Effects of moisture content and temperature during storage on germination of the achenes of Bidens gardneri Baker

Bidens gardneri is a herbaceous species of the cerrados, whose seeds are light sensitive at 25 °C, but they become indifferent to light when stored in soil. In this work the effects of moisture content, temperature and light (during storage) upon light sensitivity during germination were studied. Ripe achenes were collected in the cerrados of Itirapina and Moji Guaçu, State of São Paulo, Brazil. The storage conditions of the achenes varied in each experiment. Achenes were stored in darkness or light, in closed bottles, at 4 °C, 20/30 °C or 25 °C. Achenes were imbibed for 24 h at 4 °C, 25 °C or 20/30 °C (in darkness) and then stored for 1, 10, 20, 30 and 40 days (40 days only for 4 °C and 25 °C). Germination tests were conducted at 25 °C and 20/30 °C. The achenes not previously imbibed showed sensitivity to light during germination. High moisture content did not affect light sensitivity of the achenes during germination but high moisture content together with storage temperatures of 25 °C and 20/30 °C had a deleterious effect upon the longevity of the achenes. Alternate temperatures during germination did not change the light sensitivity of newly collected achenes from Itirapina but changed the light sensitivity of the achenes stored imbibed at 4 °C in darkness. Alternate temperatures during storage of achenes with low moisture content did not change their photoblastism when germination was carried out at 25 °C. Alternate temperatures during storage of achenes with high moisture content followed by alternate temperatures during germination changed the light sensitivity of the achenes.

Advanced analysis and design methods for preparative chromatographic separation processes

Preparative liquid chromatography is one of the most selective separation techniques in the fine chemical, pharmaceutical, and food industries. Several process concepts have been developed and applied for improving the performance of classical batch chromatography. The most powerful approaches include various single-column recycling schemes, counter-current and cross-current multi-column setups, and hybrid processes where chromatography is coupled with other unit operations such as crystallization, chemical reactor, and/or solvent removal unit. To fully utilize the potential of stand-alone and integrated chromatographic processes, efficient methods for selecting the best process alternative as well as optimal operating conditions are needed. In this thesis, a unified method is developed for analysis and design of the following singlecolumn fixed bed processes and corresponding cross-current schemes: (1) batch chromatography, (2) batch chromatography with an integrated solvent removal unit, (3) mixed-recycle steady state recycling chromatography (SSR), and (4) mixed-recycle steady state recycling chromatography with solvent removal from fresh feed, recycle fraction, or column feed (SSR–SR). The method is based on the equilibrium theory of chromatography with an assumption of negligible mass transfer resistance and axial dispersion. The design criteria are given in general, dimensionless form that is formally analogous to that applied widely in the so called triangle theory of counter-current multi-column chromatography. Analytical design equations are derived for binary systems that follow competitive Langmuir adsorption isotherm model. For this purpose, the existing analytic solution of the ideal model of chromatography for binary Langmuir mixtures is completed by deriving missing explicit equations for the height and location of the pure first component shock in the case of a small feed pulse. It is thus shown that the entire chromatographic cycle at the column outlet can be expressed in closed-form. The developed design method allows predicting the feasible range of operating parameters that lead to desired product purities. It can be applied for the calculation of first estimates of optimal operating conditions, the analysis of process robustness, and the early-stage evaluation of different process alternatives. The design method is utilized to analyse the possibility to enhance the performance of conventional SSR chromatography by integrating it with a solvent removal unit. It is shown that the amount of fresh feed processed during a chromatographic cycle and thus the productivity of SSR process can be improved by removing solvent. The maximum solvent removal capacity depends on the location of the solvent removal unit and the physical solvent removal constraints, such as solubility, viscosity, and/or osmotic pressure limits. Usually, the most flexible option is to remove solvent from the column feed. Applicability of the equilibrium design for real, non-ideal separation problems is evaluated by means of numerical simulations. Due to assumption of infinite column efficiency, the developed design method is most applicable for high performance systems where thermodynamic effects are predominant, while significant deviations are observed under highly non-ideal conditions. The findings based on the equilibrium theory are applied to develop a shortcut approach for the design of chromatographic separation processes under strongly non-ideal conditions with significant dispersive effects. The method is based on a simple procedure applied to a single conventional chromatogram. Applicability of the approach for the design of batch and counter-current simulated moving bed processes is evaluated with case studies. It is shown that the shortcut approach works the better the higher the column efficiency and the lower the purity constraints are.

Development of Generic Simulation Model for Mobile Working Machines

This master’s thesis has been done for Drive! –project in which a new electric motor solution for mobile working machines is developed. Generic simulation model will be used as marketing and development tool. It can be used to model a wide variety of different vehicles with and without electric motor and to show customer the difference between traditionally build vehicles and those with new electric motor solution. Customers can also use simulation model to research different solutions for their own vehicles. At the start of the project it was decided that MeVEA software would be used as main simulation program and Simulink will only be used to simulate the operation of electrical components. Development of the generic model started with the research of these two software applications, simulation models which are made with them and how these simulation models can be build faster. Best results were used for building of generic simulation model. Finished generic model can be used to produce new tractor models for real-time simulations in short notice. All information about model is collected to one datasheet which can be easily filled by the user. After datasheet is filled a script will automatically build new simulation model in seconds. At the moment generic model is capable of building simulation models for wide variety of different tractors but it can be easily altered for other vehicle types too which would also benefit greatly from electric drive solution. Those could be for example wheel loaders and harvesters.

Novel virtual environment and real-time simulation based methods for improving life-cycle efficiency of non-road mobile machinery

Virtual environments and real-time simulators (VERS) are becoming more and more important tools in research and development (R&D) process of non-road mobile machinery (NRMM). The virtual prototyping techniques enable faster and more cost-efficient development of machines compared to use of real life prototypes. High energy efficiency has become an important topic in the world of NRMM because of environmental and economic demands. The objective of this thesis is to develop VERS based methods for research and development of NRMM. A process using VERS for assessing effects of human operators on the life-cycle efficiency of NRMM was developed. Human in the loop simulations are ran using an underground mining loader to study the developed process. The simulations were ran in the virtual environment of the Laboratory of Intelligent Machines of Lappeenranta University of Technology. A physically adequate real-time simulation model of NRMM was shown to be reliable and cost effective in testing of hardware components by the means of hardware-in-the-loop (HIL) simulations. A control interface connecting integrated electro-hydraulic energy converter (IEHEC) with virtual simulation model of log crane was developed. IEHEC consists of a hydraulic pump-motor and an integrated electrical permanent magnet synchronous motorgenerator. The results show that state of the art real-time NRMM simulators are capable to solve factors related to energy consumption and productivity of the NRMM. A significant variation between the test drivers is found. The results show that VERS can be used for assessing human effects on the life-cycle efficiency of NRMM. HIL simulation responses compared to that achieved with conventional simulation method demonstrate the advances and drawbacks of various possible interfaces between the simulator and hardware part of the system under study. Novel ideas for arranging the interface are successfully tested and compared with the more traditional one. The proposed process for assessing the effects of operators on the life-cycle efficiency will be applied for wider group of operators in the future. Driving styles of the operators can be analysed statistically from sufficient large result data. The statistical analysis can find the most life-cycle efficient driving style for the specific environment and machinery. The proposed control interface for HIL simulation need to be further studied. The robustness and the adaptation of the interface in different situations must be verified. The future work will also include studying the suitability of the IEHEC for different working machines using the proposed HIL simulation method.

Mekaanisten laitteiden eheydenhallinta öljynjalostamolla

Mekaaniset laitteet ja putkistot muodostavat valtaosan jalostusprosessissa tarvittavista laitteista. Määrän ja käyttötarkoituksen perusteella voidaan sanoa, että laitteiden ja putkistojen eheyttä on pidettävä prosessiturvallisuuden sekä jalostustoiminnan kannattavuuden perustana. Laitteiden ja putkistojen on toimittava haasteellisissa olosuhteissa pitkiä aikoja. Tämä asettaa mekaanisten laitteiden eheydelle erityisvaatimuksia. Näiden vaatimusten toteuttaminen, ylläpito ja seuranta käyttöiän ajan voidaan varmistaa vain eheyden hallintaan liittyvillä toimenpiteillä. Toimenpiteet jakautuvat suunnitteluun, hankintaan, valmistukseen, käyttöön ja kunnossapitoon näiden erityispiirteiden mukaisesti. Työssä on kuvattu eheyden hallinnan keskeiset toimijat ja toiminta sekä asioita ja ilmiöitä eheyden hallintaan liittyen. Työn aikana on saatu kerättyä arvokasta kokemusta ja konkreettisia esimerkkejä siitä, miten eheyteen voidaan vaikuttaa tai miten eheyden menetys vaikuttaa toimintaan. Eheys ja sen hallinta ovat pysyvästi läsnä jalostustoiminnassa. Tulevienkin vuosien haasteet liittyvät eheyteen ja sen hallintaan. Tämän työn tärkeä viesti on, että eheydenhallinta kuuluu kaikille, sitä ei voida ulkoistaa.

Intensification of Operation of Inclined Plate Settler at Fertilizer Plant

Fertilizer plant’s process waters contain high concentrations of nitrogen compounds, such as ammonium and nitrate. Phosphorus and fluorine, which originate from phosphoric acid and rock phosphate (apatite) used in fertilizer production, are also present. Phosphorus and nitrogen are the primary nutrients causing eutrophication of surface waters. At fertilizer plant process waters are held in closed internal circulation. In a scrubber system process waters are used for washing exhaust gases from fertilizer reactors and dry gases from granulation drums as well as for cooling down the fertilizer slurry in neutralization reactor. Solids in process waters are separated in an inclined plate settler by gravitational sedimentation. However, the operation of inclined plate settler has been inadequate. The aim of this thesis was to intensify the operation of inclined plate settler and thus the solids separation e.g. through coagulation and/or flocculation process. Chemical precipitation was studied to reduce the amount of dissolved species in process waters. Specific interest was in precipitation of nitrogen, phosphorus, and fluorine containing specimens. Amounts of phosphorus and fluorine were reduced significantly by chemical precipitation. When compared to earlier studies, annual chemical costs were almost eight times lower. Instead, nitrogen compounds are readily dissolved in water, thus being difficult to remove by precipitation. Possible alternative techniques for nitrogen removal are adsorption, ion exchange, and reverse osmosis. Settling velocities of pH adjusted and flocculated process waters were sufficient for the operation of inclined plate settler. Design principles of inclined plate settler are also presented. In continuation studies, flow conditions in inclined plate settler should be modelled with computational fluid dynamics and suitability of adsorbents, ion exchange resins, and membranes should be studied in laboratory scale tests.

Weld joint characteristics by nano-materials addition

The need for industries to remain competitive in the welding business, has created necessity to develop innovative processes that can exceed customer’s demand. Significant development in improving weld efficiency, during the past decades, still have their drawbacks, specifically in the weld strength properties. The recent innovative technologies have created smallest possible solid material known as nanomaterial and their introduction in welding production has improved the weld strength properties and to overcome unstable microstructures in the weld. This study utilizes a qualitative research method, to elaborate the methods of introducing nanomaterial to the weldments and the characteristic of the welds produced by different welding processes. The study mainly focuses on changes in the microstructural formation and strength properties on the welded joint and also discusses those factors influencing such improvements, due to the addition of nanomaterials. The effect of nanomaterial addition in welding process modifies the physics of joining region, thereby, resulting in significant improvement in the strength properties, with stable microstructure in the weld. The addition of nanomaterials in the welding processes are, through coating on base metal, addition in filler metal and utilizing nanostructured base metal. However, due to its insignificant size, the addition of nanomaterials directly to the weld, would poses complications. The factors having major influence on the joint integrity are dispersion of nanomaterials, characteristics of the nanomaterials, quantity of nanomaterials and selection of nanomaterials. The addition of nanomaterials does not affect the fundamental properties and characteristics of base metals and the filler metal. However, in some cases, the addition of nanomaterials lead to the deterioration of the joint properties by unstable microstructural formations. Still research are ongoing to achieve high joint integrity, in various materials through different welding processes and also on other factors that influence the joint strength.

Experimentation on Wind Powered Hydraulic Heating System

It is common knowledge of the world’s dependency on fossil fuel for energy, its unsustainability on the long run and the changing trend towards renewable energy as an alternative energy source. This aims to cut down greenhouse gas emission and its impact on the rate of ecological and climatic change. Quite remarkably, wind energy has been one of many focus areas of renewable energy sources and has attracted lots of investment and technological advancement. The objective of this research is to explore wind energy and its application in household heating. This research aims at applying experimental approach in real time to study and verify a virtually simulated wind powered hydraulic house heating system. The hardware components comprise of an integrated hydraulic pump, flow control valve, hydraulic fluid and other hydraulic components. The system design and control applies hardware in-the-loop (HIL) simulation setup. Output signal from the semi-empirical turbine modelling controls the integrated motor to generate flow. Throttling the volume flow creates pressure drop across the valve and subsequently thermal power in the system to be outputted using a heat exchanger. Maximum thermal power is achieved by regulating valve orifice to achieve optimum system parameter. Savonius rotor is preferred for its low inertia, high starting torque and ease of design and maintenance characteristics, but lags in power efficiency. A prototype turbine design is used; with power output in range of practical Savonius turbine. The physical mechanism of the prototype turbine’s augmentation design is not known and will not be a focus in this study.

Enhancing Security of Linux OS against Administrators

Inside cyber security threats by system administrators are some of the main concerns of organizations about the security of systems. Since operating systems are controlled and managed by fully trusted administrators, they can negligently or intentionally break the information security and privacy of users and threaten the system integrity. In this thesis, we propose some solutions for enhancing the security of Linux OS by restricting administrators’ access to superuser’s privileges while they can still manage the system. We designed and implemented an interface for administrators in Linux OS called Linux Admins’ User Interface (LAUI) for managing the system in secure ways. LAUI along with other security programs in Linux like sudo protect confidentiality and integrity of users’ data and provide a more secure system against administrators’ mismanagement. In our model, we limit administrators to perform managing tasks in secure manners and also make administrators accountable for their acts. In this thesis we present some scenarios for compromising users’ data and breaking system integrity by system administrators in Linux OS. Then we evaluate how our solutions and methods can secure the system against these administrators’ mismanagement.

Suljetun sähkönjakeluverkon regulaatio teollisuusympäristössä

Tässä työssä tutkitaan suljetun jakeluverkon regulaatiota yhden suomalaisen teollisuussähköverkon näkökulmasta ja sitä verrataan olemassa olevaan energiaviraston jakeluverkkoja koskevaan säätelymalliin. Työssä tutkitaan verkkoyhtiön kehittämän säätelymallin toimivuutta ja sitä kuinka se täyttää hyvän valvontamallin ominaispiirteet. Tässä työssä ei ole tarkoituksena esittää uutta valvontamallia, vaan tutkia ja arvioida olemassa olevia malleja. Työssä käydään läpi olemassa oleva kolmannen valvontajakson regulaatiomalli sekä muutokset, joita on esitetty tuleville valvontakausille. Työssä taustoitetaan valvontatoimintaa myös yleisen talousteorian ja valvontateorioiden avulla. Tämän taustoituksen avulla tarkastellaan teollisuussähköverkkojen erityisiä ominaisuuksia ja edelleen tutkitun teollisuussähköverkon korkeita käyttövaatimuksia ja syitä tällaisille vaatimuksille. Verkkoyhtiön käyttämä tariffimalli kuvataan myös sen liittyessä sääntelyyn saumattomasti. Työssä todistettiin mallin toimivuus tämän kaltaisessa toimintaympäristössä, jossa käyntivarmuusvaatimus on erittäin korkea. Havainnoissa myös korostuu mallin pitkäjänteisyys ja ennustettavuus. Laskentaesimerkkien avulla arvioidaan liittymähinnoittelun kohtuullisuutta asiakkaalle ja mallin toimivuutta yleensä. Näissä tarkasteluissa havaittiin, että yleisellä tasolla liittymähinnoittelu on kohtuullista asiakkaalle ja se mahdollistaa asiakkaan pääomien tehokkaamman käytön kuin ilman verkkoyhtiötä. Kehittämiskohteina tuodaan esille keskeytyksistä aiheutuvien haittojen käsittely ja se, ettei tällaiseen verkkoympäristöön ole tällä hetkellä toimivaa mittaria, jolla voitaisiin arvioida kuinka hyvin verkkoyhtiö toimii.

Conformational analysis of antibody binding site using EDMA methods /

Euclidean distance matrix analysis (EDMA) methods are used to distinguish whether or not significant difference exists between conformational samples of antibody complementarity determining region (CDR) loops, isolated LI loop and LI in three-loop assembly (LI, L3 and H3) obtained from Monte Carlo simulation. After the significant difference is detected, the specific inter-Ca distance which contributes to the difference is identified using EDMA.The estimated and improved mean forms of the conformational samples of isolated LI loop and LI loop in three-loop assembly, CDR loops of antibody binding site, are described using EDMA and distance geometry (DGEOM). To the best of our knowledge, it is the first time the EDMA methods are used to analyze conformational samples of molecules obtained from Monte Carlo simulations. Therefore, validations of the EDMA methods using both positive control and negative control tests for the conformational samples of isolated LI loop and LI in three-loop assembly must be done. The EDMA-I bootstrap null hypothesis tests showed false positive results for the comparison of six samples of the isolated LI loop and true positive results for comparison of conformational samples of isolated LI loop and LI in three-loop assembly. The bootstrap confidence interval tests revealed true negative results for comparisons of six samples of the isolated LI loop, and false negative results for the conformational comparisons between isolated LI loop and LI in three-loop assembly. Different conformational sample sizes are further explored by combining the samples of isolated LI loop to increase the sample size, or by clustering the sample using self-organizing map (SOM) to narrow the conformational distribution of the samples being comparedmolecular conformations. However, there is no improvement made for both bootstrap null hypothesis and confidence interval tests. These results show that more work is required before EDMA methods can be used reliably as a method for comparison of samples obtained by Monte Carlo simulations.

Cloning and Characterisation of the human gene gremlin promoter

L’ostéoarthrose (OA) est une maladie articulaire invalidante caractérisée par la perte de l’intégrité du cartilage articulaire. Les recherches tentent de comprendre les mécanismes moléculaires de la maladie afin de trouver des inhibiteurs efficaces pouvant prévenir la dégradation du cartilage articulaire. Les BMPs (bone morphogenic proteins) jouent un rôle dans le processus pathophysiologique de cette maladie. Cette étude cible le rôle d’un antagoniste des BMPs, le gremlin. Nous avons étudié la régulation de l’expression de gremlin par le clonage et la caractérisation de son promoteur et en déterminant si gremlin pouvait jouer un rôle autre qu’antagoniste des BMP, en affectant l’expression d’autres gènes par l’activation d’une cascade de signalisation dans la cellule. Les résultats ont identifié une région importante dans le promoteur de gremlin qui affecte son activité basale et induite, et ont montré que le gremlin ne pouvait pas affecter l’expression génique et l’activation de signalisation intracellulaire indépendamment des BMPs. Cette étude démontre que le rôle de gremlin dans l’OA en est un essentiellement d’antagoniste des BMPs.

Les R-loops et leurs conséquences sur l'expression génique chez Escherichia coli.

Des variations importantes du surenroulement de l’ADN peuvent être générées durant la phase d’élongation de la transcription selon le modèle du « twin supercoiled domain ». Selon ce modèle, le déplacement du complexe de transcription génère du surenroulement positif à l’avant, et du surenroulement négatif à l’arrière de l’ARN polymérase. Le rôle essentiel de la topoisomérase I chez Escherichia coli est de prévenir l’accumulation de ce surenroulement négatif générée durant la transcription. En absence de topoisomérase I, l’accumulation de ce surenroulement négatif favorise la formation de R-loops qui ont pour conséquence d’inhiber la croissance bactérienne. Les R-loops sont des hybrides ARN-ADN qui se forment entre l’ARN nouvellement synthétisé et le simple brin d’ADN complémentaire. Dans les cellules déficientes en topoisomérase I, des mutations compensatoires s’accumulent dans les gènes qui codent pour la gyrase, réduisant le niveau de surenroulement négatif du chromosome et favorisant la croissance. Une des ces mutations est une gyrase thermosensible qui s’exprime à 37 °C. La RNase HI, une enzyme qui dégrade la partie ARN d’un R-loop, peut aussi restaurer la croissance en absence de topoisomérase I lorsqu’elle est produite en très grande quantité par rapport à sa concentration physiologique. En présence de topoisomérase I, des R-loops peuvent aussi se former lorsque la RNase HI est inactive. Dans ces souches mutantes, les R-loops induisent la réponse SOS et la réplication constitutive de l’ADN (cSDR). Dans notre étude, nous montrons comment les R-loops formés en absence de topoisomérase I ou RNase HI peuvent affecter négativement la croissance des cellules. Lorsque la topoisomérase I est inactivée, l’accumulation d’hypersurenroulement négatif conduit à la formation de nombreux R-loops, ce qui déclenche la dégradation de l’ARN synthétisé. Issus de la dégradation de l’ARNm de pleine longueur, des ARNm incomplets et traductibles s’accumulent et causent l’inhibition de la synthèse protéique et de la croissance. Le processus par lequel l’ARN est dégradé n’est pas encore complètement élucidé, mais nos résultats soutiennent fortement que la RNase HI présente en concentration physiologique est responsable de ce phénotype. Chose importante, la RNase E qui est l’endoribonuclease majeure de la cellule n’est pas impliquée dans ce processus, et la dégradation de l’ARN survient avant son action. Nous montrons aussi qu’une corrélation parfaite existe entre la concentration de RNase HI, l’accumulation d’hypersurenroulement négatif et l’inhibition de la croissance bactérienne. Lorsque la RNase HI est en excès, l’accumulation de surenroulement négatif est inhibée et la croissance n’est pas affectée. L’inverse se produit Lorsque la RNase HI est en concentration physiologique. En limitant l’accumulation d’hypersurenroulement négatif, la surproduction de la RNase HI prévient alors la dégradation de l’ARN et permet la croissance. Quand la RNase HI est inactivée en présence de topoisomérase I, les R-loops réduisent le niveau d’expression de nombreux gènes, incluant des gènes de résistance aux stress comme rpoH et grpE. Cette inhibition de l’expression génique n’est pas accompagnée de la dégradation de l’ARN contrairement à ce qui se produit en absence de topoisomérase I. Dans le mutant déficient en RNase HI, la diminution de l’expression génique réduit la concentration cellulaire de différentes protéines, ce qui altère négativement le taux de croissance et affecte dramatiquement la survie des cellules exposées aux stress de hautes températures et oxydatifs. Une inactivation de RecA, le facteur essentiel qui déclenche la réponse SOS et le cSDR, ne restaure pas l’expression génique. Ceci démontre que la réponse SOS et le cSDR ne sont pas impliqués dans l’inhibition de l’expression génique en absence de RNase HI. La croissance bactérienne qui est inhibée en absence de topoisomérase I, reprend lorsque l’excès de surenroulement négatif est éliminé. En absence de RNase HI et de topoisomérase I, le surenroulement négatif est très relaxé. Il semble que la réponse cellulaire suite à la formation de R-loops, soit la relaxation du surenroulement négatif. Selon le même principe, des mutations compensatoires dans la gyrase apparaissent en absence de topoisomérase I et réduisent l’accumulation de surenroulement négatif. Ceci supporte fortement l’idée que le surenroulement négatif joue un rôle primordial dans la formation de R-loop. La régulation du surenroulement négatif de l’ADN est donc une tâche essentielle pour la cellule. Elle favorise notamment l’expression génique optimale durant la croissance et l’exposition aux stress, en limitant la formation de R-loops. La topoisomérase I et la RNase HI jouent un rôle important et complémentaire dans ce processus.

Polymorphisme de la capside des papillomavirus appartenant à l’espèce 9 des alphapapillomavirus

Le gène L1 encode pour la protéine majeure de la capside des papillomavirus humains (VPH). L’information relative au polymorphisme de L1 pour les types autres que VPH- 16 est jusqu’ici limitée. Cet ouvrage explore le polymorphisme de L1 en comparant les séquences des types phylogénétiquement apparentés VPH-31, -33, -35 à VPH-16. Des spécimens génitaux recueillis de 732 femmes VIH-séropositives et 323 VIHséronégatives ont été criblés à le recherche d’ADN de VPH par PCR consensus au niveau du gène L1. Les échantillons positifs pour VPH-16 (n=74), -31 (n=74), -33 (n=37) et -35 (n=58) étaient analysés par PCR-séquençage pour la totalité du gène L1. Le nombre de nucléotides substitués pour L1 variait de 19 pour VPH-33 à 52 pour VPH-31. Le rapport du nombre de variantes sur le nombre d’isolats testés était plus élevé pour VPH-31 (56.4%, p=0.05) et VPH-35 (60.3%, p=0.04) comparativement à VPH-16 (40.5%), alors que ce ratio était inférieur pour VPH-33 mais sans différence statistiquement significative (24.3%, p=0.14). La distance entre les variantes était plus grande à l’intérieur des cinq boucles présumément exposées à la surface de la protéine L1 que dans la séquence à l’extérieur (p<0.01) Des variations synonymes étaient observées chez 1.7% (95% CI 1.1- 2.3) des nucléotides intra-boucles et 2.4% (95% CI 1.2-3.7) de ceux extra-boucles. Les variations non-synonymes étaient rencontrées pour 1.8% (95% CI 1.1-2.5) des nucléotides intra-boucles et 0.2% (95% CI 0-0.4) pour les nucléotides extra-boucles. Les ratios dN/dS étaient inférieurs à 1.0 pour les régions extra-boucles et encore davantage pour les régions intra-boucles. Ces résultats suggèrent que les séquences des régions hypervariables de L1 ont été sélectionnées positivement.

Conception de miARN artificiels basée sur la caractérisation de la boucle de régulation miR-20/E2F

La biologie moléculaire et, plus spécifiquement, la régulation de l’expression génique ont été révolutionnées par la découverte des microARN (miARN). Ces petits ARN d’une vingtaine de nucléotides sont impliqués dans la majorité des processus cellulaires et leur expression est dérégulée dans plusieurs maladies, comme le cancer. Un miARN reconnaît ses cibles principalement par son noyau, ce qui lui permet de réguler simultanément la traduction de centaines d’ARN messagers. Nos travaux ont montré l’existence d’une boucle de rétro-activation négative, entre deux miARN du polycistron miR-17-92 et trois facteurs de transcription de la famille E2F. E2F1, 2 et 3 induisent la transcription de miR-20 et miR-17 qui par la suite inhibent leur traduction. Nos résultats suggèrent l’implication de cette boucle dans la résistance à l’apoptose induite par E2F1 dans les cellules du cancer de la prostate, ce qui expliquerait en partie le potentiel oncogénique du polycistron miR-17-92. L’étude de ce motif de régulation nous a donc permis de réaliser le potentiel incroyable qu’ont les miARN à inhiber la traduction de plusieurs gènes. Basé sur les règles de reconnaissance des miARN, nous avons développé et validé MultiTar. Cet outil bioinformatique permet de trouver la séquence d’un miARN artificiel ayant le potentiel d’inhiber la traduction de gènes d’intérêts choisis par l’utilisateur. Afin de valider MultiTar, nous avons généré des multitargets pouvant inhiber l’expression des trois E2F, ce qui nous a permis de comparer leur efficacité à celle de miR-20. Nos miARN artificiels ont la capacité d’inhiber la traduction des E2F et de neutraliser leur fonction redondante de la progression du cycle cellulaire de façon similaire ou supérieur à miR-20. La fonctionnalité de notre programme, ouvre la voie à une stratégie flexible pouvant cibler le caractère multigénique de différents processus cellulaires ou maladies complexes, tel que le cancer. L’utilisation de miARN artificiels pourrait donc représenter une alternative intéressante aux stratégies déjà existantes, qui sont limitées à inhiber des cibles uniques. En plus d’élucider un réseau de régulation complexe impliquant les miARN, nous avons pu tirer profit de leur potentiel d’inhibition par la conception de miARN artificiels.