91. List of tests for validation : round 1, grant agreement N. 773139Špela Alič, Géraldine Anthoine, A Chabirand, Anne-Marie Chappé, Tanja Dreo, Tjaša Jakomin, L Laurenson, Tadeja Lukežič, Nataša Mehle, E Metz-Verschure, H Mouaziz, J Oorspronk, Manca Pirc, Maja Ravnikar, Naomi te Braak, Jenny Tomlinson, Marcel Westenberg, 2019, treatise, preliminary study, study Abstract: We prepared a list of methods and tests for validation in test performance study (TPS) Round 1, both for laboratory and on-site use, for 6 selected pests: Erwinia amylovora, Pantoea stewartiisubsp. stewartii, citrus tristeza virus, plum pox virus, Fusarium circinatum and Bursaphelenchus xylophilus. The listed tests were first validated in preliminary studies by TPS organizers in order to select the final tests for TPS, based on the scope and criteria prepared in D1.1.
Keywords: pests, tests
Published in DiRROS: 03.09.2024; Views: 37; Downloads: 26
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92. Analysis of subcellular energy metabolism in five Lacertidae lizards across varied environmental conditionsAnamarija Žagar, Urban Dajčman, Rodrigo Megía-Palma, Tatjana Simčič, Frederico Barroso, Senka Baškiera, Miguel A. Carretero, 2024, original scientific article Abstract: Aerobic respiration is the main energy source for most eukaryotes, and efficient mitochondrial energy transfer greatly influences organismal fitness. To survive environmental changes, cells have evolved to adjust their biochemistry. Thus, measuring energy metabolism at the subcellular level can enhance our understanding of individual performance, population dynamics, and species distribution ranges. We investigated three important metabolic traits at the subcellular level in five lacertid lizard species sampled from different elevations, from sea level up to 2000 m. We examined hemoglobin concentration, two markers of oxidative stress (catalase activity and carbonyl concentration) and maximum rate of metabolic respiration at the subcellular level (potential metabolic activity at the electron transport system). The traits were analysed in laboratory acclimated adult male lizards to investigate the adaptive metabolic responses to the variable environmental conditions at the local sampling sites. Potential metabolic activity at the cellular level was measured at four temperatures – 28 °C, 30 °C, 32 °C and 34 °C – covering the range of preferred body temperatures of the species studied. Hemoglobin content, carbonyl concentration and potential metabolic activity did not differ significantly among species. Interspecific differences were found in the catalase activity, Potential metabolic activity increased with temperature in parallel in all five species. The highest response of the metabolic rate with temperature (Q10) and Arrhenius activation energy (Ea) was recorded in the high-mountain species Iberolacerta monticola.
Keywords: physiology, lacertids, aerobic respiration, interspecific variability, hemoglobin, zoology
Published in DiRROS: 03.09.2024; Views: 30; Downloads: 858
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93. List of criteria the reference materials have to meet for use in validation studies : grant agreement N. 773139, DELIVERABLE N° 3.1 – V2Anne-Marie Chappé, A Chabirand, P. Dahlin, C. de Krom, Tanja Dreo, Pascal Gentit, L Laurenson, F. Peter, D. Spadaro, René van der Vlugt, E. van Veen, Marcel Westenberg, 2019, treatise, preliminary study, study Abstract: A list of general minimum criteria was developed to be used in preparation of reference materials to be used in interlaboratory testing, including validations through test performance studies. The list was based on previously identified criteria in standards including ISO standards, EPPO guidelines, deliverables of relevant projects, related fields, and own experience of project partners. Several additional criteria were proposed: ‘availability’, ‘purity’ and ‘commutability’. These criteria result from a series of discussions, taking into account previous work and relevant international standards. Where relevant, each criterion was first defined as a series of levels from the highest to lowest ranking with the lowest ranking considered to be the minimum. Depending on the intended use, the reference material may need to fulfil higher levels of selected criteria or some criteria may not be relevant at all. The criteria were tested by the organizers of the TPS in round 1 of validation within VALITEST project which include bacteria, viruses, nematodes and fungi. The systematic and structured approach of describing RMs was found to be useful in promoting transparent descriptions of the RMs used and comparability of TPSs, as well as a step toward implementing FAIR data principles. The criteria defined here are applicable, potentially with minor modification, beyond the scope of this deliverable and project to other pests and other uses of RMs
Keywords: pests, tests
Published in DiRROS: 03.09.2024; Views: 42; Downloads: 847
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94. Hitra analiza tveganja fitoplazme na leskah : 'Candidatus Phytoplasma fragariae' - fitoplazme iz skupine 16SrV, katere največja podobnost je s sevi FD-D in FD70Nataša Mehle, 2019, treatise, preliminary study, study Abstract: Glavni sklepi:
Skupna ocena tveganja:
'Ca. Phytoplasma fragariae' in/ ali fitoplazme skupine 16SrV (z največjo podobnostjo s sevi, ki na vinski trti povzročajo zlato trsno rumenico) so bile odkrite v propadajočih leskah iz geografsko ločenih nasadov v Sloveniji. V nekaterih nasadih je obseg propadanja lesk relativno velik.
Glede na vzorec pojavljanja propadlih in propadajočih lesk v nekaterih proučevanih nasadih je zelo verjetno, da imamo prenašalca, ki fitoplazme učinkovito prenaša znotraj nasada, kakor zelo verjetno tudi med nasadi in morda tudi iz drugih rastlin, ki rastejo v okolici. Možnost vnosa z vegetativno razmnoženim materialom, in možnost širjenja v nasadu s koreninskimi mostički, nista izključeni.
V vseh nasadih kjer je ena izmed proučevanih fitoplazem že prisotna (ali bo do vnosa še prišlo), lahko v primeru, da se ne uvedejo fitosanitarni ukrepi, pride do razširjanja v velikem obsegu. Ker okuženi grmi prej ali slej propadejo, bo škoda za lastnika intenzivnega nasada velika, posledično to lahko predstavlja tudi gospodarsko škodo za Slovenijo.
Fitosanitarni ukrepi:
S trenutnim znanjem o fitoplazmah na leski, je v primeru potrjene okužbe s fitoplazmami, pravilen ukrep težko določiti. S fitoplazmami okužene leske je vsekakor smiselno izruvati (s koreninami) in uničiti takoj ko se jih odkrije, saj obstaja velika verjetnost, da imamo v Sloveniji učinkovitega prenašalca teh fitoplazem.
V primeru sajenja novih sadik je priporočljivo, da se sadi le sadike, ki izhajajo iz preverjeno neokuženih matičnih dreves. Matična drevesa bi bilo smiselno testirati na prisotnost fitoplazem tudi v primeru, če nimajo bolezenskih znamenj, saj obstaja možnost, da so fitoplazme kljub temu prisotne v rastlini.
Ukrep glede tretiranja prenašalcev ne moremo predlagati, saj prenašalec pomemben za leske še
ni poznan oziroma potrjen. Enako ni znano če obstajajo sorte, ki bi bile tržno zanimive in so hkrati odporne na okužbo s fitoplazmami.
Keywords: fitoplazme, leska
Published in DiRROS: 03.09.2024; Views: 41; Downloads: 617
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95. Development of draft Standard Operating Procedures (SOPs) available for the production of the reference materials identified in task 3.1 : grant agreement N. 773139Anne-Marie Chappé, A Chabirand, P. Dahlin, C. de Krom, Tanja Dreo, Pascal Gentit, L Laurenson, F. Peter, D. Spadaro, A.D. van Diepeningen, René van der Vlugt, E. van Veen, Marcel Westenberg, 2019, treatise, preliminary study, study Abstract: A general standard operating procedure (SOP) for the production of reference material (RM) for use in plant health diagnostics was developed. The general SOP was designed based on (limited) information on existing SOPs and guidelines available with the consortium partners. The general SOP describes the different steps required in the production process, ranging from the different possible sources of the reference material, tests to confirm its identity, possibly required multiplication steps to the actual production process. For each step in the process, criteria and critical points are identified. The criteria that reference material has to meet, and their minimum required levels as identified and described in Deliverable 3.1 of WP3 form an import basis of the final production process.
Keywords: plant health diagnostics
Published in DiRROS: 03.09.2024; Views: 36; Downloads: 25
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96. Predicting GPP in Carpathian Beech Forests: Uncovering spatial and temporal patterns using a regression model with climatic, topographic and additional featuresAzim Missarov, Jakub Kašpar, Kamil Král, O. Brovkina, M. Švik, 2024, published scientific conference contribution abstract Keywords: gross primary product, regression model, remote sensing, temperature, precipitation, digital elevation model
Published in DiRROS: 03.09.2024; Views: 47; Downloads: 9
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97. Phenological trends of European beech stands along the Carpathian arc : a 20-year MODIS based analysisM. Švik, O. Brovkina, Tatjana Veljanovski, Matjaž Čater, 2024, published scientific conference contribution abstract Keywords: European beech, phenology, remote sensing, time series, vegetation index
Published in DiRROS: 03.09.2024; Views: 53; Downloads: 7
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98. Revizija biodiverzitete v Krajinskem parku Ljubljansko barje : pilotna akcijaNataša Mori, Al Vrezec, Davorin Tome, Urška Ratajc, 2020, treatise, preliminary study, study Abstract: Pilotna akcija “Revizija biodiverzitete v kopenskih, negozdnih okoljih Krajinskega parka Ljubljansko barje« je bila izvedena v okviru projekta "Od podatkov o biodiverziteti do odločanja" (Interreg Evropa; BID-REX; 2016-2021). Projekt BIDREX je naslavljal problematiko uporabe podatkov o biodiverziteti v procesih odločanja na področju varstva narave. Namen pilotne akcije je bil testirati metodo »Revizija biodiverzitete«, ki so jo razvili na Univerzi Vzhodne Anglije in uspešno uporabili že na treh naravovarstveno pomembnih območjih Velike Britanije. Osnovni cilj pilotne akcije je bil ugotoviti, katero biodiverziteto in kako uspešno jo varujejo trenutni naravovarstveni ukrepi na Ljubljanskem barju, s poudarjenim pogledom na shemo Kmetijsko-okoljsko-podnebna plačila (KOPOP). Metodo smo zaradi razlik v obsegu biodiverzitetnih podatkov v primerjavi z originalno metodo prilagodili ter poskusno izvedli le na biodiverziteti kopenskih, negozdnih okolij Ljubljanskega Barja. Ta območja so na Barju namreč najbolj razširjena in se zanje izvaja največ naravovarstvenih ukrepov.
V pilotni akciji smo najprej zbrali podatke o vseh vrstah v Krajinskem parku Ljubljansko barje ter s pomočjo sodelujočih strokovnjakov identificirali, katere vrste so, poleg Natura 2000 kvalifikacijskih vrst, prednostne, torej pomembne za varovanje na Ljubljanskem barju. V nadaljevanju smo, ponovno s pomočjo sodelujočih strokovnjakov, izvedli ekološko karakterizacijo in analizo občutljivosti prednostnih vrst na človekove dejavnosti. Nato smo prednostne vrste združili v “upravljalske cehe” – skupine vrst, ki za ohranjanje potrebujejo podobne naravovarstvene ukrepe.
Ugotovili smo, da za večino prednostnih vrst, ki živijo na Barju primanjkuje novejših podatkov, ter natančnejših prostorskih podatkov, redki so sistematični popisi, s tem je povezano tudi slabo poznavanje razširjenosti in ekoloških potreb večine vrst. Zaradi teh razlogov je ekološka karakterizacija večine prednostnih vrst potekala na podlagi najboljše ocene strokovnjaka. V upravljalskih cehih, ki smo jih oblikovali smo identificirali indikatorske vrste – vrste, za katere obstaja največ podatkov o razširjenosti na Ljubljanskem barju, oziroma smo ocenili, da bi lahko služile kot pokazatelj stanja celotnega ceha. V vsakem cehu smo določili tudi krovno vrsto - to je vrsta, za katero se že izvajajo naravovarstveni ukrepi, oziroma bi bilo priporočljivo, da se načrtujejo.
Keywords: biodiverziteta, Ljubljansko barje, naravovarstvo, določitev upravljalskih cehov
Published in DiRROS: 03.09.2024; Views: 28; Downloads: 311
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99. Graph topological transformations in space-filling cell aggregatesTanmoy Sarkar, Matej Krajnc, 2024, original scientific article Abstract: Cell rearrangements are fundamental mechanisms driving large-scale deformations of living tissues. In three-dimensional (3D) space-filling cell aggregates, cells rearrange through local topological transitions of the network of cell-cell interfaces, which is most conveniently described by the vertex model. Since these transitions are not yet mathematically properly formulated, the 3D vertex model is generally difficult to implement. The few existing implementations rely on highly customized and complex software-engineering solutions, which cannot be transparently delineated and are thus mostly non-reproducible. To solve this outstanding problem, we propose a reformulation of the vertex model. Our approach, called Graph Vertex Model (GVM), is based on storing the topology of the cell network into a knowledge graph with a particular data structure that allows performing cell-rearrangement events by simple graph transformations. Importantly, when these same transformations are applied to a two-dimensional (2D) polygonal cell aggregate, they reduce to a well-known T1 transition, thereby generalizing cell-rearrangements in 2D and 3D space-filling packings. This result suggests that the GVM’s graph data structure may be the most natural representation of cell aggregates and tissues. We also develop a Python package that implements GVM, relying on a graph-database-management framework Neo4j. We use this package to characterize an order-disorder transition in 3D cell aggregates, driven by active noise and we find aggregates undergoing efficient ordering close to the transition point. In all, our work showcases knowledge graphs as particularly suitable data models for structured storage, analysis, and manipulation of tissue data.
Keywords: 3D vertex models, cell, software-engineering
Published in DiRROS: 03.09.2024; Views: 25; Downloads: 1329
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100. Recommendations for testing water samples, in particular for tomato brown rugose fruit virusKatarina Bačnik, Ion Gutiérrez-Aguirre, Maja Ravnikar, Nataša Mehle, 2020, treatise, preliminary study, study Abstract: Water can be an important source of plant pathogenic viruses. Usually they are present in low concentrations, but environmental waters still represent a potential pathway for virus transmission. Already over 30 years ago, plant viruses have been shown to be present in environmental waters in considerable amounts (Koenig, 1986). Since then, many questions concerning the origin, survival, and spread of plant viruses by water have been raised, especially in the light of increased irrigation and use of hydroponic systems in agriculture (Mehle and Ravnikar 2012). The majority of the plant pathogenic viruses recovered from environmental waters so far are very stable. They can infect plants via the roots without the aid of a vector and often have a wide host range (Mehle and Ravnikar 2012). The release of such viruses from plants can lead to their diffusion in streams, rivers and lakes, thereby ensuring the long-distance spread of viruses that would otherwise remain restricted to limited areas (Mehle et al., 2014; Mehle and Ravnikar, 2012).
Published in DiRROS: 03.09.2024; Views: 39; Downloads: 14
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