Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Geometrical frustration of phase-separated domains in Coscinodiscus diatom frustules.

ABSTRACT: Diatoms are single-celled organisms with a cell wall made of silica, called the frustule. Even though their elaborate patterns have fascinated scientists for years, little is known about the biological and physical mechanisms underlying their organization. In this work, we take a top-down approach and examine the micrometer-scale organization of diatoms from the Coscinodiscus family. We find two competing tendencies of organization, which appear to be controlled by distinct biological pathways. On one hand, micrometer-scale pores organize locally on a triangular lattice. On the other hand, lattice vectors tend to point globally toward a center of symmetry. This competition results in a frustrated triangular lattice, populated with geometrically necessary defects whose density increases near the center.

SUBMITTER: Feofilova M

PROVIDER: S-EPMC9351504 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Geometrical frustration of phase-separated domains in <i>Coscinodiscus</i> diatom frustules.

Feofilova Maria M Schüepp Silvan S Schmid Roman R Hacker Florian F Spanke Hendrik T HT Bain Nicolas N Jensen Katharine E KE Dufresne Eric R ER

Proceedings of the National Academy of Sciences of the United States of America 20220729 31

Diatoms are single-celled organisms with a cell wall made of silica, called the frustule. Even though their elaborate patterns have fascinated scientists for years, little is known about the biological and physical mechanisms underlying their organization. In this work, we take a top-down approach and examine the micrometer-scale organization of diatoms from the Coscinodiscus family. We find two competing tendencies of organization, which appear to be controlled by distinct biological pathways. ...[more]

PMID: 35905319

Similar Datasets

Diatom frustules protect DNA from ultraviolet light.

Project description:The evolutionary causes for generation of nano and microstructured silica by photosynthetic algae are not yet deciphered. Diatoms are single photosynthetic algal cells populating the oceans and waters around the globe. They generate a considerable fraction (20-30%) of all oxygen from photosynthesis, and 45% of total primary production of organic material in the sea. There are more than 100,000 species of diatoms, classified by the shape of the glass cage in which they live, and which they build during algal growth. These glass structures have accumulated for the last 100 million of years, and left rich deposits of nano/microstructured silicon oxide in the form of diatomaceous earth around the globe. Here we show that reflection of ultraviolet light by nanostructured silica can protect the deoxyribonucleic acid (DNA) in the algal cells, and that this may be an evolutionary cause for the formation of glass cages.

| S-EPMC5865130 | biostudies-literature

Tunable geometrical frustration in magnonic vortex crystals.

Project description:A novel approach to investigate geometrical frustration is introduced using two-dimensional magnonic vortex crystals. The frustration of the crystal can be manipulated and turned on and off dynamically on the timescale of milliseconds. The vortices are studied using scanning transmission x-ray microscopy and ferromagnetic resonance spectroscopy. They are arranged analogous to the nanomagnets in artificial spin-ice systems. The polarization state of the vortices is tuned in a way that geometrical frustration arises. We demonstrate that frustrated polarization states and non-frustrated states can be tuned to the crystal by changing the frequency of the state formation process.

| S-EPMC5760707 | biostudies-literature

Geometrical frustration yields fiber formation in self-assembly.

Project description:Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales [1, 2]. Nevertheless, even particles without optimized shapes can robustly form well-defined morphologies. This is the case in numerous medical conditions where normally soluble proteins aggregate into fibers [3, 4]. Beyond the diversity of molecular mechanisms involved [5, 6], we propose that fibers generically arise from the aggregation of irregular particles with short-range interactions. Using a minimal model of ill-fitting, sticky particles, we demonstrate robust fiber formation for a variety of particle shapes and aggregation conditions. Geometrical frustration plays a crucial role in this process, and accounts for the range of parameters in which fibers form as well as for their metastable character.

| S-EPMC5669487 | biostudies-literature

Silica from diatom frustules as anode material for Li-ion batteries.

Project description:In spite of its insulating nature, SiO2 may be utilized as active anode material for Li-ion batteries. Synthetic SiO2 will typically require sophisticated synthesis and/or activation procedures in order to obtain a satisfactory performance. Here, we report on diatom frustules as active anode material without the need for extensive activation procedures. These are composed primarily of silica, exhibiting sophisticated porous structures. Various means of optimizing the performance were investigated. These included carbon coating, the addition of fluoroethylene carbonate (FEC) and vinylene carbonate (VC) to the carbonate-based electrolyte, as well as activation by an initial potentiostatic hold step. The highest capacity (723 mA h g-1) was obtained with composite electrodes with pristine diatom frustules and conventional carbon black as additive, with the capacity still increasing after 50 cycles. The capacity was around 624 mA h g-1 after subtraction of the contributions from the carbon black. Carbon coated diatom frustules showed a slightly lower but stable capacity after 50 cycles (600 mA h g-1 after subtraction of contributions from the carbon coating and the carbon black). By the use of electrochemical characterization methods, as well as post-mortem studies, differences in reaction mechanisms could be identified and attributed to the operating and processing parameters.

| S-EPMC9076370 | biostudies-literature

Fabrication of a Floatable Micron-Sized Enzyme Device Using Diatom Frustules

Project description:Immobilization of

| S-EPMC10268610 | biostudies-literature

Characteristic signatures of quantum criticality driven by geometrical frustration.

Project description:Geometrical frustration describes situations where interactions are incompatible with the lattice geometry and stabilizes exotic phases such as spin liquids. Whether geometrical frustration of magnetic interactions in metals can induce unconventional quantum critical points is an active area of research. We focus on the hexagonal heavy fermion metal CeRhSn, where the Kondo ions are located on distorted kagome planes stacked along the c axis. Low-temperature specific heat, thermal expansion, and magnetic Grüneisen parameter measurements prove a zero-field quantum critical point. The linear thermal expansion, which measures the initial uniaxial pressure derivative of the entropy, displays a striking anisotropy. Critical and noncritical behaviors along and perpendicular to the kagome planes, respectively, prove that quantum criticality is driven be geometrical frustration. We also discovered a spin flop-type metamagnetic crossover. This excludes an itinerant scenario and suggests that quantum criticality is related to local moments in a spin liquid-like state.

| S-EPMC4640633 | biostudies-literature

Two-Point Microrheology of Phase-Separated Domains in Lipid Bilayers.

Project description:Though the importance of membrane fluidity for cellular function has been well established for decades, methods for measuring lipid bilayer viscosity remain challenging to devise and implement. Recently, approaches based on characterizing the Brownian dynamics of individual tracers such as colloidal particles or lipid domains have provided insights into bilayer viscosity. For fluids in general, however, methods based on single-particle trajectories provide a limited view of hydrodynamic response. The technique of two-point microrheology, in which correlations between the Brownian dynamics of pairs of tracers report on the properties of the intervening medium, characterizes viscosity at length-scales that are larger than that of individual tracers and has less sensitivity to tracer-induced distortions, but has never been applied to lipid membranes. We present, to our knowledge, the first two-point microrheological study of lipid bilayers, examining the correlated motion of domains in phase-separated lipid vesicles and comparing one- and two-point results. We measure two-point correlation functions in excellent agreement with the forms predicted by two-dimensional hydrodynamic models, analysis of which reveals a viscosity intermediate between those of the two lipid phases, indicative of global fluid properties rather than the viscosity of the local neighborhood of the tracer.

| S-EPMC4547336 | biostudies-literature

Numerical and experimental investigation of light trapping effect of nanostructured diatom frustules.

Project description:Recent advances in nanophotonic light-trapping technologies offer promising solutions in developing high-efficiency thin-film solar cells. However, the cost-effective scalable manufacturing of those rationally designed nanophotonic structures remains a critical challenge. In contrast, diatoms, the most common type of phytoplankton found in nature, may offer a very attractive solution. Diatoms exhibit high solar energy harvesting efficiency due to their frustules (i.e., hard porous cell wall made of silica) possessing remarkable hierarchical micro-/nano-scaled features optimized for the photosynthetic process through millions of years of evolution. Here we report numerical and experimental studies to investigate the light-trapping characteristic of diatom frustule. Rigorous coupled wave analysis (RCWA) and finite-difference time-domain (FDTD) methods are employed to investigate the light-trapping characteristics of the diatom frustules. In simulation, placing the diatom frustules on the surface of the light-absorption materials is found to strongly enhance the optical absorption over the visible spectrum. The absorption spectra are also measured experimentally and the results are in good agreement with numerical simulations.

| S-EPMC4496668 | biostudies-literature

Revealing the static and dynamic nanomechanical properties of diatom frustules-Nature's glass lace.

Project description:Diatoms are single cell microalgae enclosed in silica exoskeletons (frustules) that provide inspiration for advanced hybrid nanostructure designs mimicking multi-scale porosity to achieve outstanding mechanical and optical properties. Interrogating the structure and properties of diatoms down to nanometer scale leads to breakthrough advances reported here in the nanomechanical characterization of Coscinodiscus oculus-iridis diatom pure silica frustules, as well as of air-dried and wet cells with organic content. Static and dynamic mode Atomic Force Microscopy (AFM) and in-SEM nanoindentation revealed the peculiarities of diatom response with separate contributions from material nanoscale behavior and membrane deformation of the entire valve. Significant differences in the nanomechanical properties of the different frustule layers were observed. Furthermore, the deformation response depends strongly on silica hydration and on the support from the internal organic content. The cyclic loading revealed that the average compliance of the silica frustule is 0.019 m/N and increases with increasing number of cycles. The structure-mechanical properties relationship has a direct impact on the vibrational properties of the frustule as a complex micrometer-sized mechanical system. Lessons from Nature's nanostructuring of diatoms open up pathways to new generations of nano- and microdevices for electronic, electromechanical, photonic, liquid, energy storage, and other applications.

| S-EPMC10073200 | biostudies-literature

A phase separated active subnuclear compartment safeguards repressive chromatin domains [iCLIP]

Project description:The nucleus is composed of membrane-less subnuclear compartments, containing intrinsically disordered proteins and RNAs that phase separate (PS) and contribute to specific nuclear reactions. However, whether and how different subnuclear compartments can intercommunicate remains elusive. Here we identified nuclear bodies with PS features composed of BAZ2A, a factor associating with active chromatin. BAZ2A-bodies depend on active transcription, RNAs, and the non-disordered BAZ2A RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space BAZ2A-bodies contact H3K27me3-bodies. Disruption of BAZ2A-bodies promotes BAZ2A invasion into H3K27me3-domains, causing H3K27me3-bodies loss, H3K27me3 decrease, and gene upregulation. BAZ2A-bodies formation is negatively regulated by the nuclear-speckles associated lncRNA Malat1 that interacts with BAZ2A and mediates BAZ2A association to chromatin at nuclear speckles, which do not contact BAZ2A-bodies. The results unravel how active compartments protect repressive compartments using PS mechanisms that are promoted or impaired according to the type of RNA interactions with RNA-binding proteins.

2024-04-09 | GSE225896 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data