Visualitzador de molècules d'ADN per laboratori virtual

RESUM Com a continuació del treball de final de carrera “Desenvolupament d’un laboratori virtual per a les pràctiques de Biologia Molecular” de Jordi Romero, s’ha realitzat una eina complementaria per a la visualització de molècules integrada en el propi laboratori virtual. Es tracta d’una eina per a la visualització gràfica de gens, ORF, marques i seqüències de restricció de molècules reals o fictícies. El fet de poder treballar amb molècules fictícies és la gran avantatge respecte a les solucions com GENBANK que només permet treballar amb molècules pròpies. Treballar amb molècules fictícies fa que sigui una solució ideal per a l’ensenyament, ja que dóna la possibilitat als professors de realitzar exercicis o demostracions amb molècules reals o dissenyades expressament per a l’exercici a demostrar. A més, permet mostrar de forma visual les diferents parts simultàniament o per separat, de manera que ofereix una primera aproximació interpretació dels resultats. Per altra banda, permet marcar gens, crear marques, localitzar seqüències de restricció i generar els ORF de la molècula que nosaltres creem o modificar una ja existent. Per l’implementació, s’ha continuat amb l’idea de separar la part de codi i la part de disseny en les aplicacions Flash. Per fer-ho, s’ha utilitzat la plataforma de codi lliure Ariware ARPv2.02 que proposa un marc de desenvolupament d’aplicacions Flash orientades a objectes amb el codi (classes ActionScript 2.0) separats del movieclip. Per al processament de dades s’ha fet servir Perl per ser altament utilitzat en Bioinformàtica i per velocitat de càlcul. Les dades generades es guarden en una Base de Dades en MYSQL (de lliure distribució), de la que s’extreuen les dades per generar fitxers XML, fent servir tant PHP com la plataforma AMFPHP com a enllaç entre Flash i la resta de parts.

Effect of physical activity during pregnancy on mode of delivery.

OBJECTIVE: The purpose of this study was to evaluate the effect of structured physical exercise programs during pregnancy on the course of labor and delivery. STUDY DESIGN: We conducted a systematic review and metaanalysis using the following data sources: Medline and The Cochrane Library. In our study, we used randomized controlled trials (RCT) that evaluated the effects of exercise programs during pregnancy on labor and delivery. The results are summarized as relative risks. RESULTS: In the 16 RCTs that were included there were 3359 women. Women in exercise groups had a significantly lower risk of cesarean delivery (relative risk, 0.85; 95% confidence interval [CI], 0.73-0.99). Birthweight was not significantly reduced in exercise groups. The risk of instrumental delivery was similar among groups (relative risk, 1.00; 95% CI, 0.82-1.22). Data on Apgar score, episiotomy, epidural anesthesia, perineal tear, length of labor, and induction of labor were insufficient to draw conclusions. With the use of data from 11 studies (1668 women), our analysis showed that women in the exercise groups gained significantly less weight than women in control groups (mean difference, -1.13 kg; 95% CI, -1.49 to -0.78). CONCLUSION: Structured physical exercise during pregnancy reduces the risk of cesarean delivery. This is an important finding to convince women to be active during their pregnancy and should lead the physician to recommend physical exercise to pregnant women, when this is not contraindicated.

Science, practice and patient needs: the work of the Plinius Maior Society.

The Plinius Maior Society is a European multinational, multidisciplinary group of clinicians and researchers in the alcoholism field, which strives for a comprehensive care concept in the management of alcoholism and alcohol-related problems. The Society, using evidence-based medicine, has developed a set of protocols, in the forms of guidelines, flow-charts, leaflets and booklets, for use as tools in research on and treatment of alcohol dependence, with a view to standardize clinical research procedures and to bridge the gap between the alcoholism researcher, practitioner and patient. These protocols or tools have been subjected to a review process during their preparation, and further comments on their validity will be integrated in their updates. Seven protocols have so far been developed, two of which, 'Guidelines on Evaluation of Treatment of Alcohol Dependence' and 'Detection and Management of Patients with Psychiatric and Alcohol Use Disorders', are aimed at the clinical researcher and specialists, whereas three others [in the form of decision trees (flow-charts)] are aimed at the general practitioner and other primary health care providers. These are entitled 'Alcohol Risk Assessment and Intervention in Primary Care', 'Withdrawal from Alcohol at Home' and 'Brief Intervention in Patients with Alcohol-Related Problems'. The remaining two tools are booklets aimed at the patient, one to support initiatives for detection of drinking problems and primary intervention, namely 'Do you have this Problem? Discuss it with your Doctor!', and the other to assist the patient in relapse prevention after the early stages of treatment, namely 'On the Way to Recovery'. The protocols for the general practitioners and patients have so far been produced in seven European languages, and, as with the Guidelines, feedback from target users will be collected and incorporated in future updates. The Society continually seeks to consider areas of clinical importance for its work and, as it enters the new millennium, it hopes to address and make a significant contribution to the most pressing problem in the management of alcohol dependence, namely relapse.

Extracorporeal liver support in severe alcoholic hepatitis

The severity of alcoholic hepatitis (AH) which may coexist with cirrhosis varies greatly, from asymptomatic forms which are detected in alcoholic patients without any sign of liver disease, except laboratory abnormalities, to severe forms characterised by deep jaundice, ascites, hepatic encephalopathy and low prothrombin index. In hospitalized patients the mortality could be as high as 75%. The elevated number of therapeutic proposals reported for more than forty years reveals the lack of efficacy of a particular modality. Even in the most favorable trials, the survival is already very poor and in some cases related to the development of renal failure or hepatorenal syndrome. There are some motivating reports concerning albumin dialysis as a support treatment in patients with severe AH, either alone or in combination with other pharmacological therapies. The favorable effects of albumin dialysis in patients with severe AH suggest that the procedure used alone or in combination with other therapies may have a role in this clinical condition. This will be particularly relevant to offer an alternative therapy in these patients, thus being a potential bridge to recovery or to be listed for liver transplantation.

Nutritional and feeding ecology in the Cory"s shearwater (Calonectris diomedea).

In birds, parents adjust their feeding behaviour according to breeding duties, which ultimately may lead to seasonal adjustments in nutritional physiology and hematology over the breeding season. Although avian physiology has been widely investigated in captivity, few studies have integrated individual changes in feeding and physiological ecology throughout the breeding season in wild birds. To study relationships between feeding ecology and nutritional ecophysiology in Cory"s shearwater Calonectris diomedea, we weighed and took blood samples from 28 males and 19 females during the pre-laying, egg-laying, incubation, hatching and chick-rearing periods of the breeding season. In addition, we fitted 6 birds with geolocators to track their foraging movements throughout the reproductive period. Thus, we examined individual changes in (1) nutritional condition (biochemistry metabolites); (2) oxygen carrying capacity (hematology); and (3) feeding areas and foraging effort (stable isotopes and foraging movements). Geolocators revealed a latitudinal shift in main feeding areas towards more southern and more neritic waters throughout the breeding season, which is consistent with the steady increase in δ13C signatures in the blood. Geolocators also showed a decrease in foraging effort from egg-laying to hatching, reflecting the activity decrease associated with incubation duties. Plasma metabolites, body mass and oxygen carrying capacity were associated with temporal changes in nutritional state and foraging effort in relation to recovery after migration, egg formation, fasting shifts during incubation and chick provisioning. This study shows that combining physiological and ecological approaches can help us understand the influence of breeding duties on feeding ecology and nutritional physiology in wild birds.

Metallien talteenotto kloridiliuoksesta

Diplomityön tarkoituksena oli tutkia ja kehittää menetelmä arvometallien kuten kuparin, sinkin, koboltin ja nikkelin talteenottoon metallikloridiliuoksesta. Tavoitteena oli valita taloudellisin ja ympäristöystävällisin menetelmä, jolla saadaan nämä arvometallit myyntituotteiksi. Lisäksi puhdistetun prosessiveden tuli täyttää asetetut tavoitteet. Kirjallisuustyön perusteella laskettiin viidelle eri prosessivaihtoehdolle ainetaseet HSC Sim 6.0 ohjelmalla, joka on HSC Chemistry-pohjainen prosessien simulointi- ja mallinnusohjelma. Kaikissa vaihtoehdoissa oli ensimmäisenä prosessiosana kuparin, sinkin, koboltin ja nikkelin sulfidisaostus ja sakan pesu. Sulfidisaostusta seurasi vaihtoehtoisesti joko 1) hapetus hapella ja hydroksidisaostus, 2) hapetus vetyperoksidilla ja hydroksidisaostus, 3) pelkkä hydroksidisaostus, 4) hapetus SO2/O2-kaasuseoksella ja hydroksidisaostus tai 5) karbonaattisaostus. Taselaskennan perusteella valittiin kokeelliseen osaan tutkittavat prosessivaihtoehdot, jotka olivat sulfidisaostus, hydroksidisaostus, SO2/O2- hapetus ja hydroksidisaostus sekä karbonaattisaostus. Kokeissa arvometallit saatiin talteenotettua sulfidisaostuksella selektiivisimmin lämpötilassa 55 °C ja pH:ssa 4. Näissä olosuhteissa reagenssin kulutus verrattaessa muihin tehtyihin sulfidisaostuksiin oli pienin. Sakka laskeutui ja suotautui hyvin. Loppusakan sisältämien metallien (kupari, sinkki ja koboltti) pitoisuudet olivat korkeimmat. Myös nikkelin määrä oli suuri. Mangaani ja rauta saatiin talteenotettua selektiivisimmin karbonaattisaostuksella lämpötilassa 65 °C. Sakka sisälsi eniten mangaania. Sakka laskeutui ja suotautui hyvin. Tällä menetelmällä puhdistetun prosessiveden laatu täytti asetetut tavoitteet.

Defining housing market areas using commuting and migration algorithms. Catalonia (Spain) as an applied case study

In the literature on housing market areas, different approaches can be found to defining them, for example, using travel-to-work areas and, more recently, making use of migration data. Here we propose a simple exercise to shed light on which approach performs better. Using regional data from Catalonia, Spain, we have computed housing market areas with both commuting data and migration data. In order to decide which procedure shows superior performance, we have looked at uniformity of prices within areas. The main finding is that commuting algorithms present more homogeneous areas in terms of housing prices.

Visualitzador de molècules d'ADN per laboratori virtual

Com a continuació del treball de final de carrera “Desenvolupament d’un laboratori virtual per a les pràctiques de Biologia Molecular” de Jordi Romero, s’ha realitzat una eina complementaria per a la visualització de molècules integrada en el propi laboratori virtual. Es tracta d’una eina per a la visualització gràfica de gens, ORF, marques i seqüències de restricció de molècules reals o fictícies. El fet de poder treballar amb molècules fictícies és la gran avantatge respecte a les solucions com GENBANK que només permet treballar amb molècules pròpies. Treballar amb molècules fictícies fa que sigui una solució ideal per a l’ensenyament, ja que dóna la possibilitat als professors de realitzar exercicis o demostracions amb molècules reals o dissenyades expressament per a l’exercici a demostrar. A més, permet mostrar de forma visual les diferents parts simultàniament o per separat, de manera que ofereix una primera aproximació interpretació dels resultats. Per altra banda, permet marcar gens, crear marques, localitzar seqüències de restricció i generar els ORF de la molècula que nosaltres creem o modificar una ja existent. Per l’implementació, s’ha continuat amb l’idea de separar la part de codi i la part de disseny en les aplicacions Flash. Per fer-ho, s’ha utilitzat la plataforma de codi lliure Ariware ARPv2.02 que proposa un marc de desenvolupament d’aplicacions Flash orientades a objectes amb el codi (classes ActionScript 2.0) separats del movieclip. Per al processament de dades s’ha fet servir Perl per ser altament utilitzat en Bioinformàtica i per velocitat de càlcul. Les dades generades es guarden en una Base de Dades en MYSQL (de lliure distribució), de la que s’extreuen les dades per generar fitxers XML, fent servir tant PHP com la plataforma AMFPHP com a enllaç entre Flash i la resta de parts.

Tietojärjestelmien riskit osana liiketoiminnan jatkuvuuden hallintaa

Tietojärjestelmät ovat kehittyneet kriittisiksi tekijöiksi yritysten liiketoiminnassa. Niitä on vaikea tai lähes mahdoton korvata. Toisaalta tietojärjestelmät ovat edesauttaneet yrityksiä tehostamaan toimintaansa. Yrityksen toimialalla tai koolla ei nykyään ole merkitystä erilaisten tietoteknisten järjestelmien ja sovellusten hyödyntämisessä. Riskienhallinnan avulla yritys pyrkii ennaltaehkäisemään tunnettuja riskejä. Liiketoiminnan jatkuvuudenhallinta pyrkii puolestaan varautumaan riskin aiheuttamaan liiketoiminnan häiriöön ja siitä toipumiseen. Tietojärjestelmien ollessa korvaamattomia tulee yrityksen kohdistaa resursseja ennaltaehkäiseviin toimiin, lisäksi sen on pyrittävä lyhentämään häiriöstä toipumisen aikaa. Tutkimuksen tarkoituksena oli tunnistaa kohdeyrityksen tietojärjestelmien merkittävimmät riskit, jotka uhkaavat oleellisesti liiketoiminnan jatkuvuutta. Liiketoiminnan jatkuvuuden tarkastelussa hyödynnettiin yrityksen käyttämää suorituskykymittaristoa (Balanced Score Card). Työllä tuetaan yrityksen laatujärjestelmän vaatimuksia liiketoiminnan turvaamisessa. Tutkielma toteutettiin pääasiassa teemahaastatteluiden muodossa, laadullista tutkimusmenetelmää hyödyntäen. Tutkimuksessa todettiin yrityksen tietojärjestelmien ja niiden ylläpidon olevan hyvällä tasolla. Muutamia kriittisiä vikaantumispisteitä kuitenkin havaittiin, joiden pohjalta laadittiin kehitysehdotuksia tietojärjestelmien vikasietoisuuden parantamiseksi liiketoiminnan jatkuvuudenhallinnan näkökannalta.

Biodiversity and ecosystem functioning in angiosperm communities in the Baltic Sea

The biological variation in nature is called biodiversity. Anthropogenic pressures have led to a loss of biodiversity, alarming scientists as to what consequences declining diversity has for ecosystem functioning. The general consensus is that diversity (e.g. species richness or identity) affects functioning and provides services from which humans benefit. The aim of this thesis was to investigate how aquatic plant species richness and identity affect ecosystem functioning in terms of processes such as primary production, nutrient availability, epifaunal colonization and properties e.g. stability of Zostera marina subjected to shading. The main work was carried out in the field and ranged temporally from weeklong to 3.5 months-long experiments. The experimental plants used frequently co-occur in submerged meadows in the northern Baltic Sea and consist of eelgrass (Z. marina), perfoliate pondweed (Potamogeton perfoliatus), sago pondweed (P. pectinatus), slender-leaved pondweed (P. filiformis) and horned pondweed (Zannichellia palustris). The results showed that plant richness affected epifaunal community variables weakly, but had a strong positive effect on infaunal species number and functional diversity, while plant identity had strong effects on amphipods (Gammarus spp.), of which abundances were higher in plant assemblages consisting of P. perfoliatus. Depending on the starting standardizing unit, plant richness showed varying effects on primary production. In shoot density-standardized plots, plant richness increased the shoot densities of three out of four species and enhanced the plant biomass production. Both positive complementarity and selection effects were found to underpin the positive biodiversity effects. In shoot biomass-standardized plots, richness effects only affected biomass production of one species. Negative selection was prevalent, counteracting positive complementarity, which resulted in no significant biodiversity effect. The stability of Z. marina was affected by plant richness in such that Z. marina growing in polycultures lost proportionally less biomass than Z. marina in monocultures and thus had a higher resistance to shading. Monoculture plants in turn gained biomass faster, and thereby had a faster recovery than Z. marina growing in polycultures. These results indicate that positive interspecific interactions occurred during shading, while the faster recovery of monocultures suggests that the change from shading stress to recovery resulted in a shift from positive interactions to resource competition between species. The results derived from this thesis show that plant diversity affects ecosystem functioning and contribute to the growing knowledge of plant diversity being an important component of aquatic ecosystems. Diverse plant communities sustain higher primary productivity than comparable monocultures, affect faunal communities positively and enhance stability. Richness and identity effects vary, and identity has generally stronger effects on more variables than richness. However, species-rich communities are likely to contain several species with differing effects on functions, which renders species richness important for functioning. Mixed meadows add to coastal ecosystem functioning in the northern Baltic Sea and may provide with services essential for human well-being.

Role of Th1 and Th2 cells in autoimmune demyelinating disease

Evidence is accumulating that Th1 cells play an important role in the development of multiple sclerosis (MS) and experimental allergic encephalomyelitis (EAE), whereas Th2 cells contribute to recovery from disease. A major determinant in the development of Th1 and Th2 cells is the type of antigen-presenting cell (APC) involved and its functional characteristics, e.g., the production of interleukin-12. Therefore, modulation of APC might interfere with the development of Th1 type responses and as such be beneficial for MS and EAE. The potential of cytokines, in particular interleukin-10, and glucocorticoids to exert a selective effect on APC, and as a consequence to affect the Th1-Th2 balance in EAE, is discussed

Ethological analysis of mother-pup interactions and other behavioral reactions in rats: effects of malnutrition and tactile stimulation of the pups

Mother-pup interaction, as well as other behavioral reactions were studied during the lactation period in 24 litters of Wistar rats and their dams fed either a 16% (control - C; 12 litters) or a 6% (malnourished - M; 12 litters) protein diet. The diets were isocaloric. Throughout lactation there was a 36.4% weight loss of M dams and a 63% body weight deficit in the M pups when compared to control pups. During this period, half of the litters were exposed daily to additional tactile stimulation (CS or MS), while the other half were submitted to normal rearing conditions (CN or MN). The tactile stimulation of pups (handling) consisted of holding the animal in one hand and gently touching the dorsal part of the animal's body with the fingers for 3 min. A special camera and a time-lapse video were used to record litter behavior in their home cages. Starting at 6 p.m. and ending at 6 a.m., on days 3, 6, 12, 15, 18 and 21 of lactation, photos were taken at 4-s intervals. An increase in the frequency (154.88 ± 16.19) and duration (455.86 ± 18.05 min) of suckling was observed throughout the lactation period in all groups compared to birth day (frequency 24.88 ± 2.37 and duration 376.76 ± 21.01 min), but the frequency was higher in the C (84.96 ± 8.52) than in the M group (43.13 ± 4.37); however, the M group (470.2 ± 11.87 min) spent more time suckling as compared with the C group (393.67 ± 13.09 min). The M dams showed a decreased frequency of resting position throughout the lactation period (6.5 ± 2.48) compared to birth day (25.42 ± 7.74). Pups from the C group were more frequently observed separated (73.02 ± 4.38) and interacting (258.99 ± 20.61) more with their mothers than the M pups (separated 66.94 ± 5.5 and interacting 165.72 ± 12.05). Tactile stimulation did not interact with diet condition, showing that the kind of stimulation used in the present study did not lead to recovery from the changes induced by protein malnutrition. The changes in mother-pup interaction produced by protein malnutrition of both may represent retardation in neuromotor development and a higher dependence of the pups on their mothers. These changes may represent an important means of energy saving and heat maintenance in malnourished pups.

Effect of chronic oral administration of a low dose of captopril on sodium appetite of hypothyroid rats: Influence of aldosterone treatment

Rats rendered hypothyroid by treatment with methimazole develop an exaggerated sodium appetite. We investigated here the capacity of hypothyroid rats (N = 12 for each group) to respond to a low dose of captopril added to the ration, a paradigm which induces an increase in angiotensin II synthesis in cerebral areas that regulate sodium appetite by increasing the availability of circulating angiotensin I. In addition, we determined the influence of aldosterone in hypothyroid rats during the expression of spontaneous sodium appetite and after captopril treatment. Captopril significantly increased (P<0.05) the daily intake of 1.8% NaCl (in ml/100 g body weight) in hypothyroid rats after 36 days of methimazole administration (day 36: 9.2 ± 0.7 vs day 32: 2.8 ± 0.6 ml, on the 4th day after captopril treatment). After the discontinuation of captopril treatment, daily 1.8% NaCl intake reached values ranging from 10.0 ± 0.9 to 13.9 ± 1.0 ml, 48 to 60 days after treatment with methimazole. Aldosterone treatment significantly reduced (P<0.05) saline intake before (7.3 ± 1.6 vs day 0, 14.4 ± 1.3 ml) and after captopril treatment. Our results demonstrate that, although hypothyroid rats develop a deficiency in the production of all components of the renin-angiotensin-aldosterone system, their capacity to synthesize angiotensin II at the cerebral level is preserved. The partial reversal of daily 1.8% NaCl intake during aldosterone treatment suggests that sodium retention reduces both spontaneous and captopril-induced salt appetite.

Bases políticas das transferências intergovernamentais no Brasil (1985-2004)

The politics of intergovernmental transfers in Brazil. This article examines the political economy of public resources distribution in Brazil's federal system in 1985-2004. We propose an empirical exercise to analyze how the country's federal governments deal with the tradeoff between the provision of material wellbeing to sub-national governments (the states in our study) and the pursuit of political support from the latter. To identify the determinants of the transfer of resources from the federal government to the states, a set of economic, political, and institutional variables is econometrically tested. Based upon instrumental variables estimation for panel-data models, our estimates indicate that in Brazil the pursuit of political goals prevails over social equity and economic efficiency criteria: higher levels of per capita transfers are associated with the political makeup of governing coalitions, while larger investments in infrastructure and development by the states are associated with a lower amount of per capita resources transferred to sub-national governments. Our findings also suggest a trend toward the freezing of interregional inequalities in Brazil, and show the relevance of fiscal discipline laws in discouraging the use of the administrative apparatus for electioneering.

Interactions of diploid embryonal carcinoma cells and normal cell mass cells with 2.5 day mouse embryos following aggregation

Spontaneous teratocarcinomas are ovarian or testicular tumors which have their origins in germ cells. The tumors contain a disorganized array of benign differentiated cells as well as an undifferentiated population of malignant stem cells, the embryonal carcinoma or EC cells. These pluripotent stem cells in tissue culture share many properties with the transient pluripotent cells of the early embryo, and might therefore serve as models for the investigation of developmental events ill vitro. The property of EC cells of prime interest in this study is an in vivo phenomenon. Certain EC cell lines are known to be regulated ill vivo and to differentiate normally in association with normal embryonic cells, resulting in chimeric mice. These mice have two genetically distinct cell populations, one of which is derived from the originally malignant EC cells. This has usually been accomplished by injection of the EC cells into the Day 3 blastocyst. In this study, the interactions between earlier stage embryos and EC cells have been tested by aggregating clumps of EC cells with Day 2 embryos. The few previous aggregation studies produced a high degree of abnormality in chimeric embryos, but the EC cells employed had known chromosomal abnormalities. In this study, two diploid EC cell lines (P19 and Pi0) were aggregated with 2.5 day mouse embryos, and were found to behave quite differently in the embryonic environment. P19 containing aggregates generally resorbed early, and the few embryos recovered at midgestation were normal and non-chimeric. Pi0 containing aggregates survived in high numbers to midgestation, and the Pi0 cells were very successful in colonizing the embryo. All these embryos were chimeric, and the contribution by the EC cells to each chimera was very high. However, these heavily chimeric embryos were all abnormal. Blastocyst injection had previously produced some abnormal embryos with high Pl0 contributions in addition to the live born mice, which had lower EC contributions. This study now adds more support to the hypothesis that high EC contributions may be incompatible with normal development. The possibility that the abnormalities were due to the mixing of temporally asynchronous embryonic cell types in the aggregates was tested by aggregating normal pluripotent cells taken from 3.5 day embryos with 2.5 day embryos. Early embryo loss was very high, and histological studies showed that the majority of these embryos died by 6.5 days development. Some embryos escaped this early death such that some healthy chimeras were recovered, in contrast to recovery of abnormal chimeric embryos following Pl0-morula aggregations, and non-chimeric embryos following P19-morula aggregations. This somewhat surprising adverse effect on development following aggregation of normal cell types suggests that there are developmental difficulties associated with the mixing of asynchronous cell types in aggregates. However, the greater magnitude of the adverse effects when the aggregates contained tumor derived cells suggests that EC cells should not be considered the complete equivalent of the pluripotent cells of the early embryo.