The evolution of alternative splicing patterns and regulatory mechanisms

Alternative splicing produces multiple isoforms from the same gene, thus increasing the number of transcripts of the species. Alternative splicing is a virtually ubiquitous mechanism in eukaryotes, for example more than 90% of protein-coding genes in human are alternatively spliced. Recent evolutionary studies showed that alternative splicing is a fast evolving and highly species- specific mechanism. The rapid evolution of alternative splicing was considered as a contribution to the phenotypic diversity between species. However, the function of many isoforms produced by alternative splicing remains unclear and they might be the result of noisy splicing. Thus, the functional relevance of alternative splicing and the evolutionary mechanisms of its rapid divergence among species are still poorly understood. During my thesis, I performed a large-scale analysis of the regulatory mechanisms that drive the rapid evolution of alternative splicing. To study the evolution of alternative splicing regulatory mechanisms, I used an extensive RNA-sequencing dataset comprising 12 tetrapod species (human, chimpanzee and bonobo, gorilla, orangutan, macaque, marmoset, mouse, opossum, platypus, chicken and frog) and 8 tissues (cerebellum, brain, heart, kidney, liver, testis, placenta and ovary). To identify the catalogue of alternative splicing eis-acting regulatory elements in the different tetrapod species, I used a previously defined computational approach. This approach is a statistical analysis of exons/introns and splice sites composition and relies on a principle of compensation between splice sites strength and the presence of additional regulators. With an evolutionary comparative analysis of the exonic eis-acting regulators, I showed that these regulatory elements are generally shared among primates and more conserved than non-regulatory elements. In addition, I showed that the usage of these regulatory elements is also more conserved than expected by chance. In addition to the identification of species- specific eis-acting regulators, these results may explain the rapid evolution of alternative splicing. I also developed a new approach based on evolutionary sequence changes and corresponding alternative splicing changes to identify potential splicing eis-acting regulators in primates. The identification of lineage-specific substitutions and corresponding lineage-specific alternative splicing changes, allowed me to annotate the genomic sequences that might have played a role in the alternative splicing pattern differences among primates. Finally, I showed that the identified splicing eis-acting regulator datasets are enriched in human disease-causing mutations, thus confirming their biological relevance.

Effects of winter feeding strategies with alternative feeds on the performance of mature suckler cows and their progeny

Selostus: Tasaruokinnan ja vaihtoehtoisten rehujen soveltuvuus emolehmien talvikauden ruokintaan

Towards an alternative testing strategy for nanomaterials used in nanomedicine: Lessons from NanoTEST.

In spite of recent advances in describing the health outcomes of exposure to nanoparticles (NPs), it still remains unclear how exactly NPs interact with their cellular targets. Size, surface, mass, geometry, and composition may all play a beneficial role as well as causing toxicity. Concerns of scientists, politicians and the public about potential health hazards associated with NPs need to be answered. With the variety of exposure routes available, there is potential for NPs to reach every organ in the body but we know little about the impact this might have. The main objective of the FP7 NanoTEST project ( www.nanotest-fp7.eu ) was a better understanding of mechanisms of interactions of NPs employed in nanomedicine with cells, tissues and organs and to address critical issues relating to toxicity testing especially with respect to alternatives to tests on animals. Here we describe an approach towards alternative testing strategies for hazard and risk assessment of nanomaterials, highlighting the adaptation of standard methods demanded by the special physicochemical features of nanomaterials and bioavailability studies. The work has assessed a broad range of toxicity tests, cell models and NP types and concentrations taking into account the inherent impact of NP properties and the effects of changes in experimental conditions using well-characterized NPs. The results of the studies have been used to generate recommendations for a suitable and robust testing strategy which can be applied to new medical NPs as they are developed.

On diversity effects of alternative agricultural policy reforms in Finland : an agricultural sector modelling approach

Selostus: Maatalouspolitiikkauudistusten vaikutuksista pellonkäytön diversiteettiin

Phimose : Sind topische Kortikosteroide eine Alternative zur chirurgischen Behandlung [Phimosis : are topical corticosteroids an alternative to surgical treatment?]

Hintergrund: Die physiologische Phimose ist bereits bei der Geburt vorhanden und wächst sich in den meisten Fällen aus. Während 10% der Knaben im Alter von drei Jahren noch eine Phimose haben, nimmt diese Prävalenz auf 6-8% im Alter von sieben Jahren und 1% im Alter von 16 Jahren ab. Man spricht von einer pathologischen Phimose, wenn die Vorhaut Vernarbungen infolge von wiederholten Entzündungen oder forcierten Retraktionsversuchen aufweist. Dennoch ist die Unterscheidung zwischen pathologischer und physiologischer Phimose schwierig, und eine chirurgische Behandlung (Zirkumzision, Vorhautplastik) ist häufig. Eine topische Kortikosteroidbehandlung wird seit mehreren Jahren wegen seiner anti-inflammatorischen und immunsuppressiven Wirkung (Verminderung der Kollagenproduktion) angewendet. Es gibt aber keine Evidenz bezüglich Wirksamkeit und Sicherheit dieser Behandlung.

Phimosis et corticostéroïdes topiques : une alternative au traitement chirurgical? : revue Cochrane pour le praticien

Question clinique: Une mère vous consulte avec son fils âgé de 6 ans, en bonne santé habituelle mais connu pour un phimosis. Il ne présente pas de troubles mictionnels, ni d'antécédents de balanite ou de paraphimosis. Sa mère est inquiète de voir le phimosis persister et vous demande s'il existe une alternative au traitement chirurgical. Contexte: Présent dès la naissance, le phimosis physiologique se résout spontanément dans la majorité des cas. Alors que 10% des garçons présentent un phimosis à l'âge de 3 ans, cette prévalence diminue à 6-8% à l'âge de 7 ans, pour atteindre 1% à l'âge de 16 ans. On parle de phimosis pathologique lorsque le prépuce présente des cicatrices fibreuses suite à des inflammations répétées ou des décalottages forcés. Cependant, la distinction clinique entre un phimosis pathologique et physiologique est difficile et le traitement chirurgical reste fréquent. Un traitement par corticostéroïdes topiques est utilisé depuis de nombreuses années pour son action anti-inflammatoire et immunosuppressive (diminution de la production de collagène). Pourtant, il n'existe pas de preuve quant à l'efficacité et la sécurité de ce traitement.

2,4-dichlorophenoxyacetic acid as an alternative auxin for rooting of vine rootstock cuttings

Viticulture is an important agricultural activity in semiarid northeastern Brazil, and the quality and ease of vine propagation are very important in this context. This study evaluated the use of 2,4-dichlorophenoxyacetic acid (2,4-D) as an alternative to indolebutyric acid (IBA) in the rooting of vine rootstock cuttings. The trial was conducted at the Universidade Federal de Sergipe (São Cristóvão-SE) between January and March 2010 with cuttings of the rootstocks of 'IAC-766', 'IAC-572', and 'Paulsen 1103' treated with 2,4-D or IBA applied at concentrations of 0, 1000, 2000, or 3000 rng-L-1 for 5 s and planted in a field on washed sand. At 56 days after planting, the percentages of rooted, sprouted, callused, and dead cuttings were evaluated, and also the average number and length of the rooted cuttings. The results showed that 2,4-D was not superior to IBA in the characteristics wanted for the rooting process of the vine rootstock cuttings. The vine rootstocks showed potential for propagation by cutting without auxin application. It was observed that the high concentrations were the worst for the rooting of the cuttings.

Architecture for a Session Initiation Protocol Based Presence Client

Mitä on läsnäolo? Tämä työ määrittelee läsnäolon tietyn henkilön, laitteen tai palvelun halukkuudeksi kommunikoida. Nykyään on olemassa lukuisia läsnäolotietoa levittäviä sovelluksia, joista jokainen käyttää erilaista protokollaa tehtävän suorittamiseen. Vasta viime aikoina sovellusten kehittäjät ovat huomanneet tarpeen yhdelle sovellukselle, joka kykenee tukemaan lukuisia läsnäoloprotokollia. Session Initiation Protocol (SIP) voi levittää läsnäolotietoa muiden ominaisuuksiensa lisäksi. Kun muita protokollia käytetään vain reaaliaikaiseen viestintään ja läsnäolotiedon lähetykseen, SIP pystyy moniin muihinkin asioihin. Se on alunperin suunniteltu aloittamaan, muuttamaan ja lopettamaan osapuolien välisiä multimediaistuntoja. Arkkitehtuurin toteutus käyttää kahta Symbian –käyttöjärjestelmän perusominaisuutta: asiakas-palvelin rakennetta ja kontaktitietokantaa. Asiakaspalvelin rakenne erottaa asiakkaan protokollasta tarjoten perustan laajennettavalle usean protokollan arkkitehtuurille ja kontaktitietokanta toimii läsnäolotietojen varastona. Työn tuloksena on Symbianin käyttöjärjestelmässä toimiva läsnäoloasiakas.

Annonaceae substitution rates: a codon model perspective

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

Use of alternative and complementary therapies in labor and delivery care: a cross-sectional study of midwives" training in Catalan hospitals accredited as centers for normal birth

Background: The use of complementary and alternative medicine (CAM) and complementary and alternative therapies (CAT) during pregnancy is increasing. Scientific evidence for CAM and CAT in the field of obstetrics mainly covers pain relief in labor. Midwives are responsible for labor and delivery care: hence, their knowledge of CAM and CAT is important. The aims of this study are to describe the professional profile of midwives who provide care for natural childbirth in Catalan hospitals accredited as centers for normal birth, to assess midwives" level of training in CAT and their use of these therapies, and to identify specific resources for CAT in labor wards. Methods: A descriptive, cross-sectional, quantitative method was used to assess the level of training and use of CAT by midwives working at 28 hospitals in Catalonia, Spain, accredited as public normal birth centers. Results: Just under a third of midwives (30.4%) trained in CAT after completion of basic training. They trained in an average of 5.97 therapies (SD 3.56). The number of CAT in which the midwives were trained correlated negatively with age (r = - 0.284; p < 0.001) and with their time working at the hospital in years (r = - 0.136; p = 0.036). Midwives trained in CAT considered that the following therapies were useful or very useful for pain relief during labor and delivery: relaxation techniques (64.3%), hydrotherapy (84.8%) and the application of compresses to the perineum (75.9%). The availability of resources for providing CAT during normal birth care varied widely from center to center. Conclusions: Age may influence attitudes towards training. It is important to increase the number of midwives trained in CAM for pain relief during childbirth, in order to promote the use of CAT and ensure efficiency and safety. CAT resources at accredited hospitals providing normal childbirth care should also be standardized.

Use of alternative and complementary therapies in labor and delivery care: a cross-sectional study of midwives" training in Catalan hospitals accredited as centers for normal birth

Background: The use of complementary and alternative medicine (CAM) and complementary and alternative therapies (CAT) during pregnancy is increasing. Scientific evidence for CAM and CAT in the field of obstetrics mainly covers pain relief in labor. Midwives are responsible for labor and delivery care: hence, their knowledge of CAM and CAT is important. The aims of this study are to describe the professional profile of midwives who provide care for natural childbirth in Catalan hospitals accredited as centers for normal birth, to assess midwives" level of training in CAT and their use of these therapies, and to identify specific resources for CAT in labor wards. Methods: A descriptive, cross-sectional, quantitative method was used to assess the level of training and use of CAT by midwives working at 28 hospitals in Catalonia, Spain, accredited as public normal birth centers. Results: Just under a third of midwives (30.4%) trained in CAT after completion of basic training. They trained in an average of 5.97 therapies (SD 3.56). The number of CAT in which the midwives were trained correlated negatively with age (r = - 0.284; p < 0.001) and with their time working at the hospital in years (r = - 0.136; p = 0.036). Midwives trained in CAT considered that the following therapies were useful or very useful for pain relief during labor and delivery: relaxation techniques (64.3%), hydrotherapy (84.8%) and the application of compresses to the perineum (75.9%). The availability of resources for providing CAT during normal birth care varied widely from center to center. Conclusions: Age may influence attitudes towards training. It is important to increase the number of midwives trained in CAM for pain relief during childbirth, in order to promote the use of CAT and ensure efficiency and safety. CAT resources at accredited hospitals providing normal childbirth care should also be standardized.

Dual role of LldR in regulation of the lldPRD operon, involved in l-Lactate metabolism in Escherichia coli.

The lldPRD operon of Escherichia coli, involved in L-lactate metabolism, is induced by growth in this compound. We experimentally identified that this system is transcribed from a single promoter with an initiation site located 110 nucleotides upstream of the ATG start codon. On the basis of computational data, it had been proposed that LldR and its homologue PdhR act as regulators of the lldPRD operon. Nevertheless, no experimental data on the function of these regulators have been reported so far. Here we show that induction of an lldP-lacZ fusion by L-lactate is lost in an lldR mutant, indicating the role of LldR in this induction. Expression analysis of this construct in a pdhR mutant ruled out the participation of PdhR in the control of lldPRD. Gel shift experiments showed that LldR binds to two operator sites, O1 (positions 105 to 89) and O2 (positions 22 to 38), with O1 being filled at a lower concentration of LldR. L-Lactate induced a conformational change in LldR that did not modify its DNA binding activity. Mutations in O1 and O2 enhanced the basal transcriptional level. However, only mutations in O1 abolished induction by L-lactate. Mutants with a change in helical phasing between O1 and O2 behaved like O2 mutants. These results were consistent with the hypothesis that LldR has a dual role, acting as a repressor or an activator of lldPRD. We propose that in the absence of L-lactate, LldR binds to both O1 and O2, probably leading to DNA looping and the repression of transcription. Binding of L-lactate to LldR promotes a conformational change that may disrupt the DNA loop, allowing the formation of the transcription open complex.