scholarly journals Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Diyan Li ◽  
Chunyou Ning ◽  
Jiaman Zhang ◽  
Yujie Wang ◽  
Qianzi Tang ◽  
...  

AbstractFolliculogenesis is a complex biological process involving a central oocyte and its surrounding somatic cells. Three-dimensional chromatin architecture is an important transcription regulator; however, little is known about its dynamics and role in transcriptional regulation of granulosa cells during chicken folliculogenesis. We investigate the transcriptomic dynamics of chicken granulosa cells over ten follicular stages and assess the chromatin architecture dynamics and how it influences gene expression in granulosa cells at three key stages: the prehierarchical small white follicles, the first largest preovulatory follicles, and the postovulatory follicles. Our results demonstrate the consistency between the global reprogramming of chromatin architecture and the transcriptomic divergence during folliculogenesis, providing ample evidence for compartmentalization rearrangement, variable organization of topologically associating domains, and rewiring of the long-range interaction between promoter and enhancers. These results provide key insights into avian reproductive biology and provide a foundational dataset for the future in-depth functional characterization of granulosa cells.

2021 ◽  
Vol 4 (3) ◽  
pp. 49
Author(s):  
Tomas Zelenka ◽  
Charalampos Spilianakis

The functional implications of the three-dimensional genome organization are becoming increasingly recognized. The Hi-C and HiChIP research approaches belong among the most popular choices for probing long-range chromatin interactions. A few methodical protocols have been published so far, yet their reproducibility and efficiency may vary. Most importantly, the high frequency of the dangling ends may dramatically affect the number of usable reads mapped to valid interaction pairs. Additionally, more obstacles arise from the chromatin compactness of certain investigated cell types, such as primary T cells, which due to their small and compact nuclei, impede limitations for their use in various genomic approaches. Here we systematically optimized all the major steps of the HiChIP protocol in T cells. As a result, we reduced the number of dangling ends to nearly zero and increased the proportion of long-range interaction pairs. Moreover, using three different mouse genotypes and multiple biological replicates, we demonstrated the high reproducibility of the optimized protocol. Although our primary goal was to optimize HiChIP, we also successfully applied the optimized steps to Hi-C, given their significant protocol overlap. Overall, we describe the rationale behind every optimization step, followed by a detailed protocol for both HiChIP and Hi-C experiments.


Materials ◽  
2019 ◽  
Vol 12 (17) ◽  
pp. 2762 ◽  
Author(s):  
Ruimin Shi ◽  
Bukang Wang ◽  
Zhiwei Yan ◽  
Zongyan Wang ◽  
Lei Dong

In order to explore the relationship between the surface topography parameters and friction properties of a rough contact interface under fluid dynamic pressure lubrication conditions, friction experiments were carried out. The three-dimensional surface topography of specimens was measured and characterized with a profile microscopy measuring system and scanning electron microscope. The friction coefficient showed a trend of decreasing first and then increasing with the increase in some surface topography parameters at lower pressure, such as the surface height arithmetic mean Sa, surface height distribution kurtosis Sku, surface volume average volume Vvv, and surface center area average void volume Vvc, which are the ISO 25178 international standard parameters. The effects of surface topographic parameters on friction were analyzed and the wear mechanism of the worn surface was presented. The wear characteristics of the samples were mainly characterized as strain fatigue, grinding, and scraping. The results provide a theoretical basis for the functional characterization of surface topography.


2019 ◽  
Vol 13 (3) ◽  
Author(s):  
Prabhuti Kharel ◽  
Likitha Somasekhar ◽  
Amy Vecheck ◽  
Kunal Mitra

Bioprinting is a technique of creating 3D cell-laden structures by accurately dispensing biomaterial to form complex synthetic tissue. The printed constructs aim to mimic the native tissue by preserving the cell functionality and viability within the printed structure. The 3D bioprinting system presented in this paper aims to facilitate the process of 3D bioprinting through its ability to control the environmental parameters within an enclosed printing chamber. This design of the bioprinter targets to eliminate the need for a laminar flow hood, by regulating the necessary environmental conditions important for cell survival, especially during long duration prints. A syringe-based extrusion (SBE) deposition method comprising multiple nozzles is integrated into the system. This allows for a wider selection of biomaterials that can be used for the formation of the extracellular matrix (ECM). Tissue constructs composed of alginate-gelatin hydrogels were mixed with fibrinogen and human endothelial cells which were then characterized and compared using two methodologies: casted and bioprinted. Furthermore, vasculature was incorporated in the bioprinted constructs using sacrificial printing. Structural and functional characterization of the constructs were performed by assessing rheological, mechanical properties, and analyzing live-dead assay measurements.


iScience ◽  
2020 ◽  
Vol 23 (8) ◽  
pp. 101434
Author(s):  
Yu-Ting L. Dingle ◽  
Volha Liaudanskaya ◽  
Liam T. Finnegan ◽  
Kyler C. Berlind ◽  
Craig Mizzoni ◽  
...  

1998 ◽  
Vol 538 ◽  
Author(s):  
A. El-Azab

AbstractThe present work aims at studying the image stress and image Peach-Koehler force fields for three-dimensional dislocation configurations in a single crystal of finite volume. It is shown that the image stress field is significant within the entire crystal volume, and that the image Peach-Koehler force can be of the same order of magnitude as the direct interaction force calculated from the infinite domain solution. The results demonstrate that image stress gives rise to long-range interaction forces that are important in meso-scale dynamics of dislocation structures.


2015 ◽  
Vol 104 (3) ◽  
pp. e309
Author(s):  
Y. Wu ◽  
D.F. Albertini ◽  
Q. Wang ◽  
D.H. Barad ◽  
V.A. Kushnir ◽  
...  

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