Phylogenetics, taxon delimitation and phylogenetic diversity

Throughout the history of Linnean taxonomy, species have been described with varying degrees of justification. Many descriptions have been based on only a few ambiguous morphological characters. Moreover, species have been considered natural, well-defined units whereas higher taxa have been treated as disparate, non-existent creations. In the present thesis a few such cases were studied in detail. Often the species-level descriptions were based on only a few specimens and the variation previously thought to be interspecific was found to be intraspecific. In some cases morphological characters were sufficient to resolve the evolutionary relationships between the taxa, but generally more resolution was gained by the addition of molecular evidence. However, both morphological and molecular data were found to be deceptive in some cases. The DNA sequences of morphologically similar specimens were found to differ distinctly in some cases, whereas in other closely related species the morphology of specimens with identical DNA sequences differed substantially. This study counsels caution when evolutionary relationships are being studied utilizing only one source of evidence or a very limited number of characters (e.g. barcoding). Moreover, it emphasizes the importance of high quality data as well as the utilization of proper methods when making scientific inferences. Properly conducted analyses produce robust results that can be utilized in numerous interesting ways. The present thesis considered two such extensions of systematics. A novel hypothesis on the origin of bioluminescence in Elateriformia beetles is presented, tying it to the development of the clicking mechanism in the ancestors of these animals. An entirely different type of extension of systematics is the proposed high value of the white sand forests in maintaining the diversity of beetles in the Peruvian Amazon. White sand forests are under growing pressure from human activities that lead to deforestation. They were found to harbor an extremely diverse beetle fauna and many taxa were specialists living only in this unique habitat. In comparison to the predominant clay soil forests, considerably more elateroid beetles belonging to all studied taxonomic levels (species, genus, tribus, and subfamily) were collected in white sand forests. This evolutionary diversity is hypothesized to be due to a combination of factors: (1) the forest structure, which favors the fungus-plant interactions important for the elateroid beetles, (2) the old age of the forest type favoring survival of many evolutionary lineages and (3) the widespread distribution and fragmentation of the forests in the Miocene, favoring speciation.

The Risk of Cancer Associated with Immunosuppressive Therapy for Skin Diseases

The possible carcinogenic risk of immunosuppressive therapies is an important issue in everyday clinical practise. Carcinogenesis is a slow multi step procedure, thus a long latency period is needed before cancer develops. PUVA therapy is used for many skin diseases including psoriasis, early stage cutaneous T cell lymphoma, atopic dermatitis, palmoplantar pustulosis and chronic eczema. There has been concern about the increased melanoma risk associated to PUVA therapy, which has previously been associated with an increased risk on non-melanoma skin cancer, especially squamous cell carcinoma. The increased risk of basal cell carcinoma (BCC) is also documented but it is modest compared to squamous cell carcinoma (SCC). This thesis evaluated melanoma and noncutaneous cancer risk associated to PUVA, and the persistence of nonmelanoma cancer risk after the cessation of PUVA treatment. Also, the influence of photochemotherapy to the development of secondary cancers in cutaneous T cell lymphoma and the role of short term cyclosporine in later cancer development in inflammatory skin diseases were evaluated. The first three studies were performed on psoriasis patients. The risk of melanoma started to increase 15 years after the first treatment with PUVA. The risk was highest among persons who had received over 250 treatments compared to those under 250 treatments. In noncutaneous cancer, the overall risk was not increased (RR=1.08,95% CI=0.93-1.24), but significant increases in risk were found in thyroid cancer, breast cancer and in central nervous system neoplasms. These cancers were not associated to PUVA. The increased risk of SCC was associated to high cumulative UVA exposure in the PUVA regimen. The patients with high risk had no substantial exposure to other carcinogens. In BCC there was a similar but more modest tendency. In the two other studies, the risk of all secondary cancers (SIR) in CTCL patients was 1.4 (95% CI=1.0-1.9). In separate sites, the risk of lung cancer, Hodgkin and non-Hodgkin lymphomas were increased. PUVA seemed not to contribute to any extent to the appearance of these cancers. The carcinogenity of short-term cyclosporine was evaluated in inflammatory skin diseases. No increased risk for any type of cancer including the skin cancers was detected. To conclude, our studies confirm the increased skin cancer risk related to PUVA treatment in psoriasis patients. In clinical practice, this has led to a close and permanent follow-up of patients treated with PUVA. In CTCL patients, PUVA treatment did not contribute to the development of secondary cancers. We could not detect any increase in the risk of cancer in patients treated with short term cyclosporine, unlike in organ transplant patients under such long-term therapy.

Future chemistry teachers use of knowledge dimensions and high-order cognitive skills in pre-laboratory concept maps

This poster describes a pilot case study, which aim is to study how future chemistry teachers use knowledge dimensions and high-order cognitive skills (HOCS) in their pre-laboratory concept maps to support chemistry laboratory work. The research data consisted of 168 pre-laboratory concept maps that 29 students constructed as a part of their chemistry laboratory studies. Concept maps were analyzed by using a theory based content analysis through Anderson & Krathwohls' learning taxonomy (2001). This study implicates that novice concept mapper students use all knowledge dimensions and applying, analyzing and evaluating HOCS to support the pre-laboratory work.

Metsänomistajille tarjottavat palvelut, palveluntarjoajat ja palvelukentän rakenne

Suomessa metsänomistajille on tarjolla neljäntyyppisiä eri palveluita metsänhoidossa, puukaupassa, omaisuudenhoidossa ja informaatiopalveluissa. Palveluita tarjoaa joukko hyvin erikokoisia organisaatioita, joista osa toimii markkinalähtöisesti toisten tarjotessa palveluitaan lakiperusteisesti. Metsäalan palvelumarkkinat ovat nyt murrosvaiheessa, ja muutoksia on tapahtumassa sekä tarjonta- että kysyntäkentässä. Metsänomistajille tarjottavien palveluiden markkinoita ei tarjoajanäkökulmasta ole aiemmin tutkittu kattavasti. Tutkimukset ovat usein keskittyneet suppeasti johonkin palvelulajiin, eikä kokonaiskuvausta palvelumarkkinoista omaisuudenhoitopalvelut mukaan lukien ole ollut tarjolla. Tarjoajakenttään on odotettavissa muutoksia, sillä metsäalan palvelumarkkinoiden rahoituspohjaa ollaan muuttamassa, jolloin markkinoiden kilpailu vapautuu nykytilanteeseen verrattuna. Muutokset koskevat etenkin lakisääteisten organisaatioiden toimintaa, mutta ne tulevat vaikuttamaan koko toimialaan. Kysyntäkentässä aiempi tutkimus on ollut kattavampaa. Etenkin metsänomistajarakenteen muutosta, joka johtuu pääasiassa metsätilojen siirtymisestä kaupungistuneelle sukupolvelle, on tutkittu runsaasti. Lisäksi palveluiden kysyntään vaikuttavia tekijöitä ja palvelun eri laatu-ulottuvuuksia on tutkittu. Voidaan kuitenkin epäillä, kyetäänkö markkinoilla tarjoamaan sellaisia palveluita, jotka todella kattavasti tyydyttävät metsänomistajien tarpeita ja pystyvät tarjoamaan sellaisia hyötyjä, joista ollaan valmiita maksamaan. Tässä tutkimuksessa on tarkasteltu nykyisiä metsäpalvelumarkkinoita, sillä kokonaiskuvan luominen nykytilanteesta tarjoaa pohjan tulevien muutoksien ennakoimiselle. Tutkimusmenetelmänä on käytetty kvalitatiivista sisällönanalyysiä, ja tarkastelun kohteena on ollut palveluntarjoajien metsänomistajille suuntaama markkinointimateriaali – pääasiassa tarjoajien internetissä oleva materiaali. Markkinointimateriaalien tukena on käytetty palveluorganisaatioiden edustajien ja alan asiantuntijoiden teemahaastatteluita. Palveluita ja organisaatioita on tarkasteltu niiden asiakkaan kokemien hyötyjen pohjalta, joita markkinoinnissa palveluihin ja palveluntarjoajiin on pyritty liittämään. Teoreettisesti taustalla on käytetty mallia kuluttajan valintakriteereistä hankintapäätöstä tehtäessä. Tulosten perusteella on löydettävissä kysynnän kannalta kriittisiä palveluita, joiden ympärille palvelukokonaisuuksia on rakennettu. Metsänomistamisen odotetaan olevan kannattavaa, joten eräs palveluntarjonnan haasteista syntyy alan tarpeesta rahoittaa itsensä mielekkäällä aikajänteellä. Tämä luo tarpeen tuloja synnyttävien palveluiden yhdistämiseen kokonaisuuksiksi kustannuksia aiheuttavien, mutta muita hyötyjä tuottavien palveluiden kanssa. Tarjoajien kannalta tärkeää on kyetä luomaan asiakkaita hyödyttäviä palvelukokonaisuuksia muuttuville markkinoille.

Molecular Characterization of Viruses Causing the Cassava Brown Streak Disease Epidemic in Eastern Africa

Cassava brown streak disease (CBSD) was described for the first time in Tanganyika (now Tanzania) about seven decades ago. Tanganyika (now Tanzania) about seven decades ago. It was endemic in the lowland areas of East Africa and inland parts of Malawi and caused by Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae). However, in 1990s CBSD was observed at high altitude areas in Uganda. The causes for spread to new locations were not known.The present work was thus initiated to generate information on genetic variability, clarify the taxonomy of the virus or viruses associated with CBSD in Eastern Africa as well as to understand the evolutionary forces acting on their genes. It also sought to develop a molecular based diagnostic tool for detection of CBSD-associated virus isolates. Comparison of the CP-encoding sequences of CBSD-associated virus isolates collected from Uganda and north-western Tanzania in 2007 and the partial sequences available in Genbank revealed occurrence of two genetically distinct groups of isolates. Two isolates were selected to represent the two groups. The complete genomes of isolates MLB3 (TZ:Mlb3:07) and Kor6 (TZ:Kor6:08) obtained from North-Western (Kagera) and North-Eastern (Tanga) Tanzania, respectively, were sequenced. The genomes were 9069 and 8995 nucleotides (nt), respectively. They translated into polyproteins that were predicted to yield ten mature proteins after cleavage. Nine proteins were typical in the family Potyviridae, namely P1, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP, but the viruses did not contain HC-Pro. Interestingly, genomes of both isolates contained a Maf/HAM1-like sequence (HAM1h; 678 nucleotides, 25 kDa) recombined between the NIb and CP domains in the 3’-proximal part of the genomes. HAM1h was also identified in Euphorbia ringspot virus (EuRSV) whose sequence was in GenBank. The HAM1 gene is widely spread in both prokaryotes and eukaryotes. In yeast (Saccharomyces cerevisiae) it is known to be a nucleoside triphosphate (NTP) pyrophosphatase. Novel information was obtained on the structural variation at the N-termini of polyproteins of viruses in the genus Ipomovirus. Cucumber vein yellowing virus (CVYV) and Squash vein yellowing virus (SqVYV) contain a duplicated P1 (P1a and P1b) but lack the HC-Pro. On the other hand, Sweet potato mild mottle virus (SPMMV), has a single but large P1 and has HC-Pro. Both virus isolates (TZ:Mlb3:07 & TZ:Kor6:08) characterized in this study contained a single P1 and lacked the HC-Pro which indicates unique evolution in the family Potyviridae. Comparison of 12 complete genomes of CBSD-associated viruses which included two genomes characterized in this study, revealed genetic identity of 69.0–70.3% (nt) and amino acid (aa) identities of 73.6–74.4% at polyprotein level. Comparison was also made among 68 complete CP sequences, which indicated 69.0-70.3 and 73.6-74.4 % identity at nt and aa levels, respectively. The genetic variation was large enough for dermacation of CBSD-associated virus isolates into two distinct species. The name CBSV was retained for isolates that were related to CBSV isolates available in database whereas the new virus described for the first time in this study was named Ugandan cassava brown streak virus (UCBSV) by the International Committee on Virus Taxonomy (ICTV). The isolates TZ:Mlb3:07 and TZ:Kor6:08 belong to UCBSV and CBSV, respectively. The isolates of CBSV and UCBSV were 79.3-95.5% and 86.3-99.3 % identitical at nt level, respectively, suggesting more variation amongst CBSV isolates. The main sources of variation in plant viruses are mutations and recombination. Signals for recombination events were detected in 50% of isolates of each virus. Recombination events were detected in coding and non-coding (3’-UTR) sequences except in the 5’UTR and P3. There was no evidence for recombination between isolates of CBSV and UCBSV. The non-synonomous (dN) to synonomous (dS) nucleotide substitution ratio (ω) for the HAM1h and CP domains of both viruses were ≤ 0.184 suggesting that most sites of these proteins were evolving under strong purifying selection. However, there were individual amino acid sites that were submitted to adaptive evolution. For instance, adaptive evolution was detected in the HAM1h of UCBSV (n=15) where 12 aa sites were under positive selection (P< 0.05) but not in CBSV (n=12). The CP of CBSV (n=23) contained 12 aa sites (p<0.01) while only 5 aa sites in the CP gene of UCBSV were predicted to be submitted to positive selection pressure (p<0.01). The advantages offered by the aa sites under positive selection could not be established but occurrence of such sites in the terminal ends of UCBSV-HAMIh, for example, was interpreted as a requirement for proteolysis during polyprotein processing. Two different primer pairs that simultaneously detect UCBSV and CBSV isolates were developed in this study. They were used successfully to study distribution of CBSV, UCBSV and their mixed infections in Tanzania and Uganda. It was established that the two viruses co-infect cassava and that incidences of co-infection could be as high as 50% around Lake Victoria on the Tanzanian side. Furthermore, it was revealed for the first time that both UCBSV and CBSV were widely distributed in Eastern Africa. The primer pair was also used to confirm infection in a close relative of cassava, Manihot glaziovii (Müller Arg.) with CBSV. DNA barcoding of M. glaziovii was done by sequencing the matK gene. Two out of seven M. glaziovii from the coastal areas of Korogwe and Kibaha in north eastern Tanzania were shown to be infected by CBSV but not UCBSV isolates. Detection in M. glaziovii has an implication in control and management of CBSD as it is likely to serve as virus reservoir. This study has contributed to the understanding of evolution of CBSV and UCBSV, which cause CBSD epidemic in Eastern Africa. The detection tools developed in this work will be useful in plant breeding, verification of the phytosanitary status of materials in regional and international movement of germplasm, and in all diagnostic activities related to management of CBSD. Whereas there are still many issues to be resolved such as the function and biological significance of HAM1h and its origin, this work has laid a foundation upon which the studies on these aspects can be based.

Reacting to Complex Threats – the Securitization in the Speeches of Anders Fogh Rasmussen based on NATO´s New Strategic Concept

The purpose of this master´s thesis is to analyze how NATO Secretary General Anders Fogh Rasmussen is trying to justify the existence of the military alliance through the use of security arguments. I am puzzled by the question: why does NATO still exist – what is NATO’s raison d'être. The New Strategic Concept (2010) forms the base for his argumentation. This thesis focuses on the security argumentation of NATO which is examined by analyzing the speeches the Secretary General. The theoretical framework of this study is based on constructivist approach to international security examining the linguistic process of securitization. Issues become securitized after Anders Fogh Rasmussen names them as threats. This thesis focuses on the securitization process relating to NATO and analyses what issues Rasmussen raises to the security agenda. Research data consists of the speeches by Anders Fogh Rasmussen. They are analyzed through J.L. Austin’s speech act taxonomy and Chaïm Perelman’s argumentation theories. The thesis will concentrate on the formulation and articulation of these threats which are considered and coined as “new threats” in contemporary international relations. I am conducting this research through the use of securitization theory. This study illustrates that the threats are constructed by NATO’s member-states in unison, but the resolutions are sounded through Rasmussen’s official speeches and transcripts. . Based on the analysis it can be concluded that Rasmussen is giving reasons for the existence of NATO. This takes place by making use of speech acts and different rhetorical techniques. The results of the analysis indicate that NATO remains an essential organization for the West and the rest of the world according to the Secretary General.