Life without Phd? – Phd Oxygen Sensor Proteins in Hypoxic Carcinoma Cell Survival

The microenvironment within the tumor plays a central role in cellular signaling. Rapidly proliferating cancer cells need building blocks for structures as well as nutrients and oxygen for energy production. In normal tissue, the vasculature effectively transports oxygen, nutrient and waste products, and maintains physiological pH. Within a tumor however, the vasculature is rarely sufficient for the needs of tumor cells. This causes the tumor to suffer from lack of oxygen (hypoxia) and nutrients as well as acidification, as the glycolytic end product lactate is accumulated. Cancer cells harbor mutations enabling survival in the rough microenvironment. One of the best characterized mutations is the inactivation of the von Hippel-Lindau protein (pVHL) in clear cell renal cell carcinoma (ccRCC). Inactivation causes constitutive activation of hypoxia-inducible factor HIF which is an important survival factor regulating glycolysis, neovascularization and apoptosis. HIFs are normally regulated by HIF prolyl hydroxylases (PHDs), which in the presence of oxygen target HIF α-subunit to ubiquitination by pVHL and degradation by proteasomes. In my thesis work, I studied the role of PHDs in the survival of carcinoma cells in hypoxia. My work revealed an essential role of PHD1 and PHD3 in cell cycle regulation through two cyclin-dependent kinase inhibitors (CKIs) p21 and p27. Depletion of PHD1 or PHD3 caused a cell cycle arrest and subjected the carcinoma cells to stress and impaired the survival.

Hiokkeen laatuvaihteluja aiheuttavat tekijät ja vaihteluiden vaimentamismahdollisuudet

Myllykoski Paper Oy:n hiokkeen laadussa ja prosessivesien ominaisuuksissa tapahtuu vaihtelua ajan suhteen. Tämä käy ilmi useiden vuosien aikana kerätyistä laatuseurantatiedoista. Diplomityön tavoitteena oli selvittää hiokkeen ja kierto-vesien laatuun vaikuttavat tekijät ja kehittää laadunvaihtelua hillitseviä toimenpi-teitä. Työn kirjallisuusosassa pyrittiin löytämään tekijöitä, jotka voivat aiheuttaa valmiin hiokkeen laatuun vaihtelua. Lähtökohtaisesti laatuvaihteluita aiheuttavat tekijät jaettiin raaka-aine- tai prosessivaihteluksi. Työn kokeellisessa osassa selvitettiin eri hioke- ja prosessivesiominaisuuksien kehittymistä tarkastelemalla eri mittaussuureista kerättyjä aineistoja erilaisin aika-välein. Aluksi tarkasteltiin hiokkeen ja vesien ominaisuuksia viiden vuoden ajan-jaksolla, josta siirryttiin tarkastelemaan lyhyempiä aikavälejä. Käytetty mittausaineisto oli peräisin DW-tietovarastosta ja PHD-reaaliaikatietokannasta. Työn tuloksista kävi muun muassa ilmi, että painehiokkeen lujuusominaisuudet ovat hienoisesti alentuneet viimeisen viiden vuoden aikana. Muutos selittyy hiokkeen pitkäkuituosuuden ja kuitupuun keskimääräisen läpimitan alenemisella. Lisäksi valkaisemattomien hiokkeiden vaaleudet ovat alentuneet samallakun prosessivedet ovat muuttuneet likaisemmiksi. Kehitykseen on vaikuttanut vesikiertojen kasvanut sulkemisaste ja uusi peroksidivalkaisulaitos. Jatkotoimenpide-ehdotukset painottuvat pääosin vesiajotilanteiden hallintaan. Vesiajoaiheuttaa aina suuria muutoksia niin hiokkeen kuin myös kiertovesien laatuun.

Molluscan radiations and landscape evolution in Miocene Amazonia

This PhD study aims to exploit the rich archive provided by the Miocene mollusc fauna of the Pebas Formation and other inland Miocene Amazonian formations to reconstruct landscape evolution and biotic development in lowland Amazonia during the Neogene. Over 160 samples from more than 70 Pebas Formation outcrops mostly collected by the author were processed for this study. Additional samples were collected in Andean areas of Colombia and Venezuela and further material from other northwestern South American basins was studied in museums. Pebas Formation samples and well log data made available by Occidental Peru from three wells in the Marañon Basin in Peru were also investigated. During this study four genera and 74 species from the Pebas Formation have been described and a further 13 species have been introduced in open nomenclature, and several species were reported for the first time. The number of mollusc species attributed to the Pebas fauna has increased from around 50 to 156. The Pebas fauna is characterised as aquatic, endemic and extinct, and is a typical representative of a long-lived lake fauna. Fluvial taxa are not common, (marginal) marine taxa are rare. An additional molluscan fauna from the Miocene Solimões Formation of Brazil, containing 13 fresh water species was also described. The newly documented fauna was used to improve biostratigraphic framework of Miocene Amazonian deposits. Twelve mollusc zones were introduced, the upper eleven of which cover a time interval of approximately seven million years covered previously by only three pollen zones. An age model calculated for the borehole data indicates that the Pebas Formation was deposited between c. 24 and 11 Ma. The areal distribution of the outcropping mollusc zones uncovered a broad dome structure, termed here the Iquitos-Araracuara anteclise in the study area. The structure appears to have influenced river courses and also contributed to edaphic heterogeneity that may have been in part responsible for the current high biodiversity in the study area. The Pebas system was a huge system (> one million km2) dominated by relatively shallow lakes, but also containing swamps and rivers. The system was fed by rivers draining the emergent Andes in the west and lowlands and cratons to the east. The Pebas system was located at sea level and was open to marine settings through a northern portal running through the Llanos Basin and East Venezuela Basin towards the Caribbean. Cyclical baselevel changes possibly related to Mylankhovitch cycles, have been documented in depositional sequences of the Pebas Formation. The composition of the Pebasian mollusc fauna implies that the system was mostly a fresh water system. Such an interpretation is matched by strontium isotope ratios as well as very negative δ18O ratios found in the shells, but is at odds with oligohaline and mesohaline ichnofacies found in the same strata. The mollusc fauna of the Pebas Formation diversified through most of the existence of the lake system. The diversification was mostly the result of in-situ cladogenesis. The success of some of the Pebasian endemic clades is explained by adaptation to fresh water, low oxygen, common unconsolidated lake bottoms (soup grounds) as well as high predation intensity. Maximum diversity was reached at the base of the late Middle to early Late Miocene Grimsdalea pollen zone, some 13 Ma. At the time some 85 species co-occurred, 67 of which are considered as Pebasian endemics. A subsequent drop in species richness coincides with indications of elevated salinities, although a causal relation still needs to be established. Apparently the Pebas fauna went (almost) entirely extinct with the replacement of the lake system into a fluvio-tidal system during the Early Late Miocene, some 11 Ma.

The Detector Control Systems for the CMS Resistive Plate Chamber at LHC

The RPC Detector Control System (RCS) is the main subject of this PhD work. The project, involving the Lappeenranta University of Technology, the Warsaw University and INFN of Naples, is aimed to integrate the different subsystems for the RPC detector and its trigger chain in order to develop a common framework to control and monitoring the different parts. In this project, I have been strongly involved during the last three years on the hardware and software development, construction and commissioning as main responsible and coordinator. The CMS Resistive Plate Chambers (RPC) system consists of 912 double-gap chambers at its start-up in middle of 2008. A continuous control and monitoring of the detector, the trigger and all the ancillary sub-systems (high voltages, low voltages, environmental, gas, and cooling), is required to achieve the operational stability and reliability of a so large and complex detector and trigger system. Role of the RPC Detector Control System is to monitor the detector conditions and performance, control and monitor all subsystems related to RPC and their electronics and store all the information in a dedicated database, called Condition DB. Therefore the RPC DCS system has to assure the safe and correct operation of the sub-detectors during all CMS life time (more than 10 year), detect abnormal and harmful situations and take protective and automatic actions to minimize consequential damages. The analysis of the requirements and project challenges, the architecture design and its development as well as the calibration and commissioning phases represent themain tasks of the work developed for this PhD thesis. Different technologies, middleware and solutions has been studied and adopted in the design and development of the different components and a big challenging consisted in the integration of these different parts each other and in the general CMS control system and data acquisition framework. Therefore, the RCS installation and commissioning phase as well as its performance and the first results, obtained during the last three years CMS cosmic runs, will be

Conversioni al cattolicesimo a Roma tra Sei e Settecento. La presenza degli scandinavi nell’Ospizio dei Convertendi.

In my PhD dissertation, I have examined a group of people of Scandinavian origin received by Ospizio dei Convertendi. This group has been hitherto largely unknown to historical research. The Ospizio was an institute founded by the Oratorian Congregation in Rome in 1673 to provide religious instruction and material aid to both recent and aspirant converts to Roman Catholicism. My research traces the profile of converts and a typology of motives, examining different factors which influenced the conversion process. I show that the key factors were often of a social rather than a religious nature. Moreover, I have analyzed the hospice in the context of Counter-Reformation charity as well. In terms of numbers, the Scandinavians formed a somewhat marginal yet not insignificant group within the Roman hospice. Out of a total of 2203 guests received between 1673 and 1706, 4.6 % were Scandinavians: 74 Swedes (including Finland and Livonia) and 27 Danes (including Norway). They came from a rigorously Protestant region which reacted to Catholicism with severe legislative measures. Converts to Catholicism risked confiscation of their goods, expulsion or even capital punishment. Since both Sweden and Denmark were practically impenetrable to Catholicism at the time and clandestine missionary attempts often failed before they had even properly started, the Roman Catholic Church shifted its interest towards Northerners arriving in Rome, a preferred destination for young noblemen, artists and migrant craftsmen. The material related to Ospizio dei Convertendi, conserved in the Vatican archives, is a scarcely known yet unusually rich source, not only for the religious history of our continent, but also for social history and the study of migration in early modern Europe. It contains a wealth of information about members of the subordinate classes, of their travels and lives in Europe. The profile delineated in these documents is of individuals who had a wide range of different professions and different aspirations. These documents encompass a vast social spectrum that was highly mobile on a continent which by that time had become pluriconfessional. Therefore, these migrants faced the complex religious reality in their everyday life. The principal corpus of my research consists of two types of manuscript sources created for administrative and in a way also for apologetic purposes of the Roman Catholic Church. My starting point is the Primo registro generale of Ospizio dei Convertendi. This is a volume in which the following information about each guest was registered: name, nationality, city of origin, age, sex, profession, confession professed before converting, date of arrival, departure, abjuration and baptism. Typically, the convert was male, originating from Stockholm or Copenhagen, from 21 to 30 years of age. The biggest occupational groups in descending order were soldiers, noblemen, craftsmen and sailors. Thus the data reflects a multiform reality of interurban and long distance migration, ideals regarding the education of young noblemen and gentry as well as the need of European armies to hire foreign mercenaries in their various campaigns. Against this background the almost total absence of women is hardly surprising: there is only one woman in the material I have studied. The second main source, Nota degl’ospiti ricevuti e spese fatte per essi, sheds more light on the choices of the converts, their motivations and their lives outside Scandinavia before reaching Rome. This narrative material permits an analysis which completes but also goes far beyond the columns of the Institute’s general register. This material consists of reports written by Catholic priests based on an interview conducted upon each guest’s arrival. The material frequently includes information on what the converts would do following their departure from the Institute as well. These sources have a specific narrative form and contain short biographies, list reasons for converting and information about the journey from the North to the Mediterranean - a journey which in many cases took several years. Moreover, they show that certain unorthodox practices such as calling on the saints and pleading for help from them were not uncommon in the Protestant popular religion. The recording of information on conversions from Protestantism to Catholicism reflects both religious and social interest on the part of the receiving institute. The information obtained was used for the purposes of religious teaching, for finding adequate ways of inserting the convert into Italian society so that he could earn a living, and to find effective methods to convert others with a similar cultural and geographical background. The stories recorded were based on interviews with the newly-arrived, information obtained from a travel companion or fellow countrymen, or from written documents the aspirant converts carried with them. These sources illustrate, although sometimes in rather simplified ways, the circumstances and motivations which were relevant to the choice of changing one’s confession. In addition, I have examined petitions addressed to the hospice and other Roman authorities in order to get financial aid. These petitions were written by Italian scrittori, and they contain certain conventions and topoi of presenting the conversion with the purpose of improving the chances of obtaining financial aid. It is through these filters, which may seem initially almost invisible, that the remote voice of the converts reaches us. The results of the analysis are particularly interesting because they disagree with some of the principal conclusions of previous work on the subject. First, earlier research has focused almost exclusively on the conversions of noblemen, and has argued, second, that the Queen Christina of Sweden was the driving force behind their change of confession. The sources examined for this dissertation present a profile of long-distance migrants, many of them members of the subordinate classes, who were looking for ways to make their living in Europe. These people had in many cases left their country of origin several years earlier and not for religious reasons, so, crucially, we are not dealing with confessional migration in these cases. Rather, conversion was a complex process, intricately tied up with strategies of survival, integration and upward social mobility. At the same time, while these components are significant on their own right, they do not necessarily point to the absence of motivations of a more clearly religious nature.

Molecular Evolution of Metazoan Hypoxia-inducing Factors

Most metazoans rely on aerobic energy production, which is dependent on adequate oxygen supply. In the case of reduced oxygen supply (hypoxia), the most profound changes in gene expression are mediated by transcription factors named hypoxia-inducible factors (HIF alpha). These proteins are post-translationally regulated by prolyl-4-hydroxylase (PHD) enzymes that are direct “sensors” of cellular oxygen levels. This thesis examines the molecular evolution of metazoan HIF systems. In early metazoans the HIF system emerged from pre-existing PHD oxygen sensors and early bHLH-PAS transcription factors. In invertebrates our analysis revealed an unexpected diversity of PHD genes and HIF alpha sequence characteristics. An early branching vertebrate, the epaulette shark (Hemiscyllium ocellatum) was chosen for sequencing and hypoxia preconditioning studies of HIF alpha and PHD genes. As no quantitative PCR reference genes were available, this thesis includes the first study of reference genes in cartilaginous fish species. Applying multiple statistical analysis we also discoveredthat commonly used reference gene software may perform poorly with some data sets. Novel reference genes allowed accurate measurements of the mRNAlevels of the studied target genes. Cartilaginous fishes have three genomic duplicates of both HIF alpha and PHD genes like mammals and teleost fishes. Combining functional divergence and selection analyses it was possible to describe how sequence changes in both HIF alpha and PHD duplicates may have contributed to the differential oxygen sensitivityof HIF alphas. Additionally, novel teleost HIF-1 alpha sequences were produced and used to reveal the molecular evolution of HIF-1 alpha in this lineage rich with hypoxia tolerant species.

Studies on 68Ga-Based Agents for PET Imaging of Cancer and Inflammation

Studies on ⁶⁸Ga-Based Agents for PET Imaging of Cancer and Inflammation Positron emission tomography (PET) is based on the use of radiolabeled agents and facilitates in vivo imaging of biological processes, such as cancer. Because the detection of cancer is demanding and is often obscured by inflammation, there is a demand for better PET imaging agents. The aim was to preliminarily evaluate new PET agents for imaging cancer and inflammation using experimental models. ⁶⁸Ga-chloride and peptides, ⁶⁸Ga-labeled through 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA), targeting matrix metalloproteinase-9 (MMP-9) were tested for tumor imaging. In addition, a ⁶⁸Ga-DOTA-conjugated peptide targeting vascular adhesion protein-1 (VAP-1), was tested for inflammation imaging. The ⁶⁸Ga-based imaging agents described here showed potential features by passing the essential in vitro tests, proceeding further to preclinical in vivo evaluation and being able to visualize the target. The target uptake and target-to-background ratios of ⁶⁸Ga-based agents were, however, not optimal. ⁶⁸Ga-chloride showed slow clearance caused by its binding to blood transferrin. In the case of ⁶⁸Ga-DOTA-peptides low in vivo stability and/or low lipophilicity led to too rapid blood clearance and urinary excretion. The properties of ⁶⁸Ga-labeled peptides are modifiable, as shown with matrix metalloproteinase-9 targeting ligands. In the conclusion of this PhD thesis, ⁶⁸Ga-based agents for PET imaging of cancer and inflammation could be applied in the development of drugs, earlier diagnostics and following-up of the efficacy of therapies.

Quasiconformal mappings and inequalities involving special functions

This PhD thesis in Mathematics belongs to the field of Geometric Function Theory. The thesis consists of four original papers. The topic studied deals with quasiconformal mappings and their distortion theory in Euclidean n-dimensional spaces. This theory has its roots in the pioneering papers of F. W. Gehring and J. Väisälä published in the early 1960’s and it has been studied by many mathematicians thereafter. In the first paper we refine the known bounds for the so-called Mori constant and also estimate the distortion in the hyperbolic metric. The second paper deals with radial functions which are simple examples of quasiconformal mappings. These radial functions lead us to the study of the so-called p-angular distance which has been studied recently e.g. by L. Maligranda and S. Dragomir. In the third paper we study a class of functions of a real variable studied by P. Lindqvist in an influential paper. This leads one to study parametrized analogues of classical trigonometric and hyperbolic functions which for the parameter value p = 2 coincide with the classical functions. Gaussian hypergeometric functions have an important role in the study of these special functions. Several new inequalities and identities involving p-analogues of these functions are also given. In the fourth paper we study the generalized complete elliptic integrals, modular functions and some related functions. We find the upper and lower bounds of these functions, and those bounds are given in a simple form. This theory has a long history which goes back two centuries and includes names such as A. M. Legendre, C. Jacobi, C. F. Gauss. Modular functions also occur in the study of quasiconformal mappings. Conformal invariants, such as the modulus of a curve family, are often applied in quasiconformal mapping theory. The invariants can be sometimes expressed in terms of special conformal mappings. This fact explains why special functions often occur in this theory.

Functional studies on bacterial nucleotide-regulated inorganic pyrophosphatases

CBS domains are ~60 amino acid tandemly repeated regulatory modules forming a widely distributed domain superfamily. Found in thousands of proteins from all kingdoms of life, CBS domains have adopted a variety of functions during evolution, one of which is regulation of enzyme activity through binding of adenylate-containing compounds in a hydrophobic cavity. Mutations in human CBS domain-containing proteins cause hereditary diseases. Inorganic pyrophosphatases (PPases) are ubiquitous enzymes, which pull pyrophosphate (PPi) producing reactions forward by hydrolyzing PPi into phosphate. Of the two nonhomologous soluble PPases, dimeric family II PPases, belonging to the DHH family of phosphoesterases, require a transition metal and magnesium for maximal activity. A quarter of the almost 500 family II PPases, found in bacteria and archaea, contain a 120-250 amino acid N-terminal insertion, comprised of two CBS domains separated in sequence by a DRTGG domain. These enzymes are thus named CBS-PPases. The function of the DRTGG domain in proteins is unknown. The aim of this PhD thesis was to elucidate the structural and functional differences of CBS-PPases in comparison to family II PPases lacking the regulatory insert. To this end, we expressed, purified and characterized the CBS-PPases from Clostridium perfringens (cpCBS-PPase) and Moorella thermoacetica (mtCBS-PPase), the latter lacking a DRTGG domain. Both enzymes are homodimers in solution and display maximal activity against PPi in the presence of Co2+ and Mg2+. Uniquely, the DRTGG domain was found to enable tripolyphosphate hydrolysis at rates similar to that of PPi. Additionally, we found that AMP and ADP inhibit, while ATP and AP4A activate CBSPPases, thus enabling regulation in response to changes in cellular energy status. We then observed substrate- and nucleotide-induced conformational transitions in mtCBS-PPase and found that the enzyme exists in two differentially active conformations, interconverted through substrate binding and resulting in a 2.5-fold enzyme activation. AMP binding was shown to produce an alternate conformation, which is reached through a different pathway than the substrate-induced conformation. We solved the structure of the regulatory insert from cpCBS-PPase in complex with AMP and AP4A and proposed that conformational changes in the loops connecting the catalytic and regulatory domains enable activity regulation. We examined the effects of mutations in the CBS domains of mtCBS-PPase on catalytic activity, as well as, nucleotide binding and inhibition.

First dice your dill – new methods and techniques in sample handling

This book is dedicated to celebrate the 60th birthday of Professor Rainer Huopalahti. Professor Rainer “Repe” Huopalahti has had, and in fact is still enjoying a distinguished career in the analysis of food and food related flavor compounds. One will find it hard to make any progress in this particular field without a valid and innovative sample handling technique and this is a field in which Professor Huopalahti has made great contributions. The title and the front cover of this book honors Professor Huopahti’s early steps in science. His PhD thesis which was published on 1985 is entitled “Composition and content of aroma compounds in the dill herb, Anethum graveolens L., affected by different factors”. At that time, the thesis introduced new technology being applied to sample handling and analysis of flavoring compounds of dill. Sample handling is an essential task that in just about every analysis. If one is working with minor compounds in a sample or trying to detect trace levels of the analytes, one of the aims of sample handling may be to increase the sensitivity of the analytical method. On the other hand, if one is working with a challenging matrix such as the kind found in biological samples, one of the aims is to increase the selectivity. However, quite often the aim is to increase both the selectivity and the sensitivity. This book provides good and representative examples about the necessity of valid sample handling and the role of the sample handling in the analytical method. The contributors of the book are leading Finnish scientists on the field of organic instrumental analytical chemistry. Some of them are also Repe’ s personal friends and former students from the University of Turku, Department of Biochemistry and Food Chemistry. Importantly, the authors all know Repe in one way or another and are well aware of his achievements on the field of analytical chemistry. The editorial team had a great time during the planning phase and during the “hard work editorial phase” of the book. For example, we came up with many ideas on how to publish the book. After many long discussions, we decided to have a limited edition as an “old school hard cover book” – and to acknowledge more modern ways of disseminating knowledge by publishing an internet version of the book on the webpages of the University of Turku. Downloading the book from the webpage for personal use is free of charge. We believe and hope that the book will be read with great interest by scientists working in the fascinating field of organic instrumental analytical chemistry. We decided to publish our book in English for two main reasons. First, we believe that in the near future, more and more teaching in Finnish Universities will be delivered in English. To facilitate this process and encourage students to develop good language skills, it was decided to be published the book in English. Secondly, we believe that the book will also interest scientists outside Finland – particularly in the other member states of the European Union. The editorial team thanks all the authors for their willingness to contribute to this book – and to adhere to the very strict schedule. We also want to thank the various individuals and enterprises who financially supported the book project. Without that support, it would not have been possible to publish the hardcover book.

Numbers and Languages

The thesis presents results obtained during the authors PhD-studies. First systems of language equations of a simple form consisting of just two equations are proved to be computationally universal. These are systems over unary alphabet, that are seen as systems of equations over natural numbers. The systems contain only an equation X+A=B and an equation X+X+C=X+X+D, where A, B, C and D are eventually periodic constants. It is proved that for every recursive set S there exists natural numbers p and d, and eventually periodic sets A, B, C and D such that a number n is in S if and only if np+d is in the unique solution of the abovementioned system of two equations, so all recursive sets can be represented in an encoded form. It is also proved that all recursive sets cannot be represented as they are, so the encoding is really needed. Furthermore, it is proved that the family of languages generated by Boolean grammars is closed under injective gsm-mappings and inverse gsm-mappings. The arguments apply also for the families of unambiguous Boolean languages, conjunctive languages and unambiguous languages. Finally, characterizations for morphisims preserving subfamilies of context-free languages are presented. It is shown that the families of deterministic and LL context-free languages are closed under codes if and only if they are of bounded deciphering delay. These families are also closed under non-codes, if they map every letter into a submonoid generated by a single word. The family of unambiguous context-free languages is closed under all codes and under the same non-codes as the families of deterministic and LL context-free languages.

Proceedings of the PDM2013 conference, LUT 24.-25.4.2013

The 1st PDM Forum for Finland-Russia Collaboration was held at Lappeenranta University of Technology, Finland, during 25.-26.4.2013. The forum brought together leading academics, practitioners, advisors, engineers, industrial experts, and software vendors from Finland and Russia. The forum can be seen as a new integrating element between Russian and Finnish industries and universities. Over border connections between Russia and Finland may also bring new contacts and ideas to develop and expand businesses. Meeting different universities professors, PhD students, and companies’ agents facilitates the sharing and discussion of current PDM (Product Data Management) issues.