Identification of DNA-Methylated CpG Islands Associated With Gene Silencing in the Adult Body Tissues of the Ogye Chicken Using RNA-Seq and Reduced Representation Bisulfite Sequencing

Conclusion In conclusion, genes that display a correlation between DNA methylation and their expression in specific tissues are responsible for significant changes in not only in developmental stages but also in adult tissues. We made this finding by using tissues that are not in developmental stages, but have developed in adults. This can either represent a change that occurs at the developmental stage, or it can be the result of epigenetic changes. This study presents a methodology that can be used by other researchers using omics data combined with different types of NGS data, and provides them with the opportunity to use our transcriptome and DNA methylome landscapes. Ethics Statement This study was carried out in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) and was approved by the National Institute of Animal Science, Rural Development Administration, South Korea (Approval No: 2014-080). Animal preparation and experiments were conducted in accordance with protocols approved under the guidance of the IACUC. Author Contributions NK designed and supervised this project. W-JL and KK analyzed the data and drafted the manuscript. J-YK and SJ interpreted and visualized the results. All authors reviewed and approved the final manuscript. Funding This work was supported by grants from the National Research Foundation of Korea (NRF-2014M3C9A3064552) and the KRIBB Initiative Program and Agriculture Science and Technology Developme...
Source: Frontiers in Genetics - Category: Genetics & Stem Cells Source Type: research

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Conclusion: Our study demonstrated that the aberrant expression of CDCA gene family members plays an indispensable role in tumorigenesis. PMID: 31955607 [PubMed - as supplied by publisher]
Source: Future Medicine: Biomarkers in Medicine - Category: Internal Medicine Tags: Biomark Med Source Type: research
Publication date: Available online 20 January 2020Source: Carbohydrate PolymersAuthor(s): Nadezhda E. Ustyuzhanina, Maria I. Bilan, Andrey S. Dmitrenok, Alexander S. Shashkov, Nora M.A. Ponce, Carlos A. Stortz, Nikolay E. Nifantiev, Anatolii I. UsovAbstractFucosylated chondroitin sulfate (FCS) HeSp was isolated from the Patagonian sea cucumber Hemioedema spectabilis. Ion-exchange chromatography was applied for purification of the FCS from the crude extract of sulfated polysaccharides. Analysis of monosaccharide and sulfate content of HeSp revealed the molar ratio of GlcA:GalNAc:Fuc:SO3Na as 1.15:1:1.1:3.9. Molecular weight...
Source: Carbohydrate Polymers - Category: Biomedical Science Source Type: research
Increases in the number of cell therapies in the preclinical and clinical phases have prompted the need for reliable and noninvasive assays to validate transplant function in clinical biomanufacturing. We developed a robust characterization methodology composed of quantitative bright-field absorbance microscopy (QBAM) and deep neural networks (DNNs) to noninvasively predict tissue function and cellular donor identity. The methodology was validated using clinical-grade induced pluripotent stem cell–derived retinal pigment epithelial cells (iPSC-RPE). QBAM images of iPSC-RPE were used to train DNNs that predicted iPSC-...
Source: Journal of Clinical Investigation - Category: Biomedical Science Authors: Source Type: research
Cancer immune evasion is achieved through multiple layers of immune tolerance mechanisms including immune editing, recruitment of tolerogenic immune cells, and secretion of immunosuppressive cytokines. Recent success with immune checkpoint inhibitors in cancer immunotherapy suggests a dysfunctional immune synapse as a pivotal tolerogenic mechanism. Tumor cells express immune synapse proteins to suppress the immune system, which is often modulated by epigenetic mechanisms. When the methylation status of key immune synapse genes was interrogated, we observed disproportionately hypermethylated costimulatory genes and hypometh...
Source: Journal of Clinical Investigation - Category: Biomedical Science Authors: Source Type: research
The advent of human induced pluripotent stem cells (iPSCs) provided a means for avoiding ethical concerns associated with the use of cells isolated from human embryos. The number of labs now using iPSCs to generate photoreceptor, retinal pigmented epithelial (RPE), and more recently choroidal endothelial cells has grown exponentially. However, for autologous cell replacement to be effective, manufacturing strategies will need to change. Many tasks carried out by hand will need simplifying and automating. In this issue of the JCI, Schaub and colleagues combined quantitative brightfield microscopy and artificial intelligence...
Source: Journal of Clinical Investigation - Category: Biomedical Science Authors: Source Type: research
Increased rates of locoregional recurrence are observed in patients with basal-like breast cancer (BC) despite the use of radiation therapy (RT); therefore, approaches that result in radiosensitization of basal-like BC are critically needed. Using patients’ tumor gene expression data from 4 independent data sets, we correlated gene expression with recurrence to find genes significantly correlated with early recurrence after RT. The highest-ranked gene, TTK, was most highly expressed in basal-like BC across multiple data sets. Inhibition of TTK by both genetic and pharmacologic methods enhanced radiosensitivity in mul...
Source: Journal of Clinical Investigation - Category: Biomedical Science Authors: Source Type: research
The protein-protein interaction between menin and mixed lineage leukemia 1 (MLL1) plays a critical role in acute leukemias with translocations of the MLL1 gene or with mutations in the nucleophosmin 1 (NPM1) gene. As a step toward clinical translation of menin-MLL1 inhibitors, we report development of MI-3454, a highly potent and orally bioavailable inhibitor of the menin-MLL1 interaction. MI-3454 profoundly inhibited proliferation and induced differentiation in acute leukemia cells and primary patient samples with MLL1 translocations or NPM1 mutations. When applied as a single agent, MI-3454 induced complete remission or ...
Source: Journal of Clinical Investigation - Category: Biomedical Science Authors: Source Type: research
CONCLUSION We identified a population of HCV-specific CD4+ T cells with a follicular T helper cell signature that is maintained after therapy-induced elimination of persistent infection and may constitute an important target population for vaccination efforts to prevent reinfection and immunotherapeutic approaches for persistent viral infections.FUNDING Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), the National Institute of Allergy and Infectious Diseases (NIAID), the European Union, the Berta-Ottenstein-Programme for Advanced Clinician Scientists, and the ANRS.
Source: Journal of Clinical Investigation - Category: Biomedical Science Authors: Source Type: research
Publication date: Available online 21 January 2020Source: Sensors and Actuators B: ChemicalAuthor(s): Ying Li, Pengchao Zhang, Tao Li, Rui Hu, Jiang Zhu, Ting He, Yunhuang Yang, Maili LiuAbstractCancer cells’ MMP9 activity plays vital roles in tumor development. Tumor cells are in an adhesion profile during cell-cell and cell-matrix interaction. However, it is challenging for current platforms (e.g., typical droplet systems) to measure MMP9 secreted by single cells in an adhesion profile and retrieve the cells of interest for downstream analysis. Herein, we report a single-cell protease sensor (SCPS) based on ‘...
Source: Sensors and Actuators B: Chemical - Category: Chemistry Source Type: research
Publication date: 15 May 2020Source: Journal of Alloys and Compounds, Volume 823Author(s): Jinzhi Jia, Xu Dong Liu, Xiaojia Li, Linhong Cao, Meng Zhang, Botao Wu, Xiuwen ZhouAbstractThe morphology and size of nanostructures have been considered to be directly related to capacitive performance. Additionally, hydrothermal synthesis is a common method to control nanostructures. In practice, researchers paid more attention to the direct effect of “useful ions” on morphology or size of nanostructures, e.g. the combination and decomposition processes of H+ and WO42− to form WO3. Unfortunately, the effects of ot...
Source: Journal of Alloys and Compounds - Category: Chemistry Source Type: research
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