UniPathway: a resource for the exploration and annotation of metabolic pathways.

UniPathway (http://www.unipathway.org) is a fully manually curated resource for the representation and annotation of metabolic pathways. UniPathway provides explicit representations of enzyme-catalyzed and spontaneous chemical reactions, as well as a hierarchical representation of metabolic pathways. This hierarchy uses linear subpathways as the basic building block for the assembly of larger and more complex pathways, including species-specific pathway variants. All of the pathway data in UniPathway has been extensively cross-linked to existing pathway resources such as KEGG and MetaCyc, as well as sequence resources such as the UniProt KnowledgeBase (UniProtKB), for which UniPathway provides a controlled vocabulary for pathway annotation. We introduce here the basic concepts underlying the UniPathway resource, with the aim of allowing users to fully exploit the information provided by UniPathway.

The role of culture in international students' image formation: the emergence of expected and perceived university image

Tämän tutkimuksen tavoitteena oli selvittää, vaikuttaako kansainvälisen opiskelijan kulttuuritausta opiskelijan odotetun ja koetun yliopistoimagon muodostumiseen. Jotta kulttuurin vaikutuksia yliopistoimagoon voitiin tutkia, tutkimuksessa tunnistettiin yliopistoimagon muodostumiseen oleellisesti vaikuttavat tekijät. Kulttuurin roolia organisaation imagon muodostumisessa ei ole tutkittu aiemmissa tieteellisissä julkaisuissa. Näin ollen tämän tutkimuksen voidaan katsoa edistäneen nykyistä imagotutkimusta. Tutkimuksen kohdeyliopistona oli Lappeenrannan teknillinen yliopisto (LTY). Tutkimuksen empiirinen osa toteutettiin kvantitatiivisena Internet - pohjaisena kyselytutkimuksena tilastollisen analyysin menetelmin. Otos (N=179) koostui kaikista Lappeenrannan teknillisessä yliopistossa lukuvuonna 2005-2006 opiskelleista kansainvälisistä opiskelijoista. Kyselyyn vastasi 68,7 % opiskelijoista. Johtopäätöksenä voidaan todeta, että kulttuurilla ei ole merkittävää vaikutusta yliopistoimagon muodostumiseen. Tutkimuksessa saatiin selville, että yliopiston Internet-sivujen laatu vaikuttaa positiivisesti odotetun yliopistoimagon muodostumiseen, kun taas koettuun yliopistoimagoon vaikuttavat positiivisesti odotettu yliopistoimago, pedagoginen laatu sekä opetusympäristö. Markkinoinnin näkökulmasta tulokset voidaan vetää yhteen toteamalla, että yliopistojen ei tarvitsisi räätälöidä tutkimuksessa tunnistettuja imagoon vaikuttavia tekijöitä eri kulttuureistatulevia opiskelijoita varten.

The Boundaries of a Firm in the Pulp and Paper Industry: Complementarities of the Resource-Based View and Transaction Cost Economics

Tämän tutkimuksen tarkoituksena on tutkia sellu- ja paperiteollisuuden toimintojen luonnetta sekä miten yrityksen rajapinnat ovat muodostuneet ko. teollisuudenalalla. Tutkimus on eksploratiivinen ja luonteeltaan kvalitatiivinen. Tutkimuksen aineisto kerättiin yrityksissä tehdyillä teemahaastatteluilla. Sellu- ja paperitehtaan toimintojen analysoinnissa käytetään resurssiperusteista näkemystä ja transaktiokustannusteoriaa. Tutkimuksen yritysten rakennetta voidaan pitää varsin konservatiivisena. Teoreettinen kehys pystyi selittämään varsinaisen tuotannon järjestämistä varsin hyvin. Tukitoiminnoissa löytyi ristiriitoja teorian ja todellisuuden välillä. Tuotantotoiminnot kannattaa pitää yrityksen sisällä, koska ne täyttävät VRIN-attribuutit ja niihin liittyy korkeita transaktiokustannuksia. Suurin osa tukitoiminnoista voidaan luokitella triviaaleiksi. Joitain tukitoimintoja voidaan kuitenkin luokitella strategisesti tärkeiksi, ja voidaan päätellä, että ne pitäisi pitää yrityksen sisällä. Tässä suhteessa tulokset olivat kuitenkin ristiriitaisia, ja lisätutkimuksia tarvittaisiin lopullisten johtopäätösten tekemiseen.

The Reflections of Strategic Orientation on profitability - A resource-based study in pulp and paper industry

Tutkielman tavoitteena oli analysoida erilaisia strategisia orientaatioita sellu- ja paperiteollisuudessa. Sellu- ja paperiteollisuus on kohtaamassa strategisia haasteita, jotka ulottuvat syvälle sen rakenteisiin. Yritykset ovat valinneet erilaisia lähestymistapoja organisoidessaan tuotantoa ja kansainvälistä arvoketjuaan tässä muuttuvassa ympäristössä. Tutkimukseen valittiin 30 suurinta sellu- ja paperiteollisuudessa toimivaa yritystä ja mahdollisia syitä kannattavuuseroihin yritysten välillä analysoitiin. Yritysten strategista orientaatiota tarkasteltiin vertailemalla muun muassa seuraavia tekijöitä: vertikaalinen integraatioaste, tuotevalikoiman laajuus, tuotantokapasiteetin levinneisyys ja tuotantokapasiteetin ikä. Kannattavuutta mitattiin erilaisilla talouden tunnusluvuilla (liikevoitto, oman pääoman tuotto-%, koko pääoman tuotto-%). Tulosten mukaan yrityksiä voidaan ryhmitellä strategisen orientaation perusteella ja ryhmien välillä on kannattavuuseroja.

Evaluation of the integrity of human corneal epithelium maintained in organ-culture during eye banking using Corneamax®

Purpose: Mediums have been developed to conserve corneal endothelium in organ-culture during eye banking. CorneaMax® is used by 25% of Eye Bank in Europe. Only little is known about conservation of corneal epithelium with this medium during banking. Its preservation could be of interest in clinic to cure corneal disease with stem cells deficiency. Therefore, we wanted to examine the integrity of human corneal epithelium maintained in CorneaMax®. Methods: Human corneas, considered unsuitable for transplantation, were obtained from the Eye Bank in Lausanne. Average post-mortem time was 14 hours. Cornoscleral rings were maintained in organ-culture in Corneamax® at 32°C. Samples were formalin-fixed after period ranging from 0 (D0) to 35 days (D35, N=5 for each time points) and stained with H&E. Proliferation and apoptosis were evaluated by immunostaining with antibody against Ki67 and Caspase3 respectively. Results: Corneas, which were not in organ-cultured (D0), showed different morphology, including intact epithelium with 5 to 7 layers, but also completely denuded basement membrane. In two cases, at D0, the epithelium lost its adherence to the basal lamina of the cornea creating a large epithelial sheet. During the two first days, corneas and limbus area lost totally their epithelium, except for some remaining limbal basal cells. From day 2 to day 10, regeneration of the epithelium took place, starting from the limbal region in direction to the central cornea. From day 10 to day 35, corneal epithelium appeared as an atrophic epithelium, consisting of only two cell layers. Proliferation happened in the whole cornea during the 35 days of organ-culture, as shown by Ki67 positive cells. Apoptosis was rarely detected in the corneal epithelium. Conclusions: Corneas maintained in CorneaMax® showed a complete disappearance of the corneal epithelium during the two first days and a conservation of limbal basal cells in the limbal region. These remaining cells allowed a full regeneration of the tissue, leading to an atrophic epithelium, composed of only two cell layers. This atrophic epithelium could be seen in all the organ-cultured corneas during the 35 days of conservation. This study is a first step to develop medium in organ-culture in order to conserve corneal epithelial cells.

Forensic science culture

Heretofore the issue of quality in forensic science is approached through a quality management policy whose tenets are ruled by market forces. Despite some obvious advantages of standardization of methods allowing interlaboratory comparisons and implementation of databases, this approach suffers from a serious lack of consideration for forensic science as a science. A critical study of its principles and foundations, which constitutes its culture, enables to consider the matter of scientific quality through a new dimension. A better understanding of what pertains to forensic science ensures a better application and improves elementary actions within the investigative and intelligence processes as well as the judicial process. This leads to focus the attention on the core of the subject matter: the physical remnants of the criminal activity, namely, the traces that produce information in understanding this activity. Adapting practices to the detection and recognition of relevant traces relies on the apprehension of the processes underlying forensic science tenets (Locard, Kirk, relevancy issue) and a structured management of circumstantial information (directindirect information). This is influenced by forensic science education and training. However, the lack of homogeneity with regard to the scientific nature and culture of the discipline within forensic science practitioners and partners represents a real challenge. A sound and critical reconsideration of the forensic science practitioner's roles (investigator, evaluator, intelligence provider) and objectives (prevention, strategies, evidence provider) within the criminal justice system is a means to strengthen the understanding and the application of forensic science. Indeed, the whole philosophy is aimed at ensuring a high degree of excellence, namely, a dedicated scientific quality.

From the Resource-Base to Firm Boundaries in the Electricity Network Business - Case Lappeenrannan Energia Oy

Tutkielman tavoitteena oli selvittääcase -yrityksen resurssi- ja kyvykkyyspohjaa resurssiperustaisen näkemyksen mukaan, sekä yrityksen rajoja transaktiokustannusteorian mukaan. Tutkimusongelmia lähestyttiin kirjallisuuskatsauksella, puoli-strukturoiduilla teemahaastatteluilla, sekä kyselylomakkeilla. Tutkielman päätuloksiksi voidaan Tukea löydetty resurssikuilu, resurssien ja kyvykkyyksien tutkinta, sekä kyselylomakkeiden rakentaminen ja käyttö. Tutkielman paljastamasta kuilusta voidaan erottaa kolme päähaastetta; ikääntyvät sähköverkot, ikääntyvä henkilökunta ja liiketoimintaosaamisen puute. Lisäksi resurssien ja kyvykkyyksien tutkinta nosti esille organisaation rutiineja ja prosesseja, ja kyselylomakkeet osoittautuivat varsin toimiviksi tutkimuksen kontekstissa. Yhteenvetona voidaan todeta, että sähköverkkoliiketoiminta ja case yritys ovat suuren rakennemuutoksen alla, joka tuo mukanaan suuria haasteita myös lähitulevaisuudessa.

In vitro culture of Spondias mombin L. nodal segments

Spondias mombin L. shoot cultures were initiated from nodal explants taken from plants propagated by seeds. Explants coming from 4-6 months old plants, previously disinfected, were cultivated on WPM medium supplemented with a wide range of concentrations of BAP (0.0, 0.22, 0.44, 2.22 and 4.44 muM) and NAA (0.0, 0.27 and 2.70 muM). After four weeks, the responses obtained were axillary shoot and root formation. The first response were preferentially induced with the medium containing only BAP, regardless of the BAP concentration. The addition of NAA on medium reduced significantly axillary shoot formation and induced rhizogenesis. Roots were formed on nodal explant basis, preferentially on medium supplemented with 4.44 muM NAA. The medium supplemented with BAP reduced significantly root formation.

Sexual dimorphism in a dioecious population of the wind-pollinated herb Mercurialis annua: the interactive effects of resource availability and competition.

Background and Aims Male-biased sex allocation commonly occurs in wind-pollinated hermaphroditic plants, and is often positively associated with size, notably in terms of height. Currently, it is not well established whether a corresponding pattern holds for dioecious plants: do males of wind-pollinated species exhibit greater reproductive allocation than females? Here, sexual dimorphism is investigated in terms of life history trade-offs in a dioecious population of the wind-pollinated ruderal herb Mercurialis annua.Methods The allocation strategies of males and females grown under different soil nutrient availability and competitive (i.e. no, male or female competitor) regimes were compared.Key Results Male reproductive allocation increased disproportionately with biomass, and was greater than that of females when grown in rich soils. Sexual morphs differentially adjusted their reproductive allocation in response to local environmental conditions. In particular, males reduced their reproductive allocation in poor soils, whereas females increased theirs, especially when competing with another female rather than growing alone. Finally, males displayed smaller above-ground vegetative sizes than females, but neither nutrient availability nor competition had a strong independent effect on relative size disparities between the sexes.Conclusions Selection appears to favour plasticity in reproductive allocation in dioecious M. annua, thereby maintaining a relatively constant size hierarchy between sexual morphs. In common with other dioecious species, there seems to be little divergence in the niches occupied by males and females of M. annua.

An experience beyond continuous assessment activities: virtual tour to the medieval medicinal plant garden of the Pedralbes monastery

[eng] The group of teaching innovation in the area of Botany (GIBAF), University of Barcelona (UB), is raised each year to design new accreditation activities under continuous evaluation framework. We present the experience carried out during the academic year 2008-09 in the course of Pharmaceutical Botany. The aim has been to involve students for a semester in the authorship of a tutored project immediately useful and of easy permanence, beyond its assessment proving usefulness. The Medicinal Plants Garden of the Monastery of Pedralbes has been used as a resource and a collaboration agreement has been signed between the UB faculty and the Institute of Culture of Barcelona. The students have developed the work using the Moodle platform CampusvirtualUB into five stages which included preparation of files by students that have been modified in some steps following the various feedbacks from teachers. At the beginning of the activity, students were provided with a complete schedule of activities, the schedule for its implementation, and a total of 18 forced-use library resources. Finally, through Google sites, a website has been implemented, allowing for a virtual tour of the garden, documenting by referenced literature 50 medicinal plants for their nomenclature, botanical description, distribution, uses historical, current and future) and toxicity. The result of the activity was presented at a public ceremony in the Monastery of Pedralbes and is available at: http://sites.google.com/site/jardimedievalpedralbes/ [spa] El grupo de innovación docente integrado por profesores del área de Botánica (GIBAF) de la Universidad de Barcelona (UB) se plantea cada curso el diseño de nuevas actividades acreditativas en el marco de la evaluación continuada. Se presenta la experiencia llevada a cabo durante el curso 2008-09 en la asignatura Botánica Farmacéutica. El objetivo ha sido implicar durante un semestre a los estudiantes en la autoría de un proyecto tutorizado de inmediata utilidad y clara perdurabilidad, más allá de su utilidad acreditativa. Como recurso se ha utilizado el Jardín de Plantas Medicinales del Monasterio de Pedralbes y se ha firmado un convenio de colaboración docente entre la UB y el Instituto de Cultura de Barcelona. Los estudiantes han realizado el trabajo utilizando la plataforma Moodle del Campus virtual de la UB en cinco etapas que han incluido la confección de unas fichas que se han ido modificando en función de las diversas retroacciones de los profesores. Al inicio de la actividad, se facilitó a los estudiantes el cronograma completo de la actividad, la pauta para su realización, así como un total de 18 recursos bibliográficos de uso obligado. Finalmente, a través de GoogleSites, se ha realizado una web que permite realizar un paseo virtual por el jardín, documentando de forma referenciada para las 50 plantas medicinales su nomenclatura, descripción botánica, distribución, usos (históricos, actuales y futuros) y toxicidad. El resultado de la actividad fue presentado en un acto público en el Monasterio de Pedralbes y puede consultarse en: http://sites.google.com/site/jardimedievalpedralbes/

Role of mutations in the phosphoprotein on RNA polymerase activity of canine distemper virus following cell culture adaptation

Abstract: The canine distemper virus A75/17 wild-type strain, which is unable to replicate in cell lines, was adapted to growth in Vero cells. Sequence comparison between the A75/17 and the Vero cell-adapted A75/17-V virus revealed 7 amino acid differences between the 2 viruses. Three of these were located in the matrix protein, three in the phosphoprotein also changing the V protein but not the C protein and one in the large protein. The phosphoprotein and the large protein constituted the viral RNA polymerase whose activity was studied by transfection experiments using a reverse genetic system with a plasmid encoding a minireplicon and expression plasmids encoding the nucleocapsid protein and the viral RNA polymerase subunits. Surprinsingly, the enzyme of A75/17 CDV was significantly more active in cell lines compared to the polymerase of A75/17-V CDV. The decrease in overall enzyme activity was found to be due to both decreased replication and transcription activity. This polymerase attenuation was confirmed in CHO cells infection stably expressing the dog SLAM receptor mainly found in dog's lymphoid organs and allowing both virus strains to enter these cells at the same efficiency. A75/17-V CDV replicated more slowly in CHODogSLAM cells than A75/17 CDV and syncytium formation was significantly decreased compared to A75/17 infected CHODogSLAM cells.. Cell culture adaptation lead to an attenuated virus strain both in vitro and in vivo with decreased polymerase activity and syncytium forming capability showing an important role of the polymerase in determining the phenoytpe of the virus. In addition, this reduced phenotype of A75/17-V CDV was shown to be due to the P mutations in the P protein only, showing an important function of the polycistronic P gene in the adaptation process. The role of the matrix protein was found not to have any effect on polymerase activity, however its participation in the adaptation process still needs to be elucidated. The accessory proteins V and C were shown to act on polymerase activity, but their functions in virus pathogenicity and in inhibiting the interferon system have not been studied in this thesis. The V proteins have an activating effect on the polymerase of both the A75/17 and the A75/17-V CDV strains. Although the C protein amino acid sequence was not changed during adaptation of wild-type canine distemper virus in Vero cells, the C protein was demonstrated to have opposite effects on polymerase activity of both virus strains suggesting a different interaction of the C protein with the proteins forming the polymerase complex, which could modulate polymeras activity. These effects were demonstrated by transfection experiments and studying recombinant viruses not expressing the C protein. Thus, the abrogation of the C protein decrease the activity of the wild-type polymerase. In contrast, the polymerase activity of the Vero cell- adapted virus is enhanced in the absence of the C protein and this has also been demonstrated with a recombinant virus, which grew faster in the first 48 hours of infection. Future studies will focus on the generation of recombinant wild-type viruses, which should be very helpful in understanding the molecular mechanisms underlying the adaptation process and the loss of pathogenicity.