Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Method of Three-Dimensional Micro-Rotational Flow Generation for Biological Applications.

ABSTRACT: We report a convenient method to create a three-dimensional micro-rotational fluidic platform for biological applications in the direction of a vertical plane (out-of-plane) without contact in an open space. Unlike our previous complex fluidic manipulation system, this method uses a micro-rotational flow generated near a single orifice when the solution is pushed from the orifice by using a single pump. The three-dimensional fluidic platform shows good potential for fluidic biological applications such as culturing, stimulating, sorting, and manipulating cells. The pattern and velocity of the micro-rotational flow can be controlled by tuning the parameters such as the flow rate and the liquid-air interface height. We found that bio-objects captured by the micro-rotational flow showed self-rotational motion and orbital motion. Furthermore, the path length and position, velocity, and pattern of the orbital motion of the bio-object could be controlled. To demonstrate our method, we used embryoid body cells. As a result, the orbital motion had a maximum length of 2.4 mm, a maximum acceleration of 0.63 m/s², a frequency of approximately 0.45 Hz, a maximum velocity of 15.4 mm/s, and a maximum rotation speed of 600 rpm. The capability to have bio-objects rotate or move orbitally in three dimensions without contact opens up new research opportunities in three-dimensional microfluidic technology.

SUBMITTER: Yalikun Y

PROVIDER: S-EPMC6190094 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Numerical and Experimental Analyses of Three- Dimensional Unsteady Flow around a Micro-Pillar Subjected to Rotational Vibration.

Project description:The steady streaming (SS) phenomenon is gaining increased attention in the microfluidics community, because it can generate net mass flow from zero-mean vibration. We developed numerical simulation and experimental measurement tools to analyze this vibration-induced flow, which has been challenging due to its unsteady nature. The validity of these analysis methods is confirmed by comparing the three-dimensional (3D) flow field and the resulting particle trajectories induced around a cylindrical micro-pillar under circular vibration. In the numerical modeling, we directly solved the flow in the Lagrangian frame so that the substrate with a micro-pillar becomes stationary, and the results were converted to a stationary Eulerian frame to compare with the experimental results. The present approach enables us to avoid the introduction of a moving boundary or infinitesimal perturbation approximation. The flow field obtained by the micron-resolution particle image velocimetry (micro-PIV) measurement supported the three-dimensionality observed in the numerical results, which could be important for controlling the mass transport and manipulating particulate objects in microfluidic systems.

| S-EPMC6316184 | biostudies-literature

Three-fold rotational defects in two-dimensional transition metal dichalcogenides.

Project description:As defects frequently govern the properties of crystalline solids, the precise microscopic knowledge of defect atomic structure is of fundamental importance. We report a new class of point defects in single-layer transition metal dichalcogenides that can be created through 60° rotations of metal-chalcogen bonds in the trigonal prismatic lattice, with the simplest among them being a three-fold symmetric trefoil-like defect. The defects, which are inherently related to the crystal symmetry of transition metal dichalcogenides, can expand through sequential bond rotations, as evident from in situ scanning transmission electron microscopy experiments, and eventually form larger linear defects consisting of aligned 8-5-5-8 membered rings. First-principles calculations provide insights into the evolution of rotational defects and show that they give rise to p-type doping and local magnetic moments, but weakly affect mechanical characteristics of transition metal dichalcogenides. Thus, controllable introduction of rotational defects can be used to engineer the properties of these materials.

| S-EPMC4396367 | biostudies-literature

Three-dimensional rotational angiography in children with an aortic coarctation.

Project description:BackgroundChildren with aortic coarctations (CoA) are increasingly percutaneously treated. Good visualisation of the CoA is mandatory and can be obtained with three-dimensional rotational angiography (3DRA). This study aims to compare the diagnostic and therapeutic additional value of 3DRA with conventional biplane angiography (CA) in children with a CoA.MethodsPatients undergoing percutaneous treatment of CoA with balloon angioplasty (BA) or stent between 2003 and 2015, were retrospectively reviewed on success rate, complications, radiation and technical settings. Diagnostic quality of CA and 3DRA and additional value of 3DRA were scored.ResultsIn total, 134 patients underwent 183 catheterisations, 121 CA and 62 3DRA-guided. Median age was 0.52 years in the BA group and 11.19 years in the stent group. 3DRA was superior to CA in displaying the left ventricle (p = 0.008), ascending aorta (p < 0.001), aortic arch (p = 0.005) and coronary arteries (p < 0.001). In the BA group, 3DRA had a significantly higher success rate than CA (100.0 % versus 68.9 %, p = 0.016). All stent interventions were successful. Complication rates did not differ significantly. The median total dose area product did not significantly differ between CA and 3DRA in the BA (27.88 μGym2/kg versus 15.81 μGym2/kg, p = 0.275) or stent group (37.34 μGym2/kg versus 45.24 μGym2/kg, p = 0.090). 3DRA was of additional value in 96.8 % of the interventions.Conclusions3DRA is superior to CA in diagnostic quality and not associated with increased radiation exposure. It provides high additional value in guiding CoA related interventions.

| S-EPMC5065539 | biostudies-literature

Three-dimensional chromatin landscapes in MLLr AML [Micro-C]

Project description:Rearrangements of the mixed lineage leukemia (MLLr) gene are frequently associated with both pediatric and adult leukemia. However, the treatment options for these aggressive MLLr leukemias are limited due to the genomic complexity and dynamics of 3D structure in oncogene transcription and leukemia development. Here, we use Micro-C and transcriptome profiling to examine the MLLr-driven aberrant 3D genome architecture in gene-edited MLL-AF9 AML samples with biologically matched healthy donors. Recurrent and MLLr-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing in the same AML samples also revealed extensive and recurrent MLLr-specific promoter–enhancer and promoter–silencer loops. Overall, this study highlights the critical regulatory elements and provides rational and effective targeting strategy in MLLr AML.

2024-02-20 | GSE244471 | GEO

Application of symmetry adapted function method for three-dimensional reconstruction of octahedral biological macromolecules.

Project description:A method for three-dimensional (3D) reconstruction of macromolecule assembles, that is, octahedral symmetrical adapted functions (OSAFs) method, was introduced in this paper and a series of formulations for reconstruction by OSAF method were derived. To verify the feasibility and advantages of the method, two octahedral symmetrical macromolecules, that is, heat shock protein Degp(24) and the Red-cell L Ferritin, were utilized as examples to implement reconstruction by the OSAF method. The schedule for simulation was designed as follows: 2000 random orientated projections of single particles with predefined Euler angles and centers of origins were generated, then different levels of noises that is signal-to-noise ratio (S/N) = 0.1, 0.5, and 0.8 were added. The structures reconstructed by the OSAF method were in good agreement with the standard models and the relative errors of the structures reconstructed by the OSAF method to standard structures were very little even for high level noise. The facts mentioned above account for that the OSAF method is feasible and efficient approach to reconstruct structures of macromolecules and have ability to suppress the influence of noise.

| S-EPMC2817395 | biostudies-literature

Three-dimensional flow in Kupffer's Vesicle.

Project description:Whilst many vertebrates appear externally left-right symmetric, the arrangement of internal organs is asymmetric. In zebrafish, the breaking of left-right symmetry is organised by Kupffer's Vesicle (KV): an approximately spherical, fluid-filled structure that begins to form in the embryo 10 hours post fertilisation. A crucial component of zebrafish symmetry breaking is the establishment of a cilia-driven fluid flow within KV. However, it is still unclear (a) how dorsal, ventral and equatorial cilia contribute to the global vortical flow, and (b) if this flow breaks left-right symmetry through mechanical transduction or morphogen transport. Fully answering these questions requires knowledge of the three-dimensional flow patterns within KV, which have not been quantified in previous work. In this study, we calculate and analyse the three-dimensional flow in KV. We consider flow from both individual and groups of cilia, and (a) find anticlockwise flow can arise purely from excess of cilia on the dorsal roof over the ventral floor, showing how this vortical flow is stabilised by dorsal tilt of equatorial cilia, and (b) show that anterior clustering of dorsal cilia leads to around 40 % faster flow in the anterior over the posterior corner. We argue that these flow features are supportive of symmetry breaking through mechano-sensory cilia, and suggest a novel experiment to test this hypothesis. From our new understanding of the flow, we propose a further experiment to reverse the flow within KV to potentially induce situs inversus.

| S-EPMC4980428 | biostudies-literature

Spatiotemporal mapping of three dimensional rotational dynamics of single ultrasmall gold nanorods.

Project description:Spatiotemporal mapping of the position and orientation of nano-machinery inside complex and dynamic cellular environments is essential for the detailed understanding of many bio-physical processes. For the genuine observation of such biomolecular dynamics with high signal to noise ratio and reduced disturbance from the labeling probes, reduction in the size of nano-bio labels and simplification of techniques for their observation are important. Here we achieve this using polarized dark field scattering micro-spectroscopy (PDFSMS), in its simplest form so that it is deployable in several experiments. We not only locate tiny gold nanorods (GNRs) of size 30 (length) × 10 nm (diameter) inside HEK293 cells but also demonstrate mapping of their in-situ polarization patterns using a novel method. Real time observations of rotating GNR with DFSMS and PDFSMS are used to resolve in-plane and out-of-plane rotational modes of GNR. We have shown that PDFSMS itself can provide complete information about the state of GNR. A step ahead, we demonstrate the application of PDFSMS to track three dimensional rotational dynamics of transferrin-conjugated GNRs inside live HEK293 cells. These first-time observations of the three dimensional intracellular rotational dynamics of tiny GNRs using PDFSMS present a new landmark in single particle scattering spectroscopy.

| S-EPMC4121602 | biostudies-literature

A three-dimensional method for morphological analysis and flow velocity estimation in microvasculature on-a-chip.

Project description:Three-dimensional (3D) imaging techniques (e.g., confocal microscopy) are commonly used to visualize in vitro models, especially microvasculature on-a-chip. Conversely, 3D analysis is not the standard method to extract quantitative information from those models. We developed the μVES algorithm to analyze vascularized in vitro models leveraging 3D data. It computes morphological parameters (geometry, diameter, length, tortuosity, eccentricity) and intravascular flow velocity. μVES application to microfluidic vascularized in vitro models shows that they successfully replicate functional features of the microvasculature in vivo in terms of intravascular fluid flow velocity. However, wall shear stress is lower compared to in vivo references. The morphological analysis also highlights the model's physiological similarities (vessel length and tortuosity) and shortcomings (vessel radius and surface-over-volume ratio). The addition of the third dimension in our analysis produced significant differences in the metrics assessed compared to 2D estimations. It enabled the computation of new indices, such as vessel eccentricity. These μVES capabilities can find application in analyses of different in vitro vascular models, as well as in vivo and ex vivo microvasculature.

| S-EPMC10487341 | biostudies-literature

Untethered micro-robotic coding of three-dimensional material composition.

Project description:Complex functional materials with three-dimensional micro- or nano-scale dynamic compositional features are prevalent in nature. However, the generation of three-dimensional functional materials composed of both soft and rigid microstructures, each programmed by shape and composition, is still an unsolved challenge. Here we describe a method to code complex materials in three-dimensions with tunable structural, morphological and chemical features using an untethered magnetic micro-robot remotely controlled by magnetic fields. This strategy allows the micro-robot to be introduced to arbitrary microfluidic environments for remote two- and three-dimensional manipulation. We demonstrate the coding of soft hydrogels, rigid copper bars, polystyrene beads and silicon chiplets into three-dimensional heterogeneous structures. We also use coded microstructures for bottom-up tissue engineering by generating cell-encapsulating constructs.

| S-EPMC3947548 | biostudies-literature

Prevascularization of natural nanofibrous extracellular matrix for engineering completely biological three-dimensional prevascularized tissues for diverse applications.

Project description:Self-sustainability after implantation is one of the critical obstacles facing large engineered tissues. A preformed functional vascular network provides an effective solution for solving the mass transportation problem. With the support of mural cells, endothelial cells (ECs) can form microvessels within engineered tissues. As an important mural cell, human mesenchymal stem cells (hMSCs) not only stabilize the engineered microvessel network, but also preserve their multi-potency when grown under optimal culture conditions. A prevascularized hMSC/extracellular matrix (ECM) sheet fabricated by the combination of hMSCs, ECs and a naturally derived nanofibrous ECM scaffold offers great opportunity for engineering mechanically strong and completely biological three-dimensional prevascularized tissues. The objective of this study was to create a prevascularized hMSC/ECM sheet by co-culturing ECs and hMSCs on a nanofibrous ECM scaffold. Physiologically low oxygen (2% O2 ) was introduced during the 7 day hMSC culture to preserve the stemness of hMSCs and thereby their capability to secrete angiogenic factors. The ECs were then included to form microvessels under normal oxygen (20% O2 ) for up to 7 days. The results showed that a branched and mature vascular network was formed in the co-culture condition. Angiogenic factors vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF) and angiopoietin-1 (Ang-1) were significantly increased by low-oxygen culture of hMSCs, which further stabilized and supported the maturation of microvessels. A differentiation assay of the prevascularized ECM scaffold demonstrated a retained hMSC multi-potency in the hypoxia cultured samples. The prevascularized hMSC/ECM sheet holds great promise for engineering three-dimensional prevascularized tissues for diverse applications.

| S-EPMC5771986 | 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