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  • Mäntylä, Jorma Allan (Matemaattisten aineiden opettajien liitto MAOL ry, 2009)
    Tarkastelun kohteena on Galileo Galilein ja John Miltonin tapaaminen 1638 sekä Galilein inkvisitio-oikeudenkäynnin vaikutus John Miltonin käsitykseen sananvapaudesta. Artikkelia on täydennetty 2009.
  • Copenhagen, D.R.; Donner, K.; Reuter, T. (Blackwell, 1987)
    1. The performance of ganglion cells in detecting flashes of light near the absolute threshold was studied in an isolated eye-cup preparation of toad retina. Retinal ganglion cells, through which all visual information from the rods must flow to the brain, are in a key position for evaluating the still unproven hypothesis that the absolute light sensitivity is limited by rod noise (Barlow, 1956). 2. The dark-adapted threshold intensity for these cells, which were selected on the basis of their high sensitivity, averaged 0.029 Rh* flash-1 (range 0.008- 0.062), where Rh* signifies one photoisomerization per rod. On average, 46 photoisomerizations were needed per receptive field per flash to evoke a threshold response (range 16-84). 3. In the threshold region, frequency of responses versus mean flash intensity was determined. Threshold performance could be described by theoretical frequency of response curves, allowing intrinsic noise to be estimated in terms of an equivalent rate of photoisomerization-like (dark) events. In two completely characterized cells the rate of dark events corresponded to 0.03 and 0.06 Rh*DS-1, where Rh*D signifies one dark event per rod. 4. Threshold elevations produced by dim backgrounds were studied. The results of these experiments are consistent with a dark event rate equivalent to 0.046 Rh*DS-1, or 0.037 Rh*DS-1 after correcting for a probable decrease in summation time. 5. The rate of actual dark events (0.028 Rh*DS-1, 20 degrees C) measured in Bufo rods (Baylor, Lamb & Yau, 1980) is close to the equivalent rates determined here. Thus, for the ganglion cells signalling the dimmest lights, the dark events in rods appear to be the most significant intrinsic retinal noise source limiting detection.
  • Koivula, M.; Niemelä, J. (Blackwell, 2003)
    In order to study the ecological effects of logging combined with mechanical soil preparation, we sampled carabid beetles with pitfall trapping in nine spruce-dominated stands in central Finland in 1995–1998. Three of the stands were left intact as controls. Three 1600-m2 openings per stand were logged in the winter 1995–1996 into six stands. In three of these stands, light soil preparation was applied. Logging affected the species assemblages, but soil preparation per se had no clear effects. Open-habitat species increased in abundance in the openings one year after logging, but catches of generalist species in the different treatments did not differ from each other. A forest species, Calathus micropterus, was least abundant in the prepared openings. The amounts of logging residue, exposed mineral soil and aggregated humus, as well as the abundance of red wood ants, significantly explained variation in carabid assemblages.
  • Rizzo, A.F.; Korkeala, H.; Mononen, I. (American Society for Microbiology, 1987)
    Cellular fatty acids and monosaccharides in a group of 14 lactobacilli were analyzed by gas chromatography and the identity of the components was confirmed by gas chromatography-mass spectrometry. From the same bacterial sample, both monosaccharides and fatty acids were liberated by methanolysis, and in certain experiments, fatty acids alone were released by basic hydrolysis. The results indicate that basic hydrolysis gave more comprehensive information about the fatty acids, but the analysis of monosaccharides was found to be much more useful in distinguishing between different species of lactobacilli. The method described allowed differentiation of 11 of 14 Lactobacillus species, and even single colonies isolated from agar plates could be used for analysis without subculturing.
  • Ylä-Ajos, Maria; Tuominen, Satu; Hänninen, Laura; Ruusunen, Marita; Puolanne, Eero; Valros, Anna (TAYLOR & FRANCIS LTD, 2012)
    1. Investigations were made into the breast and leg muscle energy metabolism, and the quality of breast meat of turkeys after controlled atmosphere stunning or stun-killing (CAS) with various gas mixtures. In addition, the effect on meat quality of an increase in the chilling rate of turkey breast meat after hypercapnic or anoxic stun-killing was studied. 2. A total of 35 turkey toms within two replicate pens were individually stunned during consecutive weeks using one of 4 CAS methods. The stunning gases tested were high CO2 concentration (60% CO2 in air), high N2 concentration (98% N2, 2% O2), a mixture of 76% N2 and 24% CO2, and a biphasic method (first minute in mixture containing 40% CO2, 30% N2, and 30% O2; followed by two minutes in a mixture containing 60% CO2 in air). 3. The birds stunned with N2 displayed the highest initial reduction in muscle pH, but after 4 h post mortem there were no differences in pH values associated with the various CAS methods. 4. The CAS method alone had no statistically significant effect on the quality of turkey breast muscle when the chilling speed was rapid (0°C for 4 h, followed by storage at 4°C). When the chilling rate was slowed (20°C for4 h followed by storage at 4°C), a significant decrease in cooking loss and in Warner-Bratzler shear force was recorded for birds stun-killed with CO2. 5. This study shows that anoxic stun-killing with N2 had no adverse effects on meat quality despite the rapid post mortem pH decrease. The CAS with N2 allows rapid cooling of carcases without the risk of cold shortening, whereas with CO2-stun-killing of turkeys, the rate of chilling should be slower. Concerning meat quality, all the CAS methods tested were suitable for stunning turkeys.
  • Väliverronen, Esa (Viestinnän laitos, 2007)
    Tässä kirjassa tutkin sitä, millaisten tarinoiden, kuvien ja vertauskuvien kautta biotekniikasta ja geenitutkimuksen sovelluksista on kerrottu mediassa. Tärkeimpänä aineistoa ovat YLE:n ja MTV3: n geeniperimää ja biotekniikkaa käsittelevät tv-uutiset vuosilta 1985–2000. Nämä runsaat 200 uutisjuttuja antavat kiinnostavan läpileikkauksen aiheen käsittelystä ja muutoksista runsaan kymmenen vuoden aikana. Televisiouutisten lisäksi käytän aiheen taustoituksessa ja kahdessa tapausanalyysissa laajempaa media-aineistoa kuten sanoma- ja aikakauslehtiä ja tv-dokumentteja. Nämä tapaukset ovat paljon julkisuutta saaneet siirtogeeninen Huomen -lehmä sekä ihmisen geeniperimää kartoittanut Human Genome -projekti. Satunnaisemmin viittaan myös muutamiin elokuviin ja mainoksiin.
  • Enroth, Johannes (Puutarhaliitto, 2012)
  • Katayama, Shintaro; Skoog, Tiina; Jouhilahti, Eeva-Mari; Siitonen, H. A; Nuutila, Kristo; Tervaniemi, Mari H; Vuola, Jyrki; Johnsson, Anna; Lönnerberg, Peter; Linnarsson, Sten; Elomaa, Outi; Kankuri, Esko; Kere, Juha (BioMed Central, 2015)
    Abstract Background Keratinocytes (KCs) are the most frequent cells in the epidermis, and they are often isolated and cultured in vitro to study the molecular biology of the skin. Cultured primary cells and various immortalized cells have been frequently used as skin models but their comparability to intact skin has been questioned. Moreover, when analyzing KC transcriptomes, fluctuation of polyA+ RNA content during the KCs’ lifecycle has been omitted. Results We performed STRT RNA sequencing on 10 ng samples of total RNA from three different sample types: i) epidermal tissue (split-thickness skin grafts), ii) cultured primary KCs, and iii) HaCaT cell line. We observed significant variation in cellular polyA+ RNA content between tissue and cell culture samples of KCs. The use of synthetic RNAs and SAMstrt in normalization enabled comparison of gene expression levels in the highly heterogenous samples and facilitated discovery of differences between the tissue samples and cultured cells. The transcriptome analysis sensitively revealed genes involved in KC differentiation in skin grafts and cell cycle regulation related genes in cultured KCs and emphasized the fluctuation of transcription factors and non-coding RNAs associated to sample types. Conclusions The epidermal keratinocytes derived from tissue and cell culture samples showed highly different polyA+ RNA contents. The use of SAMstrt and synthetic RNA based normalization allowed the comparison between tissue and cell culture samples and thus proved to be valuable tools for RNA-seq analysis with translational approach. Transciptomics revealed clear difference both between tissue and cell culture samples and between primary KCs and immortalized HaCaT cells.
  • Majumder, Mamun; Kumar, Ashwini; Heckman, Caroline; Kankainen, Matti; Pesonen, Sari; Jäger , Elke; Karbach , Julia; Joensuu, Timo; Kairemo, Kalevi; Partanen, Kaarina; Alanko, Tuomo; Hemminki, Akseli; Backman, Charlotta; Dienel, Kasper; von Euler, Mikael; Hakonen, Tiina; Juhila, Juuso; Ranki, Tuuli; Vassilev, Lotta; Vuolanto, Antti; Jaderberg, Magnus (BioMed Central Ltd, 2014)
  • Tiraboschi, Ettore; Guirado, Ramon; Greco, Dario; Auvinen, Petri; Fernando Maya-Vetencourt, Jose; Maffei, Lamberto; Castren, Eero (HINDAWI PUBLISHING CORPORATION, 2013)
  • Friedman, Sy-David; Hyttinen, Tapani; Kulikov, Vadim (American Mathematical Society, 2014)
    Memoirs of the American Mathematical Society
    The field of descriptive set theory is mainly concerned with studying subsets of the space of all countable binary sequences. In this paper we study the generalization where countable is replaced by uncountable. We explore properties of generalized Baire and Cantor spaces, equivalence relations and their Borel reducibility. The study shows that the descriptive set theory looks very dierent in this generalized setting compared to the classical, countable case. We also draw the connection between the stability theoretic complexity of first-order theories and the descriptive set theoretic complexity of their isomorphism relations. Our results suggest that Borel reducibility on uncountable structures is a model theoretically natural way to compare the complexity of isomorphism relations.
  • Kiljunen, Saija; Pajunen, Maria I; Dilks, Kieran; Storf, Stefanie; Pohlschroder, Mechthild; Savilahti, Harri (BioMed Central Ltd, 2014)
    Abstract Background Archaea share fundamental properties with bacteria and eukaryotes. Yet, they also possess unique attributes, which largely remain poorly characterized. Haloferax volcanii is an aerobic, moderately halophilic archaeon that can be grown in defined media. It serves as an excellent archaeal model organism to study the molecular mechanisms of biological processes and cellular responses to changes in the environment. Studies on haloarchaea have been impeded by the lack of efficient genetic screens that would facilitate the identification of protein functions and respective metabolic pathways. Results Here, we devised an insertion mutagenesis strategy that combined Mu in vitro DNA transposition and homologous-recombination-based gene targeting in H. volcanii. We generated an insertion mutant library, in which the clones contained a single genomic insertion. From the library, we isolated pigmentation-defective and auxotrophic mutants, and the respective insertions pinpointed a number of genes previously known to be involved in carotenoid and amino acid biosynthesis pathways, thus validating the performance of the methodologies used. We also identified mutants that had a transposon insertion in a gene encoding a protein of unknown or putative function, demonstrating that novel roles for non-annotated genes could be assigned. Conclusions We have generated, for the first time, a random genomic insertion mutant library for a halophilic archaeon and used it for efficient gene discovery. The library will facilitate the identification of non-essential genes behind any specific biochemical pathway. It represents a significant step towards achieving a more complete understanding of the unique characteristics of halophilic archaea.
  • Shikano, Takahito; Laine, Veronika N.; Herczeg, Gabor; Vilkki, Johanna; Merilä, Juha (GENETICS SOC AM, 2013)
  • Haukkala, Ari; Konttinen, Hanna; Hankonen, Nelli; Perola, Markus; Kääriäinen, Helena; Salomaa, Veikko (BioMed Central, 2015)
    Abstract Background The role and meaning of genetic information has grown considerably in the recent decades. We examined changes in causal beliefs about morbidity as well as the associations between causal beliefs, health behaviors and obesity, and health outcome beliefs from 1982 to 2002. Methods In five population-based risk-factor surveys (the FINRISK Studies) of individuals aged 25 to 64 years conducted from 1982 to 2002 (n = 37,503), respondents chose the most important cause of morbidity from a list of ten alternatives. Health outcome beliefs were assessed with two items. Physical inactivity and smoking status were based on self-reports and obesity was based on measured height and weight. Results The prevalence of those who endorse genetic factors as the most important cause of morbidity increased from 4% in 1982 to 10% in 1992 and remained at that level until 2002. During the study period, lack of exercise and overweight increased, whereas inappropriate diet and stress diminished as causal beliefs about morbidity. Smokers and physically inactive were more likely to endorse genetic than behavioral causes of morbidity, whereas obese respondents were more likely to choose overweight over genetic causes of morbidity. Those who endorse genetic factors as the most important cause had more pessimistic outcome beliefs about health behavior changes, but these outcome beliefs became more positive in all causal belief groups during the study period. Conclusion Despite increased public discussion of genomics, the relative proportion of those who endorse genetic factors as the most important cause of morbidity has remained low. However, within this group beliefs about benefits of health behavior changes have become more positive. This could indicate that increase in genomic health information does not lead to more negative appraisals of efficacy of lifestyle changes.
  • Aivelo, Tuomas Juho Eero; Uitto, Anna Eliisa (Naturfagsenteret, 2015)
    Genetics is a fast-developing field and it has been argued that genetics education is lagging behind. Genetics education has for example been suspected of indoctrinating strong genetic determinism. As the updating of the national upper secondary school curricula is about to start, we decided to study how the current curriculum manifests in Finnish biology textbooks. We studied the main four textbooks for historical gene models and definitions of genes using content analysis. Hybrid models were pervasive in textbooks. The textbooks expressed sometimes even strong genetic determinism, which might be linked to the dominance of older historical models in the textbooks. We also found instances of determinism which we call ‘weak determinism’: genes were depicted as more important factor than environment in relation to the expressed properties. Subsequently, there were no modern gene models found. We suggest gene models should be presented explicitly to reduce misconceptions about genes. We argue that genetics education needs to take more into account than environmental effects and there needs to be more emphasis on the temporal and developmental aspect of genotype-phenotype link. Specifically in Finland this could be done by a more explicit formulation of the national curriculum.
  • Csöndes, Izabella; Cseh, András; Taller, János; Poczai, Péter (Springer Netherlands, 2012)
  • Petersen, Jessica L.; Mickelson, James R.; Cothran, E. Gus; Andersson, Lisa S.; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; Machado, Artur da Camara; Distl, Ottmar; Felicetti, Michela; Fox-Clipsham, Laura; Graves, Kathryn T.; Guerin, Gerard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A.; Mikko, Sofia; Orr, Nicholas; Penedo, M. Cecilia T.; Piercy, Richard J.; Raekallio, Marja; Rieder, Stefan; Roed, Knut H.; Silvestrelli, Maurizio; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; Wade, Claire M.; McCue, Molly E. (PUBLIC LIBRARY OF SCIENCE, 2013)
  • Baig, Abiyad; McNally, Alan; Dunn, Steven; Paszkiewicz, Konrad H; Corander, Jukka; Manning, Georgina (BioMed Central, 2015)
    Abstract Background Campylobacter jejuni is a major zoonotic pathogen, causing gastroenteritis in humans. Invasion is an important pathogenesis trait by which C. jejuni causes disease. Here we report the genomic analysis of 134 strains to identify traits unique to hyperinvasive isolates. Methods A total of 134 C. jejuni genomes were used to create a phylogenetic tree to position the hyperinvasive strains. Comparative genomics lead to the identification of mosaic capsule regions. A pan genome approach led to the discovery of unique loci, or loci with unique alleles, to the hyperinvasive strains. Results Phylogenetic analysis showed that the hyper-invasive phenotype is a generalist trait. Despite the fact that hyperinvasive strains are only distantly related based on the whole genome phylogeny, they all possess genes within the capsule region with high identity to capsule genes from C. jejuni subsp. doylei and C. lari. In addition there were genes unique to the hyper-invasive strains with identity to non-C. jejuni genes, as well as allelic variants of mainly pathogenesis related genes already known in the other C. jejuni. In particular, the sequence of flagella genes, flgD-E and flgL were highly conserved amongst the hyper-invasive strains and divergent from sequences in other C. jejuni. A novel cytolethal distending toxin (cdt) operon was also identified as present in all hyper-invasive strains in addition to the classic cdt operon present in other C. jejuni. Conclusions Overall, the hyper-invasive phenotype is strongly linked to the presence of orthologous genes from other Campylobacter species in their genomes, notably within the capsule region, in addition to the observed association with unique allelic variants in flagellar genes and the secondary cdt operon which is unlikely under random sharing of accessory alleles in separate lineages.