Identifying protein-coding genes in genomic sequences.

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.

Nationalisme économique et réalisme mercantile : la politique énergétique russe sous Poutine (2000-2008)

Mon travail met en évidence la restructuration de l'industrie énergétique russe sous les deux mandats Poutine (2000-2008) via le rôle prédominant de l'État dans une perspective historique. Une nouvelle élite politique russe (les Silovikis) issue des structures de force de l'Etat favorise le nationalisme économique axé sur le rétablissement de l'autorité du gouvernement central au sein de l'industrie énergétique nationale au détriment des pouvoirs régionaux, des sociétés privées étrangères et des oligarques indépendants. Dans cette perspective, on peut citer "l'affaire Youkos" en 2003 caractérisée par l'arrestation de l'oligarque Mikhaïl Khodorkhovsky; les tentatives silovikiennes de reprendre l'ascendant sur les compagnies pétrolières régionales Tatneft et Bachneft gérées par les gouvernements tatar et bachkir, la pression fiscale envers les majors pétrolières étrangères à l'instar du conflit russo- britannique relatif à la joint-venture TNK-BP. Quant à la politique énergétique étrangère russe, elle est inspirée par line vision réaliste mercantile; le gouvernement silovikien vise à défendre l'intérêt national, le prestige et la puissance de la Russie via ses "champions" énergétiques Rosneft et Gazprom utilisés comme levier politique, notamment à l'égard des pays de la CEI considéré par Moscou comme sa sphère d'influence historique. Dans cette perspective, nous pouvons mentionner l'interruption des approvisionnements pétroliers et gaziers russes à l'Ukraine, aux Etats baltes ou encore à la Géorgie; la concurrence entre les majors russes et étrangères en Asie centrale / Caucase pour les champs pétrolifères et les tracés de pipelines (nouveau «Grand Jeu»); la diversification des marchés russes à l'exportation à travers la promotion de nouveaux pipelines partant des champs pétrolifères sibériens vers la Chine et l'océan Pacifique.¦My work highlights the restructuration of the Russian energy industry under the 2 Putin madates (2000-2008) by the predominant role of the state in a historical perspective. A new Russian politic elite (Siloviki) from state structure forces promotes the economic nationalism focused on the reestablishment of the central governmental authority in the national energy industry against regional powers, private foreign companies and independent oligarchs. In this perspective, we can mention the "Yukos Affair" in 2003 with the arrest of the oligarch Mikhail Khodorkhovsky; the silovikian attempts to take over the regional oil companies Tatneft and Bachneft handled by the Tatar and Bashkir governments; the fiscal silovikian pressure against foreign companies such as the Russo-Britannic joint- venture TNK-BP. As for the Russian energy Foreign policy, it is inspired by a mercantile realism vision; the silovikian government aims to defend the national interest, the prestige and the power of Russia through its energy companies Rosneft and Gazprom as a political leverage especially toward the CEI Countries considered by Moscow as it historical sphere of influence. In this perspective, we can mention the interruption of Russian oil&gas supply toward Ukraine, Baltic states or Georgia; the competition between Russian and foreign companies in Central Asia/Caucasus for oil and gas fields and pipeline routes (new "Great Game"); the diversification of Russian export markets through the promotion ο new pipelines from Siberian oil&gas fields to China and the Pacific Ocean.

Sociogenetics of fire ants

RÉSUMÉ GRAND PUBLIC La complexité des sociétés d'insectes (telles que les abeilles, les termites ou les fourmis) a depuis longtemps fasciné l'Homme. Depuis le débfit du XIXème siècle, de nombreux travaux observationnels, comportementaux et théoriques leur on été consacrés afin de mieux les décrire et comprendre. L'avènement de la biologie moléculaire à la fin du XXèrne siècle a offert de nouveaux outils scientifiques pour identifier et étudier les gènes et molécules impliqués dans le développement et le comportement des êtres vivants. Alors que la majorité de ces études s'est focalisée sur des organismes de laboratoire tel que la mouche ou les nématodes, l'utilisation de ces outils est restée marginale jusqu'à présent dans l'étude des sociétés d'insectes. Lors de ma thèse, j'ai développé des outils moléculaires permettant de déterminer le niveau d'activité de zo,ooo gènes chez la fourmi de feu, Solenopsis invicta, ainsi qu'une base de données et un portail en ligne regroupant les informations relatives à l'étude génétique des fourmis: Fourmidable. J'ai ensuite utilisé ces outils dans le cadre d'une étude comportementale chez la fourmis S. invicta. Dans les sociétés d'insectes, une hiérarchie peut déterminer le statut reproducteur des individus. Suite à la mort d'un dominant, les subordonnés entrent en compétition en vue d'améliorer leur statut. Un tel phénomène se produit au sein des colonies de S. invicta contenant une unique reine mère, des milliers d'ouvrières et des centaines de reines vierges ailées. A la mort de la reine mère, un grand nombre de reines vierges tentent de la remplacer en arrachant leurs ailes et en activant leurs organes reproducteurs plutôt que de partir en vol nuptial. Ces tentatives sont le plus souvent arrêtées par les ouvrières qui exécutent la plupart de ces reines sur la base de signaux olfactifs produits lors de l'activation des organes reproducteurs. Afin de mieux comprendre les mécanismes moléculaires impliqués, j'ai étudié l'activité de gènes au sein des reines au début de ce processus. J'ai ainsi déterminé que des gènes impliqués dans communication olfactive, le développement des organes reproducteurs et la métabolisation de l'hormone juvénile sont activês à ce moment là. La vitesse à laquelle les reines perdent leurs ailes ainsi que les niveaux d'expression de gènes sont ensuite liés à leur probabilité de survie. ABSTRACT : Honeybees, termites and ants occupy the "pinnacle of social evolution" with societies of a complexity that rivals our own. Humans have long been fascinated by social insects, but studying them has been mostly limited to observational and behavioral experiments. The advent of molecular biology first made it possible to investigate the molecular-genetic basis of development in model systems such as the fruit fly Drosophila melarcogaster or the roundworm Caenorhabditis elegans and subsequently their behavior. Molecular and genomic tools are now becoming available for the study of social insects as well. To permit genomic research on the fire ant, Solenopsis invicta, we developed a cDNA microarray that can simultaneously determine the expression levels of approximately 1oooo genes. These genes were assembled and bioinformatically annotated using custom pipelines. The obtained data formed the cornerstones for Fourmidable, a web portal centralizing sequence, gene annotation and gene expression data as well as laboratory protocols for research on ants. In many animals living in groups the reproductive status of individuals is determined by their social status. In species with social hierarchies, the death of dominant individuals typically upheaves the social hierarchy and provides an opportunity for subordinate individuals to improve their social status. Such a phenomenon occurs in the monogyne form of S. invicta, where colonies typically contain a single wingless reproductive queen, thousands of workers and hundreds of winged non-reproductive virgin queens. Upon the death of the mother queen, many virgin queens shed their wings and initiate reproductive development instead of departing on a mating flight. Workers progressively execute almost all of them over the following weeks. The workers base their collective decision on pheromonal cues associated with the onset of reproductive development of the virgin queens which occurs after orphaning. We used the aforementioned tools to determine that genes putatively involved in processes including olfactory signaling, reproductive development and Juvenile Hormone metabolism are differentially expressed at the onset of competition. Additionally, we found that queens that initiate reproductive development faster and, to a certain extent, shed their wings faster after orphaning are more likely to become replacement queens. These results provide candidate genes that are putatively linked to competition outcome. To determine the extent to which specific genes affect different aspects of life in ant colonies, functional tests such as gene activation and silencing will still be required. We conclude by discussing some of the challenges and opportunities for molecular-genetic research on ants. RÉSUMÉ Les sociétés d'abeilles, de termites et de fourmis sont d'une complexité proche de celle de la nôtre et ont depuis longtemps fasciné l'Homme. Cependant, leur étude était jusqu'à présent limitée aux observations et expériences comportementales. L'avènement de la biologie moléculaire a d'abord rendu possible l'étude moléculaire et génétique du développement d'organismes modèles tels que la mouche Drosophila melanogaster ou le nématode Caenorhabditis elegans, puis dans un second temps de leur comportement. De telles études deviennent désormais possibles pour les insectes sociaux. Nous avons développé une puce à ADN permettant de déterminer simultanément les niveaux d'expression de 1oooo gènes de la fourmi de feu, Solenopsís invicta. Ces gènes ont été séquencés puis assemblés et annotés à l'aide de pipelines que nous avons développés. En se basant sur les informations obtenues, nous avons créé un portail web, Fourmidable. Ce portail vise à centraliser toutes les informations de séquence, d'annotation et d'expression de gènes, ainsi que les protocoles de laboratoire utilisés pour la recherche sur les fourmis. Par la suite, nous avons utilisé les outils développés pour étudier un aspect particulier de S. invicta. Chez les animaux grégaires, une hiérarchie sociale peut déterminer le statut reproducteur des individus. Suite à la mort d'un individu dominant, les individus subordonnés peuvent entrer en compétition en vue d'améliorer leur statut. Un tel phénomène se produit au sein des colonies monogynes de S. invicta, qui contiennent habituellement une unique reine mère, des milliers d'ouvrières et des centaines de reines vierges ailées. Suite à la mort de la reine mère, dominante, un grand nombre de reines vierges, subordonnées, perdent leurs ailes et activent leurs organes reproducteurs au lieu de partir en vol nuptial. Au cours des semaines suivantes, les ouvrières exécutent la plupart de ces reines sur la base de signaux olfactifs produits lors de l'activation des organes reproducteurs. Afin de mieux comprendre les mécanismes moléculaires impliqués, nous avons étudié l'expression de gènes au début de cette compétition. Nous avons identifié 297 gènes différemment exprimés, dont l'annotation indique qu'ils seraient impliqués dans des processus biologiques dont la communication olfactive, le développement des organes reproducteurs et la métabolisation de l'hormone juvénile. Par la suite, nous avons déterminé que la vitesse à laquelle les reines perdent leurs ailes en début de compétition ainsi que les niveaux d'expression de gènes sont corrélés à la probabilité de survie des reines. Nous concluons en discutant des opportunités offertes par la recherche génétique sur les fourmis ainsi que les défis qu'elle devra surmonter.

The GENCODE pseudogene resource.

BACKGROUND: Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data. RESULTS: As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection. CONCLUSIONS: At one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.

Iowa Transportation Laws, HR-234, 1985

Research project HR-234 was sponsored by the Iowa Highway Research Board and the Iowa Department of Transportation. In the preparation of this compilation of highway and street laws of Iowa, an attempt has been made to include those sections of the Code to which reference is frequently required by the Department of Transportation, counties, cities and towns in their conduct of highway and street administration, construction and maintenance. Because of the broad scope of highway and street work and the many interrelated provisions of Iowa law, and in the interests of keeping this volume in a convenient and usable size, some Code provisions which have some bearing on the principal subject were of necessity omitted. The volume has been compiled in loose leaf form with the expectation that periodic updates will keep the reader informed regarding changes in the law and/or new laws. A general index is provided at the end of the text of this volume. Each major topic is divided into relevant subtopics and are accompanied by appropriate Code sections. This publication is offered with the hope and belief that it will prove to be of value and assistance to those concerned with the problems of establishing, maintaining and administering a highway and street system. The reader is cautioned to consult legal counsel on all matters beyond the scope of this text.

Embankment Quality Phase II Final Report, TR-401, 1999

Phase II research included the following: (1) develop and evaluate alternative soil design and embankment construction specifications based on soil type, moisture, density, stability, and compaction process; (2) assess various quality control and acceptance procedures with a variety of in-situ test methods including the Dual-mass Dynamic Cone Penetrometer (DCP); and (3) develop and design rapid field soil identification methods. At the start of the research, soils were divided into cohesive and cohesionless soil types, with each category being addressed separately. Cohesionless soils were designated as having less than 36% fines content (material passing the No. 200 sieve) and cohesive soils as having greater than 36% fines content. Subsequently, soil categories were refined based not only on fines content but soil plasticity as well. Research activities included observations of fill placement, in-place moisture and density testing, and dual-mass DCP index testing on several highway embankment projects throughout Iowa. Experiments involving rubber-tired and vibratory compaction, lift thickness changes, and disk aeration were carried out for the full range of Iowa soils. By testing for soil stability the DCP was found to be a valuable field tool for quality control, whereby shortcomings from density testing (density gradients) were avoided. Furthermore, critical DCP index values were established based on soil type and compaction moisture content.

ConnectomeViewer - Multi-Modal Multi-Level Network Visualization and Analysis.

Introduction: The field of Connectomic research is growing rapidly, resulting from methodological advances in structural neuroimaging on many spatial scales. Especially progress in Diffusion MRI data acquisition and processing made available macroscopic structural connectivity maps in vivo through Connectome Mapping Pipelines (Hagmann et al, 2008) into so-called Connectomes (Hagmann 2005, Sporns et al, 2005). They exhibit both spatial and topological information that constrain functional imaging studies and are relevant in their interpretation. The need for a special-purpose software tool for both clinical researchers and neuroscientists to support investigations of such connectome data has grown. Methods: We developed the ConnectomeViewer, a powerful, extensible software tool for visualization and analysis in connectomic research. It uses the novel defined container-like Connectome File Format, specifying networks (GraphML), surfaces (Gifti), volumes (Nifti), track data (TrackVis) and metadata. Usage of Python as programming language allows it to by cross-platform and have access to a multitude of scientific libraries. Results: Using a flexible plugin architecture, it is possible to enhance functionality for specific purposes easily. Following features are already implemented: * Ready usage of libraries, e.g. for complex network analysis (NetworkX) and data plotting (Matplotlib). More brain connectivity measures will be implemented in a future release (Rubinov et al, 2009). * 3D View of networks with node positioning based on corresponding ROI surface patch. Other layouts possible. * Picking functionality to select nodes, select edges, get more node information (ConnectomeWiki), toggle surface representations * Interactive thresholding and modality selection of edge properties using filters * Arbitrary metadata can be stored for networks, thereby allowing e.g. group-based analysis or meta-analysis. * Python Shell for scripting. Application data is exposed and can be modified or used for further post-processing. * Visualization pipelines using filters and modules can be composed with Mayavi (Ramachandran et al, 2008). * Interface to TrackVis to visualize track data. Selected nodes are converted to ROIs for fiber filtering The Connectome Mapping Pipeline (Hagmann et al, 2008) processed 20 healthy subjects into an average Connectome dataset. The Figures show the ConnectomeViewer user interface using this dataset. Connections are shown that occur in all 20 subjects. The dataset is freely available from the homepage (connectomeviewer.org). Conclusions: The ConnectomeViewer is a cross-platform, open-source software tool that provides extensive visualization and analysis capabilities for connectomic research. It has a modular architecture, integrates relevant datatypes and is completely scriptable. Visit www.connectomics.org to get involved as user or developer.

Iowa System of Bridge Deck Rehabilitation with Cathodic Protection, HR-1044, 1986

Bridge deck and substructure deterioration due to the corrosive effects of deicing chemicals on reinforcing steel is a problem facing many transportation agencies. The main concern is protection of older bridges with uncoated reinforcing steel. Many different methods have been tried over the past years to repair bridge decks. The Iowa system of bridge deck rehabilitation has proven to be very effective. It consists of scarifying the deck surface, removing any deteriorated concrete, and overlaying with low slump dense concrete. Another rehabilitation method that has emerged is cathodic protection. It has been used for many years in the protection of underground pipelines and in 1973 was first installed on a bridge deck. Cathodic protection works by applying an external source of direct current to the embedded reinforcing steel, thereby changing the electrochemical process of corrosion. The corroding steel, which is anodic, is protected by changing it to a cathodic state. The technology involved in cathodic protection as applied to bridge decks has improved over the last 12 years. One company marketing new technology in cathodic protection systems is Raychem Corporation of Menlo Park, California. Their system utilizes a Ferex anode mesh that distributes the impressed direct current over the deck surface. Ferex mesh was selected because it seemed readily adaptable to the Iowa system of bridge deck rehabilitation. The bridge deck would be scarified, deteriorated concrete removed, Ferex anode mesh installed, and overlaid with low slump dense concrete. The Federal Highway Administration (FHWA) promotes cathodic protection under Demonstration Project No. 34, "Cathodic Protection for Reinforced Concrete Bridge Decks."

Oulun Energian kaukolämpöverkoston ja -tuotannon kehitys vuosina 2006 - 2020

Tässä diplomityössä on tarkasteltu Oulun Energian kaukolämpötoiminnan kehitystä lähitulevaisuudessa. Työn yhteydessä selvitettiin nykyisessä tilanteessa mitoituslämpötilaa -32 oC vastaava tehotilastollisen analyysin avulla ja laadittiin kasvuennuste kaukolämmityksen tehontarpeesta seuraavalle viidelletoista vuodelle. Kasvuennusteen perusteella on tehty tarkastelu kaukolämmön varatehon riittävyydestä. Verkoston tehonsiirtokykyä nykyisissä ja tulevaisuuden kuormitustilanteissa on tarkasteltu Process VisioninGrades Heating -verkostolaskentaohjelmiston avulla. Tarkastelun perusteella kaukolämpöverkoston siirtokyky on kohtalaisen hyvä. Verkoston ongelmakohtia ovat länsi-itäsuunnassa olevat siirtolinjat. Varatehon määrä tulee laskemaan lähivuosina alle suositeltavan määrän, mikäli uutta lämmöntuotantokapasiteettia ei rakenneta. Alkuvaiheessa paras ratkaisu tilanteen korjaamiseksi olisi uusien lämpökeskusten rakentaminen sekä kaupungin etelä- että itä-osiin. 2010-luvulla tarve uuden voimalaitoksen rakentamiselle kaukolämpötehon tarpeen kattamiseksi tulee kasvamaan.

Viranomaisvaatimusten mukaisten putkistojen hankinta, asennus ja korjaus

Tämän työn tarkoituksena oli kirjallisuustutkimuksen ja aikaisemmin valmistuneiden putkitöiden avulla määritellä ohjeistus viranomaisvaatimusten mukaisten putkistojen valmistamista varten. Tarkasteluesimerkkeinä oli kolme erilaista putkityötä. Näiden seikkojen kautta vahvistui käsitys ohjeistuksen tarpeellisuudesta, mikä oli jo työn tavoitteissa yhtenä päämääränä. Aluksi selvitetään lainsäädäntöä ja sitä, mitä laki vaati putkistoilta. Seuraavaksi tarkastellaan standardeja valmistuksen näkökannalta ja siitä seurauksena syntyi valmistusohje. Sen jälkeen käsitellään putkistoista tehtyjä dokumentaatioita, joita oli jo valmistettu lainsäädännön vaihtumisen jälkeen. Kokoamalla em. tutkimukset on saatu aikaiseksi ohjeistus, jota seuraamallavalmistaja voi valmistaa putkiston, joka täyttää lain ja asetuksen vaatimuksen.Tässä työssä ei tarkasteltu tuotannon tehostamista asennusolosuhteissa eikä laatutavoitteita. Tuloksena syntyi ohjeistus, joka huomioi erilaiset lait ja asetukset, kun kyseessä on putkistojen hankinta, asennus tai korjaus putkistoissa, joita viranomaismääräykset ja asetukset valvovat. Putkistojen asennuksen ja tuotannon tehostaminen sekä automatisoinnin tai mekanisoinnin käyttö hitsauksessa ja hitsauksen laadun varmistus voivat olla tämän diplomityön jälkeisiä tutkimusaiheita.

Jyväskylän kaukolämpöverkon kehittäminen

Kaukolämmitys on yleisin Suomessa käytetty lämmitysmuoto ja sen osuus koko lämmitysmarkkinoista on noin 50 %. Kaukolämmön varsinainen tuotanto ja jakelu alkoivat Suomessa vuonna 1957 ja Jyväskylässä vuonna 1960. Jyväskylässä kaukolämmön piiriin kuuluivuoden 2006 loppuun mennessä noin 3200 asiakasta. Suurin tuntiteho laitoksilta oli noin 375 MW. Vuonna 2020 suurimman tuntitehon on ennustettu olevan noin 480 MW, mikä tarkoittaa asiakasmäärän ja verkon pituuden merkittävää kasvua. Jyväskylän kaukolämpöverkon nykytilanne on hyvä. Verkostolaskennan tulosten perusteella lämpö saadaan siirtymään nykyisillä laitoksilla ja verkon laitteilla jokaiselle asiakkaalle niin normaalitilanteessa kuin päälaitoksen häiriötilanteessa. Häiriötilanteessa paikallisia ongelmia voi esiintyä, mutta niihin voidaan vaikuttaa parantavasti esimerkiksi verkon staattisen paineen nostolla. Jyväskylän kaukolämpöverkon tulevaisuuden näkymät ovat erinomaiset. Laskennan perusteella verkkoa voidaan laajentaa kaikille laskennassa mukana olleille alueille ilman suurempia ongelmia. Uuden tuotantokapasiteetin, verkonlaajentumisen ja asiakasmäärän kasvun aiheuttamat kehitystarpeet saatiin selvitetyksi ja tulokset olivat aikaisempien tutkimusten suuntaisia. Tulevaisuutta ajatellen verkkoon joudutaan tekemään muutamia muutoksia suunniteltujen uusien yhteyksien lisäksi. Uuteen linjaan, joka yhdistää Palokan verkon toisen yhteyden kautta Jyväskylän pääverkkoon, rakennetaan mahdollisesti pumppaamo. Lisäkuristusventtiilejä tarvitaan viiteen eri paikkaan turvaamaan riittävän suuret kaukolämpöveden paluupaineet. Osa venttiileistä olisi suositeltavaa asentaa jo nykytilanteessa, sillä niiden hankinta parantaisi verkon nykytilaa.

Blind docking of 260 protein-ligand complexes with EADock 2.0.

Molecular docking softwares are one of the important tools of modern drug development pipelines. The promising achievements of the last 10 years emphasize the need for further improvement, as reflected by several recent publications (Leach et al., J Med Chem 2006, 49, 5851; Warren et al., J Med Chem 2006, 49, 5912). Our initial approach, EADock, showed a good performance in reproducing the experimental binding modes for a set of 37 different ligand-protein complexes (Grosdidier et al., Proteins 2007, 67, 1010). This article presents recent improvements regarding the scoring and sampling aspects over the initial implementation, as well as a new seeding procedure based on the detection of cavities, opening the door to blind docking with EADock. These enhancements were validated on 260 complexes taken from the high quality Ligand Protein Database [LPDB, (Roche et al., J Med Chem 2001, 44, 3592)]. Two issues were identified: first, the quality of the initial structures cannot be assumed and a manual inspection and/or a search in the literature are likely to be required to achieve the best performance. Second the description of interactions involving metal ions still has to be improved. Nonetheless, a remarkable success rate of 65% was achieved for a large scale blind docking assay, when considering only the top ranked binding mode and a success threshold of 2 A RMSD to the crystal structure. When looking at the five-top ranked binding modes, the success rate increases up to 76%. In a standard local docking assay, success rates of 75 and 83% were obtained, considering only the top ranked binding mode, or the five top binding modes, respectively.

Lisäainetehtaan tuotantoprosessin kehittäminen

Tämän diplomityön tarkoituksena oli Finnsementti osakeyhtiöön kuuluvan betonin lisäaineita valmistavan tehtaan tuotantoprosessin kehittäminen. Työssä laadittiin myynnin kasvuennusteen perusteella suunnitelma, jonka mukaan määriteltiin betonin lisäaineille ja raaka-aineille sopivat varastosäiliöt. Suunnitelman perusteella määriteltiin kiinteät putkilinjat sekä kirkkaille että tummille nesteille, jolloin materiaalihäviöt saatiin pienemmiksi ja putkilinjojen pesun tarve väheni. Lisäksi työssä otettiin huomioon tuotantoprosessin automatisointi. Suunnitellusta projektista laadittiin alustava kustannusarvio, toteutusaikataulu sekä sijoituspiirustus, putkisto-instrumentointikaavio ja 3D-piirrokset. Projektin kustannusarvioksi saatiin noin 290 tuhatta markkaa ja projektin pituudeksi noin 11 viikkoa.

Quantitative proteomics in the characterization of T helper lymphocyte differentiation

The term proteome is used to define the complete set of proteins expressed in cells or tissues of an organism at a certain timepoint. Respectively, proteomics is used to describe the methods, which are used to study such proteomes. These methods include chromatographic and electrophoretic techniques for protein or peptide fractionation, mass spectrometry for their identification, and use of computational methods to assist the complicated data analysis. A primary aim in this Ph.D. thesis was to set-up, optimize, and develop proteomics methods for analysing proteins extracted from T-helper (Th) lymphocytes. First, high-throughput LC-MS/MS and ICAT labeling methods were set-up and optimized for analysing the microsomal fraction proteins extracted from Th lymphocytes. Later, iTRAQ method was optimized to study cytokine regulated protein expression in the nuclei of Th lymphocytes. High-throughput LC-MS/MS analyses, like ICAT and iTRAQ, produce large quantities of data and robust software and data analysis pipelines are needed. Therefore, different software programs used for analysing such data were evaluated. Moreover, a pre-filtering algorithm was developed to classify good-quality and bad-quality spectra prior to the database searches. Th-lymphocytes can differentiate into Th1 or Th2 cells based on surrounding antigens, co-stimulatory molecules, and cytokines. Both subsets have individual cytokine secretion profiles and specific functions. Th1 cells participate in the cellular immunity against intracellular pathogens, while Th2 cells have important role in the humoral immunity against extracellular parasites. An abnormal response of Th1 and Th2 cells and imbalance between the subsets are charasteristic of several diseases. Th1 specific reactions and cytokines have been detected in autoimmune diseases, while Th2 specific response and cytokine profile is common in allergy and asthma. In this Ph. D. thesis mass spectrometry-based proteomics was used to study the effects of Th1 and Th2 promoting cytokines IL-12 and IL-4 on the proteome of Th lymphocytes. Characterization of microsomal fraction proteome extracted from IL-12 treated lymphobasts and IL-4 stimulated cord blood CD4+ cells resulted in finding of cytokine regulated proteins. Galectin-1 and CD7 were down-regulated in IL-12 treated cells, while IL-4 stimulation decreased the expression of STAT1, MXA, GIMAP1, and GIMAP4. Interestingly, the transcription of both GIMAP genes was up-regulated in Th1 polarized cells and down-regulated in Th2 promoting conditions.

Simulation-based evaluation of susceptibility distortion correction methods in diffusion MRI for connectivity analysis

Connectivity analysis on diffusion MRI data of the whole- brain suffers from distortions caused by the standard echo- planar imaging acquisition strategies. These images show characteristic geometrical deformations and signal destruction that are an important drawback limiting the success of tractography algorithms. Several retrospective correction techniques are readily available. In this work, we use a digital phantom designed for the evaluation of connectivity pipelines. We subject the phantom to a âeurooetheoretically correctâeuro and plausible deformation that resembles the artifact under investigation. We correct data back, with three standard methodologies (namely fieldmap-based, reversed encoding-based, and registration- based). Finally, we rank the methods based on their geometrical accuracy, the dropout compensation, and their impact on the resulting connectivity matrices.