MECHANISMS AND EFFECTS OF MITOCHONDRIAL DNA INSTABILITY AND COPY NUMBER MANIPULATION

Defects in mitochondrial DNA (mtDNA) maintenance cause a range of human diseases, including autosomal dominant progressive external ophthalmoplegia (adPEO). This study aimed to clarify the molecular background of adPEO. We discovered that deoxynucleoside triphosphate (dNTP) metabolism plays a crucial in mtDNA maintenance and were thus prompted to search for therapeutic strategies based on the modulation of cellular dNTP pools or mtDNA copy number. Human mtDNA is a 16.6 kb circular molecule present in hundreds to thousands of copies per cell. mtDNA is compacted into nucleoprotein clusters called nucleoids. mtDNA maintenance diseases result from defects in nuclear encoded proteins that maintain the mtDNA. These syndromes typically afflict highly differentiated, post-mitotic tissues such as muscle and nerve, but virtually any organ can be affected. adPEO is a disease where mtDNA molecules with large-scale deletions accumulate in patients tissues, particularly in skeletal muscle. Mutations in five nuclear genes, encoding the proteins ANT1, Twinkle, POLG, POLG2 and OPA1, have previously been shown to cause adPEO. Here, we studied a large North American pedigree with adPEO, and identified a novel heterozygous mutation in the gene RRM2B, which encodes the p53R2 subunit of the enzyme ribonucleotide reductase (RNR). RNR is the rate-limiting enzyme in dNTP biosynthesis, and is required both for nuclear and mitochondrial DNA replication. The mutation results in the expression of a truncated form of p53R2, which is likely to compete with the wild-type allele. A change in enzyme function leads to defective mtDNA replication due to altered dNTP pools. Therefore, RRM2B is a novel adPEO disease gene. The importance of adequate dNTP pools and RNR function for mtDNA maintenance has been established in many organisms. In yeast, induction of RNR has previously been shown to increase mtDNA copy number, and to rescue the phenotype caused by mutations in the yeast mtDNA polymerase. To further study the role of RNR in mammalian mtDNA maintenance, we used mice that broadly overexpress the RNR subunits Rrm1, Rrm2 or p53R2. Active RNR is a heterotetramer consisting of two large subunits (Rrm1) and two small subunits (either Rrm2 or p53R2). We also created bitransgenic mice that overexpress Rrm1 together with either Rrm2 or p53R2. In contrast to the previous findings in yeast, bitransgenic RNR overexpression led to mtDNA depletion in mouse skeletal muscle, without mtDNA deletions or point mutations. The mtDNA depletion was associated with imbalanced dNTP pools. Furthermore, the mRNA expression levels of Rrm1 and p53R2 were found to correlate with mtDNA copy number in two independent mouse models, suggesting nuclear-mitochondrial cross talk with regard to mtDNA copy number. We conclude that tight regulation of RNR is needed to prevent harmful alterations in the dNTP pool balance, which can lead to disordered mtDNA maintenance. Increasing the copy number of wild-type mtDNA has been suggested as a strategy for treating PEO and other mitochondrial diseases. Only two proteins are known to cause a robust increase in mtDNA copy number when overexpressed in mice; the mitochondrial transcription factor A (TFAM), and the mitochondrial replicative helicase Twinkle. We studied the mechanisms by which Twinkle and TFAM elevate mtDNA levels, and showed that Twinkle specifically implements mtDNA synthesis. Furthermore, both Twinkle and TFAM were found to increase mtDNA content per nucleoid. Increased mtDNA content in mouse tissues correlated with an age-related accumulation of mtDNA deletions, depletion of mitochondrial transcripts, and progressive respiratory dysfunction. Simultaneous overexpression of Twinkle and TFAM led to a further increase in the mtDNA content of nucleoids, and aggravated the respiratory deficiency. These results suggested that high mtDNA levels have detrimental long-term effects in mice. These data have to be considered when developing and evaluating treatment strategies for elevating mtDNA copy number.

Measurement of the tt̅ cross section in pp̅ collisions at √s=1.96 TeV using dilepton events with a lepton plus track selection

This paper reports a measurement of the cross section for the pair production of top quarks in ppbar collisions at sqrt(s) = 1.96 TeV at the Fermilab Tevatron. The data was collected from the CDF II detector in a set of runs with a total integrated luminosity of 1.1 fb^{-1}. The cross section is measured in the dilepton channel, the subset of ttbar events in which both top quarks decay through t -> Wb -> l nu b where l = e, mu, or tau. The lepton pair is reconstructed as one identified electron or muon and one isolated track. The use of an isolated track to identify the second lepton increases the ttbar acceptance, particularly for the case in which one W decays as W -> tau nu. The purity of the sample may be further improved at the cost of a reduction in the number of signal events, by requiring an identified b-jet. We present the results of measurements performed with and without the request of an identified b-jet. The former is the first published CDF result for which a b-jet requirement is added to the dilepton selection. In the CDF data there are 129 pretag lepton + track candidate events, of which 69 are tagged. With the tagging information, the sample is divided into tagged and untagged sub-samples, and a combined cross section is calculated by maximizing a likelihood. The result is sigma_{ttbar} = 9.6 +/- 1.2 (stat.) -0.5 +0.6 (sys.) +/- 0.6 (lum.) pb, assuming a branching ratio of BR(W -> ell nu) = 10.8% and a top mass of m_t = 175 GeV/c^2.

Search for standard model Higgs boson production in association with a W boson using a neural network discriminant at CDF

We present a search for standard model Higgs boson production in association with a W boson in proton-antiproton collisions at a center of mass energy of 1.96 TeV. The search employs data collected with the CDF II detector that correspond to an integrated luminosity of approximately 1.9 inverse fb. We select events consistent with a signature of a single charged lepton, missing transverse energy, and two jets. Jets corresponding to bottom quarks are identified with a secondary vertex tagging method, a jet probability tagging method, and a neural network filter. We use kinematic information in an artificial neural network to improve discrimination between signal and background compared to previous analyses. The observed number of events and the neural network output distributions are consistent with the standard model background expectations, and we set 95% confidence level upper limits on the production cross section times branching fraction ranging from 1.2 to 1.1 pb or 7.5 to 102 times the standard model expectation for Higgs boson masses from 110 to $150 GeV/c^2, respectively.

Searching the inclusive ℓγE̸T+b-quark signature for radiative top quark decay and non-standard-model processes

In a search for new phenomena in a signature suppressed in the standard model of elementary particles (SM), we compare the inclusive production of events containing a lepton, a photon, significant transverse momentum imbalance (MET), and a jet identified as containing a b-quark, to SM predictions. The search uses data produced in proton-antiproton collisions at 1.96 TeV corresponding to 1.9 fb-1 of integrated luminosity taken with the CDF detector at the Fermilab Tevatron. We find 28 lepton+photon+MET+b events versus an expectation of 31.0+4.1/-3.5 events. If we further require events to contain at least three jets and large total transverse energy, simulations predict that the largest SM source is top-quark pair production with an additional radiated photon, ttbar+photon. In the data we observe 16 ttbar+photon candidate events versus an expectation from SM sources of 11.2+2.3/-2.1. Assuming the difference between the observed number and the predicted non-top-quark total is due to SM top quark production, we estimate the ttg cross section to be 0.15 +- 0.08 pb.

Study of multi-muon events produced in p\bar{p} interactions at \sqrt{s}=1.96 TeV

We report the results of a study of multi-muon events produced at the Fermilab Tevatron collider and acquired with the CDF II detector using a dedicated dimuon trigger. The production cross section and kinematics of events in which both muon candidates are produced inside the beam pipe of radius 1.5 cm are successfully modeled by known processes which include heavy flavor production. In contrast, we are presently unable to fully account for the number and properties of the remaining events, in which at least one muon candidate is produced outside of the beam pipe, in terms of the same understanding of the CDF II detector, trigger, and event reconstruction.

Governance theory as a framework for empirical research : a case study on local environmental policy-making in Helsinki, Finland

Governance has been one of the most popular buzzwords in recent political science. As with any term shared by numerous fields of research, as well as everyday language, governance is encumbered by a jungle of definitions and applications. This work elaborates on the concept of network governance. Network governance refers to complex policy-making situations, where a variety of public and private actors collaborate in order to produce and define policy. Governance is processes of autonomous, self-organizing networks of organizations exchanging information and deliberating. Network governance is a theoretical concept that corresponds to an empirical phenomenon. Often, this phenomenon is used to descirbe a historical development: governance is often used to describe changes in political processes of Western societies since the 1980s. In this work, empirical governance networks are used as an organizing framework, and the concepts of autonomy, self-organization and network structure are developed as tools for empirical analysis of any complex decision-making process. This work develops this framework and explores the governance networks in the case of environmental policy-making in the City of Helsinki, Finland. The crafting of a local ecological sustainability programme required support and knowledge from all sectors of administration, a number of entrepreneurs and companies and the inhabitants of Helsinki. The policy process relied explicitly on networking, with public and private actors collaborating to design policy instruments. Communication between individual organizations led to the development of network structures and patterns. This research analyses these patterns and their effects on policy choice, by applying the methods of social network analysis. A variety of social network analysis methods are used to uncover different features of the networked process. Links between individual network positions, network subgroup structures and macro-level network patterns are compared to the types of organizations involved and final policy instruments chosen. By using governance concepts to depict a policy process, the work aims to assess whether they contribute to models of policy-making. The conclusion is that the governance literature sheds light on events that would otherwise go unnoticed, or whose conceptualization would remain atheoretical. The framework of network governance should be in the toolkit of the policy analyst.

Prosopis, an Alien among the Sacred Trees of South India

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

On the use of weather radar for mesoscale applications in northern conditions

Mesoscale weather phenomena, such as the sea breeze circulation or lake effect snow bands, are typically too large to be observed at one point, yet too small to be caught in a traditional network of weather stations. Hence, the weather radar is one of the best tools for observing, analyzing and understanding their behavior and development. A weather radar network is a complex system, which has many structural and technical features to be tuned, from the location of each radar to the number of pulses averaged in the signal processing. These design parameters have no universal optimal values, but their selection depends on the nature of the weather phenomena to be monitored as well as on the applications for which the data will be used. The priorities and critical values are different for forest fire forecasting, aviation weather service or the planning of snow ploughing, to name a few radar-based applications. The main objective of the work performed within this thesis has been to combine knowledge of technical properties of the radar systems and our understanding of weather conditions in order to produce better applications able to efficiently support decision making in service duties for modern society related to weather and safety in northern conditions. When a new application is developed, it must be tested against ground truth . Two new verification approaches for radar-based hail estimates are introduced in this thesis. For mesoscale applications, finding the representative reference can be challenging since these phenomena are by definition difficult to catch with surface observations. Hence, almost any valuable information, which can be distilled from unconventional data sources such as newspapers and holiday shots is welcome. However, as important as getting data is to obtain estimates of data quality, and to judge to what extent the two disparate information sources can be compared. The presented new applications do not rely on radar data alone, but ingest information from auxiliary sources such as temperature fields. The author concludes that in the future the radar will continue to be a key source of data and information especially when used together in an effective way with other meteorological data.

Markov random fields and spatial smoothing in improving of forest inventory estimates

Markov random fields (MRF) are popular in image processing applications to describe spatial dependencies between image units. Here, we take a look at the theory and the models of MRFs with an application to improve forest inventory estimates. Typically, autocorrelation between study units is a nuisance in statistical inference, but we take an advantage of the dependencies to smooth noisy measurements by borrowing information from the neighbouring units. We build a stochastic spatial model, which we estimate with a Markov chain Monte Carlo simulation method. The smooth values are validated against another data set increasing our confidence that the estimates are more accurate than the originals.

Luonnonhoitopellot maatalousympäristön luonnon monimuotoisuuden edistämisessä

Luonnonhoitopellot lisättiin uutena vapaaehtoisena toimenpiteenä maatalouden ympäristötukeen vuonna 2009. Luonnonhoitopeltoihin kuuluvat monivuotiset nurmipellot sekä niitty-, riista- ja maisemakasveilla kylvetyt pellot. Toimenpiteen avulla pyritään suojelemaan ja lisäämään maatalousympäristön luonnon monimuotoisuutta sekä muun muassa vähentämään maatalouden ravinnehuuhtoumia. Vuonna 2010 luonnonhoitopeltoja oli yli seitsemän prosenttia Suomen viljelyalasta. Luonnonhoitopeltojen ympäristövaikutusten arvioiminen ja toimenpiteen kehittäminen on tärkeää, jotta toimenpiteeseen käytettävät varat eivät valu hukkaan. Tämän tutkimuksen tavoitteena oli selvittää, millainen merkitys luonnonhoitopelloilla on maatalousympäristön monimuotoisuuden kannalta; millaiset luonnonhoitopellot ovat monimuotoisuuden kannalta arvokkaimpia; ja kuinka toimenpidettä kannattaa kehittää. Kysymyksiin pyrittiin vastaamaan tutkimalla putkilokasvilajistoa, -lajirikkautta ja kasvillisuuden rakennetta erilaisilla luonnonhoitopelloilla, sekä vertaamalla luonnonhoitopeltojen kasvillisuutta pientareiden ja niittyjen kasvillisuuteen. Maastotyö luonnonhoitopelloilla tehtiin kesällä 2010 Uudenmaan ja Pohjois-Pohjanmaan ELY-keskusalueilla. Lisäksi tutkimuslohkoista kerättiin tietoja viljelijäkyselyn kautta. Niittypellot osoittautuivat tutkimuksessa lajirikkaimmaksi luonnonhoitopeltotyypiksi, mikä selittynee lähinnä sillä, että ne kylvetään heikosti kilpailukykyisellä siemenseoksella. Nurmi- ja niittypelloilla lohkon viljavuus korreloi negatiivisesti lajirikkauden kanssa. Lajikoostumukseltaan kaikki luonnonhoitopellot eroavat toisistaan sekä maatalousympäristön puoliluonnontilaisista elinympäristöistä, ja lisäävät siten monimuotoisuutta maisematasolla. Luonnonhoitopeltojen lajisto ei ole kuitenkaan suojelun kannalta erityisen arvokasta. Toimenpiteen maatalousympäristöä rikastuttavaa vaikutusta vähentää, että tällä hetkellä valtaosa luonnonhoitopelloista on monivuotisia nurmipeltoja. Luonnonhoitopeltojen siemenseoksia kehittämällä, perustamis- ja hoitomenetelmiä tutkimalla ja neuvontaan panostamalla voidaan lisätä luonnonhoitopeltojen arvoa niin luonnon, viljelijän kuin yhteiskunnankin kannalta.

Plant communities of field margins : the effects of management and environmental factors on species composition and diversity

Agri-environmental schemes have so far resulted in only minor positive implications for the biodiversity of agricultural environments, in contrast to what has been expected. Land-use intensification has decreased landscape heterogeneity and the amount of semi-natural habitats. Field margins are uncultivated areas of permanent vegetation located adjacent to fields. Since the number of these habitats is high, investing in their quality may result in more diverse agricultural landscapes. Field margins can be considered as multifunctional habitats providing agronomic, environmental and wildlife services. This thesis aimed at examining the plant communities of different types of field margin habitats and the factors affecting their species diversity and composition. The importance of edaphic, spatial and management factors was studied on regional, landscape and habitat scales. Vegetation surveys were conducted on regional and landscape scales and a field experiment on cutting management was conducted on a habitat scale. In field margin plant communities, species appeared to be indicators of high or intermediate soil fertility and moist soil conditions. The plant species diversity found was rather low, compared with most species-rich agricultural habitats in Finland, such as dry meadows. Among regions, land-use history, main production line, natural species and human induced distribution, climate and edaphic factors were elements inducing differences in species composition. The lowest regional species diversity of field margins was related to intensive and long-term cereal production. Management by cutting and removal or grazing had a positive effect on plant species diversity. The positive effect of cutting and removal on species richness was also dependent on the adjacent source of colonizing species. Therefore, in species-poor habitats and landscapes, establishment of margins with diverse seed mixtures can be recommended for enhancing the development of species richness. However, seed mixtures should include only native species preferably local origin. Management by cutting once a year for 5 years did not result in a decline in dominance of a harmful weed species, Elymus repens, showing that E. repens probably needs cutting more frequently than once per year. Agri-environmental schemes should include long-term contracts with farmers for the establishment, and management by cutting and removal or grazing, of field margins that are several metres wide. In such schemes, the timing and frequency of management should be planned so as not to harm other taxa, such as the insects and birds that are dependent on these habitats. All accidental herbicide drifts to field margins should be avoided when spraying the cultivated area to minimize the negative effects of sprayings on vegetation. The harmful effects of herbicides can be avoided by organic farming methods.

Integration of miRNA and mRNA expression with DNA copy number of Ewing sarcoma cell lines

Ewing sarcoma is an aggressive and poorly differentiated malignancy of bone and soft tissue. It primarily affects children, adolescents, and young adults, with a slight male predominance. It is characterized by a translocation between chromosomes 11 and 22 resulting in the EWSR1-FLI1fusion transcription factor. The aim of this study is to identify putative Ewing sarcoma target genes through an integrative analysis of three microarray data sets. Array comparative genomic hybridization is used to measure changes in DNA copy number, and analyzed to detect common chromosomal aberrations. mRNA and miRNA microarrays are used to measure expression of protein-coding and miRNA genes, and these results integrated with the copy number data. Chromosomal aberrations typically contain also bystanders in addition to the driving tumor suppressor and oncogenes, and integration with expression helps to identify the true targets. Correlation between expression of miRNAs and their predicted target mRNAs is also evaluated to assess the results of post-transcriptional miRNA regulation on mRNA levels. The highest frequencies of copy number gains were identified in chromosome 8, 1q, and X. Losses were most frequent in 9p21.3, which also showed an enrichment of copy number breakpoints relative to the rest of the genome. Copy number losses in 9p21.3 were found have a statistically significant effect on the expression of MTAP, but not on CDKN2A, which is a known tumor-suppressor in the same locus. MTAP was also down-regulated in the Ewing sarcoma cell lines compared to mesenchymal stem cells. Genes exhibiting elevated expression in association with copy number gains and up-regulation compared to the reference samples included DCAF7, ENO2, MTCP1, andSTK40. Differentially expressed miRNAs were detected by comparing Ewing sarcoma cell lines against mesenchymal stem cells. 21 up-regulated and 32 down-regulated miRNAs were identified, includingmiR-145, which has been previously linked to Ewing sarcoma. The EWSR1-FLI1 fusion gene represses miR-145, which in turn targets FLI1 forming a mutually repressive feedback loop. In addition higher expression linked to copy number gains and compared to mesenchymal stem cells, STK40 was also found to be a target of four different miRNAs that were all down-regulated in Ewing sarcoma cell lines compared to the reference samples. SLCO5A1 was identified as the only up-regulated gene within a frequently gained region in chromosome 8. This region was gained in over 90 % of the cell lines, and also with a higher frequency than the neighboring regions. In addition, SLCO5A1 was found to be a target of three miRNAs that were down-regulated compared to the mesenchymal stem cells.

Sneutrino-antisneutrino oscillations at colliders

Modern elementary particle physics is based on quantum field theories. Currently, our understanding is that, on the one hand, the smallest structures of matter and, on the other hand, the composition of the universe are based on quantum field theories which present the observable phenomena by describing particles as vibrations of the fields. The Standard Model of particle physics is a quantum field theory describing the electromagnetic, weak, and strong interactions in terms of a gauge field theory. However, it is believed that the Standard Model describes physics properly only up to a certain energy scale. This scale cannot be much larger than the so-called electroweak scale, i.e., the masses of the gauge fields W^+- and Z^0. Beyond this scale, the Standard Model has to be modified. In this dissertation, supersymmetric theories are used to tackle the problems of the Standard Model. For example, the quadratic divergences, which plague the Higgs boson mass in the Standard model, cancel in supersymmetric theories. Experimental facts concerning the neutrino sector indicate that the lepton number is violated in Nature. On the other hand, the lepton number violating Majorana neutrino masses can induce sneutrino-antisneutrino oscillations in any supersymmetric model. In this dissertation, I present some viable signals for detecting the sneutrino-antisneutrino oscillation at colliders. At the e-gamma collider (at the International Linear Collider), the numbers of the electron-sneutrino-antisneutrino oscillation signal events are quite high, and the backgrounds are quite small. A similar study for the LHC shows that, even though there are several backrounds, the sneutrino-antisneutrino oscillations can be detected. A useful asymmetry observable is introduced and studied. Usually, the oscillation probability formula where the sneutrinos are produced at rest is used. However, here, we study a general oscillation probability. The Lorentz factor and the distance at which the measurement is made inside the detector can have effects, especially when the sneutrino decay width is very small. These effects are demonstrated for a certain scenario at the LHC.