Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.

Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.

New opportunities in vasopressin and oxytocin research: a perspective from the amygdala.

In the present review, we discuss how the evolution of oxytocin and vasopressin from a single ancestor peptide after gene duplication has stimulated the development of the vertebrate social brain. Separate production sites became possible with a hypothalamic development, which, interestingly, is triggered by the same transcription factors that underlie the development of various subcortical regions where vasopressin and oxytocin receptors are adjacently expressed and which are connected by inhibitory circuits. The opposite modulation of their output by vasopressin and oxytocin could thus create a dynamic equilibrium for rapid responsiveness to external stimuli. At the level of the individual, nurturing early in life can long-lastingly program oxytocin signaling, maintaining a capability of learning and sensitivity to external stimuli that contributes to development of social behavior in adulthood. Oxytocin and vasopressin are thus important for the development of a vertebrate brain that supports bonding between individuals and building of an interactive community.

The 16p11.2 rearrangments genetic paradigms for obesity and neurodevelopmental disorders.

Recent discoveries of recurrent and reciprocal Copy Number Variants (CNVs) using genome- wide studies have led to a new understanding of the etiology of neuropsychiatric disorders. CNVs represent loss (deletion) or gain (duplication) of genomic material. This thesis work is focused on CNVs at the 16p11.2 BP4-BP5 locus, which are among the most frequent etiologies of neurodevelopmental disorders and have been associated with Autism Spectrum Disorders (ASD), schizophrenia, cognitive impairment, alterations of brain size as well as obesity and underweight. Because deletion and duplication of the 16p11.2 locus occur frequently and recurrently (with the same breakpoints), CNVs at this locus represent a powerful paradigm to understand how a genomic region may modulate cognitive and behavioral traits as well as the relationship and shared mechanisms between distinct psychiatric diagnoses such as ASD and schizophrenia. The present dissertation includes three studies: 1) The first project aims at identifying structural brain-imaging endophenotypes in 16p11.2 CNVs carriers at risk for ASD and schizophrenia. The results show that gene dosage at the 16p11.2 locus modulates global brain volumes and neural circuitry, including the reward system, language and social cognition circuits. 2) The second investigates the neuropsychological profile in 16p11.2 deletion and duplication carriers. While deletion carriers show specific deficits in language and inhibition, the profile of duplication carriers is devoid of specific weaknesses and presents enhanced performance in a verbal memory task. 3) The third study on food-related behaviors in 16p11.2 deletion and duplication carriers shows that alterations of the reponse to satiety are present in CNV carriers before the onset of obesity, pointing toward a potential mechanism driving the Body Mass Index increase in deletion carriers. Dysfunctions in the reward system and dopaminergic circuitries could represent a common mechanism playing a role in the phenotype and could be investigated in future studies. Our data strongly suggest that complex cognitive traits correlate to gene dosage in humans. Larger studies including expression data would allow elucidating the contribution of specific genes to these different gene dosage effects. In conclusion, a systematic and careful investigation of cognitive, behavioral and intermediate phenotypes using a gene dosage paradigm has allowed us to advance our understanding of the 16p11.2 BP4-BP5 locus and its effects on neurodevelopment. -- La récente découverte de variations du nombre de copies (CNVs pour 'copy number variants') dans le génome humain a amélioré nos connaissances sur l'étiologie des troubles neuropsychiatriques. Un CNV représente une perte (délétion) ou un gain (duplication) de matériel génétique sur un segment chromosomique. Ce travail de thèse est focalisé sur les CNVs réciproques (délétion et duplication) dans la région 16p11.2 BP4-BP5. Ces CNVs sont une cause fréquente de troubles neurodéveloppementaux et ont été associés à des phénotypes « en miroir » tels que obésité/sous-poids ou macro/microcéphalie mais aussi aux troubles du spectre autistique (TSA), à la schizophrénie et au retard de développement/déficience intellectuelle. La fréquence et la récurrence de la délétion et de la duplication aux mêmes points de cassure font de ces CNVs un paradigme unique pour étudier la relation entre dosage génique et les traits cognitifs et comportementaux, ainsi que les mécanismes partagés par des troubles psychiatriques apparemment distincts tels que les TSA et la schizophrénie. Ce travail de thèse comporte trois études distinctes : 1) l'étude en neuroimagerie structurelle identifie les endophénotypes chez les porteurs de la délétion ou de la duplication. Les résultats montrent une influence du dosage génique sur le volume cérébral total et certaines structures dans les systèmes de récompense, du langage et de la cognition sociale. 2) L'étude des profils neuropsychologiques chez les porteurs de la délétion ou de la duplication montre que la délétion est associée à des troubles spécifiques du langage et de l'inhibition alors que les porteurs de la duplication ne montrent pas de faiblesse spécifique mais des performances mnésiques verbales supérieures à leur niveau cognitif global. 3) L'étude sur les comportements alimentaires met en évidence une altération de la réponse à la satiété qui est présente avant l'apparition de l'obésité. Un dysfonctionnement dans le système de récompense et les circuits dopaminergiques pourrait représenter un mécanisme commun aux différents phénotypes observés chez ces individus porteurs de CNVs au locus 16p11.2. En conclusion, l'utilisation du dosage génique comme outil d'investigation des phénotypes cliniques et endophénotypes nous a permis de mieux comprendre le rôle de la région 16p11.2 BP4-BP5 dans le neurodéveloppement.

Guideline adaptation: a methodology to enhance efficiency in guideline development and improve utilization.

BACKGROUND: Developing and updating high-quality guidelines requires substantial time and resources. To reduce duplication of effort and enhance efficiency, we developed a process for guideline adaptation and assessed initial perceptions of its feasibility and usefulness. METHODS: Based on preliminary developments and empirical studies, a series of meetings with guideline experts were organised to define a process for guideline adaptation (ADAPTE) and to develop a manual and a toolkit made available on a website (http://www.adapte.org). Potential users, guideline developers and implementers, were invited to register and to complete a questionnaire evaluating their perception about the proposed process.

Functional and evolutionary analysis of DXL1, a non-essential gene encoding a 1-deoxy-D-xylulose 5-phosphate synthase like protein in Arabidopsis thaliana

The synthesis of 1-deoxy-D-xylulose 5-phosphate (DXP), catalyzed by the enzyme DXP synthase (DXS), represents a key regulatory step of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis. In plants DXS is encoded by small multigene families that can be classified into, at least, three specialized subfamilies. Arabidopsis thaliana contains three genes encoding proteins with similarity to DXS, including the well-known DXS1/CLA1 gene, which clusters within subfamily I. The remaining proteins, initially named DXS2 and DXS3, have not yet been characterized. Here we report the expression and functional analysis of A. thaliana DXS2. Unexpectedly, the expression of DXS2 failed to rescue Escherichia coli and A. thaliana mutants defective in DXS activity. Coherently, we found that DXS activity was negligible in vitro, being renamed as DXL1 following recent nomenclature recommendation. DXL1 is targeted to plastids as DXS1, but shows a distinct expression pattern. The phenotypic analysis of a DXL1 defective mutant revealed that the function of the encoded protein is not essential for growth and development. Evolutionary analyses indicated that DXL1 emerged from DXS1 through a recent duplication apparently specific of the Brassicaceae lineage. Divergent selective constraints would have affected a significant fraction of sites after diversification of the paralogues. Furthermore, amino acids subjected to divergent selection and likely critical for functional divergence through the acquisition of a novel, although not yet known, biochemical function, were identified. Our results provide with the first evidences of functional specialization at both the regulatory and biochemical level within the plant DXS family.

Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes

Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the evolutionary impact of lineage-specific gene loss. Here, we show that identifying lineage-specific gene loss after genome duplication is important for understanding the evolution of gene subfunctions in surviving paralogs and for improving functional connectivity among human and model organism genomes. We examine the general principles of gene loss following duplication, coupled with expression analysis of the retinaldehyde dehydrogenase Aldh1a gene family during retinoic acid signaling in eye development as a case study. Humans have three ALDH1A genes, but teleosts have just one or two. We used comparative genomics and conserved syntenies to identify loss of ohnologs (paralogs derived from genome duplication) and to clarify uncertain phylogenies. Analysis showed that Aldh1a1 and Aldh1a2 form a clade that is sister to Aldh1a3-related genes. Genome comparisons showed secondarily loss of aldh1a1 in teleosts, revealing that Aldh1a1 is not a tetrapod innovation and that aldh1a3 was recently lost in medaka, making it the first known vertebrate with a single aldh1a gene. Interestingly, results revealed asymmetric distribution of surviving ohnologs between co-orthologous teleost chromosome segments, suggesting that local genome architecture can influence ohnolog survival. We propose a model that reconstructs the chromosomal history of the Aldh1a family in the ancestral vertebrate genome, coupled with the evolution of gene functions in surviving Aldh1a ohnologs after R1, R2, and R3 genome duplications. Results provide evidence for early subfunctionalization and late subfunction-partitioning and suggest a mechanistic model based on altered regulation leading to heterochronic gene expression to explain the acquisition or modification of subfunctions by surviving ohnologs that preserve unaltered ancestral developmental programs in the face of gene loss.

Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms.

Based on Darwin's concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions, and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host's factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT) that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms (ARMs).

Web services to link interlibrary software with OCLC WorldShare

Purpose - This article describes the use of web services to interconnect the GTBib interlibrary loan program with the OCLC WorldShare platform. Design/methodology/approach - We describe the current problem of duplication of procedures in libraries that have added their collections to the OCLC WorldCat catalogue in recent years and are therefore more likely to receive interlibrary loan requests through the WorldShare Platform. Findings - A solution that uses web services to insert and retrieve requests between the two systems is presented. Autonomous agents periodically check the status of the requests and keep them updated and synchronized. These agents also inform the library staff of any variation or inconsistency that is detected. Practical Implications - This technology reduces process management time by making it unnecessary to introduce the request data in both systems. Agents are used to check the consistency of statuses between the two systems, thus avoiding errors and omissions and improving the efficiency of the whole interlibrary loan process. Originality/value - This paper describes in detail the technical aspects of the solution as a reference for the development of future applications.

Automatisointiin ja monistettavuuteen perustuvan palvelumallin soveltaminen tietojärjestelmätoimituksissa

Ohjelmistotuotannon yleinen ongelma on se, että toimitusprojektien läpivientiajat pitkittyvät. Kilpailun kiristyessä ohjelmistoalalla on alettu kiinnittää erityistä huomiota projektien eri vaiheiden tehostamiseen. Process Vision Oy kehittää energiatietojärjestelmiä Suomen energia-alan yrityksille. Yrityksessä on kehitetty vuonna 2010 palvelumalli, jonka avulla pyritään nopeuttamaan toimitusprojektien eri vaiheita. Valtioneuvosto valmisteli vuonna 2009 tuntimittausasetuksen, joka määritti sääntöjä mittaustiedon hallintaan energia-alalla. Kyseisen asetuksen pohjalta Energiateollisuus julkaisi vuonna 2010 ohjeistuksen, joka selkeyttää asetuksen sisällön vaatimuksia jakeluverkonhaltijoille ja sähkön myyjille. Process Vision Oy on valmistellut ohjeistuksen pohjalta tuntimittauspaketin, joka sisältää ohjeistuksen mukaiset toiminnot GENERIS-järjestelmässä. Tässä diplomityössä määritellään Process Vision Oy:n palvelumallin mukaiset standardikomponentit tuntimittauspaketin toimitusprojekteja varten. Työn tavoitteena on kehittää mahdollisimman pitkälle tuotteistettu tuntimittauspaketin toimitus uusille ja vanhoille asiakkaille. Työn lopussa pohditaan miten hyvin palvelumalli soveltuu tuntimittauspaketin toimitusprojekteihin. Lisäksi työssä kartoitetaan yrityksessä käytössä olevien automatisointityökalujen kehitystarpeita. Työn tuloksena saatiin määriteltyä GENERIS-objektit ja konfiguraatiot, jotka toimitetaan tuntimittauspaketin mukana. Työn ohessa sisällytettiin yrityksen Suomen taseselvitysjärjestelmien asennusohjeeseen tuntimittauspaketin toiminnallisuuksien konfigurointi. Uusien vientimäärittelyjen avulla voidaan tuntimittauspaketin toiminnallisuudet toimittaa jatkossa tehokkaammin kuin aiemmin.

Cisto de duplicação gástrica com parênquima pancreático ectópico em adulto assintomático

The authors describe a rare case of a gastric duplication cyst in a 55-year-old man. The past history revealed that the patient was treated one year before for gastroduodenal ulcer. The cyst was discovered incidentally at upper gastrointestinal endoscopy. Biopsies showed inflammation without evidence of tumor. On abdominal ultrasonography and CT scan, a left upper quadrant mass was noted. At laparotomy, a mass measuring 6,0 cm in contact with the stomach was excised. Histopathology showed a gastric duplication cyst containing pancreatic mucosa.

Duplicação uretral em homem adulto

Urethral duplication is a rare congenital anomaly. The clinical presentation and treatment varies because of the different anatomical patterns of this abnormality. We report a case of this entity in the adult male patient. The clinical, radiological and endoscopic findings, as well as the treatment are discussed.

Transfer of Administrative HR Services to Global Service Center in Poland

Liiketoimintaa tukevien palvelujen etätuotanto edustaa uutta kansainvälistymisen muotoa. Kehittyvien markkinoiden nousu yhdistettynä yritysten arvoketjutoimintojen kansainvälistymiseen on luonut yrityksille kasvavan paineen etsiä parasta sijaintia toiminnoilleen. Monikansalliset yritykset ovat yhä useammin korvanneet paikallisia henkilöstöpalvelujaan siirtymällä globaaliin malliin jaettujen palvelujen tuotannossa. Tämä diplomityö on toteutettu tukeakseen UPM:n henkilöstöhallintoa globaalin palvelukeskuksen perustamisessa Puolaan. Tutkimuksen tavoitteena on laajentaa käsitystä henkilöstöpalvelujen tarjontamallin uudistamiseen johtaneista tekijöistä ja motiiveista. Empiirisen tutkimuksen tärkein tavoite on tukea rekrytoinnin hallinnollisten töiden siirtoa globaaliin palvelukeskukseen palvelun laadun säilyessä vähintään aikaisemmalla tasolla. Tutkimuksen tulokset painottavat strategista näkökulmaa muutokseen. Strategiset syyt UPM:n henkilöstöhallinnon globaalin palvelukeskuksen perustamiselle sisältävät ylikapasiteetin ja päällekkäisten toimintojen vähentämisen eri maissa. Muutos lisää palvelun joustavuutta sekä edesauttaa toiminnan läpinäkyvyyttä, ennustettavuutta ja kustannusten valvontaa. Onnistuneesti toteutetut jaetut palvelut voivat toimia hyvänä lähtökohtana tehokkaiden henkilöstöpalvelujen tuottamiselle.

Developing sustainable research data management services: an institutional collaboration

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Chronic effect of antidopaminergic drugs or estrogen on male Wistar rat lactotrophs and somatotrophs

The aim of the present study was to evaluate the effect of antidopaminergic agents on the somatotrophs in the presence of hyperprolactinemia. Adult male Wistar rats were divided into 6 groups: a control group and five groups chronically treated (60 days) with haloperidol, fluphenazine, sulpiride, metoclopramide or estrogen. Somatotrophs and lactotrophs were identified by immunohistochemistry and the data are reported as percent of total anterior pituitary cells counted. The drugs significantly increased the percentage of lactotrophs: control (mean ± SD) 21.3 ± 4.4, haloperidol 27.8 ± 2.2, fluphenazine 34.5 ± 3.6, sulpiride 32.7 ± 3.5, metoclopramide 33.4 ± 5.5 and estrogen 42.4 ± 2.8. A significant reduction in somatotrophs was observed in animals treated with haloperidol (23.1 ± 3.0), fluphenazine (22.1 ± 1.1) and metoclopramide (24.2 ± 3.0) compared to control (27.3 ± 3.8), whereas no difference was observed in the groups treated with sulpiride (25.0 ± 2.2) and estrogen (27.1 ± 2.8). In the groups in which a reduction occurred, this may have simply been due to dilution, secondary to lactotroph hyperplasia. In view of the duplication of the percentage of prolactin-secreting cells, when estrogen was applied, the absence of a reduction in the percent of somatotrophs suggests a replication effect on this cell population. These data provide additional information about the direct or indirect effect of drugs which, in addition to interfering with the dopaminergic system, may act on other pituitary cells as well as on the lactotrophs.

Mutations in the SRY, DAX1, SF1 and WNT4 genes in Brazilian sex-reversed patients

In most mammals, male development is triggered by the transient expression of the SRY gene, which initiates a cascade of gene interactions ultimately leading to the formation of a testis from the indifferent fetal gonad. Mutation studies have identified several genes essential for early gonadal development. We report here a molecular study of the SRY, DAX1, SF1 and WNT4 genes, mainly involved in sexual determination, in Brazilian 46,XX and 46,XY sex-reversed patients. The group of 46,XX sex-reversed patients consisted of thirteen 46,XX true hermaphrodites and four 46,XX males, and was examined for the presence of the SRY gene and for the loss of function (inactivating mutations and deletions) of DAX1 and WNT4 genes. In the second group consisting of thirty-three 46,XY sex-reversed patients we investigated the presence of inactivating mutations in the SRY and SF1 genes as well as the overexpression (duplication) of the DAX1 and WNT4 genes. The SRY gene was present in two 46,XX male patients and in none of the true hermaphrodites. Only one mutation, located outside homeobox domain of the 5' region of the HMG box of SRY (S18N), was identified in a patient with 46,XY sex reversal. A novel 8-bp microdeletion of the SF1 gene was identified in a 46,XY sex-reversed patient without adrenal insufficiency. The dosage of DAX1 and WNT4 was normal in the sex-reversed patients studied. We conclude that these genes are rarely involved in the etiology of male gonadal development in sex-reversed patients, a fact suggesting the presence of other genes in the sex determination cascade.