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PubMed2006

Building a European biomedical grid on cancer: the ACGT Integrated Project.

This paper presents the needs and requirements that led to the formation of the ACGT (Advancing Clinico Genomic Trials) integrated project, its vision and methodological approaches of the project. The ultimate objective of the ACGT project is the development of a European biomedical grid for cancer research, based on the principles of open access and open source, enhanced by a set of interoperable tools and services which will facilitate the seamless and secure access to and analysis of multi-level clinico-genomic data, enriched with high-performing knowledge discovery operations and services. By doing so, it is expected that the influence of genetic variation in oncogenesis will be revealed, the molecular classification of cancer and the development of individualised therapies will be promoted, and finally the in-silico tumour growth and therapy response will be realistically and reliably modelled. Its main design decisions and results at its current stage of development are presented.

Biomedical Research↗
PubMed2005

Genetic diversity among alfalfa (Medicago sativa) cultivars coming from a breeding program, using SSR markers.

Alfalfa (Medicago sativa) is an autotetraploid, allogamous and heterozygous species whose cultivars are synthetic populations. The breeders apply selection pressure for some agronomic traits within a breeding pool to increase the frequency of favorable individuals. The objective of this study was to investigate the differentiation level among seven cultivars originating from one breeding program, and between these cultivars and the breeding pool, with eight SSR markers. These highly polymorphic and codominant markers, together with recent population genetic statistics extended to autotetraploids, offer tools to analyse genetic diversity in alfalfa. The number of alleles per locus varied between 3 and 24. All loci were at a panmictic equilibrium in the cultivars, except one, probably because of null alleles. With seven SSR loci, each cultivar was at panmictic equilibrium. The mean gene diversity was high, ranging from 0.665 to 0.717 in the cultivars. The parameter F(ST) indicated a low but significant diversity among cultivars. Among 21 pairs of cultivars, 15 were significantly different. The breeding pool also had a high diversity, and was significantly different from each cultivar except the most recent one. Considering the characteristics of the breeding program and the mode of cultivar elaboration, we found that they were unable to generate a large variety differentiation. Estimation of population genetics parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources.

Breeding↗
PubMed2002

Searching for RNA genes using base-composition statistics.

The hypothesis that genomic regions rich in non-protein-coding RNAs (ncRNAs) can be identified using local variations in single-base and dinucleotide statistics has been investigated. (G+C)%, (G-C)% difference, (A-T)% difference and dinucleotide-frequency statistics were compared among seven classes of ncRNAs and three genomes. Significant variations were observed in (G+C)% and, in Methanococcus jannaschii, in the frequency of the dinucleotide 'CG'. Screening programs based on these two base-composition statistics were developed. With (G+C)% screening alone, a 1% fraction of the M.jannaschii genome containing all 44 known transfer RNAs, ribosomal RNAs and signal recognition particle RNAs could be identified. When (G+C)% combined with CG dinucleotide-frequency screening was used, 43 of the 44 known M.jannaschii structural ncRNAs were again identified, while the number of presumably false hits overlapping a known or putative protein-coding gene was reduced from 15 to 6. In addition, 19 candidate ncRNAs were identified including one with significant homology to several known archaeal RNaseP RNAs.

Animals↗
PubMed2004

Mutation screen of the glutamate decarboxylase-67 gene and haplotype association to unipolar depression.

Abnormally low concentrations of brain gamma-aminobutyric acid (GABA) have been reported in unipolar depression. Almost all of the brain GABA is synthesized by glutamate decarboxylase (GAD) enzymes (GAD67 and GAD65). These enzymes, therefore, play a central role in brain GABA homeostasis. We screened all the 17 exons of the GAD67 gene for mutations using single strand conformation polymorphism (SSCP) or denaturing high pressure liquid chromatography (dHPLC) in a sample of 43 individuals diagnosed with major unipolar depression or other disorders with putative GABAergic dysfunction. We identified eight novel variants (five synonymous base substitutions, two insertion/deletions and one tandem repeat). Three relatively common (minor allele frequency >20%) single nucleotide polymorphisms (SNPs), located in the 5' non-coding region (exon 0), intron 8, and the 3' non-coding region (exon 16) of the gene, were genotyped in 103 European-American (EA) subjects with depression and 125 EA psychiatrically screened controls. Linkage disequilibrium (LD) and haplotype frequencies were estimated using the 3LOCUS program. Significant LD was observed between the intron 8 SNP and the exon 16 SNP and between the exon 0 SNP and the exon 16 SNP. Three common GAD67 haplotypes were observed in this population, which accounted for >90% of the possible GAD67 three-locus haplotypes. Comparison of SNP and haplotype frequencies between individuals with depression and controls revealed no differences. These results demonstrate a significant within-gene LD for GAD67 in the EA population and begin to establish a haplotype map for this gene. Furthermore, these results suggest that common genetic variation within the GAD67 gene does not play a major role in the predisposition to unipolar depression.

DNA↗
PubMed2000

Mach's phenomenalism and the British reception of Mendelism.

The assimilation of Mendel's paper into Britain took place in an Edwardian social context. This paper concentrates on the interplay of empirical and philosophical issues in this reception. A feature of the British reception of mendelism, not duplicated elsewhere, was the role of phenomenalist philosophies of science as developed by the physicist-mathematician and scientific methodologist Karl Pearson from the philosophical positions of Austrian physicist Ernst Mach and British mathematician William Clifford. Pearson's philosophy of science forms the background to his subsequent collaboration with the zoologist W.F.R. Weldon. In this collaborative work, Pearson developed powerful statistical techniques for analyzing Weldon's empirical data on organic variation. Pearson's statistical analysis of causation and his rejection of hidden entities and causes in the explanation of evolutionary change formed the philosophical component of this program. The arguments of Pearson and Weldon were first brought to bear against the pre-Mendel 'discontinuist' analyses of variation of William Bateson. The introduction of Mendel's paper into these empirical and methodological debates consequently resulted in mathematically sophisticated attacks on Mendel's claims by Pearson and Weldon. This paper summarizes this history and argues for the creative importance of this biometrical resistance to Mendelism.

Animals↗
PubMed2003

Update on the global distribution of genotypes of wild type measles viruses.

Molecular characterization of measles viruses is an important component of measles surveillance because these studies enhance our ability to identify the source and transmission pathways of the virus. Molecular surveillance is most beneficial when it is possible to observe the change in virus genotypes over time in a particular region. Such information can help to document the interruption of transmission of measles virus and thus provide an important method for assessing the effectiveness of vaccination programs. It is recommended that virus surveillance be conducted during all phases of measles control and be expanded to give an accurate description of the global distribution of measles genotypes. This review provides updated information on the circulation patterns of measles genotypes and examples of the utility of virologic surveillance.

Genetic Variation↗
PubMed1999

Genetically distinct dog-derived and human-derived Sarcoptes scabiei in scabies-endemic communities in northern Australia.

Overcrowding is a significant factor contributing to endemic infection with Sarcoptes scabiei in human and animal populations. However, since scabies mites from different host species are indistinguishable morphologically, it is unclear whether people can be infected from scabies-infested animals. Molecular fingerprinting was done using three S. scabiei-specific single locus hypervariable microsatellite markers, with a combined total of 70 known alleles. Multilocus analysis of 712 scabies mites from human and dog hosts in Ohio, Panama and Aboriginal communities in northern Australia now shows that genotypes of dog-derived and human-derived scabies cluster by host species rather than by geographic location. Because of the apparent genetic separation between human scabies and dog scabies, control programs for human scabies in endemic areas do not require resources directed against zoonotic infection from dogs.

Alleles↗
PubMed2004

BAPS 2: enhanced possibilities for the analysis of genetic population structure.

UNLABELLED: Bayesian statistical methods based on simulation techniques have recently been shown to provide powerful tools for the analysis of genetic population structure. We have previously developed a Markov chain Monte Carlo (MCMC) algorithm for characterizing genetically divergent groups based on molecular markers and geographical sampling design of the dataset. However, for large-scale datasets such algorithms may get stuck to local maxima in the parameter space. Therefore, we have modified our earlier algorithm to support multiple parallel MCMC chains, with enhanced features that enable considerably faster and more reliable estimation compared to the earlier version of the algorithm. We consider also a hierarchical tree representation, from which a Bayesian model-averaged structure estimate can be extracted. The algorithm is implemented in a computer program that features a user-friendly interface and built-in graphics. The enhanced features are illustrated by analyses of simulated data and an extensive human molecular dataset. AVAILABILITY: Freely available at http://www.rni.helsinki.fi/~jic/bapspage.html.

Algorithms↗
PubMed2002

Variant analysis and immunogenicity prediction of envelope gene of HCV strains from China.

The putative envelope protein E2 of hepatitis C virus (HCV) is the most variable antigenic fragment in the whole viral genome and is responsible mainly for the large inter- and intra-individual heterogeneity of the infecting virus. To analyze variation and immunogenicity of HCV envelope genes of HCV strains from China, the serum samples from 12 Chinese patients with chronic hepatitis C from 10 cities of China were amplified, sequenced directly, and compared with international strains reported previously. Variant analysis and immunogenicity prediction were then carried out with computer programs. The results suggested that HCV envelope genes show diversity in the north and the south of China and that they vary among different genotypes. Therefore, the diversity among different genotypes and derived areas should be calculated for HCV vaccine design; simultaneously, domains characterized by the hydrophilicity and the conserved immunogenicity could be targeted, for example, the domain of aa434-444, aa408-414, aa449-462 in the envelope region and aa399-406 in HVR1. These data may hold the key for future development of HCV vaccine in China.

Amino Acid Sequence↗
PubMed1991

Use of recombinant inbred strains to identify quantitative trait loci in psychopharmacology.

Unlike simple Mendelian characteristics, individual differences in complex quantitative phenotypes studied in psychopharmacology are generally distributed continuously and are likely to be influenced by many genes. Recombinant inbred (RI) strains are valuable not only for their traditional use of detecting major gene segregation and linkage but also for identifying associations between quantitative traits and quantitative trait loci (QTL) that account for relatively small amounts of variation in phenotypes as well as loci that account for greater amounts of variation. When applied to published data on genetic markers and on amphetamine, alcohol, and morphine responses in BXD RI strains (RI strains developed from the cross between C57BL/6J and DBA/2J progenitor inbred strains), the RI QTL approach identified several significant associations beyond known major gene effects. Together, significant associations explain more than half of the genetic variance for these measures. The RI QTL approach is especially valuable for investigating the QTL underpinnings of genetic correlations among measures. It is recommended that psychopharmacogenetic research focus on the BXD RI strains. The cumulative and integrative nature of such a program of research is the major benefit of the RI QTL association approach for molecular genetic analysis of psychopharmacological processes, their physiological infrastructure, and their interface with other behavioral and biological systems.

Animals↗
PubMed2005

Central corneal thickness is highly heritable: the twin eye studies.

PURPOSE: A classic twin study was performed to determine the heritability of central corneal thickness (CCT), an important parameter in glaucoma assessment. METHODS: The concordance of CCT between monozygotic (MZ) and dizygotic (DZ) twins was compared. A total of 256 twin pairs (131 MZ and 125 DZ) were recruited from three centers: the Twin Eye Study in Tasmania, the Brisbane Adolescent Twin Study, and the Twins U.K. Adult Registry held at St. Thomas' Hospital in London. As part of an extensive ophthalmic evaluation, CCT was measured by ultrasound pachymetry. Structural equation modeling with the Mx program (Department of Psychiatry, Medical College of Virginia, Richmond, VA) was used to determine the heritability of CCT. RESULTS: The mean age of subjects was 38 years (range, 8-81). The mean CCT of all eyes examined was 544.5 +/- 37.3 mum (SD). The CCT measurements correlated more highly in MZ twins than in DZ twins, with intraclass correlation coefficients of 0.95 and 0.52, respectively, suggesting a strong genetic influence. A model of additive genetic and unique environmental effects provided the best fit, yielding a heritability of 0.95 (95% confidence interval [CI], 0.93-0.96) with the remaining variation being attributable to unique environmental factors. CONCLUSIONS: In this study of Australian and U.K. twins, genetic factors were shown to be of major importance in CCT, with a heritability of 0.95.

Adolescent↗
PubMed2000

[Obesity in the child].

The prevalence of childhood obesity increases dramatically in all industrialized countries. As in adults, it is defined by an increase in fat mass. The United States seem to be facing the most difficult situation. However, rapid changes in the way of life leads to consider that, in a near future, as much as 25% of the children in Europe could be concerned as well. A new epidemiological tool designed by the International Obesity Task Force takes as reference criteria the body mass index and will allow comparisons between countries as well as it will take into account the physiological variations of fat mass during growth. GENETICS AND ENVIRONMENT: A NEW PUZZLE: Inactivity seems to account as much as increased or unbalanced food intakes. While genetics account for a part of the disease at the population level, its role remains unclear in individuals. Most complications occur early in life, in a silent and progressive way. All these aspects do not only open fields of research but also provide new understanding and therapeutic basis for clinicians. PREVENTION: A PUBLIC HEALTH PRIORITY: Prevention has become a priority which should be based on early individual surveillance and Health Policy programs based on "National Recommendations for the diagnosis, prevention and treatment of obesity". All professionals dealing in one way or another with children lifestyle are concerned as well as do the families.

Adolescent↗
PubMed1982

Quantitative two-dimensional protein electrophoresis for studies of inborn errors of metabolism.

High-resolution electrophoretic methods and sensitive protein-detection techniques permit new approaches to understanding and diagnosis of the inborn errors of metabolism. These approaches encompass: the search for protein alterations that represent primary mutations effects; observation of alterations in protein patterns due to secondary effects, as might occur in major metabolic pathway abnormalities; and identification of protein polymorphisms that are genetically linked to an inborn metabolic disease. With the aid of computer analysis of the electrophoretograms, all three approaches are being developed. Protein density and position are evaluated with an interactive computer program that requires that gel polypeptides be indexed by the investigator. Proteins on the gels are made visible with an inexpensive, rapid silver stain, which can be used quantitatively. The Lesch-Nyhan syndrome, one of a few neuropsychiatric diseases for which the molecular defect is known, was chosen for study with these techniques. Four hundred proteins were analyzed for positional or quantitative variation. Eleven significant (2p less than 0.01) quantitative differences were found in autoradiograms from gels of phytohemagglutinin-stimulated lymphocytes. Specific patterns of polypeptide variation are now being sought in an expanded clinical study primarily focusing on Huntington's disease. Large studies are required to establish the specificity of observed alterations. As the number and variety of analyses increase, a correlative catalog of molecular variation and polymorphism will be generated.

Autoradiography↗
PubMed1994

Variability of serum thyroglobulin levels is determined by a major gene.

OBJECTIVE: There are large variations in the circulating concentrations of thyroglobulin. The purpose of this study was to explore the possibility of a genetic basis for the variability of serum concentration of thyroglobulin (Tg) in euthyroid individuals. DESIGN: The serum concentration of thyroglobulin (Tg) varies several-fold in euthyroid individuals. Other circulating proteins also show wide normal ranges of concentration and these variations have been shown to have a genetic as well as an environmental basis. To explore the possibility of a genetic basis for variability in serum Tg levels, an analysis was made of serum Tg levels in 44 pairs of identical twins and 66 nuclear families who were euthyroid and thyroid autoantibody negative (thereby eliminating subclinical autoimmune thyroid disease and Tg autoantibody interference with the Tg assay). RESULTS: Each pair of identical twins tended to have a similar Tg level and the overall correlation was highly significant (r = 0.734, P < 0.001). There was no relation between Tg and TSH levels in the twins (r = 0.119; P = 0.366). Segregation analysis of the 66 families showed that where both parents had Tg levels above the overall median for the subjects (males, 19 micrograms/l; females, 33 micrograms/l), 73% of the offspring also had concentrations above these levels, compared with 30% of the offspring when one parent had a high Tg level and only 16% in families where neither parent had a high Tg level. CONCLUSIONS: Complex segregation analysis using the computer program Pointer suggested that variability in Tg levels was the result of a major dominant-like gene effect (accounting for 80% of the variability) combined with a multifactorial component. Thyroglobulin, a template for thyroid hormone production, is also a major thyroid autoantigen and inherited variations in serum Tg levels may have implications for the pathogenesis of autoimmune thyroid disease.

Adolescent↗
PubMed1989

Evaluation of production and reproduction of sheep, goat and alpaca genotypes in the Small Ruminant Collaborative Research Support Program.

Research has been conducted as part of the Small Ruminant Collaborative Research Support Program (SR-CRSP) on evaluation of genetic resources and methods of effecting genetic improvement of small ruminants in the participating countries. In Kenya, the focus has been on development of a dual-purpose goat for milk and meat production in farming areas, utilizing two locally adapted breeds, Galla and East African, and two imported dairy breeds, Anglo-Nubian and Toggenburg, into a single stock. That research now has reached the stage of field testing. In Morocco, the performance of a highly prolific breed of sheep, the D'Man, and of a less prolific but larger breed, commonly raised under extensive management, the Sardi, and of their F1, F2 and backcross progeny has been evaluated for several reproduction and growth traits. Prolificacy of the D'Man was transmitted additively, but there was favorable heterosis for age at puberty, fertility and growth rate, resulting in substantial heterosis in total performance. In Indonesia, a high degree of variability in prolificacy in sheep appears to be due to segregation of a gene with large effect on ovulation rate, similar in some respects to the Booroola gene. In Peru, work has involved evaluation of effectiveness of current selection programs and estimation of phenotypic and genetic parameters, in unimproved and improved types of sheep, with a limited amount of work also on alpacas. Fiber production is the principal economic trait in alpacas. There also has been work on evaluation of hair sheep in Brazil, Kenya and Indonesia.

Animals↗
PubMed2006

In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

BACKGROUND: Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effects on splicing of other sequence variations are difficult to predict. Loosely defined exonic and intronic sequences have been shown to affect splicing efficiency by means of silencing and enhancement mechanisms. Thus, nucleotide substitutions in these sequences can induce aberrant splicing. Web-based resources have recently been developed to facilitate the identification of nucleotide changes that could alter splicing. However, computer predictions do not always correlate with in vivo splicing defects. The issue of unclassified variants in cancer predisposing genes is very important both for the correct ascertainment of cancer risk and for the understanding of the basic mechanisms of cancer gene function and regulation. Therefore we aimed to verify how predictions that can be drawn from in silico analysis correlate with results obtained in an in vivo splicing assay. RESULTS: We analysed 99 hMLH1 and hMSH2 missense mutations with six different algorithms. Transfection of three different cell lines with 20 missense mutations, showed that a minority of them lead to defective splicing. Moreover, we observed that some exons and some mutations show cell-specific differences in the frequency of exon inclusion. CONCLUSION: Our results suggest that the available algorithms, while potentially helpful in identifying splicing modulators especially when they are located in weakly defined exons, do not always correspond to an obvious modification of the splicing pattern. Thus caution must be used in assessing the pathogenicity of a missense or silent mutation with prediction programs. The variations observed in the splicing proficiency in three different cell lines suggest that nucleotide changes may dictate alternative splice site selection in a tissue-specific manner contributing to the widely observed phenotypic variability in inherited cancers.

Adaptor Proteins, Signal Transducing↗
PubMed2005

Economic evaluation for conservation of farm animal genetic resources.

The decline in biodiversity of farm animal genetic resources (AnGR) has come to the forefront of concern in the discussion of animal conservation and breeding programmes. To improve decision-making regarding conservation and breeding programmes, a number of evaluation techniques of farm AnGR are available. This paper presents an overview of the different values associated to AnGR and of the techniques for their measurement being employed in the economic literature. Those include linear programming and farm simulation models, dynamic models estimating the value of research and development and econometric models estimating the demand for breed characteristics. While farm programming and simulation models are fairly well developed, they do have large data requirements. Alternatively, contingent valuation methods are available, in particular when the goal is to capture non-market values embedded in breeds.

Animal Husbandry↗
PubMed1988

Heterologous expression of excitability proteins: route to more specific drugs?

Many clinically important drugs act on the intrinsic membrane proteins (ion channels, receptors, and ion pumps) that control cell excitability. A major goal of pharmacology has been to develop drugs that are more specific for a particular subtype of excitability molecule. DNA cloning has revealed that many excitability proteins are encoded by multigene families and that the diversity of previously recognized pharmacological subtypes is matched, and probably surpassed, by the diversity of messenger RNAs that encode excitability molecules. In general, the diverse subtypes retain their properties when the excitability proteins are expressed in foreign cells such as oocytes and mammalian cell lines. Such heterologous expression may therefore become a tool for testing drugs against specific subtypes. In a systematic research program to exploit this possibility, major considerations include alternative processing of messenger RNA for excitability proteins, coupling to second-messenger systems, and expression of enough protein to provide material for structural studies.

Animals↗