scholarly journals Imaging chromatin interactions at sub-kilobase resolution Via Tn5-FISH

2019 ◽  
Author(s):  
Xu Zhang ◽  
Jing Niu ◽  
Guipeng Li ◽  
Qionghai Dai ◽  
Dayong Jin ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Cost Effective ◽  
Imaging Method ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Cytogenetic Changes ◽  
Chromatin Configuration ◽  
Clinical Detection ◽  
Tn5 Transposase

ABSTRACTThere is increasing interest in understanding how the three-dimensional organization of the genome is regulated. Different strategies have been employed to identify chromatin interactions genome wide. However, due to the current limitations in resolving genomic contacts, visualization and validation of these genomic loci with sub-kilobase resolution remain the bottleneck for many years. Here, we describe Tn5 transposase-based Fluorescence in situ Hybridization (Tn5-FISH), a Polymerase Chain Reaction (PCR)-based, cost-effective imaging method, which achieved the co-localization of genomic loci with sub-kilobase resolution, to fine dissect genome architecture at sub-kilobase resolution and to verify chromatin interactions detected by Chromatin Configuration Capture (3C)-derivative methods. Especially, Tn5-FISH is very useful to verify short-range chromatin interactions inside of contact domain and Topologically Associated Domain (TAD). It also offers one powerful molecular diagnosis tool for clinical detection of cytogenetic changes in cancers.

scholarly journals HiCRes: a computational method to estimate and predict the resolution of HiC libraries

2020 ◽  
Author(s):  
Claire Marchal ◽  
Nivedita Singh ◽  
Ximena Corso-Díaz ◽  
Anand Swaroop
Keyword(s):  
Expression Patterns ◽  
Three Dimensional ◽  
Computational Method ◽  
Mathematical Concepts ◽  
Regulate Gene Expression ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
A Cell ◽  
Cell Type Specific ◽  
Human And Mouse

AbstractThree-dimensional (3D) conformation of the chromatin is crucial to stringently regulate gene expression patterns and DNA replication in a cell-type specific manner. HiC is a key technique for measuring 3D chromatin interactions genome wide. Estimating and predicting the resolution of a library is an essential step in any HiC experimental design. Here, we present the mathematical concepts to estimate the resolution of a library and predict whether deeper sequencing would enhance the resolution. We have developed HiCRes, a docker pipeline, by applying these concepts to human and mouse HiC libraries.

Three-dimensional (3D) velocity map imaging: from technique to application

2022 ◽  
Author(s):  
Gihan Basnayake ◽  
Yasashri Ranathunga ◽  
Suk Kyoung Lee ◽  
Wen Li
Keyword(s):  
Three Dimensional ◽  
Cost Effective ◽  
Velocity Map Imaging ◽  
Imaging Method ◽  
Translational Energy ◽  
Ion Imaging ◽  
Standard Tool ◽  
Recent Advancement ◽  
Acquisition Speed ◽  
Energy And Angular Distributions

Abstract The velocity map imaging (VMI) technique was first introduced by Eppink and Parker in 1997, as an improvement to the original ion imaging method by Houston and Chandler in 1987. The method has gained huge popularity over the past two decades and has become a standard tool for measuring high-resolution translational energy and angular distributions of ions and electrons. VMI has evolved gradually from 2D momentum measurements to 3D measurements with various implementations and configurations. The most recent advancement has brought unprecedented 3D performance to the technique in terms of resolutions (both spatial and temporal), multi-hit capability as well as acquisition speed while maintaining many attractive attributes afforded by conventional VMI such as being simple, cost-effective, visually appealing and versatile. In this tutorial we will discuss many technical aspects of the recent advancement and its application in probing correlated chemical dynamics.

scholarly journals MAPPING OF LONG-RANGE CHROMATIN INTERACTIONS BY PROXIMITY LIGATION ASSISTED CHIP-SEQ

2016 ◽  
Author(s):  
Rongxin Fang ◽  
Miao Yu ◽  
Guoqiang Li ◽  
Sora Chee ◽  
Tristin Liu ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Embryonic Stem ◽  
Cost Effective ◽  
Eukaryotic Cells ◽  
Proximity Ligation ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Cost Effective Method ◽  
Highly Sensitive ◽  
State Of Art

AbstractWe report a highly sensitive and cost-effective method for genome-wide identification of chromatin interactions in eukaryotic cells. Combining proximity ligation with chromatin immunoprecipitation and sequencing, the method outperforms the state of art approach in sensitivity, accuracy and ease of operation. Application of the method to mouse embryonic stem cells improves mapping of enhancer-promoter interactions.

A one-step, cost-effective green method to in situ fabricate Ni(OH)2 hexagonal platelets on Ni foam as binder-free supercapacitor electrode materials

2015 ◽  
Vol 3 (5) ◽  
pp. 1953-1960 ◽  
Author(s):  
Lingjie Li ◽  
Jing Xu ◽  
Jinglei Lei ◽  
Jie Zhang ◽  
Frank McLarnon ◽  
...  
Keyword(s):  
High Performance ◽  
Electrode Materials ◽  
Three Dimensional ◽  
Cost Effective ◽  
Ni Foam ◽  
Supercapacitor Electrode ◽  
One Step ◽  
Binder Free ◽  
Supercapacitor Electrode Materials

The Ni(OH)2 hexagonal platelets were in situ fabricated on Ni foam as a binder-free supercapacitor electrode material with high performance and excellent cycling stability by a one-step, cost-effective, green hydrothermal treatment of three-dimensional (3D) Ni foam in a 15 wt% H2O2 aqueous solution.

Three-dimensional islet graft histology: panoramic imaging of neural plasticity in sympathetic reinnervation of transplanted islets under the kidney capsule

2014 ◽  
Vol 306 (5) ◽  
pp. E559-E570 ◽  
Author(s):  
Jyuhn-Huarng Juang ◽  
Shih-Jung Peng ◽  
Chien-Hung Kuo ◽  
Shiue-Cheng Tang
Keyword(s):  
Blood Vessels ◽  
Neural Plasticity ◽  
Sympathetic Innervation ◽  
Three Dimensional ◽  
Resolving Power ◽  
Imaging Method ◽  
Kidney Capsule ◽  
Panoramic Imaging ◽  
Syngeneic Islet Transplantation

Microscopic examination of transplanted islets in an ectopic environment provides information to evaluate islet engraftment, including revascularization and reinnervation. However, because of the dispersed nature of blood vessels and nerves, global visualization of the graft neurovascular network has been difficult. In this research we revealed the neurovascular network by preparing transparent mouse islet grafts under the kidney capsule with optical clearing to investigate the sympathetic reinnervation via three-dimensional confocal microscopy. Normoglycemic and streptozotocin-induced diabetic mice were used in syngeneic islet transplantation, with both groups maintaining euglycemia after transplantation. Triple staining of insulin/glucagon, blood vessels, and tyrosine hydroxylase (sympathetic marker) was used to reveal the graft microstructure, vasculature, and sympathetic innervation. Three weeks after transplantation, we observed perigraft sympathetic innervation similar to the peri-islet sympathetic innervation in the pancreas. Six weeks after transplantation, prominent intragraft, perivascular sympathetic innervation was achieved, resembling the pancreatic intraislet, perivascular sympathetic innervation in situ. Meanwhile, in diabetic recipients, a higher graft sympathetic nerve density was found compared with grafts in normoglycemic recipients, indicating the graft neural plasticity in response to the physiological difference of the recipients and the resolving power of this imaging approach. Overall, this new graft imaging method provides a useful tool to identify the islet neurovascular complex in an ectopic environment to study islet engraftment.

scholarly journals Building stone quarries: resource evaluation by block modelling and unmanned aerial photogrammetric surveys

2021 ◽  
Vol 81 (1) ◽  
Author(s):  
Maxim Bogdanowitsch ◽  
Luís Sousa ◽  
Siegfried Siegesmund
Keyword(s):  
Three Dimensional ◽  
Block Size ◽  
Cost Effective ◽  
Building Stone ◽  
Raw Material ◽  
Factors Affecting ◽  
Conditioning Factors ◽  
Full Characterization ◽  
Three Dimensional Models

AbstractThe production of building stones shown an exponential growth in last decades as consequences of the demand and developments in the extraction and processing techniques. From the several conditioning factors affecting this industry, the geological constrains at quarry scale stands out as one of most important. Globalization and increasing competition in the building stone market require large raw material blocks to keep further processing as cost-effective as possible. Therefore, the potential extraction volume of in-situ stone blocks plays an important role in the yield of a dimensional stone quarry. The full characterization of the fracturing in the quarries comes up as fundamental in the assessment of the in-situ blocks volume/shape and potential extracted raw blocks. Identify the joint sets present, their spacing and the differences across the quarry demands a continuous assess during the quarry live span. Information from unmanned aerial vehicles helps in the field survey, namely trough digital surface models, orthophotos, and three-dimensional models. Also, the fracturing modelling by specific software programs is crucial to improve the block size assessment and the increase the quarry yield. In this research fracturing of twenty-one quarries of granite, limestone, marble, and slate from Portugal were assessed by combining field surveys with new techniques. From the studied quarries several cases were selected and presented to highlight the importance of this combined methodology in the fracturing assessment and how they can be helpful in the maximization of the resources and quarry management.

scholarly journals Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture

2019 ◽  
Author(s):  
Yizhou Zhu ◽  
Yousin Suh
Keyword(s):  
Regulatory Elements ◽  
Interaction Networks ◽  
Chromatin Interaction ◽  
Resolution Limit ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Regulatory Genome ◽  
Contact Domain

AbstractThe resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here we report two 3C-derived methods, Tri-4C and Tri-HiC, which utilize mult-restriction enzyme digestions for ultrafine mapping of targeted and genome-wide chromatin interaction, respectively, at up to one hundred basepair resolution. Tri-4C identified CRE loop interaction networks and quantifatively revealed their alterations underlying dynamic gene control. Tri-HiC uncovered global fine-gage regulatory interaction networks, identifying > 20-fold more enhancer:promoter (E:P) loops than in situ HiC. In addition to vasly improved identification of subkilobase-sized E:P loops, Tri-HiC also uncovered interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically-associated domain (TAD) boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high resolution interactome maps required for characterizing fine-gage regulatory chromatin interactions in analysis of development, homeostasis and disease.

scholarly journals Amplification-free Library Preparation Improves Quality of Hi-C Analysis

2019 ◽  
Author(s):  
Longjian Niu ◽  
Wei Shen ◽  
Yingzhang Huang ◽  
Na He ◽  
Yuedong Zhang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Three Dimensional ◽  
Pcr Amplification ◽  
Interaction Network ◽  
Human Cells ◽  
Chromatin Interaction ◽  
Library Preparation ◽  
Amplification Bias ◽  
Chromatin Interactions

AbstractPCR amplification of Hi-C libraries introduces unusable duplicates and results in a biased representation of chromatin interactions. We present a simplified, fast, and economically efficient Hi-C library preparation procedure that generates sufficient non-amplified ligation products for deep sequencing from 30 million Drosophila cells. Comprehensive analysis of the resulting data indicates that amplification-free Hi-C preserves higher complexity of chromatin interaction and lowers sequencing depth dramatically for the same number of unique paired reads. For human cells which has a large genome, this method recovers an amount of ligated fragments enough for direct high-throughput sequencing without amplification on as low as 250 thousand of cells. Comparison with published in situ Hi-C on millions of human cells reveals that amplification introduces distance-dependent amplification bias, which results in increasing background noise level against genomic distance. With amplification bias avoided, our method may produce a chromatin interaction network more faithfully reflecting the real three-dimensional genomic architecture.

Correlated Studies of Cellular Interactions Using TEM, Freeze Etching, and SEM

1974 ◽  
Vol 32 ◽  
pp. 320-321
Author(s):  
J. P. Revel
Keyword(s):  
Developmental Stages ◽  
Three Dimensional ◽  
Cell Movement ◽  
Cellular Interactions ◽  
Serial Sections ◽  
Cell Sheets ◽  
Freeze Etching ◽  
Early Developmental

Movement of individual cells or of cell sheets and complex patterns of folding play a prominent role in the early developmental stages of the embryo. Our understanding of these processes is based on three- dimensional reconstructions laboriously prepared from serial sections, and from autoradiographic and other studies. Many concepts have also evolved from extrapolation of investigations of cell movement carried out in vitro. The scanning electron microscope now allows us to examine some of these events in situ. It is possible to prepare dissections of embryos and even of tissues of adult animals which reveal existing relationships between various structures more readily than used to be possible vithout an SEM.

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