Wolfram WeckwerthUniversity of Vienna | UniWien · Department of Ecogenomics and Systems Biology
Wolfram Weckwerth
Prof. Dr.
Director of Vienna Metabolomics Center (VIME)
https://metabolomics.univie.ac.at/
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526
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Introduction
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September 2008 - present
Publications
Publications (526)
Chickpea is the world's fourth largest grown legume crop, which significantly contributes to food security by providing calories and dietary protein globally. However, the increased frequency of drought stress has significantly reduced chickpea production in recent years. Here, we have performed a field experiment with 36 diverse chickpea genotypes...
Wheat (Triticum spp.) is a primary dietary staple food for humanity. Many wheat genetic resources with variable genomes have a record of domestication history and are widespread throughout the world. To develop elite wheat varieties, agronomical and stress-responsive trait characterization is foremost for evaluating existing germ-plasm to promote b...
Advanced sequencing techniques have propelled molecular biology research into what is often termed the post-genomics era. Consequently, there is a heightened focus on unraveling the functional connections between individual genes and their ultimate phenotype, an area referred to as predictive genomics. To support this quest, we developed an intuiti...
Physical inactivity and a weak fitness status have become a global health concern. Metabolomics, as an integrative systematic approach, might link to individual fitness at the molecular level. In this study, we performed blood samples metabolomics analysis of a cohort of elderly people with different treatments. By defining two groups of fitness an...
Potato, the most important non-cereal crop, is highly water and space efficient but susceptible to abiotic stress such as heat, drought, or flooding. Climate change is severely increasing the likelihood of such stresses to occur individually, sequentially, or simultaneously. However, the understanding of acclimation to abiotic stress in crops in ge...
Cyanobacterium Nostoc commune is a filamentous terrestrial prokaryotic organism widely distributed, which suggest its high adaptive potential to environmental or abiotic stress. Physiological parameters and proteomic analysis were performed in two accession of N. commune with the aim to elucidate the differences of physiological trails between dist...
Whilst policymaking will always remain a highly political process, especially amidst crises, evidence-based pandemic management can benefit from adopting a socioecological perspective that integrates multi- and trans-disciplinary insights: from biology, biomedicine, mathematics, statistics, social and behavioural sciences, as well as the perspectiv...
Deregulation of mitochondrial functions in hepatocytes contributes to many liver diseases, such as nonalcoholic fatty liver disease (NAFLD). Lately, it was referred to as MAFLD (metabolism-associated fatty liver disease). Hesperetin (Hst), a bioactive flavonoid constituent of citrus fruit, has been proven to attenuate NAFLD. However, a potential co...
The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean acid metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait...
Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overview of the concept of Polygenic Risk Scores (PRS). We elucidate the historical advancements of PRS, their advan...
Phosphoglycerate dehydrogenase (PHGDH) has emerged as a crucial factor in macromolecule synthesis, neutralizing oxidative stress, and regulating methylation reactions in cancer cells, lymphocytes, and endothelial cells. However, the role of PHGDH in tumor-associated macrophages (TAMs) is poorly understood. Here, we found that the T helper 2 (Th2) c...
The growing food demand in the world due to the increasing population and decreasing availability of agricultural land requires new crops that are more productive and resistant to harsher environmental conditions. Thus, rapid and effective exploration, identification, and validation of an important trait, gene, molecular mediator, and protein inter...
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1–4, based on the polymorphisms of 3’ external transcribed sequences. The variants are known to be differentially expressed during plant development. We created a m...
The need for increasing for crop productivity leads to a higher usage of synthetic fertilizers, which has tremendous effects on the environment. Nitrogen (N) is a crucial plant macronutrient, but the production of synthetic N fertilizer and its leakage into aquatic systems represent sources of environmental damage. To reduce the usage of synthetic...
The study presents an innovative pipeline for detecting horizontal gene transfer (HGT) among a collection of sequenced genomes from gut microbiota. Herein, chicken and porcine gut microbiota were analyzed. Based on statistical analysis, we propose that nearly identical genes co-shared between distinct genera can be evidence for a previous event of...
The development of next-generation sequencing and single-cell technology has generated vast genome-scale multi-omics datasets. Dedicated mathematical algorithms are required to dissect intricate molecular causality within metabolic networks using these datasets. Based on the network analysis, recent research has introduced the inverse differential...
The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain‐filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type‐specific proteome and metabolome inventory of developing wheat endo...
The metabolome is the biochemical basis of plant form and function, but we know little about its macroecological variation across the plant kingdom. Here, we used the plant functional trait concept to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five metabolic functiona...
The pathogenicity of intracellular plant pathogenic bacteria is associated with the action of pathogenicity factors/effectors, but their physiological roles for most phytoplasma species, including ‘Candidiatus Phytoplasma solani’ are unknown. Six putative pathogenicity factors/effectors from six different strains of ‘Ca. P. solani’ were selected by...
Whole-genome duplication has shaped the evolution of angiosperms and other organisms, and is important for many crops. Structural reorganization of chromosomes and repatterning of gene expression are frequently observed in allopolyploids, with physiological and ecological consequences. Recurrent origins from different parental populations are wides...
Motivation:
One central goal of systems biology is to infer biochemical regulations from large-scale OMICS data. Many aspects of cellular physiology and organismal phenotypes can be understood as results of metabolic interaction network dynamics. Previously, we have proposed a convenient mathematical method which addresses this problem using metab...
Comprehensive analysis of lipids is becoming a forefront of clinical data analysis. Due to significant technical advancements, lipidomics is emerging in clinical diagnostics for improvement and earlier detection of a broad range of diseases. However, in order to understand the biological complexities and interrelationships between the molecules, it...
Plant growth promoting bacteria can confer resistance to various types of stress and increase agricultural yields. The mechanisms they employ are diverse. One of the most important genes associated with the increase in plant biomass and stress resistance is acdS , which encodes a 1-aminocyclopropane-1-carboxylate- or ACC-deaminase. The non-proteino...
Acclimation and adaptation of metabolism to a changing environment are key processes for plant survival and reproductive success. In the present study, 241 natural accessions of Arabidopsis (Arabidopsis thaliana) were grown under two different temperature regimes, 16 °C and 6 °C, and growth parameters were recorded, together with metabolite profile...
Inflammation is thought to be a key cause of many chronic diseases and cancer. However, current therapeutic agents to control inflammation have limited long-term use potential due to various side-effects. This study aimed to examine the preventive effects of norbergenin, a constituent of traditional anti-inflammatory recipes, on LPS-induced proinfl...
Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought‐responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought‐tolerant), and ICC 1882 (...
One central goal of systems biology is to infer biochemical regulations from large-scale OMICS data. Many aspects of cellular physiology and organism phenotypes could be understood as a result of the metabolic interaction network dynamics. Previously, we have derived a mathematical method addressing this problem using metabolomics data for the inve...
Roots are sensors evolved to simultaneously respond to manifold signals, which allow the plant to survive. Root growth responses, including the modulation of directional root growth, were shown to be differently regulated when the root is exposed to a combination of exogenous stimuli compared to an individual stress trigger. Several studies pointed...
The metabolome is the biochemical basis of plant form and function, but we know little about its macroecological variation across the plant kingdom. Here, we used the plant functional trait concept to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five metabolic functiona...
Heat stress drastically affects anther tissues resulting in poor plant fertility, necessitating an urgent need to determine the key proteome regulation associated with mature anther in response to heat stress. We identified several genotype - specific protein alterations in rice anthers of Moroberekan (Japonica, heat sensitive), IR64 (Indica, moder...
Chloroplast development is initiated by light-signals triggering the expression of nuclear encoded chloroplast genes in a first phase, followed by massive structural changes in the transition from proplastids to mature chloroplasts in the second phase. While the molecular players involved in the first phase are currently emerging, regulatory compon...
Isomeric compounds are present in the human body as well as in drugs and exhibit different physiological functions, making their measurement important in clinical science. Isomer measurement is often difficult even when applying chromatographic separation. To accommodate this, affinity-based sample preparation, such as Immunoprecipitation (IP) and...
The traceability of palm oil to determine its geographical origins within the palm oil supply chains is of importance to ensure quality and sustainable production. The current traceability systems are insufficient, thus requiring a more viable and effective approach to improve the traceability framework of the palm oil supply chain. In this study,...
Machine learning has become a powerful tool for systems biologists, from diagnosing cancer to optimizing kinetic models and predicting the state, growth dynamics, or type of a cell. Potential predictions from complex biological data sets obtained by “omics” experiments seem endless, but are often not the main objective of biological research. Often...
Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N2O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is...
Macrophages are prominent immune cells in the tumor microenvironment that can be educated into pro-tumoral phenotype by tumor cells to favor tumor growth and metastasis. The mechanisms that mediate a mutualistic relationship between tumor cells and macrophages remain poorly characterized. Here, we have shown in vitro that different human and murine...
Is data-driven analysis sufficient for understanding the COVID-19 pandemic and for justifying public health regulations? In this paper, we argue that such analysis is insufficient. Rather what is needed is the identification and implementation of over-arching hypothesis-related and/or theory-based rationales to conduct effective SARS-CoV2/COVID-19...
Background:
Birch pollen-related apple allergy is the most frequent IgE-mediated food allergy in Central-Northern Europe with Mal d 1 as major allergen. Its concentration in apples varies with the cultivar and storage time. Year-round appealing, hypoallergenic cultivars still are needed to satisfy the nutritional needs of affected individuals. We...
Plants rely on fine-tuning organ movement to ensure their survival and productivity. Even subtle loss of directional growth orchestration can result in a huge impact when the plant is impaired to adapt to everchanging environment, where it is exposed to manifold exogenous stimuli simultaneously. We present a newly designed chamber to obtain live im...
Murine macrophages activated by the Toll-like receptor 4 agonist lipopolysaccharide (LPS) polarize to the M1 type by inducing proinflammatory marker proteins and changing their energy metabolism to increased aerobic glycolysis and reduced respiration. We here show that the aliphatic isothiocyanate sulforaphane (Sfn) diminishes M1 marker expression...
Common ragweed (Ambrosia artemisiifolia) is an invasive plant with allergenic pollen. Due to environmental changes, ragweed pollen (RWP) airborne concentrations are predicted to quadruple in Europe by 2050 and more than double allergic sensitization of Europeans by 2060. We developed an experimental RWP model of allergy in BALB/c mice to evaluate h...
Metabolite analysis reveals new challenges in human health care. This human health care connects to the immune system and presents opportunities for the prevention and detection of early hidden disease symptoms. Predicting the concentration of immune metabolites and confirming relationships between concentrations of individual metabolites have the...
In Pseudomonas aeruginosa, the RNA chaperone Hfq and the catabolite repression protein Crc act in concert to regulate numerous genes during carbon catabolite repression (CCR). After alleviation of CCR, the RNA CrcZ sequesters Hfq/Crc, which leads to a rewiring of gene expression to ensure the consumption of less preferred carbon and nitrogen source...
Roots secrete a vast array of low molecular weight compounds into the soil broadly referred to as root exudates. It is a key mechanism by which plants and soil microbes interact in the rhizosphere. The effect of drought stress on the exudation process and composition is rarely studied, especially in cereal crops. This study focuses on comparative m...
Catechin is an extensively investigated plant flavan-3-ol with a beneficial impact on human health that is often associated with antioxidant activities and iron coordination complex formation. The aim of this study was to explore these properties with FeII and FeIII using a combination of nanoelectrospray-mass spectrometry, differential pulse volta...
Directional root growth control is crucial for plant fitness. The degree of root growth deviation depends on several factors, whereby exogenous growth conditions have a profound impact. The perception of mechanical impedance by wild-type roots results in the modulation of root growth traits, and it is known that gravitropic stimulus influences dist...
Legumes are the most important crop plants in agriculture, contributing 27% of the world's primary food production. However, productivity and production of Legumes is reduced due to increasing environmental stress. Hence, there is a pressing need to understand the molecular mechanism involved in stress response and legumes adaptation. Proteomics pr...
A major aim of ecology is to upscale attributes of individuals to understand processes at population, community and ecosystem scales. Such attributes are typically described using functional traits, that is, standardised characteristics that impact fitness via effects on survival, growth and/or reproduction. However, commonly used functional traits...
Prediction models that rely on time series data are often affected by diminished predictive accuracy. This occurs from the causal relationships of the data that shift over time. Thus, the changing weights that are used to create prediction models lose their informational value. One way to correct this change is by using concept drift information. T...
Rapidly evolving space exploration makes understanding the short- and long- term effects of microgravity on humans, plants, and microorganisms an important task. The ubiquitous presence of the gravitational force has had an influence on the development of all living entities on Earth, and short- and long-term changes in perceived gravitational forc...
The root is the below-ground organ of a plant, and it has evolved multiple signaling pathways that allow adaptation of architecture, growth rate, and direction to an ever-changing environment. Roots grow along the gravitropic vector towards beneficial areas in the soil to provide the plant with proper nutrients to ensure its survival and productivi...
A novel bacterium, designated strain Msb3 T , was recently isolated from leaves of the yam family plant Dioscorea bulbifera ( Dioscoreaceae ). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % s...
Crop production systems need to expand their outputs sustainably to feed a burgeoning human population. Advances in genome sequencing technologies combined with efficient trait mapping procedures accelerate the availability of beneficial alleles for breeding and research. Enhanced interoperability between different omics and phenotyping platforms,...
Cereal grain germination provides the basis for crop production and requires a tissue-specific interplay between the embryo and endosperm during heterotrophic germination involving signalling, protein secretion, and nutrient uptake until autotrophic growth is possible. High salt concentrations in soil are one of the most severe constraints limiting...