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Forzieri G, Dutrieux LP, Elia A, Eckhardt B, Caudullo G, Taboada FÁ, Andriolo A, Bălăcenoiu F, Bastos A, Buzatu A, Dorado FC, Dobrovolný L, Duduman ML, Fernandez-Carrillo A, Hernández-Clemente R, Hornero A, Ionuț S, Lombardero MJ, Junttila S, Lukeš P, Marianelli L, Mas H, Mlčoušek M, Mugnai F, Nețoiu C, Nikolov C, Olenici N, Olsson PO, Paoli F, Paraschiv M, Patočka Z, Pérez-Laorga E, Quero JL, Rüetschi M, Stroheker S, Nardi D, Ferenčík J, Battisti A, Hartmann H, Nistor C, Cescatti A, Beck PSA. The Database of European Forest Insect and Disease Disturbances: DEFID2. Glob Chang Biol 2023; 29:6040-6065. [PMID: 37605971 DOI: 10.1111/gcb.16912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/23/2023]
Abstract
Insect and disease outbreaks in forests are biotic disturbances that can profoundly alter ecosystem dynamics. In many parts of the world, these disturbance regimes are intensifying as the climate changes and shifts the distribution of species and biomes. As a result, key forest ecosystem services, such as carbon sequestration, regulation of water flows, wood production, protection of soils, and the conservation of biodiversity, could be increasingly compromised. Despite the relevance of these detrimental effects, there are currently no spatially detailed databases that record insect and disease disturbances on forests at the pan-European scale. Here, we present the new Database of European Forest Insect and Disease Disturbances (DEFID2). It comprises over 650,000 harmonized georeferenced records, mapped as polygons or points, of insects and disease disturbances that occurred between 1963 and 2021 in European forests. The records currently span eight different countries and were acquired through diverse methods (e.g., ground surveys, remote sensing techniques). The records in DEFID2 are described by a set of qualitative attributes, including severity and patterns of damage symptoms, agents, host tree species, climate-driven trigger factors, silvicultural practices, and eventual sanitary interventions. They are further complemented with a satellite-based quantitative characterization of the affected forest areas based on Landsat Normalized Burn Ratio time series, and damage metrics derived from them using the LandTrendr spectral-temporal segmentation algorithm (including onset, duration, magnitude, and rate of the disturbance), and possible interactions with windthrow and wildfire events. The DEFID2 database is a novel resource for many large-scale applications dealing with biotic disturbances. It offers a unique contribution to design networks of experiments, improve our understanding of ecological processes underlying biotic forest disturbances, monitor their dynamics, and enhance their representation in land-climate models. Further data sharing is encouraged to extend and improve the DEFID2 database continuously. The database is freely available at https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/FOREST/DISTURBANCES/DEFID2/.
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Affiliation(s)
- Giovanni Forzieri
- Department of Civil and Environmental Engineering, University of Florence, Florence, Italy
- European Commission, Joint Research Centre, Ispra, Italy
| | | | | | - Bernd Eckhardt
- European Commission, Joint Research Centre, Ispra, Italy
| | | | - Flor Álvarez Taboada
- DRACONES Research Group, Universidad de León, León, Spain
- Sustainable Forestry and Environmental Management Unit, University of Santiago de Compostela, Lugo, Spain
| | - Alessandro Andriolo
- Ufficio Pianificazione Forestale, Amministrazione Provincia Bolzano, Bolzano, Italy
| | - Flavius Bălăcenoiu
- National Institute for Research and Development in Forestry "Marin Drăcea" (INCDS), Voluntari, Romania
| | - Ana Bastos
- Department of Biogeochemical Processes, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | - Andrei Buzatu
- National Institute for Research and Development in Forestry "Marin Drăcea" (INCDS), Craiova, Romania
| | - Fernando Castedo Dorado
- DRACONES Research Group, Universidad de León, León, Spain
- Sustainable Forestry and Environmental Management Unit, University of Santiago de Compostela, Lugo, Spain
| | - Lumír Dobrovolný
- University Forest Enterprise Masaryk Forest Křtiny, Mendel University in Brno, Brno, Czech Republic
| | - Mihai-Leonard Duduman
- Applied Ecology Laboratory, Forestry Faculty, "Ștefan cel Mare" University of Suceava, Suceava, Romania
| | | | | | - Alberto Hornero
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
- Faculty of Engineering and Information Technology (FEIT), The University of Melbourne, Melbourne, Victoria, Australia
| | - Săvulescu Ionuț
- Department of Geomorphology-Pedology-Geomatics, Faculty of Geography, University of Bucharest, Bucharest, Romania
| | - María J Lombardero
- Sustainable Forestry and Environmental Management Unit, University of Santiago de Compostela, Lugo, Spain
| | - Samuli Junttila
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Petr Lukeš
- Czechglobe-Global Change Research Institute, CAS, Brno, Czech Republic
- Ústav pro hospodářskou úpravu lesů-Forest Management Institute (FMI), Brno-Žabovřesky, Czech Republic
| | - Leonardo Marianelli
- CREA Research Centre for Plant Protection and Certification, Florence, Italy
| | - Hugo Mas
- Laboratori de Sanitat Forestal, Servei d'Ordenació i Gestió Forestal, Conselleria d'Agricultura, Desenvolupament Rural, Emergència Climàtica i Transició Ecològica, Generalitat Valenciana, Valencia, Spain
| | - Marek Mlčoušek
- Czechglobe-Global Change Research Institute, CAS, Brno, Czech Republic
- Ústav pro hospodářskou úpravu lesů-Forest Management Institute (FMI), Brno-Žabovřesky, Czech Republic
| | - Francesco Mugnai
- Department of Civil and Environmental Engineering, University of Florence, Florence, Italy
| | - Constantin Nețoiu
- National Institute for Research and Development in Forestry "Marin Drăcea" (INCDS), Craiova, Romania
| | - Christo Nikolov
- National Forest Centre, Forest Research Institute, Zvolen, Slovakia
| | - Nicolai Olenici
- National Institute for Research and Development in Forestry "Marin Drăcea" (INCDS), Voluntari, Romania
| | - Per-Ola Olsson
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Francesco Paoli
- CREA Research Centre for Plant Protection and Certification, Florence, Italy
| | - Marius Paraschiv
- National Institute for Research and Development in Forestry "Marin Drăcea" (INCDS), Brașov, Romania
| | - Zdeněk Patočka
- Department of Forest Management and Applied Geoinformatics, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Eduardo Pérez-Laorga
- Laboratori de Sanitat Forestal, Servei d'Ordenació i Gestió Forestal, Conselleria d'Agricultura, Desenvolupament Rural, Emergència Climàtica i Transició Ecològica, Generalitat Valenciana, Valencia, Spain
| | - Jose Luis Quero
- Department of Forest Engineering, University of Córdoba, Córdoba, Spain
| | - Marius Rüetschi
- Department of Land Change Science, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Sophie Stroheker
- Swiss Forest Protection, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Davide Nardi
- DAFNAE-Entomology, University of Padova, Padova, Italy
| | - Ján Ferenčík
- Research Station Tatra National Park, Tatranská Lomnica, Slovakia
| | | | - Henrik Hartmann
- Department of Biogeochemical Processes, Max-Planck Institute for Biogeochemistry, Jena, Germany
- Insitute for Forest Protection, Julius Kühn-Institute, Federal Research Federal Research Center for Cultivated Plants, Quedlinburg, Germany
| | - Constantin Nistor
- Department of Geomorphology-Pedology-Geomatics, Faculty of Geography, University of Bucharest, Bucharest, Romania
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Calders K, Brede B, Newnham G, Culvenor D, Armston J, Bartholomeus H, Griebel A, Hayward J, Junttila S, Lau A, Levick S, Morrone R, Origo N, Pfeifer M, Verbesselt J, Herold M. StrucNet: a global network for automated vegetation structure monitoring. Remote Sens Ecol Conserv 2023; 9:587-598. [PMID: 38505271 PMCID: PMC10946942 DOI: 10.1002/rse2.333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 03/21/2024]
Abstract
Climate change and increasing human activities are impacting ecosystems and their biodiversity. Quantitative measurements of essential biodiversity variables (EBV) and essential climate variables are used to monitor biodiversity and carbon dynamics and evaluate policy and management interventions. Ecosystem structure is at the core of EBVs and carbon stock estimation and can help to inform assessments of species and species diversity. Ecosystem structure is also used as an indirect indicator of habitat quality and expected species richness or species community composition. Spaceborne measurements can provide large-scale insight into monitoring the structural dynamics of ecosystems, but they generally lack consistent, robust, timely and detailed information regarding their full three-dimensional vegetation structure at local scales. Here we demonstrate the potential of high-frequency ground-based laser scanning to systematically monitor structural changes in vegetation. We present a proof-of-concept high-temporal ecosystem structure time series of 5 years in a temperate forest using terrestrial laser scanning (TLS). We also present data from automated high-temporal laser scanning that can allow upscaling of vegetation structure scanning, overcoming the limitations of a typically opportunistic TLS measurement approach. Automated monitoring will be a critical component to build a network of field monitoring sites that can provide the required calibration data for satellite missions to effectively monitor the structural dynamics of vegetation over large areas. Within this perspective, we reflect on how this network could be designed and discuss implementation pathways.
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Affiliation(s)
- Kim Calders
- CAVElab – Computational & Applied Vegetation Ecology, Department of EnvironmentGhent UniversityCoupure links 653Ghent9000Belgium
- School of Forest Sciences, University of Eastern FinlandJoensuu80101Finland
| | - Benjamin Brede
- Helmholtz Center Potsdam GFZ German Research Centre for GeosciencesSection 1.4 Remote Sensing and GeoinformaticsTelegrafenbergPotsdam14473Germany
| | | | - Darius Culvenor
- Environmental Sensing SystemsBentleigh EastVictoria3165Australia
| | - John Armston
- Department of Geographical SciencesUniversity of MarylandCollege ParkMarylandUSA
| | - Harm Bartholomeus
- Laboratory of Geo‐Information Science and Remote SensingWageningen UniversityWageningen6708 PBthe Netherlands
| | - Anne Griebel
- Hawkesbury Institute for the Environment, Western Sydney UniversityLocked Bag 1797PenrithNew South Wales2751Australia
| | - Jodie Hayward
- CSIRO564 Vanderlin DriveBerrimahNorthern Territory0828Australia
| | - Samuli Junttila
- School of Forest Sciences, University of Eastern FinlandJoensuu80101Finland
| | - Alvaro Lau
- Laboratory of Geo‐Information Science and Remote SensingWageningen UniversityWageningen6708 PBthe Netherlands
| | - Shaun Levick
- CSIRO564 Vanderlin DriveBerrimahNorthern Territory0828Australia
| | - Rosalinda Morrone
- Climate and Earth Observation GroupNational Physical LaboratoryHampton Road, TeddingtonLondonUK
| | - Niall Origo
- Climate and Earth Observation GroupNational Physical LaboratoryHampton Road, TeddingtonLondonUK
| | - Marion Pfeifer
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastle Upon TyneNE1 7RUUK
| | - Jan Verbesselt
- Laboratory of Geo‐Information Science and Remote SensingWageningen UniversityWageningen6708 PBthe Netherlands
| | - Martin Herold
- Helmholtz Center Potsdam GFZ German Research Centre for GeosciencesSection 1.4 Remote Sensing and GeoinformaticsTelegrafenbergPotsdam14473Germany
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Li S, Brandt M, Fensholt R, Kariryaa A, Igel C, Gieseke F, Nord-Larsen T, Oehmcke S, Carlsen AH, Junttila S, Tong X, d’Aspremont A, Ciais P. Deep learning enables image-based tree counting, crown segmentation, and height prediction at national scale. PNAS Nexus 2023; 2:pgad076. [PMID: 37065619 PMCID: PMC10096914 DOI: 10.1093/pnasnexus/pgad076] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/28/2023] [Accepted: 02/27/2023] [Indexed: 04/18/2023]
Abstract
Sustainable tree resource management is the key to mitigating climate warming, fostering a green economy, and protecting valuable habitats. Detailed knowledge about tree resources is a prerequisite for such management but is conventionally based on plot-scale data, which often neglects trees outside forests. Here, we present a deep learning-based framework that provides location, crown area, and height for individual overstory trees from aerial images at country scale. We apply the framework on data covering Denmark and show that large trees (stem diameter >10 cm) can be identified with a low bias (12.5%) and that trees outside forests contribute to 30% of the total tree cover, which is typically unrecognized in national inventories. The bias is high (46.6%) when our results are evaluated against all trees taller than 1.3 m, which involve undetectable small or understory trees. Furthermore, we demonstrate that only marginal effort is needed to transfer our framework to data from Finland, despite markedly dissimilar data sources. Our work lays the foundation for digitalized national databases, where large trees are spatially traceable and manageable.
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Affiliation(s)
- Sizhuo Li
- To whom correspondence should be addressed: ;
| | | | - Rasmus Fensholt
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen 1350, Denmark
| | - Ankit Kariryaa
- Department of Computer Science, University of Copenhagen, Copenhagen 2100, Denmark
| | - Christian Igel
- Department of Computer Science, University of Copenhagen, Copenhagen 2100, Denmark
| | - Fabian Gieseke
- Department of Computer Science, University of Copenhagen, Copenhagen 2100, Denmark
- Department of Information Systems, University of Münster, Münster 48149, Germany
| | - Thomas Nord-Larsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen 1350, Denmark
| | - Stefan Oehmcke
- Department of Computer Science, University of Copenhagen, Copenhagen 2100, Denmark
| | - Ask Holm Carlsen
- Department of Earth Observations, The Danish Agency for Data Supply and Infrastructure, Copenhagen 2400, Denmark
| | - Samuli Junttila
- Department of Forest Sciences, University of Eastern Finland, Joensuu 80101, Finland
| | - Xiaoye Tong
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen 1350, Denmark
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4
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Saarinen N, Kankare V, Huuskonen S, Hynynen J, Bianchi S, Yrttimaa T, Luoma V, Junttila S, Holopainen M, Hyyppä J, Vastaranta M. Effects of Stem Density on Crown Architecture of Scots Pine Trees. Front Plant Sci 2022; 13:817792. [PMID: 35356110 PMCID: PMC8959813 DOI: 10.3389/fpls.2022.817792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Trees adapt to their growing conditions by regulating the sizes of their parts and their relationships. For example, removal or death of adjacent trees increases the growing space and the amount of light received by the remaining trees enabling their crowns to expand. Knowledge about the effects of silvicultural practices on crown size and shape and also about the quality of branches affecting the shape of a crown is, however, still limited. Thus, the aim was to study the crown structure of individual Scots pine trees in forest stands with varying stem densities due to past forest management practices. Furthermore, we wanted to understand how crown and stem attributes and also tree growth affect stem area at the height of maximum crown diameter (SAHMC), which could be used as a proxy for tree growth potential. We used terrestrial laser scanning (TLS) to generate attributes characterizing crown size and shape. The results showed that increasing stem density decreased Scots pine crown size. TLS provided more detailed attributes for crown characterization compared with traditional field measurements. Furthermore, decreasing stem density increased SAHMC, and strong relationships (Spearman's correlations > 0.5) were found between SAHMC and crown and stem size and also stem growth. Thus, this study provided quantitative and more comprehensive characterization of Scots pine crowns and their growth potential. The combination of a traditional growth and yield study design and 3D characterization of crown architecture and growth potential can open up new research possibilities.
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Affiliation(s)
- Ninni Saarinen
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Ville Kankare
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | | | - Jari Hynynen
- Natural Resources Institute Finland, Helsinki, Finland
| | | | - Tuomas Yrttimaa
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Ville Luoma
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Samuli Junttila
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Markus Holopainen
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Juha Hyyppä
- Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute, Masala, Finland
| | - Mikko Vastaranta
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
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5
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Saarinen N, Calders K, Kankare V, Yrttimaa T, Junttila S, Luoma V, Huuskonen S, Hynynen J, Verbeeck H. Understanding 3D structural complexity of individual Scots pine trees with different management history. Ecol Evol 2021; 11:2561-2572. [PMID: 33767821 PMCID: PMC7981231 DOI: 10.1002/ece3.7216] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 12/04/2022] Open
Abstract
Tree functional traits together with processes such as forest regeneration, growth, and mortality affect forest and tree structure. Forest management inherently impacts these processes. Moreover, forest structure, biodiversity, resilience, and carbon uptake can be sustained and enhanced with forest management activities. To assess structural complexity of individual trees, comprehensive and quantitative measures are needed, and they are often lacking for current forest management practices. Here, we utilized 3D information from individual Scots pine (Pinus sylvestris L.) trees obtained with terrestrial laser scanning to, first, assess effects of forest management on structural complexity of individual trees and, second, understand relationship between several tree attributes and structural complexity. We studied structural complexity of individual trees represented by a single scale-independent metric called "box dimension." This study aimed at identifying drivers affecting structural complexity of individual Scots pine trees in boreal forest conditions. The results showed that thinning increased structural complexity of individual Scots pine trees. Furthermore, we found a relationship between structural complexity and stem and crown size and shape as well as tree growth. Thus, it can be concluded that forest management affected structural complexity of individual Scots pine trees in managed boreal forests, and stem, crown, and growth attributes were identified as drivers of it.
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Affiliation(s)
- Ninni Saarinen
- Department of Forest SciencesUniversity of HelsinkiHelsinkiFinland
- School of Forest SciencesUniversity of Eastern FinlandJoensuuFinland
| | - Kim Calders
- CAVElab ‐ Computational & Applied Vegetation EcologyDepartment of EnvironmentFaculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Ville Kankare
- Department of Forest SciencesUniversity of HelsinkiHelsinkiFinland
- School of Forest SciencesUniversity of Eastern FinlandJoensuuFinland
| | - Tuomas Yrttimaa
- Department of Forest SciencesUniversity of HelsinkiHelsinkiFinland
- School of Forest SciencesUniversity of Eastern FinlandJoensuuFinland
| | - Samuli Junttila
- Department of Forest SciencesUniversity of HelsinkiHelsinkiFinland
- School of Forest SciencesUniversity of Eastern FinlandJoensuuFinland
| | - Ville Luoma
- Department of Forest SciencesUniversity of HelsinkiHelsinkiFinland
| | | | - Jari Hynynen
- Natural Resources Institute FinlandHelsinkiFinland
| | - Hans Verbeeck
- CAVElab ‐ Computational & Applied Vegetation EcologyDepartment of EnvironmentFaculty of Bioscience EngineeringGhent UniversityGentBelgium
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6
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Rosser J, Bachmann B, Jordan C, Ribitsch I, Haltmayer E, Gueltekin S, Junttila S, Galik B, Gyenesei A, Haddadi B, Harasek M, Egerbacher M, Ertl P, Jenner F. Microfluidic nutrient gradient-based three-dimensional chondrocyte culture-on-a-chip as an in vitro equine arthritis model. Mater Today Bio 2019; 4:100023. [PMID: 32159153 PMCID: PMC7061638 DOI: 10.1016/j.mtbio.2019.100023] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/27/2023] Open
Abstract
In this work, we describe a microfluidic three-dimensional (3D) chondrocyte culture mimicking in vivo articular chondrocyte morphology, cell distribution, metabolism, and gene expression. This has been accomplished by establishing a physiologic nutrient diffusion gradient across the simulated matrix, while geometric design constraints of the microchambers drive native-like cellular behavior. Primary equine chondrocytes remained viable for the extended culture time of 3 weeks and maintained the low metabolic activity and high Sox9, aggrecan, and Col2 expression typical of articular chondrocytes. Our microfluidic 3D chondrocyte microtissues were further exposed to inflammatory cytokines to establish an animal-free, in vitro osteoarthritis model. Results of our study indicate that our microtissue model emulates the basic characteristics of native cartilage and responds to biochemical injury, thus providing a new foundation for exploration of osteoarthritis pathophysiology in both human and veterinary patients.
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Affiliation(s)
- J Rosser
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - B Bachmann
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - C Jordan
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - I Ribitsch
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - E Haltmayer
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - S Gueltekin
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - S Junttila
- BIOCOMP, Bioinformatics & Scientific Computing VBCF, Vienna Biocenter Core Facilities GmbH, GmbH, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - B Galik
- BIOCOMP, Bioinformatics & Scientific Computing VBCF, Vienna Biocenter Core Facilities GmbH, GmbH, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - A Gyenesei
- BIOCOMP, Bioinformatics & Scientific Computing VBCF, Vienna Biocenter Core Facilities GmbH, GmbH, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - B Haddadi
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - M Harasek
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - M Egerbacher
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - P Ertl
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - F Jenner
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
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7
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Junttila S, Sugano J, Vastaranta M, Linnakoski R, Kaartinen H, Kukko A, Holopainen M, Hyyppä H, Hyyppä J. Can Leaf Water Content Be Estimated Using Multispectral Terrestrial Laser Scanning? A Case Study With Norway Spruce Seedlings. Front Plant Sci 2018; 9:299. [PMID: 29568306 PMCID: PMC5853165 DOI: 10.3389/fpls.2018.00299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
Changing climate is increasing the amount and intensity of forest stress agents, such as drought, pest insects, and pathogens. Leaf water content, measured here in terms of equivalent water thickness (EWT), is an early indicator of tree stress that provides timely information about the health status of forests. Multispectral terrestrial laser scanning (MS-TLS) measures target geometry and reflectance simultaneously, providing spatially explicit reflectance information at several wavelengths. EWT and leaf internal structure affect leaf reflectance in the shortwave infrared region that can be used to predict EWT with MS-TLS. A second wavelength that is sensitive to leaf internal structure but not affected by EWT can be used to normalize leaf internal effects on the shortwave infrared region and improve the prediction of EWT. Here we investigated the relationship between EWT and laser intensity features using multisensor MS-TLS at 690, 905, and 1,550 nm wavelengths with both drought-treated and Endoconidiophora polonica inoculated Norway spruce seedlings to better understand how MS-TLS measurements can explain variation in EWT. In our study, a normalized ratio of two wavelengths at 905 and 1,550 nm and length of seedling explained 91% of the variation (R2) in EWT as the respective prediction accuracy for EWT was 0.003 g/cm2 in greenhouse conditions. The relation between EWT and the normalized ratio of 905 and 1,550 nm wavelengths did not seem sensitive to a decreased point density of the MS-TLS data. Based on our results, different EWTs in Norway spruce seedlings show different spectral responses when measured using MS-TLS. These results can be further used when developing EWT monitoring for improving forest health assessments.
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Affiliation(s)
- Samuli Junttila
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Centre of Excellence in Laser Scanning Research, Finnish Geospatial Research Institute (FGI), Masala, Finland
| | - Junko Sugano
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Mikko Vastaranta
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Centre of Excellence in Laser Scanning Research, Finnish Geospatial Research Institute (FGI), Masala, Finland
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Riikka Linnakoski
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Harri Kaartinen
- Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute (FGI), Masala, Finland
- Department of Geography and Geology, University of Turku, Turku, Finland
| | - Antero Kukko
- Centre of Excellence in Laser Scanning Research, Finnish Geospatial Research Institute (FGI), Masala, Finland
- Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute (FGI), Masala, Finland
| | - Markus Holopainen
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Centre of Excellence in Laser Scanning Research, Finnish Geospatial Research Institute (FGI), Masala, Finland
| | - Hannu Hyyppä
- Centre of Excellence in Laser Scanning Research, Finnish Geospatial Research Institute (FGI), Masala, Finland
- Department of Built Environment, Aalto University, Aalto, Finland
| | - Juha Hyyppä
- Centre of Excellence in Laser Scanning Research, Finnish Geospatial Research Institute (FGI), Masala, Finland
- Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute (FGI), Masala, Finland
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8
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Linnakoski R, Sugano J, Junttila S, Pulkkinen P, Asiegbu FO, Forbes KM. Effects of water availability on a forestry pathosystem: fungal strain-specific variation in disease severity. Sci Rep 2017; 7:13501. [PMID: 29044133 PMCID: PMC5647412 DOI: 10.1038/s41598-017-13512-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/25/2017] [Indexed: 01/02/2023] Open
Abstract
Norway spruce is one of the most important commercial forestry species in Europe, and is commonly infected by the bark beetle-vectored necrotrophic fungus, Endoconidiophora polonica. Spruce trees display a restricted capacity to respond to environmental perturbations, and we hypothesized that water limitation will increase disease severity in this pathosystem. To test this prediction, 737 seedlings were randomized to high (W+) or low (W−) water availability treatment groups, and experimentally inoculated with one of three E. polonica strains or mock-inoculated. Seedling mortality was monitored throughout an annual growing season, and total seedling growth and lesion length indices were measured at the experiment conclusion. Seedling growth was greater in the W+ than W− treatment group, demonstrating limitation due to water availability. For seedlings infected with two of the fungal strains, no differences in disease severity occurred in response to water availability. For the third fungal strain, however, greater disease severity (mortality and lesion lengths) occurred in W− than W+ seedlings. While the co-circulation in nature of multiple E. polonica strains of varying virulence is known, this is the first experimental evidence that water availability can alter strain-specific disease severity.
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Affiliation(s)
- Riikka Linnakoski
- Department of Forest Sciences, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Junko Sugano
- Department of Forest Sciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Samuli Junttila
- Department of Forest Sciences, University of Helsinki, FI-00014, Helsinki, Finland.,Centre of Excellence in Laser Scanning Research, Finnish Geospatial Research Institute FGI, FI-02430 Masala, Finland
| | - Pertti Pulkkinen
- Natural Resources Institute Finland (Luke), FI-12600 Läyliäinen, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Kristian M Forbes
- Department of Virology, University of Helsinki, FI-00290, Helsinki, Finland
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9
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Budzyńska PM, Niemelä M, Sarapulov AV, Kyläniemi MK, Nera KP, Junttila S, Laiho A, Mattila PK, Alinikula J, Lassila O. IRF4 Deficiency Leads to Altered BCR Signalling Revealed by Enhanced PI3K Pathway, Decreased SHIP Expression and Defected Cytoskeletal Responses. Scand J Immunol 2016; 82:418-28. [PMID: 26173778 DOI: 10.1111/sji.12343] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 07/07/2015] [Indexed: 12/13/2022]
Abstract
The graded expression of transcription factor interferon regulatory factor 4 (IRF4) regulates B cell development and is critical for plasma cell differentiation. However, the mechanisms, by which IRF4 elicits its crucial tasks, are largely unknown. To characterize the molecular targets of IRF4 in B cells, we established an IRF4-deficient DT40 B cell line. We found that in the absence of IRF4, the expression of several molecules involved in BCR signalling was altered. For example, the expression of B cell adaptor for PI3K (BCAP) was upregulated, whereas the SHIP (SH2-containing Inositol 5?-Phosphatase) expression was downregulated. These molecular unbalances were accompanied by increased BCR-induced calcium signalling, attenuated B cell linker protein (BLNK) and ERK activity and enhanced activity of PI3K/protein kinase B (Akt) pathway. Further, the IRF4-deficient cells showed dramatically diminished cytoskeletal responses to anti-IgM cross-linking. Our results show that IRF4 has an important role in the regulation of BCR signalling and help to shed light on the molecular mechanisms of B cell development and germinal centre response.
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Affiliation(s)
- P M Budzyńska
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland.,Turku Doctoral Programme of Biomedical Sciences, University of Turku, Turku, Finland
| | - M Niemelä
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - A V Sarapulov
- Institute of Biomedicine, Department of Pathology, University of Turku, Turku, Finland
| | - M K Kyläniemi
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - K-P Nera
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - S Junttila
- The Finnish Microarray and Sequencing Center, Turku Centre for Biotechnology, Turku, Finland
| | - A Laiho
- The Finnish Microarray and Sequencing Center, Turku Centre for Biotechnology, Turku, Finland
| | - P K Mattila
- Institute of Biomedicine, Department of Pathology, University of Turku, Turku, Finland
| | - J Alinikula
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - O Lassila
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
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10
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Abstract
The culture medium of Streptomyces xanthochromogenes JH903 was found to show selective activity against DNA-repair-deficient Escherichia coli CM871 strain. In this report we describe a simple method to locate and isolate DNA binding compounds from the fermentation broth. The method is based on the retention of DNA-reacting compounds in cellulose complexed with DNA, and purification of these compounds with thin-layer chromatography. Screening of microbial metabolites from chloroform extracts of fermentation media resulted in detection of five genotoxic fractions.
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Affiliation(s)
- J Holmalahti
- Department of Pharmaceutical Chemistry, University of Kuopio, Finland
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11
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Ihlebekk H, Eilertsen S, Junttila S, Grindal G, Moe R. CONTROL OF PLANT HEIGHT IN CAMPANULA ISOPHYLLA BY TEMPERATURE ALTERNATIONS; INVOLVEMENT OF GAS. ACTA ACUST UNITED AC 1995. [DOI: 10.17660/actahortic.1995.394.38] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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