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    • Several versions

    The effect of tree architecture on conduit diameter and frequency from small distal roots to branch tips in Betula pendula , Picea abies and Pinus sylvestris

    Lintunen, Anna, Kalliokoski, Tuomo, Niinemets, Ülo
    Tree Physiology, 2010, Vol. 30(11), pp.1433-1447 [Peer Reviewed Journal]

    • Several versions

    Comparability of Mixed IC 50 Data – A Statistical Analysis

    Kalliokoski, Tuomo, Kramer, Christian, Vulpetti, Anna, Gedeck, Peter
    PLoS ONE, 2013, Vol.8(4) [Peer Reviewed Journal]

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    Belowground interspecific competition in mixed boreal forests: fine root and ectomycorrhiza characteristics along stand developmental stage and soil fertility gradients

    Kalliokoski, Tuomo, Pennanen, Taina, Nygren, Pekka, Sievänen, Risto, Helmisaari, Heljä-Sisko
    Plant and Soil, 2010, Vol.330(1), pp.73-89 [Peer Reviewed Journal]
    Springer Science & Business Media B.V.
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    Title: Belowground interspecific competition in mixed boreal forests: fine root and ectomycorrhiza characteristics along stand developmental stage and soil fertility gradients
    Author: Kalliokoski, Tuomo; Pennanen, Taina; Nygren, Pekka; Sievänen, Risto; Helmisaari, Heljä-Sisko
    Subject: Fine root biomass ; Fine root length ; Root morphology ; Ectomycorrhizal diversity ; Fungal biomass
    Description: We studied fine roots and ectomycorrhizas in relation to aboveground tree and stand characteristics in five mixed Betula pendula Roth, Picea abies (L.) H. Karst., and Pinus sylvestris L. stands in Southern Finland. The stands formed gradients of developmental stage (15-, 30-, and 50-year-old stands) in the stands of medium fertility, and of site fertility in the young stands (30-year-old fertile, medium fertile, and least fertile stands). The biomass of the external hyphae of ectomycorrhizas (ECM) was the highest, and the diversity of the fungal community the lowest, in the most fertile stand. The vertical distributions of fine roots of the three tree species were mostly overlapping, indicating high inter-specific belowground competition in the stands. We did not find any clear trends in the fine root biomass (FRB) or length across the stand developmental stages. The FRB of the conifers varied with site fertility, whereas in B. pendula it was almost constant. In contrast to the conifers, the specific root length (SRL) of B. pendula clearly increased from the most fertile to the least fertile stand. This indicates differences in the primary nutrient acquisition strategy between conifers and B. pendula .
    Is part of: Plant and Soil, 2010, Vol.330(1), pp.73-89
    Identifier: 0032-079X (ISSN); 1573-5036 (E-ISSN); 10.1007/s11104-009-0177-9 (DOI)

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    Tree roots as self-similar branching structures: axis differentiation and segment tapering in coarse roots of three boreal forest tree species

    Kalliokoski, Tuomo, Sievänen, Risto, Nygren, Pekka
    Trees, 2010, Vol.24(2), pp.219-236 [Peer Reviewed Journal]
    Springer Science & Business Media B.V.
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    Title: Tree roots as self-similar branching structures: axis differentiation and segment tapering in coarse roots of three boreal forest tree species
    Author: Kalliokoski, Tuomo; Sievänen, Risto; Nygren, Pekka
    Subject: Developmental stage ; Fractal root model ; Mixed stand ; Root architecture ; Site type
    Description: We applied a fractal root model to the 3D architecture of the coarse root systems of Betula pendula Roth, Picea abies (L.) H. Karst., and Pinus sylvestris L. in mixed boreal forests. Our dataset consisted of 60 root systems excavated in five different mixed forest stands. We analyzed the variability of the model parameters with respect to species, site type, and different root axes. According to our results, the cross-sectional area of root segments (i.e. second power of diameter) was a suitable variable for analyzing the values of parameters of the fractal model. The parameter values varied with generation and order of root segments; the roots thus did not follow the simple fractal branching. The variation of parameters along the root axes showed the existence of a zone of rapid tapering in all tree species. The model was, with parameter values analyzed from the data, moderately capable of accounting for the main coarse root characteristics. It was important for model predictions to take into account the tapering of root segments. We conclude that, in boreal forests, tree root systems are the output of the axis-specific morphogenetic branching rules and functional adaptation to spatial heterogeneity in the soil.
    Is part of: Trees, 2010, Vol.24(2), pp.219-236
    Identifier: 0931-1890 (ISSN); 1432-2285 (E-ISSN); 10.1007/s00468-009-0393-1 (DOI)

    • Several versions

    Early root growth and architecture of fast- and slow-growing Norway spruce ( Picea abies ) families differ—potential for functional adaptation

    Hamberg, Leena, Velmala, Sannakajsa M, Sievänen, Risto, Kalliokoski, Tuomo, Pennanen, Taina
    Tree Physiology, 2017, Vol. 38(6), pp.853-864 [Peer Reviewed Journal]

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    Effects of nutrient optimization on intra-annual wood formation in Norway spruce

    Kalliokoski, Tuomo, Mäkinen, Harri, Jyske, Tuula, Nöjd, Pekka, Linder, Sune, Ryan, Michael
    Tree Physiology, 2013, Vol. 33(11), pp.1145-1155 [Peer Reviewed Journal]

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    Intra-annual tracheid formation of Norway spruce provenances in southern Finland

    Kalliokoski, Tuomo, Reza, Mehedi, Jyske, Tuula, Mäkinen, Harri, Nöjd, Pekka
    Trees, 2012, Vol.26(2), pp.543-555 [Peer Reviewed Journal]
    Springer Science & Business Media B.V.
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    Title: Intra-annual tracheid formation of Norway spruce provenances in southern Finland
    Author: Kalliokoski, Tuomo; Reza, Mehedi; Jyske, Tuula; Mäkinen, Harri; Nöjd, Pekka
    Subject: Cambial activity ; Origin ; Picea abies ; Seasonal dynamics ; Temperature ; Xylogenesis
    Description: We studied the intra-annual wood formation in a Norway spruce provenance experiment in southern Finland from 2004–2008. Two Finnish provenances, northern and southern, as well as German and Hungarian provenances were included. Timing of tracheid formation and differentiation, and tracheid dimensions were determined from periodically extracted microcores. The aim was to determine the differences between the years and provenances in the timing of the xylogenesis and in the xylem characteristics. Year-to-year variation was high both in timing of tracheid formation and xylem characteristics, while between-provenance differences were small. The onset of tracheid formation varied from early May to late June in different trees in different years. The onset of tracheid formation was not closely related to the annual variations of temperature sum. In all the years, daily temperatures exceeded the threshold +5°C for several weeks before the onset of tracheid formation. The highest tracheid formation rate occurred after the summer solstice in all years and generally coincided with the highest daily temperatures during the growing season. Tracheid production ceased early in 2006 due to a mid-summer drought. Cell differentiation continued late in autumn as non-mature tracheids were still observed around mid-September. No clear differences between the provenances in the timing of tracheid formation were observed, although the Finnish provenances tended to initiate tracheid formation slightly earlier than the other provenances. The tree-ring widths of the Finnish provenances were also wider, while tracheid diameter of the German provenance was slightly smaller. Our results indicate that between-tree variation in the timing of wood formation is high compared with the latitude effect of seed source.
    Is part of: Trees, 2012, Vol.26(2), pp.543-555
    Identifier: 0931-1890 (ISSN); 1432-2285 (E-ISSN); 10.1007/s00468-011-0616-0 (DOI)

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    Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

    Khan Suleiman A, Faisal Ali, Mpindi John, Parkkinen Juuso A, Kalliokoski Tuomo, Poso Antti, Kallioniemi Olli P, Wennerberg Krister, Kaski Samuel
    BMC bioinformatics, 01 May 2012, Vol.13(1), p.112 [Peer Reviewed Journal]

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    Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

    Khan, Suleiman, Ali, Faisal, Mpindi, John, Parkkinen, Juuso, Kalliokoski, Tuomo, Poso, Antti, Kallioniemi, Olli, Wennerberg, Krister, Kaski, Samuel
    arXiv.org, Dec 27, 2011
    © ProQuest LLC All rights reserved, Engineering Database, Publicly Available Content Database, ProQuest Engineering Collection, ProQuest Technology Collection, ProQuest SciTech Collection, Materials Science & Engineering Database, ProQuest Central (new), ProQuest Central Korea, SciTech Premium Collection, Technology Collection, ProQuest Central Essentials, ProQuest One Academic, Engineering Collection (ProQuest)
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    Title: Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs
    Author: Khan, Suleiman; Ali, Faisal; Mpindi, John; Parkkinen, Juuso; Kalliokoski, Tuomo; Poso, Antti; Kallioniemi, Olli; Wennerberg, Krister; Kaski, Samuel
    Contributor: Kaski, Samuel (pacrepositoryorg)
    Subject: Gene Expression ; Proteins ; Organic Chemistry ; Decoding ; Gene Expression ; Cancer ; Biological Effects ; Bonding Strength ; Impact Analysis ; Biological Properties ; Drugs ; Biological Activity ; Hydrogen Bonding ; Quantitative Analysis ; Deoxyribonucleic Acid–DNA ; Biomolecules ; Applications
    Description: Detailed and systematic understanding of the biological effects of millions of available compounds on living cells is a significant challenge. As most compounds impact multiple targets and pathways, traditional methods for analyzing structure-function relationships are not comprehensive enough. Therefore more advanced integrative models are needed for predicting biological effects elicited by specific chemical features. As a step towards creating such computational links we developed a data-driven chemical systems biology approach to comprehensively study the relationship of 76 structural 3D-descriptors (VolSurf, chemical space) of 1159 drugs with the gene expression responses (biological space) they elicited in three cancer cell lines. The analysis covering 11350 genes was based on data from the Connectivity Map. We decomposed these biological response profiles into components, each linked to a characteristic chemical descriptor profile. The integrated quantitative analysis of the chemical...
    Is part of: arXiv.org, Dec 27, 2011
    Identifier: 2331-8422 (E-ISSN)

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    Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

    Khan, Suleiman A., Faisal, Ali, Mpindi, John Patric, Parkkinen, Juuso A., Kalliokoski, Tuomo, Poso, Antti, Kallioniemi, Olli P., Wennerberg, Krister, Kaski, Samuel
    Cornell University
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    Title: Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs
    Author: Khan, Suleiman A.; Faisal, Ali; Mpindi, John Patric; Parkkinen, Juuso A.; Kalliokoski, Tuomo; Poso, Antti; Kallioniemi, Olli P.; Wennerberg, Krister; Kaski, Samuel
    Subject: Quantitative Biology - Biomolecules ; Statistics - Applications
    Description: Detailed and systematic understanding of the biological effects of millions of available compounds on living cells is a significant challenge. As most compounds impact multiple targets and pathways, traditional methods for analyzing structure-function relationships are not comprehensive enough. Therefore more advanced integrative models are needed for predicting biological effects elicited by specific chemical features. As a step towards creating such computational links we developed a data-driven chemical systems biology approach to comprehensively study the relationship of 76 structural 3D-descriptors (VolSurf, chemical space) of 1159 drugs with the gene expression responses (biological space) they elicited in three cancer cell lines. The analysis covering 11350 genes was based on data from the Connectivity Map. We decomposed these biological response profiles into components, each linked to a characteristic chemical descriptor profile. The integrated quantitative analysis of the chemical and biological spaces was more informative about protein-target based drug similarity than either dataset separately. We identified ten major components that link distinct VolSurf features across multiple compounds to specific biological activity types. For example, component 2 (hydrophobic properties) strongly links to DNA damage response, while component 3 (hydrogen bonding) connects to metabolic stress. Individual structural and biological features were often linked to one cell line only, such as leukemia cells (HL-60) specifically responding to cardiac glycosides. In summary, our approach identified specific chemical structures shared across multiple drugs causing distinct biological responses. The decoding of such systematic chemical-biological relationships is necessary to build better models of drug effects, including unidentified types of molecular properties with strong biological effects. Comment: 10 pages, 7 figures, 2 tables
    Identifier: 1112.6015 (ARXIV ID)