The Transcriptional Regulation of Retrotransposon BARE

The purpose of this research project was to understand the steps of the retrotransposon BARE (BArley REtrotransposon) life cycle, from regulation of transcription to Virus-Like Particle (VLP) formation and ultimate integration back into the genome. Our study concentrates mainly on BARE1 transcriptional regulation because transcription is the crucial first step in the retrotransposon life cycle. The BARE element is a Class I LTR (Long Terminal Repeat) retrotransposon belonging to the Copia superfamily and was originally isolated in our research group. The LTR retrotransposons are transcribed from promoters in the LTRs and encode proteins for packaging of their transcripts, the reverse transcription of the transcripts into cDNA, and integration of the cDNA back into the genome. BARE1 is translated as a single polyprotein and cleaved into the capsid protein (GAG), integrase (IN), and reverse transcriptase-RNaseH (RT-RH) by the integral aspartic proteinase (AP). The BARE retrotransposon family comprises more than 104 copies in the barley (Hordeum vulgare) genome. The element is bound by long terminal repeats (LTRs, 1829 bp) containing promoters required for replication, signals for RNA processing, and motifs necessary for the integration of the cDNA. Members of the BARE1 subfamily are transcribed, translated, and form virus-like particles. Several basic questions concerning transcription are explored in the thesis: BARE1 transcription control, promoter choice in different barley tissues, start and termination sites for BARE transcripts, and BARE1 transcript polyadenylation (I). Polyadenylation is an important step during mRNA maturation, and determines its stability and translatability among other characteristics. Our work has found a novel way used by BARE1 to make extra GAG protein, which is critical for VLP formation. The discovery that BARE1 uses one RNA population for protein synthesis and another RNA population for making cDNA has established the most important step of the BARE1 life cycle (III). The relationship between BARE1 and BARE2 has been investigated. Besides BARE, we have examined the retrotransposon Cassandra (II), which uses a very different transcriptional mechanism and a fully parasitic life cycle. In general, this work is focused on BARE1 promoter activity, transcriptional regulation including differential promoter usage and RNA pools, extra GAG protein production and VLP formation. The results of this study give new insights into transcription regulation of LTR retrotransposons.

Yhteisestä toiminnasta yhteiseen kieleen : keskustelunanalyyttinen tutkimus toisen kielen oppimisesta kielikylpypäiväkodin arkitilanteissa

This dissertation examines how Finnish-speaking children learn Swedish in an immersion kindergarten where the method of Canadian immersion is used. Within the framework of conversation analysis, this study explores how second language learning is situated in interaction and evidenced in the participants´ verbal and non-verbal behavior. The database consists of 40 hours of videotaped data collected in naturally occurring situations in a group of 15 four-year-old children during the first two years of their immersion. Due to the immersion method, all the children share the same L1, in this case Finnish, and the teachers understand Finnish. However, they speak only Swedish to the children in all situations and Swedish is learned in interaction without formal teaching. The aim of the study is to discover how the children´s second language competence gradually increases when they participate in interaction with the Swedish-speaking teachers. The study also sheds light on the methodological question of how second language learning can be analyzed with the method of conversation analysis. The focus is on showing how the second language is learned in interaction, especially on how learning is achieved collaboratively. In this study, the emerging second language competence is explored by investigating how the children show understanding of the teachers´ non-verbal and verbal actions during the first and the second semester of the immersion. The children´s use of Swedish is analyzed by investigating how they recycle lexical items and later even syntactic structures from the teachers´ Swedish turns. The results show that the teachers´ actions are largely understood by the children even at the beginning of the immersion. The analyzes of the children´s responsive turns reveal that they interpret the teachers´ turns on the basis of non-verbal cues at first. Especially at the beginning of the immersion, the participants orient to the progress of interaction and not to problems in understanding. Even in situations where the next actions show that the children do not understand what is said, they tend to display understanding rather than non-understanding. This behavior changes, however, when the children´s competence in their second language increases. At the second semester, the children both show understanding of the teachers´ verbal turns and also display their non-understanding by initiating repair when they do not understand. Understanding of the teachers´ verbal turns, including their syntactic structure, is manifested in the ways the children tie their turns to the teachers´ turns. Recycling, on the other hand, proves to be the way by which the children start to speak the second language. In this study, the children´s common L1 is evidenced to be an important resource in interaction. It allows the children to participate in their individual ways and to share their experiences both with each other and with the teachers. It also enables them to co-construct conversations that lead to collaborative learning. Moreover, the uninhibited use of L1 proves to be an important analytic tool that makes the immersion data especially fruitful for conversation analytic research on second language learning, since the children´s interpretations of the second language are in evidence even when they do not speak the second language.

HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Tietokone ikäihmisen arjessa

The aged people in the target group of my study belong to generation, which has experienced the shift from agricultural society via industrial society up to the society which has been described as information society. They have grown up concurrently with the technological development, but during the recent years the technological development has accelerated. One can say that the older the target study group has come the more information technological skills they need to possess to be equal actors in our society. However, especially in case of aged people the learning and maintaining of skills in information technology has mainly been left dependent on their personal motivation. The purpose of this report is to study the use of computers in the life of the aged people. The report studies the will and ability of the aged people to learn the skill of using computers, and the new possibilities which this brings into their lives. The study questions are the following: 1) Why the aged people start to use computers? 2) How the aged people benefit information technology in their own life? 3) How computers have extended the environment of the aged people? 4) What kind of problems the aged people have experienced in use of computers? The research material consists of group interviews and individual interviews (total of 23 people). The interview material has been collected among the participants on information technology courses of the Senior University of Helsinki University during years 2004-2005. The research method used is theme interviewing. In addition, the material of opinions about information technology of people born in decades of 1920 and 1930, gathered as part of the Ikihyvä Päijät-Häme 2002 -research has been used. On basis of this research one can say that the aged people do have motivation to study the use of computers, although many interviewees commented that they also have met problems in use of computers. The motivation has grown also because the fear that without the skills to use computers they could drift into outsiders of the society, whereas instead as skilled computer users they felt to be equal citizens compared with the younger age groups, and that they can maintain their independence and autonomy. Especially, the independent use of banking routines over the Internet and use of emails seem to give them a position as modern actors. Many interview statements also underline that computers will bring both joy and benefit to the users. Studying the use of computers is a new and interesting hobby, which can fill the hole left in the life after leaving the working life. Using skills of text processing and processing of pictures one can, for example, record the traditional knowledge of the family and ancestry to the younger generations, and write articles or even books on the professional area of ones own. Single people emphasize that computers can even act as companionship substitutes. One can use Internet for virtual traveling, which provides a new dimension in use of computers. Internet can also be used to maintain family relationships, especially between grandparents and remote grandchildren. Typical problems in use of computers appeared to be that reaching the right professional helpdesk advisers of the service providers is difficult and requires lots of time and patience. However, the interviewees were not willing to give up their computers, because they had already used to these. Keywords: digital divide, aging, Internet, usability, motivation, information technology, information society.

A Circuit-Based Proof of Toda′s Theorem

We present a simple proof of Toda′s result (Toda (1989), in "Proceedings, 30th Annual IEEE Symposium on Foundations of Computer Science," pp. 514-519), which states that circled plus P is hard for the Polynomial Hierarchy under randomized reductions. Our approach is circuit-based in the sense that we start with uniform circuit definitions of the Polynomial Hierarchy and apply the Valiant-Vazirani lemma on these circuits (Valiant and Vazirani (1986), Thoeret. Comput. Sci.47, 85-93).

Osallistuminen ja läpinäkyvyys kuntatasolla : tapaustutkimus Nicaraguasta

In this Master's thesis I go through the principals of the good governance. I apply these principals to the Nicaraguan context and especially in two rural municipalities in Chontales department. I clarify the development of the space of participation in Nicaraguan municipal level. I start my examination from the period when Somoza dictatorship ended and first open elections were held, and I end it to the municipal eleccions held in November 2008. These elections were robbed in 33 municipalities and because of this there started a crisis in Nicaragua and among the actors of development cooperation. As a methods of research I use two types of interview in the thesis, the interviews for the citizens and interviews for the experts. These interviews answer to my questions of the methods of participation. I also review the level of the trust of a citizen to an authority by asking if s/he voted in the municipal eleccions in November 2008. Furthermore, I define the work of municipal government in the point of view of the citizen. I also find out if a citizen wants to take more part in the decision making in her/his municipal. I have classified the types of citizens by the interviews I made. Due to this classification I explain how many people actually have opportunity to participate the dialogue of the municipal decision making and how many can follow the activity of the municipal governance. The result is that after the elections in November 2008 only one typed group can freely take part in the dialogue. This does not apply the principals of good governance, especially in subterms of participation and transparency. The incidents after the municipal elections have affected strongly on the co-operation of Finland and Nicaragua. Because of the fault of the elections Finland like the other co-operative countries brought down the directly paid budget support. This has caused a great economical crisis in Nicaragua which the covering will take a long time. The Master's thesis is a case study of two rural municipalities called Santo Tómas and Villa Sandino. Santo Tómas has a sandinista municipal government which is not legitimate. In Villa Sandino the government is liberal and legitimate.

Koti keskellä kaupunkia : Keskusta lapsiperheen asuinalueena, esimerkkeinä Tukholma ja Helsinki

Families with children have traditionally moved to suburbs. In the last 20 years a modest counter process has however been recognized. Families with an urban lifestyle stay in the city centres. This study looks at the phenomenon through two cases, Stockholm and Helsinki. In the first case it has already been observed that the city centre has grown in popularity among families with children. Therefore it serves as a basis for the study and as well as a point of comparison. Stockholm’s city centre is expanding as new neighbourhoods have been built and are being planned. In the city centre of Helsinki the building of two large neighbourhoods for 30 000 inhabitants will start in a few years. The first aim of the study is to look closer at what has really happened in the city centre of Stockholm, why families choose to live there with their children and how the City of Stockholm has reacted to the change. The main sources of information are secondary sources, statistics and interviews with planners, politicians and experts in the field. The main object is to look at the situation in the city centre of Helsinki. Can a preference for urban residential environments be observed in Helsinki? What are the reasons for a family to choose the city centre as a living place? How does the everyday life of a family in the city centre appear? How are these families taken into account in the planning of the city? The main sources of information here are statistics, interviews with dwellers in the neighbourhood Kruununhaka and interviews with planners. In Stockholm the birth rate has grown constantly during the 2000s and is highest in the city centre. Some of the families still move elsewhere, but many of them do not. One of the most important reasons for living in the city centre is short working distances which give working parents more time with their children. Another reason is a preference of an urban, active lifestyle. Families prefer to live close to everything, childcare, schools, shops and entertainments. The popularity of the city centre among families with children has taken politicians and planners by surprise. Helsinki has not experienced a baby boom like Stockholm. However the negative changes in the birth rate have been more modest in the central areas than in the suburbs. Statistics show, that many families move away from the city centre as the children grow. Families who stay in the city centre especially appreciate closeness to public and private services and good public transportation which means that they are not dependent on using the car. Further they find that the city centre has a tolerant climate and is a safe and beautiful place to live in. The families enjoy the social life of the neighbourhood and feel that it makes a good climate to raise children in. However they are concerned with traffic safety and the lack of stimulus in the playgrounds of the neighbourhood parks. Two large neighbourhoods with homes for about 30 000 inhabitants are now planned in the former Port Districts in the city centre of Helsinki. The other one, Jätkäsaari has been planned to become an attractive alternative for families with children. Traffic safety has been one of the main objects for the planning. The other, Kalasatama, has been planned to attract all groups in society.

Properties of ion assisted deposited titania films

Thin films of titanium dioxide have been deposited using ion assisted deposition with oxygen ions in the energy range 100�500 eV and current densities up to 100 ?A/cm2. It has been observed that the refractive index of the films increases up to 300 eV and the extinction coefficient increased only nominally up to 300 eV. Optical band gap calculations have shown a strong dependence of the gap on the energy of incident ions. Beyond a critical energy and current density of the ions the refractive index and extinction coefficient of the films start deteriorating. It has also been found that beyond the critical values the optical band gap value decreases. The maximum refractive index obtained was 2.49 at an energy of 300 eV and 50 ?A/cm2 current density. Post?deposition annealing of the films at 500?°C resulted in a slight increase in refractive index without affecting the extinction coefficient. X?ray diffraction studies revealed a monophasic anatase structure in these films. ?

Studies on a stove for powdery biomass

The sawdust stove, classically known for several decades, is considered here in a scientific study. The poor ignition characteristics and smoky start up are related to improper geometric dimensions. Based on a parametric study, the startup procedure and the dimensions of the stove were modified to achieve a smooth start up. Also, the range of acceptable fuels was enlarged to include tiny unprocessed dry twigs, weeds and wood sticks o the extent of about 50%, with the rest being sawdust-like material. The efficiency of the stove was measured to be 30–40%, depending on the relative size and shape of the vessel and the power level of the stove. A simple procedure for designing this class of stove for various power levels, as well as burning times, is presented. A new concept of multiport design is also discussed.

A quasi-steady performance prediction model for dynamic characteristics of a volute pump

A performance prediction model generally applicable for volute-type centrifugal pumps has been extended to predict the dynamic characteristics of a pump during its normal starting and stopping periods. Experiments have been conducted on a volute pump with different valve openings to study the dynamic behaviour of the pump during normal start-up and stopping, when a small length of discharge pipeline is connected to the discharge flange of the pump. Such experiments have also been conducted when the test pump was part of a hydraulic system, an experimental rig, where it is pumping against three similar pumps, known as supply pumps, connected in series, with the supply pumps kept idle or running. Instantaneous rotational speed, flowrate, and delivery and suction pressures of the pump were recorded and it was observed in all the tested cases that the change of pump behaviour during the transient period was quasi-steady, which validates the quasi-steady approach presented in this paper. The nature of variation of parameters during the transients has been discussed. The model-predicted dynamic head-capacity curves agree well with the experimental data for almost all the tested cases.

Cloning and sequence of a cDNA encoding a novel hybrid prolme-rich protein associated with cytokinin-induced haustoria formation in Cuscuta reflexa

A complete cDNA encoding a novel hybrid Pro-rich protein (HyPRP) was identified by differentially screening 3x10(4) recombinant plaques of a Cuscuta reflexa cytokinin-induced haustorial cDNA library constructed in lambda gt10. The nucleotide (nt) sequence consists of: (i) a 424-bp 5'-non coding region having five start codons (ATGs) and three upstream open reading frames (uORFs); (ii) an ORF of 987 bp with coding potential for a 329-amino-acid (aa) protein of M(r), 35203 with a hydrophobic N-terminal region including a stretch of nine consecutive Phe followed by a Pro-rich sequence and a Cys-rich hydrophobic C terminus; and (iii) a 178-bp 3'-UTR (untranslated region). Comparison of the predicted aa sequence with the NBRF and SWISSPROT databases and with a recent report of an embryo-specific protein of maize [Jose-Estanyol et al., Plant Cell 4 (1992) 413-423] showed it to be similar to the class of HyPRPs encoded by genes preferentially expressed in young tomato fruits, maize embryos and in vitro-cultured carrot embryos. Northern analysis revealed an approx. 1.8-kb mRNA of this gene expressed in the subapical region of the C. reflexa vine which exhibited maximum sensitivity to cytokinin in haustorial induction.

The cDNA sequence of cytochrome b5 associated with cytokinin-induced haustoria formation in Cuscuta reflexa

A cDNA clone isolated by differentially screening a cytokinin-induced haustorial cDNA library of Cuscuta reflexa was sequenced and identified as the gene coding for cytochrome b(5), based on the similarity of the deduced amino-acid sequence with that of the cauliflower (60% identity) and tobacco (78% identity) proteins. The 5'-UTR is unusually long (720 bp) and contains 14 potential start codons (ATG) and 10 short ORFs.

Centrifugal pump transient characteristics and analysis using the method of characteristics

A theoretical and experimental study has been carried out on the transient characteristics of a centrifugal pump during starting and stopping periods. Experiments have been conducted on a volute pump with different valve openings to study the dynamic behaviour of the pump during normal start up and stopping, when a small length of discharge pipe line is connected to discharge flange of the pump. Similar experiments have also been conducted when the test pump was part of a hydraulic system to study the system effect on the transient characteristics. Instantaneous rotational speed, flowrate, and delivery and suction pressures of the pump are recorded and it is observed in ail the tested cases that the change of pump behaviour during the transient period is quasi-steady. The dynamic characteristics of the pump have been analysed by a numerical model using the method of characteristics. The model is presented and the results are compared with the experimental data. As the model contains speed acceleration and unsteady discharge terms, the model can be applied for analyses of purely unsteady cases where the pump dynamic characteristics show considerable departure from their steady-state characteristics.

Towards building an intelligent decision support system for project management

Management of large projects, especially the ones in which a major component of R&D is involved and those requiring knowledge from diverse specialised and sophisticated fields, may be classified as semi-structured problems. In these problems, there is some knowledge about the nature of the work involved, but there are also uncertainties associated with emerging technologies. In order to draw up a plan and schedule of activities of such a large and complex project, the project manager is faced with a host of complex decisions that he has to take, such as, when to start an activity, for how long the activity is likely to continue, etc. An Intelligent Decision Support System (IDSS) which aids the manager in decision making and drawing up a feasible schedule of activities while taking into consideration the constraints of resources and time, will have a considerable impact on the efficient management of the project. This report discusses the design of an IDSS that helps in project planning phase through the scheduling phase. The IDSS uses a new project scheduling tool, the Project Influence Graph (PIG).

Reduction of electric are furnace slags in stainless steelmaking - Part 1 Observations

Simultaneous reduction of iron and chromium oxides from synthetic electric are furnace stainless steelmaking slag in a graphite crucible has been studied. Above the melting point of iron the reduction of iron oxide leads to a carbon saturated Fe-C melt, but below the melting point of iron initially solid iron or iron carbide forms on the crucible surface. Only when a certain number of Fe-C droplets are formed does the reduction of chromium oxide start to form an Fe-Cr-C alloy. The reaction proceeds with pronounced foaming which depends on the basicity, temperature, and iron oxide content of the slag. IS/1352a (C) 1998 The Institute of Materials.