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196 results match your criteria: "Kavli institute of nanoscience Delft[Affiliation]"
Front Neurosci
December 2024
Department of Quantum Nanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands.
Neuronal activity in the highly organized networks of the central nervous system is the vital basis for various functional processes, such as perception, motor control, and cognition. Understanding interneuronal connectivity and how activity is regulated in the neuronal circuits is crucial for interpreting how the brain works. Multi-electrode arrays (MEAs) are particularly useful for studying the dynamics of neuronal network activity and their development as they allow for real-time, high-throughput measurements of neural activity.
View Article and Find Full Text PDFACS Appl Mater Interfaces
December 2024
dsm-firmenich Science & Research, Biotechnology, Alexander Fleminglaan 1, Delft 2613 AX, The Netherlands.
The biofabrication of recombinant structural proteins with a range of mechanical or structural features usually relies on the generation of protein libraries displaying variations in terms of amino acid composition, block structure, molecular weight, or physical/chemical cross-linking sites. This approach, while highly successful in generating a wealth of knowledge regarding the links between design features and material properties, has some inherent limitations related to its low throughput. This slows down the pace of the development of recombinant structural proteins.
View Article and Find Full Text PDFSci Adv
December 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2629HZ, Netherlands.
Eukaryotes carry three types of structural maintenance of chromosome (SMC) protein complexes, condensin, cohesin, and SMC5/6, which are ATP-dependent motor proteins that remodel the genome via DNA loop extrusion (LE). SMCs modulate DNA supercoiling but remains incompletely understood how this is achieved. Using a single-molecule magnetic tweezers assay that directly measures how much twist is induced by individual SMCs in each LE step, we demonstrate that all three SMC complexes induce the same large negative twist (i.
View Article and Find Full Text PDFNano Lett
December 2024
Quantum Engineering Laboratory, Department of Electrical and Systems Engineering, University of Pennsylvania, 200 S. 33rd St., Philadelphia, Pennsylvania 19104, United States.
Nuclear quadrupolar resonance (NQR) spectroscopy reveals chemical bonding patterns in materials and molecules through the unique coupling between nuclear spins and local fields. However, traditional NQR techniques require macroscopic ensembles of nuclei to yield a detectable signal, which obscures molecule-to-molecule variations. Solid-state spin qubits, such as the nitrogen-vacancy (NV) center in diamond, facilitate the detection and control of individual nuclei through their local magnetic couplings.
View Article and Find Full Text PDFNucleic Acids Res
November 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Massweg 9, 2629HZ Delft, Netherlands.
The ParABS system plays a critical role in bacterial chromosome segregation. The key component of this system, ParB, loads and spreads along DNA to form a local protein-DNA condensate known as a partition complex. As bacterial chromosomes are heavily supercoiled due to the continuous action of RNA polymerases, topoisomerases and nucleoid-associated proteins, it is important to study the impact of DNA supercoiling on the ParB-DNA partition complex formation.
View Article and Find Full Text PDFACS Nano
October 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2629 HZ, The Netherlands.
Development
September 2024
Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, Utrecht 3584, The Netherlands.
The intricate dynamics of Hes expression across diverse cell types in the developing vertebrate embryonic tail have remained elusive. To address this, we have developed an endogenously tagged Hes1-Achilles mouse line, enabling precise quantification of dynamics at the single-cell resolution across various tissues. Our findings reveal striking disparities in Hes1 dynamics between presomitic mesoderm (PSM) and preneural tube (pre-NT) cells.
View Article and Find Full Text PDFNat Commun
August 2024
Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany.
Nucleic Acids Res
August 2024
Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
BRCA2 is an essential tumor suppressor protein involved in promoting faithful repair of DNA lesions. The activity of BRCA2 needs to be tuned precisely to be active when and where it is needed. Here, we quantified the spatio-temporal dynamics of BRCA2 in living cells using aberration-corrected multifocal microscopy (acMFM).
View Article and Find Full Text PDFBiophys Rev (Melville)
June 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands.
Cell migration is a fundamental process for life and is highly dependent on the dynamical and mechanical properties of the cytoskeleton. Intensive physical and biochemical crosstalk among actin, microtubules, and intermediate filaments ensures their coordination to facilitate and enable migration. In this review, we discuss the different mechanical aspects that govern cell migration and provide, for each mechanical aspect, a novel perspective by juxtaposing two complementary approaches to the biophysical study of cytoskeletal crosstalk: live-cell studies (often referred to as top-down studies) and cell-free studies (often referred to as bottom-up studies).
View Article and Find Full Text PDFbioRxiv
May 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
Peptide phytohormones are decorated with post-translational modifications (PTMs) that are crucial for receptor recognition. Tyrosine sulfation on these hormones is essential for plant growth and development1. Measuring the occurrence and position of sulfotyrosine is, however, compromised by major technical challenges during isolation and detection2.
View Article and Find Full Text PDFNat Commun
April 2024
NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
Nat Commun
April 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, van der Maasweg 9, Delft, the Netherlands.
Neuronal network formation is facilitated by recognition between synaptic cell adhesion molecules at the cell surface. Alternative splicing of cell adhesion molecules provides additional specificity in forming neuronal connections. For the teneurin family of cell adhesion molecules, alternative splicing of the EGF-repeats and NHL domain controls synaptic protein-protein interactions.
View Article and Find Full Text PDFNat Commun
April 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands.
Nat Commun
March 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands.
Bacterial chromosomes are folded into tightly regulated three-dimensional structures to ensure proper transcription, replication, and segregation of the genetic information. Direct visualization of chromosomal shape within bacterial cells is hampered by cell-wall confinement and the optical diffraction limit. Here, we combine cell-shape manipulation strategies, high-resolution fluorescence microscopy techniques, and genetic engineering to visualize the shape of unconfined bacterial chromosome in real-time in live Bacillus subtilis cells that are expanded in volume.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
March 2024
Van 't Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam 1090 GD, The Netherlands.
Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H[Formula: see text]O/D[Formula: see text]O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H[Formula: see text]O and D[Formula: see text]O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers.
View Article and Find Full Text PDFNat Commun
March 2024
QuTech, Delft University of Technology, PO Box 5046, 2600, GA Delft, The Netherlands.
Spins associated to optically accessible solid-state defects have emerged as a versatile platform for exploring quantum simulation, quantum sensing and quantum communication. Pioneering experiments have shown the sensing, imaging, and control of multiple nuclear spins surrounding a single electron spin defect. However, the accessible size of these spin networks has been constrained by the spectral resolution of current methods.
View Article and Find Full Text PDFJ Cell Sci
March 2024
Department of Physiology and Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, T6G 2S2, Canada.
In this Perspective, Journal of Cell Science invited researchers working on cell and tissue polarity to share their thoughts on unique, emerging or open questions relating to their field. The goal of this article is to feature 'voices' from scientists around the world and at various career stages, to bring attention to innovative and thought-provoking topics of interest to the cell biology community. These voices discuss intriguing questions that consider polarity across scales, evolution, development and disease.
View Article and Find Full Text PDFNanoscale
February 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
Nat Commun
January 2024
Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany.
It is estimated that two-thirds of all proteins in higher organisms are composed of multiple domains, many of them containing discontinuous folds. However, to date, most in vitro protein folding studies have focused on small, single-domain proteins. As a model system for a two-domain discontinuous protein, we study the unfolding/refolding of a slow-folding double mutant of the maltose binding protein (DM-MBP) using single-molecule two- and three-color Förster Resonance Energy Transfer experiments.
View Article and Find Full Text PDFACS Photonics
December 2023
4-th Physics Institute and Research Center SCoPE, University of Stuttgart, 70569 Stuttgart, Germany.
The creation and manipulation of optical vortices, both in free space and in two-dimensional systems such as surface plasmon polaritons (SPPs), has attracted widespread attention in nano-optics due to their robust topological structure. Coupled with strong spatial confinement in the case of SPPs, these plasmonic vortices and their underlying orbital angular momentum (OAM) have promise in novel light-matter interactions on the nanoscale with applications ranging from on-chip particle manipulation to tailored control of plasmonic quasiparticles. Until now, predominantly integer OAM values have been investigated.
View Article and Find Full Text PDFFEMS Microbiol Rev
January 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology; Van der Maasweg 9, Delft, the Netherlands.
Bacterial cells require DNA segregation machinery to properly distribute a genome to both daughter cells upon division. The most common system involved in chromosome and plasmid segregation in bacteria is the ParABS system. A core protein of this system - partition protein B (ParB) - regulates chromosome organization and chromosome segregation during the bacterial cell cycle.
View Article and Find Full Text PDFNucleic Acids Res
February 2024
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands.
Transcription-coupled supercoiling of DNA is a key factor in chromosome compaction and the regulation of genetic processes in all domains of life. It has become common knowledge that, during transcription, the DNA-dependent RNA polymerase (RNAP) induces positive supercoiling ahead of it (downstream) and negative supercoils in its wake (upstream), as rotation of RNAP around the DNA axis upon tracking its helical groove gets constrained due to drag on its RNA transcript. Here, we experimentally validate this so-called twin-supercoiled-domain model with in vitro real-time visualization at the single-molecule scale.
View Article and Find Full Text PDFNat Commun
November 2023
Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Protein misfolding and aggregation play central roles in the pathogenesis of various neurodegenerative diseases (NDDs), including Huntington's disease, which is caused by a genetic mutation in exon 1 of the Huntingtin protein (Httex1). The fluorescent labels commonly used to visualize and monitor the dynamics of protein expression have been shown to alter the biophysical properties of proteins and the final ultrastructure, composition, and toxic properties of the formed aggregates. To overcome this limitation, we present a method for label-free identification of NDD-associated aggregates (LINA).
View Article and Find Full Text PDFScience
November 2023
Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands.
A potential mechanism of DNA loop extrusion by molecular motors is discussed.
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