Biomedical subjects

Stephan Weise

Publications and source records attributed to Stephan Weise.

4 recordsLinked to original sources

PubMed2026

Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation.

MOTIVATION: The AGENT project established a network of actively cooperating European genebanks, integrating genomic and phenotypic data from accessions of wheat and barley. Due to specific storage demands for phenotypic and genotypic data, the project used separate database instances and backend technologies to manage integrated phenotypic and genotypic data. RESULTS: We discuss the challenges encountered when integrating dispersed data to serve through a single interface such as the Plant Breeding Application Programming Interface, BrAPI. We examine how the consistent mappability of genebank data to the BrAPI model can enable the implementation of effective services. The advantages of BrAPI in transparently linking distributed data entities through embedded, unique identifiers are highlighted. We present a technical solution involving a BrAPI proxy, which combines and merges separate BrAPI endpoints. Finally, we demonstrate the AGENT BrAPI implementation with an illustrative example that validates a suggested SNP for a trait from the literature by linking phenotypic, genotypic and passport data. AVAILABILITY AND IMPLEMENTATION: The BrAPI proxy implementation and documentation is available at the Python Package Index (https://pypi.org/project/brapi-proxy) and archived in Zenodo (doi: 10.5281/zenodo.19436445). SUPPLEMENTARY INFORMATION: A Jupyter Notebook file for the validation example using a marker-trait relationship found in the literature.

Phenotype↗

PubMed2006

Meta-All: a system for managing metabolic pathway information.

BACKGROUND: Many attempts are being made to understand biological subjects at a systems level. A major resource for these approaches are biological databases, storing manifold information about DNA, RNA and protein sequences including their functional and structural motifs, molecular markers, mRNA expression levels, metabolite concentrations, protein-protein interactions, phenotypic traits or taxonomic relationships. The use of these databases is often hampered by the fact that they are designed for special application areas and thus lack universality. Databases on metabolic pathways, which provide an increasingly important foundation for many analyses of biochemical processes at a systems level, are no exception from the rule. Data stored in central databases such as KEGG, BRENDA or SABIO-RK is often limited to read-only access. If experimentalists want to store their own data, possibly still under investigation, there are two possibilities. They can either develop their own information system for managing that own data, which is very time-consuming and costly, or they can try to store their data in existing systems, which is often restricted. Hence, an out-of-the-box information system for managing metabolic pathway data is needed. RESULTS: We have designed META-ALL, an information system that allows the management of metabolic pathways, including reaction kinetics, detailed locations, environmental factors and taxonomic information. Data can be stored together with quality tags and in different parallel versions. META-ALL uses Oracle DBMS and Oracle Application Express. We provide the META-ALL information system for download and use. In this paper, we describe the database structure and give information about the tools for submitting and accessing the data. As a first application of META-ALL, we show how the information contained in a detailed kinetic model can be stored and accessed. CONCLUSION: META-ALL is a system for managing information about metabolic pathways. It facilitates the handling of pathway-related data and is designed to help biochemists and molecular biologists in their daily research. It is available on the Web at http://bic-gh.de/meta-all and can be downloaded free of charge and installed locally.

Database Management Systems↗

PubMed2006

Farmers' perception on the importance of variegated grasshopper (Zonocerus variegatus (L.)) in the agricultural production systems of the humid forest zone of Southern Cameroon.

BACKGROUND: Zonocerus variegatus (Linnaeus, 1758) (Orthoptera: Pyrgomorphidae) is known as an agricultural pest in West and Central Africa. However, its importance in the agricultural production system in Cameroon has not been investigated. The study assesses farmers' perception on the importance of Z. variegatus in the agricultural production systems of the humid forest zone of Southern Cameroon. METHODS: Research was carried out in 5 villages of each of three Agro-Ecological, Cultural and Demographic Blocks (AECD-Blocks) of the Forest Margin Benchmark Area (FMBA). In each village, a semi-structured survey was used; male and female groups of farmers were interviewed separately. RESULTS: Z. variegatus is present throughout the humid forest zone of Southern Cameroon, where it is ranked as the third most economically important insect pest of agriculture. In the farmers' opinion, Z. variegatus is a polyphagous insect with little impact on young perennial crops. The length of the pre-farming fallow does not affect Z. variegatus pest pressure in the following crops. The increased impact of the grasshopper observed today in the fields, compared to what existed 10 years ago is as a result of deforestation and increase in surface of herbaceous fallow. The damage caused by Z. variegatus is higher in fields adjacent to C. odorata and herbaceous fallows than in those adjacent to forests and shrubby fallows. The fight against this grasshopper is often done through physical methods carried out by hand, for human consumption. The farmers highlight low usage of the chemical methods and a total absence of biological and ecological methods. CONCLUSION: Farmers' perception have contributed to understanding the status of Z. variegatus in the humid forest zone of Southern Cameroon. The results are in general similar to those obtained in other countries.

Adolescent↗

PubMed2006

Soil-plant hydrology of indigenous and exotic trees in an Ethiopian montane forest.

Fast-growing exotic trees are widely planted in the tropics to counteract deforestation; however, their patterns of water use could be detrimental to overall ecosystem productivity through their impact on ecosystem water budget. In a comparative field study on seasonal soil-plant water dynamics of two exotic species (Cupressus lusitanica Mill. and Eucalyptus globulus Labill.) and the indigenous Podocarpus falcatus (Thunb.) Mirb. in south Ethiopia, we combined a 2.5-year record for climate and soil water availability, natural-abundance oxygen isotope ratios (delta(18)O) of soil and xylem water, destructive root sampling and transpiration measurements. Soil was generally driest under C. lusitanica with its dense canopy and shallow root system, particularly following a relatively low-rainfall wet season, with the wettest soil under E. globulus. Wet season transpiration of C. lusitanica was twice that of the other species. In the dry season, P. falcatus and C. lusitanica reduced transpiration by a factor of six and two, respectively, whereas E. globulus showed a fivefold increase. In all species, there was a shift in water uptake to deeper soil layers as the dry season progressed, accompanied by relocation of live fine root biomass (LFR) of C. lusitanica and P. falcatus to deeper layers. Under P. falcatus, variability in soil matric potential, narrow delta(18)O depth gradients and high LFR indicated fast water redistribution. Subsoil water uptake was important only for E. globulus, which had low topsoil LFR and tap roots exploiting deep water. Although P. falcatus appeared better adapted to varying soil water availability than the exotic species, both conifers decreased growth substantially during dry weather. Growth of E. globulus was largely independent of topsoil water content, giving it the potential to cause substantial dry-season groundwater depletion.

Biological Transport↗