Regulation of strawberry growth and development

Strawberries (Fragaria sp.) are adapted to diverse environmental conditions from the tropics to about 70ºN, so different responses to environmental conditions can be found. Most genotypes of garden strawberry (F. x ananassa Duch.) and woodland strawberry (F. vesca L.) are short-day (SD) plants that are induced to flowering by photoperiods under a critical limit, but also various photoperiod x temperature interactions can be found. In addition, continuously flowering everbearing (EB) genotypes are found. In addition to flowering, axillary bud differentiation in strawberry is regulated by photoperiod. In SD conditions, axillary buds differentiate to rosette-like structures called "branch crowns", whereas in long-day conditions (LD) they form runners, branches with 2 long internodes followed by a daughter plant (leaf rosette). The number of crown branches determines the yield of the plant, since inflorescences are formed from the apical meristems of the crown. Although axillary bud differentiation is an important developmental process in strawberries, its environmental and hormonal regulation has not been characterized in detail. Moreover, the genetic mechanisms underlying axillary bud differentiation and regulation of flowering time in these species are almost completely unresolved. These topics have been studied in this thesis in order to enhance strawberry research, cultivation and breeding. The results showed that 8-12 SD cycles suppressed runner initiation from the axillary buds of the garden strawberry cv. Korona with the concomitant induction of crown branching, and 3 weeks of SD was sufficient for the induction of flowering in the main crown. Furthermore, a second SD treatment given a few weeks after the first SD period can be used to induce flowering in the primary branch crowns and to induce the formation of secondary branches. Thus, artificial SD treatments effectively stimulate crown branching, providing one means for the increase of cropping (yield) potential in strawberry. It was also shown by growth regulation applications, quantitave hormone analysis and gene expression analysis that gibberellin (GA) is one of the key signals involved in the photoperiod control of shoot differentiation. The results indicate that photoperiod controls GA activity specifically in axillary buds, thereby determining bud fate. It was further shown that chemical control of GA biosynthesis by prohexadione-calcium can be utilized to prevent excessive runner formation and induce crown branching in strawberry fields. Moreover, ProCa increased berry yield up to 50%, showing that it is an easier and more applicable alternative to artificial SD treatments for controlling strawberry crown development and yield. Finally, flowering gene pathways in Fragaria were explored by searching for homologs of 118 Arabidopsis thaliana flowering-time genes. In total, 66 gene homologs were identified, and they distributed to all known flowering pathways, suggesting the presence of these pathways also in strawberry. Expression analysis of selected genes revealed that the mRNA of putative floral identity gene APETALA1 accumulated in the shoot apex of the EB genotype after the induction of flowering, whereas it was absent in vegetative SD genotype, indicating the usefulness of this gene product as the marker of floral initiation. The present data enables the further exploration of strawberry flowering pathways with genetic transformation, gene mapping and transcriptomics methods.

Indexing Heterogeneous XML for Full-Text Search

XML documents are becoming more and more common in various environments. In particular, enterprise-scale document management is commonly centred around XML, and desktop applications as well as online document collections are soon to follow. The growing number of XML documents increases the importance of appropriate indexing methods and search tools in keeping the information accessible. Therefore, we focus on content that is stored in XML format as we develop such indexing methods. Because XML is used for different kinds of content ranging all the way from records of data fields to narrative full-texts, the methods for Information Retrieval are facing a new challenge in identifying which content is subject to data queries and which should be indexed for full-text search. In response to this challenge, we analyse the relation of character content and XML tags in XML documents in order to separate the full-text from data. As a result, we are able to both reduce the size of the index by 5-6\% and improve the retrieval precision as we select the XML fragments to be indexed. Besides being challenging, XML comes with many unexplored opportunities which are not paid much attention in the literature. For example, authors often tag the content they want to emphasise by using a typeface that stands out. The tagged content constitutes phrases that are descriptive of the content and useful for full-text search. They are simple to detect in XML documents, but also possible to confuse with other inline-level text. Nonetheless, the search results seem to improve when the detected phrases are given additional weight in the index. Similar improvements are reported when related content is associated with the indexed full-text including titles, captions, and references. Experimental results show that for certain types of document collections, at least, the proposed methods help us find the relevant answers. Even when we know nothing about the document structure but the XML syntax, we are able to take advantage of the XML structure when the content is indexed for full-text search.

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.

From the river to the open sea - a critical life phase of young Atlantic salmon migrating from the Simojoki river

Long-term monitoring data collected from wild smolts of Atlantic salmon (Salmo salar) in the Simojoki river, northern Finland, were used in studying the relationships between the smolt size and age, smolt and postsmolt migration, environmental conditions and postsmolt survival. The onset of the smolt run was significantly dependent on the rising water temperature and decreasing discharge of the river in the spring. The mean length of smolts migrating early in the season was commonly higher and the mean age always older than among smolts migrating later. Many of the smolts migrating early in the season and almost all smolts migrating later had started their new growth in spring in the river before their sea entry. Among postsmolts, the time required for emigration from the estuary was dependent on the sea surface temperature (SST) off the river, being significantly shorter in years with warm than cold sea temperatures. After leaving the estuary, the postsmolts migrated southwards along the eastern coast of the northern Gulf of Bothnia, the geographical distribution of the tag recoveries coinciding with the warm thermal zone in spring in the coastal area. After arriving in the southern Gulf of Bothnia in late summer the postsmolts mostly migrated near the western coast, reaching the Baltic Main Basin in late autumn. Until the early 1990s there was only a weak positive association between smolt length and postsmolt survival. However, following a subsequent decrease in the mean smolt size, a significant positive dependence was observed between smolt size and the reported recapture rate of tagged salmon. The differences in recapture rates between smolts tagged during the first and second half of the annual migration season were insignificant, indicating that the seasonal variation in smolt size and age seem to be too small to affect survival. Among the climatic factors examined, the summer SST in the Gulf of Bothnia was most clearly related to the survival of the wild postsmolts. Postsmolt survival appeared to be highest in years when the SST in June in the Bothnian Bay varied between 9 and 12 ºC. In addition, the survival of wild postsmolts showed a significant positive dependence on the SST in July in the Bothnian Sea, but not on the abundance of the prey fish (0+ herring, Clupea harengus and sprat, Sprattus sprattus) in the Bothnian Sea and in the Baltic Main Basin. The results suggest, that if the incidence of extreme weather conditions were to increase due to climatic changes, it would probably reduce the postsmolt survival of wild salmon populations. For improving the performance of hatchery-reared smolts, it could be useful to examine opportunities to produce smolts that are in their smolt traits and abilities more similar to the wild smolts described in this thesis.

Identification of the fungal catabolic D-galacturonate pathway

Pectin is a natural polymer consisting mainly of D-galacturonic acid monomers. Microorganisms living on decaying plant material can use D-galacturonic acid for growth. Although bacterial pathways for D-galacturonate catabolism had been described previously, no eukaryotic pathway for D-galacturonate catabolism was known at the beginning of this work. The aim of this work was to identify such a pathway. In this thesis the pathway for D-galacturonate catabolism was identified in the filamentous fungus Trichoderma reesei. The pathway consisted of four enzymes: NADPH-dependent D-galacturonate reductase (GAR1), L-galactonate dehydratase (LGD1), L-threo-3-deoxy-hexulosonate aldolase (LGA1) and NADPH-dependent glyceraldehyde reductase (GLD1). In this pathway D-galacturonate was converted to pyruvate and glycerol via L-galactonate, L-threo-3-deoxy-hexulosonate and L-glyceraldehyde. The enzyme activities of GAR1, LGD1 and LGA1 were present in crude mycelial extract only when T. reesei was grown on D-galacturonate. The activity of GLD1 was equally present on all the tested carbon sources. The corresponding genes were identified either by purifying and sequencing the enzyme or by expressing genes with homology to other similar enzymes in a heterologous host and testing the activities. The new genes that were identified were expressed in Saccharomyces cerevisiae and resulted in active enzymes. The GAR1, LGA1 and GLD1 were also produced in S. cerevisiae as active enzymes with a polyhistidine-tag, and purified and characterised. GAR1 and LGA1 catalysed reversible reactions, whereas only the forward reactions were observed for LGD1 and GLD1. When gar1, lgd1 or lga1 was deleted in T. reesei the deletion strain was unable to grow with D-galacturonate as the only carbon source, demonstrating that all the corresponding enzymes were essential for D-galacturonate catabolism and that no alternative D-galacturonate pathway exists in T. reesei. A challenge for biotechnology is to convert cheap raw materials to useful and more valuable products. Filamentous fungi are especially useful for the conversion of pectin, since they are efficient producers of pectinases. Identification of the fungal D-galacturonate pathway is of fundamental importance for the utilisation of pectin and its conversion to useful products.

The viral coat protein is regulated by HSP70 and HSP40 in Potato virus A infection

Plus-stranded (plus) RNA viruses multiply within a cellular environment as tightly integrated units and rely on the genetic information carried within their genomes for multiplication and, hence, persistence. The minimal genomes of plus RNA viruses are unable to encode the molecular machineries that are required for virus multiplication. This sets requisites for the virus, which must form compatible interactions with host components during multiplication to successfully utilize primary metabolites as building blocks or metabolic energy, and to divert the protein synthesis machinery for production of viral proteins. In fact, the emerging picture of a virus-infected cell displays tight integration with the virus, from simple host and virus protein interactions through to major changes in the physiological state of the host cell. This study set out to develop a method for the identification of host components, mainly host proteins, that interact with proteins of Potato virus A (PVA; Potyvirus) during infection. This goal was approached by developing affinity-tag based methods for the purification of viral proteins complexed with associated host proteins from infected plants. Using this method, host membrane-associated viral ribonucleoprotein (RNP) complexes were obtained, and several host and viral proteins could be identified as components of these complexes. One of the host proteins identified using this strategy was a member of the heat shock protein 70 (HSP70) family, and this protein was chosen for further analysis. To enable the analysis of viral gene expression, a second method was developed based on Agrobacterium-mediated virus genome delivery into plant cells, and detection of virally expressed Renilla luciferase (RLUC) as a quantitative measure of viral gene expression. Using this method, it was observed that down-regulation of HSP70 caused a PVA coat protein (CP)-mediated defect associated with replication. Further experimentation suggested that CP can inhibit viral gene expression and that a distinct translational activity coupled to replication, referred to as replication-associated translation (RAT), exists. Unlike translation of replication-deficient viral RNA, RAT was dependent on HSP70 and its co-chaperone CPIP. HSP70 and CPIP together regulated CP turnover by promoting its modification by ubiquitin. Based on these results, an HSP70 and CPIP-driven mechanism that functions to regulate CP during viral RNA replication and/or translation is proposed, possibly to prevent premature particle assembly caused by CP association with viral RNA.

Studies on Aerosol Particle Emission, Sampling and Authenticity

Emissions of coal combustion fly ash through real scale ElectroStatic Precipitators (ESP) were studied in different coal combustion and operation conditions. Sub-micron fly-ash aerosol emission from a power plant boiler and the ESP were determined and consequently the aerosol penetration, as based on electrical mobility measurements, thus giving thereby an indication for an estimate on the size and the maximum extent that the small particles can escape. The experimentals indicate a maximum penetration of 4% to 20 % of the small particles, as counted on number basis instead of the normally used mass basis, while simultaneously the ESP is operating at a nearly 100% collection efficiency on mass basis. Although the size range as such seems to appear independent of the coal, of the boiler or even of the device used for the emission control, the maximum penetration level on the number basis depends on the ESP operating parameters. The measured emissions were stable during stable boiler operation for a fired coal, and the emissions seemed each to be different indicating that the sub-micron size distribution of the fly-ash could be used as a specific characteristics for recognition, for instance for authenticity, provided with an indication of known stable operation. Consequently, the results on the emissions suggest an optimum particle size range for environmental monitoring in respect to the probability of finding traces from the samples. The current work embodies also an authentication system for aerosol samples for post-inspection from any macroscopic sample piece. The system can comprise newly introduced new devices, for mutually independent use, or, for use in a combination with each other, as arranged in order to promote the sampling operation length and/or the tag selection diversity. The tag for the samples can be based on naturally occurring measures and/or added measures of authenticity in a suitable combination. The method involves not only military related applications but those in civil industries as well. Alternatively to the samples, the system can be applied to ink for note printing or other monetary valued papers, but also in a filter manufacturing for marking fibrous filters.

Geant4 Hadronic Cascade Models and CMS Data Analysis : Computational Challenges in the LHC era

This work belongs to the field of computational high-energy physics (HEP). The key methods used in this thesis work to meet the challenges raised by the Large Hadron Collider (LHC) era experiments are object-orientation with software engineering, Monte Carlo simulation, the computer technology of clusters, and artificial neural networks. The first aspect discussed is the development of hadronic cascade models, used for the accurate simulation of medium-energy hadron-nucleus reactions, up to 10 GeV. These models are typically needed in hadronic calorimeter studies and in the estimation of radiation backgrounds. Various applications outside HEP include the medical field (such as hadron treatment simulations), space science (satellite shielding), and nuclear physics (spallation studies). Validation results are presented for several significant improvements released in Geant4 simulation tool, and the significance of the new models for computing in the Large Hadron Collider era is estimated. In particular, we estimate the ability of the Bertini cascade to simulate Compact Muon Solenoid (CMS) hadron calorimeter HCAL. LHC test beam activity has a tightly coupled cycle of simulation-to-data analysis. Typically, a Geant4 computer experiment is used to understand test beam measurements. Thus an another aspect of this thesis is a description of studies related to developing new CMS H2 test beam data analysis tools and performing data analysis on the basis of CMS Monte Carlo events. These events have been simulated in detail using Geant4 physics models, full CMS detector description, and event reconstruction. Using the ROOT data analysis framework we have developed an offline ANN-based approach to tag b-jets associated with heavy neutral Higgs particles, and we show that this kind of NN methodology can be successfully used to separate the Higgs signal from the background in the CMS experiment.

Optical Tweezers for Single Molecule Biology

Molecular machinery on the micro-scale, believed to be the fundamental building blocks of life, involve forces of 1-100 pN and movements of nanometers to micrometers. Micromechanical single-molecule experiments seek to understand the physics of nucleic acids, molecular motors, and other biological systems through direct measurement of forces and displacements. Optical tweezers are a popular choice among several complementary techniques for sensitive force-spectroscopy in the field of single molecule biology. The main objective of this thesis was to design and construct an optical tweezers instrument capable of investigating the physics of molecular motors and mechanisms of protein/nucleic-acid interactions on the single-molecule level. A double-trap optical tweezers instrument incorporating acousto-optic trap-steering, two independent detection channels, and a real-time digital controller was built. A numerical simulation and a theoretical study was performed to assess the signal-to-noise ratio in a constant-force molecular motor stepping experiment. Real-time feedback control of optical tweezers was explored in three studies. Position-clamping was implemented and compared to theoretical models using both proportional and predictive control. A force-clamp was implemented and tested with a DNA-tether in presence of the enzyme lambda exonuclease. The results of the study indicate that the presented models describing signal-to-noise ratio in constant-force experiments and feedback control experiments in optical tweezers agree well with experimental data. The effective trap stiffness can be increased by an order of magnitude using the presented position-clamping method. The force-clamp can be used for constant-force experiments, and the results from a proof-of-principle experiment, in which the enzyme lambda exonuclease converts double-stranded DNA to single-stranded DNA, agree with previous research. The main objective of the thesis was thus achieved. The developed instrument and presented results on feedback control serve as a stepping stone for future contributions to the growing field of single molecule biology.

Hantavirus glycoprotein GN in virion assembly and regulation of interferon response

Hantaviruses have a tri-segmented negative-stranded RNA genome. The S segment encodes the nucleocapsid protein (N), M segment two glycoproteins, Gn and Gc, and the L segment the RNA polymerase. Gn and Gc are co-translationally cleaved from a precursor and targeted to the cis-Golgi compartment. The Gn glycoprotein consists of an external domain, a transmembrane domain and a C-terminal cytoplasmic domain. In addition, the S segment of some hantaviruses, including Tula and Puumala virus, have an open reading frame (ORF) encoding a nonstructural potein NSs that can function as a weak interferon antagonist. The mechanisms of hantavirus-induced pathogenesis are not fully understood but it is known that both hemorrhagic fever with renal syndrome (HFRS) and hantavirus (cardio) pulmonary syndrome (HCPS) share various features such as increased capillary permeability, thrombocytopenia and upregulation of TNF-. Several hantaviruses have been reported to induce programmed cell death (apoptosis), such as TULV-infected Vero E6 cells which is known to be defective in interferon signaling. Recently reports describing properties of the hantavirus Gn cytoplasmic tail (Gn-CT) have appeared. The Gn-CT of hantaviruses contains animmunoreceptor tyrosine-based activation motif (ITAM) which directs receptor signaling in immune and endothelial cells; and contain highly conserved classical zinc finger domains which may have a role in the interaction with N protein. More functions of Gn protein have been discovered, but much still remains unknown. Our aim was to study the functions of Gn protein from several aspects: synthesis, degradation and interaction with N protein. Gn protein was reported to inhibit interferon induction and amplication. For this reason, we also carried out projects studying the mechanisms of IFN induction and evasion by hantavirus. We first showed degradation and aggresome formation of the Gn-CT of the apathogenic TULV. It was reported earlier that the degradation of Gn-CT is related to the pathogenicity of hantavirus. We found that the Gn-CT of the apathogenic hantaviruses (TULV, Prospect Hill virus) was degraded through the ubiquitin-proteasome pathway, and TULV Gn-CT formed aggresomes upon treatment with proteasomal inhibitor. Thus the results suggest that degradation and aggregation of the Gn-CT may be a general property of most hantaviruses, unrelated to pathogenicity. Second, we investigated the interaction of TULV N protein and the TULV Gn-CT. The Gn protein is located on the Golgi membrane and its interaction with N protein has been thought to determine the cargo of the hantaviral ribonucleoprotein which is an important step in virus assembly, but direct evidence has not been reported. We found that TULV Gn-CT fused with GST tag expressed in bacteria can pull-down the N protein expressed in mammalian cells; a mutagenesis assay was carried out, in which we found that the zinc finger motif in Gn-CT and RNA-binding motif in N protein are indispensable for the interaction. For the study of mechanisms of IFN induction and evasion by Old World hantavirus, we found that Old World hantaviruses do not produce detectable amounts of dsRNA in infected cells and the 5 -termini of their genomic RNAs are monophosphorylated. DsRNA and tri-phosphorylated RNA are considered to be critical activators of innate immnity response by interacting with PRRs (pattern recognition receptors). We examined systematically the 5´-termini of hantavirus genomic RNAs and the dsRNA production by different species of hantaviruses. We found that no detectable dsRNA was produced in cells infected by the two groups of the old world hantaviruses: Seoul, Dobrava, Saaremaa, Puumala and Tula. We also found that the genomic RNAs of these Old World hantaviruses carry 5´-monophosphate and are unable to trigger interferon induction. The antiviral response is mainly mediated by alpha/beta interferon. Recently the glycoproteins of the pathogenic hantaviruses Sin Nombre and New York-1 viruses were reported to regulate cellular interferon. We found that Gn-CT can inhibit the induction of IFN activation through Toll-like receptor (TLR) and retinoic acid-inducible gene I-like RNA helicases (RLH) pathway and that the inhibition target lies at the level of TANK-binding kinase 1 (TBK-1)/ IKK epislon complex and myeloid differentiation primary response gene (88) (MyD88) / interferon regulatory factor 7 (IRF-7) complex.

Una gramática descriptiva del chabacano de Ternate

This dissertation is a descriptive grammar of Ternate Chabacano, a Spanish-lexifier Creole spoken by 3.000 people in the town of Ternate, Philippines. The dissertation offers an analysis of the phonological, morphological, and syntactic system of the language. It includes an overview of the historical background, the current situation of the speech community and a collection of annotated texts. Ternate Chabacano shares many characteristics with its main adstrate language Tagalog as well as the dialectal varieties of Spanish. At present, English also exerts an influence, nevertheless mainly affecting its lexicon. The description offered is based on fieldwork conducted in Ternate. Spoken language collected through thematic interviews forms the main type of the material analysed. Information regarding the informants and text types is included in the examples. Ternate Chabacano has a five-vowel system and 17 consonant phonemes. The morphology of the language is largely isolating. Clitics are used extensively for expressing adverbial relations. The verbal system is based on the preverbal markers that express the category of tense, modality and aspect, among which aspect is the main dimension. Complex predicates and verbal chains are used in order to further distinguish aspect and modality, as well as changes of voice and valency. Intransitive verbs express motion, states, and reflexive actions, even though the majority of verbs can occur in both intransitive and transitive clauses. Ternate Chabacano is a nominative-accusative type language but the typological configuration of the Philippine languages influences the marking of its constituents. A case in point is constituted by the nominal determination system. The basic constituent order in a clause is VSO. Equative and attibutive clauses are formed by juxtaposition while the locative clauses feature a copula. Indefinite terms are expressed through existential constructions. The negation of existential clauses differs from standard negation but both are intensified in the same way. In spoken discourse, tag-questions are common. Pragmatic elements and social formulas reflect largely the corresponding Tagalog expressions. Coordination and subordination occur typically without overt markers but a variety of markers exists for expressing different relations, especially those made explicit by adverbial clauses. Verbal chains form a continuum from serial verbs to complementation and ultimately to coordination.

Part-of-Speech Tagging using Parallel Weighted Finite-State Transducers

We use parallel weighted finite-state transducers to implement a part-of-speech tagger, which obtains state-of-the-art accuracy when used to tag the Europarl corpora for Finnish, Swedish and English. Our system consists of a weighted lexicon and a guesser combined with a bigram model factored into two weighted transducers. We use both lemmas and tag sequences in the bigram model, which guarantees reliable bigram estimates.