Análisis de una iniciativa estudiantil de investigación surgida en Criptogamia, una asignatura optativa de segundo ciclo de Biología = Analysis of a students’ research initiative originating in Cryptogamy, an elective course in the last two years of the Biology degree

Presentamos una experiencia exitosa de aprendizaje que partió de Criptogamia (asignatura optativa de segundo ciclo de Biología), que dio lugar a un proyecto de investigación gestionado por los propios alumnos. La iniciativa se consolidó estableciendo una Asociación de Estudiantes centrada en investigación y divulgación. En poco tiempo, los participantes han presentado comunicaciones científicas, y organizado actividades dirigidas a diversos públicos, dentro y fuera de la comunidad universitaria. Actualmente se plantea una colaboración multidisciplinar con otros organismos de investigación y la extensión de su ámbito de estudio. Abordamos su incidencia en el aprendizaje en varios aspectos: científico (técnicas específicas, rigor, búsqueda de información e interpretación de resultados), comunicativo (estructuración y presentación de la información obtenida, para diversos públicos), y organizativo, incluyendo el trabajo en equipo. Aunque de carácter espontáneo, esta experiencia muestra rasgos evaluables en cuanto a sus posibilidades para otras asignaturas. Analizamos las características y planteamiento de esta optativa, el perfil de sus alumnos, y el contexto universitario que la acoge. Detectamos como factores principales los aspectos participativos de la asignatura, la cohesión del grupo, el carácter voluntario de la implicación, los beneficios percibidos por los estudiantes, y la disponibilidad de recursos humanos (supervisión) y materiales (equipamiento y subvenciones).

X-chromosome tiling path array detection of copy number variants in patients with chromosome X-linked mental retardation

Background: Aproximately 5–10% of cases of mental retardation in males are due to copy number variations (CNV) on the X chromosome. Novel technologies, such as array comparative genomic hybridization (aCGH), may help to uncover cryptic rearrangements in X-linked mental retardation (XLMR) patients. We have constructed an X-chromosome tiling path array using bacterial artificial chromosomes (BACs) and validated it using samples with cytogenetically defined copy number changes. We have studied 54 patients with idiopathic mental retardation and 20 controls subjects. Results: Known genomic aberrations were reliably detected on the array and eight novel submicroscopic imbalances, likely causative for the mental retardation (MR) phenotype, were detected. Putatively pathogenic rearrangements included three deletions and five duplications (ranging between 82 kb to one Mb), all but two affecting genes previously known to be responsible for XLMR. Additionally, we describe different CNV regions with significant different frequencies in XLMR and control subjects (44% vs. 20%). Conclusion:This tiling path array of the human X chromosome has proven successful for the detection and characterization of known rearrangements and novel CNVs in XLMR patients.

Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p<0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.

Some last thoughts on compositional data analysis

One of the disadvantages of old age is that there is more past than future: this,however, may be turned into an advantage if the wealth of experience and, hopefully,wisdom gained in the past can be reflected upon and throw some light on possiblefuture trends. To an extent, then, this talk is necessarily personal, certainly nostalgic,but also self critical and inquisitive about our understanding of the discipline ofstatistics. A number of almost philosophical themes will run through the talk: searchfor appropriate modelling in relation to the real problem envisaged, emphasis onsensible balances between simplicity and complexity, the relative roles of theory andpractice, the nature of communication of inferential ideas to the statistical layman, theinter-related roles of teaching, consultation and research. A list of keywords might be:identification of sample space and its mathematical structure, choices betweentransform and stay, the role of parametric modelling, the role of a sample spacemetric, the underused hypothesis lattice, the nature of compositional change,particularly in relation to the modelling of processes. While the main theme will berelevance to compositional data analysis we shall point to substantial implications forgeneral multivariate analysis arising from experience of the development ofcompositional data analysis…

The lender of last resort: A 21st Century approach

The object of this paper is to analyze rigorously the role of a Lender ofLast Resort by providing a framework where the distinction betweeninsolvency and illiquidity is not clearly cut. Determining the optimalLender of Last Resort policy requires a careful modeling of the structureof the interbank market and of the closure policy. In our set up, theresults depend upon the existence of moral hazard. If the main source ofmoral hazard is the banks lack of incentives to screen loans, then theLender of Last Resort may have to intervene to improve the e¢ciency of anunsecured interbank market; if instead, the main source of moral hazard isloans monitoring, then the interbank market should be secured and theLender of Last Resort should never intervene.

Firms vs. insiders as traders of last resort

We explore the role of corporate insiders vs. firms as traders of last resort. We develop a simple model of insider trading in which insiders provide price support, as well as liquidity, in security markets. Consistent with the model predictions we find that in the US markets insiders trading activities have a clear impact on return distributions. Furthermore, we provide empirical evidence on insiders transactions and firm transactions affecting returns in a different manner. In particular, while insiders transactions (both purchases and sales) have a strong impact on skewness in the short run and to a lesser extent in short run volatility, company repurchases only have a clear impact on volatility, both in the short and the long run. We provide explanations for this asymmetry.

A flood geodatabase and its climatological applications: the case of Catalonia for the last century

Floods are the natural hazards that produce the highest number of casualties and material damage in the Western Mediterranean. An improvement in flood risk assessment and study of a possible increase in flooding occurrence are therefore needed. To carry out these tasks it is important to have at our disposal extensive knowledge on historical floods and to find an efficient way to manage this geographical data. In this paper we present a complete flood database spanning the 20th century for the whole of Catalonia (NE Spain), which includes documentary information (affected areas and damage) and instrumental information (meteorological and hydrological records). This geodatabase, named Inungama, has been implemented on a GIS (Geographical Information System) in order to display all the information within a given geographical scenario, as well as to carry out an analysis thereof using queries, overlays and calculus. Following a description of the type and amount of information stored in the database and the structure of the information system, the first applications of Inungama are presented. The geographical distribution of floods shows the localities which are more likely to be flooded, confirming that the most affected municipalities are the most densely populated ones in coastal areas. Regarding the existence of an increase in flooding occurrence, a temporal analysis has been carried out, showing a steady increase over the last 30 years.

Mitologia i literatura a "Suddenly Last Summer" de Tennessee Williams: tot lluitant contra Venus i Èdip

The aim of this article is to analyze accurately the role played by two classical references, Venus and Oedipus, in Tennessee Williams¿s Suddenly Last Summer, in accordance with the usual nature of studies on Classical Tradition ¿Greek and Roman- and focusing in this case on the relationship between literature and mythology. It is thanks to Venus and Oedipus that the playwright succeeds in showing the magnitude of men¿s and women¿s tragedy, which from his point of view is simply that they have failed to see either kindness in the face of God or to feel his loving and fatherly providence.

Literature and Mythology in Tennessee Williams's "Suddenly Last Summer": Fighting against Venus and Oedipus

The aim of this article is to analyze accurately the role played by two classical references, Venus and Oedipus, in Tennessee Williams Suddenly Last Summer, in accordance with the usual nature of studies on Classical Tradition a Greek and Roman- and focusing in this case on the relationship between literature and mythology. It is thanks to Venus and Oedipus that the playwright succeeds in showing the magnitude of mens and womens tragedy, which from his point of view is simply that they have failed to see either kindness in the face of God or to feel his loving and fatherly providence.

Mitología y Literatura en "Suddenly Last Summer" de Tennessee Williams: luchando contra Venus y Edipo

The aim of this article is to analyze accurately the role played by two classical references, Venus and Oedipus, in Tennessee Williams's Suddenly Last Summer, in accordance with the usual nature of studies on Classical Tradition -Greek and Roman- and focusing in this case on the relationship between literature and mythology. It is thanks to Venus and Oedipus that the playwright succeeds in showing the magnitude of men¿s and women¿s tragedy, which from his point of view is simply that they have failed to see either kindness in the face of God or to feel his loving and fatherly providence.

Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

Background: MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample.Results: Through simulation studies we have shown that our proposed method outperforms two existing methods that are based on simple threshold rules or iterative regression. We have illustrated the method using a controlled MLPA assay in which targeted regions are variable in copy number in individuals suffering from different disorders such as Prader-Willi, DiGeorge or Autism showing the best performace.Conclusion: Using the proposed mixed-model, we are able to determine thresholds to decide whether a region is altered. These threholds are specific for each individual, incorporating experimental variability, resulting in improved sensitivity and specificity as the examples with real data have revealed.

Identifying the parent-of-origin of de novo SNVs in schizophrenia

Several studies over the last few years have shown that newly arising (de novo) mutations contribute to the genetics of schizophrenia (SZ), autism (ASD) and other developmental disorders. The strongest evidence comes from studies of de novo Copy Number Variation (CNV), where the rate of new mutations is shown to be increased in cases when compared to controls [23, 24]. Research on de novo point mutations and small insertion-deletions (indels) has been more limited, but with the development of next-generation sequencing (NGS) technology, such studies are beginning to provide preliminary evidence that de novo single-nucleotide mutations (SNVs) might also increase risk of SZ and ASD [25, 26] Advanced paternal age is a major source of new mutations in human beings [27] and could thus be associated with increased risk for developing SZ, ASD or other developmental disorders. Indeed, advanced paternal age is found to be a risk factor for developing SZ and ASD in the offspring [28, 29] and new mutations related to advanced paternal age have been implicated as a cause of sporadic cases in several autosomal dominant diseases, some neurodevelopmental diseases, including SZ and ASD, and social functioning. New single-base substitutions occur at higher rates at males compared to females and this difference increases with paternal age. This is due to the fact that sperm cells go through a much higher number of cell divisions (~840 by the age of 50), which increases the risk for DNA copy errors in the male germ line [30] . By contrast, the female eggs (oocytes) undergo only 24 cell divisions and all but the last occur during foetal life. The aim of my project is to determine the parent-of-origin of de novo SNVs, using large samples of parent-offspring trios affected with schizophrenia (SZ). From whole exome sequencing of 618 Bulgarian proband-offspring trios affected, nearly 1000 de novo (SNVs or small indels) have been identified and from these, the parent-of-origin of at least 60% of the mutations (N=600) can be established. This project is contained in a main one that consists on the determination of the parental origin of different types of de novo mutations (SNVs, small indels and large CNVs).

Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip

Background: Recent studies in pigs have detected copy number variants (CNVs) using the Comparative Genomic Hybridization technique in arrays designed to cover specific porcine chromosomes. The goal of this study was to identify CNV regions (CNVRs) in swine species based on whole genome SNP genotyping chips. Results: We used predictions from three different programs (cnvPartition, PennCNV and GADA) to analyze data from the Porcine SNP60 BeadChip. A total of 49 CNVRs were identified in 55 animals from an Iberian x Landrace cross (IBMAP) according to three criteria: detected in at least two animals, contained three or more consecutive SNPs and recalled by at least two programs. Mendelian inheritance of CNVRs was confirmed in animals belonging to several generations of the IBMAP cross. Subsequently, a segregation analysis of these CNVRs was performed in 372 additional animals from the IBMAP cross and its distribution was studied in 133 unrelated pig samples from different geographical origins. Five out of seven analyzed CNVRs were validated by real time quantitative PCR, some of which coincide with well known examples of CNVs conserved across mammalian species. Conclusions: Our results illustrate the usefulness of Porcine SNP60 BeadChip to detect CNVRs and show that structural variants can not be neglected when studying the genetic variability in this species.

The use of tricyclic antidepressants in the treatment of temporomandibular joint disorders: systematic review of the literature of the last 20 years

Many therapies have been proposed for the management of temporomandibular disorders, including the use of different drugs. However, lack of knowledge about the mechanisms behind the pain associated with this pathology, and the fact that the studies carried out so far use highly disparate patient selection criteria, mean that results on the effectiveness of the different medications are inconclusive. This study makes a systematic review of the literature published on the use of tricyclic antidepressants for the treatment of temporomandibular disorders, using the SORT criteria (Strength of recommendation taxonomy) to consider the level of scientific evidence of the different studies. Following analysis of the articles, and in function of their scientific quality, a type B recommendation is given in favor of the use of tricyclic antidepressants for the treatment of temporomandibular disorders.

Macrofossils in Raraku Lake (Easter Island) integrated with sedimentary and geochemical records towards a palaeoecological synthesis for the last 34,000 years

Macrofossil analysis of a composite 19 m long sediment core from Rano Raraku Lake (Easter Island)was related to litho-sedimentary and geochemical features of the sediment. Strong stratigraphical patterns are shown by indirect gradient analyses of the data. The good correspondence between the stratigraphical patterns derived from macrofossil (Correspondence Analysis) and sedimentary and geochemical data (Principal Component Analysis) shows that macrofossil associations provide sound palaeolimnological information in conjunction with sedimentary data. The main taphonomic factors in fluencing the macrofossil assemblages are run-off from the catchment, the littoral plant belt, and the depositional environment within the basin. Five main stages during the last 34,000 calibrated years BP (cal yr BP) are characterised from the lithological, geochemical, and macrofossil data. From 34 to 14.6 cal kyr BP (last glacial period) the sediments were largely derived from the catchment, indicating a high energy lake environment with much erosion and run-off bringing abundant plant trichomes, lichens, and mosses into the centre of Raraku Lake.