Visual completion in an illusory figure

The visual systems of humans and animals represent physical reality in a modified way, depending on the specific demands that the species in question has for survival. The ability to perceive visual illusions is found in independently evolved visual systems, from honeybees to humans. In humans, the ability emerges early, at the age of four months. Thus the perception of illusion is likely to reflect visual processes of fundamental importance for object perception in natural vision. The experiments reported in this thesis employed various modifications of the Kanizsa triangle, a drawn configuration composed of three black disks with missing sectors on a white background. The sectors appear to form the tips of a triangle. The visual system completes the physically empty area between the disks, generally called inducers, with giving the perception of an illusory triangle. The illusory triangle consists of an illusory surface bounded by illusory contours; the triangle appears brighter than and to lie above the background. If the sectors are coloured, the colour fills the illusory area, a phenomenon known as neon colour spreading . We investigated spatial limitations on the perception of Kanizsa-type illusions and how other stimuli and viewing parameters affected these limitations. We also studied complex configurations thick, bent, mobile and chromatic inducers - to determine whether illusions combining several attributes can be perceived. The results suggest that the visual system is highly effective in completing a percept. The perception of an illusory figure is spatially scale invariant when perceived at threshold. The processing time and the number of fixations modify the percept, making the perception of the illusion more probable in various viewing conditions. Furthermore, the fact that the illusion can be perceived when only one inducer is physically present at any given moment indicates the potential of single inducers. Apparently, modelling illusory figure perception will require a combination of low-level, local processes and higher-level integrative processes. Our studies with stimuli combining several attributes relevant to object perception demonstrate that the perception of an illusory figure is flexible and is maintained also when it contains colour and volume and when shown in movement. All in all, the results confirm the assumed importance of the visual processes related with the perception of illusory figures in everyday viewing. This is indicated by the variety of inducer modifications that can be made without destroying the percept. Furthermore, the illusion can acquire additional attributes from such modifications. Due to individual differences in the perception of illusory figures, universal values for absolute performance are not always meaningful, but stable trends and general relations do exist.

Social perception and cognition : processing of gestures, postures and facial expressions in the human brain

Humans are a social species with the internal capability to process social information from other humans. To understand others behavior and to react accordingly, it is necessary to infer their internal states, emotions and aims, which are conveyed by subtle nonverbal bodily cues such as postures, gestures, and facial expressions. This thesis investigates the brain functions underlying the processing of such social information. Studies I and II of this thesis explore the neural basis of perceiving pain from another person s facial expressions by means of functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG). In Study I, observing another s facial expression of pain activated the affective pain system (previously associated with self-experienced pain) in accordance with the intensity of the observed expression. The strength of the response in anterior insula was also linked to the observer s empathic abilities. The cortical processing of facial pain expressions advanced from the visual to temporal-lobe areas at similar latencies (around 300 500 ms) to those previously shown for emotional expressions such as fear or disgust. Study III shows that perceiving a yawning face is associated with middle and posterior STS activity, and the contagiousness of a yawn correlates negatively with amygdalar activity. Study IV explored the brain correlates of interpreting social interaction between two members of the same species, in this case human and canine. Observing interaction engaged brain activity in very similar manner for both species. Moreover, the body and object sensitive brain areas of dog experts differentiated interaction from noninteraction in both humans and dogs whereas in the control subjects, similar differentiation occurred only for humans. Finally, Study V shows the engagement of the brain area associated with biological motion when exposed to the sounds produced by a single human being walking. However, more complex pattern of activation, with the walking sounds of several persons, suggests that as the social situation becomes more complex so does the brain response. Taken together, these studies demonstrate the roles of distinct cortical and subcortical brain regions in the perception and sharing of others internal states via facial and bodily gestures, and the connection of brain responses to behavioral attributes.

Expression Analysis of Host-Induced Genes and Proteins of Potato Pathogen Pectobacterium atrosepticum

Pectobacterium atrosepticum on Gram-negatiivinen bakteeri, joka aiheuttaa perunan tyvi- ja märkämätää. P. atrosepticum bakteerin optimilämpötila on melko alhainen ja se on yleinen lauhkeilla alueilla. Tyvimätä leviää pääasiassa siemenperunan välityksellä ja siksi se on ongelma erityisesti siemenperunan tuotannossa. P. atrosepticum kannan SCRI1043 genomi on julkaistu ja sitä tutkitaan malliorganismina märkä- ja tyvimädän taudinaiheuttamisen ymmärtämiseksi. Tämä opportunistinen taudinaiheuttaja voi elää isäntäkasvissa kuukausia piilevänä, aiheuttamatta näkyviä oireita. Suotuisissa olosuhteissa bakteerit alkavat jakautua ja tuottaa kasvin kudoksia hajottavia entsyymejä. Mädäntyvä kasvimassa tarjoaa ravinteita bakteerien kasvuun ja mahdollistaa isäntäkasvin asuttamisen. Soluseiniä hajottavien entsyymien merkitys taudinaiheuttamisessa on hyvin tunnettu, mutta oireettomasta jaksosta ja taudin alkuvaiheista tiedätään vain vähän. Bakteerin genomi sisältää monia toksiineja, adhesiineja, hemolysiineja ja muita proteiineja, joilla saattaa olla merkitys taudinaiheuttamisessa. Tässä työssä käytettiin proteomiikkaa ja mikrosiruanalysiä P. atrosepticum bakteerin erittyvien proteiinien ja geeniekspression tutkimiseen. Proteiinit, jotka eritetään ulos bakteerista, toimivat todennäköisesti taudinaiheuttamisessa, koska ne ovat suorassa kontaktissa isäntäkasvin kanssa. Analyysit suoritettiin olosuhteissa, jotka muistuttavat kasvin soluvälitilaa: matala pH, vähän ravinteita ja matala lämpötila. Isäntäkasvin läsnäolon vaikutusta proteiinien tuottoon ja geeniekspressioon tutkittiin lisäämällä perunauutetta kasvatusalustaan. Tutkimuksessa tunnistettiin P. atrosepticum bakteerin monia jo tunnettuja ja mahdollisesti taudinaiheuttamiseen liittyviä proteiineja. Perunauute lisäsi hiljattain tunnistetun, proteiinien eritysreittiä (tyyppi VI sekreetio, T6SS) koodaavien geenien ilmentymistä. Lisäksi bakteerin havaittiin erittävän useita T6SS:n liittyviä proteiineja kasvualustaan, johon oli lisätty perunauutetta. T6SS:n merkitys bakteereille on vielä epäselvä ja sen vaikutuksesta taudinaiheuttamiseen on julkaistu ristiriitaisia tuloksia. Märkä- ja tyvimädän ymmärtäminen molekulaarisella tasolla luo pohjan tautien kontrollointiin tähtäävään soveltavaan tutkimukseen. Tämä tutkimus lisää tietoa kasvi-patogeeni- interaktiosta ja sitä voidaan tulevaisuudessa käyttää hyväksi esimerkiksi diagnostiikassa, resistenttien perunalajikkeiden jalostuksessa tai viljely- ja varastointiolosuhteiden parantamisessa.

Potato virus A as a heterologous protein expression tool in plants

Viruksien käyttö tuotekehityksen ja tutkimuksen vaatimien proteiinien tuottamiseen, syötävien rokotteiden kehittämiseen ja geeniterapiaan edustavat kasvavia biotekniikan sovellusalueita. Perunan A-virus (PVA) kuuluu potyviruksiin, joiden proteiinit tuotetaan aluksi yhtenä suurena molekyylinä, joka pilkotaan yksittäisiksi proteiineiksi viruksen itsensä tuottamilla entsyymeillä. Siten virusgenomiin lisätty vieras geeni käännetään proteiiniksi virusproteiinien mukana. Lopputuloksena kaikkia proteiineja tuotetaan kasvisoluissa samansuuruinen määrä. Lisäksi, viruksen proteiinikuoren koontimekanismi sallii perintöaineksen merkittävän lisäyksen ilman että viruksen tartutuskyky merkittävästi heikkenee. Koska virus monistuu ja leviää koko kasviin, jo melko pieni määrä kasveja riittää huomattavan proteiinimäärän tuottamiseen esimerkiksi säännösten mukaisessa kasvihuoneessa. Tämän työn tarkoituksena oli muuntaa PVA:n genomia siten, että virus soveltuisi yhden vieraan proteiinin tai useiden erilaisten proteiinien samanaikaiseen tuottamiseen kasveissa. Aluksi kokeiltiin viruksen replikaasia ja kuoriproteiinia koodaavien genomialueiden välistä kohtaa ja ihmisestä peräisi olevaa geeniä, joka tuotti S-COMT-entsyymiä (katekoli-O-metyylitransferaasi). Sen aktiivisuuden rajoittaminen auttaa Parkinsonintaudin hoidossa. Kasvissa tuotettua S-COMT:ia voitaisiin käyttää lääkekehityksessä estolääkkeiden testaukseen. Kahden viikon kuluttua tartutuksesta tupakan lehdissä oli entsymaattisesti aktiivista S-COMT:ia n. 1 % lehden liukoisista proteiineista. PVA:n P1-proteiinia koodaavalta alueelta oli paikannettu kohta, johon ehkä voitaisiin siirtää vieras geeni. Asia varmistettiin siirtämällä tähän kohtaan meduusan geeni, joka tuottaa UV-valossa vihreänä fluoresoivaa proteiinia (GFP). GFP-geeniä kantava PVA levisi kasvissa ja lisääntyi n. 30-50 %:iin viruksen normaalista pitoisuudesta. Koko kasvi fluoresoi vihreänä UV-valossa. Vieras geeni voidaan sijoittaa myös potyviruksen P1- ja HCpro-proteiineja koodaavien alueiden väliin. Samaan PVA-genomiin siirrettiin kolme geeniä, yksi kuhunkin kolmesta kloonauskohdasta: GFP-geeni P1:n sisälle, merivuokon lusiferaasigeeni P1/HCpro-kohtaan ja bakteerin beta-glukuronidaasigeeni (GUS) replikaasi/kuoriproteiini-kohtaan. Virusgenomin ja itse viruksen pituudet kasvoivat 38 %, mutta virus säilytti tartutuskykynsä. Se levisi kasveissa saavuttaen n. 15 % viruksen normaalista pitoisuudesta. Kaikki kolme vierasta proteiinia esiintyivät lehdissä aktiivisina.

Rhizoctonia solani as a potato pathogen : Variation of isolates in Finland and host response

Rhizoctonia solani is a soil inhabiting basidiomycetous fungus able to induce a wide range of symptoms in many plant species. This genetically complex species is divided to 13 anastomosis groups (AG), of which AG-3 is specialized to infect potato. However, also a few other AGs are able to infect or live in close contact with potato. On potato, R. solani infection causes two main types of diseases including stem canker observed as a dark brown lesions on developing stems and stolons, and black scurf that develops on new tubers close to the time of harvest. These disease symptoms are collectively called a ‘Rhizoctonia disease complex’. Between the growing seasons R. solani survives in soil and plant debri as sclerotia or as the sclerotia called black scurf on potato tubers which when used as seed offer the main route for dispersal of the fungus to new areas. The reasons for the dominance of AG-3 on potato seem to be attributable to its highly specialization to potato and its ability to infect and form sclerotia efficiently at low temperatures. In this study, a large nationwide survey of R. solani isolates was made in potato crops in Finland. Almost all characterized isolates belonged to AG-3. Additionally, three other AGs (AG-2-1, AG-4 and AG-5) were found associated with symptoms on potato plants but they were weaker pathogens on potato than AG-3 as less prone to form black scurf. According to phylogenetic analysis of the internal transcribed sequences (ITS) of the ribosomal RNA genes the Finnish AG-3 isolates are closely related to each other even though a wide variation of physiological features was observed between them. Detailed analysis of the ITS regions revealed single nucleotide polymorphism in 14 nucleotide positions of ITS-1 and ITS-2. Additionally, compensatory base changes on ITS-2 were detected which suggests that potato-infecting R. solani AG-3 could be considered as a separate species instead of an AG of R. solani. For the first time, molecular defence responses were studied and detected during the early phases of interaction between R. solani AG-3 and potato. Extensive systemic signalling for defence exploiting several known defence pathways was activated as soon as R. solani came into close contact with the base of a sprout. The defence response was strong enough to protect vulnerable sprout tips from new attacks by the pathogen. These results at least partly explain why potato emergence is eventually successful even under heavy infection pressure by R. solani.

Algorithms for 13C metabolic flux analysis

The metabolism of an organism consists of a network of biochemical reactions that transform small molecules, or metabolites, into others in order to produce energy and building blocks for essential macromolecules. The goal of metabolic flux analysis is to uncover the rates, or the fluxes, of those biochemical reactions. In a steady state, the sum of the fluxes that produce an internal metabolite is equal to the sum of the fluxes that consume the same molecule. Thus the steady state imposes linear balance constraints to the fluxes. In general, the balance constraints imposed by the steady state are not sufficient to uncover all the fluxes of a metabolic network. The fluxes through cycles and alternative pathways between the same source and target metabolites remain unknown. More information about the fluxes can be obtained from isotopic labelling experiments, where a cell population is fed with labelled nutrients, such as glucose that contains 13C atoms. Labels are then transferred by biochemical reactions to other metabolites. The relative abundances of different labelling patterns in internal metabolites depend on the fluxes of pathways producing them. Thus, the relative abundances of different labelling patterns contain information about the fluxes that cannot be uncovered from the balance constraints derived from the steady state. The field of research that estimates the fluxes utilizing the measured constraints to the relative abundances of different labelling patterns induced by 13C labelled nutrients is called 13C metabolic flux analysis. There exist two approaches of 13C metabolic flux analysis. In the optimization approach, a non-linear optimization task, where candidate fluxes are iteratively generated until they fit to the measured abundances of different labelling patterns, is constructed. In the direct approach, linear balance constraints given by the steady state are augmented with linear constraints derived from the abundances of different labelling patterns of metabolites. Thus, mathematically involved non-linear optimization methods that can get stuck to the local optima can be avoided. On the other hand, the direct approach may require more measurement data than the optimization approach to obtain the same flux information. Furthermore, the optimization framework can easily be applied regardless of the labelling measurement technology and with all network topologies. In this thesis we present a formal computational framework for direct 13C metabolic flux analysis. The aim of our study is to construct as many linear constraints to the fluxes from the 13C labelling measurements using only computational methods that avoid non-linear techniques and are independent from the type of measurement data, the labelling of external nutrients and the topology of the metabolic network. The presented framework is the first representative of the direct approach for 13C metabolic flux analysis that is free from restricting assumptions made about these parameters.In our framework, measurement data is first propagated from the measured metabolites to other metabolites. The propagation is facilitated by the flow analysis of metabolite fragments in the network. Then new linear constraints to the fluxes are derived from the propagated data by applying the techniques of linear algebra.Based on the results of the fragment flow analysis, we also present an experiment planning method that selects sets of metabolites whose relative abundances of different labelling patterns are most useful for 13C metabolic flux analysis. Furthermore, we give computational tools to process raw 13C labelling data produced by tandem mass spectrometry to a form suitable for 13C metabolic flux analysis.

Revision of the family Alycidae (Acariformes, Acari), with special reference to European species

The thesis provides a proposal to divide Alycidae G. Canestrini & Fanzago into two subfamilies and four tribes. This new hierarchy is based on a reassessment and reranking of new and previously known synapomorphies of the clusters concerned by cladistic analysis, using 60 morphological characters for 48 ingroup species. The basic characters of the taxa are illustrated either by SEM micrographs (Scanning Electron Microscopy) or by outline drawings. The presented classification includes the definitions of Alycini G. Canestrini & Fanzago new rank; Bimichaeliini Womersley new rank; Petralycini new rank; and the (re)descriptions of Alycus C.L. Koch, Pachygnathus Dugès, Amphialycus Zachvatkin, Bimichaelia Thor and Laminamichaelia gen. nov. The species described or redescribed are: Pachygnathus wasastjernae sp. nov. from Kvarken (Merenkurkku), Finland; Pachygnathus villosus Dugès (in Oken); Alycus roseus C.L. Koch; Alycus denasutus (Grandjean) comb. and stat. nov.; Alycus trichotus (Grandjean) comb. nov.; Alycus marinus (Schuster) comb. nov.; Amphialycus (Amphialycus) pentophthalmus Zachvatkin; Amphialycus (Amphialycus) leucogaster (Grandjean); and Amphialycus (Orthacarus) oblongus (Halbert) comb. nov.; Bimichaelia augustana (Berlese); Bimichaelia sarekensis Trägårdh; Laminamichaelia setigera (Berlese) comb. nov.; Laminamichelia arbusculosa (Grandjean) comb. nov.; Laminamichelia subnuda (Berlese) comb. nov. and Petralycus unicornis Grandjean. Fourteen nominal species were found to be junior synonymies. The importance of sensory organs in taxonomy is well recognized, but inclusion of the elaborate skin pattern seemed to improve essentially the usefulness of the prodorsal sensory area. The detailed pictures of the prodorsa of the European alycids could be used like passport photographs for the species. A database like this of prodorsa of other mite taxa as well might be an answer to future needs of species identification in soil zoology, ecology and conservation.

Interactions between harmful algae and calanoid copepods in the Baltic Sea

The aim of the studies reported in this thesis was to examine the feeding interactions between calanoid copepods and toxic algae in the Baltic Sea. The central questions in this research concerned the feeding, survival and egg production of copepods exposed to toxic algae. Furthermore, the importance of copepods as vectors in toxin transfer was examined. The haptophyte Prymnesium parvum, which produces extracellular toxins, was the only studied species that directly harmed copepods. Beside this, it had allelopathic effects (cell lysis) on non-toxic Rhodomonas salina. Copepods that were exposed to P. parvum filtrates died or became severely impaired, although filtrates were not haemolytic (indicative of toxicity in this study). Monospecific Prymnesium cell suspensions, in turn, were haemolytic and copepods in these treatments became inactive, although no clear effect on mortality was detected. These results suggest that haemolytic activity may not be a good proxy of the harmful effects of P. parvum. In addition, P. parvum deterred feeding, and low egestion and suppressed egg production were consequently observed in monospecific suspensions of Prymnesium. Similarly, ingestion and faecal pellet production rates were suppressed in high concentration P. parvum filtrates and in mixtures of P. parvum and R. salina. These results indicate that the allelopathic effects of P. parvum on other algal species together with lowered viability as well as suppressed production of copepods may contribute to bloom formation and persistence. Furthermore, the availability of food for planktivorous animals may be affected due to reduced copepod productivity. Nodularin produced by Nodularia spumigena was transferred to Eurytemora affinis via grazing on filaments of small N. spumigena and by direct uptake from the dissolved pool. Copepods also acquired nodularin in fractions where N. spumigena filaments were absent. Thus, the importance of microbial food webs in nodularin transfer should be considered. Copepods were able to remove particulate nodularin from the system, but at the same time a large proportion of the nodularin disappeared. This indicates that copepods may possess effective mechanisms to remove toxins from their tissues. The importance of microorganisms, such as bacteria, in the degradation of cyanobacterial toxins could also be substantial. Our results were the first reports of the accumulation of diarrhetic shellfish toxins (DSTs) produced by Dinophysis spp. in copepods. The PTX2 content in copepods after feeding experiments corresponded to the ingestion of <100 Dinophysis spp. cells. However, no DSTs were recorded from field-collected copepods. Dinophysis spp. was not selected by the copepods and consumption remained low. It seems thus likely that copepods are an unimportant link in the transfer of DSTs in the northern Baltic Sea.

Outer Membrane Protease/Adhesin PgtE of Salmonella enterica: Role in Salmonella-Host Interaction

Salmonella enterica serovar Typhimurium is a common cause of gastroenteritis in humans and, occasionally, also causes systemic infection. During systemic infection an important characteristic of Salmonella is its ability to survive and replicate within macrophages. The outer membrane protease PgtE of S. enterica is a member of the omptin family of outer membrane aspartate proteases, which are beta-barrel proteins with five surface-exposed loops. The main goals of this study were to characterize biological substrates and pathogenesis-associated functions of PgtE and to determine the conditions where PgtE is fully active. In this study we found that PgtE requires rough lipopolysaccharide (LPS) to be functional but is sterically inhibited by the long O-antigen side chain in smooth LPS. Salmonella isolates normally are smooth with a long oligosaccharide O-antigen, and PgtE remains functionally cryptic in wild-type Salmonella cultivated in vitro. Interestingly, our results showed that due to increased expression of PgtE and to reduced length of the LPS O-antigen chains, the wild-type Salmonella expresses highly functional PgtE when isolated from mouse macrophage-like J774A.1 cells. Salmonella is thought to be continuously released from macrophages to infect new ones, and our results suggest that PgtE is functional during these transient extracellular growth phases. Six novel host protein substrates were identified for PgtE in this work. PgtE was previously known to activate human plasminogen (Plg) to plasmin, a broad-spectrum serine protease, and in this study PgtE was shown to interfere with the Plg system by inactivating the main inhibitor of plasmin, alpha2-antiplasmin. PgtE also interferes with another important proteolytic system of mammals by activating pro-matrix metalloproteinase-9 to an active gelatinase. PgtE also directly degrades gelatin, a component of extracellular matrices. PgtE also increases bacterial resistance against complement-mediated killing in human serum and enhances survival of Salmonella within murine macrophages as well as in the liver and spleen of intraperitoneally infected mice. Taken together, the results in this study suggest that PgtE is a virulence factor of Salmonella that has adapted to interfere with host proteolytic systems and to modify extracellular matrix; these features likely assist the migration of Salmonella during systemic salmonellosis.

Diffusive and ship-mediated spread of dinoflagellates in the Baltic Sea with Prorocentrum minimum as a special case

In this thesis the role played by expansive and introduced species in the phytoplankton ecology of the Baltic Sea was investigated. The aims were threefold. First, the studies investigated the resting stages of dinoflagellates, which were transported into the Baltic Sea via shipping and were able to germinate under the ambient, nutrient-rich, brackish water conditions. The studies also estimated which factors favoured the occurrence and spread of P. minimum in the Baltic Sea and discussed the identification of this morphologically variable species. In addition, the classification of phytoplankton species recently observed in the Baltic Sea was discussed. Incubation of sediments from four Finnish ports and 10 ships ballast tanks revealed that the sediments act as sources of living dinoflagellates and other phytoplankton. Dinoflagellates germinated from all ports detected and from 90% of ballast tanks. The concentrations of cells germinating from ballast tank sediments were mostly low compared with the acceptable cell concentrations set by the International Maritime Organization s (IMO s) International Convention for the Control and Management of Ships Ballast Water and Sediments. However, the IMO allows such high concentrations of small cells in the discharged ballast water that the total number of cells in large ballast water tanks can be very high. Prorocentrum minimum occurred in the Baltic Sea annually but with no obvious trend in the 10-year timespan from 1993 to 2002. The species occurred under wide ranges of temperatures and salinities and the abundance of the species was positively related especially to the presence of organic nitrogen and phosphorus. This indicated that the species was favoured by increased organic nutrient loading and runoff from land and rivers. The cell shape of P. minimum varied from triangular to oval-round, but morphological fine details indicated that only one morphospecies was present. P. minimum also is, according to present knowledge, the only potentially harmful phytoplankton species that has recently expanded widely into new areas of the Baltic Sea.

Invertebrate predation and trophic cascades in a pelagic food web : The multiple roles of Chaoborus flavicans (Meigen) in a clay-turbid lake

In lake ecosystems, both fish and invertebrate predators have dramatic effects on their prey communities. Fish predation selects large cladocerans while invertebrate predators prefer prey of smaller size. Since invertebrate predators are the preferred food items for fish, their occurrence at high densities is often connected with the absence or low number of fish. It is generally believed that invertebrate predators can play a significant role only if the density of planktivorous fish is low. However, in eutrophic clay-turbid Lake Hiidenvesi (southern Finland), a dense population of predatory Chaoborus flavicans larvae coexists with an abundant fish population. The population covers the stratifying area of the lake and attains a maximum population density of 23000 ind. m-2. This thesis aims to clarify the effects of Chaoborus flavicans on the zooplankton community and the environmental factors facilitating the coexistence of fish and invertebrate predators. In the stratifying area of Lake Hiidenvesi, the seasonal succession of cladocerans was exceptional. The spring biomass peak of cladocerans was missing and the highest biomass occurred in midsummer. In early summer, the consumption rate by chaoborids clearly exceeded the production rate of cladocerans and each year the biomass peak of cladocerans coincided with the minimum chaoborid density. In contrast, consumption by fish was very low and each study year cladocerans attained maximum biomass simultaneously with the highest consumption by smelt (Osmerus eperlanus). The results indicated that Chaoborus flavicans was the main predator of cladocerans in the stratifying area of Lake Hiidenvesi. The clay turbidity strongly contributed to the coexistence of chaoborids and smelt at high densities. Turbidity exceeding 30 NTU combined with light intensity below 0.1 μE m-2 s-1provides an efficient daytime refuge for chaoborids, but turbidity alone is not an adequate refuge unless combined with low light intensity. In the non-stratifying shallow basins of Lake Hiidenvesi, light intensity exceeds this level during summer days at the bottom of the lake, preventing Chaoborus forming a dense population in the shallow parts of the lake. Chaoborus can be successful particularly in deep, clay-turbid lakes where they can remain high in the water column close to their epilimnetic prey. Suspended clay alters the trophic interactions by weakening the link between fish and Chaoborus, which in turn strengthens the effect of Chaoborus predation on crustacean zooplankton. Since food web management largely relies on manipulations of fish stocks and the cascading effects of such actions, the validity of the method in deep clay-turbid lakes may be questioned.

Epidemiology and Treatment Options of Primary Biliary Cirrhosis

Primary biliary cirrhosis (PBC) is caused by an autoimmune inflammation of the small bile ducts. It results to destruction of bile ducts, accumulation of the bile in the liver, and cirrhosis. The prevalence and incidence of PBC is increasing in the Western world. The prevalence is highest in the USA (402 per million) and incidence in Scotland (49/million/year). Our aim was to assess the epidemiology of PBC in Finland. Patients for the epidemiological study were searched from the hospital discharge records from year 1988 to 1999.The prevalence rose from 103 to 180/million from 1988 to 1999, an annual increase of 5.1%. The incidence rose from 12 to 17 /million/year, an annual increase of 3.5%. The age at death increased markedly from 65 to 76 years. The risk of liver related deaths diminished over time. The treatment of PBC is based on Ursodeoxycholic acid (UDCA). During 20 years 50% of patients end up with cirrhosis. Our treatment option was to combine budesonide, a potent corticosteroid with a high first pass metabolism in the liver, to UDCA and evaluate the liver effects and systemic effects such as bone mass density (BMD) changes. Our aim was to find out if combination of laboratory tests would serve as a surrogate marker for PBC and help reducing the need for liver biopsy. Non-cirrhotic PBC patients were randomized to receive budesonide 6 mg/day combined to UDCA 15 mg /kg/day or UDCA alone for three years. The combination therapy with UDCA and budesonide was effective: stage improved 22%, fibrosis 25%, and inflammation 32%. In the UDCA group the changes were: 20% deterioriation in stage and 70% in fibrosis, but a 10% improvement in inflammation. BMD in femoral neck decreased by 3.6% in the combination group and by 1.9% in the UDCA group. The reductions in lumbar spine were 2.8% and 0.7%. Pharmacokinetics did not differ between the stages of PBC. HA, PIIINP, bile acids, and AST were significantly different within stages I-III and could differentiate the mild fibrosis (F0F1) from the moderate (F2F3). The combination of these individual markers (PBC-score) further improved the accuracy. The area under the ROC of the PBC score, using a cut of value 66, had a sensitivity of 81.4% and a specificity of 65.2% to classify the stage of PBC. The prevalence of PBC in Finland increases, which results from increasing incidence and improved survival. The combination of budesonide and UDCA improves liver histology compared to UDCA alone in non-cirrhotic stages of PBC. The treatment may reduce BMD. Hyaluronic acid, PIIINP, AST, and bile acids may serve as tools to monitor the treatment response in the early stages of PBC. The budesonide and UDCA combination therapy is an option for those patients who do not receive full response from UDCA and are still at the non-cirrhotic stage of PBC.

Conjunctival Melanoma in Finland 1967-2000: a population-based study

Eighty-five new cases of conjunctival melanoma (CM) were diagnosed in Finland between 1967 and 2000. The annual crude incidence of CM was 0.51 per million inhabitants. The average age-adjusted incidence of 0.54 doubled during the study period, analogous to the increase in the incidence of cutaneous malignant melanoma during this period, suggesting a possible role for ultraviolet radiation in its pathogenesis. Nonlimbal tumors were more likely than limbal ones to recur and they were associated with decreased survival. Increasing tumor thickness and recurrence of the primary tumor were other clinical factors related to death from CM. The histopathologic specimens of 85 patients with CM melanoma were studied for cell type, mitotic count, tumor-infiltrating lymphocytes and macrophages, mean vascular density, extravascular matrix loops and networks, and mean diameter of the ten largest nucleoli (MLN). The absence of epithelioid cells, increasing mitotic count and small MLN were associated with shorter time to recurrence according to the Cox univariate regression. None of the histopathologic variables was associated with mortality from CM. Four (5%) patients had a CM limited to the cornea without evidence of a tumor other than primary acquired melanosis of the conjunctiva. Because there are no melanocytes in the cornea, the origin of these melanomas most likely is the limbal conjunctiva. All four corneally displaced CM were limited to the epithelium, and none of the patients developed metastases. An anatomic sub-classification based on my patients and world literature was developed for corneally displaced CM. In 20 patients the metastatic pattern could be determined. Ten patients had initial systemic metastases detected, nine had initial regional metastases, and in one case the two types were detected simultaneously. The patients most likely to develop either type of initial metastases were those with nonlimbal conjunctival melanoma, those with a primary tumor more than 2 mm thick, and those with a recurrent conjunctival melanoma. Approximately two thirds of the patients had limbal CM, a location associated with good prognosis. One third, however, had a primary CM originating outside the limbus. In these patients the chance of developing local recurrences as well as systemic metastases was significantly higher than in patients with limbal CM. Each recurrence accompanies an increased risk of developing metastases, and recurrences contribute to death along with increasing tumor thickness and nonlimbal tumor location. In my data, an equal number of patients with initial locoregional and systemic metastasis existed. Patients with limbal primary tumors less than 2 mm in thickness rarely experienced metastases, unless the tumor recurred. Consequently, the patients most likely to benefit from sentinel lymph node biopsy are those who have nonlimbal tumors, CM that are over 2 mm thick, or recurrent CM. The histopathology of CM differs from that of uveal melanoma. Microvascular factors did not prove to be of prognostic importance, possibly due to the fact that CM at least as often disseminates first to the regional lymph nodes, unlike uveal melanoma that almost always disseminates hematogenously.

Rekonnektio Maan magnetosfäärissä

Tässä väitöskirjassa perehdytään magneettisen rekonnektion ilmenemismuotoihin ja vaikutuksiin Maan magnetosfäärissä. Keskeisenä tutkimusvälineenä käytetään magnetohydrodynaamista (MHD) Gumics-magnetosfäärisimulaatiota. Työssä kehitetään myös uusia menetelmiä simulaatiossa ilmenevän rekonnektion tunnistamiseksi ja mittaamiseksi. MHD-simulaatio sopii suuren mittakaavan ilmiöiden tarkasteluun, joten kuvaa rekonnektiosta täydennetään pienen mittakaavan piirteiden osalta Cluster-satelliittien avulla. Tärkein tutkimuksen tuoma edistysaskel menetelmien saralla on rekonnektioviivan paikallistaminen topologisesti erityyppisten magneettikenttäviivojen alueiden liitoskohdassa olevana erottajaviivana neljän kentän tienoon menetelmää käyttäen. Tämä topologinen lähestymistapa on hyödyllinen erityisesti magnetopausilla, jonka monimutkainen geometria tekee magneettikentän paikalliseen käyttäytymiseen perustuvien rekonnektioviivan etsintätapojen soveltamisen hankalaksi. Topologisesti määritelty rekonnektioviiva on myös helppo tunnistaa magnetosfäärin globaalin konvektion solmukohdaksi. Magnetopausin rekonnektioviivan käyttäytyminen Gumicsissa noudattaa komponenttirekonnektio-olettamaan pohjautuvia teoreettisia ennusteita. Rekonnektion kvantitatiivinen tarkastelu Gumics-simulaatiossa perustuu energian muuntumiseen, joka lasketaan Poyntingin vektorin divergenssinä tai Poyntingin vuona valitun umpinaisen pinnan läpi. Rekonnektioon liittyvän energian muuntumisen jakautumista magnetopausilla tarkastellaan energian muuntumisen pintatiheyden avulla ja rekonnektion kokonaismäärää rekonnektiotehon avulla. Magnetopausin ja pyrstön rekonnektiotehot ovat simulaatiossa samaa suuruusluokkaa. Tärkeimmät magnetopausin rekonnektiotehoa säätelevät parametrit ovat aurinkotuulen nopeus ja aurinkotuulen magneettikentän suunta. Magnetopausin rekonnektio puolestaan säätelee energian ja aineen pääsyä magnetosfääriin, joskaan magnetopausin läpäisevät vuot eivät ole aivan suoraan verrannollisia rekonnektiotehoon. Pyrstön rekonnektioteho sen sijaan on suoraan verrannollinen magnetopausilta tulevaan energiavuohon; pyrstörekonnektio Gumicsissa on siis ulkoista pakotetta seuraava passiivinen energian käsittelijä. Simulaation tuottama rekonnektio on realistinen magnetosfäärin globaalissa mittakaavassa tarkasteltuna, mutta satelliittihavainnot paljastavat rekonnektiosta simulaation erottelukykyä pienimittakaavaisempia piirteitä. Havaintopuolella tämän väitöstutkimuksen tärkein löytö on protonien diffuusioalueen rakenteeseen kuuluvien Hallin kenttien kääntyminen pyrstön virtalevyn aaltoilun mukana.