The Gerbera cDNA Microarray: A Tool for Large-Scale Identification of Genes Involved in Flower Development

During the past ten years, large-scale transcript analysis using microarrays has become a powerful tool to identify and predict functions for new genes. It allows simultaneous monitoring of the expression of thousands of genes and has become a routinely used tool in laboratories worldwide. Microarray analysis will, together with other functional genomics tools, take us closer to understanding the functions of all genes in genomes of living organisms. Flower development is a genetically regulated process which has mostly been studied in the traditional model species Arabidopsis thaliana, Antirrhinum majus and Petunia hybrida. The molecular mechanisms behind flower development in them are partly applicable in other plant systems. However, not all biological phenomena can be approached with just a few model systems. In order to understand and apply the knowledge to ecologically and economically important plants, other species also need to be studied. Sequencing of 17 000 ESTs from nine different cDNA libraries of the ornamental plant Gerbera hybrida made it possible to construct a cDNA microarray with 9000 probes. The probes of the microarray represent all different ESTs in the database. From the gerbera ESTs 20% were unique to gerbera while 373 were specific to the Asteraceae family of flowering plants. Gerbera has composite inflorescences with three different types of flowers that vary from each other morphologically. The marginal ray flowers are large, often pigmented and female, while the central disc flowers are smaller and more radially symmetrical perfect flowers. Intermediate trans flowers are similar to ray flowers but smaller in size. This feature together with the molecular tools applied to gerbera, make gerbera a unique system in comparison to the common model plants with only a single kind of flowers in their inflorescence. In the first part of this thesis, conditions for gerbera microarray analysis were optimised including experimental design, sample preparation and hybridization, as well as data analysis and verification. Moreover, in the first study, the flower and flower organ-specific genes were identified. After the reliability and reproducibility of the method were confirmed, the microarrays were utilized to investigate transcriptional differences between ray and disc flowers. This study revealed novel information about the morphological development as well as the transcriptional regulation of early stages of development in various flower types of gerbera. The most interesting finding was differential expression of MADS-box genes, suggesting the existence of flower type-specific regulatory complexes in the specification of different types of flowers. The gerbera microarray was further used to profile changes in expression during petal development. Gerbera ray flower petals are large, which makes them an ideal model to study organogenesis. Six different stages were compared and specifically analysed. Expression profiles of genes related to cell structure and growth implied that during stage two, cells divide, a process which is marked by expression of histones, cyclins and tubulins. Stage 4 was found to be a transition stage between cell division and expansion and by stage 6 cells had stopped division and instead underwent expansion. Interestingly, at the last analysed stage, stage 9, when cells did not grow any more, the highest number of upregulated genes was detected. The gerbera microarray is a fully-functioning tool for large-scale studies of flower development and correlation with real-time RT-PCR results show that it is also highly sensitive and reliable. Gene expression data presented here will be a source for gene expression mining or marker gene discovery in the future studies that will be performed in the Gerbera Laboratory. The publicly available data will also serve the plant research community world-wide.

The role of MADS and TCP transcription factors in Gerbera hybrida flower development

Angiosperms represent a huge diversity in floral structures. Thus, they provide an attractive target for comparative developmental genetics studies. Research on flower development has focused on few main model plants, and studies on these species have revealed the importance of transcription factors, such as MADS-box and TCP genes, for regulating the floral form. The MADS-box genes determine floral organ identities, whereas the TCP genes are known to regulate flower shape and the number of floral organs. In this study, I have concentrated on these two gene families and their role in regulating flower development in Gerbera hybrida, a species belonging to the large sunflower family (Asteraceae). The Gerbera inflorescence is comprised of hundreds of tightly clustered flowers that differ in their size, shape and function according to their position in the inflorescence. The presence of distinct flower types tells Gerbera apart from the common model species that bear only single kinds of flowers in their inflorescences. The marginally located ray flowers have large bilaterally symmetrical petals and non-functional stamens. The centrally located disc flowers are smaller, have less pronounced bilateral symmetry and carry functional stamens. Early stages of flower development were studied in Gerbera to understand the differentiation of flower types better. After morphological analysis, we compared gene expression between ray and disc flowers to reveal transcriptional differences in flower types. Interestingly, MADS-box genes showed differential expression, suggesting that they might take part in defining flower types by forming flower-type-specific regulatory complexes. Functional analysis of a CYCLOIDEA-like TCP gene GhCYC2 provided evidence that TCP transcription factors are involved in flower type differentiation in Gerbera. The expression of GhCYC2 is ray-flower-specific at early stages of development and activated only later in disc flowers. Overexpression of GhCYC2 in transgenic Gerbera-lines causes disc flowers to obtain ray-flower-like characters, such as elongated petals and disrupted stamen development. The expression pattern and transgenic phenotypes further suggest that GhCYC2 may shape ray flowers by promoting organ fusion. Cooperation of GhCYC2 with other Gerbera CYC-like TCP genes is most likely needed for proper flower type specification, and by this means for shaping the elaborate inflorescence structure. Gerbera flower development was also approached by characterizing B class MADS-box genes, which in the main model plants are known regulators of petal and stamen identity. The four Gerbera B class genes were phylogenetically grouped into three clades; GGLO1 into the PI/GLO clade, GDEF2 and GDEF3 into the euAP3 clade and GDEF1 into the TM6 clade. Putative orthologs for GDEF2 and GDEF3 were identified in other Asteraceae species, which suggests that they appeared through an Asteraceae-specific duplication. Functional analyses indicated that GGLO1 and GDEF2 perform conventional B-function as they determine petal and stamen identities. Our studies on GDEF1 represent the first functional analysis of a TM6-like gene outside the Solanaceae lineage and provide further evidence for the role of TM6 clade members in specifying stamen development. Overall, the Gerbera B class genes showed both commonalities and diversifications with the conventional B-function described in the main model plants.

Lumometsän syli : Anni Swanin satusymbolismi 1896-1923

Lumometsän syli, Anni Swanin satusymbolismi 1896-1923 on suomenkielisen satukirjallisuuden poetiikkaa ja 1900-luvun alun modernia naiseutta selvittävä feministiseen tutkimustraditioon liittyvä tutkimus. Sen kohteena ovat lasten- ja nuortenkirjailija Anni Swanin (1875-1958) satukokoelmat vuosilta 1901-1923 ja Uusi Suometar -lehden sadunomaiset novellit vuosilta 1896-1904. Tutkimus tuo uutta tietoa lastenkirjallisuuden osalta 1900-luvun alun modernin ihmisen problematiikasta. Se sisältää naissubjektin kehityskaaren ja sisäisen kasvun kohti naistaiteilijuutta. Yksityiskohtaisen tarkastelun kohteina ovat sadut Veli ja sisar (1917), Ihmekukka (1905), Marjaanan helmikruunu (1912), Aaltojen salaisuus (1901), Jääkukka (1905), Tyttö ja kuolema (1917), Merenkuningatar ja hänen poikansa (1905), Lumolinna (1905) ja Tarina Kultasirkasta (1901). Tutkimuksessa tarkastellaan Swanin satujen poeettista kieltä ja naiseuden tematiikkaa ranskalaisen postmodernin ajan feministisen viitekehyksen valossa. Siinä keskeisiä ovat Julia Kristevan psykoanalyyttispohjaiset näkemykset ja Hélène Cixous´n sekä Luce Irigarayn ajatukset feminiinisestä kirjoituksesta. Sadut kontekstualisoidaan ajankohdan symbolistiseen taidevirtaukseen ja Suomen taiteen kultakauteen. Satuja tulkitaan naiskirjailijan lajina ja erityisenä naisen metaforisen ilmaisun muotona. Satujen feministinen lukutapa purkaa perinteisiä lukemiskonventioita ja merkitsee satutekstin lukemista "toisin". Se avaa varhaista modernia naiseutta ja sille ominaista naisen ilmaisukielen erityisyyttä sekä mykkää ei-kielellistä, melankolian ilmaisua. Tutkimus tuo esiin uudenlaisen naiskirjailijan aistimusvoimaisen kielen. Swanin satusymbolismi on luonnon kauneuden synesteettista ja aistimusvoimaista kerrontaa, jolle on luonteenomaista aistiestetiikka, metaforisuus, metonymisyys ja metamorfoosit. Swan vahvistaa osaltaan naisen sankaruutta, omaa ilmaisukieltä ja ääntä. Tuloksena paljastuu satuperinteeseen verrattuna uudenlaisia tyttöyden, äitiyden, naistaiteilijuuden ja perheen malleja ja niiden representaatioita. Satumallit osoittautuvat aikanaan moderneiksi tyttösankareiksi, osin ambivalenteiksi uudenlaista naiseutta ja suhteessa oloa heijastaviksi ja ovat siten varhaisia feministisen sadun tunnusmerkkejä. Tutkimus selvittää, miten Swan rakentaa omaperäisen satusymboliikan. Satumetsä on luonnonkauniin suomalaismetsän symbolinen mielenmaisema ja samanaikaisesti sadun myyttis-symbolinen topos. Swanin luontokäsitys sisältää luonnonsuojelun ja varhaisen ekokriittisen näkemyksen. Tutkimus osoittaa Swanin satujen kytkeytyvän 1900-luvun alun modernismiin ja Suomen taiteen kultakauteen. Swan on suomenkielisen symbolistisen taidesadun kehittäjä ja feministisen sadun aloittaja.

Secondary metabolites in Gerbera hybrida

Plants produce a diversity of secondary metabolites, i.e., low-molecular-weight compounds that have primarily ecological functions in plants. The flavonoid pathway is one of the most studied biosynthetic pathways in plants. In order to understand biosynthetic pathways fully, it is necessary to isolate and purify the enzymes of the pathways to study individual steps and to study the regulatory genes of the pathways. Chalcone synthases are key enzymes in the formation of several groups of flavonoids, including anthocyanins. In this study, a new chalcone synthase enzyme (GCHS4), which may be one of the main contributors to flower colour, was characterised from the ornamental plant Gerbera hybrida. In addition, four chalcone synthase-like genes and enzymes (GCHS17, GCHS17b, GCHS26 and GCHS26b) were studied. Spatial expression of the polyketide synthase gene family in gerbera was also analysed with quantitative RT-PCR from 12 tissues, including several developmental stages and flower types. A previously identified MYB transcription factor from gerbera, GMYB10, which regulates the anthocyanin pathway, was transferred to gerbera and the phenotypes were analysed. Total anthocyanin content and anthocyanidin profiles of control and transgenic samples were compared spectrophotometrically and with HPLC. The overexpression of GMYB10 alone was able to change anthocyanin pigmentation: cyanidin pigmentation was induced and pelargonidin pigmentation was increased. The gerbera 9K cDNA microarray was used to compare the gene expression profiles of transgenic tissues against the corresponding control tissues to reveal putative target genes for GMYB10. GMYB10 overexpression affected the expression of both early and late biosynthetic genes in anthocyanin-accumulating transgenic tissues, including the newly isolated gene GCHS4. Two new MYB domain factors, named as GMYB11 and GMYB12, were also upregulated. Gene transfer is not only a powerful tool for basic research, but also for plant breeding. However, crop improvement by genetic modification (GM) remains controversial, at least in Europe. Many of the concerns relating to both human health and to ecological impacts relate to changes in the secondary metabolites of GM crops. In the second part of this study, qualitative and quantitative differences in cytotoxicity and metabolic fingerprints between 225 genetically modified Gerbera hybrida lines and 42 non-GM Gerbera varieties were compared. There was no evidence for any major qualitative and quantitative changes between the GM lines and non-GM varieties. The developed cell viability assays offer also a model scheme for cell-based cytotoxicity screening of a large variety of GM plants in standardized conditions.

Developing Peer-To-Peer Web Applications

As the virtual world grows more complex, finding a standard way for storing data becomes increasingly important. Ideally, each data item would be brought into the computer system only once. References for data items need to be cryptographically verifiable, so the data can maintain its identity while being passed around. This way there will be only one copy of the users family photo album, while the user can use multiple tools to show or manipulate the album. Copies of users data could be stored on some of his family members computer, some of his computers, but also at some online services which he uses. When all actors operate over one replicated copy of the data, the system automatically avoids a single point of failure. Thus the data will not disappear with one computer breaking, or one service provider going out of business. One shared copy also makes it possible to delete a piece of data from all systems at once, on users request. In our research we tried to find a model that would make data manageable to users, and make it possible to have the same data stored at various locations. We studied three systems, Persona, Freenet, and GNUnet, that suggest different models for protecting user data. The main application areas of the systems studied include securing online social networks, providing anonymous web, and preventing censorship in file-sharing. Each of the systems studied store user data on machines belonging to third parties. The systems differ in measures they take to protect their users from data loss, forged information, censorship, and being monitored. All of the systems use cryptography to secure names used for the content, and to protect the data from outsiders. Based on the gained knowledge, we built a prototype platform called Peerscape, which stores user data in a synchronized, protected database. Data items themselves are protected with cryptography against forgery, but not encrypted as the focus has been disseminating the data directly among family and friends instead of letting third parties store the information. We turned the synchronizing database into peer-to-peer web by revealing its contents through an integrated http server. The REST-like http API supports development of applications in javascript. To evaluate the platform s suitability for application development we wrote some simple applications, including a public chat room, bittorrent site, and a flower growing game. During our early tests we came to the conclusion that using the platform for simple applications works well. As web standards develop further, writing applications for the platform should become easier. Any system this complex will have its problems, and we are not expecting our platform to replace the existing web, but are fairly impressed with the results and consider our work important from the perspective of managing user data.

Mehiläisten (Apis mellifera) kukkavierailut mansikalla (Fragaria x ananassa) ja vadelmalla (Rubus idaeus) sekä kukkavierailuihin vaikuttavat tekijät

Hyönteispölytys lisää monien ristipölytteisten viljelykasvien siemensatoa sekä parantaa sadon laatua. Marjakasveilla, kuten mansikalla ja vadelmalla marjojen koko suurenee sekä niiden laatu paranee onnistuneen pölytyksen seurauksena. Aiempien havaintojen mukaan mansikan kukat eivät pääsääntöisesti houkuttele mehiläisiä, kun taas vadelma on yksi mehiläisten pääsatokasveista. Tutkimuksen tarkoituksena oli selvittää, miten tehokkaasti mehiläiset vierailevat mansikalla sekä vadelmalla, keskittyen kukkakohtaisiin käynteihin tuntia kohti. Mehiläisiä voidaan käyttää Gliocladium catenulatum-vektoreina torjuttaessa mansikan ja vadelman harmaahometta (Botrytis cinerea). Kukkavierailujen perusteella arvioidaan, onko vektorilevitys riittävän tehokas torjumaan harmaahometta ja miten hyvin mehiläisiä voidaan käyttää pölytyspalveluihin, etenkin mansikalla. Havainnot kerättiin kuudelta eri tilalta Sisä-Savosta kesällä 2007. Kukkavierailuja laskettiin mansikan ja vadelman kukinnan aikana erilaisissa sääolosuhteissa, eri kellonaikoina ja eri etäisyyksillä mehiläispesistä. Kukat valittiin satunnaisesti, ja valintaperusteena oli kukan avonaisuus. Tarkkailuaika riippui mehiläisten lentoaktiivisuudesta. Mansikan koko havaintojakson keskiarvoksi tuli 1,75 käyntiä kukkaa kohti tunnissa. Vadelmalla vastaava luku oli 4,27, joten keskiarvojen perusteella vadelma oli houkuttelevampi kuin mansikka. Kasvukauden vaiheella ei ollut eroja vierailuihin kummallakaan kasvilla, mutta vuorokaudenajan suhteen vierailuja oli enemmän aamupäivällä kuin iltapäivällä. Lämpötila korreloi positiivisesti vierailutiheyden kanssa kummallakin kasvilla. Sääolosuhteet rajoittivat havaintojen keräämistä ja kesä oli erittäin sateinen. Mehiläiset vierailivat kukissa riittävästi haastavissakin sääolosuhteissa niin, että harmaahometorjunta onnistui. Vektorilevitystä suunnitellessa, etenkin mansikalla, tulee ottaa huomioon pesien sijoittelu sekä riittävä lukumäärä. Pesien ravinnontarpeen tulee olla suuri, jotta mehiläiset keräisivät ravintoa kukista mahdollisimman tehokkaasti. Pesiin voidaan lisätä tarvittaessa avosikiöitä tai poistaa siitepölyvarastoja ravinnonkeruuaktiivisuuden lisäämiseksi. Lisätutkimusta tarvitaan pesien sijoittelun, kilpailevien kasvien sekä mansikkalajikkeiden houkuttelevuuden vaikutuksesta vierailutiheyteen. Suomalaisten mansikkalajikkeiden meden sekä siitepölyneritystä olisi myös hyvä selvittää.

Development of tissue culture and virus-induced gene silencing for Calendula officinalis

Calendula officinalis is grown widely as an ornamental plant across Europe. It belongs to the large. Asteraceae family. In this study, the aim was to explore the possibilities to use Calendula officinalis as a new model organism for flower development and secondary mechanism studies in Asteraceae. Tissue culture of Calendula officinalis was established using nine different cultivars. Murashige & Skoog (MS) medium with four different combinations of plant growth regulators were tested. Of all these combinations, the medium containing 1mg/l BAP, 0.1 mg/l IAA, and 1mg/l Zeatin achieved highest frequency of adventitious shoot regeneration from hypocotyl and cotyledon explants. Virus-induced gene silencing is a recent developed genetic tool for charactering the gene functions in plants, and extends the range of host plants that are not accessible for Agrobacterium transformation. Here, tobacco rattle virus (TRV)-based VIGS technique was tested in calendula (cv. Single Orange). We used TRV carrying Gerbera hybrid phytoene desaturase (PDS) gene fragment to induce PDS silencing in calendula. Vacuum infiltration and syringe infiltration methods both resulted in photo-bleaching phenotypes in leaves, bracts and petals. Loss-of-function phenotypes occurred on calendula 13 days post-infiltration. In conclusion, the data indicates that calendula explants can be regenerated through tissue culture which is a prerequisite for development of stable transformation methods. However, further optimization is still needed to improve the frequency. In addition, VIGS was applied to silence PDS marker gene expression indicating that this method has potential for gene functional studies in future.

Arabidopsis GRI is involved in the regulation of cell death induced by extracellular ROS

Reactive oxygen species (ROS) have important functions in plant stress responses and development. In plants, ozone and pathogen infection induce an extracellular oxidative burst that is involved in the regulation of cell death. However, very little is known about how plants can perceive ROS and regulate the initiation and the containment of cell death. We have identified an Arabidopsis thaliana protein, GRIM REAPER (GRI), that is involved in the regulation of cell death induced by extracellular ROS. Plants with an insertion in GRI display an ozone-sensitive phenotype. GRI is an Arabidopsis ortholog of the tobacco flower-specific Stig1 gene. The GRI protein appears to be processed in leaves with a release of an N-terminal fragment of the protein. Infiltration of the N-terminal fragment of the GRI protein into leaves caused cell death in a superoxide-and salicylic acid-dependent manner. Analysis of the extracellular GRI protein yields information on how plants can initiate ROS-induced cell death during stress response and development.