61. Minimum performance parameters to select tests for validation and selection of laboratories for TPS : grant agreement N. 773139, deliverable N° 1.1Špela Alič, Géraldine Anthoine, A Chabirand, Anne-Marie Chappé, Tanja Dreo, L Laurenson, Tadeja Lukežič, Nataša Mehle, H Mouaziz, Manca Pirc, Maja Ravnikar, Jenny Tomlinson, Marcel Westenberg, 2019, elaborat, predštudija, študija Povzetek: The aim of deliverable 1.1. is to prepare criteria to select tests for validation and to select laboratories for TPS (test performance study). Criteria for selection of tests for the TPS for each pest have been set (see Tables 7-12). These criteria have been divided in five groups: 1) validation data, 2) applicability, 3) protocols, 4) chemicals and 5) equipment. For selection of participants for the TPS selection criteria have also been set (see Table 13). Amongst the most important criteria for selection for participants of TPS are technical expertise for the pest group and the method, authorization to work with the specific pest and that the participating laboratory has quality assurance in place. These criteria enable evaluation of whether participants are proficient to perform the tests, have the necessary equipment and a permit to work with viable regulated organism. The scope of the testing for specific pests was set and common rules for each selection process was defined.
Ključne besede: pests, tests
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62. 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, elaborat, predštudija, študija Povzetek: 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.
Ključne besede: pests, tests
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63. 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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: physiology, lacertids, aerobic respiration, interspecific variability, hemoglobin, zoology
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64. 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, elaborat, predštudija, študija Povzetek: 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
Ključne besede: pests, tests
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65. 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, elaborat, predštudija, študija Povzetek: 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.
Ključne besede: fitoplazme, leska
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66. 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, elaborat, predštudija, študija Povzetek: 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.
Ključne besede: plant health diagnostics
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67. 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, objavljeni povzetek znanstvenega prispevka na konferenci Ključne besede: gross primary product, regression model, remote sensing, temperature, precipitation, digital elevation model
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68. Phenological trends of European beech stands along the Carpathian arc : a 20-year MODIS based analysisM. Švik, O. Brovkina, Tatjana Veljanovski, Matjaž Čater, 2024, objavljeni povzetek znanstvenega prispevka na konferenci Ključne besede: European beech, phenology, remote sensing, time series, vegetation index
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69. Revizija biodiverzitete v Krajinskem parku Ljubljansko barje : pilotna akcijaNataša Mori, Al Vrezec, Davorin Tome, Urška Ratajc, 2020, elaborat, predštudija, študija Povzetek: 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.
Ključne besede: biodiverziteta, Ljubljansko barje, naravovarstvo, določitev upravljalskih cehov
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70. Graph topological transformations in space-filling cell aggregatesTanmoy Sarkar, Matej Krajnc, 2024, izvirni znanstveni članek Povzetek: 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.
Ključne besede: 3D vertex models, cell, software-engineering
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