Biology subjects

van Genderen, E.

Publications and source records attributed to van Genderen, E..

4 recordsLinked to original sources

bioRxiv2026

Replacing H2O with D2O in cryo-EM reduces radiation damage in biological samples

Radiation damage limits the resolution achievable in electron microscopy of biological specimens. Hydrogen is the most abundant atom in these specimens, and its low mass maximizes the recoil energy it receives from incident electrons, making it the atom most readily lost under the beam. Substitution of hydrogen by deuterium halves this recoil energy and makes the bonds involved slightly harder to break, yet its protective effect on vitrified protein crystals has not been tested. Using cryogenic electron diffraction at 200 kV, we show that hen egg-white lysozyme crystals grown directly in D2O withstand a dose 1.7 times higher than crystals grown in H2O before their Bragg intensity at 10-7[A] falls to 1/e (13.2 {+/-} 1.0 against 7.7 {+/-} 0.4 e-/[A]2), with every D2O-grown crystal outlasting every H2O-grown crystal. The protection is achieved with deuteration confined mainly to the solvent and the exchangeable hydrogens at the protein surface, which form the hydrogen bonds that hold the crystal lattice together. The protein itself need not be deuterated by expression in deuterated media. Direct crystallization in D2O involves only a single substitution in the mother liquor and offers an accessible strategy to extend the usable dose in electron diffraction of protein crystals.

biophysics↗

bioRxiv2025

Feeder-free culture of naive human pluripotent stem cells retaining embryonic, extraembryonic and blastoid generation potential

Conventional human pluripotent stem cells (hPSCs) are widely used to study early embryonic development, generate somatic cells, and model diseases, with differentiation potential aligned to a post-implantation epiblast identity. In the past decade, naive hPSCs, representing a pre-implantation stage, have been derived. Naive hPSCs efficiently differentiate towards embryonic and extraembryonic lineages such as trophectoderm, primitive endoderm, and extraembryonic mesoderm, and also self-organize into blastocyst-like structures called blastoids. However, their culture typically relies on mouse embryonic fibroblasts (MEFs), which are variable, resource-intensive, and can confound analyses. We report the long-term maintenance of naive hPSCs in a feeder-free, serum-coated system. We successfully expanded for up to 25 passages 8 different naive hPSCs lines across 5 laboratories. Growth rate, clonogenicity, and gene expression profiles on serum coating were comparable to MEF-based cultures, but serum coating eliminated fibroblast contamination. Naive hPSCs cultured on serum exhibited more efficient germ layer specification, retained trophectoderm potential and high blastoid formation efficiency. Exome sequencing revealed fewer mutations in serum-cultured cells, and mass spectrometry identified extracellular matrix proteins such as vitronectin, fibronectin, and collagens in the serum coating. Overall, serum coating offers a scalable, cost-effective and therefore widely applicable alternative for naive hPSC culture, maintaining developmental potential, reducing DNA mutations, and eliminating MEF-related confounding factors. We believe serum coating will expand the use of naive hPSCs to large-scale studies and facilitate the investigation of mechanistic insights into developmental and disease modelling.

cell biology↗

bioRxiv2021

Epiblast morphogenesis is controlled by selective mRNA decay triggered by LIN28A relocation

The embryonic progression from naive to primed pluripotency is accompanied by the rapid decay of pluripotency-associated mRNAs and a concomitant radical morphogenetic sequence of epiblast polarization, rosette formation and lumenogenesis. The mechanisms triggering and linking these events remain poorly understood. Guided by machine learning and metabolic RNA sequencing, we identified RNA binding proteins (RBPs), especially LIN28A, as primary mRNA decay factors. Using mRNA-RBP interactome capture, we revealed a dramatic increase in LIN28A mRNA binding during the naive-rosette-primed pluripotency transition, driven by its nucleolar-to-cytoplasmic translocation. Cytoplasmic LIN28A binds to 3UTRs of pluripotency-associated mRNAs to directly stimulate their decay and drive lumenogenesis. Accordingly, forced nuclear retention of LIN28A impeded lumenogenesis, impaired gastrulation, and caused an unforeseen embryonic multiplication. Selective mRNA decay, driven by nucleo-cytoplasmic RBP translocation, therefore acts as an intrinsic mechanism linking cell identity switches to the control of embryonic growth and morphogenesis.

developmental biology↗

bioRxiv2020

A lipocalin mediates unidirectional haem biomineralization in malaria parasites

During blood stage development, malaria parasites are challenged with the detoxification of enormous amounts of haem released during the proteolytic catabolism of erythrocytic haemoglobin. They tackle this problem by sequestering haem into bioinert crystals known as haemozoin. The mechanisms underlying this biomineralization process remain enigmatic. Here, we demonstrate that both rodent and human malaria parasite species secrete and internalize a lipocalin-like protein, PV5, to control haem crystallization. Transcriptional deregulation of PV5 in the rodent parasite Plasmodium berghei results in inordinate elongation of haemozoin crystals, while conditional PV5 inactivation in the human malaria agent Plasmodium falciparum causes excessive multi-directional crystal branching. Although haemoglobin processing remains unaffected, PV5-deficient parasites generate less haemozoin. Electron diffraction analysis indicates that despite the distinct changes in crystal morphology neither the crystalline order nor unit cell of haemozoin are affected by impaired PV5 function. Deregulation of PV5 expression renders P. berghei hypersensitive to the antimalarial drugs artesunate, chloroquine, and atovaquone, resulting in accelerated parasite clearance following drug treatment in vivo. Together, our findings demonstrate the Plasmodium-tailored role of a lipocalin family member in haemozoin formation and underscore the haem biomineralization pathway as an attractive target for therapeutic exploitation. SIGNIFICANCEDuring blood stage development, the malaria parasite replicates inside erythrocytes of the vertebrate host, where it engulfs and digests most of the available haemoglobin. This results in release of the oxygen-binding prosthetic group haem, which is highly toxic in its unbound form. The parasite crystallizes the haem into an insoluble pigment called haemozoin, a process that is vital for parasite survival and which is exploited in antimalarial therapy. We demonstrate that the parasite uses a protein called PV5 in haemozoin formation and that interfering with PV5 expression can increase the parasites sensitivity to antimalarial drugs during blood infection. An improved understanding of the mechanisms underlying haem sequestration will provide valuable insights for future drug development efforts.

microbiology↗