Fission yeast rad51 and dmc1, two efficient DNA recombinases forming helical nucleoprotein filaments.

Homologous recombination is important for the repair of double-strand breaks during meiosis. Eukaryotic cells require two homologs of Escherichia coli RecA protein, Rad51 and Dmc1, for meiotic recombination. To date, it is not clear, at the biochemical level, why two homologs of RecA are necessary during meiosis. To gain insight into this, we purified Schizosaccharomyces pombe Rad51 and Dmc1 to homogeneity. Purified Rad51 and Dmc1 form homo-oligomers, bind single-stranded DNA preferentially, and exhibit DNA-stimulated ATPase activity. Both Rad51 and Dmc1 promote the renaturation of complementary single-stranded DNA. Importantly, Rad51 and Dmc1 proteins catalyze ATP-dependent strand exchange reactions with homologous duplex DNA. Electron microscopy reveals that both S. pombe Rad51 and Dmc1 form nucleoprotein filaments. Rad51 formed helical nucleoprotein filaments on single-stranded DNA, whereas Dmc1 was found in two forms, as helical filaments and also as stacked rings. These results demonstrate that Rad51 and Dmc1 are both efficient recombinases in lower eukaryotes and reveal closer functional and structural similarities between the meiotic recombinase Dmc1 and Rad51. The DNA strand exchange activity of both Rad51 and Dmc1 is most likely critical for proper meiotic DNA double-strand break repair in lower eukaryotes.

Electroluminiscence and optical amplification in silicon nanostructures: towards the integration of electronics and photonics

This line of research of my group intends to establish a Silicon technological platform in the field of photonics allowing the development of a wide set of applications. Particularly, what is still lacking in Silicon Photonics is an efficient and integrable light source such an LED or laser. Nanocrystals in silicon oxide or nitride matrices have been recently demonstrated as competitive materials for both active components (electrically and optically driven light emitters and optical amplifiers) and passive ones (waveguides and modulators). The final goal is the achievement of a complete integration of electronic and optical functions in the same CMOS chip. The first part of this paper will introduce the structural and optical properties of LEDs fabricated from silicon nanostructures. The second will treat the interaction of such nanocrystals with rare-earth elements (Er), which lead to an efficient hybrid system emitting in the third window of optical fibers. I will present the fabrication and assessment of optical waveguide amplifiers at 1.54 ¿m for which we have been able to demonstrate recently optical gain in waveguides made from sputtered silicon suboxide materials.

The ubiquitin-like protein LC3 regulates the Rho-GEF activity of AKAP-Lbc.

AKAP-Lbc is a member of the A-kinase anchoring protein (AKAP) family that has been recently associated with the development of pathologies, such as cardiac hypertrophy and cancer. We have previously demonstrated that, at the molecular level, AKAP-Lbc functions as a guanine nucleotide exchange factor (GEF) that promotes the specific activation of RhoA. In the present study, we identified the ubiquitin-like protein LC3 as a novel regulatory protein interacting with AKAP-Lbc. Mutagenesis studies revealed that LC3, through its NH(2)-terminal alpha-helical domain, interacts with two binding sites located within the NH(2)-terminal regulatory region of AKAP-Lbc. Interestingly, LC3 overexpression strongly reduced the ability of AKAP-Lbc to interact with RhoA, profoundly impairing the Rho-GEF activity of the anchoring protein and, as a consequence, its ability to promote cytoskeletal rearrangements associated with the formation of actin stress fibers. Moreover, AKAP-Lbc mutants that fail to interact with LC3 show a higher basal Rho-GEF activity as compared with the wild type protein and become refractory to the inhibitory effect of LC3. This suggests that LC3 binding maintains AKAP-Lbc in an inactive state that displays a reduced ability to promote downstream signaling. Collectively, these findings provide evidence for a previously uncharacterized role of LC3 in the regulation of Rho signaling and in the reorganization of the actin cytoskeleton.

Scaffold attachment factor B1 directly interacts with nuclear receptors in living cells and represses transcriptional activity.

Transcriptional activity relies on coregulators that modify the chromatin structure and serve as bridging factors between transcription factors and the basal transcription machinery. Using the DE domain of human peroxisome proliferator-activated receptor gamma (PPARgamma) as bait in a yeast two-hybrid screen of a human adipose tissue library, we isolated the scaffold attachment factor B1 (SAFB1/HET/HAP), which was previously shown to be a corepressor of estrogen receptor alpha. We show here that SAFB1 has a very broad tissue expression profile in human and is also expressed all along mouse embryogenesis. SAFB1 interacts in pull-down assays not only with PPARgamma but also with all nuclear receptors tested so far, albeit with different affinities. The association of SAFB1 and PPARgamma in vivo is further demonstrated by fluorescence resonance energy transfer (FRET) experiments in living cells. We finally show that SAFB1 is a rather general corepressor for nuclear receptors. Its change in expression during the early phases of adipocyte and enterocyte differentiation suggests that SAFB1 potentially influences cell proliferation and differentiation decisions.

SAT Modulo Linear Arithmetic for Solving Polynomial

Polynomial constraint solving plays a prominent role in several areas of hardware and software analysis and verification, e.g., termination proving, program invariant generation and hybrid system verification, to name a few. In this paper we propose a new method for solving non-linear constraints based on encoding the problem into an SMT problem considering only linear arithmetic. Unlike other existing methods, our method focuses on proving satisfiability of the constraints rather than on proving unsatisfiability, which is more relevant in several applications as we illustrate with several examples. Nevertheless, we also present new techniques based on the analysis of unsatisfiable cores that allow one to efficiently prove unsatisfiability too for a broad class of problems. The power of our approach is demonstrated by means of extensive experiments comparing our prototype with state-of-the-art tools on benchmarks taken both from the academic and the industrial world.

Diagnosing Patients Combining Principal Components Analysis and Case Based Reasoning

This paper addresses the application of a PCA analysis on categorical data prior to diagnose a patients data set using a Case-Based Reasoning (CBR) system. The particularity is that the standard PCA techniques are designed to deal with numerical attributes, but our medical data set contains many categorical data and alternative methods as RS-PCA are required. Thus, we propose to hybridize RS-PCA (Regular Simplex PCA) and a simple CBR. Results show how the hybrid system produces similar results when diagnosing a medical data set, that the ones obtained when using the original attributes. These results are quite promising since they allow to diagnose with less computation effort and memory storage

The cAMP response element binding protein-2 (CREB-2) can interact with the C/EBP-homologous protein (CHOP).

cAMP response element binding protein-2 (CREB-2) is a basic leucine zipper (bZIP) factor that was originally described as a repressor of CRE-dependent transcription but that can also act as a transcriptional activator. Moreover, CREB-2 is able to function in association with the viral Tax protein as an activator of the human T-cell leukemia virus type I (HTLV-I) promoter. Here we show that CREB-2 is able to interact with C/EBP-homologous protein (CHOP), a bZIP transcription factor known to inhibit CAAT/enhancer-dependent transcription. Cotransfection of CHOP with CREB-2 results in decreased activation driven by the cellular CRE motif or the HTLV-I proximal Tax-responsive element, confirming that CREB-2 and CHOP can interact with each other in vivo.

Bootstrapping a statistical speech translator from a rule-based one

We describe a series of experiments in which we start with English to French and English to Japanese versions of an Open Source rule-based speech translation system for a medical domain, and bootstrap correspondign statistical systems. Comparative evaluation reveals that the rule-based systems are still significantly better than the statistical ones, despite the fact that considerable effort has been invested in tuning both the recognition and translation components; also, a hybrid system only marginally improved recall at the cost of a los in precision. The result suggests that rule-based architectures may still be preferable to statistical ones for safety-critical speech translation tasks.

The adaptor complex 2 directly interacts with the alpha 1b-adrenergic receptor and plays a role in receptor endocytosis.

Using the yeast two-hybrid system, we identified the mu 2 subunit of the clathrin adaptor complex 2 as a protein interacting with the C-tail of the alpha 1b-adrenergic receptor (AR). Direct association between the alpha 1b-AR and mu 2 was demonstrated using a solid phase overlay assay. The alpha 1b-AR/mu 2 interaction occurred inside the cells, as shown by the finding that the transfected alpha 1b-AR and the endogenous mu 2 could be coimmunoprecipitated from HEK-293 cell extracts. Mutational analysis of the alpha 1b-AR revealed that the binding site for mu 2 does not involve canonical YXX Phi or dileucine motifs but a stretch of eight arginines on the receptor C-tail. The binding domain of mu 2 for the receptor C-tail involves both its N terminus and the subdomain B of its C-terminal portion. The alpha 1b-AR specifically interacted with mu 2, but not with the mu 1, mu 3, or mu 4 subunits belonging to other AP complexes. The deletion of the mu 2 binding site in the C-tail markedly decreased agonist-induced receptor internalization as demonstrated by confocal microscopy as well as by the results of a surface receptor biotinylation assay. The direct association of the adaptor complex 2 with a G protein-coupled receptor has not been reported so far and might represent a common mechanism underlying clathrin-mediated receptor endocytosis.

Hybridikäytön mitoitus liikkuvan työkoneen energian talteenottojärjestelmäksi

Työssä tarkastellaan sähköisiä energian talteenottomahdollisuuksia liikkuvissa työkoneissa. Työssä esitetään kolme erityyppistä liikkuvaan työkoneeseen soveltuvaa sähköisen energian talteenottojärjestelmää sekä mitoitetaan hybridikäyttö kahdelle erityyppiselle työkonesovellukselle kuormituskäyrien perusteella. Lisäksi työssä lasketaan hybridijärjestelmää käyttämällä saavutettava energiansäästö nykyiseen käyttöön verrattuna.

Time-series forecasting of pollutant concentration levels using particle swarm optimization and artificial neural networks

This study evaluates the application of an intelligent hybrid system for time-series forecasting of atmospheric pollutant concentration levels. The proposed method consists of an artificial neural network combined with a particle swarm optimization algorithm. The method not only searches relevant time lags for the correct characterization of the time series, but also determines the best neural network architecture. An experimental analysis is performed using four real time series and the results are shown in terms of six performance measures. The experimental results demonstrate that the proposed methodology achieves a fair prediction of the presented pollutant time series by using compact networks.

Kaivoslastauskoneen hybridisointianalyysi virtuaali- ja in-loop -simuloinnin avulla

Työssä tutkitaan raskaiden työkoneiden hybridisointimitoitusta simuloimalla. Työssä esitetään simulation-in-the-loop-simulointiin perustuva järjestelmä, jolla esimerkkitapauksena oleva kaivoslastauskone työympäristöineen voidaan mallintaa mekaaniselta osaltaan monikappaledynamiikkaan perustuvalla ohjelmistolla ja hybridijärjestelmän osalta Simulinkissa. Yhdistetty simulointi mahdollistaa hybridityökoneen virtuaalimallin ohjaamisen käyttäjän toimesta reaaliajassa. Simuloinnista saadaan tuloksena mm. työsykli, jota voidaan käyttää hybridisointimitoitukseen. Hybridisointi toteutetaan kahdella erilaisella kokoonpanolla, joista analysoidaan suorituskykyä sekä polttoaineen kulutusta. Tuloksia verrataan pelkästään dieselmoottoria voimanlähteenä käyttävään lastauskoneeseen. Työssä tehty tutkimus osoittaa, että (sarja-) hybridisoinnilla voidaan saavuttaa merkittäviä etuja raskaiden työkoneiden polttoainetehokkuudessa. Dieselmoottoria voidaan ajaa sellaisessa staattisessa toimintapisteessä, jonka hyötysuhde on korkea riippumatta työkoneen kuormituksesta. Saavutettu hyöty on toteutetussa tutkimuksessa parhaimmillaan jopa 56 % vähennys polttoaineenkulutuksessa. Lisäksi tarvittava dieselin nimellisteho pienenee huomattavasti. Tutkimuksen osana esitellään myös Hardware-in-the-Loop -laitteisto, jonka avulla voidaan liittää oikea sähkömoottori ja taajuudenmuuttaja osaksi virtuaalisesti simuloitua työkonetta.

Energy Efficiency of a Diesel-Electric MobileWorking Machine

The power demand of many mobile working machines such as mine loaders, straddle carriers and harvesters varies significantly during operation, and typically, the average power demand of a working machine is considerably lower than the demand for maximum power. Consequently, for most of the time, the diesel engine of a working machine operates at a poor efficiency far from its optimum efficiency range. However, the energy efficiency of dieseldriven working machines can be improved by electric hybridization. This way, the diesel engine can be dimensioned to operate within its optimum efficiency range, and the electric drive with its energy storages responds to changes in machine loading. A hybrid working machine can be implemented in many ways either as a parallel hybrid, a series hybrid or a combination of these two. The energy efficiency of hybrid working machines can be further enhanced by energy recovery and reuse. This doctoral thesis introduces the component models required in the simulation model of a working machine. Component efficiency maps are applied to the modelling; the efficiency maps for electrical machines are determined analytically in the whole torque–rotational speed plane based on the electricalmachine parameters. Furthermore, the thesis provides simulation models for parallel, series and parallel-series hybrid working machines. With these simulation models, the energy consumption of the working machine can be analysed. In addition, the hybridization process is introduced and described. The thesis provides a case example of the hybridization and dimensioning process of a working machine, starting from the work cycle of the machine. The selection and dimensioning of the hybrid system have a significant impact on the energy consumption of a hybrid working machine. The thesis compares the energy consumption of a working machine implemented by three different hybrid systems (parallel, series and parallel-series) and with different component dimensions. The payback time of a hybrid working machine and the energy storage lifetime are also estimated in the study.

Lämmöntuotanto älykkäässä energiaverkossa

Energiaverkon edistäminen tulee olemaan tulevaisuudessa suuressa roolissa niin Suomessa kuin maailmalla. Tällöin yhtenä vaihtoehtona on älykkyyden tuominen koko energiajärjestelmään niin sähkön kuin lämmönkin osalta. Tällöin voidaan vähentää kulutushuippujen aikaista energian käyttöä ja saada koko verkoston energiankulutus profiili tasaiseksi. Tässä työssä tarkastellaan spot-sähkön hyödyntämismahdollisuuksia lämmöntuotannossa. Työssä kehitetyn mallinnustyökalun avulla tutkittiin erilaisia ajotapoja ja erilaisten järjestelmien kokonaiskustannuksia. Työssä esitellään esimerkkilaskennan avulla spot-sähkön käytöstä syntyviä kustannuksia ja keinoja vaikuttaa niihin eri järjestelmä muutoksin. Malli mahdollistaa erilaisten järjestelmien ja niiden ajotapojen tutkimista. Mallilla voidaan myös tutkia erilaisten alueiden kulutuskäyttäytymistä ja hyödyntää sitä kustannuslaskelmiin. Voidaan todeta, että työssä muodostunut malli on toimiva ja sitä voidaan hyödyntää alueellisten lämmöntuotantojärjestelmien ajotapojen optimointiin.

Sähköverkosta irti olevan pienhybridijärjestelmän toteutus

Lappeen siniset –partiolippukunnalla on käytössään leiripaikka Humaljärvellä, Lappeenrannassa. Leiripaikalla ei ole liityntää sähköverkkoon, joten leiripaikalle on asennettu kaksi erillistä aurinkovoimalla toimivaa sähköjärjestelmää. Leiripaikan sähköistetyt rakennukset ovat pääkämppä ja saunan sekä vanhan kämpän muodostama kokonaisuus. Aurinkopaneeleilla tuotettu sähköenergia varastoidaan akustoihin. Lippukunta on havainnot käytössä, ettei talvella tuotettu aurinkoenergia riitä kattamaan pääkämpän sähkönkulutusta, joten leiripaikalle on päätetty hankkia tuulivoimala lisäämään tuotantoa. Tässä kandidaatin työssä esitellään hybridijärjestelmään kuuluvien aurinko- ja tuulivoiman toimintaperiaatteita sekä näiden komponentteja. Aurinko- ja tuulivoimalla tuotetulle sähköenergialle lasketaan arviot, joita verrataan leiripaikan sähköjärjestelmän arvioituun kulutukseen. Leiripaikalle tulevaa tuuliturbiinia ja sen lataussäädintä testataan laboratoriossa, jotta varmistutaan niiden soveltuvuudesta sekä toimivuudesta kohteeseen. Testausten ja laitteiden datalehtien avulla suunnitellaan leiripaikalle toimiva hybridijärjestelmä, joka kattaa leiripaikan ympärivuotisen sähkönkulutuksen.