Cab45 is required for Ca(2+)-dependent secretory cargo sorting at the trans-Golgi network

Ca(2+) import into the lumen of the trans-Golgi network (TGN) by the secretory pathway calcium ATPase1 (SPCA1) is required for the sorting of secretory cargo. How is Ca(2+) retained in the lumen of the Golgi, and what is its role in cargo sorting? We show here that a soluble, lumenal Golgi resident protein, Cab45, is required for SPCA1-dependent Ca(2+) import into the TGN; it binds secretory cargo in a Ca(2+)-dependent reaction and is required for its sorting at the TGN.

TRPM5-mediated calcium uptake regulates mucin secretion from human colon goblet cells

Mucin 5AC (MUC5AC) is secreted by goblet cells of the respiratory tract and, surprisingly, also expressed de novo in mucus secreting cancer lines. siRNA-mediated knockdown of 7343 human gene products in a human colonic cancer goblet cell line (HT29-18N2) revealed new proteins, including a Ca(2+)-activated channel TRPM5, for MUC5AC secretion. TRPM5 was required for PMA and ATP-induced secretion of MUC5AC from the post-Golgi secretory granules. Stable knockdown of TRPM5 reduced a TRPM5-like current and ATP-mediated Ca(2+) signal. ATP-induced MUC5AC secretion depended strongly on Ca(2+) influx, which was markedly reduced in TRPM5 knockdown cells. The difference in ATP-induced Ca(2+) entry between control and TRPM5 knockdown cells was abrogated in the absence of extracellular Ca(2+) and by inhibition of the Na(+)/Ca(2+) exchanger (NCX). Accordingly, MUC5AC secretion was reduced by inhibition of NCX. Thus TRPM5 activation by ATP couples TRPM5-mediated Na(+) entry to promote Ca(2+) uptake via an NCX to trigger MUC5AC secretion

Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes

BACKGROUND: Understanding how alternative phenotypes arise from the same genome is a major challenge in modern biology. Eusociality in insects requires the evolution of two alternative phenotypes - workers, who sacrifice personal reproduction, and queens, who realize that reproduction. Extensive work on honeybees and ants has revealed the molecular basis of derived queen and worker phenotypes in highly eusocial lineages, but we lack equivalent deep-level analyses of wasps and of primitively eusocial species, the latter of which can reveal how phenotypic decoupling first occurs in the early stages of eusocial evolution. RESULTS: We sequenced 20 Gbp of transcriptomes derived from brains of different behavioral castes of the primitively eusocial tropical paper wasp Polistes canadensis. Surprisingly, 75% of the 2,442 genes differentially expressed between phenotypes were novel, having no significant homology with described sequences. Moreover, 90% of these novel genes were significantly upregulated in workers relative to queens. Differential expression of novel genes in the early stages of sociality may be important in facilitating the evolution of worker behavioral complexity in eusocial evolution. We also found surprisingly low correlation in the identity and direction of expression of differentially expressed genes across similar phenotypes in different social lineages, supporting the idea that social evolution in different lineages requires substantial de novo rewiring of molecular pathways. CONCLUSIONS: These genomic resources for aculeate wasps and first transcriptome-wide insights into the origin of castes bring us closer to a more general understanding of eusocial evolution and how phenotypic diversity arises from the same genome.

Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.

Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis

Invasive candidiasis is the most commonly reported invasive fungal infection worldwide. Although Candida albicans remains the main cause, the incidence of emerging Candida species, such as C. parapsilosis is increasing. It has been postulated that C. parapsilosis clinical isolates result from a recent global expansion of a virulent clone. However, the availability of a single genome for this species has so far prevented testing this hypothesis at genomic scales. We present here the sequence of three additional strains from clinical and environmental samples. Our analyses reveal unexpected patterns of genomic variation, shared among distant strains, that argue against the clonal expansion hypothesis. All strains carry independent expansions involving an arsenite transporter homolog, pointing to the existence of directional selection in the environment, and independent origins of the two clinical isolates. Furthermore, we report the first evidence for the existence of recombination in this species. Altogether, our results shed new light onto the dynamics of genome evolution in C. parapsilosis.

SICA2 : la experiencia de integración CRIS/RI en el ámbito regional de Andalucía

El proyecto SICA2, presentado por Beatriz Barros y Miguel Ángel Aguirre, de la Consejería de Economía, Innovación y Ciencia de la Junta de Andalucía, supone una innovadora extensión del concepto de CRIS universitario a un ámbito regional para el conjunto de las universidades andaluzas. El sistema de recogida y validación de la información científica en tiempo real se basa en una primera fase SICA que organiza la investigación en unidades mínimas o 'Grupos PAIDI' y que ya implementó el estándar CVN para las nueve universidades andaluzas que forman parte del proyecto. Esta segunda fase de integración tiene además prevista su prolongación en el repositorio institucional Reposit-AN de ámbito igualmente regional que se alimentará de los metadatos procedentes del sistema CRIS de la Junta de Andalucía y se presentará oficialmente a final de año.

Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina)

The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, ~13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts.

Comparative transcriptomics of early dipteran development

BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). RESULTS: We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. CONCLUSIONS: We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).

Comparative genomics of emerging pathogens in the Candida glabrata clade

BACKGROUND: Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens have recently been described within this group: C. nivariensis and C. bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts. RESULTS: Our results indicate that the two new pathogens are more closely related to the non-pathogenic N. delphensis than to C. glabrata. We uncover duplications and accelerated evolution that specifically affected genes in the lineage preceding the group containing N. delphensis and the three pathogens, which may provide clues to the higher propensity of this group to infect humans. Finally, the number of Epa-like adhesins is specifically enriched in the pathogens, particularly in C. glabrata. CONCLUSIONS: Remarkably, some features thought to be the result of adaptation of C. glabrata to a pathogenic lifestyle, are present throughout the Nakaseomyces, indicating these are rather ancient adaptations to other environments. Phylogeny suggests that human pathogenesis evolved several times, independently within the clade. The expansion of the EPA gene family in pathogens establishes an evolutionary link between adhesion and virulence phenotypes. Our analyses thus shed light onto the relationships between virulence and the recent genomic changes that occurred within the Nakaseomyces.

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.

Kiinteistön sähköisen huoltokirjan kehittäminen

Ympäristöministeriö edellyttää kaikilta vuoden 2000 jälkeen valmistuneilta tai peruskorjatuilta asuinkiinteistöiltä huoltokirjaa. Huoltokirja on kiinteistön ylläpitoon liittyvä asiakirjakokonaisuus, johon kootaan kaikki tarvittavat tiedot kiinteistöstä ja sen hoidosta. Tämän diplomityön tavoitteena oli toteuttaa sähköinen huoltokirjajärjestelmä asuinkiinteistöille. Järjestelmän haluttiin palvelevan isännöitsijöiden ja huoltoyhtiöiden lisäksi myös kiinteistön omistajia, asukkaita, rakennuttajia ja kiinteistön välittäjiä. Tästä syystä järjestelmästä haluttiin Internet-selaimella käytettävä verkkopalvelu. Diplomityöhön kuului järjestelmän suunnittelu, toteutus ja testaus. Työn lopputuloksena syntynyt Pihapiiri.com järjestelmä otettiin käyttöön syksyllä 2002. Projektin aikanahavaittiin, että huoltokirjoja koskevat määrittelyt ja standardit olivat vasta kehitteillä. e-EHYT-hanke (elinkaarihallinnan yhteiset ydintie dot sähköisissä huoltokirjoissa) on merkittävä edistysaskel huoltokirjajärjestelmien sisällön ja tiedonsiirron standardoinnissa. Uusissa tuotekehityshankkeissa ja nykyisten huoltokirjajärjestelmien jatkokehityshankkeissa on olennaista huomioida e-EHYT-määritysten sekä yhteistyöverkoston merkitys. Käyttäjät ovat kritisoineet markkinoilla olevia tuotteita liian tarkoiksi. Liian teknisiä ja raskaita ratkaisuja tulee välttää varsinkin silloin kun tuotetta suunnitellaan asunto-osakeyhtiöille ja pientalo-omistajille.

Rakennusinvestointien käsittelyprosessin tehostaminen

Suomen valtionhallinnon maaliskuussa 2005 julkaisemat tuloksellisuuden tavoitteet koskettavat kaikkia hallinnonaloja. Maa- ja metsätalousministeriön ohjeistamat Työvoima- ja elinkeinokeskusten maaseutuosastot ovat yksikköjä, joita vaikuttavuus- ja tuloksellisuustavoitteet velvoittavat. Tehokasta elintarviketuotantoa ja maatalouden kustannuskehityksen hallintaa voidaan tarkastella kiinteiden tuotannontekijöiden, kuten maatalousrakennusten ja investointituilla tuetun rakentamisen, vaikuttavuuden kautta. Työn tavoitteena oli tehostaa rakennusinvestointien käsittelyprosessia: kehittää sekä tehostamisen menetelmiä että työväline toiminnan ohjaukseen maa- ja metsätalousministeriölle. Ratkaisuja etsittiin teorian ja empirian pohjalta kehitettävien käsitteistöjen ja menetelmien avulla. Teoriaosuudessa haettiin kirjallisuudesta välineitä joilla prosesseja voitaisiin analysoida, mitata ja kehittää. Prosessimallinnukset, Italian vastaavan järjestelmän tutkimus ja Suomen rakennustoimelle tehty kysely muodostavat empiirisen aineiston, jonka perusteella lopulliset tehostamisen keinot ja konstruktiot kehitettiin. Tehostamisen menetelmäksi kehitettiinaluehallinnolle sovellettu suorituskyvyn mittausjärjestelmä, panosprisma. Tuloksellisuus, vaikuttavuus ja laatu riippuvat työn tuottamisen lähtökohdista. Prosessia voidaan tehostaa kiinnittämällä huomiota tulosohjaukseen, asiakirjojen saatavuuteen ja laatuun, neuvonnan oikea-aikaiseen ajoittuvuuteen ja riittävyyteen sekä tietojärjestelmien kehittämiseen. Näiden avulla voidaan saavuttaa käsittelyprosessin aika- ja kustannussäästöjä, tukivarojen käyttöön saaminen ja hyödynnettävyys paranevat ja tukipäätöksen tuottamisen asiakaspalveluprosessi tehostuu.

Language variation in source texts and their translations: the case of L3 in film translation

In addition to the two languages essentially involved in translation, that of the source text (L1) and that of the target text (L2), we propose a third language (L3) to refer to any other language(s) found in the text. L3 may appear in the source text (ST) or the target text (TT), actually appearing more frequently inSTs in our case studies. We present a range of combinations for the convergence and divergence of L1, L2 and L3, for the case of feature films and their translations using examples from dubbed and subtitled versions of films, but we are hopeful that our tentative conclusions may be relevant to other modalities of translation, audiovisual and otherwise. When L3 appears in an audiovisual ST,we find a variety of solutions whereby L3 is deleted from or adapted to the TT.In the latter case, L3 might be rendered in a number of ways, depending on factors such as the audience’s familiarity with L3, and the possibility that L3 inthe ST is an invented language.

Ympäristövaikutusten velvoitetarkkailun tulosten epävarmuuden arviointi

Tämä diplomityö tehtiin Neste Oil Oyj:n Kehittäminen ja Laboratoriot yksikön HSE-palveluille. Työn tavoitteena oli arvioida Neste Oilin ympäristövaikutusten velvoitetarkkailujen mittaustulosten epävarmuutta. Tarkastelu koski ilmanlaadun SO2-, NO2-, TRS- sekä O3-mittauksia, ympäristömelumittauksia sekä pohjavesinäytteenottoa. Ympäristönsuojelulaki (86/2000) velvoittaa tuotantolaitoksia selvittämään toimintansa ympäristövaikutukset. Myös esimerkiksi akkreditoitaessa menetelmiä mittausepävarmuus on tunnettava. On arvioitu, että tulevaisuudessa direktiivit tulevat tiukentamaan päästöraja-arvoja ja mittausepävarmuuden käsite tulee käyttöön kaikilla ympäristösektoreilla.Tässä työssä ilmanlaadun mittausepävarmuus arvioitiin vertaamalla Neste Oilin mittaustuloksia Ilmatieteenlaitoksen vertailumittausten ja kalibrointien tuloksiin. Ympäristömelun mittausepävarmuus arvioitiin Ympäristöministeriön ympäristömelunmittausohjeen (1/1995)mukai-sesti. Pohjavesinäytteenoton mittausepävarmuus arvioitiin laskemalla haitta-aineiden ajallisen vaihtelun, näytteenottomenetelmien, näytteiden kuljetuksenja säilytyksen aiheuttaman kontaminaation sekä analyysivaiheen epävarmuustekijöiden yhdistetty mittausepävarmuus. Tarkastelussa todettiin, että ilmanlaadunmittaustulokset eivät poikenneet merkittävästi vertai-lumittausten ja kalibrointien tuloksista. Menetelmien laajennetuksi mittausepävarmuudeksi saatiin 6-8 %. Ympäristömelun mittausepävarmuus vastasi ympäristömelunmittausohjeessa esitettyjä arvoja ja vaihtelivat 2-10 dB:n välillä, riippuen mittausetäisyydestä ja mittauskertojen lukumäärästä. Pohjavesinäytteenoton mittausepävarmuudelle ei ole asetettu laatutavoitteita. Tässä tarkastelussa pohjavesinäytteenoton mittausepävarmuudeksi saatiin 33 %.