Alternative electron transfer routes involved in photoprotection of cyanobacteria

In oxygenic photosynthesis, the highly oxidizing reactions of water splitting produce reactive oxygen species (ROS) and other radicals that could damage the photosynthetic apparatus and affect cell viability. Under particular environmental conditions, more electrons are produced in water oxidation than can be harmlessly used by photochemical processes for the reduction of metabolic electron sinks. In these circumstances, the excess of electrons can be delivered, for instance, to O2, resulting in the production of ROS. To prevent detrimental reactions, a diversified assortment of photoprotection mechanisms has evolved in oxygenic photosynthetic organisms. In this thesis, I focus on the role of alternative electron transfer routes in photoprotection of the cyanobacterium Synechocystis sp. PCC 6803. Firstly, I discovered a novel subunit of the NDH-1 complex, NdhS, which is necessary for cyclic electron transfer around Photosystem I, and provides tolerance to high light intensities. Cyclic electron transfer is important in modulating the ATP/NADPH ratio under stressful environmental conditions. The NdhS subunit is conserved in many oxygenic phototrophs, such as cyanobacteria and higher plants. NdhS has been shown to link linear electron transfer to cyclic electron transfer by forming a bridge for electrons accumulating in the Ferredoxin pool to reach the NDH-1 complexes. Secondly, I thoroughly investigated the role of the entire flv4-2 operon in the photoprotection of Photosystem II under air level CO2 conditions and varying light intensities. The operon encodes three proteins: two flavodiiron proteins Flv2 and Flv4 and a small Sll0218 protein. Flv2 and Flv4 are involved in a novel electron transport pathway diverting electrons from the QB pocket of Photosystem II to electron acceptors, which still remain unknown. In my work, it is shown that the flv4-2 operon-encoded proteins safeguard Photosystem II activity by sequestering electrons and maintaining the oxidized state of the PQ pool. Further, Flv2/Flv4 was shown to boost Photosystem II activity by accelerating forward electron flow, triggered by an increased redox potential of QB. The Sll0218 protein was shown to be differentially regulated as compared to Flv2 and Flv4. Sll0218 appeared to be essential for Photosystem II accumulation and was assigned a stabilizing role for Photosystem II assembly/repair. It was also shown to be responsible for optimized light-harvesting. Thus, Sll0218 and Flv2/Flv4 cooperate to protect and enhance Photosystem II activity. Sll0218 ensures an increased number of active Photosystem II centers that efficiently capture light energy from antennae, whilst the Flv2/Flv4 heterodimer provides a higher electron sink availability, in turn, promoting a safer and enhanced activity of Photosystem II. This intertwined function was shown to result in lowered singlet oxygen production. The flv4-2 operon-encoded photoprotective mechanism disperses excess excitation pressure in a complimentary manner with the Orange Carotenoid Protein-mediated non-photochemical quenching. Bioinformatics analyses provided evidence for the loss of the flv4-2 operon in the genomes of cyanobacteria that have developed a stress inducible D1 form. However, the occurrence of various mechanisms, which dissipate excitation pressure at the acceptor side of Photosystem II was revealed in evolutionarily distant clades of organisms, i.e. cyanobacteria, algae and plants.

From protein structure to function with bioinformatics

It has long been known that amino acids are the building blocks for proteins and govern their folding into specific three-dimensional structures. However, the details of this process are still unknown and represent one of the main problems in structural bioinformatics, which is a highly active research area with the focus on the prediction of three-dimensional structure and its relationship to protein function. The protein structure prediction procedure encompasses several different steps from searches and analyses of sequences and structures, through sequence alignment to the creation of the structural model. Careful evaluation and analysis ultimately results in a hypothetical structure, which can be used to study biological phenomena in, for example, research at the molecular level, biotechnology and especially in drug discovery and development. In this thesis, the structures of five proteins were modeled with templatebased methods, which use proteins with known structures (templates) to model related or structurally similar proteins. The resulting models were an important asset for the interpretation and explanation of biological phenomena, such as amino acids and interaction networks that are essential for the function and/or ligand specificity of the studied proteins. The five proteins represent different case studies with their own challenges like varying template availability, which resulted in a different structure prediction process. This thesis presents the techniques and considerations, which should be taken into account in the modeling procedure to overcome limitations and produce a hypothetical and reliable three-dimensional structure. As each project shows, the reliability is highly dependent on the extensive incorporation of experimental data or known literature and, although experimental verification of in silico results is always desirable to increase the reliability, the presented projects show that also the experimental studies can greatly benefit from structural models. With the help of in silico studies, the experiments can be targeted and precisely designed, thereby saving both money and time. As the programs used in structural bioinformatics are constantly improved and the range of templates increases through structural genomics efforts, the mutual benefits between in silico and experimental studies become even more prominent. Hence, reliable models for protein three-dimensional structures achieved through careful planning and thoughtful executions are, and will continue to be, valuable and indispensable sources for structural information to be combined with functional data.

Cost-plus-loss analyses of forest inventory strategies based on kNN-assigned reference sample plot data

Abstract

APROS code benchmarking inboiling water reactor accident analyses

Diplomityö käsittelee kiehutusvesilaitosten transienttien ja onnettomuuksien analysointia APROS-ohjelmiston avulla. Työ on tehty Teollisuuden Voima Oy:n (TVO) Olkiluoto 1 ja 2 laitosyksiköiden mallin pohjalta. Raportissa esitetään ohjelmiston käyttämiä yhtälöitäja laskentamalleja yleisellä tasolla. Työssä esitellään laitoksen yleispiirteet turvallisuustoimintoineen ja kuvataan ohjelmaan suureksi osaksi aiemmin luotua laskentamallia. Työssä on luetteloitu voimassa olevatlisensiointianalyysit, joiden joukosta on valittu laskentatapauksia ohjelmiston suorituskyvyn arviointia varten. Lisäksi työhön on valittu laskentatapauksia muilla kuin lisensointiin käytetyillä ohjelmilla lasketuista analyyseistä. Lisäksi on suoritettu vertailulaskuja konservatiivisen ja realistisen mallin erojen esille saamiseksi. Laskentatapauksia ovat mm. ylipainetransientti, jäähdytteen menetysonnettomuus ja oletettavissa oleva käyttöhäiriö, jossa pikasulku ei toimi (ATWS). Diplomityön edetessä laitosmallia on kehitetty edelleen lisäämällä joitakin järjestelmiä ja tarkentamalla joidenkin komponenttien kuvausta. Työssä ilmeni, että APROS soveltuu jäähdytteenmenetysonnettomuuden ja suojarakennuksen yhtäaikaiseen analyysiin. APROS.n vaste nopeisiin transientteihin jäi kuitenkin vertailutasosta. Tämän työn perusteella APROS-mallia kehitys jatkuu edelleen siten, että se soveltuisi entistä paremmin myös nopeiden transienttien ja ATWS-tilanteiden kuvaamiseen. Työssä olevaa lisensointianalyysien kuvausta tullaan käyttämään hyväksi selvitettäessä laitoksen turvallisuuden väliarviossa tarvittavien analyysien määrää ja laatua. Nyt saatuja kokemuksia voidaan hyödyntää myös mahdollisen kolmiulotteisen sydänmallin hankinnassa APROS-ohjelmistoon. Tässä diplomityössä esitettyjä parannuksia voidaan käyttää hyväksi SAFIRtutkimusohjelman hankkeiden suunnittelussa.

Ecological and Epidemiological Analyses of Multiple Sclerosis Relapse Rate

The underlying cause of many human autoimmune diseases is unknown, but several environmental factors are implicated in triggering the self-destructive immune reactions. Multiple Sclerosis (MS) is a chronic autoimmune disease of the central nervous system, potentially leading to persistent neurological deterioration. The cause of MS is not known, and apart from immunomodulatory treatments there is no cure. In the early phase of the disease, relapsing-remitting MS (RR-MS) is characterized by unpredictable exacerbations of the neurological symptoms called relapses, which can occur at different intervals ranging from 4 weeks to several years. Microbial infections are known to be able to trigger MS relapses, and the patients are instructed to avoid all factors that might increase the risk of infections and to properly use antibiotics as well as to take care of dental hygiene. Among those environmental factors which are known to increase susceptibility to infections, high ambient air inhalable particulate matter levels affect all people within a geographical region. During the period of interest in this thesis, the occurrence of MS relapses could be effectively reduced by injections of interferon, which has immunomodulatory and antiviral properties. In this thesis, ecological and epidemiological analyses were used to study the possible connection between MS relapse occurrence, population level viral infections and air quality factors, as well as the effects of interferon medication. Hospital archive data were collected retrospectively from 1986-2001, a period in time ranging from when interferon medication first became available until just before other disease-modifying MS therapies arrived on the market. The grouped data were studied with logistic regression and intervention analysis, and individual patient data with survival analysis. Interferons proved to be effective in the treatment of MS in this observational study, as the amount of MS exacerbations was lower during interferon use as compared to the time before interferon treatment. A statistically significant temporal relationship between MS relapses and inhalable particular matter (PM₁₀) concentrations was found in this study, which implies that MS patients are affected by the exposure to PM₁₀. Interferon probably protected against the effect of PM₁₀, because a significant increase in the risk of exacerbations was only observed in MS patients without interferon medication following environmental exposure to population level specific viral infections and PM₁₀. Apart from being antiviral, interferon could thus also attenuate the enhancement of immune reactions caused by ambient air PM₁₀. The retrospective approach utilizing carefully constructed hospital records proved to be an economical and reliable source of MS disease information for statistical analyses.

Characterization of novel genes predominantly expressed in the epididymis – from genome analyses to genetically modified mice

In mammals, post-testicular sperm maturation taking place in the epididymis is required for the spermatozoa to acquire the abilities required to fertilize the egg in vivo. The epididymal epithelial cells secrete proteins and other small molecules into the lumen, where they interact with the spermatozoa and enable necessary maturational changes. In this study different in silico, in vitro and in vivo approaches were utilized in order to find novel genes responsible for the function of the epididymis and post-testicular sperm maturation in the mouse. Available online genomic databases were analyzed to identify genes potentially expressed in the epididymis, gene expression profiling was performed by studying their expression in different mouse tissues, and significance of certain genes to fertility was assessed by generating genetically modified mouse models. A recently discovered Pate (prostate and testis expression) gene family was found to be predominantly expressed in the epididymis. It represents one of the largest known gene families expressed in the epididymis, and the members code for proteins potentially involved in defense against microorganisms. Through genetically modified mouse models CRISP4 (cysteine-rich secretory protein 4) was identified to regulate sperm acrosome reaction, and BMYC to inhibit the expression of the Myc proto-oncogene in the developing testis. A mouse line expressing iCre recombinase specifically in the epididymis was also generated. This model can be used to generate conditional, epididymis-specific knock-out models, and will be a valuable tool in fertility studies.

18F-Labeled Presynaptic Dopaminergic Tracers. Synthesis, Radiochemical Analyses, and Preclinical Evaluation of [18F]FDOPA and [18F]CFT

Dysfunction of the dopaminergic system in brain is involved in several pathological conditions such as Parkinson’s disease and depression. 2β-Carbomethoxy-3β-(4-[18F] fluorophenyl)tropane ([18F]CFT) and 6-[18F]fluoro-L-dopa ([18F]FDOPA) are tracers for imaging the dopaminergic function with positron emission tomography (PET). Peripheral uptake of [18F]FDOPA is also used in the localization and diagnosis of neuroendocrine tumors. [18F]FDOPA and [18F]CFT can be synthesized by electrophilic fluorodestannylation. However, the specific radioactivity (SA) in the electrophilic fluorination is low with traditional synthetic methods. In this study, [18F]FDOPA and [18F]CFT were synthesized using post-target-produced [18F]F2 as an electrophilic fluorination agent. With this method, tracers are produced with sufficient SA for neuroreceptor studies. Specific aims in this study were to replace Freon-11 in the production of [18F]FDOPA due to the ozone depleting properties of this solvent, to determine pharmacological specificity and selectivity of [18F]CFT with respect to monoamine transporters, and to compare the ability of these tracers to reflect the degree of nigral neuronal loss in rats in which the dopaminergic system in the brain had been unilaterally destroyed by 6- OHDA. Post-target-produced [18F]F2 was successfully used in the production of [18F]FDOPA and [18F]CFT. The SA achieved was substantially higher than in previous synthetic methods. Deuterated compounds, CD2Cl2, CDCl3 and C3D6O, were found to be suitable solvents for replacing Freon-11. Both [18F]FDOPA and [18F]CFT demonstrated nigrostriatal dopaminergic hypofunction and correlated with the number of nigral dopaminergic neurons in the 6-OHDA lesioned rat. However, the dopamine transporter (DAT) tracer [18F]CFT was more sensitive than the dopamine synthesis tracer [18F]FDOPA in detecting these defects because of the higher non-specific uptake of [18F]FDOPA. [18F]CFT can also be used for imaging the norepinephrine transporter (NET) because of the specific uptake into the locus coeruleus. The observation that [18F]CFT exhibits specific uptake in the pancreas warrants further studies in humans with respect to potential utility in pancreatic imaging

Analyses of the usefulness of Software Defined Storage Solutions for Web-based Digital Preservation Applications

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014