Persistent organic pollutants in sediments and fish from Lake Victoria, Uganda

This thesis describes the occurrence and sources of selected persistent organic pollutants (POPs) such as polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and hexachlorocyclohexanes (HCHs) in the northern watershed of Lake Victoria. Sediments and fish were collected from three highly polluted embayments (i.e. Murchison Bay, Napoleon Gulf and Thurston Bay) of the lake. The analysis for PCDD/Fs, PCBs and PBDEs was done using a high resolution mass spectrometer coupled to a gas chromatograph (GC), and a GC equipped with an electron capture detector was used for HCHs. Total (Σ) PCDD/Fs, PCBs and PBDEs in sediments ranged from 3.19 to 478, 313 to 4325 and 60.8 to 179 pg g-1 dry weight (dw), respectively. The highest concentrations of pollutants were found at sites close to industrial areas and wastewater discharge points. The maximum concentrations of PCDD/Fs, PCBs, PBDEs and HCHs in fish muscle homogenates were 49, 779, 495 and 45,900 pg g-1 wet weight (ww), respectively. The concentrations of the pollutants in Nile perch (Lates niloticus) were significantly greater than those in Nile tilapia (Oreochromis niloticus), possibly due to differences in trophic level and dietary feeding habits among fish species. World Health Organization-toxic equivalency quotient (WHO2005-TEQ) values in the sediments were up to 4.24 pg g-1 dw for PCDD/Fs and 0.55 pg TEQ g-1 dw for the 12 dioxin-like PCBs (dl-PCBs). 23.1% of the samples from the Napoleon Gulf were above the interim sediment quality guideline value of 0.85 pg WHO-TEQ g-1 dw set by the Canadian Council for Ministers of the Environment. The WHO2005-TEQs in fish were 0.001-0.16 pg g-1 for PCDD/Fs and 0.001-0.31 pg g-1 ww for dl- PCBs. The TEQ values were within a permissible level of 3.5 pg g−1 ww recommended by the European Commission. Based on the Commission set TEQs and minimum risk level criteria formulated by the Agency for Toxic Substances and Disease Registry, the consumption of fish from Lake Victoria gives no indication of health risks associated to PCDD/Fs and PCBs. Principal component analysis (PCA) indicated that anthropogenic activities such as agricultural straw open burning, medical waste incinerators and municipal solid waste combustors were the major sources of PCDD/Fs in the watershed of Lake Victoria. The ratios of α-/γ-HCH varied from 0.89 to 1.68 suggesting that the highest HCH residues mainly came from earlier usage and fresh γ-HCH (lindane). In the present study, the concentration of POPs in fish were not significantly related to those in sediments, and the biota sediment accumulation factor (BSAF) concept was found to be a poor predictor of the bioavailability and bioaccumulation of environmental pollutants.

From genotype to phenotype : diversity and population structure of Flavobacterium psychrophilum

Flavobacterium psychrophilum is the etiological agent of bacterial cold-water disease (BCWD) causing high fish mortalities and significant economic losses to the freshwater salmonid aquaculture industry around the world. Today BCWD outbreaks are mainly treated with environmentally hazardous antimicrobial agents and alternative preventative measures are urgently needed in order to ensure the well-being of animals and the sustainability of aquaculture. The diversity of pathogenic bacteria challenges the development of universal control strategies and in many cases the pathogen population structure, i.e. the total genetic diversity of the species must be taken into account. This work integrates the tools of modern molecular biology and conventional phenotypic microbiology to gain knowledge about the diversity and population structure of F. psychrophilum. The present work includes genetic characterization of a large collection of isolates collected from diverse origins and years, from aquaculture in a whole region including different countries, and provides the first international validation of a universal multilocus sequence typing (MLST) approach for unambiguous genetic typing of F. psychrophilum. Population structure analyses showed that the global F. psychrophilum population is subdivided into pathogenic species-specific clones, of which one particular genetic lineage, clonal complex CC-ST2, has been responsible for the majority of BCWD outbreaks in rainbow trout (Oncorhynchus mykiss) in European aquaculture facilities over several decades. Genotypic and phenotypic population heterogeneity affecting antimicrobial resistance in F. psychrophilum within BCWD outbreaks was discovered. Specific genotypes were associated with severe infections in farmed rainbow trout and Atlantic salmon (Salmo salar), and in addition to high adherence, antimicrobial resistance was strongly associated with outbreak strains. The study brought additional support for the hypothesis of an epidemic F. psychrophilum population structure, where recombination is an important force for the generation and maintenance of genetic diversity, and a significant contribution towards mapping the genetic diversity of this important fish pathogen. Evidence indicating dissemination of virulent strains with commercial movement of fish and fish products was strengthened.

Automatic recognition of fish from video sequences

The problem of automatic recognition of the fish from the video sequences is discussed in this Master’s Thesis. This is a very urgent issue for many organizations engaged in fish farming in Finland and Russia because the process of automation control and counting of individual species is turning point in the industry. The difficulties and the specific features of the problem have been identified in order to find a solution and propose some recommendations for the components of the automated fish recognition system. Methods such as background subtraction, Kalman filtering and Viola-Jones method were implemented during this work for detection, tracking and estimation of fish parameters. Both the results of the experiments and the choice of the appropriate methods strongly depend on the quality and the type of a video which is used as an input data. Practical experiments have demonstrated that not all methods can produce good results for real data, whereas on synthetic data they operate satisfactorily.

Spatial and temporal variation in fish populations and assemblages in coastal waters of the northern Baltic Proper

The distribution and traits of fish are of interest both ecologically and socio-economically. In this thesis, phenotypic and structural variation in fish populations and assemblages was studied on multiple spatial and temporal scales in shallow coastal areas in the archipelago of the northern Baltic Proper. In Lumparn basin in Åland Islands, the fish assemblage displayed significant seasonal variation in depth zone distribution. The results indicate that investigating both spatial and temporal variation in small scale is crucial for understanding patterns in fish distribution and community structure in large scale. The local population of Eurasian perch Perca fluviatilis L displayed habitat-specific morphological and dietary variation. Perch in the pelagic zone were on average deeper in their body shape than the littoral ones and fed on fish and benthic invertebrates. The results differ from previous studies conducted in freshwater habitats, where the pelagic perch typically are streamlined in body shape and zooplanktivorous. Stable isotopes of carbon and nitrogen differed between perch with different stomach contents, suggesting differentiation of individual diet preferences. In the study areas Lumparn and Ivarskärsfjärden in Åland Islands and Galtfjärden in Swedish east coast, the development in fish assemblages during the 2000’s indicated a general shift towards higher abundances of small-bodied lower-order consumers, especially cyprinids. For European pikeperch Sander lucioperca L., recent declines in adult fish abundances and high mortalities (Z = 1.06–1.16) were observed, which suggests unsustainably high fishing pressure on pikeperch. Based on the results it can be hypothesized that fishing has reduced the abundances of large predatory fish, which together with bottom-up forcing by eutrophication has allowed the lower-order consumer species to increase in abundances. This thesis contributes to the scientific understanding of aquatic ecosystems with new descriptions on morphological and dietary adaptations in perch in brackish water, and on the seasonal variation in small-scale spatial fish distribution. The results also demonstrate anthropogenic effects on coastal fish communities and underline the urgency of further reducing nutrient inputs and regulating fisheries in the Baltic Sea region.

Nichesourcing The Uralic Languages For The Benefit Of Linguistic Research And Lingual Societies

The emerging technologies have recently challenged the libraries to reconsider their role as a mere mediator between the collections, researchers, and wider audiences (Sula, 2013), and libraries, especially the nationwide institutions like national libraries, haven’t always managed to face the challenge (Nygren et al., 2014). In the Digitization Project of Kindred Languages, the National Library of Finland has become a node that connects the partners to interplay and work for shared goals and objectives. In this paper, I will be drawing a picture of the crowdsourcing methods that have been established during the project to support both linguistic research and lingual diversity. The National Library of Finland has been executing the Digitization Project of Kindred Languages since 2012. The project seeks to digitize and publish approximately 1,200 monograph titles and more than 100 newspapers titles in various, and in some cases endangered Uralic languages. Once the digitization has been completed in 2015, the Fenno-Ugrica online collection will consist of 110,000 monograph pages and around 90,000 newspaper pages to which all users will have open access regardless of their place of residence. The majority of the digitized literature was originally published in the 1920s and 1930s in the Soviet Union, and it was the genesis and consolidation period of literary languages. This was the era when many Uralic languages were converted into media of popular education, enlightenment, and dissemination of information pertinent to the developing political agenda of the Soviet state. The ‘deluge’ of popular literature in the 1920s to 1930s suddenly challenged the lexical orthographic norms of the limited ecclesiastical publications from the 1880s onward. Newspapers were now written in orthographies and in word forms that the locals would understand. Textbooks were written to address the separate needs of both adults and children. New concepts were introduced in the language. This was the beginning of a renaissance and period of enlightenment (Rueter, 2013). The linguistically oriented population can also find writings to their delight, especially lexical items specific to a given publication, and orthographically documented specifics of phonetics. The project is financially supported by the Kone Foundation in Helsinki and is part of the Foundation’s Language Programme. One of the key objectives of the Kone Foundation Language Programme is to support a culture of openness and interaction in linguistic research, but also to promote citizen science as a tool for the participation of the language community in research. In addition to sharing this aspiration, our objective within the Language Programme is to make sure that old and new corpora in Uralic languages are made available for the open and interactive use of the academic community as well as the language societies. Wordlists are available in 17 languages, but without tokenization, lemmatization, and so on. This approach was verified with the scholars, and we consider the wordlists as raw data for linguists. Our data is used for creating the morphological analyzers and online dictionaries at the Helsinki and Tromsø Universities, for instance. In order to reach the targets, we will produce not only the digitized materials but also their development tools for supporting linguistic research and citizen science. The Digitization Project of Kindred Languages is thus linked with the research of language technology. The mission is to improve the usage and usability of digitized content. During the project, we have advanced methods that will refine the raw data for further use, especially in the linguistic research. How does the library meet the objectives, which appears to be beyond its traditional playground? The written materials from this period are a gold mine, so how could we retrieve these hidden treasures of languages out of the stack that contains more than 200,000 pages of literature in various Uralic languages? The problem is that the machined-encoded text (OCR) contains often too many mistakes to be used as such in research. The mistakes in OCRed texts must be corrected. For enhancing the OCRed texts, the National Library of Finland developed an open-source code OCR editor that enabled the editing of machine-encoded text for the benefit of linguistic research. This tool was necessary to implement, since these rare and peripheral prints did often include already perished characters, which are sadly neglected by the modern OCR software developers, but belong to the historical context of kindred languages and thus are an essential part of the linguistic heritage (van Hemel, 2014). Our crowdsourcing tool application is essentially an editor of Alto XML format. It consists of a back-end for managing users, permissions, and files, communicating through a REST API with a front-end interface—that is, the actual editor for correcting the OCRed text. The enhanced XML files can be retrieved from the Fenno-Ugrica collection for further purposes. Could the crowd do this work to support the academic research? The challenge in crowdsourcing lies in its nature. The targets in the traditional crowdsourcing have often been split into several microtasks that do not require any special skills from the anonymous people, a faceless crowd. This way of crowdsourcing may produce quantitative results, but from the research’s point of view, there is a danger that the needs of linguists are not necessarily met. Also, the remarkable downside is the lack of shared goal or the social affinity. There is no reward in the traditional methods of crowdsourcing (de Boer et al., 2012). Also, there has been criticism that digital humanities makes the humanities too data-driven and oriented towards quantitative methods, losing the values of critical qualitative methods (Fish, 2012). And on top of that, the downsides of the traditional crowdsourcing become more imminent when you leave the Anglophone world. Our potential crowd is geographically scattered in Russia. This crowd is linguistically heterogeneous, speaking 17 different languages. In many cases languages are close to extinction or longing for language revitalization, and the native speakers do not always have Internet access, so an open call for crowdsourcing would not have produced appeasing results for linguists. Thus, one has to identify carefully the potential niches to complete the needed tasks. When using the help of a crowd in a project that is aiming to support both linguistic research and survival of endangered languages, the approach has to be a different one. In nichesourcing, the tasks are distributed amongst a small crowd of citizen scientists (communities). Although communities provide smaller pools to draw resources, their specific richness in skill is suited for complex tasks with high-quality product expectations found in nichesourcing. Communities have a purpose and identity, and their regular interaction engenders social trust and reputation. These communities can correspond to research more precisely (de Boer et al., 2012). Instead of repetitive and rather trivial tasks, we are trying to utilize the knowledge and skills of citizen scientists to provide qualitative results. In nichesourcing, we hand in such assignments that would precisely fill the gaps in linguistic research. A typical task would be editing and collecting the words in such fields of vocabularies where the researchers do require more information. For instance, there is lack of Hill Mari words and terminology in anatomy. We have digitized the books in medicine, and we could try to track the words related to human organs by assigning the citizen scientists to edit and collect words with the OCR editor. From the nichesourcing’s perspective, it is essential that altruism play a central role when the language communities are involved. In nichesourcing, our goal is to reach a certain level of interplay, where the language communities would benefit from the results. For instance, the corrected words in Ingrian will be added to an online dictionary, which is made freely available for the public, so the society can benefit, too. This objective of interplay can be understood as an aspiration to support the endangered languages and the maintenance of lingual diversity, but also as a servant of ‘two masters’: research and society.

Diel patterns and tissue-specificity of environmental responses in fish

Humans are profoundly changing aquatic environments through climate change and the release of nutrients and chemicals. To understand the effects of these changes on natural populations, knowledge on individuals’ environmental responses is needed. At the molecular level, the environmental responses are partly mediated by chances in messenger RNA and protein levels. In this thesis I study messenger RNA and protein responses to an assortment of environmental stressors in fish. As daily (diel) rhythms are known to be ubiquitous in different tissues, I particularly focus on diel patterns in the responses. The studied species are the three-spined stickleback (Gasterosteus aculeatus L.) and the Arctic char (Salvelinus alpinus L.), both of which have circumpolar distribution in the Northern hemisphere. In the first two studies, three-spined sticklebacks were exposed to both the non-steroidal anti-inflammatory drug diclofenac and low-oxygen conditions (hypoxia), and their responses measured at separate time points in the liver and gills. The results show how the seemingly unrelated environmental stressors, hypoxia and anti-inflammatory drugs, can have harmful combined effects that differ from the effects of each stressor alone. Moreover, both stressors disturbed natural diel patterns in gene expression. In the third study, I studied the responses of three-spined sticklebacks to two test chemicals: one used in hormonal medicine (17α-ethinyl-oestradiol) and one used as a plasticizer and solvent chemical (di-n-butyl phthalate). The results suggest that the phthalate can affect genes related to spermatogenesis in fish testes, while estrogen-mimicking compounds can lead to numerous disturbances in the endocrine system. In the final study, the temperature-dependence of diel rhythms in messenger RNA levels were evaluated in the liver tissue of the Arctic char, a cold-adapted salmonid. The results show that cold acclimation repressed diel rhythms in gene expression compared to warm-acclimated fish, in which the expression of hundreds of genes was rhythmic, suggesting the circadian clock of the Arctic fish species can be sensitive to temperature. Overall, the results of the thesis indicate that fishes’ responses to abiotic factors interact with their diel rhythms, and more studies on the consequences of these interactions are needed to comprehensively understand human impacts on ecosystems.

Catalogue Of the main groups of Ephemera Collection

The Ephemera Collection has been organised in groups based on the topic. The collection also includes groups formed on the basis of the publication type.