associations between phenotypes and SNPs in dense genetic maps. Our approach uses a genetic algorithm (GA) to construct logic trees consisting of Boolean expressions involving strings or blocks of SNPs. These blocks or nodes of the logic trees consist of SNPs in high linkage disequilibrium (LD), that is, SNPs that are highly correlated with each other due to evolutionary processes. At each generation of our GA, a population of logic tree models is modified using selection, cross-over and mutation moves. Logic trees are selected for the next generation using a fitness function based on the marginal likelihood in a Bayesian regression frame-work. Mutation and cross-over moves use LD measures to pro pose changes to the trees, and facilitate the movement through the model space. We demonstrate our method and the flexibility of logic tree structure with variable nodal lengths on simulated data from a coalescent model, as well as data from a candidate gene study of quantitative genetic variation.

Algorithms↗

PubMed2006

Education in medical genetics for non-genetic health care providers in Sweden.

We investigated the content and extent of education in medical/clinical genetics among Swedish universities, university colleges and colleges of health providing undergraduate education for medical doctors and nurses. In addition, selected medical specialist training programmes and programmes for midwives and district nurses were analysed to detect elements of education or training in medical/clinical genetics. The main results are that, although basic cell biology is taught during the first semesters in all education, there is little or no genetics taught during the clinical parts of the educational programmes. Moreover, with regard to post-graduate education, it is almost absent. There is a need to improve education and training in genetics for all health care professionals to meet the expected increase in genetic issues in clinical medicine.

Education, Medical↗

PubMed2005

Architectures of genetic medicine: comparing genetic testing for breast cancer in the USA and the UK.

This paper compares the development of genetic testing for breast cancer (BRCA testing) in the USA and the UK. It argues that national political cultures played an important role in how these genetic testing technologies were shaped, and that the shapes of these technologies had important implications for the users of these systems. In order to demonstrate the roles of national social and political elements in the development of new genetic testing technologies, I introduce the concept of a technology's architecture, which is made up of components and the specific ways in which these components are assembled to fulfill particular functions. In the USA, four very different BRCA testing systems initially emerged. However, one biotechnology company, Myriad Genetics, eventually used its legal and economic position to become the sole provider of testing. It offered BRCA testing the way many other laboratory tests were provided in the USA, available to anyone through any physician. The shape of this testing service had important implications for its participants, defining the client as a consumer who could demand access to any of Myriad's laboratory services, but could not choose among testing systems. In the UK, the government-run National Health Service provided testing through regional genetics clinics, using family history information to assess risk and triage care. Clients in the UK were defined as citizens and patients, who had the right to equal access to the testing system but could not demand any specific services.

Breast Neoplasms↗