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Methods in molecular exercise physiology
Published in Adam P. Sharples, James P. Morton, Henning Wackerhage, Molecular Exercise Physiology, 2022
Adam P. Sharples, Daniel C. Turner, Stephen Roth, Robert A. Seaborne, Brendan Egan, Mark Viggars, Jonathan C. Jarvis, Daniel J. Owens, Jatin G. Burniston, Piotr P. Gorski, Claire E. Stewart
For a genome-wide approach, ChIP-on-chip was the first widespread method in which DNA fragments are analysed via a microarray analysis. However, with rapid development of NGS, ChIP-sequencing has become the more common methodology employed. In this process, DNA fragments are purified from the ChIP protocol detailed above and used for generating DNA sequencing libraries. Nonetheless, both approaches provide information regarding the binding location and amount of binding of the histone modification of choice (e.g. the histone mark used for the antibody immunoprecipitation step) (29). Each of these protocols however is costly, and produces a large amount of data and requires advanced expertise in bioinformatics and data analysis (30). To overcome these limitations, researchers are now able to analyse the purified DNA fragments via quantitative PCR (qPCR), in a far more targeted approach. This protocol relies heavily on the researchers knowing exactly the region in the genome they wish to target, and the ability to design PCR primers to investigate this area. ChIP protocols require large quantities of starting material, are relatively labour-intensive and, for sequencing protocols, require large amounts of sequencing data in order to reliably determine meaningful differences across datasets.
Role of Histone Methyltransferase in Breast Cancer
Published in Meenu Gupta, Rachna Jain, Arun Solanki, Fadi Al-Turjman, Cancer Prediction for Industrial IoT 4.0: A Machine Learning Perspective, 2021
Surekha Manhas, Zaved Ahmed Khan
G9a’s role also has implications in various aspects associated with T-cell-based biology. However, genome mapping studies on the G9a binding or H3K9me2 deposition in immunity-providing cells has not performed due to some technical issues. A comprehensive descriptive H3K9me2 marks genome analysis in the case of resting immune cells by means of using ChIP-on-chip based methods, which illustrate that the epigenetic H3K9me2 mark is highly enriched on those genes that are strongly associated with numerous specific pathways, such as GATA3 transcription, T-cell-dependent receptor-based signaling, and IL-4 signaling [60].
Portable High-Frequency Ultrasound Imaging System Design and Hardware Considerations
Published in Iniewski Krzysztof, Integrated Microsystems, 2017
Insoo Kim, Hyunsoo Kim, Flavio Griggio, Richard L. Tutwiler, Thomas N. Jackson, Susan Trolier-McKinstry, Kyusun Choi
Therefore, low-voltage high-frequency ultrasound transducer arrays are crucial in portable high-frequency ultrasound imaging systems. The low-voltage transducers make the imaging system capable of integrating front-end electronics with transducers without charge-pump circuitry and RF coaxial cables. In addition, receiver protection devices are likely to be unnecessary because the transmit voltage is of the same magnitude as the CMOS logic voltage level. The integrated electronics also produces better signal integrity and noise immunity than conventional, analog, front-end electronics, which consist of discrete chipsets. Digital signal interfacing has wide acceptance for much higher signal-to-noise ratio (SNR) compliance than analog signal interfacing. In conventional systems, substantial efforts are necessary to control SNR in analog signal interfacing. However, in the integrated system, only chip-to-chip interfacing is necessary via digital signals because all analog signal processing occurs inside the chip and chips produce only digital outputs.
Organ-on-a-chip technologies that can transform ophthalmic drug discovery and disease modeling
Published in Expert Opinion on Drug Discovery, 2019
Jasmin C. Haderspeck, Johanna Chuchuy, Stefan Kustermann, Stefan Liebau, Peter Loskill
Su et al. developed a microfluidic chip to analyze retinal synaptic regeneration, which they called the retinal synaptic regeneration chip (RSR-chip) [74]. The RSR-chip contained two micro-chambers linked by multiple arrays of microchannels (see Figure 3(f)). Two cell populations derived from murine precursor cells were seeded separately into micro-chambers and after 3 days, axons emerged that grew from one population towards the other. Formation of retinal synaptic connections in response to secreted cytokines could be detected in the RSR-chip. Moreover, an oriented network of synapses was generated, and an automated method enabled simple analysis and enumeration of synaptic connectivity. The functionality of the chip was validated by testing the system with different amounts of glycine, which acts as an inhibitory transmitter in the retina. Furthermore, the electrophysiological activity of the retina could be monitored via immunodetection of pERK (phosphorylated extracellular-related kinase). The main purposes of this chip were to study the mechanism of synaptogenesis and to screen factors supporting retinal regeneration.
Applications of MALDI-TOF mass spectrometry in clinical proteomics
Published in Expert Review of Proteomics, 2018
Viviana Greco, Cristian Piras, Luisa Pieroni, Maurizio Ronci, Lorenza Putignani, Paola Roncada, Andrea Urbani
Similarly, SELDI platform consists of a SELDI chip coupled with a mass analyzer and software for data acquisition. SELDI chips (Protein chips arrays) are derivatized target surfaces with different chemical properties, as cation and anion exchanges, immobilized metal affinity chromatography, or antibody-antigen. According to the chemical characteristics of the chip, SELDI is a simple top-down analysis based on selective adsorption of proteins on chromatographic surfaces to reduce sample complexity and to characterize biofluid proteomics profiling [85]. This approach was used primarily to identify peptidomic and proteomic serum profiling of ovarian cancer patients [86]. However, low reproducibility, limited number of acquired MS peaks, chip-to-chip variability and low data resolution make SELDI unsuitable for routine application [85]. To date, SELDI-TOF MS platform continues to be used especially in biomarker research studies such as for antiphospholipid syndrome [87], primary biliary cirrhosis [88], and several others disorders [89–91]. On the other side, the ease of use and higher accuracy of MALDI results in a more suitable approach to the identification of peptides and proteins.
On the potential of micro-flow LC-MS/MS in proteomics
Published in Expert Review of Proteomics, 2022
Yangyang Bian, Chunli Gao, Bernhard Kuster
Despite the many attractions that micro-flow LC-MS/MS has to offer, there is no doubt that these come at the price of lower absolute sensitivity compared to nano-flow LC-MS/MS. This is because of the reduced electrospray ionization efficiency that occurs because of the much larger droplets that are formed at higher flow rates [95,96]. One option to improve ESI efficiency at higher flow rates is to use a multiple-spray emitter. Mao et al. developed a silicon-based microfluidic multi-nozzle emitter array chip (MEA chip) [97–99] that has been commercialized by Newomics as the M3 Emitter. Using such emitters, the same laboratory developed an intact protein measurement assay to analyze human plasma [100]. The high sensitivity (0.1–1.0 fmol of protein) and speed of analysis (1–5 min) was equivalent to an enzyme-linked immunosorbent assay (ELISA). Rochat et al. [101] reported a micro-flow LC-MS/MS workflow for plasma peptidomics where peptides were separated on a 0.3 mm i.d. × 100 mm C18 column at 10 μL/min. The authors compared three ESI sources: the HESI-II probe with a 50 μm i.d. micron needle, the EASY-Spray source with a 20 μm i.d. emitter, and the multi-nozzle M3 emitter and concluded that the latter delivered the highest sensitivity. Based on the same concept, Shen et al. fabricated a multi-emitter array that showed a 4–6 times improvement in signal-to-noise ratio compared to ESI from a classical electrospray needle [102]. At the time of writing, there were only few publications available that reported results from the analysis of complex proteomic samples. Hence, more studies are required to fully assess how successful multi-nozzle ESI sources are for proteomic applications.