Publications by authors named "Petr Holub"

29 Publications

  • Page 1 of 1

Ecometabolomics for a Better Understanding of Plant Responses and Acclimation to Abiotic Factors Linked to Global Change.

Metabolites 2020 Jun 9;10(6). Epub 2020 Jun 9.

Spain National Research Council (CSIC), Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Spain.

The number of ecometabolomic studies, which use metabolomic analyses to disentangle organisms' metabolic responses and acclimation to a changing environment, has grown exponentially in recent years. Here, we review the results and conclusions of ecometabolomic studies on the impacts of four main drivers of global change (increasing frequencies of drought episodes, heat stress, increasing atmospheric carbon dioxide (CO) concentrations and increasing nitrogen (N) loads) on plant metabolism. Ecometabolomic studies of drought effects confirmed findings of previous target studies, in which most changes in metabolism are characterized by increased concentrations of soluble sugars and carbohydrate derivatives and frequently also by elevated concentrations of free amino acids. Secondary metabolites, especially flavonoids and terpenes, also commonly exhibited increased concentrations when drought intensified. Under heat and increasing N loads, soluble amino acids derived from glutamate and glutamine were the most responsive metabolites. Foliar metabolic responses to elevated atmospheric CO concentrations were dominated by greater production of monosaccharides and associated synthesis of secondary metabolites, such as terpenes, rather than secondary metabolites synthesized along longer sugar pathways involving N-rich precursor molecules, such as those formed from cyclic amino acids and along the shikimate pathway. We suggest that breeding for crop genotypes tolerant to drought and heat stress should be based on their capacity to increase the concentrations of C-rich compounds more than the concentrations of smaller N-rich molecules, such as amino acids. This could facilitate rapid and efficient stress response by reducing protein catabolism without compromising enzymatic capacity or increasing the requirement for re-transcription and de novo biosynthesis of proteins.
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http://dx.doi.org/10.3390/metabo10060239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7345909PMC
June 2020

BBMRI-ERIC's contributions to research and knowledge exchange on COVID-19.

Eur J Hum Genet 2020 06 22;28(6):728-731. Epub 2020 May 22.

BBMRI-ERIC, Neue Stiftingtalstraße 2/B/6, 8010, Graz, Austria.

During the COVID-19 pandemic, the European biobanking infrastructure is in a unique position to preserve valuable biological material complemented with detailed data for future research purposes. Biobanks can be either integrated into healthcare, where preservation of the biological material is a fork in clinical routine diagnostics and medical treatment processes or they can also host prospective cohorts or material related to clinical trials. The paper discussed objectives of BBMRI-ERIC, the European research infrastructure established to facilitate access to quality-defined biological materials and data for research purposes, with respect to the COVID-19 crisis: (a) to collect information on available European as well as non-European COVID-19-relevant biobanking resources in BBMRI-ERIC Directory and to facilitate access to these via BBMRI-ERIC Negotiator platform; (b) to help harmonizing guidelines on how data and biological material is to be collected to maximize utility for future research, including large-scale data processing in artificial intelligence, by participating in activities such as COVID-19 Host Genetics Initiative; (c) to minimize risks for all involved parties dealing with (potentially) infectious material by developing recommendations and guidelines; (d) to provide a European-wide platform of exchange in relation to ethical, legal, and societal issues (ELSI) specific to the collection of biological material and data during the COVID-19 pandemic.
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http://dx.doi.org/10.1038/s41431-020-0634-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242892PMC
June 2020

Extending the Minimum Information About BIobank Data Sharing Terminology to Describe Samples, Sample Donors, and Events.

Biopreserv Biobank 2020 Jun 17;18(3):155-164. Epub 2020 Apr 17.

THL Biobank, Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland.

The Minimum Information About BIobank data Sharing (MIABIS) was initiated in 2012. MIABIS aims to create a common biobank terminology to facilitate data sharing in biobanks and sample collections. The MIABIS Core terminology consists of three components describing biobanks, sample collections, and studies, in which information on samples and sample donors is provided at aggregated form. However, there is also a need to describe samples and sample donors at an individual level to allow more elaborate queries on available biobank samples and data. Therefore the MIABIS terminology has now been extended with components describing samples and sample donors at an individual level. The components were defined according to specific scope and use cases by a large group of experts, and through several cycles of reviews, according to the new MIABIS governance model of BBMRI-ERIC (Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium). The guiding principles applied in developing these components included the following terms: model should consider only samples of human origin, model should be applicable to all types of samples and all sample donors, and model should describe the current status of samples stored in a given biobank. A minimal set of standard attributes for defining samples and sample donors is presented here. We added an "event" component to describe attributes that are not directly describing samples or sample donors but are tightly related to them. To better utilize the generic data model, we suggest a procedure by which interoperability can be promoted, using specific MIABIS profiles. The MIABIS sample and donor component extensions and the new generic data model complement the existing MIABIS Core 2.0 components, and substantially increase the potential usability of this terminology for better describing biobank samples and sample donors. They also support the use of individual level data about samples and sample donors to obtain accurate and detailed biobank availability queries.
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http://dx.doi.org/10.1089/bio.2019.0129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310316PMC
June 2020

Application of organic carbon affects mineral nitrogen uptake by winter wheat and leaching in subsoil: Proximal sensing as a tool for agronomic practice.

Sci Total Environ 2020 May 7;717:137058. Epub 2020 Feb 7.

Global Change Research Institute of the Czech Academy of Sciences, Bělidla 4a, CZ-603 00 Brno, Czech Republic; Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.

We tested the hypothesis that application of stable forms of organic carbon (C) into the soil reduces leaching of nitrogen (N). We also examined the potential to estimate N leaching employing N-sensitive spectral reflectance indices. During three growing seasons 2013-2015, field experiment at two experimental sites combining application of distinct N doses (0 (N), 35 (N), 70 (N), and 140 (N) kg N ha) and two stable forms of organic C (lignohumate and compost) was established to measure N uptake by winter wheat and its leaching to subsoil layers. The spectral reflectance at canopy level was measured simultaneously with N content in leaf dry matter at the beginning of the grain filling phase. At full maturity, the above-ground biomass, grain yield, and grain protein content were evaluated. That data was used to calculate N uptake in grain. The N dose led to increased N uptake by grain of 64% and 73% in the wetter years 2013 and 2014, respectively, and even by 118% in the drier year 2015 in comparison with the N treatment. N leaching to subsoil increased substantially with higher N dose, but only in wetter years 2013 (by 74%) and 2014 (by 87%). By contrast, no effect of N dose on leached N was found in the dry year 2015. The application of organic C along with the N dose substantially reduced N leaching by 26% and 29% in 2014 and 2015, respectively. Moreover, we demonstrated that normalized red-edge spectral reflectance index (NRERI) is able to predict N uptake by wheat and it can serve as an indicator of N leaching in heavy-rainfall years. Our results thus point towards possible agronomic practices and use of remote-sensing techniques to reduce groundwater contamination by N-based fertilizers.
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http://dx.doi.org/10.1016/j.scitotenv.2020.137058DOI Listing
May 2020

Distinct seasonal dynamics of responses to elevated CO in two understorey grass species differing in shade-tolerance.

Ecol Evol 2019 Dec 29;9(24):13663-13677. Epub 2019 Nov 29.

Global Change Research Institute of the Czech Academy of Sciences Brno Czech Republic.

Understorey plant communities are crucial to maintain species diversity and ecosystem processes including nutrient cycling and regeneration of overstorey trees. Most studies exploring effects of elevated CO concentration ([CO]) in forests have, however, been done on overstorey trees, while understorey communities received only limited attention.The hypothesis that understorey grass species differ in shade-tolerance and development dynamics, and temporally exploit different niches under elevated [CO], was tested during the fourth year of [CO] treatment. We assumed stimulated carbon gain by elevated [CO] even at low light conditions in strongly shade-tolerant , while its stimulation under elevated [CO] in less shade-tolerant was expected only in early spring when the tree canopy is not fully developed.We found evidence supporting this hypothesis. While elevated [CO] stimulated photosynthesis in mainly in the peak of the growing season (by 55%-57% in July and August), even at low light intensities (50 µmol m s), stimulatory effect of [CO] in was found mainly under high light intensities (200 µmol m s) at the beginning of the growing season (increase by 171% in May) and gradually declined during the season. Elevated [CO] also substantially stimulated leaf mass area and root-to-shoot ratio in , while only insignificant increases were observed in .Our physiological and morphological analyses indicate that understorey species, differing in shade-tolerance, under elevated [CO] exploit distinct niches in light environment given by the dynamics of the tree canopy.
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http://dx.doi.org/10.1002/ece3.5738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6953567PMC
December 2019

Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC.

Appl Clin Inform 2019 08 11;10(4):679-692. Epub 2019 Sep 11.

Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany.

Background: High-quality clinical data and biological specimens are key for medical research and personalized medicine. The Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) aims to facilitate access to such biological resources. The accompanying ADOPT BBMRI-ERIC project kick-started BBMRI-ERIC by collecting colorectal cancer data from European biobanks.

Objectives: To transform these data into a common representation, a uniform approach for data integration and harmonization had to be developed. This article describes the design and the implementation of a toolset for this task.

Methods: Based on the semantics of a metadata repository, we developed a lexical bag-of-words matcher, capable of semiautomatically mapping local biobank terms to the central ADOPT BBMRI-ERIC terminology. Its algorithm supports fuzzy matching, utilization of synonyms, and sentiment tagging. To process the anonymized instance data based on these mappings, we also developed a data transformation application.

Results: The implementation was used to process the data from 10 European biobanks. The lexical matcher automatically and correctly mapped 78.48% of the 1,492 local biobank terms, and human experts were able to complete the remaining mappings. We used the expert-curated mappings to successfully process 147,608 data records from 3,415 patients.

Conclusion: A generic harmonization approach was created and successfully used for cross-institutional data harmonization across 10 European biobanks. The software tools were made available as open source.
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http://dx.doi.org/10.1055/s-0039-1695793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739205PMC
August 2019

Distinct Morphological, Physiological, and Biochemical Responses to Light Quality in Barley Leaves and Roots.

Front Plant Sci 2019 14;10:1026. Epub 2019 Aug 14.

Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia.

Light quality modulates plant growth, development, physiology, and metabolism through a series of photoreceptors perceiving light signal and related signaling pathways. Although the partial mechanisms of the responses to light quality are well understood, how plants orchestrate these impacts on the levels of above- and below-ground tissues and molecular, physiological, and morphological processes remains unclear. However, the re-allocation of plant resources can substantially adjust plant tolerance to stress conditions such as reduced water availability. In this study, we investigated in two spring barley genotypes the effect of ultraviolet-A (UV-A), blue, red, and far-red light on morphological, physiological, and metabolic responses in leaves and roots. The plants were grown in growth units where the root system develops on black filter paper, placed in growth chambers. While the growth of above-ground biomass and photosynthetic performance were enhanced mainly by the combined action of red, blue, far-red, and UV-A light, the root growth was stimulated particularly by supplementary far-red light to red light. Exposure of plants to the full light spectrum also stimulates the accumulation of numerous compounds related to stress tolerance such as proline, secondary metabolites with antioxidative functions or jasmonic acid. On the other hand, full light spectrum reduces the accumulation of abscisic acid, which is closely associated with stress responses. Addition of blue light induced accumulation of γ-aminobutyric acid (GABA), sorgolactone, or several secondary metabolites. Because these compounds play important roles as osmolytes, antioxidants, UV screening compounds, or growth regulators, the importance of light quality in stress tolerance is unequivocal.
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http://dx.doi.org/10.3389/fpls.2019.01026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6703096PMC
August 2019

Leveraging European infrastructures to access 1 million human genomes by 2022.

Nat Rev Genet 2019 11 27;20(11):693-701. Epub 2019 Aug 27.

ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK.

Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.
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http://dx.doi.org/10.1038/s41576-019-0156-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115898PMC
November 2019

Ozone flux and ozone deposition in a mountain spruce forest are modulated by sky conditions.

Sci Total Environ 2019 Jul 1;672:296-304. Epub 2019 Apr 1.

Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00 Brno, Czech Republic. Electronic address:

In order to understand the main driving factors of ozone (O) deposition we tested the hypothesis that sky conditions (cloudy, partly cloudy, and clear sky) modulate O flux in forest ecosystems via stomatal regulation. The hypothesis is based on the fact that complex microclimate conditions under cloudy sky usually stimulate stomatal conductance. O fluxes were inferred from a concentration gradient in a mountainous Norway spruce forest in the Czech Republic (Central Europe) for years 2012-2016 and measured directly by eddy-covariance during the summer of 2017. Daily and seasonal O depositions were calculated separately for days with cloudy, partly cloudy, and clear sky conditions. The data show unequivocally that more O is taken up under cloudy and partially cloudy skies. Moreover, we found significant interactive effects of sky conditions and season on O flux. Though there are other mechanisms and pathways involved in the transport of O to the plant-soil system, the highest O deposition was associated to the highest stomatal conductance during partly cloudy and cloudy sky conditions in all seasons, while lower O ecosystem fluxes were observed under clear sky conditions despite the highest O concentrations at this time. These findings suggest that forests growing at sites where conditions are predominantly cloudy are expected to deposit higher extent of O than less-cloudy forests being thus more threatened by phytotoxic O.
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http://dx.doi.org/10.1016/j.scitotenv.2019.03.491DOI Listing
July 2019

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

Gigascience 2019 02;8(2)

Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, Germany.

Background: Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution.

Findings: PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm.

Conclusions: PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.
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http://dx.doi.org/10.1093/gigascience/giy149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377398PMC
February 2019

Induction of phenolic compounds by UV and PAR is modulated by leaf ontogeny and barley genotype.

Plant Physiol Biochem 2019 Jan 11;134:81-93. Epub 2018 Aug 11.

Global Change Research Institute CAS, v. v. i., Bělidla 986/4a, CZ 60300 Brno, Czech Republic. Electronic address:

We investigated the effect of leaf ontogeny and barley genotype on the accumulation of phenolic compounds (PhCs) induced by ultraviolet (UV) and photosynthetically active radiation (PAR). We hypothesized that different groups of PhCs are induced in leaves differing in ontogeny, and that this has consequences for protective functions and the need for other protection mechanisms. Generally, lower constitutive contents of PhCs (under conditions of UV exclusion and reduced PAR) were found in a UV-sensitive genotype (Barke) compared to a tolerant genotype (Bonus). However, UV and PAR induced accumulation of PhCs exceeded the constitutive amounts several fold. Specifically, lutonarin, 3-feruloylquinic acid, unidentified hydroxycinnamic acid and luteolin derivatives were markedly enhanced by high PAR and UV irradiances. Leaves developed during UV and PAR treatments had higher PhCs contents than mature leaves already fully developed at the onset of the UV and PAR treatment. UV and PAR treatments had, however, a minor effect on saponarin and unidentified apigenin derivatives which occur particularly in mature leaves of the tolerant genotype Bonus. In addition, high UV and PAR intensities increased the total content of xanthophylls (VAZ), while chlorophyll content was reduced, particularly in developing leaves. A redundancy analysis revealed positive associations between most of PhCs and VAZ and a negative association between total chlorophylls and carotenoids. Non-linear relationships between VAZ and lutonarin and other PhCs indicate that VAZ accumulation can compensate for the insufficient efficiency of anti-oxidative protection mediated by PhCs. Accordingly, we conclude that UV and PAR-induced accumulation of PhCs is affected by leaf ontogeny, however, this effect is compound-specific.
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http://dx.doi.org/10.1016/j.plaphy.2018.08.012DOI Listing
January 2019

Ultraviolet radiation modulates C:N stoichiometry and biomass allocation in Fagus sylvatica saplings cultivated under elevated CO concentration.

Plant Physiol Biochem 2019 Jan 3;134:103-112. Epub 2018 Aug 3.

Global Change Research Institute CAS, Bělidla 986/4a, CZ-603 00, Brno, Czech Republic; Mendel University in Brno, Zemědělská 1, CZ-613 00, Brno, Czech Republic. Electronic address:

Under the conditions of ongoing climate change, terrestrial ecosystems will be simultaneously exposed to a permanent rise in atmospheric CO concentration and increasing variability of such environmental factors as temperature, precipitation, and UV radiation. This will result in numerous interactions. The interactive effects caused by exposure to such multiple environmental factors are not yet well understood. We tested the hypotheses that enhanced UV radiation reduces the stimulatory effect of elevated CO concentration on plant biomass production and that it alters biomass allocation in broadleaved European beech (Fagus sylvatica L.) saplings. Our results after 2 years of exposure confirmed interactive effects of CO concentration and UV radiation on biomass production, and particularly on biomass allocation to roots and aboveground biomass. The strongest stimulatory effect of elevated CO on aboveground biomass and roots was found under ambient UV radiation, while both low and high UV doses reduced this stimulation. Nitrogen content in the roots and the distribution of nitrogen among leaves and roots were also significantly affected by interaction of CO concentration and UV radiation. The observed changes in leaf and root C:N stoichiometry were associated with altered morphological traits, and particularly with a change in the proportion of fine roots. As the biomass allocation and especially the proportion of fine roots can play an important role in effective water and nutrient use and acclimation to future climates, it is essential to obtain a deeper understanding of the links between C:N stoichiometry and biomass accumulation.
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http://dx.doi.org/10.1016/j.plaphy.2018.07.038DOI Listing
January 2019

Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health.

Biopreserv Biobank 2018 Apr 23;16(2):97-105. Epub 2018 Jan 23.

1 BBMRI-ERIC , Graz, Austria .

The known challenge of underutilization of data and biological material from biorepositories as potential resources for medical research has been the focus of discussion for over a decade. Recently developed guidelines for improved data availability and reusability-entitled FAIR Principles (Findability, Accessibility, Interoperability, and Reusability)-are likely to address only parts of the problem. In this article, we argue that biological material and data should be viewed as a unified resource. This approach would facilitate access to complete provenance information, which is a prerequisite for reproducibility and meaningful integration of the data. A unified view also allows for optimization of long-term storage strategies, as demonstrated in the case of biobanks. We propose an extension of the FAIR Principles to include the following additional components: (1) quality aspects related to research reproducibility and meaningful reuse of the data, (2) incentives to stimulate effective enrichment of data sets and biological material collections and its reuse on all levels, and (3) privacy-respecting approaches for working with the human material and data. These FAIR-Health principles should then be applied to both the biological material and data. We also propose the development of common guidelines for cloud architectures, due to the unprecedented growth of volume and breadth of medical data generation, as well as the associated need to process the data efficiently.
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http://dx.doi.org/10.1089/bio.2017.0110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906729PMC
April 2018

BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration.

Bioinformatics 2017 Nov;33(22):3627-3634

Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.

Motivation: Biobanks are indispensable for large-scale genetic/epidemiological studies, yet it remains difficult for researchers to determine which biobanks contain data matching their research questions.

Results: To overcome this, we developed a new matching algorithm that identifies pairs of related data elements between biobanks and research variables with high precision and recall. It integrates lexical comparison, Unified Medical Language System ontology tagging and semantic query expansion. The result is BiobankUniverse, a fast matchmaking service for biobanks and researchers. Biobankers upload their data elements and researchers their desired study variables, BiobankUniverse automatically shortlists matching attributes between them. Users can quickly explore matching potential and search for biobanks/data elements matching their research. They can also curate matches and define personalized data-universes.

Availability And Implementation: BiobankUniverse is available at http://biobankuniverse.com or can be downloaded as part of the open source MOLGENIS suite at http://github.com/molgenis/molgenis.

Contact: m.a.swertz@rug.nl.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btx478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870622PMC
November 2017

A Decentralized IT Architecture for Locating and Negotiating Access to Biobank Samples.

Stud Health Technol Inform 2017 ;243:75-79

German Cancer Research Center, Heidelberg.&BBMRI.de.

There is a need among researchers for the easy discoverability of biobank samples. Currently, there is no uniform way for finding samples and negotiate access. Instead, researchers have to communicate with each biobank separately. We present the architecture for the BBMRI-CS IT platform, whose goal is to facilitate sample location and access. We chose a decentral approach, which allows for strong data protection and provides the high flexibility needed in the highly heterogeneous landscape of European biobanks. This is the first implementation of a decentral search in the biobank field. With the addition of a Negotiator component, it also allows for easy communication and a follow-through of the lengthy approval process for accessing samples.
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April 2018

Four simple recommendations to encourage best practices in research software.

F1000Res 2017 13;6. Epub 2017 Jun 13.

Software Sustainability Institute, Web and Internet Science, University of Southampton, Southampton, UK.

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.
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http://dx.doi.org/10.12688/f1000research.11407.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490478PMC
June 2017

Conception and Implementation of an Austrian Biobank Directory Integration Framework.

Biopreserv Biobank 2017 Aug 5;15(4):332-340. Epub 2017 Apr 5.

1 Department of Medical Statistics, Informatics and Health Economics, Medical University of Innsbruck , Innsbruck, Austria .

Introduction: Sample collections and data are hosted within different biobanks at diverse institutions across Europe. Our data integration framework aims at incorporating data about sample collections from different biobanks into a common research infrastructure, facilitating researchers' abilities to obtain high-quality samples to conduct their research. The resulting information must be locally gathered and distributed to searchable higher level information biobank directories to maximize the visibility on the national and European levels. Therefore, biobanks and sample collections must be clearly described and unambiguously identified. We describe how to tackle the challenges of integrating biobank-related data between biobank directories using heterogeneous data schemas and different technical environments.

Methods: To establish a data exchange infrastructure between all biobank directories involved, we propose the following steps: (A) identification of core entities, terminology, and semantic relationships, (B) harmonization of heterogeneous data schemas of different Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) directories, and (C) formulation of technical core principles for biobank data exchange between directories.

Results: (A) We identified the major core elements to describe biobanks in biobank directories. Since all directory data models were partially based on Minimum Information About BIobank Data Sharing (MIABIS) 2.0, the MIABIS 2.0 core model was used for compatibility. (B) Different projection scenarios were elaborated in collaboration with all BBMRI.at partners. A minimum set of mandatory and optional core entities and data items was defined for mapping across all directory levels. (C) Major core data exchange principles were formulated and data interfaces implemented by all biobank directories involved.

Discussion: We agreed on a MIABIS 2.0-based core set of harmonized biobank attributes and established a list of data exchange core principles for integrating biobank directories on different levels. This generic approach and the data exchange core principles proposed herein can also be applied in related tasks like integration and harmonization of biobank data on the individual sample and patient levels.
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http://dx.doi.org/10.1089/bio.2016.0113DOI Listing
August 2017

Asymmetric responses of primary productivity to precipitation extremes: A synthesis of grassland precipitation manipulation experiments.

Glob Chang Biol 2017 10 9;23(10):4376-4385. Epub 2017 May 9.

Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.

Climatic changes are altering Earth's hydrological cycle, resulting in altered precipitation amounts, increased interannual variability of precipitation, and more frequent extreme precipitation events. These trends will likely continue into the future, having substantial impacts on net primary productivity (NPP) and associated ecosystem services such as food production and carbon sequestration. Frequently, experimental manipulations of precipitation have linked altered precipitation regimes to changes in NPP. Yet, findings have been diverse and substantial uncertainty still surrounds generalities describing patterns of ecosystem sensitivity to altered precipitation. Additionally, we do not know whether previously observed correlations between NPP and precipitation remain accurate when precipitation changes become extreme. We synthesized results from 83 case studies of experimental precipitation manipulations in grasslands worldwide. We used meta-analytical techniques to search for generalities and asymmetries of aboveground NPP (ANPP) and belowground NPP (BNPP) responses to both the direction and magnitude of precipitation change. Sensitivity (i.e., productivity response standardized by the amount of precipitation change) of BNPP was similar under precipitation additions and reductions, but ANPP was more sensitive to precipitation additions than reductions; this was especially evident in drier ecosystems. Additionally, overall relationships between the magnitude of productivity responses and the magnitude of precipitation change were saturating in form. The saturating form of this relationship was likely driven by ANPP responses to very extreme precipitation increases, although there were limited studies imposing extreme precipitation change, and there was considerable variation among experiments. This highlights the importance of incorporating gradients of manipulations, ranging from extreme drought to extreme precipitation increases into future climate change experiments. Additionally, policy and land management decisions related to global change scenarios should consider how ANPP and BNPP responses may differ, and that ecosystem responses to extreme events might not be predicted from relationships found under moderate environmental changes.
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http://dx.doi.org/10.1111/gcb.13706DOI Listing
October 2017

Toward Global Biobank Integration by Implementation of the Minimum Information About BIobank Data Sharing (MIABIS 2.0 Core).

Biopreserv Biobank 2016 Aug 15;14(4):298-306. Epub 2016 Mar 15.

6 BBMRI-ERIC , Graz, Austria .

Biobanks are the biological back end of data-driven medicine, but lack standards and generic solutions for interoperability and information harmonization. The move toward a global information infrastructure for biobanking demands semantic interoperability through harmonized services and common ontologies. To tackle this issue, the Minimum Information About BIobank data Sharing (MIABIS) was developed in 2012 by the Biobanking and BioMolecular Resources Research Infrastructure of Sweden (BBMRI.se). The wide acceptance of the first version of MIABIS encouraged evolving it to a more structured and descriptive standard. In 2013 a working group was formed under the largest infrastructure for health in Europe, Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), with the remit to continue the development of MIABIS (version 2.0) through a multicountry governance process. MIABIS 2.0 Core has been developed with 22 attributes describing Biobanks, Sample Collections, and Studies according to a modular structure that makes it easier to adhere to and to extend the standard. This integration standard will make a great contribution to the discovery and exploitation of biobank resources and lead to a wider and more efficient use of valuable bioresources, thereby speeding up the research on human diseases. Many within the European Union have accepted MIABIS 2.0 Core as the "de facto" biobank information standard.
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http://dx.doi.org/10.1089/bio.2015.0070DOI Listing
August 2016

BBMRI-ERIC: the novel gateway to biobanks. From humans to humans.

Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2016 Mar;59(3):379-84

BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria.

BBMRI-ERIC, the Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium, is a new form of umbrella organization for biobanking in Europe. For rare and common diseases alike, it aims at providing fair access to quality-controlled human biological samples and associated biomedical and biomolecular data. Such access enables basic mechanisms underlying diseases to be studied, which is indispensable for the development of new biomarkers and drugs. In the context of the European Research Area (ERA), biobanks, which were identified as a particular European strength, contribute to Europe's cohesion policy through capacity-building in the BBMRI-ERIC member countries.
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http://dx.doi.org/10.1007/s00103-015-2301-8DOI Listing
March 2016

Ultraviolet and photosynthetically active radiation can both induce photoprotective capacity allowing barley to overcome high radiation stress.

Plant Physiol Biochem 2015 Aug 7;93:74-83. Epub 2015 Jan 7.

Global Change Research Center AS CR, v.v.i., Bělidla 4a, CZ 60300 Brno, Czech Republic. Electronic address:

The main objective of this study was to determine the effects of acclimation to ultraviolet (UV) and photosynthetically active radiation (PAR) on photoprotective mechanisms in barley leaves. Barley plants were acclimated for 7 days under three combinations of high or low UV and PAR treatments ([UV-PAR-], [UV-PAR+], [UV+PAR+]). Subsequently, plants were exposed to short-term high radiation stress (HRS; defined by high intensities of PAR - 1000 μmol m(-2) s(-1), UV-A - 10 W m(-2) and UV-B 2 W m(-2) for 4 h), to test their photoprotective capacity. The barley variety sensitive to photooxidative stress (Barke) had low constitutive flavonoid content compared to the resistant variety (Bonus) under low UV and PAR intensities. The accumulation of lutonarin and 3-feruloylquinic acid, but not of saponarin, was greatly enhanced by high PAR and further increased by UV exposure. Acclimation of plants to both high UV and PAR intensities also increased the total pool of xanthophyll-cycle pigments (VAZ). Subsequent exposure to HRS revealed that prior acclimation to UV and PAR was able to ameliorate the negative consequences of HRS on photosynthesis. Both total contents of epidermal flavonols and the total pool of VAZ were closely correlated with small reductions in light-saturated CO2 assimilation rate and maximum quantum yield of photosystem II photochemistry caused by HRS. Based on these results, we conclude that growth under high PAR can substantially increase the photoprotective capacity of barley plants compared with plants grown under low PAR. However, additional UV radiation is necessary to fully induce photoprotective mechanisms in the variety Barke. This study demonstrates that UV-exposure can lead to enhanced photoprotective capacity and can contribute to the induction of tolerance to high radiation stress in barley.
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http://dx.doi.org/10.1016/j.plaphy.2015.01.001DOI Listing
August 2015

Morphological, biochemical and physiological traits of upper and lower canopy leaves of European beech tend to converge with increasing altitude.

Tree Physiol 2015 Jan 9;35(1):47-60. Epub 2015 Jan 9.

Global Change Research Centre, Academy of Sciences of the Czech Republic, Bělidla 4a, CZ-60300 Brno, Czech Republic

The present work has explored for the first time acclimation of upper versus lower canopy leaves along an altitudinal gradient. We tested the hypothesis that restrictive climatic conditions associated with high altitudes reduce within-canopy variations of leaf traits. The investigated beech (Fagus sylvatica L.) forest is located on the southern slope of the Hrubý Jeseník Mountains (Czech Republic). All measurements were taken on leaves from upper and lower parts of the canopy of mature trees (>85 years old) growing at low (400 m above sea level, a.s.l.), middle (720 m a.s.l.) and high (1100 m a.s.l.) altitudes. Compared with trees at higher altitudes, those growing at low altitudes had lower stomatal conductance, slightly lower CO(2) assimilation rate (A(max)) and leaf mass per area (LMA), and higher photochemical reflectance index, water-use efficiency and Rubisco content. Given similar stand densities at all altitudes, the different growth conditions result in a more open canopy and higher penetration of light into lower canopy with increasing altitude. Even though strong vertical gradients in light intensity occurred across the canopy at all altitudes, lower canopy leaves at high altitudes tended to acquire the same morphological, biochemical and physiological traits as did upper leaves. While elevation had no significant effect on nitrogen (N) and carbon (C) contents per unit leaf area, LMA, or total content of chlorophylls and epidermal flavonoids in upper leaves, these increased significantly in lower leaves at higher altitudes. The increases in N content of lower leaves were coupled with similar changes in A(max). Moreover, a high N content coincided with high Rubisco concentrations in lower but not in upper canopy leaves. Our results show that the limiting role of light in lower parts of the canopy is reduced at high altitudes. A great capacity of trees to adjust the entire canopy is thus demonstrated.
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http://dx.doi.org/10.1093/treephys/tpu104DOI Listing
January 2015

The effect of nitrogen addition on biomass production and competition in three expansive tall grasses.

Environ Pollut 2012 Nov 24;170:211-6. Epub 2012 Jul 24.

Global Change Research Centre, Academy of Sciences of the Czech Republic, Brno, Czech Republic.

A large increase of grasses Calamagrostis epigejos, Bromus inermis and Brachypodium pinnatum has often been observed in many regions enriched by higher nitrogen (N) wet deposition inputs. Competitive relationships between these grasses under enhanced N loads have not yet been studied. Therefore an outdoor experiment was established which involved monocultures of Calamagrostis, Bromus and Brachypodium and their 1:1 mixtures in containers under two N treatments, i.e., unfertilized and fertilized (+50 kg N ha(-1)). In monocultures, the total aboveground biomass of Calamagrostis, Bromus and Brachypodium were 1.1, 3.6 and 2.5 times higher respectively due to enhanced N fertilization. Relative crowding and aggressivity coefficients indicate that Calamagrostis and Bromus dominate when mixed with Brachypodium at both levels of N availability. When mixed with Bromus, Calamagrostis is the poorer competitor at lower N loads, however, it can be dominating in N fertilized treatments.
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http://dx.doi.org/10.1016/j.envpol.2012.07.007DOI Listing
November 2012

Interannual variation in root production in grasslands affected by artificially modified amount of rainfall.

ScientificWorldJournal 2012 2;2012:805298. Epub 2012 May 2.

Department of Vegetation Ecology, Institute of Botany, Academy of Sciences of the Czech Republic, Lidická 25, 602 00 Brno, Czech Republic.

The effect of different amounts of rainfall on the below-ground plant biomass was studied in three grassland ecosystems. Responses of the lowland (dry Festuca grassland), highland (wet Cirsium grassland), and mountain (Nardus grassland) grasslands were studied during five years (2006-2010). A field experiment based on rainout shelters and gravity irrigation simulated three climate scenarios: rainfall reduced by 50% (dry), rainfall increased by 50% (wet), and the natural rainfall of the current growing season (ambient). The interannual variation in root increment and total below-ground biomass reflected the experimentally manipulated amount of precipitation and also the amount of current rainfall of individual years. The effect of year on these below-ground parameters was found significant in all studied grasslands. In comparison with dry Festuca grassland, better adapted to drought, submontane wet Cirsium grassland was more sensitive to the different water inputs forming rather lower amount of below-ground plant matter at reduced precipitation.
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http://dx.doi.org/10.1100/2012/805298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353563PMC
October 2012

Secure and pervasive collaborative platform for medical applications.

Stud Health Technol Inform 2007 ;126:229-38

Institute of Computer Science, Masaryk University, Czech Republic.

Providing secure, extensible, pervasive and easy to implement collaborative environment for medical applications poses significant challenge for state-of-the-art computer systems and networks. In this paper, we describe such a collaborative environment developed for Ithanet project, based on Grid authentication mechanisms. Significant effort has been put into developing a system, that is capable of deployment across tightly secured networking environments as implemented in vast majority of hospitals. The environment is extensible enough to incorporate Grid-service based collaborative systems like AccessGrid.
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September 2007