Novel insulated gamma and lentis retroviral vectors towards safer genetic modification of stem cells

In otherwise successful gene therapy trials insertional mutagenesis has resulted in leukemia. The identification of new short synthetic genetic insulator elements (GIE) which would both prevent such activation effects and shield the transgene from silencing, is a main challenge. Previous attempts with e.g. b-globin HS4, have met with poor efficacy and genetic instability. We have investigated potential improvement with two new candidate synthetic GIEs in SIN-gamma and lentiviral vectors. With each constructs two internal promoters have been tested: either the strong Fr- MuLV-U3 or the housekeeping hPGK.We could identify a specific combination of insulator 2 repeats which translates into best functional activity, high titers and boundary effect in both gammaretro and lentivectors. In target cells a dramatic shift of expression is observed with an homogenous profile the level of which strictly depends on the promoter strength. These data remain stable in both HeLa cells over three months and cord blood HSCs for two months, irrespective of the multiplicity of infection (MOI). In comparison, control native and SIN vectors expression levels show heterogeneous, depend on the MOI and prove unstable. We have undertaken genotoxicity assessment in comparing integration patterns ingenuity in human target cells sampled over three months using high-throughput pyro-sequencing. Data will be presented. Further genotoxicity assessment will include in vivo studies. We have established insulated vectors which harbour both boundary and enhancer-blocking effect and show stable in prolonged in vitro culture conditions. Work performed with support of EC-DG research FP6-NoE, CLINIGENE: LSHB-CT-2006-018933

Vuosaaren sataman palon-, öljyn- ja vaarallisten aineiden torjuntasuunnitelmat

Työn tavoitteena oli laatiavuonna 2008 valmistuvaan Vuosaaren satamaan palon-, öljyn- ja vaarallisten aineiden torjuntasuunnitelmat. Suunnitelmat perustuvat eri lain-säädännön sekä sataman ympäristöluvan vaatimuksiin. Ne otetaan käyttöön jo sata-man rakentamisen yhteydessä. Suunnitelmissa on Vuosaaren satamassa työskentelevälle henkilöstölle toimintaohjei-ta erilaisten onnettomuuksien varalle. Suunnitelmat täyttävät viranomaisten niille asettamat vaatimukset. Liitteillä on tarkentavia piirroksia ja toimintaohjeita, joita voi tarvittaessa hyödyntää työpisteissä tai torjuntakonteissa. Suunnitelmien laadinnassa ovat olleet mukana Helsingin Sataman ao. toiminnasta vastaavat henkilöt sekä eri viranomaiset (ympäristö- ja pelastusviranomaiset). Varsinainen diplomityö on kuvaus ja tiivistelmä eri suunnitelmista ja siitä, miten ne ovat syntyneet.

Satamatoimintojen käyttöönoton logistiikka

Työn tavoitteena oli selvittää Vuosaaren sataman käyttöönoton ja Helsingin nykyisten tavarasatamien siirron samanaikaissuutta siten, että palvelu toimii koko ajan. Tässä tutkimuksessa Vuosaaren satamalle muodostettiin erilaisia käyttöönottomalleja, joista kartoitettiin hyviä ja huonoja puolia. Ennen käyttöönottomallien muodostamista selvitettiin, mitä satamatoiminnot ovat Helsingin satamassa tällä hetkellä ja miten satamatoiminnot muuttuvat siirryttäessä Vuosaaren satamaan. Tämä tutkimus on ensiaskel ennen kokonaisvaltaista Vuosaaren sataman käyttöönoton ja nykyisten tavarasatamien siirron suunnittelua.

Yhteiskunnalliset vaikutustavoitteet julkisessa hankintaprosessissa

Tämän Pro gradu -tutkielman tavoitteena on analysoida julkisiin hankintoihin ja yhteiskunnallisiin vaikutuksiin liittyviä käsitteitä, käsitejärjestelmiä ja tutkimustuloksia. Työ on toteutettu käsitetutkimuksena, jolloin tarkoituksena on löytää ajattelun välineitä. Hankkeen yhteiskunnallisia vaikutuksia ovat muunmuassa ympäristövaikutukset sekä ihmisiin kohdistuvat vaikutukset. Näiden vaikutusten huomioiminen hankintavaiheessa mahdollistaa tarkemman kuvan saamisen hankkeen kokonaistaloudellisista vaikutuksista. Työn case -osuuskäsittelee Vuosaaren satamanhanketta, joka on yksi suurimmista julkisista investointihankkeista. Satamahanke toteutetaan laajassa eri tahojen yhteistyössä. Politikointi on ollut vahvasti mukana Vuosaaren satamanhankkeessa ja tietyt poliittiset voimat ovat pyrkineet edesauttamaan hankkeen toteutumista. Toisaalta tietytryhmät ovat pyrkineet estämään, tai hidastamaan hankkeen toteutumista.

Satamatoimintojen suunnittelu Kemin satamissa

Kemissä on meneillään Kukoistava Ajos -projekti, jonka tarkoituksena on kehittää Ajoksen satamaa vastaamaan tulevaisuuden vaatimuksiin. Yhtenä osana suunnitelmaan kuuluu Kemin satamien laivausten keskittäminen Ajoksen satamaan. Tämän työn tavoitteena oli satamatoimintojen suunnittelu Kukoistavan Ajoksen liikenteelle kemiläisen satama-operaattorin Kemi Shipping Oy:n näkökulmasta. Parhaan toimintomallin selvittäminen aloitettiin kartoittamalla ratkaistavien kysymysten kaikki erilaiset toteutusmahdollisuudet. Näistä vaihtoehdoista muodostettiin eri tilanteisiin soveltuvia kokonaismalleja, joita vertailtiin analysoimalla niiden vaikutusta työvoiman ja työkoneiden tarpeeseen, kuljetuksiin ja rakentamiseen ja sitä kautta kustannuksiin. Työn tuloksena saatiin aikaan esitys satamatoimintojen toteuttamisesta Kukoistavan Ajoksen tavaraliikenteelle. Lisäksi muodostettiin esitys nykyisen toimintamallin muuttamiseksi ennen lopullista siirtymistä Kukoistavan Ajoksen mallin toteuttamiseen.

Do mediterranean genera not included in Tachet et al. (2002) have mediterranean trait characteristics?

Do mediterranean genera not included in Tachet et al. 2002 have mediterranean trait characteristics? Multiple-trait databases are increasingly used in community ecology in different regions of the world. In Europe, Tachet et al.(2002) compiled an aquatic macroinvertebrate database for 473 taxa using information on 11 biological traits described by 63 categories. However, less studied regions, at the time of the compilation of the database, such as the mediterranean Basin, can harbour exclusive genera, which were not included in Tachet"s database. In a large-scale study across the mediterranean Basin, we found 44 genera that were not included in Tachet"s database (NEW genera). Our main aim was to compile trait information for these NEW genera and assess whether these genera had specific traits that could explain their exclusivity to the Mediterranean region. We compared the trait characteristics of NEW genera to those of genera only found in Mediterranean or temperate regions that were included in the Tachet"s database (MED and TEM genera, respectively). We found that NEW genera had more mediterranean characteristics than TEM genera and that some trait categories of NEW genera were even more mediterranean-like than the traits of MED genera (e.g., diapause). Therefore, our results suggest that the specific biological traits of these NEW genera allow them to cope successfully and exclusively with the harsh environmental conditions of the mediterranean climate rivers, which could partially explain their absence in Tachet"s database. Other explanations, such as the limited dispersal ability of these NEW genera to reach and colonize temperate Europe or the rarity of these NEW genera, should also be considered. We provide biological traits of the NEW genera to be used in future studies on the mediterranean river ecology.

Lastaus- ja jakelutoiminnan kehittäminen paperitehtaalla

Stora Enso Oyj:n Anjalan paperitehdas on vuoden 2008 alussa muutosten keskellä; tehtaalla pysäytetään yksi paperikone, ja samalla kahden käyntiin jäävän paperikoneen tuoteportfoliota muutetaan. Näin ollen tehtaalla on tarve päivittää logistista strategiaa ja kehittää tehtaan lähtölogistiikan toimintoja. Tämän diplomityön tavoitteena oli määrittää Anjalan paperitehtaan lastausaseman resurssit tehtaalla toteutettavan rakennemuutoksen jälkeisessä tilanteessa sekä tuoda esille ja pohtia tehtaan lähtölogistiikan toimintojen mahdollisia kehitystoimenpiteitä. Työssä pohdittiin rakennemuutoksen vaikutuksia lastausaseman resursseihin niin auto- kuin junalastauksenkin osalta sekä käsiteltiin mahdollisia logististen järjestelyjen kehitystoimenpiteitä. Lastausaseman resurssit todettiin riittäviksi. Keskeisimmiksi ja tärkeimmiksi kehitystoimenpiteiksi työssä nähtiin tehdas-satama -toimituksissa käytettävien autokuljetusten määrän kasvattaminen, Stora Enson systeemiliikenteen junalastausten kehittäminen sekä Anjalan paperitehtaan ja Inkeroisten kartonkitehtaan yhteisen kuljetussuunnittelijan toimen käynnistäminen.

Molecular profiling of non-small cell lung cancer by histologic subtype

Background: A substantial proportion of NSCLC has been shown to harbour specific molecular alterations affecting tumour proliferation and resulting in sensitivity to inhibition of the corresponding activated oncogenic pathway by targeted therapies. Comprehensive tumor profiling can diagnose such alterations and may identify new alterations opening additional treatment options for all distinct NSCLC subtypes. Methods: Over 6,700 non-small cell lung cancer cases referred to Caris Life Sciences between 2009 and 2014 were evaluated; clinical diagnoses and detailed tumor pathology were collected from referring physicians. Specific profiling was performed per physician request and included a combination of sequencing (Sanger, NGS or pyrosequencing), protein expression (IHC), gene amplification/rearrangement (CISH or FISH), and/or RNA fragment analysis within potential cancer-related genes and pathways. Results: Patients were grouped into cohorts according to histological subtype - adenocarcinoma (AD) (n=4,286), squamous cell carcinoma (SCC) (n=1,280), large cell carcinoma (LCC) (n=153) and bronchioalveolar carcinoma (BAC) (n=94). Protein overexpression of cMET (>2+ in >50% cells) was higher in AD (35.9%) compared to other subgroups (12-20%) while RRM1 and TOP2A levels were lower in AD. ALK or ROS1 were rearranged in 5.3% of patients with AD compared to 3.7% of patients with LCC and 1.2% of patients with SCC. EGFR mutations were found at low prevalence in both the LCC (0%) and SCC cohorts (2.8%) compared to 21% in AD. Similar lower rates of BRAF mutations were observed in the LCC and SCC cohorts compared to AD (0%, 1.1% and 5.1%). Pathway analysis showed activating mutations in the ERK pathway in 40% of patients with AD. Only 10-12% of patients with LCC or SCC had activating mutations in the ERK pathway. Conclusions: Despite the limitations of this retrospective series, we report comprehensive profiling of the largest cohort of NSCLC. Tumor profiling reveals that ADs may be more addicted to the ERK pathway than other histological subtypes. Drugs which target cMET may also have most utility in AD. Full analysis by histological subtype and additional correlative data on protein expression, gene copy number and mutations will be presented.

Spiders on a Hot Volcanic Roof: Colonisation Pathways and Phylogeography of the Canary Islands Endemic Trap-Door Spider Titanidiops canariensis (Araneae, Idiopidae)

Studies conducted on volcanic islands have greatly contributed to our current understanding of how organisms diversify. The Canary Islands archipelago, located northwest of the coast of northern Africa, harbours a large number of endemic taxa. Because of their low vagility, mygalomorph spiders are usually absent from oceanic islands. The spider Titanidiops canariensis, which inhabits the easternmost islands of the archipelago, constitutes an exception to this rule. Here, we use a multi-locus approach that combines three mitochondrial and four nuclear genes to investigate the origins and phylogeography of this remarkable trap-door spider. We provide a timeframe for the colonisation of the Canary Islands using two alternative approaches: concatenation and species tree inference in a Bayesian relaxed clock framework. Additionally, we investigate the existence of cryptic species on the islands by means of a Bayesian multi-locus species delimitation method. Our results indicate that T. canariensis colonised the Canary Islands once, most likely during the Miocene, although discrepancies between the timeframes from different approaches make the exact timing uncertain. A complex evolutionary history for the species in the archipelago is revealed, which involves two independent colonisations of Fuerteventura from the ancestral range of T. canariensis in northern Lanzarote and a possible back colonisation of southern Lanzarote. The data further corroborate a previously proposed volcanic refugium, highlighting the impact of the dynamic volcanic history of the island on the phylogeographic patterns of the endemic taxa. T. canariensis includes at least two different species, one inhabiting the Jandia peninsula and central Fuerteventura and one spanning from central Fuerteventura to Lanzarote. Our data suggest that the extant northern African Titanidiops lineages may have expanded to the region after the islands were colonised and, hence, are not the source of colonisation. In addition, T. maroccanus may harbour several cryptic species.

Langattoman tietoliikenneverkon toteuttaminen satama-alueelle

Tässä työssä toteutetaan IEEE 802.16-2004 standardiin perustuva langaton WiMAX tietoliikenneverkko, sekä tutkitaan etenemismallien soveltuvuutta satama-alueelle. Myös muiden verkkoratkaisujen soveltuvuutta pohditaan. Lisäksi tutkitaan sääolosuhteiden sekä päätelaitteen liikkumisnopeuden vaikutuksia yhteyteen. Satama-alueella on teräksestä valmistettuja merikontteja pinottuina päällekkäin, ja ne vaikeuttavat langattomien signaalien etenemistä. Merikonttien pinot säilyttävät tietyn maksimikorkeuden johtuen työkoneiden rajallisesta kyvystä pinota niitä. Langattomien signaalien etenemiselle erilaisissa ympäristöissä on kehitetty etenemismalleja. Etenemisallien avulla voidaan pyrkiä ennustamaan signaalin vahvuutta eri etäisyyksillä tukiasemasta. Etenemismallit kuvaavat ympäristön aiheuttamaa signaalin vaimenemista erilaisten muuttujien avulla. Langattoman tietoliikenneverkon toteutus ongelmatilanteineen dokumentoitiin ja alueella tehtiin kuuluvuusmittauksia. Löydettiin etenemismalli ja muuttujat, joiden avulla lasketut tulokset vastasivat mitattuja tuloksia hyvin. Myös sääolosuhteiden sekä päätelaitteen liikkumisnopeuden vaikutusta signaalin vahvuuteen tutkittiin. Vesi- ja lumisateen sekä sumun vaikutuksen todettiin olevan merkityksetön verkon käyttämällä 3.5 GHz taajuusalueella. Myöskään päätelaitteen liikkumisnopeuden ei todettu vaikuttavan toiminnallisuuteen 20-30 kilometrin tuntinopeudella, jolla työkoneet alueella liikkuvat.

RAPD analysis of genetic variability in a multiprovenance base population of Eucalyptus grandis hill ex maiden

This study aimed to evaluate the genetic variability among individuals of a base population of Eucalyptus grandis and to build a molecular marker database for the analyzed populations. The Eucalyptus grandis base population comprised 327 individuals from Coff's Harbour, Atherton and Rio Claro. A few plants came from other sites (Belthorpe MT. Pandanus, Kenilworth, Yabbra, etc.). Since this base population had a heterogeneous composition, the groups were divided according to geographic localization (latitude and longitude), and genetic breeding level. Thus, the influence of those two factors (geographic localization and genetic breeding level) on the genetic variability detected was discussed. The RAPD technique allowed the evaluation of 70 loci. The binary matrix was used to estimate the genetic similarity among individuals using Jaccard's Coefficient. Parametric statistical tests were used to compare within-group similarity of the means. The obtained results showed that the base population had wide genetic variability and a mean genetic similarity of 0.328. Sub-group 3 (wild materials from the Atherton region) showed mean genetic similarity of 0.318. S.P.A. (from Coff's Harbour region) had a mean genetic similarity of 0.322 and was found to be very important for maintenance of variation in the base population. This can be explained since the individuals from those groups accounted for most of the base population (48.3% for it). The base population plants with genetic similarity higher than 0.60 should be phenotypically analyzed again in order to clarify the tendency of genetic variability during breeding programs.

Effectiveness of Pilotage

The objective of the pilotage effectiveness study was to come up with a process descrip-tion of the pilotage procedure, to design performance indicators based on this process description, to be used by Finnpilot, and to work out a preliminary plan for the imple-mentation of the indicators within the Finnpilot organisation. The theoretical aspects of pilotage as well as the guidelines and standards used were determined through a literature review. Based on the literature review, a process flow model with the following phases was created: the planning of pilotage, the start of pilo-tage, the act of pilotage, the end of pilotage and the closing of pilotage. The model based on the literature review was tested through interviews and observation of pilotage. At the same time an e-mail survey directed at foreign pilotage organisations, which included a questionnaire concerning their standards and management systems, operations procedures, measurement tools and their attitude to the passage planning, was conducted. The main issues in the observations and interviews were the passage plan and the bridge team co-operation. The phases of the pilotage process model emerged in both the pilotage activities and the interviews whereas bridge team co-operation was relatively marginal. Most of the pilotage organisations, who responded to the query, also use some standard-based management system. All organisations who answered the survey use some sort of a pilotage process model. According to the query, the main measuring tools for pilotage are statistical information concerning pilotage and the organisations, the customer feedback surveys, and financial results. Attitudes to-wards passage planning were mostly positive among the organisations. A workshop with pilotage experts was arranged where the process model constructed on the basis of the literature review was tuned to match practical pilotage. In the workshop it was determined that certain phases and the corresponding tasks, through which pilo-tage can be described as a process, were identifiable in all pilotage. The result of the workshop was a complemented process model, which separates incoming and outgoing traffic, as well as the fairway pilotage and harbour pilotage from each other. Addition-ally indicators divided according to the data gathering method were defined. Data con-cerning safety and traffic flow is gathered in the form of customer feedback. The pilot's own perceptions of the pilotage process are gathered through self-assessment. The measurement data which is connected to the phases of the pilotage process is generated e.g. by gathering statistics of the success of the pilot dispatches, the accuracy of the pi-lotage and the incidents that occurred during the pilotage, near misses, deviations and accidents. The measurement data is collected via the PilotWeb at the closing of the pilo-tage. A separate project and a project group with pilots also participating will be established for the deployment of the performance indicators. The phases of the project are: the definition phase, the implementation phase and the deployment phase. The purpose of the definition phase is to prepare questions for ship commanders concerning the cus-tomer feedback questionnaire and also to work out the self-assessment queries and the queries concerning the process indicators.

People and the intertidal : human induced changes, biodiversity loss, livelihood implications and management in the Western Indian Ocean

Vad händer i tidvattenzonen? Var går gränsen mellan land och hav, vad händer i tidvattenzonen och vem ansvarar för detta? I västra Indiska oceanen (VIO) kan avståndet mellan den lägsta nivån för lågvattnet och den högsta nivån för högvattnet vara flera kilometer och nivåskillnaderna upp till 6 meter och detta skapar ett stort och föränderligt område. Syftet med min avhandling är att öka förståelsen för tidvattenzonen i tropiska och subtropiska västra Indiska oceanen. Sammanfattningsvis visar mina studier att det finns ett mycket stort värde i den komplexa tidvattenzonen, men också att det här området hotas från både land och hav, genom t.ex. överexploatering, erosion och föroreningar. Uttnyttjandet av tidvattenzonen är stort och min avhandling har visat att aktiviteter såsom fiske i form av plocking av musslor och andra ryggradslösa djur och hamnaktiviteter påverkar den biologiska mångfalden negativt, vilket leder till försämrad levnadsstandard för resursutnyttjande människor i regionen. För att förbättra situationen krävs det mer forskning, miljöövervakning och bättre förvaltning av tidvattenzonen. Experter i regionen har rangordnat förslag på förvaltningsstrategier som skulle kunna testas för att förbättra miljön och skapa ett mer hållbart nyttjande. Avhandlingen visar även att det är möjligt att använda fjärranalysteknik såsom satellitbildsanalys för att kvantifiera mängden sjögräsvegetation (i form av biomassa), vilket kan ha stor betydelse för att förbättra storskalig miljöövervakning av kustnära naturtyper (habitat). I avhandlingsarbetet har jag använt mig av ett multidisciplinärt tillvägagångssätt och använt metoder såsom ekologisk och biologisk provtagning, intervjuer, observationer, diskussionsgrupper, frågeformulär och fjärranalys. Resultaten presenterade i denna avhandling ger en ökad kunskap om tidvattenzonen i utvecklingsländerna inom VIO-regionen som kan användas för att initiera och fortsätta att utveckla hållbara förvaltningsstrategier av biologiska resurser.

Interpreting marine benthic ecosystem functioning in coastal waters: validating the biological trait concept

Coastal areas harbour high biodiversity, but are simultaneously affected by rapid degradations of species and habitats due to human interactions. Such alterations also affect the functioning of the ecosystem, which is primarily governed by the characteristics or traits expressed by the organisms present. Marine benthic fauna is nvolved in numerous functions such as organic matter transformation and transport, secondary production, oxygen transport as well as nutrient cycling. Approaches utilising the variety of faunal traits to assess benthic community functioning have rapidly increased and shown the need for further development of the concept. In this thesis, I applied biological trait analysis that allows for assessments of a multitude of categorical traits and thus evaluation of multiple functional aspects simultaneously. I determined the functional trait structure, diversity and variability of coastal zoobenthic communities in the Baltic Sea. The measures were related to recruitment processes, habitat heterogeneity, large-scale environmental and taxonomic gradients as well as anthropogenic impacts. The studies comprised spatial scales from metres to thousands of kilometres, and temporal scales spanning one season as well as a decade. The benthic functional structure was found to vary within and between seagrass landscape microhabitats and four different habitats within a coastal bay, in papers I and II respectively. Expressions of trait categories varied within habitats, while the density of individuals was found to drive the functional differences between habitats. The findings in paper III unveiled high trait richness of Finnish coastal benthos (25 traits and 102 cateogries) although this differed between areas high and low in salinity and human pressure. In paper IV, the natural reduction in taxonomic richness across the Baltic Sea led to an overall reduction in function. However, functional richness in terms of number of trait categories remained comparatively high at low taxon richness. Changes in number of taxa within trait categories were also subtle and some individual categories were maintained or even increased. The temporal analysis in papers I and III highlighted generalities in trait expressions and dominant trait categories in a seagrass landscape as well as a “type organism” for the northern Baltic Sea. Some initial findings were made in all four papers on the role of common and rare species and traits for benthic community functioning. The findings show that common and rare species may not always express the same trait categories in relation to each other. Rare species in general did not express unique functional properties. In order to advance the understanding of the approach, I also assessed some issues concerning the limitations of the concept. This was conducted by evaluating the link between trait category and taxonomic richness using especially univariate measures. My results also show the need to collaborate nationally and internationally on safeguarding the utility of taxonomic and trait data. The findings also highlight the importance of including functional trait information into current efforts in marine spatial planning and biomonitoring.

Rock outcrop habitats in the Venezuelan Guayana lowlands: their main vegetation types and floristic components

The Guayana Shield, located in north-eastern South America, consists of a highly complex and composite mosaic of landscape elements. Amongst these, inselbergs are very conspicuous, because of their peculiar shape and their unusual associated vegetation. Geologically, these rock outcrops are part of the underlying ancient igneous-metamorphic basement and occur mainly in the lowlands of the periphery of the shield. As azonal habitats, inselbergs harbour a highly specialized flora. The characteristic vegetation is composed of lithophytic and savanna-like plant communities, as well as low dry forests. As a whole, the vegetation of an inselberg may be interpreted as a mosaic of marginal habitats. Therefore a large number of taxa find suitable niches in a quite condensed space. Gradients of soil depth and water availability are the main factors determining the floristic composition. A preliminary floristic inventory of the Venezuelan inselberg flora comprises 614 vascular plant species. 24% of them are endemic to the Guayana region, 15% are endemic to inselbergs of the Guayana region. The distribution patterns of these latter, eco-endemic species allows to distinguish a northern and a southern inselberg district. The two districts overlap in the Átures area, in the surroundings of Puerto Ayacucho, where a true centre of endemism is located. The distinction into two districts is emphasised by different phytogeographic relations. The southern inselberg district shows connections to the "tepui" flora, whereas the northern district reveals phytogeographic relations to the Caribbean region as well as to the Brazilian Shield. Possible explanations for the floristic interchange across the equator are discussed.