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.

Intranet Alman käytettävyydestä

Usability testing is a productive and reliable method for evaluating the usability of software. Planning and implementing the test and analyzing its results is typically considered time-consuming, whereas applying usability methods in general is considered difficult. Because of this, usability testing is often priorized lower than more concrete issues in software engineering projects. Intranet Alma is a web service, users of which consist of students and personnel of the University of Helsinki. Alma was published in 2004 at the opening ceremony of the university. It has 45 000 users, and it replaces several former university network services. In this thesis, the usability of intranet Alma is evaluated with usability testing. The testing method applied has been lightened to make its taking into use as easy as possible. In the test, six students each tried to solve nine test tasks with Alma. As a result concrete usability problems were described in the final test report. Goal-orientation was given less importance in the applied usability testing. In addition, the system was tested only with test users from the largest user group. Usability test found general usability problems that occurred no matter the task or the user. However, further evaluation needs to be done: in addition to the general usability problems, there are task-dependent problems, solving of which requires thorough gathering of users goals. In the basic structure and central functionality of Alma, for example in navigation, there are serious and often repeating usability problems. It would be of interest to verify the designed user interface solutions to these problems before taking them into use. In the long run, the goals of the users, that the software is planned to support, are worth gathering, and the software development should be based on these goals.

Kokonaisvaltainen fysiikanopetus peruskoulussa fysiikan valinnaiskurssilla

Holistic physics education in upper secondary level based on the optional course of physics Keywords: physics education, education, holistic, curriculum, world view, values A physics teacher s task is to put into practice all goals of the curriculum. Holistic physics education means in this research teaching, in which the school s common educational goals and the goals particular to the physics curriculum are taken into account. These involve knowledge, skills and personal value and attitude goals. Research task was to clarify how the educational goals involving student s values and attitudes can be carried out through the subject content of physics. How does the physics teacher communicate the modern world view through the content of the physics class? The goal of this research was to improve teaching, to find new points of view and to widen the perspective on how physics is taught. The teacher, who acted also as a researcher, planned and delivered an optional course where she could study the possibilities of holistic physics education. In 2001-2002 ten girls and two boys of the grade 9th class participated in that elective course. According to principles of action research the teacher-researcher reflected also on her own teaching action. Research method was content analysis that involved both analyzing student feedback, and relevant features of the teacher s knowledge, which are needed for planning and giving the physics lessons. In this research that means taking into account the subject matter knowledge, curriculum, didactic and the pedagogical content knowledge of the teacher. The didactic includes the knowledge of the learning process, students motivation, specific features of the physics didactics and the research of physics education. Among other things, the researcher constructed the contents of the curriculum and abstracted sentences as keywords, from which she drew a concept map. The concept maps, for instance, the map of educational goals and the mapping of the physics essence, were tools for studying contents which are included in the holistic physics education. Moreover, conclusions were reached concerning the contents of physics domains by which these can be achieved. According to this research, the contents employing the holistic physics education is as follows: perception, the essence of science, the development of science, new research topics and interactions in physics. The starting point of teaching should be connected with the student s life experiences and the approach to teaching should be broadly relevant to those experiences. The teacher-researcher observed and analyzed the effects of the experimental physics course, through the lens of a holistic physics education. The students reported that the goals of holistic physics education were achieved in the course. The discourses of the students indicated that in the experimental course they could express their opinions and feelings and make proposals and evaluations. The students had experiences about chances to affect the content of the course, and they considered the philosophical physics course interesting, it awakened questions, increased their self-esteem and helped them to become more aware of their world views. The students analytic skills developed in the interactive learning environment. The physics teacher needs broad knowledge for planning his or her teaching, which is evaluated in this research from contents maps made for the tools of the teaching. In the holistic physics education the teacher needs an open and curious mind and skills for interaction in teaching. This research indicates the importance of teaching physics in developing attitudes and values beside substance of the physics in class environment. The different points of view concerning human beings life make it possible to construct the modern world view of the students and to develop analytic skills and the self-esteem and thus help them in learning. Overall and wide points of view also help to transfer knowledge to practice. Since such contents is not employed by teaching the physics included in the standard curriculum, supplement relevant teaching material that includes such topics are needed.

Very Low Birth Weight Infants as Young Adults : Focus on aspects of cognition, behavior and sleep

Major advances in the treatment of preterm infants have occurred during the last three decades. Survival rates have increased, and the first generations of preterm infants born at very low birth weight (VLBW; less than 1500 g) who profited from modern neonatal intensive care are now in young adulthood. The literature shows that VLBW children achieve on average lower scores on cognitive tests, even after exclusion of individuals with obvious neurosensory deficits. Evidence also exists for an increased risk in VLBW children for various neuropsychiatric disorders such as attention-deficit hyperactivity disorder (ADHD) and related behavioral symptoms. Up till now, studies extending into adulthood are sparse, and it remains to be seen whether these problems persist into adulthood. The aim of this thesis was to study ADHD-related symptoms and cognitive and executive functioning in young adults born at VLBW. In addition, we aimed to study sleep disturbances, known to adversely affect both cognition and attention. We hypothesized that preterm birth at VLBW interferes with early brain development in a way that alters the neuropsychological phenotype; this may manifest itself as ADHD symptoms and impaired cognitive abilities in young adulthood. In this cohort study from a geographically defined region, we studied 166 VLBW adults and 172 term-born controls born from 1978 through 1985. At ages 18 to 27 years, the study participants took part in a clinic study during which their physical and psychological health was assessed in detail. Three years later, 213 of these individuals participated in a follow-up. The current study is part of a larger research project (The Helsinki Study of Very Low Birth Weight Adults), and the measurements of interest for this particular study include the following: 1) The Adult Problem Questionnaire (APQ), a self-rating scale of ADHD-related symptoms in adults; 2) A computerized cognitive test battery designed for population studies (CogState®) which measures core cognitive abilities such as reaction time, working memory, and visual learning; 3) Sleep assessment by actigraphy, the Basic Nordic Sleep Questionnaire, and the Morningness-Eveningness Questionnaire. Actigraphs are wrist-worn accelerometers that separate sleep from wakefulness by registering body movements. Contrary to expectations, VLBW adults as a group reported no more ADHD-related behavioral symptoms than did controls. Further subdivision of the VLBW group into SGA (small for gestational age) and AGA (appropriate for gestational age) subgroups, however, revealed more symptoms on ADHD subscales pertaining to executive dysfunction and emotional instability among those born SGA. Thus, it seems that intrauterine growth retardation (for which SGA served as a proxy) is a more essential predictor for self-perceived ADHD symptoms in adulthood than is VLBW birth as such. In line with observations from other cohorts, the VLBW adults reported less risk-taking behavior in terms of substance use (alcohol, smoking, and recreational drugs), a finding reassuring for the VLBW individuals and their families. On the cognitive test, VLBW adults free from neurosensory deficits had longer reaction times than did term-born peers on all tasks included in the test battery, and lower accuracy on the learning task, with no discernible effect of SGA status over and above the effect of VLBW. Altogether, on a group level, even high-functioning VLBW adults show subtle deficits in psychomotor processing speed, visual working memory, and learning abilities. The sleep studies provided no evidence for differences in sleep quality or duration between the two groups. The VLBW adults were, however, at more than two-fold higher risk for sleep-disordered breathing (in terms of chronic snoring). Given the link between sleep-disordered breathing and health sequelae, these results suggest that VLBW individuals may benefit from an increased awareness among clinicians of this potential problem area. An unexpected finding from the sleep studies was the suggestion of an advanced sleep phase: The VLBW adults went to bed earlier according to the actigraphy registrations and also reported earlier wake-up times on the questionnaire. In further study of this issue in conjunction with the follow-up three years later, the VLBW group reported higher levels of morningness propensity, further corroborating the preliminary findings of an advanced sleep phase. Although the clinical implications are not entirely clear, the issue may be worth further study, since circadian rhythms are closely related to health and well-being. In sum, we believe that increased understanding of long-term outcomes after VLBW, and identification of areas and subgroups that are particularly vulnerable, will allow earlier recognition of potential problems and ultimately lead to improved prevention strategies.

Studies of the Human Transcriptome

Gene expression is one of the most critical factors influencing the phenotype of a cell. As a result of several technological advances, measuring gene expression levels has become one of the most common molecular biological measurements to study the behaviour of cells. The scientific community has produced enormous and constantly increasing collection of gene expression data from various human cells both from healthy and pathological conditions. However, while each of these studies is informative and enlighting in its own context and research setup, diverging methods and terminologies make it very challenging to integrate existing gene expression data to a more comprehensive view of human transcriptome function. On the other hand, bioinformatic science advances only through data integration and synthesis. The aim of this study was to develop biological and mathematical methods to overcome these challenges and to construct an integrated database of human transcriptome as well as to demonstrate its usage. Methods developed in this study can be divided in two distinct parts. First, the biological and medical annotation of the existing gene expression measurements needed to be encoded by systematic vocabularies. There was no single existing biomedical ontology or vocabulary suitable for this purpose. Thus, new annotation terminology was developed as a part of this work. Second part was to develop mathematical methods correcting the noise and systematic differences/errors in the data caused by various array generations. Additionally, there was a need to develop suitable computational methods for sample collection and archiving, unique sample identification, database structures, data retrieval and visualization. Bioinformatic methods were developed to analyze gene expression levels and putative functional associations of human genes by using the integrated gene expression data. Also a method to interpret individual gene expression profiles across all the healthy and pathological tissues of the reference database was developed. As a result of this work 9783 human gene expression samples measured by Affymetrix microarrays were integrated to form a unique human transcriptome resource GeneSapiens. This makes it possible to analyse expression levels of 17330 genes across 175 types of healthy and pathological human tissues. Application of this resource to interpret individual gene expression measurements allowed identification of tissue of origin with 92.0% accuracy among 44 healthy tissue types. Systematic analysis of transcriptional activity levels of 459 kinase genes was performed across 44 healthy and 55 pathological tissue types and a genome wide analysis of kinase gene co-expression networks was done. This analysis revealed biologically and medically interesting data on putative kinase gene functions in health and disease. Finally, we developed a method for alignment of gene expression profiles (AGEP) to perform analysis for individual patient samples to pinpoint gene- and pathway-specific changes in the test sample in relation to the reference transcriptome database. We also showed how large-scale gene expression data resources can be used to quantitatively characterize changes in the transcriptomic program of differentiating stem cells. Taken together, these studies indicate the power of systematic bioinformatic analyses to infer biological and medical insights from existing published datasets as well as to facilitate the interpretation of new molecular profiling data from individual patients.

Biomassan energia-arvon nostaminen sekundäärilämmöllä kuivaamalla

Viime aikoina ilmastonmuutos, fossiilisten polttoaineiden väheneminen ja niiden hinnan nousu ovat lisänneet merkittävästi maailmanlaajuista kiinnostusta uusiutuviin energiavaroihin. Suomessa uusiutuvien energialähteiden käytössä on jo pitkään panostettu metsäteollisuuden sivutuotevirtana tuottamaan puuperäiseen biomassaan, jota metsäteollisuus käyttää energiantuotantoonsa. Metsäteollisuuden jätevesien käsittelyssä syntyy erilaisia lietteitä, jotka joko uusiokäytetään tai hävitetään polttamalla tai sijoittamalla kaatopaikalle. Erityisesti biolietteiden uusiokäyttö on hankalaa ja kaatopaikkasijoitus tulevaisuudessa mahdotonta tai ainakin kustannuksiltaan kohtuutonta. Käytännössä liete hävitetään polttamalla ja kuivaamalla siitä tulee polttoaine. Lietteiden energiakäyttö on järkevin tapa hävittää jäteliete. Lietteiden korkean vesipitoisuuden vuoksi ne tulee kuitenkin kuivata ennen polttoa. Lietteen kuivaaminen sekundäärienergiavirralla eli metsäteollisuusprosesseissa sivutuotteena muodostuvalla ns. hukkalämmöllä lisää lietteen poltosta saatavaa energiamäärää ja korvaa fossiilisten polttoaineiden käyttöä. Tutkimuksen tavoitteena oli selvittää lietteen kuivaukseen optimaalisin kuoren ja lietteen seossuhde eri kuivausparametrejä vaihdellen. Kokeellinen työ aloitettiin rakentamalla energiatekniikan koehalliin laboratoriokokoluokan kiintopetikuivuri, jossa kuivumista tutkittiin puhaltamalla polttoainepedin läpi lämmitettyä ilmaa. Kuivattavina polttoaineina olivat kuoren ja lietteen seos tai pelkkä kuori ja liete erilaisilla massoilla ja erilaisilla prosenttisilla suhteilla ja erilaisissa lämpötiloissa. Kuivumiskäyrien määritys perustui massanmuutokseen. Koelaitteessa olivat anturit lämpötilan mittausta varten, jotta lämpötila saatiin säädettyä ja seurattua kokeen edellyttämällä tavalla. Lämpötilat ja painonmuutokset tallentuivat koetta tehdessä tietokoneelle. Kuivauskokeet osoittivat, että liete-kuori seos kuivuu hyvin kiintopedissä kun lietteen massaosuus seoksessa on korkeintaan 50 %. Lietteen massaosuuden ollessa tätä suurempi kuivaaminen ei enää ole tehokasta, mikä johtuu luultavasti ilman suuresta kanavoitumisesta kuivauspedissä. Kuorta kuivatessa lämpötilan nosto 50 °C:stä 70 °C:een oli huomattavasti tehokkaampaa kuin 70 °C:stä 90 °C:een, ajallisesti ero oli noin kaksinkertainen.