Rhythmic growth explained by coincidence between internal and external cues.

Most organisms use circadian oscillators to coordinate physiological and developmental processes such as growth with predictable daily environmental changes like sunrise and sunset. The importance of such coordination is highlighted by studies showing that circadian dysfunction causes reduced fitness in bacteria and plants, as well as sleep and psychological disorders in humans. Plant cell growth requires energy and water-factors that oscillate owing to diurnal environmental changes. Indeed, two important factors controlling stem growth are the internal circadian oscillator and external light levels. However, most circadian studies have been performed in constant conditions, precluding mechanistic study of interactions between the clock and diurnal variation in the environment. Studies of stem elongation in diurnal conditions have revealed complex growth patterns, but no mechanism has been described. Here we show that the growth phase of Arabidopsis seedlings in diurnal light conditions is shifted 8-12 h relative to plants in continuous light, and we describe a mechanism underlying this environmental response. We find that the clock regulates transcript levels of two basic helix-loop-helix genes, phytochrome-interacting factor 4 (PIF4) and PIF5, whereas light regulates their protein abundance. These genes function as positive growth regulators; the coincidence of high transcript levels (by the clock) and protein accumulation (in the dark) allows them to promote plant growth at the end of the night. Thus, these two genes integrate clock and light signalling, and their coordinated regulation explains the observed diurnal growth rhythms. This interaction may serve as a paradigm for understanding how endogenous and environmental signals cooperate to control other processes.

Influence of the implanted pulse generator as reference electrode in finite element model of monopolar deep brain stimulation.

Electrical deep brain stimulation (DBS) is an efficient method to treat movement disorders. Many models of DBS, based mostly on finite elements, have recently been proposed to better understand the interaction between the electrical stimulation and the brain tissues. In monopolar DBS, clinically widely used, the implanted pulse generator (IPG) is used as reference electrode (RE). In this paper, the influence of the RE model of monopolar DBS is investigated. For that purpose, a finite element model of the full electric loop including the head, the neck and the superior chest is used. Head, neck and superior chest are made of simple structures such as parallelepipeds and cylinders. The tissues surrounding the electrode are accurately modelled from data provided by the diffusion tensor magnetic resonance imaging (DT-MRI). Three different configurations of RE are compared with a commonly used model of reduced size. The electrical impedance seen by the DBS system and the potential distribution are computed for each model. Moreover, axons are modelled to compute the area of tissue activated by stimulation. Results show that these indicators are influenced by the surface and position of the RE. The use of a RE model corresponding to the implanted device rather than the usually simplified model leads to an increase of the system impedance (+48%) and a reduction of the area of activated tissue (-15%).

The role of MIC-1/GDF15 cytokine in glioblastoma

AbstractDespite advances in diagnosis and treatment made over the past two decades, high-gradeprimary brain tumors remain incurable neoplasms. Glioblastoma (GBM) represents the mostmalignant stage of astrocytic brain tumors. Identification of diagnostic and prognostic markers ineasily accessible biological material, such as plasma or cerebro-spinal fluid (CSF), would greatlyfacilitate the management of GBM patients. Elucidation of the molecular mechanisms that underlie thefunction of the factors implicated in GBM development would pave the way towards their potentialutility in cancer-targeting therapy.MIC-1/GDF15 (Macrophage Inhibitory Cytokine-1/ Growth Differentiation Factor 15), asecreted protein of the TGF-β superfamily, emerged as a candidate marker exhibiting increasingmRNA expression during astrocytoma malignant progression. However, injection of MIC-1/GDF15over-expressing GBM cell lines into nude mice has been previously shown to completely abolish theinherent tumorigenicity.In this study, determination of MIC-1/GDF15 protein levels in the CSF of a cohort of 94patients with intracranial tumors including astrocytomas (grades II, III and IV), meningioma, andmetastasis revealed significantly increased concentrations in GBM patients as compared to controlcohort of patients treated for non-neoplastic diseases. However, MIC-1/GDF15 levels were notelevated in the matching plasma samples from these patients. Most interestingly, GBM patients withthe increased concentrations of MIC-1/GDF15 in the CSF had worse outcome.In GBM tissue, it was found that the expression of MIC-1/GDF15 gene is low. Promotermethylation of the gene may partially explain the overall low expression levels. Investigation of thecellular origin of MIC-1/GDF15 expression in GBM tissue led to the MIC-1/GDF15 protein detectionin a subpopulation of the tumor infiltrating macrophages. These findings substantiated the workinghypothesis of MIC-1/GDF15 as harboring tumor-suppressive properties in GBM. Analysis of thesignaling pathway mediated by MIC-1/GDF15 in GBM highlighted the potential role of TGF-β signaltransduction. However, the lack of the functional response to the presence of MIC-1/GDF15 in-vitrosuggested operation of a paracrine loop for suppression of tumor formation which is evident solely invivo.In conclusion, MIC-1/GDF15 protein measured in the CSF may have diagnostic andprognostic values in patients with intracranial tumors. Molecular studies collectively proposeimplication of the tumor-host interactions in mediating the MIC-1/GDF15 tumor-suppressing activityduring GBM development.RésuméMalgré les progrès durant ces deux dernières décennies dans le diagnostique et le traitementdes tumeurs du cerveau primaires, ces néoplasmes restent incurables. Le glioblastome représente laforme la plus maligne des tumeurs astrocytiques du cerveau (astrocytomes). Pour le diagnostic et lepronostic, l'identification de marqueurs présents dans des substances facilement accessibles comme leplasma où le liquide céphalorachidien (LCR) faciliterait beaucoup la prise en charge des patients. Lacompréhension des mécanismes moléculaires de facteurs impliqués dans le développement du GBMpourrait ouvrir la voie vers l'utilisation de ces mécanismes dans des thérapies ciblées.MIC-1/GDF15 (Macrophage Inhibitory Cytokine-1/ Growth Differentiation Factor 15), uneprotéine secrétée qui appartient à la superfamille TGF-β, s'est révélé être un marqueur candidat, dontl'expression d'ARN messager augmente pendant la progression des astrocytomes malins. Cependant,une précedente étude montre que l'injection des lignées cellulaires de GBM fortement productrices deMIC-1/GDF15 dans des souris immunodéprimées abolit la tumorigénicité.Dans cette étude, les mesures dans une cohorte de 94 patients atteints de tumeursintracrâniennes comprenant des astrocytomes (grades II, III et IV), méningiomes et métastases,présentent des augmentations significatives des niveaux protéiques de MIC-1/GDF15 dans le LCRdes patients atteints de GBM par rapport aux patients traités pour des maladies non cancéreuses.Cependant, les niveaux de MIC-1/GDF15 n'étaient pas spécialement élevés dans le plasma. De plus,les patients atteints d'un GBM avec des niveaux élevés de MIC-1/GDF15 dans le LCR ont survécumoins longtemps. Dans les tissus de glioblastome, on observe que le gène MIC-1/GDF15 est peuexprimé. La méthylation du promoteur explique partiellement le faible niveau d'expression du gène.La recherche l'origine cellulaire de l'expression de MIC-1/GDF15, a permis de découvrir la présencede protéines MIC-1/GDF15 dans une sous-population de macrophages qui infiltrent les tumeurs. Cetteobservation supporte l'hypothèse que MIC-1/GDF15 présentait des propriétés de suppression destumeurs de type GBM. Des études sur les voies de signalisation régulées par MIC-1/GDF15 dans lesGBMs ont souligné l'importance de la voie de transduction du signal TGF-β. Cependant, l'absence deréponse fonctionnelle à MIC-1/GDF15 in vitro suggère fortement l'activité d'une boucle paracrinepour la répression de la formation de tumeur, qui n'est observé que in vivo.En conclusion, la protéine MIC-1/GDF15 mesurée dans le LCR pourrait avoir une valeur pourle diagnostic et le pronostic chez les patients atteints de GBM. Les études moléculaires suggèrent unepossible implication de l'interaction hôte-tumeur dans l'activité anti-tumorale de MIC-1/GDF15 sur leGBM.

Molecular characterization of a human matrix attachment region epigenetic regulator.

Matrix attachment regions (MAR) generally act as epigenetic regulatory sequences that increase gene expression, and they were proposed to partition chromosomes into loop-forming domains. However, their molecular mode of action remains poorly understood. Here, we assessed the possible contribution of the AT-rich core and adjacent transcription factor binding motifs to the transcription augmenting and anti-silencing effects of human MAR 1-68. Either flanking sequences together with the AT-rich core were required to obtain the full MAR effects. Shortened MAR derivatives retaining full MAR activity were constructed from combinations of the AT-rich sequence and multimerized transcription factor binding motifs, implying that both transcription factors and the AT-rich microsatellite sequence are required to mediate the MAR effect. Genomic analysis indicated that MAR AT-rich cores may be depleted of histones and enriched in RNA polymerase II, providing a molecular interpretation of their chromatin domain insulator and transcriptional augmentation activities.

Robust power allocation algorithms for MIMO OFDM systems with imperfect CSI

This paper presents a Bayesian approach to the design of transmit prefiltering matrices in closed-loop schemes robust to channel estimation errors. The algorithms are derived for a multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) system. Two different optimizationcriteria are analyzed: the minimization of the mean square error and the minimization of the bit error rate. In both cases, the transmitter design is based on the singular value decomposition (SVD) of the conditional mean of the channel response, given the channel estimate. The performance of the proposed algorithms is analyzed,and their relationship with existing algorithms is indicated. As withother previously proposed solutions, the minimum bit error rate algorithmconverges to the open-loop transmission scheme for very poor CSI estimates.

Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers.

In shade-intolerant plants such as Arabidopsis, a reduction in the red/far-red (R/FR) ratio, indicative of competition from other plants, triggers a suite of responses known as the shade avoidance syndrome (SAS). The phytochrome photoreceptors measure the R/FR ratio and control the SAS. The phytochrome-interacting factors 4 and 5 (PIF4 and PIF5) are stabilized in the shade and are required for a full SAS, whereas the related bHLH factor HFR1 (long hypocotyl in FR light) is transcriptionally induced by shade and inhibits this response. Here we show that HFR1 interacts with PIF4 and PIF5 and limits their capacity to induce the expression of shade marker genes and to promote elongation growth. HFR1 directly inhibits these PIFs by forming non-DNA-binding heterodimers with PIF4 and PIF5. Our data indicate that PIF4 and PIF5 promote SAS by directly binding to G-boxes present in the promoter of shade marker genes, but their action is limited later in the shade when HFR1 accumulates and forms non-DNA-binding heterodimers. This negative feedback loop is important to limit the response of plants to shade.

Glucagon-like peptide-1 increases beta-cell glucose competence and proliferation by translational induction of insulin-like growth factor-1 receptor expression.

Glucagon-like peptide-1 (GLP-1) protects beta-cells against apoptosis, increases their glucose competence, and induces their proliferation. We previously demonstrated that the anti-apoptotic effect was mediated by an increase in insulin-like growth factor-1 receptor (IGF-1R) expression and signaling, which was dependent on autocrine secretion of insulin-like growth factor 2 (IGF-2). Here, we further investigated how GLP-1 induces IGF-1R expression and whether the IGF-2/IGF-1R autocrine loop is also involved in mediating GLP-1-increase in glucose competence and proliferation. We show that GLP-1 up-regulated IGF-1R expression by a protein kinase A-dependent translational control mechanism, whereas isobutylmethylxanthine, which led to higher intracellular accumulation of cAMP than GLP-1, increased both IGF-1R transcription and translation. We then demonstrated, using MIN6 cells and primary islets, that the glucose competence of these cells was dependent on the level of IGF-1R expression and on IGF-2 secretion. We showed that GLP-1-induced primary beta-cell proliferation was suppressed by Igf-1r gene inactivation and by IGF-2 immunoneutralization or knockdown. Together our data show that regulation of beta-cell number and function by GLP-1 depends on the cAMP/protein kinase A mediated-induction of IGF-1R expression and the increased activity of an IGF-2/IGF-1R autocrine loop.

Personalized drug administrations using Support Vector Machine

The decision-making process regarding drug dose, regularly used in everyday medical practice, is critical to patients' health and recovery. It is a challenging process, especially for a drug with narrow therapeutic ranges, in which a medical doctor decides the quantity (dose amount) and frequency (dose interval) on the basis of a set of available patient features and doctor's clinical experience (a priori adaptation). Computer support in drug dose administration makes the prescription procedure faster, more accurate, objective, and less expensive, with a tendency to reduce the number of invasive procedures. This paper presents an advanced integrated Drug Administration Decision Support System (DADSS) to help clinicians/patients with the dose computing. Based on a support vector machine (SVM) algorithm, enhanced with the random sample consensus technique, this system is able to predict the drug concentration values and computes the ideal dose amount and dose interval for a new patient. With an extension to combine the SVM method and the explicit analytical model, the advanced integrated DADSS system is able to compute drug concentration-to-time curves for a patient under different conditions. A feedback loop is enabled to update the curve with a new measured concentration value to make it more personalized (a posteriori adaptation).

Hes1 is a critical but context-dependent mediator of canonical Notch signaling in lymphocyte development and transformation.

Although canonical Notch signaling regulates multiple hematopoietic lineage decisions including T cell and marginal zone B cell fate specification, the downstream molecular mediators of Notch function are largely unknown. We showed here that conditional inactivation of Hes1, a well-characterized Notch target gene, in adult murine bone marrow (BM) cells severely impaired T cell development without affecting other Notch-dependent hematopoietic lineages such as marginal zone B cells. Competitive mixed BM chimeras, intrathymic transfer experiments, and in vitro culture of BM progenitors on Delta-like-expressing stromal cells further demonstrated that Hes1 is required for T cell lineage commitment, but dispensable for Notch-dependent thymocyte maturation through and beyond the beta selection checkpoint. Furthermore, our data strongly suggest that Hes1 is essential for the development and maintenance of Notch-induced T cell acute lymphoblastic leukemia. Collectively, our studies identify Hes1 as a critical but context-dependent mediator of canonical Notch signaling in the hematopoietic system.

Testing of Access Network's Internet Protocol Television Features

Testaus on tänä päivänä olennainen osa tuotekehitysprosessia koko tuotteen elinkaaren ajan, myös tietoliikennetekniikassa. Tietoverkoille asetetut tiukat vaatimukset ympärivuorokautisen toimivuuden suhteen nostavatmyös niiden testauksen tason ja laadun merkitystä. Erityisesti verkkojen uudet toiminnallisuudet, joilla ei ole vielä vuosia kestäneen käytön ja kehityksen tuomaa varmuus- ja laatutasoa, tuovat haasteita testauksen toteutukselle. Televisiokuvan välityksen Internetin yli mahdollistavat ominaisuudet ovat esimerkki tällaisista toiminnallisuuksista. Tässä diplomityössä käsitellään Tellabs Oy:n tuotekehitysosastolla vuosina 2005 ja 2006 toteutetun, erään operaattorin laajakaistaliityntäverkon päivitysprojektin testausosuutta. Kattavamman tarkastelun kohteena ovat erityisesti verkkoon lisättyjen laajakaistatelevisio- eli IPTV-toiminnallisuuksien integraatio- ja systeemitestausmenetelmät.

Cooperation of breast cancer proteins PALB2 and piccolo BRCA2 in stimulating homologous recombination.

Inherited mutations in human PALB2 are associated with a predisposition to breast and pancreatic cancers. PALB2's tumor-suppressing effect is thought to be based on its ability to facilitate BRCA2's function in homologous recombination. However, the biochemical properties of PALB2 are unknown. Here we show that human PALB2 binds DNA, preferentially D-loop structures, and directly interacts with the RAD51 recombinase to stimulate strand invasion, a vital step of homologous recombination. This stimulation occurs through reinforcing biochemical mechanisms, as PALB2 alleviates inhibition by RPA and stabilizes the RAD51 filament. Moreover, PALB2 can function synergistically with a BRCA2 chimera (termed piccolo, or piBRCA2) to further promote strand invasion. Finally, we show that PALB2-deficient cells are sensitive to PARP inhibitors. Our studies provide the first biochemical insights into PALB2's function with piBRCA2 as a mediator of homologous recombination in DNA double-strand break repair.

Stability Evaluation of a Paper Machine Wet End

Työssä analysoidaanprosessin vaikutusta paperikoneen stabiiliuteen. Kaksi modernia sanomalehtipaperikonetta analysoitiin ja sen perusteella molemmista prosesseista rakennettiin fysiikan lakeihin perustuvat simulointimallit APROS Paper simulointiohjelmistolla. Työn tavoitteena on selvittää, miten kyseisten koneiden prosessit eroavat toisistaan ja arvioida, miten havaitut erot vaikuttavat prosessien stabiiliuteen. Työssä tarkastellaan periodisten häiriöiden vaimenemista prosessissa. Simuloinnissa herätteenä käytettiin puhdasta valkoista kohinaa, jonka avulla eri taajuistenperiodisten häiriöiden vaimenemista analysoitiin. Prosessien häiriövasteet esitetään taajuuskoordinaatistossa. Suurimmat erot prosessien välillä löytyivät viirakaivosta ja sen sekoitusdynamiikasta. Perinteisen viirakaivon todettiin muistuttavan käyttäytymiseltään sarjaan kytkettyjä ideaalisekoittimia, kun taas pienempitilavuuksisen fluumin todettiin käyttäytyvän lähes kuin putkiviive. Vaikka erotprosessitilavuudessa sekä viirakaivon sekoitusdynamiikassa olivat hyvin selkeät, havaittiin vain marginaalinen ero prosessin välillä periodisten häiriöiden vaimenemisessa, koska erot viiraretentiotasoissa vaikuttivat eniten simulointituloksia. Matalammalla viiraretentiolla operoivan paperikoneen todettiin vaimentavan tehokkaammin prosessihäiriöitä. Samalla retentiotasolla pienempitilavuuksisen prosessin todettiin vaimentavan hitaita prosessihäiriöitä marginaalisesti paremmin. Tutkituista paperikoneista toisella simuloitiin viiraosan vedenpoistomuutoksenvaikutusta viiraretentioon ja paperin koostumukseen. Lisäksi arvioitiin viiraretention säädön toimivuutta. Viiraosan listakengän vedenpoiston todettiin aiheuttavan merkittäviä sakeus- ja retentiohäiriöitä, mikäli sen avulla poistettavan kiintoaineen virtaus tuplaantuisi. Viiraretention säädön todettiin estävän häiriöiden kierron prosessissa, mutta siirtävän ne suoraan rainaan. Retention säädön eikuitenkaan todettu olevan suoranainen häiriön lähde.

Painelajittimen toimintasakeuden nostaminen havupuusellun lajittelussa

Painelajittimien kyky poistaa epäpuhtauksia on parantunut erityisesti roottorien ja sihtirumpujen kehityksen myötä. Painelajittimella pystytään nykyisin poistamaan yhä pienempiä roskapartikkeleja, minkä ansiosta painelajittimilla pystytään korvaamaan pyörrepuhdistimia hienolajittelussa. Nykyään ratkaisevaa on lajittimen mahdollinen toimintasakeus ja energiankulutus, joihin voidaan vaikuttaa roottori- ja sihtiratkaisuin sekä laitteen ajotavalla. Lajittimen toimintasakeutta nostamalla voitaisiin saavuttaa etuja tuotantoprosessissa pienempien virtauksien ja prosessin paremman ajettavuuden vuoksi. Työssä tarkasteltiin painelajittimen rakenneparametreista roottorin ja sihtirummun sekä ajoparametreista syöttösakeuden, massarejektisuhteen, tuotantomäärän ja roottorin kehänopeuden vaikutusta painelajittimen toimintaan. Erityisesti tutkittiin mahdollisuuksia nostaa lajittelusakeutta ja sakeuden nostonvaikutusta lajittimen energiankulutukseen. Sellutehtaaseen rakennetussa koelajitinlinjassa pystyttiin perusrakenteeltaan nykyisenlaisella painelajittimella muuttamalla roottorin ja sihdin rakennetta sekä nostamalla roottorin kehänopeutta lajittelemaan laitteen mitoitustuotannossa massaa korkeimmillaan 4,8 %:n sakeudessa. Suurin saavutettu sakeus, jossa energiankulutusta voidaanpitää hyväksyttävänä oli 4,4%. Nykyisellä ajotavalla ja roottori- ja sihtirakenteella pystyttiin lajittelemaan massaa 3,2 %:ssa. Tuloksista voidaan päätellä, että massan lajittelu yli 5 %:n sakeudessa on mahdollista roottorirakennetta edelleen kehittämällä.

Paired activation of two components within muscarinic M3 receptor dimers is required for recruitment of beta-arrestin-1 to the plasma membrane.

beta-Arrestins regulate the functioning of G protein-coupled receptors in a variety of cellular processes including receptor-mediated endocytosis and activation of signaling molecules such as ERK. A key event in these processes is the G protein-coupled receptor-mediated recruitment of beta-arrestins to the plasma membrane. However, despite extensive knowledge in this field, it is still disputable whether activation of signaling pathways via beta-arrestin recruitment entails paired activation of receptor dimers. To address this question, we investigated the ability of different muscarinic receptor dimers to recruit beta-arrestin-1 using both co-immunoprecipitation and fluorescence microscopy in COS-7 cells. Experimentally, we first made use of a mutated muscarinic M(3) receptor, which is deleted in most of the third intracellular loop (M(3)-short). Although still capable of activating phospholipase C, this receptor loses almost completely the ability to recruit beta-arrestin-1 following carbachol stimulation in COS-7 cells. Subsequently, M(3)-short was co-expressed with the M(3) receptor. Under these conditions, the M(3)/M(3)-short heterodimer could not recruit beta-arrestin-1 to the plasma membrane, even though the control M(3)/M(3) homodimer could. We next tested the ability of chimeric adrenergic muscarinic alpha(2)/M(3) and M(3)/alpha(2) heterodimeric receptors to co-immunoprecipitate with beta-arrestin-1 following stimulation with adrenergic and muscarinic agonists. beta-Arrestin-1 co-immunoprecipitation could be induced only when carbachol or clonidine were given together and not when the two agonists were supplied separately. Finally, we tested the reciprocal influence that each receptor may exert on the M(2)/M(3) heterodimer to recruit beta-arrestin-1. Remarkably, we observed that M(2)/M(3) heterodimers recruit significantly greater amounts of beta-arrestin-1 than their respective M(3)/M(3) or M(2)/M(2) homodimers. Altogether, these findings provide strong evidence in favor of the view that binding of beta-arrestin-1 to muscarinic M(3) receptors requires paired stimulation of two receptor components within the same receptor dimer.

Jatkuvatoimisen sellukeittimen säätöjen suorituskyvyn analysointi

Työssä tarkastellaan yleisiä menetelmiä säätöpiirien suorituskyvyn analysointiin ja sovelletaan niitä jatkuvatoimisen sellukeittimen säätöihin. Esitellyt menetelmät tarjoavat keinoja myös huonon säätötuloksen syyn selvittämiseen ja vinkkejä paremman suorituskyvyn saavuttamiseksi. Analyysissä edettiin top-down periaatteen mukaisesti lähtien liikkeelle keittimen tärkeimmästä säädöstä eli kappaluvun säädöstä. Sitten etsittiin tähän vaikuttavia tekijöitä mitatuista suureista. Seuraavaksi arvioitiin tärkeimmäksi katsotun tekijän (hakepinnankorkeus) säädön suorituskyky, jossa havaittiin parannettavaa. Lopuksi hakepinnankorkeuden säädön viritystämuutettiin ja tehtiin identifiointikoe säätörakenteen uudelleen järjestelyä varten.