Seven FWF Principal Investigator Projects Grants awarded to Vienna BioCenter Researchers

Martin Leeb
Functional Gene Networks in Naïve and Formative Pluripotency

Mammalian embryo development relies on precise gene regulation to establish and maintain cell identities. Pluripotent cells transition from a naïve to a formative state before committing to specific lineages, but the molecular mechanisms behind these shifts remain unclear. A newly funded project led by Perutz group leader Martin Leeb aims to map the gene regulatory networks governing these transitions using CRISPR-based functional genomics and computational approaches. 

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Martin Leeb - Functional Gene Networks in Naïve and Formative Pluripotency 

Gerhard Herndl (Department of Functional and Evolutionary Ecology)              
The microbiome in the life cycle of jellyfish blooms

Gerhard Herndl's FWF project "The microbiome in the life cycle of jellyfish blooms" investigates the role of the microbiome in the life cycle and collapse of jellyfish blooms, which are increasing due to human impact and climate change. These blooms can collapse abruptly, causing major disruption to the ecosystem and its services, but the mechanisms behind these 'boom and bust' population dynamics remain unknown. 

The researchers hypothesise that microbiota influence bloom dynamics, with variations based on host environmental and physiological factors. Using an integrated transdisciplinary approach with field sampling, they will analyse bacteria, fungi and viruses at different bloom stages. The in situ survey will be coupled with manipulation experiments under controlled laboratory conditions to provide additional insights. This innovative study will create the first open-access jellyfish microbiome database to help predict and mitigate bloom-related ecological disturbances.

Oleg Simakov (Department of Neurosciences and Developmental Biology)
Genome topology and gene regulation in cephalopod neurons
 

Oleg Simakovs’s FWF project “Genome topology and gene regulation in cephalopod neurons” explores how genome topology influences brain cell type diversity in cephalopods, which have evolved advanced cognition and complex nervous systems independently of vertebrates. By combining expertise from three research teams, the study aims to uncover how genome organization impacts neural subtype differentiation in octopuses, squids, and cuttlefish.

Using comparative genomics and gene expression analysis, researchers will investigate the role of key transcription factors in creating neural cell diversity, revealing whether core molecular mechanisms of brain expansion are conserved or innovative. This interdisciplinary effort is the first to address complex gene regulation in cephalopod neurodevelopment, leveraging expertise in brain development, gene regulation, and genome evolution.

Ron Pinhasi (Department of Evolutionary Anthropology) 
Geochemical ENhancEment of Ancient DNA from SedImentS

Ron Pinhasi's FWF project “Geochemical Enhancement of Ancient DNA from Sediments” at the Department of Evolutionary Anthropology, aims to improve the recovery of ancient DNA (aDNA) from archaeological sediments. While paleogenomics has demonstrated that sedaDNA can reveal long-term population dynamics and migrations, challenges remain due to low DNA yields and the need to efficiently process large sample volumes.

To address these issues, the project will develop a sediment density separation protocol, an inhibition assay to determine the degree of inhibition caused by co-extracted substances and optimised sediment disaggregation techniques. The researchers will analyse Upper Paleolithic sediments from Satsurblia Cave (Georgia) and El Mirón (Spain), integrating DNA results with geochemical analyses. By combining paleogenomics and geochemistry, this innovative approach aims to refine extraction protocols, increase aDNA yields, minimise modern DNA contamination and deepen our understanding of the interactions between DNA and mineral surfaces.

Wouter Masselink (Tanaka Lab)
Mechanical principles of vertebrae regeneration

In the newly funded project, Wouter Masselink will investigate the mechanical principles involved in the regeneration of vertebrae. The vertebral column is a segmented structure crucial for supporting the vertebrate body and for allowing the body to move. In the axolotl, a salamander species with remarkable abilities to regenerate, the vertebral column can regenerate after localized injuries or when the axolotl loses its tail. This regenerative capacity makes the axolotl an ideal model for investigating both how vertebrae regenerate after injury and for understanding the formation and patterning of vertebrae. 

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Wouter Masselink - Mechanical principles of vertebrae regeneration

Daniela Pollak (Head of comparative medicine of IMBA and IMP)
Encoding gestational immune activation in the female brain

With the stand-alone grant from the FWF, Daniela Pollak will study how the activation of the immune system during pregnancy impacts the female brain and influences maternal behavior in mice. Her research will focus on understanding how immune responses alters brain circuits and the molecular pathways that control maternal care. Using advanced genetic approaches, she will monitor brain activity in response to immune activation during pregnancy. Pollak will also use single-cell analysis to understand the molecular changes at play at the individual cell level. The project aims to show how immune activation during pregnancy affects the brain’s ability to prepare for parenting, with potential insights into how infections, including COVID-19, could impact long-term maternal behaviour.

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Daniela Pollak - Encoding gestational immune activation in the female brain

Diego Rodriguez Terrones (Tanka Lab)
Transposable elements at the water to land transition

In his newly funded project, Diego Rodriguez-Terrones will investigate how transposable elements – jumping genes that move and reinsert themselves within the host’s DNA – contributed to the biological innovations that enabled animals to transition from the sea to living on land. These biological innovations, which occurred over 360 million years ago, included the transformation of fins into limbs, the development of a third heart chamber to facilitate blood flow to the lungs, and the evolution of the tongue for swallowing outside the water. 

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Diego Rodriguez Terrones - Transposable elements at the water to land transition