scholarly journals Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

2016 ◽  
Vol 26 (6) ◽  
pp. 719-731 ◽  
Author(s):  
Phillippa C. Taberlay ◽  
Joanna Achinger-Kawecka ◽  
Aaron T.L. Lun ◽  
Fabian A. Buske ◽  
Kenneth Sabir ◽  
...  
Keyword(s):  
Long Range ◽  
Three Dimensional ◽  
Cancer Genome ◽  
Epigenetic Alterations

scholarly journals 3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

2020 ◽  
Vol 49 (D1) ◽  
pp. D38-D46
Author(s):  
Kyukwang Kim ◽  
Insu Jang ◽  
Mooyoung Kim ◽  
Jinhyuk Choi ◽  
Min-Seo Kim ◽  
...  
Keyword(s):  
Cell Line ◽  
Large Scale ◽  
Three Dimensional ◽  
Cancer Cell Line ◽  
Cancer Genome ◽  
Structural Variations ◽  
3D Genome ◽  
Tightly Coupled ◽  
Regulatory Effects ◽  
The Impact

Abstract Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.

scholarly journals HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells

2021 ◽  
Vol 4 (3) ◽  
pp. 49
Author(s):  
Tomas Zelenka ◽  
Charalampos Spilianakis
Keyword(s):  
T Cells ◽  
Long Range ◽  
Three Dimensional ◽  
Cell Types ◽  
Range Interaction ◽  
Chromatin Interactions ◽  
Optimized Protocol ◽  
Long Range Interaction ◽  
Chromatin Compactness ◽  
Detailed Protocol

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.

scholarly journals Non-Markovian Quantum Optics with Three-Dimensional State-Dependent Optical Lattices

Quantum ◽  
2018 ◽  
Vol 2 ◽  
pp. 97 ◽  
Author(s):  
A. González-Tudela ◽  
J. I. Cirac
Keyword(s):  
Quantum Optics ◽  
Spectral Density ◽  
Long Range ◽  
Photon Energy ◽  
Optical Lattices ◽  
Cold Atoms ◽  
Three Dimensional ◽  
Collective Effects ◽  
State Dependent ◽  
Anisotropic Interactions

Quantum emitters coupled to structured photonic reservoirs experience unconventional individual and collective dynamics emerging from the interplay between dimensionality and non-trivial photon energy dispersions. In this work, we systematically study several paradigmatic three dimensional structured baths with qualitative differences in their bath spectral density. We discover non-Markovian individual and collective effects absent in simplified descriptions, such as perfect subradiant states or long-range anisotropic interactions. Furthermore, we show how to implement these models using only cold atoms in state-dependent optical lattices and show how this unconventional dynamics can be observed with these systems.

Dirty sea ice drives higher Mn concentrations in the Canada Basin

2021 ◽  
Author(s):  
Birgit Rogalla ◽  
Susan E. Allen ◽  
Manuel Colombo ◽  
Paul G. Myers ◽  
Kristin J. Orians
Keyword(s):  
Sea Ice ◽  
Long Range ◽  
Sediment Resuspension ◽  
Three Dimensional ◽  
Arctic Sea Ice ◽  
Canada Basin ◽  
The Arctic ◽  
Long Range Transport ◽  
Basin Surface ◽  
Range Transport

<p>The rapidly changing conditions of the Arctic sea ice system have cascading impacts on the biogeochemical cycles of the ocean. Sea ice transports sediments, nutrients, trace metals, pollutants, and gases from the extensive continental shelves into the more isolated central basins. However, it is difficult to assess the net contribution of this supply mechanism on nutrients in the surface ocean. In this study, we used Manganese (Mn), a micronutrient and tracer which can integrate source fluctuations in space and time, to understand the net impact of the long range transport of sea ice for Mn.</p><p>We developed a three-dimensional dissolved Mn model within a subdomain of the 1/12 degree Arctic and Northern Hemispheric Atlantic (ANHA12) configuration of NEMO centred on the Canadian Arctic Archipelago, and evaluated this model with in situ observations from the 2015 Canadian GEOTRACES cruises. The Mn model incorporates parameterizations for the contributions from river discharge, sediment resuspension, atmospheric deposition of aerosols directly to the ocean and via melt from sea ice, release of sediment from sea ice, and reversible scavenging, while the NEMO-TOP engine takes care of the advection and diffusion of the tracers. </p><p>Simulations with this model from 2002 to 2019 indicate that the majority of external Mn contributed annually to the Canada Basin surface is released by sediment from sea ice, much of which originates from the Siberian shelves. Reduced sea ice longevity in the Siberian shelf regions has been postulated to result in the disruption of the long range transport of sea ice by the transpolar drift. This reduced sea ice supply has the potential to decrease the Canada Basin Mn surface maximum and downstream Mn supply, with implications for other nutrients (such as Fe) contained in ice-rafted sediments as well. These results demonstrate some of the many changes to the biogeochemical supply mechanisms expected in the near-future in the Arctic Ocean and the subpolar seas.</p>

Shifted Rayleigh filter: a novel estimation filtering algorithm for pervasive underwater passive target tracking for computation in 3D by bearing and elevation measurements

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Lakshmi M. Kavitha ◽  
Rao S. Koteswara ◽  
K. Subrahmanyam
Keyword(s):  
Target Tracking ◽  
Long Range ◽  
Target Location ◽  
Unscented Kalman Filter ◽  
Three Dimensional ◽  
Content Type ◽  
Solution Convergence ◽  
Passive Target Tracking ◽  
Underwater Target ◽  
Target Motion Analysis

Purpose Marine exploration is becoming an important element of pervasive computing underwater target tracking. Many pervasive techniques are found in current literature, but only scant research has been conducted on their effectiveness in target tracking. Design/methodology/approach This research paper, introduces a Shifted Rayleigh Filter (SHRF) for three-dimensional (3 D) underwater target tracking. A comparison is drawn between the SHRF and previously proven method Unscented Kalman Filter (UKF). Findings SHRF is especially suitable for long-range scenarios to track a target with less solution convergence compared to UKF. In this analysis, the problem of determining the target location and speed from noise corrupted measurements of bearing, elevation by a single moving target is considered. SHRF is generated and its performance is evaluated for the target motion analysis approach. Originality/value The proposed filter performs better than UKF, especially for long-range scenarios. Experimental results from Monte Carlo are provided using MATLAB and the enhancements achieved by the SHRF techniques are evident.

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