Satisfaction survey with DNA cards method to collect genetic samples for pharmacogenetics studies

Background: Pharmacogenetic studies are essential in understanding the interindividual variability of drug responses. DNA sample collection for genotyping is a critical step in genetic studies. A method using dried blood samples from finger-puncture, collected on DNA-cards, has been described as an alternative to the usual venepuncture technique. The purpose of this study is to evaluate the implementation of the DNA cards method in a multicentre clinical trial, and to assess the degree of investigators' satisfaction and the acceptance of the patients perceived by the investigators.Methods: Blood samples were collected on DNA-cards. The quality and quantity of DNA recovered were analyzed. Investigators were questioned regarding their general interest, previous experience, safety issues, preferences and perceived patient satisfaction. Results: 151 patients' blood samples were collected. Genotyping of GST polymorphisms was achieved in all samples (100%). 28 investigators completed the survey. Investigators perceived patient satisfaction as very good (60.7%) or good (39.3%), without reluctance to finger puncture. Investigators preferred this method, which was considered safer and better than the usual methods. All investigators would recommend using it in future genetic studies. Conclusion: Within the clinical trial setting, the DNA-cards method was very well accepted by investigators and patients (in perception of investigators), and was preferred to conventional methods due to its ease of use and safety.

Antibiotic resistance genes in the bacteriophage DNA fraction of environmental samples

Antibiotic resistance is an increasing global problem resulting from the pressure of antibiotic usage, greater mobility of the population, and industrialization. Many antibiotic resistance genes are believed to have originated in microorganisms in the environment, and to have been transferred to other bacteria through mobile genetic elements. Among others, ß-lactam antibiotics show clinical efficacy and low toxicity, and they are thus widely used as antimicrobials. Resistance to ß-lactam antibiotics is conferred by ß-lactamase genes and penicillin-binding proteins, which are chromosomal- or plasmid-encoded, although there is little information available on the contribution of other mobile genetic elements, such as phages. This study is focused on three genes that confer resistance to ß-lactam antibiotics, namely two ß-lactamase genes (blaTEM and blaCTX-M9) and one encoding a penicillin-binding protein (mecA) in bacteriophage DNA isolated from environmental water samples. The three genes were quantified in the DNA isolated from bacteriophages collected from 30 urban sewage and river water samples, using quantitative PCR amplification. All three genes were detected in the DNA of phages from all the samples tested, in some cases reaching 104 gene copies (GC) of blaTEM or 102 GC of blaCTX-M and mecA. These values are consistent with the amount of fecal pollution in the sample, except for mecA, which showed a higher number of copies in river water samples than in urban sewage. The bla genes from phage DNA were transferred by electroporation to sensitive host bacteria, which became resistant to ampicillin. blaTEM and blaCTX were detected in the DNA of the resistant clones after transfection. This study indicates that phages are reservoirs of resistance genes in the environment.

Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands

The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700-6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.

Parametric and semiparametric estimation of sample selection models: an empirical application to the female labour force in Portugal

This comment corrects the errors in the estimation process that appear in Martins (2001). The first error is in the parametric probit estimation, as the previously presented results do not maximize the log-likelihood function. In the global maximum more variables become significant. As for the semiparametric estimation method, the kernel function used in Martins (2001) can take on both positive and negative values, which implies that the participation probability estimates may be outside the interval [0,1]. We have solved the problem by applying local smoothing in the kernel estimation, as suggested by Klein and Spady (1993).

Testing the entrepreneurial intention model on a two-country sample

This paper tests the Entrepreneurial Intention Model -which is adapted from the Theory of Planned Behavior- on a sample of 533 individuals from two quite different countries: one of them European (Spain) and the other South Asian (Taiwan). A newly developed Entrepreneurial Intention Questionnaire (EIQ) has being used which tries to overcome some of the limitations of previous instruments. Structural equations techniques were used in the empirical analysis. Results are generally satisfactory, indicating that the model is probably adequate for studying entrepreneurship. Support for the model was found not only in the combined sample, but also in each of the national ones. However, some differences arose that may indicate demographic variables contribute differently to the formation of perceptions in each culture.

Labor productivity in Europe: evidence from a sample of regions

The present paper aims at analyzing the sources of productivity in Europe to account for its recent underperformance and identify potential geographic idiosyncracies. We study the productivity performance and its sources in a sample of ten European regions belonging to four countries (France, Germany, Italy and Spain). Exploiting the increasing availability of disaggregated data at regional level in Europe, we propose both a descriptive statistics and an econometric analysis of productivity sources since 1995. Our main finding is that the sources of labor productivity are rather heterogeneous across our sample but may be associated with regional or national idiosyncracies.

Array de DNA per identificar espècies de Fusarium: ampliació d'un array existent per incloure espècies del Sud d'Europa

Projecte de recerca elaborat a partir d’una estada al Department for Feed and Food Hygiene del National Veterinary Institute, Noruega, entre novembre i desembre del 2006. Els grans de cereal poden estar contaminats amb diferents espècies de Fusarium capaces de produir metabolits secundaris altament tòxics com trichotecenes, fumonisines o moniliformines. La correcta identificació d’aquestes espècies és de gran importància per l’assegurament del risc en l’àmbit de la salut humana i animal. La identificació de Fusarium en base a la seva morfologia requereix coneixements taxonòmics i temps; la majoria dels mètodes moleculars permeten la identificació d’una única espècie diana. Per contra, la tecnologia de microarray ofereix l’anàlisi paral•lel d’un alt nombre de DNA dianes. En aquest treball, s’ha desenvolupat un array per a la identificació de les principals espècies de Fusarium toxigèniques del Nord i Sud d’Europa. S’ha ampliat un array ja existent, per a la detecció de les espècies de Fusarium productores de trichothecene i moniliformina (predominants al Nord d’Europa), amb l’addició de 18 sondes de DNA que permeten identificar les espècies toxigèniques més abundants al Sud d’Europa, les qual produeixen majoritàriament fumonisines. Les sondes de captura han estat dissenyades en base al factor d’elongació translació- 1 alpha (TEF-1alpha). L’anàlisi de les mostres es realitza mitjançant una única PCR que permet amplificar part del TEF-1alpha seguida de la hibridació al xip de Fusarium. Els resultats es visualitzen mitjançant un mètode de detecció colorimètric. El xip de Fusarium desenvolupat pot esdevenir una eina útil i de gran interès per a l’anàlisi de cereals presents en la cadena alimentària.

Aplicació de la termoquimiolisi - cromatografia de gasos - espectrometria de masses a l'estudi de la matèria orgànica del sòl

Estudi realitzat a partir d’una estada a la Université de Poitiers, França, entre 2007 i 2009. El treball s'ha centrat en dues activitats bàsiques. El treball realitzat s’ha centrat en dues activitats bàsiques. D’una banda, la posada a punt d'un protocol de fraccionament de la matèria orgànica del sòl, per extraccions successives amb solvents alcalins després d'una seqüència de pretractaments al sòl: cap pretractament, atac amb àcid (per destruir els carbonats), atac amb ditionit (per reduir els òxids de Fe i Al i facilitar l'extracció de la matèria orgànica associada a aquests compostos). El protocol dóna una visió de conjunt de la situació de la matèria orgànica del sòl, combinant aspectes físics (protecció, precipitació, oclusió per carbonats) i químics (grau d'humificació). D’altra banda, l'aprenentatge de la tècnica de termoquimiolisi-cromatografia de gasos-espectrometria de masses. Aquest era l'objectiu de l'estada a Poitiers, al qual hem donat prioritat. Ens hem centrat en l'estudi de fraccions físiques (densimètriques) obtingudes en estudis anteriors sobre sòls forestals. Les fraccions considerades són: fracció lleugera (FL), tres fraccions ocluïdes (OC1, OC2 i OC3) i fracció densa (FD). L’aplicació de la termoquimiolisi permet de caracteritzar diversos grups de substàncies, de les quals ens hem centrat en alguns indicadors bioquímics: àcids grasos, alcohols, diàcids, productes fenòlics i altres productes aromàtics, derivats de carbohidrats. L’estudi de conjunt d’aquests productes indica que és a les fraccions ocluïdes (que solen ser minoritàries a tots els horitzons) on la matèria orgànica d’origen microbià és dominant, mentre que a les fraccions lleugera (FL) i densa (FD) la matèria orgànica d’origen vegetal sembla dominant. Es preveu aplicar aquesta tècnica a l’estudi de les fraccions obtingudes a la primera part del treball, actualment congelades i a l’espera de ser processades.

Solid-phase synthesis and NMR studies of modified oligonucleotides forming triplex helix and of oligonucleopeptides mimicking the topoisomerase I-DNA covalent complex

Report for the scientific sojourn carried out at the Institut de Biologia Molecular de Barcelona of the CSIC –state agency – from april until september 2007. Topoisomerase I is an essential nuclear enzyme that modulates the topological status of DNA, facilitating DNA helix unwinding during replication and transcription. We have prepared the oligonucleotide-peptide conjugate Ac-NLeu-Asn-Tyr(p-3’TTCAGAAGC5’)-LeuC-CONH-(CH2)6-OH as model compound for NMR studies of the Topoisomerase I- DNA complex. Special attention was made on the synthetic aspects for the preparation of this challenging compound especially solid supports and protecting groups. The desired peptide was obtained although we did not achieve the amount of the conjugate needed for NMR studies. Most probably the low yield is due to the intrinsic sensitive to hydrolysis of the phosphate bond between oligonucleotide and tyrosine. We have started the synthesis and the structural characterization of oligonucleotides carrying intercalating compounds. At the present state we have obtained model duplex and quadruplex sequences modified with acridine and NMR studies are underway. In addition to this project we have successfully resolved the structure of a fusion peptide derived from hepatitis C virus envelope synthesized by the group of Dr. Haro and we have synthesized and started the characterization of a modified G-quadruplex.

Comparing population distributions from bin-aggregated sample data: an application to historical height data from France

This paper develops a methodology to estimate the entire population distributions from bin-aggregated sample data. We do this through the estimation of the parameters of mixtures of distributions that allow for maximal parametric flexibility. The statistical approach we develop enables comparisons of the full distributions of height data from potential army conscripts across France's 88 departments for most of the nineteenth century. These comparisons are made by testing for differences-of-means stochastic dominance. Corrections for possible measurement errors are also devised by taking advantage of the richness of the data sets. Our methodology is of interest to researchers working on historical as well as contemporary bin-aggregated or histogram-type data, something that is still widely done since much of the information that is publicly available is in that form, often due to restrictions due to political sensitivity and/or confidentiality concerns.

System GMM estimation with a small sample

Properties of GMM estimators for panel data, which have become very popular in the empirical economic growth literature, are not well known when the number of individuals is small. This paper analyses through Monte Carlo simulations the properties of various GMM and other estimators when the number of individuals is the one typically available in country growth studies. It is found that, provided that some persistency is present in the series, the system GMM estimator has a lower bias and higher efficiency than all the other estimators analysed, including the standard first-differences GMM estimator.

Knowledge of Catalan, public/private sector choice and earnings: Evidence from a double sample selection model

This paper explores the earnings return to Catalan knowledge for public and private workers in Catalonia. In doing so, we allow for a double simultaneous selection process. We consider, on the one hand, the non-random allocation of workers into one sector or another, and on the other, the potential self-selection into Catalan proficiency. In addition, when correcting the earnings equations, we take into account the correlation between the two selectivity rules. Our findings suggest that the apparent higher language return for public sector workers is entirely accounted for by selection effects, whereas knowledge of Catalan has a significant positive return in the private sector, which is somewhat higher when the selection processes are taken into account.

Development of specific ITS markers for plant DNA identification within herbivorous insects

DNA based techniques have proved to be very useful methods to study trophic relationships 17 between pests and their natural enemies. However, most predators are best defined as omnivores, 18 and the identification of plant-specific DNA should also allow the identification of the plant 19 species the predators have been feeding on. In this study, a PCR approach based on the 20 development of specific primers was developed as a self-marking technique to detect plant DNA 21 within the gut of one heteropteran omnivorous predator (Macrolophus pygmaeus) and two 22 lepidopteran pest species (Helicoverpa armigera and Tuta absoluta). Specific tomato primers 23 were designed from the ITS 1-2 region, which allowed the amplification of a tomato DNA 24 fragment of 332 bp within the three insect species tested in all cases (100% of detection at t = 0) 25 and did not detect DNA of other plants nor of the starved insects. Plant DNA half-lives at 25ºC 26 ranged from 5.8h, to 27.7h and 28.7h within M. pygmaeus, H. armigera and T. absoluta, 27 respectively. Tomato DNA detection within field collected M. pygmaeus suggests dietary mixing 28 in this omnivorous predator and showed a higher detection of tomato DNA in females and 29 nymphs than males. This study provides a useful tool to detect and to identify plant food sources 30 of arthropods and to evaluate crop colonization from surrounding vegetation in conservation 31 biological control programs.

Análisis de la expresión de las moléculas relacionadas con el complejo principal de histocompatibilidad de clase I y de NKG2D como respuesta al daño oxidativo del DNA en el cáncer urotelial de vejiga. Relación con las características clínico patológicas y supervivencia

Es tracta d'un estudi retrospectiu de casos de 280 pacients diagnosticats de tumor vesical primari amb un seguiment mínim de 8 anys. S'ha construït un Tissue microarray i mitjançant mètodes semiquantitatius d’inmunohistoquímica es determinarà l'expressió de les molècules MICA (MHC class I chain-related gene A) i del seu receptor NKG2D (Natural-Killer group 2-member D) a nivell tissular, relacionant-lo amb variables anatomopatològiques segons els grups de risc, hàbit tabàquic i sexe. Finalment valorarem l'expressió de MICA/NKG2D com a factor independent de recidiva / progressió tumoral. En la literatura només existeixen 2 treballs que relacionin MICA amb el càncer vesical.

Assessing the Precision of Compositional Data in a Stratified Double Stage Cluster Sample: Application to the Swiss Earnings Structure Survey

Precision of released figures is not only an important quality feature of official statistics,it is also essential for a good understanding of the data. In this paper we show a casestudy of how precision could be conveyed if the multivariate nature of data has to betaken into account. In the official release of the Swiss earnings structure survey, the totalsalary is broken down into several wage components. We follow Aitchison's approachfor the analysis of compositional data, which is based on logratios of components. Wefirst present diferent multivariate analyses of the compositional data whereby the wagecomponents are broken down by economic activity classes. Then we propose a numberof ways to assess precision