scholarly journals Assessment of the quality of accession describing metadata on plant genetic resources

2019 ◽  
Vol 3 ◽  
Author(s):  
Markus Oppermann ◽  
Stephan Weise
Keyword(s):  
Data Quality ◽  
Western Europe ◽  
Plant Genetic Resources ◽  
Ex Situ ◽  
Cultivated Plants ◽  
Research Activity ◽  
Suitable Material ◽  
Passport Data ◽  
The Individual

In the wide-ranging field of biodiversity conservation, genebanks play a major role in the preservation of cultivated plants. An important focus of genebanks is the comprehensive documentation of the maintained material. This is a prerequisite to enable users to select the most suitable material for e.g. research or breeding programs (Hoisington et al. 1999). The German Federal ex situ Genebank for Agricultural and Horticultural Crops, which is being hosted at IPK, is the largest genebank in Western Europe. Within the multitude of data associated with plant material (e.g. from various -omics areas or conservation management), the so-called passport data represent the most original and oldest data in genebanks. These metadata are often subject to heterogeneity due to historically different collection and curation, especially if they were received from different institutions around the world. This leads to difficulties in handling these data and can result in misinterpretations. In addition, there are correlations between the individual attributes of the passport data which can lead to a different importance of the individual data points for the users. Major challenges for users are to estimate completeness, correctness and reliability of these data. Thus, it is necessary to assess the quality of these data by defining a suitable set of metrics. Unfortunately, classical data quality measurement metrics, e.g. (Klier 2008), are not sufficient to fulfill the users' needs. Depending on the intention of the user, a different focus is placed on the data. Moreover, the individual attributes of the respective areas can be related to each other. Therefore, a single index value for estimating the quality of a passport record is not sufficient. Rather, it seems to be more promising to generate more differentiated quality statements. We are working on a metrics system that is sensitive to the users' focus. Through a practical set of rules of data quality metrics for accession-related data, the user will be able to influence the weighting of individual domains (e.g. geographical origin, biological status) according to their context (fit-for-use index). The presentation will discuss the background and will give an overview of the progress of this research activity.

Quality indicators for passport data in ex situ genebanks

2011 ◽  
Vol 9 (3) ◽  
pp. 478-485 ◽  
Author(s):  
Theo van Hintum ◽  
Frank Menting ◽  
Elisabeth van Strien
Keyword(s):  
Data Quality ◽  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Ex Situ ◽  
Wild Accession ◽  
Valuable Insight ◽  
Collection Site ◽  
Data Points ◽  
Passport Data

Given the increasing importance of data quality for the ex situ conservation and utilization of plant genetic resources (PGR), an indicator was created that quantifies the level of completeness of passport data. This passport data completeness index (PDCI) uses the presence or absence of data points in the documentation of a genebank accession, taking into account the presence or value of other data points. For example, a wild accession should have a well-defined collection site but no variety name. Any type of accession, wild, landrace, breeding material or modern variety, can attain a maximal score of ten for this index. The applicability of this index was tested on the complete contents of EURISCO, the European catalogue of ex situ maintained PGR containing over one million records. Analysis of the PDCI of the material in EURISCO provided valuable insight in the data quality of European collections. The PDCI can be used to identify datasets that might need additional attention and improvement or datasets that need more careful interpretation than others.

Populist Nationalism, Anti-Europeanism, Post-nationalism, and the East-West Distinction

2005 ◽  
Vol 6 (2) ◽  
pp. 371-389 ◽  
Author(s):  
Paul Blokker
Keyword(s):  
Western Europe ◽  
Structural Difference ◽  
Direct Result ◽  
Market Society ◽  
The Social ◽  
Social Belonging ◽  
Political Model ◽  
The Individual ◽  
Eastern And Western Europe

In the literature on emergent populism and nationalism in post-communist Eastern Europe, two main assumptions regarding the origins of the phenomenon can be distinguished. One line of argumentation holds that the unexpected resurgence of populism and nationalism after the collapse of the communist regimes is a direct result of the ‘valley of tears’ that characterizes the post-communist transformation from a communist, centrally planned system, to a democratic, market society. The ‘social costs’ of the transition and the still ‘incomplete’ nature of modernization make a large number of ‘modernization losers’ susceptible to mobilization by populist movements. The emergence of populist, nationalist movements should be understood as a radical form of protest against the degradation of the quality of life and widespread social dislocation and unemployment. A second explanation for the phenomenon is that populism and its naturalist, exclusivist portrayal of the nation is the result of the re-emergence of deeply, culturally ingrained perception of social belonging, and of the foundations of the polity, in which the social whole is considered prior to the individual, and in which local culture is valued differently from Western culture. In this explanation, the structural difference between Eastern and Western Europe is emphasized, a difference that can only be overcome by the former adopting the political model of the latter.

scholarly journals The Potential of Small Grains Crops in Enhancing Biofortification Breeding Strategies for Human Health Benefit

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1420
Author(s):  
Tatyana V. Shelenga ◽  
Yulia A. Kerv ◽  
Irina N. Perchuk ◽  
Alla E. Solovyeva ◽  
Elena K. Khlestkina ◽  
...  
Keyword(s):  
Plant Genetic Resources ◽  
Health Benefit ◽  
Food Sources ◽  
Cultivated Plants ◽  
Human Organism ◽  
Blood Levels ◽  
Plant Resources ◽  
The World ◽  
Small Grains

Nutrition is a source of energy, and building material for the human organism. The quality of food has an effect on the quality of individual life. Minerals and vitamins participate in various catalytic and regulatory functions of the main metabolic processes: absorption, transport, redox and biosynthesis of organic compounds, genetic information transfer, etc. Regular consumption of dietary fibers like β-glucans and oat-specific phenolics, antioxidants, and avenanthramides, stimulate innate and acquired immunity, prevent cancer, obesity, reduce glucose, total cholesterol and triglyceride blood levels and regulate the expression of cholesterol-related genes. Thus, all those compounds are vitally important for the normal functional status of the human body. A deficiency in one or another essential nutrient causes disruptions in human metabolism, thus leading to serious illnesses. Plants are the main source of essential nutrients that are bioavailable for humans. One of the most popular groups of staple crops are the small grains crops (SGC), so these crops are most often used for biofortification purposes. Exploiting the potential of plant resources, biofortification is a long-term strategy, aimed at increasing the number of essential micro- and macronutrients in major food sources and ensuring their bioavailability. The most productive way to implement such strategy is the active use of the possibilities offered by collections of plant genetic resources, including SGC, concentrated in various countries of the world. The collections of plant resources contain both cultivated plants and their wild relatives that possess the required composition of micro- and macronutrients. A complex scientific approach to studying plant germplasm collections, together with agricultural practices (soil enrichment with fertilizers with a required composition), genetic biofortification (traditional breeding, marker-assisted selection or genetic engineering tactics), and their combinations will lead to the development of new biofortified cultivars and improvement of old ones, which can be used to solve the problems of unbalanced nutrition (malnutrition or hidden hunger) in different regions of the world.

Current taxonomic composition of European genebank material documented in EURISCO

2010 ◽  
Vol 8 (2) ◽  
pp. 182-188 ◽  
Author(s):  
Theo van Hintum ◽  
Helmut Knüpffer
Keyword(s):  
Genetic Resources ◽  
Plant Genetic Resources ◽  
The United States ◽  
Taxonomic Composition ◽  
Ex Situ ◽  
United States Department ◽  
Quality Of Data ◽  
Department Of Agriculture ◽  
Food And Agriculture

Taxonomy plays an essential role in genebank documentation. It is often the first level at which users search material, and it determines the protocols used in the management of collections. Especially, when plant genetic resources information is pooled in systems such as EURISCO, the European catalogue of ex situ plant genetic resources, problems regarding technical handling of taxonomic nomenclature, such as lack of standardization and low quality of data, become apparent. These problems were studied by analysing the content of EURISCO and mapping the taxon names in EURISCO on those used in the United States Department of Agriculture genebank system GRIN-Tax. Thus, the number of spelling errors and the level of standardization could be quantified and improved. An analysis of the content of EURISCO was made, showing a highly unbalanced distribution over crops: 50% of the accessions belong to ten genera only. Mapping EURISCO on the crops listed in Annex 1 of the International Treaty on Plant Genetic Resources for Food and Agriculture showed that 67% of the accessions in EURISCO belong to crops in that list.

scholarly journals Ex situ PLANT GERMPLASM CONSERVATION REVISED AT THE LIGHT OF MECHANISMS AND METHODS OF GENETICS

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 11-24
Author(s):  
E.L. Camadro ◽  
P. Rimieri
Keyword(s):  
Genetic Resources ◽  
Higher Plants ◽  
Plant Genetic Resources ◽  
Genetic Material ◽  
Germplasm Conservation ◽  
Ex Situ ◽  
Individual Plant ◽  
Plant Germplasm ◽  
The Individual ◽  
Germplasm Banks

Plant genetic resources for food and agriculture are ex situ conserved in germplasm banks as samples (accessions) of natural or naturalized populations, either as the originally sampled propagules (mainly seeds) or their multiplications. The premises underlying ex situ conservation are that (a) it is the safest and cheapest alternative for germplasm preservation for future generations and (b) accessions are representative of the genetic diversity encountered in nature. In the past decades, ideas, alternatives and considerations have been put forward on the topic, and protocols have been devised for plant germplasm sampling, conservation and multiplication. However, limitations in the management efficiency of germplasm banks have been pointed out by international organizations. In our opinion, germplasm banks in general need to revise their functioning and management at the light of principles and methods of Genetics. To that end, it is necessary to consider the reproductive biology of higher plants -whose genetic consequences at both the individual plant and the population levels are not always either fully understood or taken into account in devising the protocols-, the genetic structures of wild and cultivated populations, and the course of the genetic material in the populations. In this paper, we discuss the three topics and provide an example of a national forage breeding program, from germplasm bank accessions as the germplasm of origin to the obtainment of commercial cultivars. Finally, we present a proposal as a base for discussion among curators, researchers and breeders. Key words: accessions, breeding, genetic resources, germplasm banks, population genetics

scholarly journals Best practices for setting up a repository of phenotypic data for European germplasm holdings

2018 ◽  
Vol 2 ◽  
pp. e25223
Author(s):  
Stephan Weise ◽  
Markus Oppermann
Keyword(s):  
Best Practices ◽  
Genetic Resources ◽  
Rating Scales ◽  
Plant Genetic Resources ◽  
Wild Relatives ◽  
Ex Situ ◽  
Phenotypic Data ◽  
Meta Information ◽  
Passport Data ◽  
Selection Of

The European Search Catalogue for Plant Genetic Resources, EURISCO, provides information about more than 1.9 million accessions of crop plants and their wild relatives, preserved ex situ by almost 400 institutes in Europe and beyond (Weise et al. 2017). EURISCO, which is being maintained on behalf of the European Cooperative Programme for Plant Genetic Resources, is based on a network of National Inventories of 43 member countries. It represents an important effort for the preservation of the world’s agrobiological diversity by providing information about the large genetic diversity kept by the collaborating institutions. Besides the classical passport data, in 2016, EURISCO started to additionally collect phenotypic data about the documented germplasm accessions. The selection of genebank material for both research and breeding purposes is increasingly carried out through the selection of specific phenotypic values, e.g. flowering time or plant height. Thus, these data are of high importance to users of plant genetic resources (PGR) since they determine the value of the respective germplasm. However, because there are no commonly agreed standards existing within the genebank community, this kind of data is very difficult to handle. In this context, the challenges range from synonymous/homonymous descriptor names over different rating scales to different/insufficient amounts of meta information, thus hampering both integration and cross-experiment comparison of data. The presentation will illustrate the approach followed within EURISCO, together with the challenges resulting therefrom. Using this as a solid basis for a discussion about the utilization of this kind of data, the presentation shall be regarded as a call for cooperation.

scholarly journals Text and Data Quality Mining in CRIS

Information ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 374 ◽  
Author(s):  
Azeroual
Keyword(s):  
Data Quality ◽  
Research Information ◽  
Essential Requirement ◽  
High Data ◽  
Scientific Institutions ◽  
Research Information System ◽  
The Individual ◽  
Bad Data ◽  
Text And Data Mining

To provide scientific institutions with comprehensive and well-maintained documentation of their research information in a current research information system (CRIS), they have the best prerequisites for the implementation of text and data mining (TDM) methods. Using TDM helps to better identify and eliminate errors, improve the process, develop the business, and make informed decisions. In addition, TDM increases understanding of the data and its context. This not only improves the quality of the data itself, but also the institution’s handling of the data and consequently the analyses. This present paper deploys TDM in CRIS to analyze, quantify, and correct the unstructured data and its quality issues. Bad data leads to increased costs or wrong decisions. Ensuring high data quality is an essential requirement when creating a CRIS project. User acceptance in a CRIS depends, among other things, on data quality. Not only is the objective data quality the decisive criterion, but also the subjective quality that the individual user assigns to the data.

Growth of Fe/ZnSe Multilayers on GaAs (001) AND (111) by Molecular Beam Epitaxy

1995 ◽  
Vol 384 ◽  
Author(s):  
H. Abad ◽  
B. T. Jonker ◽  
C. M. Cotell ◽  
S. B. Qadri ◽  
J. J. Krebs
Keyword(s):  
High Energy ◽  
Layer Growth ◽  
Ex Situ ◽  
X Ray Diffraction ◽  
Cross Sectional ◽  
Gaas Substrates ◽  
Transmission Electron ◽  
Spacer Layer ◽  
The Individual

ABSTRACTThe growth of Fe/ZnSe/Fe multilayers on (001) and (111) GaAs substrates is reported. The samples were characterized in-situ by reflection high energy electron diffraction (RHEED), and ex situ by vibrating sample magnetometry (VSM), ferromagnetic resonance (FMR), cross sectional transmission electron microscopy (TEM), and x-ray diffraction. On the (001) surface, the quality of the layers deteriorated significantly with the growth of the first ZnSe spacer layer. In Fe/ZnSe/Fe trilayer structures, TEM revealed a well-defined layered structure, with a high density of defects in both the ZnSe spacer layer and the subsequent Fe layer. VSM and FMR clearly showed the presence of two Fe films with distinct coercive fields, with the higher coercive field attributed to the lower crystalline quality of the second Fe layer. θ-2θ xray diffraction measurements performed on samples grown on (001) GaAs substrates indicated that the ZnSe spacer layer (grown on (001) Fe) grew in a (111) orientation. Growth on GaAs(111) substrates produced better RHEED patterns for all layers with little deterioration in film quality with continued layer growth, so that the magnetic properties of the individual Fe layer could not be distinguished.

scholarly journals Ex situ PLANT GERMPLASM CONSERVATION REVISED AT THE LIGHT OF MECHANISMS AND METHODS OF GENETICS

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 11-24
Author(s):  
E.L. Camadro ◽  
P. Rimieri
Keyword(s):  
Genetic Resources ◽  
Higher Plants ◽  
Plant Genetic Resources ◽  
Genetic Material ◽  
Germplasm Conservation ◽  
Ex Situ ◽  
Individual Plant ◽  
Plant Germplasm ◽  
The Individual ◽  
Germplasm Banks

Plant genetic resources for food and agriculture are ex situ conserved in germplasm banks as samples (accessions) of natural or naturalized populations, either as the originally sampled propagules (mainly seeds) or their multiplications. The premises underlying ex situ conservation are that (a) it is the safest and cheapest alternative for germplasm preservation for future generations and (b) accessions are representative of the genetic diversity encountered in nature. In the past decades, ideas, alternatives and considerations have been put forward on the topic, and protocols have been devised for plant germplasm sampling, conservation and multiplication. However, limitations in the management efficiency of germplasm banks have been pointed out by international organizations. In our opinion, germplasm banks in general need to revise their functioning and management at the light of principles and methods of Genetics. To that end, it is necessary to consider the reproductive biology of higher plants -whose genetic consequences at both the individual plant and the population levels are not always either fully understood or taken into account in devising the protocols-, the genetic structures of wild and cultivated populations, and the course of the genetic material in the populations. In this paper, we discuss the three topics and provide an example of a national forage breeding program, from germplasm bank accessions as the germplasm of origin to the obtainment of commercial cultivars. Finally, we present a proposal as a base for discussion among curators, researchers and breeders. Key words: accessions, breeding, genetic resources, germplasm banks, population genetics

Semi-automated methods for 3-D reconstruction of macromolecular complexes

1995 ◽  
Vol 53 ◽  
pp. 42-43
Author(s):  
B. Carragher ◽  
M. Whittaker
Keyword(s):  
Three Dimensional ◽  
Time Saving ◽  
Macromolecular Complexes ◽  
Symmetry Properties ◽  
Dimensional Reconstruction ◽  
Experienced Operator ◽  
Projection Images ◽  
The Individual ◽  
Natural Symmetry

Techniques for three-dimensional reconstruction of macromolecular complexes from electron micrographs have been successfully used for many years. These include methods which take advantage of the natural symmetry properties of the structure (for example helical or icosahedral) as well as those that use single axis or other tilting geometries to reconstruct from a set of projection images. These techniques have traditionally relied on a very experienced operator to manually perform the often numerous and time consuming steps required to obtain the final reconstruction. While the guidance and oversight of an experienced and critical operator will always be an essential component of these techniques, recent advances in computer technology, microprocessor controlled microscopes and the availability of high quality CCD cameras have provided the means to automate many of the individual steps.During the acquisition of data automation provides benefits not only in terms of convenience and time saving but also in circumstances where manual procedures limit the quality of the final reconstruction.

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