A priori parameterisation of the CERES soil-crop models and tests against several European data sets

Mechanistic soil-crop models have become indispensable tools to investigate the effect of management practices on the productivity or environmental impacts of arable crops. Ideally these models may claim to be universally applicable because they simulate the major processes governing the fate of inputs such as fertiliser nitrogen or pesticides. However, because they deal with complex systems and uncertain phenomena, site-specific calibration is usually a prerequisite to ensure their predictions are realistic. This statement implies that some experimental knowledge on the system to be simulated should be available prior to any modelling attempt, and raises a tremendous limitation to practical applications of models. Because the demand for more general simulation results is high, modellers have nevertheless taken the bold step of extrapolating a model tested within a limited sample of real conditions to a much larger domain. While methodological questions are often disregarded in this extrapolation process, they are specifically addressed in this paper, and in particular the issue of models a priori parameterisation. We thus implemented and tested a standard procedure to parameterize the soil components of a modified version of the CERES models. The procedure converts routinely-available soil properties into functional characteristics by means of pedo-transfer functions. The resulting predictions of soil water and nitrogen dynamics, as well as crop biomass, nitrogen content and leaf area index were compared to observations from trials conducted in five locations across Europe (southern Italy, northern Spain, northern France and northern Germany). In three cases, the model’s performance was judged acceptable when compared to experimental errors on the measurements, based on a test of the model’s root mean squared error (RMSE). Significant deviations between observations and model outputs were however noted in all sites, and could be ascribed to various model routines. In decreasing importance, these were: water balance, the turnover of soil organic matter, and crop N uptake. A better match to field observations could therefore be achieved by visually adjusting related parameters, such as field-capacity water content or the size of soil microbial biomass. As a result, model predictions fell within the measurement errors in all sites for most variables, and the model’s RMSE was within the range of published values for similar tests. We conclude that the proposed a priori method yields acceptable simulations with only a 50% probability, a figure which may be greatly increased through a posteriori calibration. Modellers should thus exercise caution when extrapolating their models to a large sample of pedo-climatic conditions for which they have only limited information.

Lipid anchoring of Arabidopsis phototropin 1 to assess the functional significance of receptor internalization: should I stay or should I go?

The phototropin 1 (phot1) blue light receptor mediates a number of adaptive responses, including phototropism, that generally serve to optimize photosynthetic capacity. Phot1 is a plasma membrane-associated protein, but upon irradiation, a fraction is internalized into the cytoplasm. Although this phenomenon has been reported for more than a decade, its biological significance remains elusive. Here, we use a genetic approach to revisit the prevalent hypotheses regarding the functional importance of receptor internalization. Transgenic plants expressing lipidated versions of phot1 that are permanently anchored to the plasma membrane were used to analyse the effect of internalization on receptor turnover, phototropism and other phot1-mediated responses. Myristoylation and farnesylation effectively prevented phot1 internalization. Both modified photoreceptors were found to be fully functional in Arabidopsis, rescuing phototropism and all other phot1-mediated responses tested. Light-mediated phot1 turnover occurred as in the native receptor. Furthermore, our work does not provide any evidence of a role of phot1 internalization in the attenuation of receptor signalling during phototropism. Our results demonstrate that phot1 signalling is initiated at the plasma membrane. They furthermore indicate that release of phot1 into the cytosol is not linked to receptor turnover or desensitization.

Loss of the RNA polymerase III repressor MAF1 confers obesity resistance.

MAF1 is a global repressor of RNA polymerase III transcription that regulates the expression of highly abundant noncoding RNAs in response to nutrient availability and cellular stress. Thus, MAF1 function is thought to be important for metabolic economy. Here we show that a whole-body knockout of Maf1 in mice confers resistance to diet-induced obesity and nonalcoholic fatty liver disease by reducing food intake and increasing metabolic inefficiency. Energy expenditure in Maf1(-/-) mice is increased by several mechanisms. Precursor tRNA synthesis was increased in multiple tissues without significant effects on mature tRNA levels, implying increased turnover in a futile tRNA cycle. Elevated futile cycling of hepatic lipids was also observed. Metabolite profiling of the liver and skeletal muscle revealed elevated levels of many amino acids and spermidine, which links the induction of autophagy in Maf1(-/-) mice with their extended life span. The increase in spermidine was accompanied by reduced levels of nicotinamide N-methyltransferase, which promotes polyamine synthesis, enables nicotinamide salvage to regenerate NAD(+), and is associated with obesity resistance. Consistent with this, NAD(+) levels were increased in muscle. The importance of MAF1 for metabolic economy reveals the potential for MAF1 modulators to protect against obesity and its harmful consequences.

Assessment of metabolic fluxes in the mouse brain in vivo using 1H-[13C] NMR spectroscopy at 14.1 Tesla.

(13)C magnetic resonance spectroscopy (MRS) combined with the administration of (13)C labeled substrates uniquely allows to measure metabolic fluxes in vivo in the brain of humans and rats. The extension to mouse models may provide exclusive prospect for the investigation of models of human diseases. In the present study, the short-echo-time (TE) full-sensitivity (1)H-[(13)C] MRS sequence combined with high magnetic field (14.1 T) and infusion of [U-(13)C6] glucose was used to enhance the experimental sensitivity in vivo in the mouse brain and the (13)C turnover curves of glutamate C4, glutamine C4, glutamate+glutamine C3, aspartate C2, lactate C3, alanine C3, γ-aminobutyric acid C2, C3 and C4 were obtained. A one-compartment model was used to fit (13)C turnover curves and resulted in values of metabolic fluxes including the tricarboxylic acid (TCA) cycle flux VTCA (1.05 ± 0.04 μmol/g per minute), the exchange flux between 2-oxoglutarate and glutamate Vx (0.48 ± 0.02 μmol/g per minute), the glutamate-glutamine exchange rate V(gln) (0.20 ± 0.02 μmol/g per minute), the pyruvate dilution factor K(dil) (0.82 ± 0.01), and the ratio for the lactate conversion rate and the alanine conversion rate V(Lac)/V(Ala) (10 ± 2). This study opens the prospect of studying transgenic mouse models of brain pathologies.

Renovação do carbono-13 em figueiras 'Roxo de Valinhos'

O objetivo do trabalho foi determinar a taxa de renovação do carbono-13 ("turnover"), dos diferentes órgãos da figueira 'Roxo de Valinhos'. O experimento foi conduzido no pomar da Faculdade de Ciências Agronômicas, FCA/UNESP, Câmpus de Botucatu-SP. Determinou-se previamente, através das trocas gasosas com um medidor aberto portátil de fotossíntese, IRGA, a principal folha fotossinteticamente ativa. Essa folha foi colocada em uma câmara onde ocorreu a injeção do gás enriquecido. O tempo de enriquecimento da folha foi de 30 minutos. Os tratamentos foram constituídos por sete plantas de figueira, que foram retiradas do solo após: 6; 24; 48; 72; 120; 168 e 360 horas do enriquecimento com 13C, e suas partes seccionadas em: gema apical, folha jovem, folhas adultas (fotossinteticamente ativas), brotações laterais, frutos e ramo. Os resultados obtidos permitiram o estabelecimento da sequência de metabolização do carbono-13 nas partições estudadas: Folhas novas > Frutos > Brotações > Folhas Adultas > Gema Apical > Ramo > Folha marcada. Plantas de figueira 'Roxo de Valinhos' apresentam reciclagem do 13C de 24 horas e um tempo de meia-vida de duração do carbono-13 inferior a 11 horas.

Tuotannonsuunnittelun ja sisäisen varastologistiikan kehittäminen tuottavuuden kannalta

Diplomityön tavoitteena on kehittää erään metsäteollisuusyrityksen tuotannon-suunnittelua ja sisäistä varastologistiikkaa tuottavuuden parantamiseksi. Työssä keskitytään välituotteista johtuvaan problematiikkaan. Ongelmana ovat suuret välituotevarastot ja toimintamalleissa sekä pelisäännöissä olevat puutteet. Työn päätavoitteena on uuden toimintamallin kehittäminen tuotannon- ja materiaalinohjaukseen. Työn teoriaosassa esitellään lyhyesti tuotannon- ja materiaalinohjausta sekä tuottavuutta. Työn empiirisessä osassa analysoidaan jatkojalostuksen tuotantoja sekä välituotevarastoja. Työssä selvitetään eri välituotteiden määrät ja varaston kiertonopeudet raaka-ainerullille. Analyysien perusteella kehitettiin uusi toimintamalli tuotannon- ja materiaalinohjaukseen. Työssä ehdotettiin myös varastoinvestointia ja jälkirullauskapasiteetin lisäystä, jotta optimaalinen toiminta olisi tulevaisuudessa mahdollista. Diplomityön seurauksena aloitetaan projekti, jonka tavoitteena on parantaa tehtaan sisäistä tehokkuutta. Vaikutukset näkyvät monissa toiminnoissa, kuten varastoissa, tuotannossa sekä myynnissä. Parannusehdotuksilla voidaan saavuttaa vuosittain muutaman miljoonan euron säästöt. Projektin yksi tärkeä tekijä on selvittää, kuinka toimintaidea olisi hyödynnettävissä yrityksen muissa tehtaissa.

Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods

Gene turnover rates and the evolution of gene family sizes are important aspects of genome evolution. Here, we use curated sequence data of the major chemosensory gene families from Drosophila-the gustatory receptor, odorant receptor, ionotropic receptor, and odorant-binding protein families-to conduct a comparative analysis among families, exploring different methods to estimate gene birth and death rates, including an ad hoc simulation study. Remarkably, we found that the state-of-the-art methods may produce very different rate estimates, which may lead to disparate conclusions regarding the evolution of chemosensory gene family sizes in Drosophila. Among biological factors, we found that a peculiarity of D. sechellia's gene turnover rates was a major source of bias in global estimates, whereas gene conversion had negligible effects for the families analyzed herein. Turnover rates vary considerably among families, subfamilies, and ortholog groups although all analyzed families were quite dynamic in terms of gene turnover. Computer simulations showed that the methods that use ortholog group information appear to be the most accurate for the Drosophila chemosensory families. Most importantly, these results reveal the potential of rate heterogeneity among lineages to severely bias some turnover rate estimation methods and the need of further evaluating the performance of these methods in a more diverse sampling of gene families and phylogenetic contexts. Using branch-specific codon substitution models, we find further evidence of positive selection in recently duplicated genes, which attests to a nonneutral aspect of the gene birth-and-death process.

Biological evidence supports an early and complex emergence of the Isthmus of Panama.

The linking of North and South America by the Isthmus of Panama had major impacts on global climate, oceanic and atmospheric currents, and biodiversity, yet the timing of this critical event remains contentious. The Isthmus is traditionally understood to have fully closed by ca. 3.5 million years ago (Ma), and this date has been used as a benchmark for oceanographic, climatic, and evolutionary research, but recent evidence suggests a more complex geological formation. Here, we analyze both molecular and fossil data to evaluate the tempo of biotic exchange across the Americas in light of geological evidence. We demonstrate significant waves of dispersal of terrestrial organisms at approximately ca. 20 and 6 Ma and corresponding events separating marine organisms in the Atlantic and Pacific oceans at ca. 23 and 7 Ma. The direction of dispersal and their rates were symmetrical until the last ca. 6 Ma, when northern migration of South American lineages increased significantly. Variability among taxa in their timing of dispersal or vicariance across the Isthmus is not explained by the ecological factors tested in these analyses, including biome type, dispersal ability, and elevation preference. Migration was therefore not generally regulated by intrinsic traits but more likely reflects the presence of emergent terrain several millions of years earlier than commonly assumed. These results indicate that the dramatic biotic turnover associated with the Great American Biotic Interchange was a long and complex process that began as early as the Oligocene-Miocene transition.

Identification-commitment inventory (ICI-Model): confirmatory factor analysis and construct validity

The aim of this study is to confirm the factorial structure of the Identification-Commitment Inventory (ICI) developed within the frame of the Human System Audit (HSA) (Quijano et al. in Revist Psicol Soc Apl 10(2):27-61, 2000; Pap Psicól Revist Col Of Psicó 29:92-106, 2008). Commitment and identification are understood by the HSA at an individual level as part of the quality of human processes and resources in an organization; and therefore as antecedents of important organizational outcomes, such as personnel turnover intentions, organizational citizenship behavior, etc. (Meyer et al. in J Org Behav 27:665-683, 2006). The theoretical integrative model which underlies ICI Quijano et al. (2000) was tested in a sample (N = 625) of workers in a Spanish public hospital. Confirmatory factor analysis through structural equation modeling was performed. Elliptical least square solution was chosen as estimator procedure on account of non-normal distribution of the variables. The results confirm the goodness of fit of an integrative model, which underlies the relation between Commitment and Identification, although each one is operatively different.

Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome.

Cerebral, ocular, dental, auricular, skeletal anomalies (CODAS) syndrome (MIM 600373) was first described and named by Shehib et al, in 1991 in a single patient. The anomalies referred to in the acronym are as follows: cerebral-developmental delay, ocular-cataracts, dental-aberrant cusp morphology and delayed eruption, auricular-malformations of the external ear, and skeletal-spondyloepiphyseal dysplasia. This distinctive constellation of anatomical findings should allow easy recognition but despite this only four apparently sporadic patients have been reported in the last 20 years indicating that the full phenotype is indeed very rare with perhaps milder or a typical presentations that are allelic but without sufficient phenotypic resemblance to permit clinical diagnosis. We performed exome sequencing in three patients (an isolated case and a brother and sister sib pair) with classical features of CODAS. Sanger sequencing was used to confirm results as well as for mutation discovery in a further four unrelated patients ascertained via their skeletal features. Compound heterozygous or homozygous mutations in LONP1 were found in all (8 separate mutations; 6 missense, 1 nonsense, 1 small in-frame deletion) thus establishing the genetic basis of CODAS and the pattern of inheritance (autosomal recessive). LONP1 encodes an enzyme of bacterial ancestry that participates in protein turnover within the mitochondrial matrix. The mutations cluster at the ATP-binding and proteolytic domains of the enzyme. Biallelic inheritance and clustering of mutations confirm dysfunction of LONP1 activity as the molecular basis of CODAS but the pathogenesis remains to be explored.

Morphological, hydrological, biogeochemical and ecological changes and challenges in river restoration - the Thur River case study

River restoration can enhance river dynamics, environmental heterogeneity and biodiversity, but the underlying processes governing the dynamic changes need to be understood to ensure that restoration projects meet their goals, and adverse effects are prevented. In particular, we need to comprehend how hydromorphological variability quantitatively relates to ecosystem functioning and services, biodiversity as well as ground-and surface water quality in restored river corridors. This involves (i) physical processes and structural properties, determining erosion and sedimentation, as well as solute and heat transport behavior in surface water and within the subsurface; (ii) biogeochemical processes and characteristics, including the turnover of nutrients and natural water constituents; and (iii) ecological processes and indicators related to biodiversity and ecological functioning. All these aspects are interlinked, requiring an interdisciplinary investigation approach. Here, we present an overview of the recently completed RECORD (REstored CORridor Dynamics) project in which we combined physical, chemical, and biological observations with modeling at a restored river corridor of the perialpine Thur River in Switzerland. Our results show that river restoration, beyond inducing morphologic changes that reshape the river bed and banks, triggered complex spatial patterns of bank infiltration, and affected habitat type, biotic communities and biogeochemical processes. We adopted an interdisciplinary approach of monitoring the continuing changes due to restoration measures to address the following questions: How stable is the morphological variability established by restoration? Does morphological variability guarantee an improvement in biodiversity? How does morphological variability affect biogeochemical transformations in the river corridor? What are some potential adverse effects of river restoration? How is river restoration influenced by catchment-scale hydraulics [GRAPHICS] and which feedbacks exist on the large scale? Beyond summarizing the major results of individual studies within the project, we show that these overarching questions could only be addressed in an interdisciplinary framework.

Liiketoimintasuhteiden hallinta allianssiohjelmien avulla kansainvälisissä IT- yrityksissä

Työn tavoitteena on selvittää kansainvälisten IT-alan yritysten allianssiohjelmien toteutuksen haasteita ja onnistuneen yhteistyön edellytyksiä Suomen markkinoilla. Erityisesti on tutkittu sopimusten, informaation vaihdon, johdon roolin, kulttuurieroavaisuuksien ja luottamuksen merkitystä yritysten välisen yhteistyön onnistumiselle. Aiheeseen on haettu pohjaa tutustumalla tieteellisiin tutkimuksiin ja haastattelemalla yritysten allianssitoiminnasta vastuussa olevia henkilöitä. Tämän jälkeen on verrattu kirjallisuudesta saatua teoreettista näkökulmaa haastattelujen perusteella muodostuneeseen käytännön näkökulmaan. Työn tuloksena on saatu selville, että syy, miksi yritykset lähtevät tekemään yhteistyötä toisten yritysten kanssa, on liikevaihdon kasvattaminen. Tämän tuloksen aikaansaamiseksi tarvitaan yhteinen kumppanistrategia, erilaisten yrityskulttuurien huomioonottaminen, yhteiset tavoitteet ja yhdessä sovitut toimintamallit tavoitteiden saavuttamiseksi. Tämän lisäksi tarvitaan toisiaan täydentäviä ratkaisuja, henkilökohtaisia suhteita, vahva johdon sitoutuminen toimintaan, yhteisiä onnistumisia, jatkuvaa kommunikaatiota kumppaneiden kesken ja keskinäistä luottamusta. Lisäksi yhteistyöyritysten tulee olla toiminnassaan joustavia, sillä markkinat ja tilanteet muuttuvat jatkuvasti.

Yrityksen jakelutoimintojen kehittäminen

Diplomityön tavoitteena oli turkiseläinrehun valmistajan, E - P:n Minkinrehu Oy:n, jakelutoimintojen nykytilan analysointi, kehityskohteiden etsiminen ja kehitystoimenpiteiden luominen. Logististen toimintojen nykytilaa pyrittiin selvittämään haastattelujen, tutustumiskäyntien sekä kerätyn aineiston avulla. Mukaan tarkasteluun otettiin myös alan kirjallisuutta. Tutkimuksen perusteella yrityksen suurimmat jakeluongelmat liittyivät puutteelliseen jakelun ja kuljetusten suunnitteluun, penis- ja lisäarvopalveluiden puuttumiseen sekä epämääräiseen jakeluhinnoittelumenetelmään. Osa ongelmista aiheutui toimialan ominaispiirteistä, kuten sesonkiluontoisuudesta, erikoisjakelukaluston käytöstä, kalliista varastointimenetelmistä ja tuotteiden pilaantumisherkkyydestä. Jakeluun liittyviä ongelmia olivat jakelun kohdistamisongelma ja paluukuormien puuttuminen. Edellä mainituista ominaispiirteistä ja ongelmista johtuen jakelu- ja kuljetuskustannukset olivat noin 4,5 miljoonaa euroa eli lähes 20 prosenttia yrityksen liikevaihdosta vuonna 2003. Toimenpide-ehdotusten mukaan yrityksen tulisi lisätä yhteistyötä sekä toimittajien että turkistarhojen eli yrityksen osakkeenomistajien kanssa. Lähitulevaisuudessa olisi paikallaan investoiminen asianmukaiseen ja tehokkaaseen jakelun ja kuljetusten suunnittelu- ja seurantajärjestelmään. Itse jakelussa tulisi siirtyä jakelureittien optimointiin ja naiden optimaalisten jakelureittien käyttöön. Tutkimuksen mukaan jakelussa tulee siirtyä joko asiakaskohtaiseen tai osareittien mukaiseen jakeluvalin harvennukseen sesonkiaikavälillä kesäkuu - joulukuu. Jakeluhinnoittelussa on unohdettava nykyinen vyöhykehinnoittelu ja otettava käyttöön tutkimuksen perusteella jakelun todellisia kustannuksia paremmin vastaava ja asiakkaita tasapuolisesti kohteleva hinnoittelumenetelmä. Yrityksen tulisi jatkossa sisäistää jatkuvan kehityksen periaatteet sekä liiketoiminnassaan että jakelutoiminnoissaan.

Suorituskyvyn analysointijärjestelmän implementointi pkt-yrityksessä

Työn tavoitteena oli kehittää prosessimalli, jonka avulla suorituskyvyn analysointijärjestelmä voidaan ottaa käyttöön pkt-yrityksessä. Lisäksi pyrittiin löytämään oikeita toimintatapoja, joilla järjestelmän suunnittelu ja käyttöönotto voidaan toteuttaa käytännössä. Samalla kartoitettiin potentiaalisia ongelmakohtia, joita implementointiprosessiin liittyy.Työn teoriaosassa käsitellään järjestelmän suunnittelua ja implementointiin vaikuttavia seikkoja. Lisäksi selvitetään suorituskyvyn mittaamisen teoriaa yleisemmin ja esitellään kirjallisuudesta löytyviä prosessimalleja implementointiin.Käytännön osassa suorituskyvyn analysointijärjestelmä suunniteltiin ja otettiin koekäyttöön kolmessa päijäthämäläisessä metallialan pkt-yrityksessä. Kohdeyritysten liikevaihto vaihtelee kymmenen ja sadan miljoonan markan välillä.Suorituskyvyn analysointijärjestelmän suunnittelun lähtökohta on, että mittariston on linkityttävä kiinteästi yrityksen strategiaan. Siten mittaristo voi ohjata yritystä strategian määrittelemään suuntaan. Ylimmän johdon vahva sitoutuminen implementointiprosessiin on ensiarvoisen tärkeää. Johdon on myös järjestettävä riittävät resurssit suunnittelutiimille, jotta onnistuminen on mahdollista. Suunniteltavan suorituskykymittariston on oltava pkt-yrityksessä helppokäyttöinen ja tietojen syöttämisen järjestelmään on oltava nopeaa, jotta siitä voi muodostua kiinteä osa yrityksen johtamista.

Secondary metabolismin in Annonaceae: potencial source of drugs

Several species of Annona (Annonaceae) are used in traditional Mexican medicine by their anti-anxiety, anticonvulsant and tranquilizing properties. It has been reported that the alkaloids isolated from some species of the Annona have affinity to serotonergic 5-HT1A receptors and modulate dopaminergic transmission, which is involved in depressive disorders. In this review it is showed the results of the antidepressant-like effect of an alkaloid extract from the aerial parts of Annona cherimola (TA) in mice. The antidepressant-like effect was evaluated in the forced swimming test. To elucidate a possible mechanism of action, experiments of synergism with antidepressant drugs, such as imipramine (IMI), clomipramine (CLIMI), and fluoxetine (FLX), were carried out. The neurotransmitter content (DA: dopamine, 5HT: serotonin and its metabolites, HVA: homovanillic acid and 5HIAA:5-hydroxyindoleacetic) in the whole brain of mice were also determined by HPLC method. The results showed that repeated treatment with TA produced antidepressant-like effects in mice. This effect was not related to an increase in locomotor activity. Administration of TA facilitated the antidepressant effect of IMI and CLIMI as well as increased the turnover of DA and 5-HT. The alkaloids: 1,2-dimethoxy-5, 6.6 to 7-tetrahydro-4H-dibenzoquinoline-3,8,9,10-tetraol, anonaine, liriodenine, and nornuciferine were the main constituents of TA.