Cyanobacteria from the Baltic Sea and Finnish lakes as an energy source and modulators of bioenergetic pathways

Cyanobacteria are a diverse group of oxygenic photosynthetic bacteria that inhabit in a wide range of environments. They are versatile and multifaceted organisms with great possibilities for different biotechnological applications. For example, cyanobacteria produce molecular hydrogen (H2), which is one of the most important alternatives for clean and sustainable energy. Apart from being beneficial, cyanobacteria also possess harmful characteristics and may become a source of threat to human health and other living organisms, as they are able to form surface blooms that are producing a variety of toxic or bioactive compounds. The University of Helsinki Culture Collection (UHCC) maintains around 1,000 cyanobacterial strains representing a large number of genera and species isolated from the Baltic Sea and Finnish lakes. The culture collection covers different life forms such as unicellular and filamentous, N2-fixing and non-N2-fixing strains, and planktonic and benthic cyanobacteria. In this thesis, the UHCC has been screened to identify potential strains for sustainable biohydrogen production and also for strains that produce compounds modifying the bioenergetic pathways of other cyanobacteria or terrestrial plants. Among the 400 cyanobacterial strains screened so far, ten were identified as high H2-producing strains. The enzyme systems involved in H2 metabolism of cyanobacteria were analyzed using the Southern hybridization approach. This revealed the presence of the enzyme nitrogenase in all strains tested, while none of them are likely to have contained alternative nitrogenases. All the strains tested, except for two Calothrix strains, XSPORK 36C and XSPORK 11A, were suggested to contain both uptake and bidirectional hydrogenases. Moreover, 55 methanol extracts of various cyanobacterial strains were screened to identify potent bioactive compounds affecting the photosynthetic apparatus of the model cyanobacterium, Synechocystis PCC 6803. The extract from Nostoc XPORK 14A was the only one that modified the photosynthetic machinery and dark respiration. The compound responsible for this effect was identified, purified, and named M22. M22 demonstrated a dual-action mechanism: production of reactive oxygen species (ROS) under illumination and an unknown mechanism that also prevailed in the dark. During summer, the Baltic Sea is occupied by toxic blooms of Nodularia spumigena (hereafter referred to as N. spumigena), which produces a hepatotoxin called nodularin. Long-term exposure of the terrestrial plant spinach to nodularin was studied. Such treatment resulted in inhibition of growth and chlorosis of the leaves. Moreover, the activity and amount of mitochondrial electron transfer complexes increased in the leaves exposed to nodularin-containing extract, indicating upregulation of respiratory reactions, whereas no marked changes were detected in the structure or function of the photosynthetic machinery. Nodularin-exposed plants suffered from oxidative stress, evidenced by oxidative modifications of various proteins. Plants initiated strategies to combat the stress by increasing the levels of alpha-tocopherol, mitochondrial alternative oxidase (AOX), and mitochondrial ascorbate peroxidase (mAPX).

Alteração do campo visual em função do uso de cabinas em tratores agrícolas

Com o objetivo de avaliar a alteração do campo visual de um trator, ocasionada pela instalação de uma cabina, foram determinadas as áreas de visibilidade nula em função da presença ou não da mesma, para cada campo visual. Os procedimentos adotados basearam-se na norma ISO 5721-1981 - Agricultural tractors - Operator's field of vision. A cabina aumentou em 34,42% a área de visibilidade nula. A relação área de projeção do trator/área total sombreada foi de 0,075 para o trator sem cabina, e 0,057 para o trator com cabina, indicando as melhores condições de visibilidade do primeiro em relação ao segundo. No que se refere aos campos visuais, a maior redução ocorreu no campo visual dos olhos e no obtido com o movimento da cabeça, em função dos suportes da cabina e da estrutura de proteção contra o capotamento. A cabina diminui o campo de visão do operador, e adequações no projeto da estrutura avaliada são necessárias para melhorar as condições de visibilidade.

Identification and characterization of new genes and pathways regulating spermatogonial cell fate

Spermatogenesis, i.e sperm production in the seminiferous tubules of the testis, is a complex process that takes over one month to complete. Life-long ability of sperm production ultimately lies in a small population of undifferentiated cells, called spermatogonial stem cells (SSCs). These cells give rise to differentiating spermatogonia, which are committed to mature into spermatozoa. SSCs represent a heterogeneous population of cells and many aspects of their basic biology are still unknown. Understanding the mechanisms behind the cell fate decision of these cells is important to gain more insights into the causes of infertility and testis cancer. In addition, an interesting new aspect is the use of testis-derived stem cells in regenerative medicine. Our data demonstrated that adult mouse testis houses a population of Nanog-expressing spermatogonia. Based on mRNA and protein analysis these cells are enriched in stage XII of the mouse seminiferous epithelial cycle. The cells derived from this stage have the highest capacity to give rise to ES cell-like cells which express Oct4 and Nanog. These cells are under tight non- GDNF regulation but their fate can be dictated by activating p21 signalling. Comparative studies suggested that these cells are regulated like ES cells. Taken together these data imply that pluripotent cells are present in the adult mammalian testis. CIP2A (cancerous inhibitor of PP2A) has been associated with tumour aggressiveness and poor prognosis. In the testis it is expressed by the descendants of stem cells, i.e. the spermatogonial progenitor cells. Our data suggest that CIP2A acts upstream of PLZF and is needed for quantitatively normal spermatogenesis. Classification of CIP2A as a cancer/testis gene makes it an attractive target for cancer therapy. Study on the CIP2A deficient mouse model demonstrates that systemic inhibition of CIP2A does not severely interfere with growth and development or tissue or organ function, except for the spermatogenic output. These data demonstrate that CIP2A is required for quantitatively normal spermatogenesis. Hedgehog (Hh) signalling is involved in the development and maintenance of many different tissues and organs. According to our data, Hh signalling is active at many different levels during rat spermatogenesis: in spermatogonia, spermatocytes and late elongating spermatids. Localization of Suppressor of Fused (SuFu), the negative regulator of the pathway, specifically in early elongating spermatids suggests that Hh signalling needs to be shut down in these cells. Introduction of Hh signalling inhibitor resulted in an increase in germ cell apoptosis. Follicle-stimulating hormone (FSH) and inhibition of receptor tyrosine kinases resulted in down-regulation of Hh signalling. These data show that Hh signalling is under endocrine and paracrine control and it promotes germ cell survival.

Avaliação de métodos alternativos à citologia no rastreamento de lesões cervicais: detecção de DNA-HPV e inspeção visual

OBJETIVO: avaliar o desempenho da citologia oncológica (CO), de captura híbrida II (CH II) e da inspeção visual com ácido acético na detecção de lesões pré-neoplásicas e neoplásicas cervicais. MÉTODOS: 2281 mulheres foram submetidas a exame clínico além da coleta de material para citologia, para CH II para detecção de DNA-HPV. Foi feita a inspeção visual do colo após aplicação do ácido acético a 5% (IVA). As mulheres com pelo menos um exame positivo eram convocadas para colposcopia, que também foi realizada em 420 mulheres com todos os exames normais. O desempenho dos testes foi calculado utilizando como padrão ouro a colposcopia com ou sem biopsia. RESULTADOS: a CO foi anormal em 209 mulheres (9,2%); a CH II foi positiva em 399 (17,5%) e em 249 (10,9%) foram encontradas alterações na IVA. Entre as 2281 mulheres avaliadas, 671 (29,4%) apresentaram pelo menos um resultado de exame positivo, embora apenas 82 (3,6%) apresentassem doença confirmada histologicamente (50 NIC1, 20 NIC2, sete NIC3 e cinco carcinomas invasores). As sensibilidades da IVA e da CH II foram semelhantes e significativamente maiores que a da CO. A especificidade da CO foi maior que a da IVA e da CH II. Nos casos com resultado de CO negativo, a IVA apresentou melhor desempenho comparada à CH II. CONCLUSÃO: o desempenho da CO associada à IVA foi melhor que o da CO associada à CH II e do que o da CO isolada.

Inspeção visual do colo uterino após aplicação de ácido acético no rastreamento das neoplasias intra-epiteliais e lesões induzidas por HPV

OBJETIVO: estimar a validade da inspeção visual após aplicação de ácido acético (IVA) no rastreamento das neoplasias intra-epiteliais cervicais (NIC) e lesões induzidas por HPV, comparando seu desempenho com o da colpocitologia e da colposcopia. MÉTODOS: estudo de validação de teste diagnóstico realizado em 893 mulheres de 18 a 65 anos, rastreadas simultaneamente com colpocitologia, IVA e colposcopia, em unidade de saúde pública de Recife, PE. A IVA foi realizada por embrocação do colo com ácido acético a 5% e observação a olho nu, com auxílio de foco clínico comum. Considerou-se como positividade o achado de qualquer lesão aceto-branca no colo. O padrão-ouro foi o histopatológico de biópsia cervical, realizado sempre que qualquer um dos três testes resultasse anormal. Foram estimados e comparados os indicadores de validade de cada teste, com os respectivos intervalos de confiança a 95%. A concordância entre os resultados dos testes foi avaliada pelo coeficiente kappa (k). RESULTADOS: das 303 mulheres biopsiadas, o estudo histopatológico foi anormal em 24. Deste total, a IVA foi positiva em 22, conferindo-lhe sensibilidade estimada de 91,7%, especificidade de 68,9%, valor preditivo positivo de 7,5% e valor preditivo negativo de 99,7%. Comparando-se os intervalos de confiança a 95%, a IVA mostrou maior sensibilidade que a colpocitologia, mas com menores especificidade e valor preditivo positivo. Houve fraca concordância entre os resultados da IVA e da colpocitologia (k=0,02) e excelente concordância com os da colposcopia (k=0,93). CONCLUSÃO: a IVA foi muito mais sensível que a colpocitologia no rastreamento das NIC e lesões HPV-induzidas e teve o mesmo desempenho da colposcopia. Sua baixa especificidade foi responsável por um elevado número de resultados falso-positivos.

Different pathways in the larval development of the crab Ucides cordatus (Decapoda, Ocypodidae) and their relation with high mortality rates by the end of massive larvicultures

One of the most limiting factors affecting the larval rearing of Ucides cordatus in the laboratory is a period of high mortality, which usually occurs late in the course of the larviculture during the metamorphosis from the zoeal to the megalopal phase. The objective of the present research was to analyze the post-embryonic development of U. cordatus on an individual basis and, in particular, to search for patterns linking disturbances in the molting process to the high larval death rates observed in massive larvicultures. A total of 50 larvae were individually reared from hatching to metamorphosis into the megalopal phase under controlled conditions, fed a combination of microalgae and rotifers. The survivorship rate was 70% until zoea V. The 35 surviving zoea V larvae followed two different pathways. Eleven underwent metamorphosis directly to megalopa, eighteen molted to zoea VI and six died as zoea V. In the last molting event, only two zoea VI larvae reached the megalopal stage, while the remaining sixteen died. In further observation under microscope, 13 of the dead zoea VI showed characteristics of the pre-molt stage and pereiopods disproportionably large in relation to the carapace. The observed pattern resembles the Molt Death Syndrome (MDS) described for other decapod species, in which larvae die in the late pre-molt phase of the molting cycle. We suggest that U. cordatus larvae develop disturbances in the molting process similar to the MDS described for other species and that these disturbances are related to a more complex pathway involving the emergence of larval stage zoea VI.

Lean daily management, visual management and continuous improvement

This thesis was part of lean adaptation project started at Outotec Lappeenranta factory in early 2013. The purpose of this thesis was to develop and propose lean tools that could be used in daily management, visual management and continuous improvement. This thesis was “outsiders” view, and as such, did not study the current processes deeply. As result of this thesis, two different Daily Management -boards were designed, one for parallel processes and one for sequential processes. In addition, methods of doing continuous improvement and daily task accountability were framed and standard work for the leaders outlined. The tools presented in this thesis are general tools which support work in lean environment. They are visual and, if used correctly, they provide a basis from which continuous improvement can be done. Lean philosophy emphasizes the deep understanding of the current situation and it would be against the lean principles to blindly implement anything developed “on the outside”. The tools presented should be reviewed and modified further by the people working on the factory floor.

Visual customer segmentation and behavior analysis : a SOM-based approach

Ett ämne som väckt intresse både inom industrin och forskningen är hantering av kundförhållanden (CRM, eng. Customer Relationship Management), dvs. en kundorienterad affärsstrategi där företagen från att ha varit produktorienterade väljer att bli mera kundcentrerade. Numera kan kundernas beteende och aktiviteter lätt registreras och sparas med hjälp av integrerade affärssystem (ERP, eng. Enterprise Resource Planning) och datalager (DW, eng. Data Warehousing). Kunder med olika preferenser och köpbeteende skapar sin egen ”signatur” i synnerhet via användningen av kundkort, vilket möjliggör mångsidig modellering av kundernas köpbeteende. För att få en översikt av kundernas köpbeteende och deras lönsamhet, används ofta kundsegmentering som en metod för att indela kunderna i grupper utgående från deras likheter. De mest använda metoderna för kundsegmentering är analytiska modeller konstruerade för en viss tidsperiod. Dessa modeller beaktar inte att kundernas beteende kan förändras med tiden. I föreliggande avhandling skapas en holistisk översikt av kundernas karaktär och köpbeteende som utöver de konventionella segmenteringsmodellerna även beaktar dynamiken i köpbeteendet. Dynamiken i en kundsegmenteringsmodell innefattar förändringar i segmentens struktur och innehåll, samt förändringen av individuella kunders tillhörighet i ett segment (s.k migrationsanalyser). Vardera förändringen modelleras, analyseras och exemplifieras med visuella datautvinningstekniker, främst med självorganiserande kartor (SOM, eng. Self-Organizing Maps) och självorganiserande tidskartor (SOTM), en vidareutveckling av SOM. Visualiseringen anteciperas underlätta tolkningen av identifierade mönster och göra processen med kunskapsöverföring mellan den som gör analysen och beslutsfattaren smidigare. Asiakkuudenhallinta (CRM) eli organisaation muuttaminen tuotepainotteisesta asiakaskeskeiseksi on herättänyt mielenkiintoa niin yliopisto- kuin yritysmaailmassakin. Asiakkaiden käyttäytymistä ja toimintaa pystytään nykyään helposti tallentamaan ja varastoimaan toiminnanohjausjärjestelmien ja tietovarastojen avulla; asiakkaat jättävät jatkuvasti piirteistään ja ostokäyttäytymisestään kertovia tietojälkiä, joita voidaan analysoida. On tavallista, että asiakkaat poikkeavat toisistaan eri tavoin, ja heidän mieltymyksensä kuten myös ostokäyttäytymisensä saattavat olla hyvinkin erilaisia. Asiakaskäyttäytymisen monimuotoisuuteen ja tuottavuuteen paneuduttaessa käytetäänkin laajalti asiakassegmentointia eli asiakkaiden jakamista ryhmiin samankaltaisuuden perusteella. Perinteiset asiakassegmentoinnin ratkaisut ovat usein yksittäisiä analyyttisia malleja, jotka on tehty tietyn aikajakson perusteella. Tämän vuoksi ne monesti jättävät huomioimatta sen, että asiakkaiden käyttäytyminen saattaa ajan kuluessa muuttua. Tässä väitöskirjassa pyritäänkin tarjoamaan holistinen kuva asiakkaiden ominaisuuksista ja ostokäyttäytymisestä tarkastelemalla kahta muutosvoimaa tiettyyn aikarajaukseen perustuvien perinteisten segmentointimallien lisäksi. Nämä kaksi asiakassegmentointimallin dynamiikkaa ovat muutokset segmenttien rakenteessa ja muutokset yksittäisten asiakkaiden kuulumisessa ryhmään. Ensimmäistä dynamiikkaa lähestytään ajallisen asiakassegmentoinnin avulla, jossa visualisoidaan ajan kuluessa tapahtuvat muutokset segmenttien rakenteissa ja profiileissa. Toista dynamiikkaa taas lähestytään käyttäen nk. segmenttisiirtymien analyysia, jossa visuaalisin keinoin tunnistetaan samantyyppisesti segmentistä toiseen vaihtavat asiakkaat. Visualisoinnin tehtävänä on tukea havaittujen kaavojen tulkitsemista sekä helpottaa tiedonsiirtoa analysoijan ja päättäjien välillä. Visuaalisia tiedonlouhintamenetelmiä, kuten itseorganisoivia karttoja ja niiden laajennuksia, käytetään osoittamaan näiden menetelmien hyödyllisyys sekä asiakkuudenhallinnassa yleisesti että erityisesti asiakassegmentoinnissa.

Visual Arts Data Skills for Researchers (VADS4R)

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

From KAPTUR to VADS4R: Exploring Research Data Management in the Visual Arts

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