scholarly journals Controlling Spatial Organization of Multiple Cell Types in Defined 3D Geometries

2012 ◽  
Vol 24 (41) ◽  
pp. 5543-5547 ◽  
Author(s):  
Halil Tekin ◽  
Jefferson G. Sanchez ◽  
Christian Landeros ◽  
Karen Dubbin ◽  
Robert Langer ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Cell Types ◽  
Multiple Cell

scholarly journals MUNIn (Multiple cell-type UNifying long-range chromatin Interaction detector): a statistical framework for identifying long-range chromatin interactions from multiple cell types

2020 ◽  
Author(s):  
Weifang Liu ◽  
Armen Abnousi ◽  
Qian Zhang ◽  
Yun Li ◽  
Ming Hu ◽  
...  
Keyword(s):  
Long Range ◽  
Spatial Organization ◽  
Critical Role ◽  
Cell Types ◽  
Chromatin Interaction ◽  
Cell Type ◽  
Statistical Framework ◽  
Chromatin Interactions ◽  
The Status ◽  
Multiple Cell

AbstractChromatin spatial organization (interactome) plays a critical role in genome function. Deep understanding of chromatin interactome can shed insights into transcriptional regulation mechanisms and human disease pathology. One essential task in the analysis of chromatin interactomic data is to identify long-range chromatin interactions. Existing approaches, such as HiCCUPS, FitHiC/FitHiC2 and FastHiC, are all designed for analyzing individual cell types. None of them accounts for unbalanced sequencing depths and heterogeneity among multiple cell types in a unified statistical framework. To fill in the gap, we have developed a novel statistical framework MUNIn (Multiple cell-type UNifying long-range chromatin Interaction detector) for identifying long-range chromatin interactions from multiple cell types. MUNIn adopts a hierarchical hidden Markov random field (H-HMRF) model, in which the status (peak or background) of each interacting chromatin loci pair depends not only on the status of loci pairs in its neighborhood region, but also on the status of the same loci pair in other cell types. To benchmark the performance of MUNIn, we performed comprehensive simulation studies and real data analysis, and showed that MUNIn can achieve much lower false positive rates for detecting cell-type-specific interactions (33.1 - 36.2%), and much enhanced statistical power for detecting shared peaks (up to 74.3%), compared to uni-cell-type analysis. Our data demonstrated that MUNIn is a useful tool for the integrative analysis of interactomic data from multiple cell types.

Tissue Engineering: Controlling Spatial Organization of Multiple Cell Types in Defined 3D Geometries (Adv. Mater. 41/2012)

2012 ◽  
Vol 24 (41) ◽  
pp. 5542-5542
Author(s):  
Halil Tekin ◽  
Jefferson G. Sanchez ◽  
Christian Landeros ◽  
Karen Dubbin ◽  
Robert Langer ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Spatial Organization ◽  
Cell Types ◽  
Multiple Cell

scholarly journals Three-dimensional reconstructions of haustoria in two parasitic plant species in the Orobanchaceae

2021 ◽  
Author(s):  
Natsumi Masumoto ◽  
Yuki Suzuki ◽  
Songkui Cui ◽  
Mayumi Wakazaki ◽  
Mayuko Sato ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Three Dimensional ◽  
Parasitic Plants ◽  
Cell Types ◽  
Striga Hermonthica ◽  
Microscopy Observation ◽  
Internal Structures ◽  
Facultative Parasite ◽  
Multiple Cell ◽  
Structural Insights

Abstract Parasitic plants infect other plants by forming haustoria, specialized multicellular organs consisting of several cell types, each of which has unique morphological features and physiological roles associated with parasitism. Understanding the spatial organization of cell types is, therefore, of great importance in elucidating the functions of haustoria. Here, we report a three-dimensional (3-D) reconstruction of haustoria from two Orobanchaceae species, the obligate parasite Striga hermonthica infecting rice (Oryza sativa) and the facultative parasite Phtheirospermum japonicum infecting Arabidopsis (Arabidopsis thaliana). In addition, field-emission scanning electron microscopy observation revealed the presence of various cell types in haustoria. Our images reveal the spatial arrangements of multiple cell types inside haustoria and their interaction with host roots. The 3-D internal structures of haustoria highlight differences between the two parasites, particularly at the xylem connection site with the host. Our study provides cellular and structural insights into haustoria of S. hermonthica and P. japonicum and lays the foundation for understanding haustorium function.

scholarly journals Systematic evaluation of chromosome conformation capture assays

2020 ◽  
Author(s):  
Betul Akgol Oksuz ◽  
Liyan Yang ◽  
Sameer Abraham ◽  
Sergey V. Venev ◽  
Nils Krietenstein ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Cell Types ◽  
Chromosome Conformation Capture ◽  
Chromatin Interaction ◽  
Systematic Evaluation ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Experimental Parameters ◽  
Genome Features ◽  
Multiple Cell

AbstractChromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of cross-linkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthens the compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results for multiple cell types and cell cycle stages. We find that cell type-specific quantitative differences in chromosome folding are not detected or underestimated by some protocols. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using conventional Hi-C, Micro-C and Hi-C 3.0 for commonly used cell lines in the 4D Nucleome Project.

scholarly journals Three-dimensional reconstructions of the internal structures of haustoria in parasitic Orobanchaceae

2020 ◽  
Author(s):  
Natsumi Masumoto ◽  
Yuki Suzuki ◽  
Songkui Cui ◽  
Mayumi Wakazaki ◽  
Mayuko Sato ◽  
...  
Keyword(s):  
Special Reference ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Parasitic Plants ◽  
Cell Types ◽  
Striga Hermonthica ◽  
Internal Structures ◽  
Facultative Parasite ◽  
Multiple Cell ◽  
Structural Insights

AbstractParasitic plants infect other plants by forming haustoria, specialized multicellular organs consisting of several cell types each of which has unique morphological features and physiological roles associated with parasitism. Understanding the spatial organization of cell types is, therefore, of great importance in elucidating the functions of haustoria. Here, we report a three-dimensional (3-D) reconstruction of haustoria from two Orobanchaceae species, the obligate parasite Striga hermonthica infecting rice and the facultative parasite Phtheirospermum japonicum infecting Arabidopsis. Our images reveal the spatial arrangements of multiple cell types inside haustoria and their interaction with host roots. The 3-D internal structures of haustoria highlight differences between the two parasites, particularly at the xylem connection site with the host. Our study provides structural insights into how organs interact between hosts and parasitic plants.One-sentence summaryThree-dimensional image reconstruction was used to visualize the spatial organization of cell types in the haustoria of parasitic plants with special reference to their interaction with host roots.

scholarly journals Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D)

2017 ◽  
Vol 114 (35) ◽  
pp. E7321-E7330 ◽  
Author(s):  
Weizhe Li ◽  
Ronald N. Germain ◽  
Michael Y. Gerner
Keyword(s):  
Quantitative Analysis ◽  
High Resolution ◽  
Spatial Organization ◽  
Quantitative Imaging ◽  
Cell Types ◽  
Cell Populations ◽  
Lymphoid Tissues ◽  
Protein Fluorescence ◽  
Cellular Analysis ◽  
Multiple Cell

Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (Ce3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling. This enhanced signal quality and capacity for extensive probe multiplexing permits quantitative analysis of distinct, highly intermixed cell populations in intact Ce3D-treated tissues via 3D histo-cytometry. We use this technology to demonstrate large-volume, high-resolution microscopy of diverse cell types in lymphoid and nonlymphoid organs, as well as to perform quantitative analysis of the composition and tissue distribution of multiple cell populations in lymphoid tissues. Combined with histo-cytometry, Ce3D provides a comprehensive strategy for volumetric quantitative imaging and analysis that bridges the gap between conventional section imaging and disassociation-based techniques.

scholarly journals Molecular and anatomical organization of the dorsal raphe nucleus

2019 ◽  
Author(s):  
Kee Wui Huang ◽  
Nicole E. Ochandarena ◽  
Adrienne C. Philson ◽  
Minsuk Hyun ◽  
Jaclyn E. Birnbaum ◽  
...  
Keyword(s):  
Neurological Disorders ◽  
Spatial Organization ◽  
Dorsal Raphe Nucleus ◽  
Cell Types ◽  
Dorsal Raphe ◽  
Raphe Nucleus ◽  
Multiple Cell ◽  
The Brain ◽  
Dorsal Raphé

ABSTRACTThe dorsal raphe nucleus (DRN) is an important source of neuromodulators in the brain and has been implicated in a wide variety of behavioral and neurological disorders. Although mostly studied as a source of serotonin, the DRN is comprised of multiple cell types that are subdivided into distinct anatomical subregions. However, the complex and incompletely characterized cellular organization of the DRN has impeded efforts to investigate the distinct circuit and behavioral functions of its subdomains. Here we used high-throughput single-cell RNA sequencing within situhybridization and viral tracing to develop a map of transcriptional and spatial profiles of cells in and around the mouse DRN. Our studies reveal the molecular and spatial organization of multiple neuron subtypes that are the cellular bases of functionally and anatomically distinct serotonergic subsystems, and provide a resource for the design of strategies for further dissection of these subsystems and their diverse functions.

scholarly journals Recapitulating complex biological signaling environments using a multiplexed, DNA-patterning approach

2020 ◽  
Vol 6 (12) ◽  
pp. eaay5696 ◽  
Author(s):  
Olivia J. Scheideler ◽  
Chun Yang ◽  
Molly Kozminsky ◽  
Kira I. Mosher ◽  
Roberto Falcón-Banchs ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Solid Phase ◽  
Cell Types ◽  
Spatial Patterning ◽  
Presentation Of Self ◽  
Dna Oligonucleotides ◽  
High Throughput Method ◽  
Multiple Cell ◽  
Spatial Presentation

Elucidating how the spatial organization of extrinsic signals modulates cell behavior and drives biological processes remains largely unexplored because of challenges in controlling spatial patterning of multiple microenvironmental cues in vitro. Here, we describe a high-throughput method that directs simultaneous assembly of multiple cell types and solid-phase ligands across length scales within minutes. Our method involves lithographically defining hierarchical patterns of unique DNA oligonucleotides to which complementary strands, attached to cells and ligands-of-interest, hybridize. Highlighting our method’s power, we investigated how the spatial presentation of self-renewal ligand fibroblast growth factor-2 (FGF-2) and differentiation signal ephrin-B2 instruct single adult neural stem cell (NSC) fate. We found that NSCs have a strong spatial bias toward FGF-2 and identified an unexpected subpopulation exhibiting high neuronal differentiation despite spatially occupying patterned FGF-2 regions. Overall, our broadly applicable, DNA-directed approach enables mechanistic insight into how tissues encode regulatory information through the spatial presentation of heterogeneous signals.

scholarly journals Multiple cell types contribute to the atherosclerotic lesion fibrous cap by PDGFRβ and bioenergetic mechanisms

2021 ◽  
Vol 3 (2) ◽  
pp. 166-181 ◽  
Author(s):  
Alexandra A. C. Newman ◽  
Vlad Serbulea ◽  
Richard A. Baylis ◽  
Laura S. Shankman ◽  
Xenia Bradley ◽  
...  
Keyword(s):  
Atherosclerotic Lesion ◽  
Cell Types ◽  
Fibrous Cap ◽  
Multiple Cell
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