Methods in general model localization

The aim of this study was to evaluate and test methods which could improve local estimates of a general model fitted to a large area. In the first three studies, the intention was to divide the study area into sub-areas that were as homogeneous as possible according to the residuals of the general model, and in the fourth study, the localization was based on the local neighbourhood. According to spatial autocorrelation (SA), points closer together in space are more likely to be similar than those that are farther apart. Local indicators of SA (LISAs) test the similarity of data clusters. A LISA was calculated for every observation in the dataset, and together with the spatial position and residual of the global model, the data were segmented using two different methods: classification and regression trees (CART) and the multiresolution segmentation algorithm (MS) of the eCognition software. The general model was then re-fitted (localized) to the formed sub-areas. In kriging, the SA is modelled with a variogram, and the spatial correlation is a function of the distance (and direction) between the observation and the point of calculation. A general trend is corrected with the residual information of the neighbourhood, whose size is controlled by the number of the nearest neighbours. Nearness is measured as Euclidian distance. With all methods, the root mean square errors (RMSEs) were lower, but with the methods that segmented the study area, the deviance in single localized RMSEs was wide. Therefore, an element capable of controlling the division or localization should be included in the segmentation-localization process. Kriging, on the other hand, provided stable estimates when the number of neighbours was sufficient (over 30), thus offering the best potential for further studies. Even CART could be combined with kriging or non-parametric methods, such as most similar neighbours (MSN).

Lahopuumäärän ennustaminen ja kartoitus lentokonelaserkeilauksen avulla

Lahopuun määrästä ja sijoittumisesta ollaan kiinnostuneita paitsi elinympäristöjen monimuotoisuuden, myös ilmakehän hiilen varastoinnin kannalta. Tutkimuksen tavoitteena oli kehittää aluepohjainen laserkeilausdataa hyödyntävä malli lahopuukohteiden paikantamiseksi ja lahopuun määrän estimoimiseksi. Samalla tutkittiin mallin selityskyvyn muuttumista mallinnettavan ruudun kokoa suurennettaessa. Tutkimusalue sijaitsi Itä-Suomessa Sonkajärvellä ja koostui pääasiassa nuorista hoidetuista talousmetsistä. Tutkimuksessa käytettiin harvapulssista laserkeilausdataa sekä kaistoittain mitattua maastodataa kuolleesta puuaineksesta. Aineisto jaettiin siten, että neljäsosa datasta oli käytössä mallinnusta varten ja loput varattiin valmiiden mallien testaamiseen. Lahopuun mallintamisessa käytettiin sekä parametrista että ei-parametrista mallinnusmenetelmää. Logistisen regression avulla erikokoisille (0,04, 0,20, 0,32, 0,52 ja 1,00 ha) ruuduille ennustettiin todennäköisyys lahopuun esiintymiselle. Muodostettujen mallien selittävät muuttujat valittiin 80 laserpiirteen ja näiden muunnoksien joukosta. Mallien selittävät muuttujat valittiin kolmessa vaiheessa. Aluksi muuttujia tarkasteltiin visuaalisesti kuvaamalla ne lahopuumäärän suhteen. Ensimmäisessä vaiheessa sopivimmiksi arvioitujen muuttujien selityskykyä testattiin mallinnuksen toisessa vaiheessa yhden muuttujan mallien avulla. Lopullisessa usean muuttujan mallissa selittävien muuttujien kriteerinä oli tilastollinen merkitsevyys 5 % riskitasolla. 0,20 hehtaarin ruutukoolle luotu malli parametrisoitiin muun kokoisille ruuduille. Logistisella regressiolla toteutetun parametrisen mallintamisen lisäksi, 0,04 ja 1,0 hehtaarin ruutukokojen aineistot luokiteltiin ei-parametrisen CART-mallinnuksen (Classification and Regression Trees) avulla. CARTmenetelmällä etsittiin aineistosta vaikeasti havaittavia epälineaarisia riippuvuuksia laserpiirteiden ja lahopuumäärän välillä. CART-luokittelu tehtiin sekä lahopuustoisuuden että lahopuutilavuuden suhteen. CART-luokituksella päästiin logistista regressiota parempiin tuloksiin ruutujen luokituksessa lahopuustoisuuden suhteen. Logistisella mallilla tehty luokitus parani ruutukoon suurentuessa 0,04 ha:sta(kappa 0,19) 0,32 ha:iin asti (kappa 0,38). 0,52 ha:n ruutukoolla luokituksen kappa-arvo kääntyi laskuun (kappa 0,32) ja laski edelleen hehtaarin ruutukokoon saakka (kappa 0,26). CART-luokitus parani ruutukoon kasvaessa. Luokitustulokset olivat logistista mallinnusta parempia sekä 0,04 ha:n (kappa 0,24) että 1,0 ha:n (kappa 0,52) ruutukoolla. CART-malleilla määritettyjen ruutukohtaisten lahopuutilavuuksien suhteellinen RMSE pieneni ruutukoon kasvaessa. 0,04 hehtaarin ruutukoolla koko aineiston lahopuumäärän suhteellinen RMSE oli 197,1 %, kun hehtaarin ruutukoolla vastaava luku oli 120,3 %. Tämän tutkimuksen tulosten perusteella voidaan todeta, että maastossa mitatun lahopuumäärän ja tutkimuksessa käytettyjen laserpiirteiden yhteys on pienellä ruutukoolla hyvin heikko, mutta vahvistuu hieman ruutukoon kasvaessa. Kun mallinnuksessa käytetty ruutukoko kasvaa, pienialaisten lahopuukeskittymien havaitseminen kuitenkin vaikeutuu. Tutkimuksessa kohteen lahopuustoisuus pystyttiin kartoittamaan kohtuullisesti suurella ruutukoolla, mutta pienialaisten kohteiden kartoittaminen ei onnistunut käytetyillä menetelmillä. Pienialaisten kohteiden paikantaminen laserkeilauksen avulla edellyttää jatkotutkimusta erityisesti tiheäpulssisen laserdatan käytöstä lahopuuinventoinneissa.

What was behind the bark? : An assessment of decay among urban Tilia, Betula and Acer trees felled as hazardous in the Helsinki City area

Old trees growing in urban environments are often felled due to symptoms of mechanical defects that could be hazardous to people and property. The decisions concerning these removals are justified by risk assessments carried out by tree care professionals. The major motivation for this study was to determine the most common profiles of potential hazard characteristics for the three most common urban tree genera in Helsinki City: Tilia, Betula and Acer, and in this way improve management practices and protection of old amenity trees. For this research, material from approximately 250 urban trees was collected in cooperation with the City of Helsinki Public Works Department during 2001 - 2004. From the total number of trees sampled, approximately 70% were defined as hazardous. The tree species had characteristic features as potential hazard profiles. For Tilia trees, hollowed heartwood with low fungal activity and advanced decay caused by Ganoderma lipsiense were the two most common profiles. In Betula spp., the primary reason for tree removal was usually lowered amenity value in terms of decline of the crown. Internal cracks, most often due to weak fork formation, were common causes of potential failure in Acer spp. Decay caused by Rigidoporus populinus often increased the risk of stem breakage in these Acer trees. Of the decay fungi observed, G. lipsiense was most often the reason for the increased risk of stem collapse. Other fungi that also caused extensive decay were R. populinus, Inonotus obliquus, Kretzschmaria deusta and Phellinus igniarius. The most common decay fungi in terms of incidence were Pholiota spp., but decay caused by these species did not have a high potential for causing stem breakage, because it rarely extended to the cambium. The various evaluations used in the study suggested contradictions in felling decisions based on trees displaying different stages of decay. For protection of old urban trees, it is crucial to develop monitoring methods so that tree care professionals could better analyse the rate of decay progression towards the sapwood and separate those trees with decreasing amounts of sound wood from those with decay that is restricted to the heartwood area.

Distribution of non-biting midges (Diptera, Chironomidae) in subarctic lakes of Finnish Lapland applications in lake classification and palaeolimnology

Climate change contributes directly or indirectly to changes in species distributions, and there is very high confidence that recent climate warming is already affecting ecosystems. The Arctic has already experienced the greatest regional warming in recent decades, and the trend is continuing. However, studies on the northern ecosystems are scarce compared to more southerly regions. Better understanding of the past and present environmental change is needed to be able to forecast the future. Multivariate methods were used to explore the distributional patterns of chironomids in 50 shallow (≤ 10m) lakes in relation to 24 variables determined in northern Fennoscandia at the ecotonal area from the boreal forest in the south to the orohemiarctic zone in the north. Highest taxon richness was noted at middle elevations around 400 m a.s.l. Significantly lower values were observed from cold lakes situated in the tundra zone. Lake water alkalinity had the strongest positive correlation with the taxon richness. Many taxa had preference for lakes either on tundra area or forested area. The variation in the chironomid abundance data was best correlated with sediment organic content (LOI), lake water total organic carbon content, pH and air temperature, with LOI being the strongest variable. Three major lake groups were separated on the basis of their chironomid assemblages: (i) small and shallow organic-rich lakes, (ii) large and base-rich lakes, and (iii) cold and clear oligotrophic tundra lakes. Environmental variables best discriminating the lake groups were LOI, taxon richness, and Mg. When repeated, this kind of an approach could be useful and efficient in monitoring the effects of global change on species ranges. Many species of fast spreading insects, including chironomids, show a remarkable ability to track environmental changes. Based on this ability, past environmental conditions have been reconstructed using their chitinous remains in the lake sediment profiles. In order to study the Holocene environmental history of subarctic aquatic systems, and quantitatively reconstruct the past temperatures at or near the treeline, long sediment cores covering the last 10000 years (the Holocene) were collected from three lakes. Lower temperature values than expected based on the presence of pine in the catchment during the mid-Holocene were reconstructed from a lake with great water volume and depth. The lake provided thermal refuge for profundal, cold adapted taxa during the warm period. In a shallow lake, the decrease in the reconstructed temperatures during the late Holocene may reflect the indirect response of the midges to climate change through, e.g., pH change. The results from three lakes indicated that the response of chironomids to climate have been more or less indirect. However, concurrent shifts in assemblages of chironomids and vegetation in two lakes during the Holocene time period indicated that the midges together with the terrestrial vegetation had responded to the same ultimate cause, which most likely was the Holocene climate change. This was also supported by the similarity in the long-term trends in faunal succession for the chironomid assemblages in several lakes in the area. In northern Finnish Lapland the distribution of chironomids were significantly correlated with physical and limnological factors that are most likely to change as a result of future climate change. The indirect and individualistic response of aquatic systems, as reconstructed using the chironomid assemblages, to the climate change in the past suggests that in the future, the lake ecosystems in the north do not respond in one predictable way to the global climate change. Lakes in the north may respond to global climate change in various ways that are dependent on the initial characters of the catchment area and the lake.

A new classification and linear sequence of extant gymnosperms

A new classification and linear sequence of the gymnosperms based on previous molecular and morphological phylogenetic and other studies is presented. Currently accepted genera are listed for each family and arranged according to their (probable) phylogenetic position. A full synonymy is provided, and types are listed for accepted genera. An index to genera assists in easy access to synonymy and family placement of genera.

Interactions between transgenic trees and mycorrhizal and pathogenic fungi

The development of biotechnology techniques in plant breeding and the new commercial applications have raised public and scientific concerns about the safety of genetically modified (GM) crops and trees. To find out the feasibility of these new technologies in the breeding of commercially important Finnish hardwood species and to estimate the ecological risks of the produced transgenic plants, the experiments of this study have been conducted as a part of a larger project focusing on the risk assessment of GM-trees. Transgenic Betula pendula and Populus trees were produced via Agrobacterium mediated transformation. Stilbene synthase (STS) gene from pine (Pinus sylvestris) and chitinase gene from sugar beet (Beta vulgaris) were transferred to (hybrid) aspen and birch, respectively, to improve disease resistance against fungal pathogens. To modify lignin biosynthesis, a 4-coumarate:coenzyme A ligase (4CL) gene fragment in antisense orientation was introduced into two birch clones. In in vitro test, one transgenic aspen line expressing pine STS gene showed increased resistance to decay fungus Phellinus tremulae. In the field, chitinase transgenic birch lines were more susceptible to leaf spot (Pyrenopeziza betulicola) than the non-transgenic control clone while the resistance against birch rust (Melampsoridium betulinum) was improved. No changes in the content or composition of lignin were detected in the 4CL antisense birch lines. In order to evaluate the ecological effects of the produced GM trees on non-target organisms, an in vitro mycorrhiza experiment with Paxillus involutus and a decomposition experiment in the field were performed. The expression of a transgenic chitinase did not disturb the establishment of mycorrhizal symbiosis between birch and P. involutus in vitro. 4CL antisense transformed birch lines showed retarded root growth but were able to form normal ectomycorrhizal associations with the mycorrhizal fungus in vitro. 4CL lines also showed normal litter decomposition. Unexpected growth reductions resulting from the gene transformation were observed in chitinase transgenic and 4CL antisense birch lines. These results indicate that genetic engineering can provide a tool in increasing disease resistance in Finnish tree species. More extensive data with several ectomycorrhizal species is needed to evaluate the consequences of transgene expression on beneficial plant-fungus symbioses. The potential pleiotropic effects of the transgene should also be taken into account when considering the safety of transgenic trees.

Prosopis, an Alien among the Sacred Trees of South India

The problematic of invasive species in an alien environment has aroused the attention of scientists all over the world for quite some time. One of the exotic tree species that has provoked special attention in the tropical drylands is Prosopis juliflora. Originating in South America, prosopis (hereafter referred to as prosopis) has been introduced in the hot and semi-arid zones of the world particularly to provide fuelwood, to stabilize sand dunes and to combat desertification. The tree has become an essential source for fuelwood and a provider of several other products and services in areas where it has become established. However, despite the numerous benefits the tree provides to rural people, in several regions prosopis has become a noxious weed with a negative impact on the environment and to the economy of farmers and landowners. In India, prosopis was introduced in Andhra Pradesh in 1877. The tree was then proclaimed as the precious child of the plant world by scientists and local people alike. The purpose of this study was to investigate the overall impact of prosopis on local rural livelihoods in the drylands of South India. Of particular interest was the examination of the different usages of the tree, especially as fuelwood, and people s perceptions of it. Furthermore, the study examined the negative impacts of the uncontrolled invasion of prosopis on croplands, and its occupation of the banks of irrigation canals and other water sources. As another central theme, this study analysed the Hindu classification system for nature and for trees in particular. In India, several tree species are regarded as sacred. This study examined the position of the exotic prosopis among sacred trees, such as the bodhi, banyan and neem trees. The principle method for collecting the field data was by using individual and thematic group interviews. These interviews were semi-structured with open ended questions. Moreover, unstructured interviews as well as general observations provided complementary information. The data were gathered during two fieldwork periods in the states of Andhra Pradesh and Tamil Nadu, in South India. The results confirmed that prosopis both provides benefits and causes hazards to different stakeholders. Farmers and agriculturalists suffer economic losses in areas where prosopis has invaded crop fields and competes with other plants for water and nutrients. On the other hand, for a significant number of poor rural people, prosopis has become an important source of livelihood benefits. This tree, which grows on government wastelands, is commonly a free resource for all and has thus become a major local source of fuelwood. It also provides several other goods and services and cash income that contributes to improve livelihoods in rural communities. Prosopis ranked lowest in the tree classificatioin system of the Hindus of South India. Although it is appreciated for many benefits it provides for poor people, it has remained an outsider compared with the indigenous tree species. On the other hand, the most sacred trees, such as the bodhi or the banyan, are completely excluded from extraction and it is seen as a sacrilege to even cut branches from any of these trees. An unexpected finding was that, in a few cases, prosopis had also been elevated to the status of a sacred tree. Goods and services from prosopis are not utilized in the most beneficial way. Silvicultural management practices are suggested that would provide additional income and employment opportunities. Interventions are recommended to control further invasion of the tree that might cause serious negative effects in the future. For Hindus, the sacred always ranks highest, even above economic gain. The conservation of sacred groves and sacred trees is a tradition that has its roots in ancient history. These socio-religious practices need to be respected and continued. Successful management of tree and forest resources depends on the willingness of the local people to manage their natural resources, and this willingness exists and has always existed in South India. Keywords: South India, drylands, livelihood, fuelwood, invasive, resource, silviculture.

Tree mortality and deadwood dynamics in late-successional boreal forests

Here I aimed at quantifying the main components of deadwood dynamics, i.e. tree mortality, deadwood pools, and their decomposition, in late-successional boreal forests. I focused on standing dead trees in three stand types dominated by Picea mariana and Abies balsamea in eastern Canada, and on standing and down dead trees in Picea abies-dominated stands in three areas in Northern Europe. Dead and living trees were measured on five sample plots of 1.6-ha size in each study area and stand type. Stem disks from dead trees were sampled to determine wood density and year of death, using dendrochronological methods. The results were applied to reconstruct past tree mortality and to model deadwood decay class dynamics. Site productivity, stand developmental stage, and the occurrence of episodic tree mortality influenced deadwood volume and quality. In all study areas tree mortality was continuous, leading to continuity in deadwood decay stage distribution. Episodic tree mortality due to either autogenic or allogenic causes influenced deadwood volume and quality in all but one study area. However, regardless of productivity and disturbance history deadwood was abundant, accounting for 20 53% of total wood volume in European study areas, and 15 27% of total standing volume in eastern Canada. Deadwood was a persistent structural component, since its expected residence time in early- and midstages of decay was 18 yr even in the area with the most rapid decomposition. The results indicated that in the absence of episodic tree mortality, stands may eventually develop to a steady state, in which deadwood volume fluctuates around an equilibrium state. However, in many forests deadwood is naturally variable, due to recurrent moderate-severity disturbances. This variability, the continuous tree mortality, and variation in rates of wood decomposition determine the dynamics and availability of deadwood as a habitat and carbon storage medium in boreal coniferous forest ecosystems.

The effects of thinning and fertilisation on wood and tracheid properties of Norway spruce (Picea abies) the results of long-term experiments

The aim of this thesis was to study the basic relationships between thinning and fertilisation, tree growth rate and wood properties of Norway spruce (Picea abies (L.) Karst.) throughout a stand rotation. The material consisted of a total of 109 trees from both long-term thinning (Heinola, 61°10'N, 26°01'E; Punkaharju, 61°49'N, 29°19'E) and fertilisation-thinning experiments (Parikkala, 61°36'N, 29°22'E; Suonenjoki, 62°45'N, 27°00'E) in Finland. Wood properties, i.e., radial increment, wood density, latewood proportion, tracheid length, cell wall thickness and lumen diameter, as well as relative lignin content, were measured in detail from the pith to the bark, as well as from the stem base towards the stem apex. Intensive thinning and fertilisation treatments of Norway spruce stands increased (8% 64%) the radial increment of studied trees at breast height (1.3 m). At the same time, a faster growth rate slightly decreased average wood density (2% 7%), tracheid length (0% 9%) and cell wall thickness (1% 17%). The faster growth resulted in only small changes (0% 9%) in lumen diameter and relative lignin content (1% 2%; lignin content was 25.4% 26%). However, the random variation in wood properties was large both between and within trees and annual rings. The results of this thesis indicate that the prevailing thinning and fertilisation treatments of Norway spruce stands in Fennoscandia may significantly enhance the radial increment of individual trees, and cause only small or no detrimental changes in wood and tracheid properties.

Evolution and detection of cyanobacterial hepatotoxin synthetase genes

Mass occurrences (blooms) of cyanobacteria are common in aquatic environments worldwide. These blooms are often toxic, due to the presence of hepatotoxins or neurotoxins. The most common cyanobacterial toxins are hepatotoxins: microcystins and nodularins. In freshwaters, the main producers of microcystins are Microcystis, Anabaena, and Planktothrix. Nodularins are produced by strains of Nodularia spumigena in brackish waters. Toxic and nontoxic strains of cyanobacteria co-occur and cannot be differentiated by conventional microscopy. Molecular biological methods based on microcystin and nodularin synthetase genes enable detection of potentially hepatotoxic cyanobacteria. In the present study, molecular detection methods for hepatotoxin-producing cyanobacteria were developed, based on microcystin synthetase gene E (mcyE) and the orthologous nodularin synthetase gene F (ndaF) sequences. General primers were designed to amplify the mcyE/ndaF gene region from microcystin-producing Anabaena, Microcystis, Planktothrix, and Nostoc, and nodularin-producing Nodularia strains. The sequences were used for phylogenetic analyses to study how cyanobacterial mcy genes have evolved. The results showed that mcy genes and microcystin are very old and were already present in the ancestor of many modern cyanobacterial genera. The results also suggested that the sporadic distribution of biosynthetic genes in modern cyanobacteria is caused by repeated gene losses in the more derived lineages of cyanobacteria and not by horizontal gene transfer. Phylogenetic analysis also proposed that nda genes evolved from mcy genes. The frequency and composition of the microcystin producers in 70 lakes in Finland were studied by conventional polymerase chain reaction (PCR). Potential microcystin producers were detected in 84% of the lakes, using general mcyE primers, and in 91% of the lakes with the three genus-specific mcyE primers. Potential microcystin-producing Microcystis were detected in 70%, Planktothrix in 63%, and Anabaena in 37% of the lakes. The presence and co-occurrence of potential microcystin producers were more frequent in eutrophic lakes, where the total phosphorus concentration was high. The PCR results could also be associated with various environmental factors by correlation and regression analyses. In these analyses, the total nitrogen concentration and pH were both associated with the presence of multiple microcystin-producing genera and partly explained the probability of occurrence of mcyE genes. In general, the results showed that higher nutrient concentrations increased the occurrence of potential microcystin producers and the risk for toxic bloom formation. Genus-specific probe pairs for microcystin-producing Anabaena, Microcystis, Planktothrix, and Nostoc, and nodularin-producing Nodularia were designed to be used in a DNA-chip assay. The DNA-chip can be used to simultaneously detect all these potential microcystin/nodularin producers in environmental water samples. The probe pairs detected the mcyE/ndaF genes specifically and sensitively when tested with cyanobacterial strains. In addition, potential microcystin/nodularin producers were identified in lake and Baltic Sea samples by the DNA-chip almost as sensitively as by quantitative real-time PCR (qPCR), which was used to validate the DNA-chip results. Further improvement of the DNA-chip assay was achieved by optimization of the PCR, the first step in the assay. Analysis of the mcy and nda gene clusters from various hepatotoxin-producing cyanobacteria was rewarding; it revealed that the genes were ancient. In addition, new methods detecting all the main producers of hepatotoxins could be developed. Interestingly, potential microcystin-producing cyanobacterial strains of Microcystis, Planktothrix, and Anabaena, co-occurred especially in eutrophic and hypertrophic lakes. Protecting waters from eutrophication and restoration of lakes may thus decrease the prevalence of toxic cyanobacteria and the frequency of toxic blooms.

Statistical and Information-Theoretic Methods for Data-Analysis

In this Thesis, we develop theory and methods for computational data analysis. The problems in data analysis are approached from three perspectives: statistical learning theory, the Bayesian framework, and the information-theoretic minimum description length (MDL) principle. Contributions in statistical learning theory address the possibility of generalization to unseen cases, and regression analysis with partially observed data with an application to mobile device positioning. In the second part of the Thesis, we discuss so called Bayesian network classifiers, and show that they are closely related to logistic regression models. In the final part, we apply the MDL principle to tracing the history of old manuscripts, and to noise reduction in digital signals.

Dessy : desktop search and synchronization

Current smartphones have a storage capacity of several gigabytes. More and more information is stored on mobile devices. To meet the challenge of information organization, we turn to desktop search. Users often possess multiple devices, and synchronize (subsets of) information between them. This makes file synchronization more important. This thesis presents Dessy, a desktop search and synchronization framework for mobile devices. Dessy uses desktop search techniques, such as indexing, query and index term stemming, and search relevance ranking. Dessy finds files by their content, metadata, and context information. For example, PDF files may be found by their author, subject, title, or text. EXIF data of JPEG files may be used in finding them. User–defined tags can be added to files to organize and retrieve them later. Retrieved files are ranked according to their relevance to the search query. The Dessy prototype uses the BM25 ranking function, used widely in information retrieval. Dessy provides an interface for locating files for both users and applications. Dessy is closely integrated with the Syxaw file synchronizer, which provides efficient file and metadata synchronization, optimizing network usage. Dessy supports synchronization of search results, individual files, and directory trees. It allows finding and synchronizing files that reside on remote computers, or the Internet. Dessy is designed to solve the problem of efficient mobile desktop search and synchronization, also supporting remote and Internet search. Remote searches may be carried out offline using a downloaded index, or while connected to the remote machine on a weak network. To secure user data, transmissions between the Dessy client and server are encrypted using symmetric encryption. Symmetric encryption keys are exchanged with RSA key exchange. Dessy emphasizes extensibility. Also the cryptography can be extended. Users may tag their files with context tags and control custom file metadata. Adding new indexed file types, metadata fields, ranking methods, and index types is easy. Finding files is done with virtual directories, which are views into the user’s files, browseable by regular file managers. On mobile devices, the Dessy GUI provides easy access to the search and synchronization system. This thesis includes results of Dessy synchronization and search experiments, including power usage measurements. Finally, Dessy has been designed with mobility and device constraints in mind. It requires only MIDP 2.0 Mobile Java with FileConnection support, and Java 1.5 on desktop machines.

Peroxidases in lignifying xylem of Norway spruce, Scots pine and silver birch

Lignin is a complex plant polymer synthesized through co-operation of multiple intracellular and extracellular enzymes. It is deposited to plant cell walls in cells where additional strength or stiffness are needed, such as in tracheary elements (TEs) in xylem, supporting sclerenchymal tissues and at the sites of wounding. Class III peroxidases (POXs) are secreted plant oxidoreductases with implications in many physiological processes such as the polymerization of lignin and suberin and auxin catabolism. POXs are able to oxidize various substrates in the presence of hydrogen peroxide, including lignin monomers, monolignols, thus enabling the monolignol polymerization to lignin by radical coupling. Trees produce large amounts of lignin in secondary xylem of stems, branches and roots. In this study, POXs of gymnosperm and angiosperm trees were studied in order to find POXs which are able to participate in lignin polymerization in developing secondary xylem i.e. are located at the site of lignin synthesis in tree stems and have the ability to oxidize monolignol substrates. Both in the gymnosperm species, Norway spruce and Scots pine, and in the angiosperm species silver birch the monolignol oxidizing POX activities originating from multiple POX isoforms were present in lignifying secondary xylem in stems during the period of annual growth. Most of the partially purified POXs from Norway spruce and silver birch xylem had highest oxidation rate with coniferyl alcohol, the main monomer in guaiacyl-lignin in conifers. The only exception was the most anionic POX fraction from silver birch, which clearly preferred sinapyl alcohol, the lignin monomer needed in the synthesis of syringyl-guaiacyl lignin in angiosperm trees. Three full-length pox cDNAs px1, px2 and px3 were cloned from the developing xylem of Norway spruce. It was shown that px1 and px2 are expressed in developing tracheids in spruce seedlings, whereas px3 transcripts were not detected suggesting low transcription level in young trees. The amino acid sequences of PX1, PX2 and PX3 were less than 60% identical to each other but showed up to 84% identity to other known POXs. They all begin with predicted N-terminal secretion signal (SS) peptides. PX2 and PX3 contained additional putative vacuolar localization determinants (VSDs) at C-terminus. Transient expression of EGFP-fusions of the SS- and VSD-peptides in tobacco protoplasts showed SS-peptides directed EGFP to secretion in tobacco cells, whereas only the PX2 C-terminal peptide seems to be a functional VSD. According to heterologous expression of px1 in Catharanthus roseus hairy roots, PX1 is a guaicol-oxidizing POX with isoelectric point (pI) approximately 10, similar to monolignol oxidizing POXs in protein extracts from Norway spruce lignifying xylem. Hence, PX1 has characteristics for participation to monolignol dehydrogenation in lignin synthesis, whereas the other two spruce POXs seem to have some other functions. Interesting topics in future include functional characterization of syringyl compound oxidizing POXs and components of POX activity regulation in trees.

Development of biogenic VOC emission inventories for the boreal forest

Luonnosta haihtuvat orgaaniset yhdisteet, joita pääsee ilmaan etenkin metsistä, voivat vaikuttaa paikalliseen ja alueelliseen ilmanlaatuun, koska ne reagoivat ilmakehässä. Niiden reaktiotuotteet voivat myös osallistua uusien hiukkasten muodostumiseen ja kasvuun, millä voi olla vaikutusta ilmakehän säteilytaseeseen ja tätä kautta myös ilmastoon. Hiukkaset absorboivat ja sirottavat auringon säteilyä ja maapallon lämpösäteilyä minkä lisäksi ne vaikuttavat pilvien säteilyominaisuuksiin, määrään ja elinikään. Koko maapallon mittakaavassa luonnosta tulevat hiilivetypäästöt ylittävät ihmistoiminnan aiheuttamat päästöt moninkertaisesti. Tämän vuoksi luonnon päästöjen arviointi on tärkeää kun halutaan kehittää tehokkaita ilmanlaatu- ja ilmastostrategioita. Tämä tutkimus käsittelee boreaalisen metsän hiilivetypäästöjä. Boreaalinen metsä eli pohjoinen havumetsä on suurin maanpäällinen ekosysteemi, ja se ulottuu lähes yhtenäisenä nauhana koko pohjoisen pallonpuoliskon ympäri. Sille on tyypillistä puulajien suhteellisen pieni kirjo sekä olosuhteiden ja kasvun voimakkaat vuodenaikaisvaihtelut. Työssä on tutkittu Suomen yleisimmän boreaalisen puun eli männyn hiilivetypäästöjen vuodenaikaisvaihtelua sekä päästöjen riippuvuutta lämpötilasta ja valosta. Saatuja tuloksia on käytetty yhdessä muiden boreaalisilla puilla tehtyjen päästömittaustulosten kanssa Suomen metsiä varten kehitetyssä päästömallissa. Malli perustuu lisäksi maankäyttötietoihin, suomen metsille kehitettyyn luokitukseen ja meteorologisiin tietoihin, joiden avulla se laskee metsien hiilivetypäästöt kasvukauden aikana. Suomen metsien päästöt koostuvat koko kasvukauden ajan suurelta osin alfa- ja beta-pineenistä sekä delta-kareenista. Kesällä ja syksyllä päästöissä on myös paljon sabineenia, jota tulee etenkin lehtipuista. Päästöt seuraavat lämpötilan keskimääräistä vaihtelua, ovat suurimmillaan maan eteläosissa ja laskevat tasaisesti pohjoiseen siirryttäessä. Metsän isopreenipäästö on suhteellisen pieni – Suomessa tärkein isopreeniä päästävä puu on vähäpäästöinen kuusi, koska runsaspäästöisten pajun ja haavan osuus metsän lehtimassasta on hyvin pieni. Tässä työssä on myös laskettu ensimmäinen arvio metsän seskviterpeenipäästöistä. Seskviterpeenipäästöt alkavat Juhannuksen jälkeen ja ovat kasvukauden aikana samaa suuruusluokkaa kuin isopreenipäästöt. Vuositasolla Suomen metsien hiilivetypäästöt ovat noin kaksinkertaiset ihmistoiminnasta aiheutuviin päästöihin verrattuna.

Studies on the Cell Wall Structure and on the Mechanical Properties of Norway Spruce

The structure and the mechanical properties of wood of Norway spruce (Picea abies [L.] Karst.) were studied using small samples from Finland and Sweden. X-ray diffraction (XRD) was used to determine the orientation of cellulose microfibrils (microfibril angle, MFA), the dimensions of cellulose crystallites and the average shape of the cell cross-section. X-ray attenuation and x-ray fluorescence measurements were used to study the chemical composition and the trace element content. Tensile testing with in situ XRD was used to characterise the mechanical properties of wood and the deformation of crystalline cellulose within the wood cell walls. Cellulose crystallites were found to be 192 284 Å long and 28.9 33.4 Å wide in chemically untreated wood and they were longer and wider in mature wood than in juvenile wood. The MFA distribution of individual Norway spruce tracheids and larger samples was asymmetric. In individual cell walls, the mean MFA was 19 30 degrees, while the mode of the MFA distribution was 7 21 degrees. Both the mean MFA and the mode of the MFA distribution decreased as a function of the annual ring. Tangential cell walls exhibited smaller mean MFA and mode of the MFA distribution than radial cell walls. Maceration of wood material caused narrowing of the MFA distribution and removed contributions observed at around 90 degrees. In wood of both untreated and fertilised trees, the average shape of the cell cross-section changed from circular via ambiguous to rectangular as the cambial age increased. The average shape of the cell cross-section and the MFA distribution did not change as a result of fertilisation. The mass absorption coefficient for x-rays was higher in wood of fertilised trees than in that of untreated trees and wood of fertilised trees contained more of the elements S, Cl, and K, but a smaller amount of Mn. Cellulose crystallites were longer in wood of fertilised trees than in that of untreated trees. Kraft cooking caused widening and shortening of the cellulose crystallites. Tensile tests parallel to the cells showed that if the mean MFA is initially around 10 degrees or smaller, no systematic changes occur in the MFA distribution due to strain. The role of mean MFA in defining the tensile strength or the modulus of elasticity of wood was not as dominant as that reported earlier. Crystalline cellulose elongated much less than the entire samples. The Poisson ratio νca of crystalline cellulose in Norway spruce wood was shown to be largely dependent on the surroundings of crystalline cellulose in the cell wall, varying between -1.2 and 0.8. The Poisson ratio was negative in kraft cooked wood and positive in chemically untreated wood. In chemically untreated wood, νca was larger in mature wood and in latewood compared to juvenile wood and earlywood.