Structural studies on enzymes of biotechnological and biomedical interest

Structural studies of proteins aim at elucidating the atomic details of molecular interactions in biological processes of living organisms. These studies are particularly important in understanding structure, function and evolution of proteins and in defining their roles in complex biological settings. Furthermore, structural studies can be used for the development of novel properties in biomolecules of environmental, industrial and medical importance. X-ray crystallography is an invaluable tool to obtain accurate and precise information about the structure of proteins at the atomic level. Glutathione transferases (GSTs) are amongst the most versatile enzymes in nature. They are able to catalyze a wide variety of conjugation reactions between glutathione (GSH) and non-polar components containing an electrophilic carbon, nitrogen or sulphur atom. Plant GSTs from the Tau class (a poorly characterized class) play an important role in the detoxification of xenobiotics and stress tolerance. Structural studies were performed on a Tau class fluorodifen-inducible glutathione transferase from Glycine max (GmGSTU4-4) complexed with GSH (2.7 Å) and a product analogue Nb-GSH (1.7 Å). The three-dimensional structure of the GmGSTU4-4-GSH complex revealed that GSH binds in different conformations in the two subunits of the dimer: in an ionized form in one subunit and a non-ionized form in the second subunit. Only the ionized form of the substrate may lead to the formation of a catalytically competent complex. Structural comparison between the GSH and Nb-GSH bound complexes revealed significant differences with respect to the hydrogen-bonding, electrostatic interaction pattern, the upper part of -helix H4 and the C-terminus of the enzyme. These differences indicate an intrasubunit modulation between the G-and Hsites suggesting an induced-fit mechanism of xenobiotic substrate binding. A novel binding site on the surface of the enzyme was also revealed. Bacterial type-II L-asparaginases are used in the treatment of haematopoietic diseases such as acute lymphoblastic leukaemia (ALL) and lymphomas due to their ability to catalyze the conversion of L-asparagine to L-aspartate and ammonia. Escherichia coli and Erwinia chrysanthemi asparaginases are employed for the treatment of ALL for over 30 years. However, serious side-effects affecting the liver and pancreas have been observed due to the intrinsic glutaminase activity of the administered enzymes. Structural studies on Helicobacter pylori L-asparaginase (HpA) were carried out in an effort to discover novel L-asparaginases with potential chemotherapeutic utility in ALL treatment. Detailed analysis of the active site geometry revealed structurally significant differences between HpA and other Lasparaginases that may be important for the biological activities of the enzyme and could be further exploited in protein engineering efforts.

Distribution and role of macrophytes in coastal lagoons : implications of critical shifts

Crossroads, crucibles and refuges are three words that may describe natural coastal lagoon environments. The words refer to the complex mix of marine and terrestrial influences, prolonged dilution due to the semi-enclosed nature and the function of a habitat for highly diverse plant and animal communities, some of which are endangered. To attain a realistic picture of the present situation, high vulnerability to anthropogenic impact should be added to the description. As the sea floor in coastal lagoons is usually entirely photic, macrophyte primary production is accentuated compared with open sea environments. There is, however, a lack of proper knowledge on the importance of vegetation for the general functioning of coastal lagoon ecosystems. The aim of this thesis is to assess the role of macrophyte diversity, cover and species identity over temporal and spatial scales for lagoon functions, and to determine which steering factors primarily restrict the qualitative and quantitative composition of vegetation in coastal lagoons. The results are linked to patterns of related trophic levels and the indicative potential of vegetation for assessment of general conditions in coastal lagoons is evaluated. This thesis includes five field studies conducted in flads and glo-flads in the brackish water northern Baltic Sea. Flads and glo-flads are defined as a Baltic variety of coastal lagoons, which due to an inlet threshold and post-glacial landuplift slowly will be isolated from the open sea. This process shrinks inlet size, increases exposure and water retention, and is called habitat isolation. The studied coastal lagoons are situated in the archipelago areas of the eastern coast of Sweden, the Åland Islands and the south-west mainland of Finland, where land-uplift amounts to ca. 5 mm/ per year. Out of 400 evaluated sites, a total of 70 lagoons varying in inlet size, archipelago position and anthropogenic influence to cover for essential environmental variation were chosen for further inventory. Vegetation composition, cover and richness were measured together with several hydrographic and morphometric variables in the lagoons both seasonally and inter-annually to cover for general regional, local and temporal patterns influencing lagoon and vegetation development. On smaller species-level scale, the effects of macrophyte species identity and richness for the fish habitat function were studied by examining the influence of plant interaction on juvenile fish diversity. Thus, the active election of plant monoand polycultures by fish and the diversity of fish in the respective culture were examined and related to plant height and water depth. The lagoons and vegetation composition were found to experience a regime shift initiated by increased habitat isolation along with land-uplift. Vegetation composition altered, richness decreased and cover increased forming a less isolated and more isolated regime, named the vascular plant regime and charophyte regime, respectively according to the dominant vegetation. As total phosphorus in the water, turbidity and the impact of regional influences decreased in parallel, the dominance of charophytes and increasing cover seemed to buffer and stabilize conditions in the charophyte regime and indicated an increased functional role of vegetation for the lagoon ecosystem. The regime pattern was unaffected by geographical differences, while strong anthropogenic impact seemed to distort the pattern due to loss of especially Chara tomentosa L. in the charophyte regime. The regimes were further found unperturbed by short-time temporal fluctuations. In fact the seasonal and inter-annual dynamics reinforced the functional difference between the regimes by the increasing role of vegetation along habitat isolation and the resemblance to lake environments for the charophyte regime. For instance, greater total phosphorus and chlorophyll a concentrations in the water in the beginning of the season in the charophyte regime compared with the vascular plant regime presented a steeper reduction to even lower values than in the vascular plant regime along the season. Despite a regional importance and positive relationship of macrophyte diversity in relation to trophic diversity, species identity was underlined in the results of this thesis, especially with decreasing spatial scale. This result was supported partly by the increased role of charophytes in the functioning of the charophyte regime, but even more explicitly by the species-specific preference of juvenile fish for tall macrophyte monocultures. On a smaller species-level scale, tall plant species in monoculture seemed to be able to increase their length, indicating that negative selection forms preferred habitat structures, which increase fish diversity. This negative relationship between plant and fish diversity suggest a shift in diversity patterns among trohic levels on smaller scale. Thus, as diversity patterns seem complex and diverge among spatial scales, it might be ambiguous to extend the understanding of diversity relationships from one trophic level to the other. All together, the regime shift described here presents similarities to the regime development in marine lagoon environments and shallow lakes subjected to nutrient enrichment. However, due to nutrient buffering by vegetation with increased isolation and water retention as a consequence of the inlet threshold, the development seems opposite to the course along an eutrophication gradient described in marine lagoons lacking an inlet threshold, where the role of vegetation decreases. Thus, the results imply devastating consequences of inlet dredging (decreasing isolation) in terms of vegetation loss and nutrient release, and call for increased conservational supervision. Especially the red listed charophytes would suffer negatively from such interference and the consequences are likely to also deteriorate juvenile fish production. The fact that a new species to Finland, Chara connivens Salzm. Ex. Braun 1835 was discovered during this study further indicates a potential of the lagoons serving as refuges for rare species.

Understanding the Racial Nature of Police and Immigrant Relations In Finland. The Case of Africans in Turku

The focus of this study is to examine the role of police and immigrants’ relations, as less is known about this process in the country. The studies were approached in two different ways. Firstly, an attempt was made to examine how immigrants view their encounters with the police. Secondly, the studies explored how aware the police are of immigrants’ experiences in their various encounters and interactions on the street level. An ancillary aim of the studies is to clarify, analyse and discuss how prejudice and stereotypes can be tackled, thereby contributing to the general debate about racism and discrimination for better ethnic relations in the country. The data in which this analysis was based is on a group of adults (n=88) from the total of 120 Africans questioned for the entire study (n=45) police cadets and (n=6) serving police officers from Turku. The present thesis is a compilation of five articles. A summary of each article findings follows, as the same data was used in all five studies. In the first study, a theoretical model was developed to examine the perceived knowledge of bias by immigrants resulting from race, culture and belief. This was also an attempt to explore whether this knowledge was predetermined in my attempt to classify and discuss as well as analyse the factors that may be influencing immigrants’ allegations of unfair treatment by the police in Turku. The main finding shows that in the first paper there was ignorance and naivety on the part of the police in their attitudes towards the African immigrant’s prior experiences with the police, and this may probably have resulted from stereotypes or their lack of experience as well as prior training with immigrants where these kinds of experience are rampant in the country (Egharevba, 2003 and 2004a). In exploring what leads to stereotypes, a working definition is the assumption that is prevalent among some segments of the population, including the police, that Finland is a homogenous country by employing certain conducts and behaviour towards ethnic and immigrant groups in the country. This to my understanding is stereotype. Historically this was true, but today the social topography of the country is changing and becoming even more complex. It is true that, on linguistic grounds, the country is multilingual, as there are a few recognised national minority languages (Swedish, Sami and Russian) as well as a number of immigrant languages including English. Apparently it is vital for the police to have a line of communication open when addressing the problem associated with immigrants in the country. The second paper moved a step further by examining African immigrants’ understanding of human rights as well as what human rights violation means or entails in their views as a result of their experiences with the police, both in Finland and in their country of origin. This approach became essential during the course of the study, especially when the participants were completing the questionnaire (N=88), where volunteers were solicited for a later date for an in-depth interview with the author. Many of the respondents came from countries where human rights are not well protected and seldom discussed publicly, therefore understanding their views on the subject can help to explain why some of the immigrants are sceptical about coming forward to report cases of batteries and assaults to the police, or even their experiences of being monitored in shopping malls in their new home and the reason behind their low level of trust in public authorities in Finland. The study showed that knowledge of human rights is notably low among some of the participants. The study also found that female respondents were less aware of human rights when compared with their male counterparts. This has resulted in some of the male participants focussing more on their traditional ways of thinking by not realising that they are in a new country where there is equality in sexes and lack of respect on gender terms is not condoned. The third paper focussed on the respondents’ experiences with the police in Turku and tried to explore police attitudes towards African immigrant clients, in addition to the role stereotype plays in police views of different cultures and how these views have impacted on immigrants’ views of discriminatory policing in Turku. The data is the same throughout the entire studies (n=88), except that some few participants were interviewed for the third paper thirty-five persons. The results showed that there is some bias in mass-media reports on the immigrants’ issues, due to selective portrayal of biases without much investigation being carried out before jumping to conclusions, especially when the issues at stake involve an immigrant (Egharevba, 2005a; Egharevba, 2004a and 2004b). In this vein, there was an allegation that the police are even biased while investigating cases of theft, especially if the stolen property is owned by an immigrant (Egharevba, 2006a, Egharevba, 2006b). One vital observation from the respondents’ various comments was that race has meaning in their encounters and interaction with the police in the country. This result led the author to conclude that the relation between the police and immigrants is still a challenge, as there is rampant fear and distrust towards the police by some segments of the participating respondents in the study. In the fourth paper the focus was on examining the respondents’ view of the police, with special emphasis on race and culture as well as the respondents’ perspective on police behaviour in Turku. This is because race, as it was relayed to me in the study, is a significant predictor of police perception (Egharevba, 2005a; Egharevba and Hannikianen, 2005). It is a known scientific fact that inter-group racial attitudes are the representation of group competition and perceived threat to power and status (Group-position theory). According to Blumer (1958) a sense of group threat is an essential element for the emergence of racial prejudice. Consequently, it was essential that we explored the existing relationship between the respondents and the police in order to have an understanding of this concept. The result indicates some local and international contextual issues and assumptions that were of importance tackling prejudice and discrimination as it exists within the police in the country. Moreover, we have to also remember that, for years, many of these African immigrants have been on the receiving end of unjust law enforcement in their various countries of origin, which has resulted in many of them feeling inferior and distrustful of the police even in their own country of origin. While discussing the issues of cultural difference and how it affects policing, we must also keep in mind the socio-cultural background of the participants, their level of language proficiency and educational background. The research data analysed in this study also confirmed the difficulties associated with cultural misunderstandings in interpreting issues and how these misunderstandings have affected police and immigrant relations in Finland. Finally, the fifth paper focussed on cadets’ attitudes towards African immigrants as well as serving police officers’ interaction with African clients. Secondly, the police level of awareness of African immigrants’ distrustfulness of their profession was unclear. For this reason, my questions in this fifth study examined the experiences and attitudes of police cadets and serving police officers as well as those of African immigrants in understanding how to improve this relationship in the country. The data was based on (n=88) immigrant participants, (n=45) police cadets and 6 serving police officers from the Turku police department. The result suggests that there is distrust of the police in the respondents’ interaction; this tends to have galvanised a heightened tension resulting from the lack of language proficiency (Egharevba and White, 2007; Egharevba and Hannikainen, 2005, and Egharevba, 2006b) The result also shows that the allegation of immigrants as being belittled by the police stems from the misconceptions of both parties as well as the notion of stop and search by the police in Turku. All these factors were observed to have contributed to the alleged police evasiveness and the lack of regular contact between the respondents and the police in their dealings. In other words, the police have only had job-related contact with many of the participants in the present study. The results also demonstrated the complexities caused by the low level of education among some of the African immigrants in their understanding about the Finnish culture, norms and values in the country. Thus, the framework constructed in these studies embodies diversity in national culture as well as the need for a further research study with a greater number of respondents (both from the police and immigrant/majority groups), in order to explore the different role cultures play in immigrant and majority citizens’ understanding of police work.

Histochemical aspects of reserves mobilization of Caesalpinia peltophoroides (Leguminosae) seeds during germination and seedlings early growth

The objective of this study was to investigate reserve mobilization in Caesalpinia peltophoroides seeds during germination and initial seedling growth. The variation in these compounds was analyzed from the pre-germination period (0 to 5 days after sowing - DAS) to the total cotyledon senescence and abscission at 35 DAS. For this histochemical tests were made on cotyledons fixed in FAA50 or included in glycol-metacrylate. To follow the mobilization of the main reserve compounds, sudan III was used to detect total lipids, xylidine Ponceau to detect total proteins, lugol to detect starch and polarized light to visualize the crystals. The lipids, present in a great quantity in the cotyledon, gradually decreased in the period studied. A greater quantity of starch was observed on the 10th DAS than in the previous periods and it was totally consumed by 30 DAS. The distribution pattern and the morphology of the protein material were very modified by 10 DAS, a period during which it was intensely consumed, remaining only parietally fragments distributed, that practically disappeared at 25 DAS. The calcium oxalate druses were not consumed during the period studied, there was only crystal agglutination.

Analysis of private natural heritage reserves as a conservation strategy for the biodiversity of the cocoa region of the southern State of Bahia, Brazil

Brazil was the first country in Latin America to establish and regulate this type of reserve, and there are currently more than 700 Private Nature Heritage Reserves (RPPN in Portuguese) officially recognized by either federal or state environmental agencies. Together, these RPPN protect more than a half million hectares of land in the country. The coastal forests in the southern part of Bahia State extend 100 to 200 km inland, gradually changing in physiognomy as they occupy the dryer inland areas. The coastal forest has been subjected to intense deforestation, and currently occupies less than 10% of its original area. For this work the creation processes of the RPPN were consulted to obtain the data creation time, size of property, the condition of the remaining forest, succession chain and the last paid tax. After that, interviews with the owners were made to confirm this data. Sixteen RPPN have been established in this region until 2005. Their sizes vary from 4.7 to 800 ha. Ten of these RPPN are located within state or federal conservation areas or their buffer zones. In spite of the numerous national and international conservation strategies and environmental policies focused on the region, the present situation of the cocoa zone is threatening the conservation of the region's natural resources. The establishment of private reserves in the cocoa region could conceivably improve these conservation efforts. This type of reserve can be established under a uniform system supported by federal legislation, and could count on private organizations.

The Changing Nature of Library Networks - Open Data or One Big Silo?

Anders Söderbäckin esitys Kirjastoverkkopäivillä 26.10.2011 Helsingissä.

Using aster multispectral imagery for mapping woody invasive species in pico da vara natural reserve (Azores Islands, Portugal)

This paper aims to assess the effectiveness of ASTER imagery to support the mapping of Pittosporum undulatum, an invasive woody species, in Pico da Vara Natural Reserve (S. Miguel Island, Archipelago of the Azores, Portugal). This assessment was done by applying K-Nearest Neighbor (KNN), Support Vector Machine (SVM) and Maximum Likelihood (MLC) pixel-based supervised classifications to 4 different geographic and remote sensing datasets constituted by the Visible, Near-Infrared (VNIR) and Short Wave Infrared (SWIR) of the ASTER sensor and by digital cartography associated to orography (altitude and "distance to water streams") of which the spatial distribution of Pittosporum undulatum directly depends. Overall, most performed classifications showed a strong agreement and high accuracy. At targeted species level, the two higher classification accuracies were obtained when applying MLC and KNN to the VNIR bands coupled with auxiliary geographic information use. Results improved significantly by including ecology and occurrence information of species (altitude and distance to water streams) in the classification scheme. These results show that the use of ASTER sensor VNIR spectral bands, when coupled to relevant ancillary GIS data, can constitute an effective and low cost approach for the evaluation and continuous assessment of Pittosporum undulatum woodland propagation and distribution within Protected Areas of the Azores Islands.

Soil sampling intensity and spatial distribution pattern of soils attributes and corn yield in no-tillage system

Taking into account that the sampling intensity of soil attributes is a determining factor for applying of concepts of precision agriculture, this study aims to determine the spatial distribution pattern of soil attributes and corn yield at four soil sampling intensities and verify how sampling intensity affects cause-effect relationship between soil attributes and corn yield. A 100-referenced point sample grid was imposed on the experimental site. Thus, each sampling cell encompassed an area of 45 m² and was composed of five 10-m long crop rows, where referenced points were considered the center of the cell. Samples were taken from at 0 to 0.1 m and 0.1 to 0.2 m depths. Soil chemical attributes and clay content were evaluated. Sampling intensities were established by initial 100-point sampling, resulting data sets of 100; 75; 50 and 25 points. The data were submitted to descriptive statistical and geostatistics analyses. The best sampling intensity to know the spatial distribution pattern was dependent on the soil attribute being studied. The attributes P and K+ content showed higher spatial variability; while the clay content, Ca2+, Mg2+ and base saturation values (V) showed lesser spatial variability. The spatial distribution pattern of clay content and V at the 100-point sampling were the ones which best explained the spatial distribution pattern of corn yield.

Tourism, poverty alleviation and nature conservation : the state of contemporary research

Artikkeli perustuu kirjallisuuskatsaukseen, joka on tehty 17 lehden 112 vertaisarvioidusta artikkelista vuosilta 2003-2007.

Distribution pattern, surface tension and contact angle of herbicides associated to adjuvants on spraying and control of Ipomoea hederifolia under rainfall incidence

ABSTRACTScarlet Morning Glory is considered to be an infesting weed that affects several crops and causes serious damage. The application of chemical herbicides, which is the primary control method, requires a broad knowledge of the various characteristics of the solution and application technology for a more efficient phytosanitary treatment. Therefore this study aimed to characterize the effect of rainfall incidence on the control of Ipomoea hederifolia, considering droplet size, surface tension, contact angle of droplets formed by herbicides liquid on vegetal and artificial surfaces, associated to adjuvants and the volumetric distribution profile of the spray jet. The addition of the adjuvants to the herbicide spraying liquid improved the application quality, as it influenced the angle formed by the spray by broadening the deposition band of the spray nozzle and thus the possible distance between the nozzles on spray boom and due the changes at droplet size, which contribute to a safety application. The rainfall occurrence affected negatively the weed control with the different spraying liquids and also the dry matter weight, suggesting that the phytosanitary product applied was washed off.

Inguinal hernias in patients of 50 years and above. Pattern and outcome

OBJECTIVE: to evaluate a one year experience with inguinal hernia repair, in patients of > 50years, with respect to the type of inguinal hernia, type of surgery, postoperative complications and recurrence. METHODS: a prospective descriptive study of patients (n=57) > 50 years operated for inguinal hernia during a one year period. Tension-free meshplasty and herniorrhaphy, using 3"x6" polypropylene mesh and 2-0 polypropylene suture, were performed in elective and emergency surgery respectively. Follow-up visits were scheduled at six weeks, three and six months postoperatively. RESULTS: the most representative age group was 61-70 years, and all patients were male. 52 (91.22%) patients had unilateral inguinal hernias, while five (8.77%) had bilateral hernias. In 50 (87.71%) patients, the hernia was uncomplicated, while seven (12.28%) patients presented with some complication such as obstruction or strangulation. Elective surgery was performed in 50 (87.71%) patients while seven (12.28%) patients were operated in emergency. Postoperatively, 50 (87.7%) patients had uneventful recovery, while seven (12.28%) patients developed some complications which were treated conservatively. Mean hospital stay was six days. One recurrence was observed and there was no peri/postoperative death. CONCLUSION: tension-free meshplasty and herniorrhaphy are safe, simple and applicable even in elderly patients after adequate pre-operative assessment and optimization. Although associated with longer hospital stay, the mortality rate is nil and complication as well as recurrence rate is low. Hence, timely repair is necessary in elderly patients even in those with comorbid conditions.

Social tagging within task management

Social tagging evolved in response to a need to tag heterogeneous objects, the automated tagging of which is usually not feasible by current technological means. Social tagging can be used for more flexible competence management within organizations. The profiles of employees can be built in the form of groups of tags, as employees tag each other, based on their familiarity of each other’s expertise. This can serve as a replacement for the more traditional competence management approaches, which usually become outdated due to social and organizational hurdles, and obsolete data. These limitations can be overcome by people tagging, as the information revealed by such tags is usually based on most recent employee interaction and knowledge. Task management as part of personal information management aims at the support of users’ individual task handling. This can include collaborating with other individuals, sharing one’s knowledge, both functional and process-related, and distributing documents and web resources. In this context, Task patterns can be used as templates that collect information and experience around tasks associated to it during run time, facilitating agility. The effective collaboration among contributors necessitates the means to find the appropriate individuals to work with on the task, and this can be made possible by using social tagging to describe individual competencies. The goal of this study is to support finding and tagging people within task management, through the effective exploitation of the work/task context. This involves the utilization of knowledge of the workers’ expertise, nature of the task/task pattern and information available from the documents and web resources attached to the task. Vice versa, task management provides an excellent environment for social tagging due to the task context that already provides suitable tags. The study also aims at assisting users of the task management solution with the collaborative construction of light-weight ontology by inferring semantic relations between tags. The thesis project aims at an implementation of people finding & tagging within the java application for task management that consumes web services, which provide the required ontology for the organization.

Evaluation of Bubble Formation and Break Up in Suppression Pools by Using Pattern Recognition Methods

During a possible loss of coolant accident in BWRs, a large amount of steam will be released from the reactor pressure vessel to the suppression pool. Steam will be condensed into the suppression pool causing dynamic and structural loads to the pool. The formation and break up of bubbles can be measured by visual observation using a suitable pattern recognition algorithm. The aim of this study was to improve the preliminary pattern recognition algorithm, developed by Vesa Tanskanen in his doctoral dissertation, by using MATLAB. Video material from the PPOOLEX test facility, recorded during thermal stratification and mixing experiments, was used as a reference in the development of the algorithm. The developed algorithm consists of two parts: the pattern recognition of the bubbles and the analysis of recognized bubble images. The bubble recognition works well, but some errors will appear due to the complex structure of the pool. The results of the image analysis were reasonable. The volume and the surface area of the bubbles were not evaluated. Chugging frequencies calculated by using FFT fitted well into the results of oscillation frequencies measured in the experiments. The pattern recognition algorithm works in the conditions it is designed for. If the measurement configuration will be changed, some modifications have to be done. Numerous improvements are proposed for the future 3D equipment.