Bioinformatics for genomics purposes

Sinds enkele jaren wordt op het RIVM genomicsonderzoek uitgevoerd. Genomics omvat grootschalig onderzoek naar het erfelijk materiaal (DNA) van organismen. Dit onderzoek levert inzicht op in de manier waarop erfelijke eigenschappen zich vertalen naar het functioneren van een cel, en uiteindelijk een heel organisme. De praktische uitvoering van genomicsexperimenten is recentelijk beschreven in rapport 340200001 "Genomics: Implementatie, toepassing en toekomst", dat in december 2006 is verschenen. Dit rapport gaat in op de bioinformatica die het RIVM heeft opgezet en ontwikkeld. Bioinformatica is de wetenschap die methoden uit de informatica gebruikt om biologische data te kunnen verwerken en analyseren. Deze specifieke kennis is nodig om de grote hoeveelheden data die genomicsexperimenten genereren, te kunnen analyseren. De verschillende stappen in de data-analyse, zoals beeldverwerking, kwaliteitscontrole, normalisatie, statistische analyse, patroonherkenning, verlopen succesvol volgens algemeen geaccepteerde methoden. De bioinformatica voor de verdere biologische interpretatie van de resultaten is wereldwijd nog volop in ontwikkeling. In samenwerking met andere instituten wordt dit onderzoeksgebied gevolgd en worden nieuwe ontwikkelingen toegepast. De komende jaren zullen er via de literatuur meer data van genomicsexperimenten beschikbaar komen. Om die te kunnen vergelijken en te combineren zijn bioinformatica-methoden beschikbaar, die zich de komende jaren verder zullen ontwikkelen. Naast genomicsdata zullen ook steeds meer andere gegevens (bijvoorbeeld eiwit- en metabolietgegevens) beschikbaar komen. Dit biedt mogelijkheden om meerdere soorten data te integreren. Deze aanpak wordt "systems biology" genoemd en is vooral interessant om tot een betere risicoschatting van stoffen te komen. Ook bestaat behoefte aan bioinformatica voor grootschalig eiwitonderzoek (proteomics), dat het RIVM wil gebruiken voor bevolkingsonderzoeken en screeningsprogramma's van micro-organismen.Genomics constitutes large-scale research on hereditary material (DNA) of organisms. The genomics research that has been carried out the last few years at the National Institute for Public Health and the Environment (RIVM) has given us insight into the way hereditary information is translated into the functioning of a cell and eventually a whole organism. Practical realization of genomics experiments has recently been described in report 340200001 "Genomics: Implementation, application, and future".analysis demands specific expertise. The last few years has seen the set-up and further development of the bioinformatics required. The various steps in the data analysis, including image analysis, quality control, normalisation, statistical analysis and pattern recognition, are carried out successfully according to generally accepted methods. The bioinformatics concerned with interpretation of the results is worldwide in full development. This field will be closely followed and new developments applied in cooperation with other institutes. More genomics experimental data will become available via the literature in the coming years. Bioinformatics methods for comparing and combining these data are available and will develop further in the future. In addition, an increasing number of other kinds of data sets (like protein or metabolite data) will become available, thereby creating possibilities for integration of multidisciplinary data. This approach is called systems biology and is especially interesting for a better risk assessment for chemicals. Furthermore, there will be a need for bioinformatics for proteomics, which the RIVM aims to use for population screening programmes and screening applications on microorganisms.RIV

Testing the boundaries of closely related daisy taxa using metabolomic profiling

Advances in high-throughput, comprehensive small molecule analytical techniques have seen the development of the field of metabolomics. The coupling of mass spectrometry with high-resolution chromatography provides extensive chemical profiles from complex biological extracts. These profiles include thousands of compounds linked to gene expression, and can be used as taxonomic characters. Studies have shown metabolite profiles to be taxon specific in a range of organisms, but few have investigated taxonomically problematic plant taxa. This study used a phenetic analysis of metabolite profiles to test taxonomic boundaries in the Olearia phlogopappa (Asteraceae) complex as delimited by morphological data. Metabolite profiles were generated from both field- and shade house-grown material, using liquid chromatography-mass spectrometry (LC-MS). Aligned profiles of 51 samples from 12 taxa gave a final dataset of over 10,000 features. Multivariate analyses of field and shade house material gave congruent results, both confirming the distinctiveness of the morphologically defined species and subspecies in this complex. Metabolomics has great potential in alpha taxonomy, especially for testing the boundaries of closely related taxa where DNA sequence data has been uninformative

Diversity of S-Alleles and Mate Availability in 3 Populations of Self-Incompatible Wild Pear (Pyrus pyraster)

Small populations of self-incompatible plants may be expected to be threatened by the limitation of compatible mating partners (i.e., S-Allee effect). However, few empirical studies have explicitly tested the hypothesis of mate limitation in small populations of self-incompatible plants. To do so, we studied wild pear (Pyrus pyraster), which possesses a gametophytic self-incompatibility system. We determined the S-genotypes in complete samplings of all adult trees from 3 populations using a PCR-RFLP approach. We identified a total of 26 different S-alleles, homologous to S-alleles of other woody Rosaceae. The functionality of S-alleles and their Mendelian inheritance were verified in artificial pollination experiments and investigations of pollen tube growth. The smallest population (N = 8) harbored 9 different S-alleles and showed a mate availability of 92.9%, whereas the 2 larger populations harbored 18 and 25 S-alleles and exhibited mate availabilities of 98.4% and 99.2%, respectively. Therefore, we conclude that even small populations of gametophytic self-incompatible plants may exhibit high diversity at the S-locus and are not immediately threatened owing to reduced mate availabilit

Application of genetic markers to the discrimination of European Black Poplar ( Populus nigra ) from American Black Poplar ( P. deltoides ) and Hybrid Poplars ( P. x canadensis ) in Switzerland

European Black Poplar (Populus nigra) is considered a rare and endangered tree species because of severe reduction of its natural riverine habitat and potential hybridisation with the related non-indigenous taxa P. deltoides and P. x canadensis. As it is difficult to distinguish these taxa solely based on their morphology, we applied a PCR-based assay with an easy-to-use and robust molecular marker set (cpDNA trnL-trnF/RsaI RFLP, nDNA win3 and nDNA POPX/MspI RFLP) in order to identify pure P. nigra. Different plant tissues could be used for fast and standardised DNA extraction. The application of the three marker types was tested on a number of different Populus taxa, and they were also used for the verification of pure P. nigra in a sample of 304 putative P. nigra individuals from Switzerland. Cross-checking of the DNA data with those using a traditional allozyme approach resulted in complete agreement. The availability of molecular identification methods is an important prerequisite for the conservation of European Black Poplar, because pure, non-introgressed plant material can then be used in restoration projects of European floodplain

Immunomodulation by maternal autoantibodies of the fetal serotoninergic 5-HT4 receptor and its consequences in early BALB/c mouse embryonic development

<p>Abstract</p> <p>Background</p> <p>The presence of functional 5-HT₄receptors in human and its involvement in neonatal lupus erythematosus (NLE) have prompted us to study the receptor expression and role during embryogenesis. Earlier we managed to demonstrate that female BALB/c mice immunized against the second extracellular loop (SEL) of the 5-HT₄receptor gave birth to pups with heart block. To explain this phenomenon we investigated the expression of 5-HT₄receptors during mouse embryogenesis. At the same time we looked whether the consequence of 5-HT₄receptor immunomodulation observed earlier is in relation to receptor expression.</p> <p>We studied the expression of 5-HT₄receptor at the mRNA level and its two isoforms 5-HT_4(a)and 5-HT_4(d)at the protein level in embryos from BALB/c mice, at 8^th, 12^th, 18^thgestation days (GD) and 1 day post natal (DPN). Simultaneously the receptor activity was inhibited by rising antibodies, in female mice against SEL of the receptor. The mice were mated and embryos were collected at 8^th, 12^th, 18^thGD and 1 DPN.</p> <p>Results</p> <p>5-HT₄receptor mRNA increased in brain from 12^thGD to 1 DPN. Its expression gradually decreased in heart and disappeared at birth. This was consistent with expression of the receptor isoforms 5-HT_{4(a) and (d)}. Abnormalities like decreased number of embryos, growth delay, spina bifida and sinus arrhythmia from 12^thGD were documented in pups of mice showing anti-5-HT₄receptor antibodies.</p> <p>Conclusion</p> <p>serotoninergic 5-HT₄receptor plays an important role in mouse foetal development. In BALB/c mice there is a direct relation between the expression of receptor and the deleterious effect of maternal anti-5-HT₄receptor autoantibodies in early embryogenesis.</p

Genetic variation in thioredoxin interacting protein (TXNIP) is associated with hypertriglyceridaemia and blood pressure in diabetes mellitus

Aims Thioredoxin interacting protein (TXNIP) is an attractive candidate gene for diabetes or diabetic dyslipidaemia, since TXNIP is the strongest glucose-responsive gene in pancreatic B-cells, TXNIP deficiency in a mouse model is associated with hyperlipidaemia and TXNIP is located in the 1q21-1q23 chromosomal Type 2 diabetes mellitus (DM) locus. We set out to investigate whether metabolic effects of TXNIP that were previously reported in a murine model are also relevant in human Type 2 DM. Methods The frequency distribution of a 3' UTR single nucleotide polymorphism (SNP) in TXNIP was investigated in subjects with normal glucose tolerance (NGT; n = 379), impaired glucose tolerance (IGT; n = 228) and Type 2 DM (n = 230). Metabolic data were used to determine the effect of this SNP on parameters associated with lipid and glucose metabolism. Results The frequency of the TXNIP variation did not differ between groups, but within the group of diabetic subjects, carriers of the TXNIP-T variant had 1.6-fold higher triglyceride concentrations (P = 0.015; n = 136) and a 5.5-mmHg higher diastolic blood pressure (P = 0.02; n = 212) than homozygous carriers of the common C-allele, whereas in non-diabetic subjects fasting glucose was 0.26 mmol/l lower (P = 0.002; n = 478) in carriers of the T-allele. Moreover, a significant interaction between plasma glucose concentrations and TXNIP polymorphism on plasma triglycerides was observed (P = 0.012; n = 544). Conclusion This is the first report to implicate TXNIP in a human disorder of energy metabolism, Type 2 diabetes. The effect of TXNIP on triglycerides is influenced by plasma glucose concentrations, suggesting that the biological relevance of TXNIP variations may be particularly relevant in recurrent episodes of hyperglycaemia

Influence of beta(2)-adrenoceptor gene polymorphisms on diet-induced thermogenesis

The sympathetic nervous system is involved in the control of energy metabolism and expenditure. Diet-induced thermogenesis is mediated partly by the ß-adrenergic component of this system. The aim of the present study was to investigate the role of genetic variation in the ß2-adrenoceptor in diet-induced thermogenesis. Data from twenty-four subjects (fourteen men and ten women; BMI 26·7(SEM 0·8) kg/m2; age 45·2(SEM1·4) years) with different polymorph-isms of the ß2-adrenoceptor at codon 16 (Gly16Gly, Gly16Arg or Arg16Arg) were recruited for this study. Subjects were given a high-carbohydrate liquid meal, and the energy expenditure, respiratory exchange ratio, and plasma concentrations of NEFA, glycerol, glucose, insulin and catecholamines were measured before and over 4 h after the meal. The AUC of energy expenditure (diet-induced thermogenesis) was not significantly different between poly-morphism groups, nor was the response of any of the other measured variables to the meal. In a multiple regression model, the only variable that explained a significant proportion (32 %) of the variation in diet-induced thermogenesis was the increase in plasma adrenaline in response to the meal (P,0·05). The ß2-adrenoceptor codon16 polymorphisms did not contribute significantly. In conclusion, an independent contribution of the codon 16 polymorphism of the ß2-adrenoceptor gene to the variation in thermogenic response to a high-carbohydrate meal could not be demonstrated. The interindividual variation in thermo-genic response to the meal was correlated with variations in the plasma adrenaline response to the meal. ß2-Adrenoceptor polymorphisms: Diet-induced thermogenesis: Catecholamines Energy expenditure (EE) is an important factor in body-weight regulation. Diet-induced thermogenesis (DIT) is the EE associ-ated with ingestion, absorption and storage of food and account

Half a Century of Wilson & Jungner: Reflections on the Governance of Population Screening.

Background: In their landmark report on the "Principles and Practice of Screening for Disease" (1968), Wilson and Jungner noted that the practice of screening is just as important for securing beneficial outcomes and avoiding harms as the formulation of principles. Many jurisdictions have since established various kinds of "screening governance organizations" to provide oversight of screening practice. Yet to date there has been relatively little reflection on the nature and organization of screening governance itself, or on how different governance arrangements affect the way screening is implemented and perceived and the balance of benefits and harms it delivers. Methods: An international expert policy workshop convened by Sturdy, Miller and Hogarth. Results: While effective governance is essential to promote beneficial screening practices and avoid attendant harms, screening governance organizations face enduring challenges. These challenges are social and ethical as much as technical. Evidence-based adjudication of the benefits and harms of population screening must take account of factors that inform the production and interpretation of evidence, including the divergent professional, financial and personal commitments of stakeholders. Similarly, when planning and overseeing organized screening programs, screening governance organizations must persuade or compel multiple stakeholders to work together to a common end. Screening governance organizations in different jurisdictions vary widely in how they are constituted, how they relate to other interested organizations and actors, and what powers and authority they wield. Yet we know little about how these differences affect the way screening is implemented, and with what consequences. Conclusions: Systematic research into how screening governance is organized in different jurisdictions would facilitate policy learning to address enduring challenges. Even without such research, informal exchange and sharing of experiences between screening governance organizations can deliver invaluable insights into the social as well as the technical aspects of governance

Novel concepts in virally induced asthma

Viruses are the predominant infectious cause of asthma exacerbations in the developed world. In addition, recent evidence strongly suggests that viral infections may also have a causal role in the development of childhood asthma. In this article, we will briefly describe the general perception of how the link between infections and asthma has changed over the last century, and then focus on very recent developments that have provided new insights into the contribution of viruses to asthma pathogenesis. Highlighted areas include the contribution of severe early life viral infections to asthma inception, genetic determinants of severe viral infections in infancy, the differences in innate and adaptive immune system cytokine responses to viral infection between asthmatic and nonasthmatic subjects, and a potential vaccine strategy to prevent severe early life virally-induced illness