Theorica Pantegni . Facsimile and Transcription of the Helsinki manuscript (Codex EÖ.II.14)

The Theorica Pantegni is a medieval medical textbook written in Latin. The author was Constantine the African (Constantinus Africanus), a monk of Tunisian origin. He compiled the work in the latter half of the eleventh century at the Benedictine monastery of Monte Cassino in Italy. - Manuscript Eö.II.14, containing the Theorica Pantegni published here, belongs today to the National Library of Finland. It can be dated to the third quarter of the twelfth century, which makes it one of the earliest surviving exemplars of the Theorica Pantegni: over seventy manuscripts of the work survive, of which about fifteen can be dated to the twelfth century. Manuscript Eö.II.14 is written in black ink on 210 parchment leaves (recto and verso), amounting to 420 pages, in pre-Gothic script. - The present text is a transcription of Ms Eö.II.14. The goal is to provide the reader with an accessible text that is faithful to the original.

NADPH-Dependent Thioredoxin System In Regulation of Chloroplast Functions

Photosynthesis, the process in which carbon dioxide is converted into sugars using the energy of sunlight, is vital for heterotrophic life on Earth. In plants, photosynthesis takes place in specific organelles called chloroplasts. During chloroplast biogenesis, light is a prerequisite for the development of functional photosynthetic structures. In addition to photosynthesis, a number of other metabolic processes such as nitrogen assimilation, the biosynthesis of fatty acids, amino acids, vitamins, and hormones are localized to plant chloroplasts. The biosynthetic pathways in chloroplasts are tightly regulated, and especially the reduction/oxidation (redox) signals play important roles in controlling many developmental and metabolic processes in chloroplasts. Thioredoxins are universal regulatory proteins that mediate redox signals in chloroplasts. They are able to modify the structure and function of their target proteins by reduction of disulfide bonds. Oxidized thioredoxins are restored via the action of thioredoxin reductases. Two thioredoxin reductase systems exist in plant chloroplasts, the NADPHdependent thioredoxin reductase C (NTRC) and ferredoxin-thioredoxin reductase (FTR). The ferredoxin-thioredoxin system that is linked to photosynthetic light reactions is involved in light-activation of chloroplast proteins. NADPH can be produced via both the photosynthetic electron transfer reactions in light, and in darkness via the pentose phosphate pathway. These different pathways of NADPH production enable the regulation of diverse metabolic pathways in chloroplasts by the NADPH-dependent thioredoxin system. In this thesis, the role of NADPH-dependent thioredoxin system in the redox-control of chloroplast development and metabolism was studied by characterization of Arabidopsis thaliana T-DNA insertion lines of NTRC gene (ntrc) and by identification of chloroplast proteins regulated by NTRC. The ntrc plants showed the strongest visible phenotypes when grown under short 8-h photoperiod. This indicates that i) chloroplast NADPH-dependent thioredoxin system is non-redundant to ferredoxinthioredoxin system and that ii) NTRC particularly controls the chloroplast processes that are easily imbalanced in daily light/dark rhythms with short day and long night. I identified four processes and the redox-regulated proteins therein that are potentially regulated by NTRC; i) chloroplast development, ii) starch biosynthesis, iii) aromatic amino acid biosynthesis and iv) detoxification of H₂O₂. Such regulation can be achieved directly by modulating the redox state of intramolecular or intermolecular disulfide bridges of enzymes, or by protecting enzymes from oxidation in conjunction with 2-cysteine peroxiredoxins. This thesis work also demonstrated that the enzymatic antioxidant systems in chloroplasts, ascorbate peroxidases, superoxide dismutase and NTRC-dependent 2-cysteine peroxiredoxins are tightly linked up to prevent the detrimental accumulation of reactive oxygen species in plants.

Novel CO2 Regulated Proteins in Synechocystis PCC 6803

The large biodiversity of cyanobacteria together with the increasing genomics and proteomics metadata provide novel information for finding new commercially valuable metabolites. With the advent of global warming, there is growing interest in the processes that results in efficient CO2 capture through the use of photosynthetic microorganisms such as cyanobacteria. This requires a detailed knowledge of how cyanobacteria respond to the ambient CO2. My study was aimed at understanding the changes in the protein profile of the model organism, Synechocystis PCC 6803 towards the varying CO₂ level. In order to achieve this goal I have employed modern proteomics tools such as iTRAQ and DIGE, recombinant DNA techniques to construct different mutants in cyanobacteria and biophysical methods to study the photosynthetic properties. The proteomics study revealed several novel proteins, apart from the well characterized proteins involved in carbon concentrating mechanisms (CCMs), that were upregulated upon shift of the cells from high CO₂ concentration (3%) to that in air level (0.039%). The unknown proteins, Slr0006 and flavodiiron proteins (FDPs) Sll0217-Flv4 and Sll0219-Flv2, were selected for further characterization. Although slr0006 was substantially upregulated under C_i limiting conditions, inactivation of the gene did not result in any visual phenotype under various environmental conditions indicating that this protein is not essential for cell survival. However, quantitative proteomics showed the induction of novel plasmid and chromosome encoded proteins in deltaslr0006 under air level CO₂ conditions. The expression of the slr0006 gene was found to be strictly dependent on active photosynthetic electron transfer. Slr0006 contains conserved dsRNA binding domain that belongs to the Sua5/YrdC/YciO protein family. Structural modelling of Slr0006 showed an alpha/beta twisted open-sheet structure and a positively charged cavity, indicating a possible binding site for RNA. The 3D model and the co-localization of Slr0006 with ribosomal subunits suggest that it might play a role in translation or ribosome biogenesis. On the other hand, deletions in the sll0217-sll218- sll0219 operon resulted in enhanced photodamage of PSII and distorted energy transfer from phycobilisome (PBS) to PSII, suggesting a dynamic photoprotection role of the operon. Constructed homology models also suggest efficient electron transfer in heterodimeric Flv2/Flv4, apparently involved in PSII photoprotection. Both Slr0006 and FDPs exhibited several common features, including negative regulation by NdhR and ambiguous cellular localization when subjected to different concentrations of divalent ions. This strong association with the membranes remained undisturbed even in the presence of detergent or high salt. My finding brings ample information on three novel proteins and their functions towards carbon limitation. Nevertheless, many pathways and related proteins remain unexplored. The comprehensive understanding of the acclimation processes in cyanobacteria towards varying environmental CO₂ levels will help to uncover adaptive mechanisms in other organisms, including higher plants.

Mapping the translation needs and practices in development co-operation projects of NGOs

Tämän pro gradu -tutkielman aiheena on kääntäminen ja viestintä vieraalla kielellä Suomen ulkoasiainministeriön rahoittamissa kansalaisjärjestöjen kehitysyhteistyöhankkeissa. Tutkielman on tarkoitus kartoittaa kyseisten kehitysyhteistyöhankkeiden kääntämiseen ja vieraskieliseen viestintään liittyviä tarpeita ja -käytäntöjä. Aihetta ei ole tutkittu laajasti muutoin, joten empiirinen osuus on erityisen merkittävässä roolissa. Tutkielman alussa esitellään ulkoasiainministeriön laatimia suomalaisten kansalaisjärjestöjen kehitysyhteistyöhankkeiden ehtoja ja ohjeita, jotka ovat kyseiselle tutkimukselle olennaisia. Tutkielman teoreettinen osuus koostuu lähinnä metodologisesta pohdinnasta, koska aiempaa tutkimustietoa on vähän. Tutkimusmetodien analysointia on painotettu myös siksi, että empiirisellä osuudella on niin suuri merkitys. Tutkielman empiirinen aineisto on yhtäältä peräisin tutkijan havainnoista, jotka saatiin omia varhaisempia hankehallinnointikokemuksia hyödyntäen sekä osallistuvan havainnoinnin menetelmää käyttäen kahden opiskelijajärjestön kehitysyhteistyöhankkeista vuosien 2009 ja 2012 välisenä aikana. Toisaalta aineisto on kerätty kyselytutkimuksen vastauksista. Kysely lähetettiin 35 suomalaiselle kansalaisjärjestölle, joiden kehitysyhteistyöhankkeita Suomen ulkoasiainministeriö rahoittaa. Järjestöt valittiin satunnaisotannalla. Empiirisen aineiston analyysistä ilmeni muun muassa, että tutkijan alkuperäinen hypoteesi kehitysyhteistyöhön liittyvien tekstien kääntämisen yleisyydestä pitää osittain paikkansa, vaikka tekstejä käännettiinkin kansalaisjärjestöissä vähemmän kuin tutkija odotti. Tutkimusaineisto ei ole kuitenkaan tarpeeksi laaja, jotta tuloksia voitaisiin yleistää, sillä kansalaisjärjestöt, niiden hankkeet, käännöstarpeet ja asiantuntemus osoittautuivat odotetusti hyvin erilaisiksi. Tulokset sisältävät asiaa myös esimerkiksi järjestöissä kääntävien ja vieraalla kielellä viestivien taustoista. Jatkotutkimukset ovat kuitenkin tarpeen, ja mahdollisia tutkimusaiheita on runsaasti.

The pH-dependent phase distribution of wood pitch components in papermaking processes

Wood contains only a very small amount of lipophilic extractives, commonly known as wood pitch. The pitch is known to cause severe problems in papermaking processes. The amount of pitch in process waters can be decreased by seasoning of the raw material prior to pulping, pulp washing, removal of pitch by flotation, adsorption of pitch onto various mineral surfaces, and retention of pitch to the fibre material by cationic polymers. The aim of this study was to determine the influence of pH on some of the methods used for pitch control. Experiments were performed using laboratory-made wood pitch emulsions with varying pH, salt concentration, hemicellulose concentration and pitch composition. These emulsions were used to study the phase distribution of resin and fatty acids, the colloidal stability of pitch with and without steric stabilisation by galactoglucomannans, and the interactions between wood pitch and mineral particles. Purification of unbleached and peroxidebleached mill process water was performed by froth flotation in combination with a foaming agent. The distribution of resin and fatty acids (RFAs) between colloidal pitch droplets and the water phase was very dependent on pH. At pH 3, almost all of the RFAs were attached to the pitch droplets, while increasing the pH led to increasing concentration of dissolved RFAs in the water phase. The presence of salt shifted the release of RFAs towards higher pH, while lower ratio of neutral pitch in the emulsion resulted in release of RFAs at lower pH. It was also seen that the dissolution and adsorption of RFAs at sudden pHchanges takes place very quickly. Colloidal pitch was more stable against electrolyte-induced aggregation at higher pH, due to its higher anionic charge. The concentration of cationic polymers needed to aggregate colloidal pitch also increased with increasing pH. The surface characteristics of solid particles, such as amount of charged groups, were very important for understanding their interactions with colloidal wood pitch. Water-soluble galactoglucomannans stabilised the colloidal pitch sterically against aggregation, but could not completely prevent interactions between wood pitch and hydrophilic particles. Froth flotation of unbleached and peroxidebleached process water showed that the pitch could be removed more effectively and selectively at low pH, compared to at neutral pH. The pitch was removed more effectively, using lower concentrations of foaming agent, from peroxide-bleached water than from unbleached water. The results show that pH has a major impact on various pulping and papermaking processes. It determines the anionic charge of the colloidal pitch and the solubility of certain pitch components. Because of this, the pH influences the effectiveness of pitch retention and removal of pitch. The results indicate that pitch problems could be diminished by acknowledging the importance of pH in various papermaking processes.

Nucleotides as Antiviral Compounds. On the Feasibility of an Esterase-dependent Prodrug Strategy for 2-5A

Nukleotidien ja oligonukleotidien analogeilla on merkittävä rooli virusten aiheuttamien tautien hoidossa. Tämän kaltaiset yhdisteet voivat estää spesifisesti virusten proteiineja tai aktivoida luontaista immuunijärjestelmää, jossa 2-5A:ksi kutsutut lyhyet 2´,5´-sitoutuneet oligomeerit ovat keskeisiä tekijöitä. Nukleotideihin ja oligonukleotideihin pohjautuvien lääkkeiden tehokkuus riippuu pääasiassa aihiolääkestrategiasta, jolla niiden sisäänottoa soluun tehostetaan. Tavanomaisessa aihiolääkestrategiassa negatiivisesti varautuneet fosfaattiryhmät suojataan rasvaliukoisilla biohajoavilla suojaryhmillä, jotta molekyyli läpäisee solukalvon helpommin. Solun sisällä aihiolääke muuttuu aktiiviseksi lääkeaineeksi, kun suojaryhmät irtoavat solun entsyymien, kuten esteraasien vaikutuksesta. Väitöskirjassa arvioitiin esteraasin katalysoiman aihiolääkestrategian soveltuvuutta 2-5A-trimeerille syntetisoimalla kaksi erilaista 2-5A-aihiolääkekandidaattia ja tutkimalla 2-5A:n purkautumista karboksiesteraasi-entsyymin vaikutuksesta. Suojaryhmäsuunnitelma perustui esteraasilabiileihin 2,2-disubstituoituihin asyylioksipropyyliryhmiin ja asyylioksimetyyliryhmiin, joilla suojattiin trimeerien fosfaatti- ja 3´-hydroksyyliryhmät. Tulokset osoittivat, että esteraasilabiilien suojaryhmien irtoaminen 2-5A:sta hidastui merkittävästi, kun yhdisteeseen kertyi negatiivista varausta. Lisäksi suojaryhmien hajotessa muodostui elektrofiilisiä alkyloivia aineita, jotka ovat mahdollisesti toksisia. Näistä syistä johtuen kehitettiin kuusi uudenlaista 2,2,-disubstituoitua 4-asyylitio- 3-oksobutyyliryhmää fosfodiestereiden suojaamiseksi. Suojaryhmät irtoavat sekä esteraasin katalysoimana, että lämpötilan vaikutuksesta. Tämä on hyödyllinen ominaisuus silloin, kun entsyymin affiniteetti negatiivisesti varattuun substraattiin heikkenee. Suojaryhmien hydrolyyttinen ja entsymaattinen stabiilisuus on helposti säädeltävissä, jotta suojauksen purkautumisen nopeus voidaan optimoida. Vapautuneet suojaryhmät eivät ole merkittävästi alkyloivia, sillä niiden ei havaittu alkyloivan glutationia.