Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Micro- and nanofluidic technologies for epigenetic profiling.

ABSTRACT: This short review provides an overview of the impact micro- and nanotechnologies can make in studying epigenetic structures. The importance of mapping histone modifications on chromatin prompts us to highlight the complexities and challenges associated with histone mapping, as compared to DNA sequencing. First, the histone code comprised over 30 variations, compared to 4 nucleotides for DNA. Second, whereas DNA can be amplified using polymerase chain reaction, chromatin cannot be amplified, creating challenges in obtaining sufficient material for analysis. Third, while every person has only a single genome, there exist multiple epigenomes in cells of different types and origins. Finally, we summarize existing technologies for performing these types of analyses. Although there are still relatively few examples of micro- and nanofluidic technologies for chromatin analysis, the unique advantages of using such technologies to address inherent challenges in epigenetic studies, such as limited sample material, complex readouts, and the need for high-content screens, make this an area of significant growth and opportunity.

SUBMITTER: Matsuoka T

PROVIDER: S-EPMC3739826 | biostudies-other | 2013 Jul

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Single molecule epigenetic analysis in a nanofluidic channel.

Project description:Epigenetic states are governed by DNA methylation and a host of modifications to histones bound with DNA. These states are essential for proper developmentally regulated gene expression and are perturbed in many diseases. There is great interest in identifying epigenetic mark placement genome wide and understanding how these marks vary among cell types, with changes in environment or according to health and disease status. Current epigenomic analyses employ bisulfite sequencing and chromatin immunoprecipitation, but query only one type of epigenetic mark at a time, DNA methylation, or histone modifications and often require substantial input material. To overcome these limitations, we established a method using nanofluidics and multicolor fluorescence microscopy to detect DNA and histones in individual chromatin fragments at about 10 Mbp/min. We demonstrated its utility for epigenetic analysis by identifying DNA methylation on individual molecules. This technique will provide the unprecedented opportunity for genome wide, simultaneous analysis of multiple epigenetic states on single molecules.

| S-EPMC2839087 | biostudies-literature

Size-Tunable Micro-/Nanofluidic Channels Fabricated by Freezing Aqueous Sucrose.

Project description:Upon freezing aqueous sucrose at temperatures higher than the eutectic point (-14 °C in this case), two phases, that is, ice and freeze concentrated solution (FCS), are spontaneously separated. FCS forms through-pore fluidic channels when thin ice septum is prepared from aqueous sucrose. Total FCS volume depends on temperature but is independent of the initial sucrose concentration. This allows us to control the size of the FCS channels simply by changing the initial sucrose concentration as long as temperature is kept constant. In this paper, we show that the size of the channel, which has a layered structure, can be controlled in a range from 50 nm to 3 ?m. Thus, the FCS channel is suitable for size-sorting of micro- and nanoparticles. We discuss the size-sorting efficiency of the channel and demonstrate the separation of particles with different sizes.

| S-EPMC6705206 | biostudies-literature

Controllable pH Manipulations in Micro/Nanofluidic Device Using Nanoscale Electrokinetics.

Project description:Recently introduced nanoscale electrokinetic phenomenon called ion concentration polarization (ICP) has been suffered from serious pH changes to the sample fluid. A number of studies have focused on the origin of pH changes and strategies for regulating it. Instead of avoiding pH changes, in this work, we tried to demonstrate new ways to utilize this inevitable pH change. First, one can obtain a well-defined pH gradient in proton-received microchannel by applying a fixed electric current through a proton exchange membrane. Furthermore, one can tune the pH gradient on demand by adjusting the proton mass transportation (i.e., adjusting electric current). Secondly, we demonstrated that the occurrence of ICP can be examined by sensing a surrounding pH of electrolyte solution. When pH > threshold pH, patterned pH-responsive hydrogel inside a straight microchannel acted as a nanojunction to block the microchannel, while it did as a microjunction when pH < threshold pH. In case of forming a nanojunction, electrical current significantly dropped compared to the case of a microjunction. The strategies that presented in this work would be a basis for useful engineering applications such as a localized pH stimulation to biomolecules using tunable pH gradient generation and portable pH sensor with pH-sensitive hydrogel.

| S-EPMC7231315 | biostudies-literature

Epigenetic changes and assisted reproductive technologies.

Project description:Children conceived by Assisted Reproductive Technologies (ART) are at moderately increased risk for a number of undesirable outcomes, including low birth weight. Whether the additional risk is associated with specific procedures used in ART or biological factors that are intrinsic to infertility has been the subject of much debate, as has the mechanism by which ART or infertility might influence this risk. The potential effect of ART clinical and laboratory procedures on the gamete and embryo epigenomes heads the list of mechanistic candidates that might explain the association between ART and undesirable clinical outcomes. The reason for this focus is that the developmental time points at which ART clinical and laboratory procedures are implemented are precisely the time points at which large-scale reorganization of the epigenome takes place during normal development. In this manuscript, we review the many human studies comparing the epigenomes of ART children with children conceived in vivo, as well as assess the potential of individual ART clinical and laboratory procedures to alter the epigenome.

| S-EPMC6961665 | biostudies-literature

Differentiation of Essential Oils Using Nanofluidic Protein Post-Translational Modification Profiling.

Project description:Current methods for the authentication of essential oils focus on analyzing their chemical composition. This study describes the use of nanofluidic protein post-translational modification (PTM) profiling to differentiate essential oils by analyzing their biochemical effects. Protein PTM profiling was used to measure the effects of four essential oils, copaiba, mandarin, Melissa, and turmeric, on the phosphorylation of MEK1, MEK2, and ERK1/2 in the MAPK signaling pathway; Akt and 4EBP1 in the pI3K/Akt/mTOR signaling pathway; and STAT3 in the JAK/STAT signaling pathway in cultured HepG2 cells. The gain or loss of the phosphorylation of these proteins served as direct read-outs for the positive or negative regulatory effects of essential oils on their respective signaling pathways. Furthermore, protein PTM profiling and GC-MS were employed side-by-side to assess the quality of the essential oils. In general, protein PTM profiling data concurred with GC-MS data on the identification of adulterated mandarin, Melissa, and turmeric essential oils. Most interestingly, protein PTM profiling data identified the differences in biochemical effects between copaiba essential oils, which were indistinguishable with GC-MS data on their chemical composition. Taken together, nanofluidic protein PTM profiling represents a robust method for the assessment of the quality and therapeutic potential of essential oils.

| S-EPMC6651569 | biostudies-literature

Nafion Film Based Micro-nanofluidic Device for Concurrent DNA Preconcentration and Separation in Free Solution.

Project description:This paper presents a Nafion film based micro-nanofluidic device for concurrent DNA preconcentration and separation. The principle of the device is based on the combination of (a) ion concentration polarization phenomenon at the junction of the microchannel and the nanochannels in the Nafion film to form opposing electrophoretic and electroosmotic forces acting on the DNAs, and (b) end-labeled free solution electrophoresis to harness the charge-to-mass ratio for molecular differentiation. The experiments successfully demonstrated concurrent preconcentration and separation of DNA mixture in free solution within 240s, yielding concentration ratios up to 1,150X and separation resolution of 1.85. The effect of applied electric field on the concentration and separation performance was also investigated. The device can be used as a key sample preparation element in conjunction with micro- or nano-fluidic sensors for microTAS functionality.

| S-EPMC4204331 | biostudies-literature

Continuous Online Protein Quality Monitoring during Perfusion Culture Production Using an Integrated Micro/Nanofluidic System.

Project description:We demonstrate a new micro/nanofluidic system for continuous and automatic monitoring of protein product size and quantity directly from the culture supernatant during a high-cell-concentration CHO cell perfusion culture. A microfluidic device enables clog-free cell retention for a bench-scale (350 mL) perfusion bioreactor that continuously produces the culture supernatant containing monoclonal antibodies (IgG1). A nanofluidic device directly monitors the protein size and quantity in the culture supernatant. The continuous-flow and fully automated operation of this nanofluidic protein analytics reduces design complexity and offers more detailed information on protein products than offline and batch-mode conventional analytics. Moreover, chemical and mechanical robustness of the nanofluidic device enables continuous monitoring for several days to a week. This continuous and online protein quality monitoring could be deployed at different steps and scales of biomanufacturing to improve product quality and manufacturing efficiency.

| S-EPMC7309224 | biostudies-literature

Increase of reaction rate and sensitivity of low-abundance enzyme assay using micro/nanofluidic preconcentration chip.

Project description:We report a novel method of increasing both the reaction rate and the sensitivity of low-abundance enzyme assay using a micro/nanofluidic preconcentration chip. The disposable preconcentration device made out of PDMS with a surface-patterned ion-selective membrane increases local enzyme/substrate concentrations for rapid monitoring of enzyme activity. As a model system, we used trypsin as the enzyme and BODIPY FL casein as the fluorogenic substrate. We demonstrated that the reaction rate of trypsin-BODIPY FL was significantly enhanced by increasing the local concentrations of both trypsin and BODIPY FL casein in the preconcentration chip. The reaction time required to turn over substrates at 1 ng/mL was only approximately 10 min compared to approximately 1 h without preconcentration, which demonstrates a significantly higher reaction rate through the increase of the concentrations of both the enzyme and substrate. Furthermore, trypsin activity can be measured down to a concentration level of 10 pg/mL, which is a approximately 100 fold enhancement in sensitivity compared to the result without the preconcentration step. This micro/nanofluidic preconcentrator chip could be used as a generic micro reaction platform to study any enzyme-substrate systems, or other biochemical reaction systems in low concentration ranges.

| S-EPMC2751807 | biostudies-literature

Size Sorting of Exosomes by Tuning the Thicknesses of the Electric Double Layers on a Micro-Nanofluidic Device.

Project description:Exosomes, a type of extracellular vesicle with a diameter of 30-150 nm, perform key biological functions such as intercellular communication. Recently, size sorting of exosomes has received increasing attention in order to clarify the correlation between their size and components. However, such sorting remains extremely difficult. Here, we propose to sort their size by controlling their electrokinetic migration in nanochannels in a micro-nanofluidic device, which is achieved by tuning the thickness of the electric double layers in the nanochannels. This approach was demonstrated experimentally for exosomes smaller than 250 nm. Using different running buffer concentrations (1 × 10-3, 1 × 10-4, and 1 × 10-5 M), most of the exosomes larger than 140, 110, and 80 nm were successfully cut off at the downstream of the nanochannels, respectively. Therefore, it is clarified that the proposed method is applicable for the size sorting of exosomes.

| S-EPMC7281254 | biostudies-literature

Deciphering ion concentration polarization-based electrokinetic molecular concentration at the micro-nanofluidic interface: theoretical limits and scaling laws.

Project description:The electrokinetic molecular concentration (EMC) effect at the micro-nanofluidic interface, which enables million-fold preconcentration of biomolecules, is one of the most compelling yet least understood nanofluidic phenomena. Despite the tremendous interests in EMC and the substantial efforts devoted, the detailed mechanism of EMC remains an enigma so far owing to its high complexity, which gives rise to the significant scientific controversies outstanding for over a decade and leaves the precise engineering of EMC devices infeasible. We report a series of experimental and theoretical new findings that decipher the mechanism of EMC. We demonstrate the first elucidation of two separate operating regimes of EMC, and establish the first theoretical model that analytically yet concisely describes the system. We further unveil the dramatically different scaling behaviors of EMC in the two regimes, thereby clarifying the long-lasting controversies. We believe this work represents important progress towards the scientific understanding of EMC and related nano-electrokinetic systems, and would enable the rational design and optimization of EMC devices for a variety of applications.

| S-EPMC6637655 | 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