In Metabolomics we measure the levels of thousands of molecules simultaneously – which allows a much better understanding of metabolism.

We integrate system-theoretical ideas with genome-scale molecular analysis using genomics, transcriptomics, proteomics and metabolomics to understand and predict the genotype- environment-phenotype-relationship (GxExP). We investigate plant, microbial, animal and human systems.


The quality of state-of-the-art metabolomics technology depends on the quality of the preparation workflows, the quality of metabolite libraries and workflows for structural elucidation of novel structures. An interdisciplinary approach is necessary to tackle this problem.

Internationally recognized labs at the University of Vienna distributed over three faculties for Chemistry, Geosciences and Life Sciences consolidate their specific and complementary metabolomics platforms and application fields to build a Vienna Metabolomics Center.


New FWF-Project:"The role of the Symbioprotein Ferritin"

08.10.2020

Stefanie Wienkoops new FWF project wants to unravel the role of Ferritin in nodule formation, symbiosis functioning and priming of drought tolerance.

Climate changes is of major concern worldwide as it result in an average global temperature increase. Heat decreases water availability, leading to longer periods of drought. Hence, an increase of only 1°C can (and is) already significantly impact on global crop production. Since decades, research strategies focus mainly on genetic engineering of molecular markers or screening for cultivars inheriting increased drought tolerance. It has been shown, however, that most of these tolerant genotypes, are often less efficient in growth and yield. Hence there is need to understand the mechanism(s) that enable stress tolerance concurrent with optimal growth performance. A trait, the so called staygreen phenotype, has been shown to be a good marker for drought tolerance. It characterizes a crop that, under drought stress conditions, keeps chlorophyll levels high. This leaf maintenance strategy protects plants from leaf-abscission and allows for a rapid recovery upon rewatering. In recent years, more and more research present evidence that habitat adapted symbioses of plants with soil microbes increases their abiotic stress tolerance while at the same time maintaining growth performance.

We recently demonstrated that the association of legumes with nitrogen fixing soil bacteria induces a staygreen phenotype in drought stressed Medicago plants. Major changes in the leaf proteome of the symbiotic primed plants (“symbioproteome”) involved in stress protection, indicate the complexity of this mechanism. Our current investigations give evidence to the hypothesis that ferritins are strongly involved in this symbiont induced leaf maintenance effect. Ferritins are known as iron storage and mobilization proteins, involved in leaf senescence and drought response. Our unpublished data revealed that ferritin is also crucial for symbiosis formation, which has not been shown thus far and needs further investigation. We therefore propose, iron is not only an important nutrient for plant growth but also crucial for nodule formation, symbiosis functioning and priming of drought tolerance. Understanding the function of Ferritin will enable smart breeding towards improved crop yield and food protection upon water scarceness.

Hence, in this project, we want to understand the mechanism of the ferritin dependent cross talk between nodule development, functioning and drought tolerance. Our approach includes reversed genetics and a comprehensive integration between multiple levels of molecular and physiological phenotyping strategies comparing different genotypes and natural accessions.

New FWF-Project "Functional characterization of TOL proteins in barley"

08.10.2020

Verena Ibls new FWF project aims to produce stress resistant barley cultivars and to help to establish barley as future food grain.

Global warming and its indirect consequences include the lack of food security as it emphasizes suboptimal growth conditions causing tremendous yield losses. Barley (Hordeum vulgare) copes well with the stress factors and carries subsequently the great potential to replace wheat as a staple food. Salinity stress as well as heat stress affect crop productivity leading to a reduced storage compound accumulation in the plant. In addition to biochemical responses to abiotic stress, the endomembrane system, specifically the endosomal sorting complex required for transport (ESCRT) machinery, are strongly affected in response to abiotic stress. Within this project, we will make a step change in our knowledge concerning the function of the (ESCRT-0) TOL proteins. Methods of plant biochemistry, proteomics, cell biology and genome editing will be combined to characterize barley TOL proteins during grain development and germination. A special focus within our approaches will be on #asnearaspossibletonature, 3#drootsystem and 3#sustainability, where first results point to the practicability of our efforts using our invented Lego® #BIBLOX. At the forefront of science, we will create urgently required insights into the function of TOL proteins in barley grain development and germination, with the ultimate aim to produce stress resistant barley cultivars and to help to establish barley as future food grain.

Madeleine Schnurer master defense announcement

23.09.2020

Madeleine will defend her thesis „Effects of heat on the endomembrane system in developing barley endosperm." on Friday, 25.9.2020 at 10:00.

Due to Covid19, the defensio it will be held online per Zoom meeting.

Join Zoom Meeting:

(the link should already work at 9:00).

Meeting ID: 822 6494 3902

 

 

Habilitation Verena Ibl

05.06.2020

Heartfelt congratulations to Dr. Verena Ibl for her recent habilitation!

Dr. Ibls habilitation colloquium on the topic "Cell Biology in Crop Seeds" was held on June 4th.

New Paper: PANOMICS meets germplasm

22.05.2020

How the germplasm can be improved for higher yield and nutrition with the current state of research: Can Green Systems Biology, Multiomics, Genome wide association studies (GWAS), Gene-editing and Speed Breeding help?

Read our recent review to get an answer for these questions.
Here we propose 3 pillars of future breeding strategies.

Read full paper for free at: https://onlinelibrary.wiley.com/doi/10.1111/pbi.13372 

"Pflanzenklänge" - Acoustic Art Installation at the botanical Garden of Vienna, 20.05.2020

13.05.2020

The life processes of plants such as root growth or photosynthesis are invisible to humans. The students of the TransArts class approach these processes with sound installations. These are found on 15 plants in the garden.

The exhibition will be on display from 20th-23th May 2020.

Guided tour by Richard Eigner und Ingeborg Lang:
20th May, 16:30-18:00
Fee: 5€ / Reduced fee: 3 €
Meeting point: Porters cabin at main entrance.

The botanical garden and exhibition can be visited for free.


Botanischer Garten der Universität Wien, Rennweg 14, 1030 Wien,
Open daily 10 - 18h

Entry through main entrance in Mechelgasse.

Newly isolated leaf dwelling symbiont of yam (Dioscorea bulbifera) can increase plant biomass when applied to tomato.

02.05.2020

Johannes B. Herpell and colleagues from the Weckwerth group found that the Betaproteobacterium Paraburkholderia sp. strain Msb3 exhibits significant growth promotion when applied to agriculturally important plants such as tomato, increasing the total dry biomass by up to 40%. The strain was isolated from leaves of the potato yam, Dioscorea bulbifera, with witch it was shown to engage in a stable long term symbiotic relationship.

TPJ Outstanding Paper Awards for Mosys Publication

28.02.2020

Our paper "Resolving subcellular plant metabolism" recently received an Outstanding Paper Awards by The Plant Journal

As of 2017 The Plant Journal initiated annual awards to the most outstanding papers in each of the three categories of articles published in the journal. The papers were voted for by the Editorial Board from a longlist drawn up from download rates, number of citations and 'Altmetric' scores. 

We are happy to announce that one of our papers has been awarded a prize for the RESOURCE ARTICLE CATEGORY first published in TPJ in 2019: "Resolving subcellular plant metabolism" by Lisa Fuertauer, Lisa Kuestner, Wolfram Weckwerth, Arnd G. Heyer and Thomas Naegele. Published in THE PLANT JOURNAL Volume 100, Issue 3, Pages 438-455.

New Project "Water's gateway to heaven"

21.02.2020

Ingeborg Lang is partner in 4-year WWTF project on 3D imaging and modeling of transient stomatal responses in plant leaves under dynamic environments.

Stomata cover less than 5 % of the leaf surface and yet, they facilitate the majority of gas exchange between the atmosphere and terrestrial vegetation. The opening of stomata is adjusted to provide carbon dioxide influx for photosynthesis and to limit water loss. Fluctuating environmental conditions infuence stomata responses and consecutively productivity and water use efficiency in crops and natural ecosystems.

In this project, we apply novel temporal 3D imaging for a better description and mechanistic understanding of stomatal movements. The combination of high resolution microCT, fluorescence microscopy and automated segmentation of images by novel computational methods allows to track stomatal movements from subcellular to whole leaf traits. We will answer long-standing questions on how to improve stomatal responses under changing environments to increase water-use efficiency and net productivity.

Targeting the cancer microenvironment

07.02.2020

In a new study published in Cell Reports the research teams of the system biologist and biochemist Wolfram Weckwerth and the immunologist Thomas Weichhart have found a novel biochemical switch involved in the polarization and proliferation of M2 macrophages. These macrophages play an important role within the immune system and in the prevention of cancer.

Scientific report on nature.com by Ibl group identifies promising targets to be genetically engineered to modulate seed storage protein accumulation

07.02.2020

Read our publication "Protein sorting into protein bodies during barley endosperm development is putatively regulated by cytoskeleton members, MVBs and the HvSNF7s" on www.nature.com/scientificreports

Read full paper for free at nature.com

New Paper "Metal accumulation in the acrocarp moss Atrichum undulatum under controlled conditions"

28.10.2019

- Fully controlled lab conditions confirm that first rain brings most contaminants.

- Weather and season are crucial in wet adsorption of metals in A. undulatum.

- Metal uptake in A. undulatum also occurs via substrate.

- Metals were not washed out, pointing to active binding to moss tissue.

- Metal sensitivity in A. undulatum depends on metal type and plant tissue.

School students visit Mosys

26.08.2019

A group of 16 year old students from BRG Wenzgasse enjoyed a trip to our department during their elective biology course.

 

After watching a presentation on GM technology by Verena Ibl, the students visited our mass spectrometry lab, greenhouse and gardens. As a last point the pupils watched students of biology carryout some experiments in plant physiology and present their outcome.

Both the visiting students and our department members enjoyed this event, which was organized by Julian Preiner.

New Paper "Toward a Unification of System-Theoretical Principles in Biology and Ecology"

07.08.2019

Theoretical Principles in Biology and Ecology—The Stochastic Lyapunov Matrix Equation and Its Inverse Application

Read full paper for free on Frontiers

The data matrix and the stochastic Lyapunov matrix equation are directly associated by multivariate properties of the system. This applies to any complex network or system and even to model predictive control of artificial intelligence systems. MIMO, multiple input multiple output.

Combination of Fasting and Metformin Impairs Tumor Growth

08.05.2019

Tumor growth can be prohibited with the right combination of fasting-induced hypoglycemia and metformin treatment. This was shown in a recent paper by Elgendy, Minucci and colleagues in collaboration with the Vienna Metabolomics Center.

In mice exposed to 24-h feeding/fasting cycles, metformin impaired tumor growth, but only when administered during fasting-induced hypoglycemia.

Synergistic anti-neoplastic effects of the metformin/hypoglycemia combination were mediated by glycogen synthase kinase 3β (GSK3β) activation downstream of PP2A, leading to a decline in the pro-survival protein MCL-1, and cell death. Mechanistically, specific activation of the PP2A-GSK3β axis was the sum of metformin-induced inhibition of CIP2A, a PP2A suppressor, and of upregulation of the PP2A regulatory subunit B56δ by low glucose, leading to an active PP2A-B56δ complex with high affinity toward GSK3β.

Get access to this paper on cell.com

Young Investigator Award to Palak Chaturvedi - Congratulations, Palak!

05.04.2019

Palak Chaturvedi receives Young Investigator Awards 2019 from University of Vienna.

The Young Investigator Award is an initiative of the Faculty of Life Sciences designed to honour young postdoctoral scientists publishing in the top journals of their field. Award recipients are selected based on their high-quality publication output.

Palak Chaturvedi has a keen interest to decipher physiological and biochemical regulation for growth and functioning of crop plants subjected to abiotic stresses including drought, heat and cold. The specific attention is given to the crop vegetative and reproductive (Male gametophyte development) physiology using high throughput multi-OMICS approaches.

(Group: Crops in a changing climate environment).

Open master thesis - research CAM photosynthesis in Costa Rica and Vienna

22.02.2019

We are looking for a master student doing system-level investigation of CAM photosynthesis both in the Costa Rica rainforest and in our lab in Vienna.

Due to global climate change the different plant photosynthesis types C3, C4 and CAM will be of utmost importance in balancing net primary as well as global food production with all its subsequent consequences on the human society.

Typical C3 crop plants are wheat, rice and potato, C4 are maize and millet, and CAM are typical tropical crop plants such as ananas. For all of them genome sequences are available and enable a system-level analysis of the different types of photosynthesis.

The only so far known tree showing CAM-type photosynthesis is restricted to Clusia species. Knowledge here is very limited, especially the system-level understanding of this highly plastic plant able to switch from C3 to CAM. The student will work on different Clusia species in the field (research field station La Gamba) and with a large collection of different ecotypes in the lab.

For more information, please, contact wolfram.weckwerth@univie.ac.at

Aerial roots of epiphytic Clusia in the tropical rain forest.

Ecosystem responses to climate change: Sedge adaptions to warmth

28.01.2019

The paper "Plastic and genetic responses of a common sedge to warming have contrasting effects on carbon cycle processes" demonstrates the capacity for plant evolution to impact ecosystem processes, and reveal a further mechanism through which plants will shape ecosystem responses to climate change.

Read full publication on Wiley Online.

Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis

28.01.2019

Using chemical imaging, we demonstrate that the Legume‐rhizobia bacteroids take up 20‐fold more sulfate than the nodule host cells. Furthermore, we show that nitrogenase biosynthesis relies on high levels of imported sulfate, making sulfur as essential as carbon for the regulation and functioning of symbiotic nitrogen fixation. Our findings establish the importance of sulfate and its active transport for the plant‐microbe interaction that is most relevant for agriculture and soil fertility.

Read full publication on Wiley online.

First combined Chlamydomonas proteomics and phosphoproteomics dataset in response to TOR inhibition

28.01.2019

In our study "Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii" we are using multivariate statistics to highlight the impact of TOR inhibition on both the proteome and the phosphoproteome.

Read full publication on Frontiers.

"10 Years Mosys" Lab Retreat

02.10.2018

During a three-day retreat at Rax mountain, we celebrated the 10th aniversary of Mosys.

 

PIs and group members presented an exciting variety of projects and outlooks.

Stefanie Wienkoop elected INPPO Vice President

21.09.2018

The International Plant Proteomics Organization (INPPO) elected Stefanie Wienkoop as new Vice President during this years Conference in Padova. Sebastian Schneider won the second poster price. Congratulations!

INPPO works to

  • Develop and intensify cooperation in the field of plant proteomics around the globe.
  • Bridge the gap between academy and industry.
  • Establish centralized databases at several locations (Americas, Europe, Asia-Pacific and Australia).
  • Organize workshops at national and international levels.
  • Bring proteomics to every laboratory working on plants around the globe.
  • Aim to outreach to the younger generation students at the school, college and university levels.
  • Help translate the proteomics knowledge into biology and vice versa.

Award for Best Poster to Julian Preiner

14.09.2018

Julian Preiner received the award for best poster at the Austrian Proteomics and Metabolomics Research Symposium APMRS 2018.

Julian is a PhD student in the Plant Systems Interaction Group (Wienkoop group) and presented his latest work on tungsten stress in legumes titled: Tungsten (W) leads to a disruption of C/N-metabolic processes in Glycine max–modified stress response through rhizobia symbiosis?

Read Abstract

APMRS 2018 in Vienna from August 29 - 31, 2018

10.09.2018

The Symposium "Building blocks of Life – from Metabolomics and Proteomics to Systems Biology" was jointly organized by The University of Vienna, Medical University of Vienna and the Austrian Academy of Sciences.

We welcomed, among our keynote speakers Hannelore Daniel, Edda Klipp, Karsten Kristiansen, Steffen Neumann and Paul Wilmes.

During our three day long conference at Syklounge Vienna, the discussed topics included

  • Human Microbiome
  • Genomics, Proteomics and Metabolomics
  • Cancer and Signal transduction
  • Health and Nutrition
  • Exposomics and Biomonitoring
  • Genome-scale Metabolic Modelling
  • Computational Mass Spectrometry
  • Innate Immune System
  • Eco-Systems Biology

Climate change and Green System Biology: Interview

10.09.2018

"How can we save our climate" asks the University of Vienna this semester. Wolfram Weckwerth gives an insight on the role which plants and Green System Biology play in this challenge.

Professorship for Thomas Nägele at LMU Munich

10.09.2018

 

 

The Ludwig-Maximilians-University Munich has appointed Dr. Nägele as professor for Evolutionary Cell Biology of Plants.

 

Congratulations, Thomas!

 

ICRISAT and VIME partner in drought tolerance research for staple food crops using systems biology approaches

10.09.2018

ICRISAT will partner the Vienna Metabolomics Center, University of Vienna, to study drought tolerance in chickpea and analyze the two-line hybrid system and epigenomics for hybrids in pigeonpea.

Agricultural and medical researchers and doctors from around the world came together from March 22 – 24, 2018, at ICRISAT to brainstorm on the connect with between microbiomes of the gut and the soil. This workshop on systems biology for human and plant nutrition aimed to elucidate the workings of microorganisms in the human body; the microbial connection between gut and brain/immune system/obesity as well as the factors influencing them (diet, genetics, environment). Experts from Ghana, India, Senegal, Mali and The Gambia presented their respective countries’ nutrition reports, highlighting the need for urgent interventions to improve nutrition. The role of plant/soil microbiomes – especially that of legumes in immune response and other physiological functions – was discussed in detail.

During the workshops, plans for joint research of ICRISAT and the Vienna Metabolomics Center were disclosed. The aim is to study drought tolerance in chickpea and analyze the two-line hybrid system and epigenomics for hybrids in pigeonpea. This study will use models to predict higher-order relationships between molecular phenotypes, interactions among each other and subsequent influence on complex traits.

www.icrisat.org/new-seeds-sown-for-systems-biology-research-at-icrisat/

Benchtop Fractionisation Method for Subcellular Metabolomics

10.09.2018

New fractionation technique for assigning metabolites to their subcellular localization developed by L. Fürtauer, W. Weckwerth and T. Nägele.

Although compartmentation is a key feature of eukaryotic cells, biological research is frequently limited by methods allowing for the comprehensive subcellular resolution of the metabolome. It has been widely accepted that such a resolution would be necessary in order to approximate cellular biochemistry and metabolic regulation, yet technical challenges still limit both the reproducible subcellular fractionation and the sample throughput being necessary for a statistically robust analysis. We present a method and a detailed protocol which is based on the non-aqueous fractionation technique enabling the assignment of metabolites to their subcellular localization.

⇒ Full Article on Frontiers

⇒ Editorial in "Laborjournal online"

Pearl millet: genome sequence published

10.09.2018

An international consortium with participation of MOSYS team members Palak Chaturvedi, Arindam Ghatak and Wolfram Weckwerth has published the genome sequence of drought- and heat-tolerant Pearl millet. The MOSYS team further developed a molecular-physiological model to explain drought and heat tolerance.

Pearl millet resists temperatures up to 42°C, unlike wheat, rice or corn. The resilient plant will be especially important in the era of global climate change. But how is this dryland cereal able to survive soaring temperatures and exceptional drought?

Wolfram Weckwerth explains: "Plant diversity and adaptation to different climatic conditions—especially important in the era of global climate change—is synonymous for the concept of natural and genetic diversity. Research tackling this natural genetic variation and the corresponding biodiversity provides one of the largest treasures of mankind.

Exactly this genetic variation of plant families, plant genera and even within one plant species is the key to cope with global climate change and dramatic consequences for agriculture.

For the purpose of sustainable research, breeding and protecting genetic diversity especially of crop plants many public non-profit research organization have formed under the umbrella of CGIAR and are active in research and building non-profit biobanks. ICRISAT, coordinator of the pearl millet genome sequencing studies, is the Indian pendant of the famous CIMMYT which started in the 60-70ies to distribute disease resistant and high yield wheat varieties under the poor farmers in the developing countries."

He further says, "the first steps to elucidate molecular mechanisms in any organism from plants to animals to microbes is to sequence and analyze their genome, proteome and metabolome. Subsequently, we draw hypotheses from these data by integration, modelling and functional interpretation.

Based on our studies we developed first molecular-physiological hypotheses to explain drought and heat tolerance of this plant. This will have a strong impact in understanding and improving plant productivity in changing climate in the next decades."

Press releases

Publication in "Nature Biotechnology"

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology, 2017; DOI: 10.1038/nbt.3943

Molecular Systems Biology University of Vienna

10.09.2018