Two-dimensional QSAR studies on arylpiperazines as high-affinity 5-HT(1A) receptor ligands

5-HT(1A) receptor plays an important role in the delayed onset of antidepressant action of a class of selective serotonin reuptake inhibitors. Moreover, 5-HT(1A) receptor levels have been shown to be altered in patients suffering from major depression. In this work, hologram quantitative structure-activity relationship (HQSAR) studies were performed on a series of arylpiperazine compounds presenting affinity to the 5-HT(1A) receptor. The models were constructed with a training set of 70 compounds. The most significant HQSAR model (q(2) = 0.81, r(2) = 0.96) was generated using atoms, bonds, connections, chirality, and donor and acceptor as fragment distinction, with fragment size of 6-9. Predictions for an external test set containing 20 compounds are in good agreement with experimental results showing the robustness of the model. Additionally, useful information can be obtained from the 2D contribution maps.

The binding of synthetic triiodo L-thyronine analogs to human transthyretin: Molecular basis of cooperative and non-cooperative ligand recognition

Transthyretin (TTR) is a tetrameric beta-sheet-rich transporter protein directly involved in human amyloid diseases. Several classes of small molecules can bind to TTR delaying its amyloid fibril formation, thus being promising drug candidates to treat TTR amyloidoses. In the present study, we characterized the interactions of the synthetic triiodo L-thyronine analogs and thyroid hormone nuclear receptor TR beta-selecfive agonists GC-1 and GC-24 with the wild type and V30M variant of human transthyretin (TTR). To achieve this aim, we conducted in vitro TTR acid-mediated aggregation and isothermal titration calorimetry experiments and determined the TTR:GC-1 and TTR:GC-24 crystal structures. Our data indicate that both GC-1 and GC-24 bind to TTR in a non-cooperative manner and are good inhibitors of TTR aggregation, with dissociation constants for both hormone binding sites (HBS) in the low micromolar range. Analysis of the crystal structures of TTRwt:GC-1(24) complexes and their comparison with the TTRwt X-ray structure bound to its natural ligand thyroxine (T4) suggests, at the molecular level, the basis for the cooperative process displayed by T4 and the non-cooperative process provoked by both GC-1 and GC-24 during binding to TTR. (C) 2010 Elsevier Inc. All rights reserved.

Pharmacophore-based 3D QSAR studies on a series of high affinity 5-HT(1A) receptor ligands

5-HT(1A) receptor antagonists have been employed to treat depression, but the lack of structural information on this receptor hampers the design of specific and selective ligands. In this study, we have performed CoMFA studies on a training set of arylpiperazines (high affinity 5-HT(1A) receptor ligands) and to produce an effective alignment of the data set, a pharmacophore model was produced using Galahad. A statistically significant model was obtained, indicating a good internal consistency and predictive ability for untested compounds. The information gathered from our receptor-independent pharmacophore hypothesis is in good agreement with results from independent studies using different approaches. Therefore, this work provides important insights on the chemical and structural basis involved in the molecular recognition of these compounds. (C) 2010 Elsevier Masson SAS. All rights reserved.

AMIN domains have a predicted role in localization of diverse periplasmic protein complexes

We describe AMIN (Amidase N-terminal domain), a novel protein domain found specifically in bacterial periplasmic proteins. AMIN domains are widely distributed among peptidoglycan hydrolases and transporter protein families. Based on experimental data, contextual information and phyletic profiles, we suggest that AMIN domains mediate the targeting of periplasmic or extracellular proteins to specific regions of the bacterial envelope.

Molecular analysis of maltotriose active transport and fermentation by Saccharomyces cerevisiae reveals a determinant role for the AGT1 permease

Incomplete and/or sluggish maltotriose fermentation causes both quality and economic problems in the ale-brewing industry. Although it has been proposed previously that the sugar uptake must be responsible for these undesirable phenotypes, there have been conflicting reports on whether all the known alpha-glucoside transporters in Saccharomyces cerevisiae (MALx1, AGT1, and MPH2 and MPH3 transporters) allow efficient maltotriose utilization by yeast cells. We characterized the kinetics of yeast cell growth, sugar consumption, and ethanol production during maltose or maltotriose utilization by several S. cerevisiae yeast strains (both MAL constitutive and AM inducible) and by their isogenic counterparts with specific deletions of the AGT1 gene. Our results clearly showed that yeast strains carrying functional permeases encoded by the MAL21, MAL31, and/or MAL41 gene in their plasma membranes were unable to utilize maltotriose. While both high-and low-affinity transport activities were responsible for maltose uptake from the medium, in the case of maltotriose, the only low-affinity (K-m, 36 +/- 2 mM) transport activity was mediated by the AGT1 permease. In conclusion, the AGT1 transporter is required for efficient maltotriose fermentation by S. cerevisiae yeasts, highlighting the importance of this permease for breeding and/or selection programs aimed at improving sluggish maltotriose fermentations.

Endocytosis of prion protein is required for ERK1/2 signaling induced by stress-inducible protein 1

The secreted cochaperone STI1 triggers activation of protein kinase A (PKA) and ERK1/2 signaling by interacting with the cellular prion (PrPC) at the cell surface, resulting in neuroprotection and increased neuritogenesis. Here, we investigated whether STI1 triggers PrPC trafficking and tested whether this process controls PrPC-dependent signaling. We found that STI1, but not a STI1 mutant unable to bind PrPC, induced PrPC endocytosis. STI1-induced signaling did not occur in cells devoid of endogenous PrPC; however, heterologous expression of PrPC reconstituted both PKA and ERK1/2 activation. In contrast, a PrPC mutant lacking endocytic activity was unable to promote ERK1/2 activation induced by STI1, whereas it reconstituted PKA activity in the same condition, suggesting a key role of endocytosis in the former process. The activation of ERK1/2 by STI1 was transient and appeared to depend on the interaction of the two proteins at the cell surface or shortly after internalization. Moreover, inhibition of dynamin activity by expression of a dominant-negative mutant caused the accumulation and colocalization of these proteins at the plasma membrane, suggesting that both proteins use a dynamin-dependent internalization pathway. These results show that PrPC endocytosis is a necessary step to modulate STI1-dependent ERK1/2 signaling involved in neuritogenesis.

Oroidin Inhibits the Activity of the Multidrug Resistance Target Pdr5p from Yeast Plasma Membranes

Oroidin was isolated from the marine sponge Agelas sventres and inhibited the activity and function of Pdr5p, an enzyme responsible for the multidrug resistance phenotype in Saccharomyces cerevisiae. This compound may help in the development of new drugs that reverse this dangerous phenotype of pathogenic yeast and fungi.

Conformational differences between the wild type and V30M mutant transthyretin modulate its binding to genistein: Implications to tetramer stability and ligand-binding

Transthyretin (TTR) is a tetrameric beta-sheet-rich transporter protein directly involved in human amyloid diseases. It was recently found that the isoflavone genistein (GEN) potently inhibits TTR amyloid fibril formation (Green et al., 2005) and is therefore a promising candidate for TTR amyloidosis treatment. Here we used structural and biophysical approaches to characterize genistein binding to the wild type (TTRwt) and to its most frequent amyloidogenic variant, the V30M mutant. In a dose-dependent manner, genistein elicited considerable increases in both mutant and TTRwt stability as demonstrated by high hydrostatic pressure (HHP) and acid-mediated dissociation/denaturation assays. TTR:GEN crystal complexes and isothermal titration calorimetry (ITC) experiments showed that the binding mechanisms of genistein to the TTRwt and to V30M are different and are dependent on apoTTR structure conformations. Furthermore, we could also identify potential allosteric movements caused by genistein binding to the wild type TTR that explains, at least in part, the frequently observed negatively cooperative process between the two sites of TTRwt when binding ligands. These findings show that TTR mutants may present different ligand recognition and therefore are of value in ligand design for inhibiting TTR amyloidosis. (C) 2010 Elsevier Inc. All rights reserved.

RailsTNE : En multimodal informationsplattform i ett interorganisatoriskt nätverk

Att utreda möjligheterna att etablera dataförsörjning riktade mot multimodala transporttjänster är idag av största intresse. Det är också intressant att försöka utnyttja de standarder som tagits fram när en dataförsörjningskedja ska etableras. Detta examensarbete genomfördes på Triona AB i Borlänge. Triona har utvecklat databasen Transport Network Engine (TNE), som idag används för att läsa in data från Nationella VägDataBasen (NVDB) och från skogsnäringen. Målet med arbetet var att ta fram en informationsmodell, som beskriver hur ett transportnät med nätanknutna data, som stödjer multimodala transporter och resor, kan lagras i TNE. En förlängning av målet blev att, utifrån ett givet användarfall, etablera dataförsörjning till TNE och lägga in de nödvändiga datamängderna. TNE bygger på ESRI:s produkter och funktionalitet för hantering av geografisk information och informationsmodell och datahantering i TNE baseras på internationella och svenska standarder. Idag finns all information om järnvägsnätet hos Banverket och det finns ingen koppling mellan Banverkets databas Baninformationssystemet (BIS) och Vägverkets databas NVDB. För att den kopplingen ska kunna ske, krävs att de båda verken kan samarbeta som två stora organisationer i ett väl fungerande nätverk. Ett så kallat interorganisatoriskt nätverk. Det akademiska syftet var att föreslå en arkitekturstrategi som stödjer ett sådant nätverk. Vi upptäckte att arkitekturstrategierna IRM och VBS är uppbyggda för att inrikta sig på enskilda organisationer, och det visade sig svårt att följa en specifik strategi inom ett nätverk med flera organisationer. I vårt användarfall måste nätverket mellan Banverket, Vägverket och Stora Enso samarbeta över organisationsgränserna. Därför behövs en strategi för ett interorganisatoriskt samarbete så att informationen kan struktureras på ett gemensamt sätt. Vi föreslår ett antal idealtypskriterier som vi utgått efter i struktureringen av systemarkitekturen. Den innehåller en informationsmodell för både väg- och järnvägsdata som följer standarden SS 63 70 04. Arbetet avgränsades till att endast innehålla de datamängder som användarfallet kräver. Vi har analyserat KombiTIF-rapporten som är ett avslutat projekt styrt av Banverket på uppdrag av Näringsdepartementet. Rapporten ger ett förslag på en lösning i form av en arena som ska göra data tillgänglig för användning. Vi väljer att se TNE-plattformen som en realisering av denna arena. Enligt vårt förslg så ska TNE-plattformen hämta in det mest grundläggande datat om järnvägsnät och nätanknuten data från BIS och standardiserad information om vägnät och nätanknuten data från NVDB via ett gränssnitt. I framtiden är det möjligt att på samma sätt ta in andra trafiknät såsom Sjöfartsverket, Luftfartsverket och Rikstrafiken. Vi arbetade efter en egen metod som vi tog fram med valda delar från andra metoder; kartläggning, perspektivanalys, verksamhetsanalys, utveckling och utvärdering. Arbetet genomfördes iterativt i de fem olika faserna.

Trätorn : Kan det vara något för svensk vindkraft i skogsmiljö?

Inom ramen för projektet Energi- och miljökompetenscentrum vid Högskolan Dalarna haren kortare förstudie kring tekniken som används av Timber Tower GmbH för högavindkrafttorn i trä gjorts. Huvudsyftet med studien har varit att titta närmare på teknikenoch dess potential för svensk landbaserad vindkraft samt utreda vad detta kan innebära förregionen.Trenden för landbaserad vindkraft i skogsmiljö går mot allt högre torn. Skogsmiljön gör attden marknära turbulensen och vindgradienten blir större än över t.ex. hav vilket gör detmer föredelaktigt att använda högre torn.Tekniken som Timber Tower GmbH använder är att bygga tornet på plats med en koniskhålstomme av plana paneler av korslimmat limträ (som annars främst används vidbyggnation av höga hus med massivträstomme). Tekniken är skyddad av ett flertalpatentansökningar varav minst en är beviljad.Vid en jämförelse mellan trätorn och svetsade ståltorn (som är den dominerandetorntekniken idag) kan det konstateras att trätornstekniken är ekonomiskt intressant.Framförallt blir trätornen mer intressanta i jämförelse med ståltornen vi ökande höjder (>100 m) pga. dess transportfördelar. Vidare bör det nämnas att de torntekniker somanvänds idag vid höjder runt 140 m och högre främst är fackverkstorn i stål ochhybridtorn med en hög bas av förspänd betong och övre delen i stål.Då ett typgodkännande av ett vindkraftverk gäller torn och turbin är det i praktiken alltidturbintillverkaren som prissätter och levererar ett komplett vindkraftverk. Medutgångspunkt i regeringens planeringsram för svensk vindkraftutbyggnad (20 TWh/årlandbaserad vindkraft 2020) kan dock marknadsvärdet för torn uppskattas till 2-3 miljarderkr/år fram till 2020. För trätorn motsvarar detta en årlig potentiell volym på ca 190 000 m3.Slutsatsen i denna korta studie är att det är tekniskt möjligt att designa ett trätorn i rimligadimensioner för en 2-3 MW turbin med navhöjd ca 140 m och att detta sannolikt även ärekonomiskt intressant. Då ett trätorn blir något lättare än motsvarande ståltorn går det åtmindre energi för att göra ett trätorn. Hur mycket mindre är dock osäkert pga. den storaspridningen i siffror för energiåtgång för stålproduktion och i praktiken blir skillnadenäven leverantörsberoende. Eftersom andelen förnyelsebar energi är betydligt större vidtillverkningen av materialet för trätornen kommer trätornet att ge en betydande sänkningpå utsläppt CO2e/kWhel jämfört med motsvarande verk med ståltorn. Ett annat argumentför trätorn är förenklade transporter jämfört med t.ex. svetsade ståltorn eller hybridtornmed prefabricerade betongelement.Om tekniken etableras kan det i förlängningen leda till en regional påverkan i form av ökatlokalt innehåll i vindkraftprojekten t.ex. genom ökade råvaruleveranser (eg. sågat ochtorkat virke), lokal produktion av korslimmat limträ eller exempelvis bildande avspecialiserade montagefirmor. Det största hindret för tekniken just nu är dessmarknadsintroduktion och acceptans samt typgodkännande tillsammans med en för svenskmarknad intressant turbinleverantör. För att få acceptans för tekniken krävs byggande ochutvärdering av minst ett verk med trätorn. En intressant storlek för marknaden är en 2-3MW turbin med navhöjd ca 140 m. Ett sådant verk skulle i så fall få det högstavindkrafttornet i Sverige och sannolikt det högsta vindkrafttornet i trä i världen. Byggandetav ett första verk med trätorn skulle sannolikt även kräva ett behov av stödfinansiering föratt täcka en projektörs ökade risk. Då flera vindkraftetableringar i regionen uppvisar godaproduktionsresultat (med Tavelberget som gott exempel) visar det att regionen ärintressant för introduktion och utvärdering av ny teknologi.

Optimization heuristic solutions, how good can they be? : With empirical applications in location problems

Combinatorial optimization problems, are one of the most important types of problems in operational research. Heuristic and metaheuristics algorithms are widely applied to find a good solution. However, a common problem is that these algorithms do not guarantee that the solution will coincide with the optimum and, hence, many solutions to real world OR-problems are afflicted with an uncertainty about the quality of the solution. The main aim of this thesis is to investigate the usability of statistical bounds to evaluate the quality of heuristic solutions applied to large combinatorial problems. The contributions of this thesis are both methodological and empirical. From a methodological point of view, the usefulness of statistical bounds on p-median problems is thoroughly investigated. The statistical bounds have good performance in providing informative quality assessment under appropriate parameter settings. Also, they outperform the commonly used Lagrangian bounds. It is demonstrated that the statistical bounds are shown to be comparable with the deterministic bounds in quadratic assignment problems. As to empirical research, environment pollution has become a worldwide problem, and transportation can cause a great amount of pollution. A new method for calculating and comparing the CO2-emissions of online and brick-and-mortar retailing is proposed. It leads to the conclusion that online retailing has significantly lesser CO2-emissions. Another problem is that the Swedish regional division is under revision and the border effect to public service accessibility is concerned of both residents and politicians. After analysis, it is shown that borders hinder the optimal location of public services and consequently the highest achievable economic and social utility may not be attained.

Data based Calibration System for Radar used by Vehicle Activated Signs

The accurate measurement of a vehicle’s velocity is an essential feature in adaptive vehicle activated sign systems. Since the velocities of the vehicles are acquired from a continuous wave Doppler radar, the data collection becomes challenging. Data accuracy is sensitive to the calibration of the radar on the road. However, clear methodologies for in-field calibration have not been carefully established. The signs are often installed by subjective judgment which results in measurement errors. This paper develops a calibration method based on mining the data collected and matching individual vehicles travelling between two radars. The data was cleaned and prepared in two ways: cleaning and reconstructing. The results showed that the proposed correction factor derived from the cleaned data corresponded well with the experimental factor done on site. In addition, this proposed factor showed superior performance to the one derived from the reconstructed data.

Inheritance beyond plain heritability : variance-controlling genes in Arabidopsis thaliana

The phenotypic effect of a gene is normally described by the mean-difference between alternative genotypes. A gene may, however, also influence the phenotype by causing a difference in variance between genotypes. Here, we reanalyze a publicly available Arabidopsis thaliana dataset [1] and show that genetic variance heterogeneity appears to be as common as normal additive effects on a genomewide scale. The study also develops theory to estimate the contributions of variance differences between genotypes to the phenotypic variance, and this is used to show that individual loci can explain more than 20% of the phenotypic variance. Two well-studied systems, cellular control of molybdenum level by the ion-transporter MOT1 and flowering-time regulation by the FRI-FLC expression network, and a novel association for Leaf serration are used to illustrate the contribution of major individual loci, expression pathways, and gene-by-environment interactions to the genetic variance heterogeneity.

Phenolic profile of Sercial and Tinta Negra Vitis vinifera L. grape skins by HPLC–DAD–ESI-MSn: novel phenolic compounds in Vitis vinifera L. grape

This study represents the first phytochemical research of phenolic components of Sercial and Tinta Negra Vitis vinifera L. The phenolic profiles of Sercial and Tinta Negra V. vinifera L. grape skins (white and red varieties, respectively) were established using high performance liquid chromatography–diode array detection–electrospray ionisation tandem mass spectrometry (HPLC–DAD–ESI-MSn), at different ripening stages (véraison and maturity). A total of 40 phenolic compounds were identified, which included 3 hydroxybenzoic acids, 8 hydroxycinnamic acids, 4 flavanols, 5 flavanones, 8 flavonols, 4 stilbenes, and 8 anthocyanins. For the white variety, in both ripening stages, hydroxycinnamic acids and flavonols were the main phenolic classes, representing about 80% of the phenolic composition. For red variety, at véraison, hydroxycinnamic acids and flavonols were also the predominant classes (71%), but at maturity, anthocyanins represented 84% of the phenolic composition. As far as we know, 10 compounds were reported for the first time in V. vinifera L. grapes, namely protocatechuic acid-glucoside, p-hydroxybenzoyl glucoside, caftaric acid vanilloyl pentoside, p-coumaric acid-erythroside, naringenin hexose derivate, eriodictyol-glucoside, taxifolin-pentoside, quercetin-glucuronide-glucoside, malylated kaempferol-glucoside, and resveratrol dimer. These novel V. vinifera L. grape components were identified based on their MSn fragmentation profile. This data represents valuable information that may be useful to oenological management and to valorise these varieties as sources of bioactive compounds.

Limiting glutamate transmission in a Vglut2-expressing subpopulation of the subthalamic nucleus is sufficient to cause hyperlocomotion

The subthalamic nucleus (STN) is a key area of the basal ganglia circuitry regulating movement. We identified a subpopulation of neurons within this structure that coexpresses Vglut2 and Pitx2, and by conditional targeting of this subpopulation we reduced Vglut2 expression levels in the STN by 40%, leaving Pitx2 expression intact. This reduction diminished, yet did not eliminate, glutamatergic transmission in the substantia nigra pars reticulata and entopeduncular nucleus, two major targets of the STN. The knock-out mice displayed hyperlocomotion and decreased latency in the initiation of movement while preserving normal gait and balance. Spatial cognition, social function, and level of impulsive choice also remained undisturbed. Furthermore, these mice showed reduced dopamine transporter binding and slower dopamine clearance in vivo, suggesting that Vglut2-expressing cells in the STN regulate dopaminergic transmission. Our results demonstrate that altering the contribution of a limited population within the STN is sufficient to achieve results similar to STN lesions and high-frequency stimulation, but with fewer side effects.