The ever increasing amount of data gathered by more growers in more years offers possibilities to... more The ever increasing amount of data gathered by more growers in more years offers possibilities to add value. Therefore—for interested parties and stakeholders—a common and controlled vocabulary of the potato domain that describes concepts, attributes, and the relations between them in a formal way using a standardised knowledge representation language is being developed: a potato ontology. The advantage is that all possible stakeholders will be able to understand the data expressed by this ontology and that software applications can process them automatically. It will also allow the application of advanced numerical techniques that may help to uncover previously unknown correlations. This version of the potato ontology aims at the domain of processing potatoes in a setting of mechanised potato production where growers have access to automated decision support systems and exchange data electronically. This paper describes the procedures to establish such an ontology where competency questions formulated by stakeholders and potential users take a central position. The potato ontology formally describes “Concepts” or “Classes”. The three main classes are those used in crop ecology: Crop, Environment and Management. Classes, e.g., biocides are a subclass of agro-chemicals, and in turn have a subclass Fungicides. The ontology also describes the “Properties” of classes, e.g., agrochemicals are produced synthetically in a factory; biocides are used to protect crops and fungicides to control fungi. The ontology also describes the “Attributes” (properties) of the concepts, e.g., all agrochemicals have attributes such as dose and time of application and mode of application. “Restrictions” may be that a particular chemical can only be applied with a certain type of equipment, or its application is restricted to a certain period or dose. The ontology also features “Instances” which are the individual data such as a particular herbicide treatment with values for field, time, dose, active ingredient, trademark, mode of application, which equipment operated by whom. The standardisation language used is the “Ontology Web Language”.
Plant species diversity is surveyed in the southern part of the Taï National Park (TNP), Côte d’I... more Plant species diversity is surveyed in the southern part of the Taï National Park (TNP), Côte d’Ivoire. This park is the largest remaining tract of pristine forest in the West African rainforest biodiversity hotspot. Plant assemblages and environment factors were surveyed in 39 temporary 625-m2 plots within three areas. The species list was completed thanks to itinerant prospections. TWINSPAN classification and detrended correspondence analysis were applied to the 39 relevés. We recorded a total of 916 plant species, including 169 West African endemics, that rises the floristic richness of TNP in 1233 species. Most plant species recorded were Guineo-Congolian species (90.9%) among which 8% were ‘Sassandrian species’, i.e. endemics of the extreme southwest Côte d’Ivoire. Eight of these endemics were exclusive of the southern part of TNP. The forest is very species-rich, particularly in Rubiaceae, Leguminosae and Euphorbiaceae. Most of the sampled species (59.5%) were erect phanerophytes with a dbh≤10 cm. We distinguished 7 plant community types, mainly determined by geomorphology and disturbance history. Lowland forests were typical dense evergreen forests with different degrees of maturity related to historical human impact. Inselbergs and swampy depressions provide an original azonal vegetation. We conclude that the southern part of TNP contributes significantly to the regional biodiversity hotspot since it includes the last remnants of primary evergreen rainforest and contains species assemblages from both higher rainfall biomes on moist soils derived from schist parent material and lower rainfall biomes on inselberg slopes and top. As anthropogenic disturbance clearly reduces biodiversity, these last remnants should be integrally protected.
A new method is described for direct monitoring of the conformational stability of proteins that ... more A new method is described for direct monitoring of the conformational stability of proteins that are physically adsorbed from solution onto a solid substrate. The adsorption-induced conformational changes of insulin are studied using a combination of hydrogen/deuterium (H/D) exchange and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The effect of the surface hydrophobicity on the adsorption-induced conformational changes in the insulin structure is probed by adsorbing insulin on a hydrophilic silica and a hydrophobic methylated silica surface before subjecting the insulin molecules to the isotopic exchange process. The present study describes the experimental procedure of this new application of MALDI. Results show that insulin is more highly and more irreversibly adsorbed to a hydrophobic methylated silica surface than to a hydrophilic silica surface. Hydrogen-exchange experiments clearly demonstrate that the strong interaction of insulin with the hydrophobic surface is accompanied by a strong increase in the H/D-exchange rates and thus in a reduction in the insulin native structural stability. In contrast, H/D-exchange rates of insulin are somewhat reduced upon adsorption on silica from solution.
The ever increasing amount of data gathered by more growers in more years offers possibilities to... more The ever increasing amount of data gathered by more growers in more years offers possibilities to add value. Therefore—for interested parties and stakeholders—a common and controlled vocabulary of the potato domain that describes concepts, attributes, and the relations between them in a formal way using a standardised knowledge representation language is being developed: a potato ontology. The advantage is that all possible stakeholders will be able to understand the data expressed by this ontology and that software applications can process them automatically. It will also allow the application of advanced numerical techniques that may help to uncover previously unknown correlations. This version of the potato ontology aims at the domain of processing potatoes in a setting of mechanised potato production where growers have access to automated decision support systems and exchange data electronically. This paper describes the procedures to establish such an ontology where competency questions formulated by stakeholders and potential users take a central position. The potato ontology formally describes “Concepts” or “Classes”. The three main classes are those used in crop ecology: Crop, Environment and Management. Classes, e.g., biocides are a subclass of agro-chemicals, and in turn have a subclass Fungicides. The ontology also describes the “Properties” of classes, e.g., agrochemicals are produced synthetically in a factory; biocides are used to protect crops and fungicides to control fungi. The ontology also describes the “Attributes” (properties) of the concepts, e.g., all agrochemicals have attributes such as dose and time of application and mode of application. “Restrictions” may be that a particular chemical can only be applied with a certain type of equipment, or its application is restricted to a certain period or dose. The ontology also features “Instances” which are the individual data such as a particular herbicide treatment with values for field, time, dose, active ingredient, trademark, mode of application, which equipment operated by whom. The standardisation language used is the “Ontology Web Language”.
Plant species diversity is surveyed in the southern part of the Taï National Park (TNP), Côte d’I... more Plant species diversity is surveyed in the southern part of the Taï National Park (TNP), Côte d’Ivoire. This park is the largest remaining tract of pristine forest in the West African rainforest biodiversity hotspot. Plant assemblages and environment factors were surveyed in 39 temporary 625-m2 plots within three areas. The species list was completed thanks to itinerant prospections. TWINSPAN classification and detrended correspondence analysis were applied to the 39 relevés. We recorded a total of 916 plant species, including 169 West African endemics, that rises the floristic richness of TNP in 1233 species. Most plant species recorded were Guineo-Congolian species (90.9%) among which 8% were ‘Sassandrian species’, i.e. endemics of the extreme southwest Côte d’Ivoire. Eight of these endemics were exclusive of the southern part of TNP. The forest is very species-rich, particularly in Rubiaceae, Leguminosae and Euphorbiaceae. Most of the sampled species (59.5%) were erect phanerophytes with a dbh≤10 cm. We distinguished 7 plant community types, mainly determined by geomorphology and disturbance history. Lowland forests were typical dense evergreen forests with different degrees of maturity related to historical human impact. Inselbergs and swampy depressions provide an original azonal vegetation. We conclude that the southern part of TNP contributes significantly to the regional biodiversity hotspot since it includes the last remnants of primary evergreen rainforest and contains species assemblages from both higher rainfall biomes on moist soils derived from schist parent material and lower rainfall biomes on inselberg slopes and top. As anthropogenic disturbance clearly reduces biodiversity, these last remnants should be integrally protected.
A new method is described for direct monitoring of the conformational stability of proteins that ... more A new method is described for direct monitoring of the conformational stability of proteins that are physically adsorbed from solution onto a solid substrate. The adsorption-induced conformational changes of insulin are studied using a combination of hydrogen/deuterium (H/D) exchange and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The effect of the surface hydrophobicity on the adsorption-induced conformational changes in the insulin structure is probed by adsorbing insulin on a hydrophilic silica and a hydrophobic methylated silica surface before subjecting the insulin molecules to the isotopic exchange process. The present study describes the experimental procedure of this new application of MALDI. Results show that insulin is more highly and more irreversibly adsorbed to a hydrophobic methylated silica surface than to a hydrophilic silica surface. Hydrogen-exchange experiments clearly demonstrate that the strong interaction of insulin with the hydrophobic surface is accompanied by a strong increase in the H/D-exchange rates and thus in a reduction in the insulin native structural stability. In contrast, H/D-exchange rates of insulin are somewhat reduced upon adsorption on silica from solution.
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