Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Auxiliary Optomechanical Tools for 3D Cell Manipulation.

ABSTRACT: Advances in laser and optoelectronic technologies have brought the general concept of optomechanical manipulation to the level of standard biophysical tools, paving the way towards controlled experiments and measurements of tiny mechanical forces. Recent developments in direct laser writing (DLW) have enabled the realization of new types of micron-scale optomechanical tools, capable of performing designated functions. Here we further develop the concept of DLW-fabricated optomechanically-driven tools and demonstrate full-3D manipulation capabilities over biological objects. In particular, we resolved the long-standing problem of out-of-plane rotation in a pure liquid, which was demonstrated on a living cell, clamped between a pair of forks, designed for efficient manipulation with holographic optical tweezers. The demonstrated concept paves the way for the realization of flexible tools for performing on-demand functions over biological objects, such as cell tomography and surgery to name just few.

SUBMITTER: Shishkin I

PROVIDER: S-EPMC7020157 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Auxiliary Optomechanical Tools for 3D Cell Manipulation.

Shishkin Ivan I Markovich Hen H Roichman Yael Y Ginzburg Pavel P

Micromachines 20200113 1

Advances in laser and optoelectronic technologies have brought the general concept of optomechanical manipulation to the level of standard biophysical tools, paving the way towards controlled experiments and measurements of tiny mechanical forces. Recent developments in direct laser writing (DLW) have enabled the realization of new types of micron-scale optomechanical tools, capable of performing designated functions. Here we further develop the concept of DLW-fabricated optomechanically-driven ...[more]

PMID: 31941107

Similar Datasets

Innovative 3D Microfluidic Tools for On-Chip Fluids and Particles Manipulation: From Design to Experimental Validation.

Project description:Micromixers are essential components in lab-on-a-chip devices, of which the low efficiency can limit many bio-application studies. Effective mixing with automation capabilities is still a crucial requirement. In this paper, we present a method to fabricate a three-dimensional (3D) poly(methyl methacrylate) (PMMA) fluidic mixer by combining computer-aided design (CAD), micromilling technology, and experimental application via manipulating fluids and nanoparticles. The entire platform consists of three microfabricated layers with a bottom reservoir-shaped microchannel, a central serpentine channel, and a through-hole for interconnection and an upper layer containing inlets and outlet. The sealing process of the three layers and the high-precision and customizable methods used for fabrication ensure the realization of the monolithic 3D architecture. This provides buried running channels able to perform passive chaotic mixing and dilution functions, thanks to a portion of the pathway in common between the reservoir and serpentine layers. The possibility to plug-and-play micropumping systems allows us to easily demonstrate the feasibility and working features of our device for tracking the mixing and dilution performances of the micromixer by using colored fluids and fluorescent nanoparticles as the proof of concept. Exploiting the good transparency of the PMMA, spatial liquid composition and better control over reaction variables are possible, and the real-time monitoring of experiments under a fluorescence microscope is also allowed. The tools shown in this paper are easily integrable in more complex lab-on-chip platforms.

| S-EPMC7912382 | biostudies-literature

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.

Project description:Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison algorithms. Yet, there has been no systematic benchmark set or decoy structures available for the 3D structure prediction of RNA, hindering the standardization of comparative tests in the modeling of RNA structure. Furthermore, there has not been a unified set of tools that allows deep and complete RNA structure analysis, and at the same time, that is easy to use. Here, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii) 3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures). This resource provides a full list of computational tools as well as a standard RNA 3D structure prediction assessment protocol for the community.

| S-EPMC7145511 | biostudies-literature

SpheroidPicker for automated 3D cell culture manipulation using deep learning.

Project description:Recent statistics report that more than 3.7 million new cases of cancer occur in Europe yearly, and the disease accounts for approximately 20% of all deaths. High-throughput screening of cancer cell cultures has dominated the search for novel, effective anticancer therapies in the past decades. Recently, functional assays with patient-derived ex vivo 3D cell culture have gained importance for drug discovery and precision medicine. We recently evaluated the major advancements and needs for the 3D cell culture screening, and concluded that strictly standardized and robust sample preparation is the most desired development. Here we propose an artificial intelligence-guided low-cost 3D cell culture delivery system. It consists of a light microscope, a micromanipulator, a syringe pump, and a controller computer. The system performs morphology-based feature analysis on spheroids and can select uniform sized or shaped spheroids to transfer them between various sample holders. It can select the samples from standard sample holders, including Petri dishes and microwell plates, and then transfer them to a variety of holders up to 384 well plates. The device performs reliable semi- and fully automated spheroid transfer. This results in highly controlled experimental conditions and eliminates non-trivial side effects of sample variability that is a key aspect towards next-generation precision medicine.

| S-EPMC8292460 | biostudies-literature

Software tools for cell culture-related 3D printed structures.

Project description:Three-dimensional (3D) printing technology allowed fast and cheap prototype fabrication in numerous segments of industry and it also became an increasingly versatile experimental platform in life sciences. Yet, general purpose software tools to control printer hardware are often suboptimal for bioprinting applications. Here we report a package of open source software tools that we developed specifically to meet bioprinting requirements: Machine movements can be (i) precisely specified using high level programming languages, and (ii) easily distributed across a batch of tissue culture dishes. To demonstrate the utility of the reported technique, we present custom fabricated, biocompatible 3D-printed plastic structures that can control cell spreading area or medium volume, and exhibit excellent optical properties even at 50 ul sample volumes. We expect our software tools to be helpful not only to manufacture customized in vitro experimental chambers, but for applications involving printing cells and extracellular matrices as well.

| S-EPMC6122815 | biostudies-literature

Tools for the Genetic Manipulation of Herpetomonas muscarum.

Project description:Trypanosomatid parasites are causative agents of important human and animal diseases such as sleeping sickness and leishmaniasis. Most trypanosomatids are transmitted to their mammalian hosts by insects, often belonging to Diptera (or true flies). With resistance to both vector-targeted pesticides and trypanocidal drugs being reported, there is a need for novel transmission blocking strategies to be developed. Studies using the blood-feeding vectors themselves are not broadly accessible, as such, new model systems are being developed to unpick insect-trypanosmatids interactions. One such case is the interactions between the model dipteran Dr osophila melanogaster and its natural trypanosomatid Herpetomonas muscarum Our previous work has found that much of the transcriptomic changes triggered in H. muscarum after ingestion by Drosophila reflect what is known for disease-causing trypanosomatids. Here we describe a set of tools to genetically manipulate the parasite and therefore create a truly tractable insect-parasite interaction system from both sides of this association. These include transgenic fluorescently tagged parasites to follow infection dynamics in the fly gut as well as iterations of plasmids that can be used for generating knock-in and knock-out strains. The tools presented in this short report will facilitate further characterization of trypanosomatid establishment in a model dipteran.

| S-EPMC7202032 | biostudies-literature

Optical vacuum cleaner by optomechanical manipulation of nanoparticles using nanostructured mesoscale dielectric cuboid.

Project description:Here, we propose the concept of an "optical vacuum cleaner" for optomechanical manipulation of nanoparticles. We utilize a dielectric cuboid to generate an optical gradient force exerted on the nanoparticles for particle's hovering and trapping. We show that the permittivity contrast between the particle and the nanohole leads to the deep subwavelength light confinement and enhancement at the opening of the nanohole located at the shadow surface of the particle. The proposed "optical vacuum cleaner" can be utilized in optomechanical manipulations on particles such as noble metal nanoparticles adsorbed on surfaces or controlling the particles taking part in cellular uptake.

| S-EPMC6726766 | biostudies-other

3D Laser Scanner for Underwater Manipulation.

Project description:Nowadays, research in autonomous underwater manipulation has demonstrated simple applications like picking an object from the sea floor, turning a valve or plugging and unplugging a connector. These are fairly simple tasks compared with those already demonstrated by the mobile robotics community, which include, among others, safe arm motion within areas populated with a priori unknown obstacles or the recognition and location of objects based on their 3D model to grasp them. Kinect-like 3D sensors have contributed significantly to the advance of mobile manipulation providing 3D sensing capabilities in real-time at low cost. Unfortunately, the underwater robotics community is lacking a 3D sensor with similar capabilities to provide rich 3D information of the work space. In this paper, we present a new underwater 3D laser scanner and demonstrate its capabilities for underwater manipulation. In order to use this sensor in conjunction with manipulators, a calibration method to find the relative position between the manipulator and the 3D laser scanner is presented. Then, two different advanced underwater manipulation tasks beyond the state of the art are demonstrated using two different manipulation systems. First, an eight Degrees of Freedom (DoF) fixed-base manipulator system is used to demonstrate arm motion within a work space populated with a priori unknown fixed obstacles. Next, an eight DoF free floating Underwater Vehicle-Manipulator System (UVMS) is used to autonomously grasp an object from the bottom of a water tank.

| S-EPMC5948579 | biostudies-literature

Tumorigenic cell selection and substrate rigidity manipulation using 2D and 3D extracellular matrices.

Project description:Soft fibrin gels are used to select tumorigenic cells and regulate the stemness and metastasis of colorectal cancer cells via mechanotransduction. This protocol details steps to produce two-dimensional (2D) and three-dimensional (3D) extracellular matrices for substrate rigidity manipulation and tumorigenic cell selection. We also describe how it can be applied to tumor mechanotransductive research by colony growth monitoring and cell isolation. For complete details on the use and execution of this protocol, please refer to Chang et al. (2022).

| S-EPMC9307683 | biostudies-literature

Tools for 3D Interactome Visualization.

Project description:In cells, intra- and intermolecular interactions of proteins confer function, and the dynamic modulation of this interactome is critical to meet the changing needs required to support life. Cross-linking and mass spectrometry (XL-MS) enable the detection of both intra- and intermolecular protein interactions in organelles, cells, tissues, and organs. Quantitative XL-MS enables the detection of interactome changes in cells due to environmental, phenotypic, pharmacological, or genetic perturbations. We have developed new informatics capabilities, the first to enable 3D visualization of multiple quantitative interactome data sets, acquired over time or with varied perturbation levels, to reveal relevant dynamic interactome changes. These new tools are integrated within release 3.0 of our online cross-linked peptide database and analysis tool suite XLinkDB. With the recent rapid expansion in XL-MS for protein structural studies and the extension to quantitative XL-MS measurements, 3D interactome visualization tools are of critical need.

| S-EPMC6519740 | biostudies-literature

MatriGrid<sup>®</sup> Based Biological Morphologies: Tools for 3D Cell Culturing.

Project description:Recent trends in 3D cell culturing has placed organotypic tissue models at another level. Now, not only is the microenvironment at the cynosure of this research, but rather, microscopic geometrical parameters are also decisive for mimicking a tissue model. Over the years, technologies such as micromachining, 3D printing, and hydrogels are making the foundation of this field. However, mimicking the topography of a particular tissue-relevant substrate can be achieved relatively simply with so-called template or morphology transfer techniques. Over the last 15 years, in one such research venture, we have been investigating a micro thermoforming technique as a facile tool for generating bioinspired topographies. We call them MatriGrid®s. In this research account, we summarize our learning outcome from this technique in terms of the influence of 3D micro morphologies on different cell cultures that we have tested in our laboratory. An integral part of this research is the evolution of unavoidable aspects such as possible label-free sensing and fluidic automatization. The development in the research field is also documented in this account.

| S-EPMC9138054 | 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