Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lung self-assembly is modulated by tissue surface tensions.

ABSTRACT: To identify cell-intrinsic properties that facilitate interaction between epithelial endodermal and mesenchymal mesodermal cells during lung morphogenesis, we developed a model of lung self-assembly that mimics fetal lung formation in structure, polarity, vasculature, and extracellular matrix expression. Three-dimensional pulmonary bodies (PBs) spontaneously self-assemble from single-cell suspensions and exhibit liquid-like properties that allow measurements of compaction rate and cohesion, and that may help to specify cellular self-organization. We hypothesized that changes in one or more of these parameters could potentially explain the lung hypoplasia associated with abnormal lung development. We examined the impact of endothelial/monocyte-activating polypeptide (EMAP) II in PBs, because EMAPII is highly expressed in lung hypoplasia. EMAPII significantly increased compaction rate and decreased overall cohesion of PBs composed of both epithelial and mesenchymal cells. Moreover, the effects of EMAPII on compaction and cohesion act exclusively through the mesenchymal cell population by interfering with fibronectin matrix assembly. We also show that EMAPII alters epithelial cell polarity and surfactant protein C expression. Our findings demonstrate, for the first time, that PBs possess liquid-like properties that can help to guide the self-assembly of fetal lungs, and that EMAPII expression can influence both mesenchymal and epithelial cells but through different molecular mechanisms.

SUBMITTER: Schwarz MA

PROVIDER: S-EPMC3095985 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Modulated self-assembly of metal-organic frameworks.

Project description:Exercising fine control over the synthesis of metal-organic frameworks (MOFs) is key to ensuring reproducibility of physical properties such as crystallinity, particle size, morphology, porosity, defectivity, and surface chemistry. The principle of modulated self-assembly - incorporation of modulator molecules into synthetic mixtures - has emerged as the primary means to this end. This perspective article will detail the development of modulated synthesis, focusing primarily on coordination modulation, from a technique initially intended to cap the growth of MOF crystals to one that is now used regularly to enhance crystallinity, control particle size, induce defectivity and select specific phases. The various mechanistic driving forces will be discussed, as well as the influence of modulation on physical properties and how this can facilitate potential applications. Modulation is also increasingly being used to exert kinetic control over self-assembly; examples of phase selection and the development of new protocols to induce this will be provided. Finally, the application of modulated self-assembly to alternative materials will be discussed, and future perspectives on the area given.

| S-EPMC8159241 | biostudies-literature

Control of gene expression by modulated self-assembly.

Project description:Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here, we capture the effects of modulated self-assembly in gene expression with a novel quantitative framework. We show that this mechanism provides precision and flexibility, two seemingly antagonistic properties, to the sensing of diverse cellular signals by systems that share common elements present in transcription factors like p53, NF-κB, STATs, Oct and RXR. Applied to the nuclear hormone receptor RXR, this framework accurately reproduces a broad range of classical, previously unexplained, sets of gene expression data and corroborates the existence of a precise functional regime with flexible properties that can be controlled both at a genome-wide scale and at the individual promoter level.

| S-EPMC3167614 | biostudies-literature

Hierarchical Self-Assembly of Metal-Ion-Modulated Chitosan Tubules.

Project description:Soft materials such as gels or biological tissues can develop via self-assembly under chemo-mechanical forces. Here, we report the instantaneous formation of soft tubular structures with a two-level hierarchy by injecting a mixture of inorganic salt and chitosan (CS) solution from below into a reactor filled with alkaline solution. Folding and wrinkling instabilities occur on the originally smooth surface controlled by the salt composition and concentration. Liesegang-like precipitation patterns develop on the outer surface on a μm length scale in the presence of calcium chloride, while the precipitate particles are distributed evenly in the bulk as corroborated by X-ray μ-CT. On the other hand, barium hydroxide precipitates out only in the thin outer layer of the CS tubule when barium chloride is introduced into the CS solution. Independent of the concentration of the weakly interacting salt, an electric potential gradient across the CS membrane develops, which vanishes when the pH difference between the two sides of the membrane diminishes.

| S-EPMC8567419 | biostudies-literature

Assembly Modulated by Particle Position and Shape: A New Concept in Self-Assembly.

Project description:In this communication we outline how the bespoke arrangements and design of micron-sized superparamagnetic shapes provide levers to modulate their assembly under homogeneous magnetic fields. We label this new approach, 'assembly modulated by particle position and shape' (APPS). Specifically, using rectangular lattices of superparamagnetic micron-sized cuboids, we construct distinct microstructures by adjusting lattice pitch and angle of array with respect to a magnetic field. Broadly, we find two modes of assembly: (1) immediate 2D jamming of the cuboids as they rotate to align with the applied field (rotation-induced jamming) and (2) aggregation via translation after their full alignment (dipole-dipole assembly). The boundary between these two assembly pathways is independent on field strength being solely a function of the cuboid's dimensions, lattice pitch, and array angle with respect to field-a relationship which we capture, along with other features of the assembly process, in a 'phase diagram'. In doing so, we set out initial design rules to build custom made assemblies. Moreover, these assemblies can be made flexible thanks to the hinged contacts of their particle building blocks. This flexibility, combined with the superparamagnetic nature of the architectures, renders our assembly method particularly appropriate for the construction of complex actuators at a scale hitherto not possible.

| S-EPMC5706238 | biostudies-other

Temperature oscillation modulated self-assembly of periodic concentric layered magnesium carbonate microparticles.

Project description:Intriguing patterns of periodic, concentric, layered, mineral microstructure are present in nature and organisms, yet they have elusive geneses. We hypothesize temperature oscillation can be an independent factor that causes the self-assembly of such patterns in mineral phases synthesized in solution. Static experiments verify that rhythmic concentric multi-layered magnesium carbonate microhemispheres can be synthesized from bicarbonate solution by temperature oscillation, without use of a chemical template, additive or gel-diffusion system. Appropriate reactant concentration and initial pH value can restrain the competitive growth of other mineral generations. Polarized light microscopy images indicate the microhemispheres are crystalline and the crystallinity increases with incubation time. The thickness of a single mineral layer of microhemisphere in microscale is precisely controlled by the waveform parameters of the temperature oscillation, while the layer number, which can reach tens to about one hundred, is constrained by the temperature oscillation period number. FT-IR spectra show that these microhemispheres synthesized under different conditions can be identified as the basic form of magnesium carbonate, hydromagnesite (Mg5(CO3)4(OH)2 ? 4H2O). SEM images exhibit the characteristic microscopic texture of the alternating dark and light rings of these microhemispheres. TEM images and ED patterns suggest the nanoflakes of microhemispheres are present in polycrystalline form with some degree of oriented assembly. The temperature oscillation modulated self-assembly may offer a new mechanism to understand the formation of layered microstructure of minerals in solution, and provide a non-invasive and programmable means to synthesize hierarchically ordered materials.

| S-EPMC3919819 | biostudies-literature

Cyclodextrin Modulated Type I Collagen Self-Assembly to Engineer Biomimetic Cornea Implants.

Project description:Collagen-rich tissues in the cornea exhibit unique and highly organized extracellular matrix ultrastructures, which contribute to its high load-bearing capacity and light transmittance. Corneal collagen fibrils are controlled during development by small leucine-rich proteoglycans (SLRPs) that regulate the fibril diameter and spacing in order to achieve the unique optical transparency. Cyclodextrins (CDs) of varying size and chemical functionality for their ability to regulate collagen assembly during vitrification process are screened in order to create biosynthetic materials that mimic the native cornea structure. Addition of βCD to collagen vitrigels produces materials with aligned fibers and lamellae similar to native cornea, resulting in mechanically robust and transparent materials. Biochemistry analysis revealed that CD interacts with hydrophobic amino acids in collagen to influence assembly and fibril organization. To translate the self-assembled collagen materials for cornea reconstruction, custom molds for gelation and vitrification are engineered to create βCD/Col implants with curvature matching that of the cornea. Acellular βCD/Col materials are implanted in a rabbit partial keratoplasty model with interrupted sutures. The implants demonstrate tissue integration and support re-epithelialization. Therefore, the addition of CD molecules regulates collagen self-assembly and provides a simple process to engineer corneal mimetic substitutes with advanced structural and functional properties.

| S-EPMC8442673 | biostudies-literature

Surface effects mediate self-assembly of amyloid-β peptides.

Project description:Here we present a label-free method for studying the mechanism of surface effects on amyloid aggregation. In this method, spin-coating is used to rapidly dry samples, in a homogeneous manner, after various incubation times. This technique allows the control of important parameters for self-assembly, such as the surface concentration. Atomic force microscopy is then used to obtain high-resolution images of the morphology. While imaging under dry conditions, we show that the morphologies of self-assembled aggregates of a model amyloid-β peptide, Aβ(12-28), are strongly influenced by the local surface concentration. On mica surfaces, where the peptides can freely diffuse, homogeneous, self-assembled protofibrils formed spontaneously and grew longer with longer subsequent incubation. The surface fibrillization rate was much faster than the rates of fibril formation observed in solution, with initiation occurring at much lower concentrations. These data suggest an alternative pathway for amyloid formation on surfaces where the nucleation stage is either bypassed entirely or too fast to measure. This simple preparation procedure for high-resolution atomic force microscopy imaging of amyloid oligomers and protofibrils should be applicable to any amyloidogenic protein species.

| S-EPMC4212779 | biostudies-literature

Surface Tensions of Alkyl Lactates with n-Alkanols or Branched Alkanols

Project description:The surface behavior of 18 binary mixtures at T = 298.15 K and at atmospheric pressure (p = 0.1

| S-EPMC9844212 | biostudies-literature

Directed block copolymer self-assembly implemented via surface-embedded electrets.

Project description:Block copolymer (BCP) nanolithography is widely recognized as a promising complementary approach to circumvent the feature size limits of conventional photolithography. The directed self-assembly of BCP thin film to form ordered nanostructures with controlled orientation and localized pattern has been the key challenge for practical nanolithography applications. Here we show that BCP nanopatterns can be directed on localized surface electrets defined by electron-beam irradiation to realize diverse features in a simple, effective and non-destructive manner. Charged electrets can generate a built-in electric field in BCP thin film and induce the formation of perpendicularly oriented microdomain of BCP film. The electret-directed orientation control of BCP film can be either integrated with mask-based patterning technique or realized by electron-beam direct-writing method to fabricate microscale arbitrary lateral patterns down to single BCP cylinder nanopattern. The electret-directed BCP self-assembly could provide an alternative means for BCP-based nanolithography, with high resolution.

| S-EPMC4756386 | biostudies-literature

Nonintuitive Surface Self-Assembly of Functionalized Molecules on Ag(111).

Project description:The fabrication of nanomaterials involves self-ordering processes of functional molecules on inorganic surfaces. To obtain specific molecular arrangements, a common strategy is to equip molecules with functional groups. However, focusing on the functional groups alone does not provide a comprehensive picture. Especially at interfaces, processes that govern self-ordering are complex and involve various physical and chemical effects, often leading to unexpected structures, as we showcase here on the example of a homologous series of quinones on Ag(111). Naively, one could expect that such quinones, which all bear the same functionalization, form similar motifs. In salient contrast, our joint theoretical and experimental study shows that profoundly different structures are formed. Using a machine-learning-based structure search algorithm, we find that this is due to a shift of the balance of three antagonizing driving forces: adsorbate-substrate interactions governing adsorption sites, adsorbate-adsorbate interactions favoring close packing, and steric hindrance inhibiting certain otherwise energetically beneficial molecular arrangements. The theoretical structures show excellent agreement with our experimental characterizations of the organic/inorganic interfaces, both for the unit cell sizes and the orientations of the molecules within. The nonintuitive interplay of similarly important interaction mechanisms will continue to be a challenging aspect for the design of functional interfaces. With a detailed examination of all driving forces, we are, however, still able to devise a design principle for self-assembly of functionalized molecules.

| S-EPMC8155339 | biostudies-literature

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