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 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 Three-dimensional testicular organoids as novel in vitro models of testicular biology and toxicology

2019 ◽  
Vol 5 (3) ◽  
Author(s):  
Sadman Sakib ◽  
Anna Voigt ◽  
Taylor Goldsmith ◽  
Ina Dobrinski
Keyword(s):  
Reproductive Biology ◽  
Monolayer Culture ◽  
Three Dimensional ◽  
Cell Types ◽  
In Vitro Models ◽  
Toxicity Screening ◽  
Current State ◽  
Potential Applications ◽  
Multiple Cell

Abstract Organoids are three dimensional structures consisting of multiple cell types that recapitulate the cellular architecture and functionality of native organs. Over the last decade, the advent of organoid research has opened up many avenues for basic and translational studies. Following suit of other disciplines, research groups working in the field of male reproductive biology have started establishing and characterizing testicular organoids. The three-dimensional architectural and functional similarities of organoids to their tissue of origin facilitate study of complex cell interactions, tissue development and establishment of representative, scalable models for drug and toxicity screening. In this review, we discuss the current state of testicular organoid research, their advantages over conventional monolayer culture and their potential applications in the field of reproductive biology and toxicology.

Multimaterial and Multiscale Three-Dimensional Bioprinter

2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Jennifer Campbell ◽  
Ian McGuinness ◽  
Holger Wirz ◽  
Andre Sharon ◽  
Alexis F. Sauer-Budge
Keyword(s):  
Mammalian Cell Culture ◽  
Life Sciences ◽  
Three Dimensional ◽  
Cell Types ◽  
3D Bioprinting ◽  
Design And Implementation ◽  
Multiple Cell ◽  
Multiple Materials ◽  
Printed Materials ◽  
The Stability

We have developed a three-dimensional (3D) bioprinting system capable of multimaterial and multiscale deposition to enable the next generation of “bottom-up” tissue engineering. This area of research resides at the interface of engineering and life sciences. As such, it entails the design and implementation of diverse elements: a novel hydrogel-based bioink, a 3D bioprinter, automation software, and mammalian cell culture. Our bioprinter has three components uniquely combined into a comprehensive tool: syringe pumps connected to a selector valve that allow precise application of up to five different materials with varying viscosities and chemistries, a high velocity/high-precision x–y–z stage to accommodate the most rapid speeds allowable by the printed materials, and temperature control of the bioink reservoirs, lines, and printing environment. Our custom-designed bioprinter is able to print multiple materials (or multiple cell types in the same material) concurrently with various feature sizes (100 μm–1 mm wide; 100 μm–1 cm high). One of these materials is a biocompatible, printable bioink that has been used to test for cell survival within the hydrogel following printing. Hand-printed (HP) controls show that our bioprinter does not adversely affect the viability of the printed cells. Here, we report the design and build of the 3D bioprinter, the optimization of the bioink, and the stability and viability of our printed constructs.

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.

scholarly journals ECOA-5. Integrative 3D spatial characterization of genomic and epigenomic intratumoral heterogeneity in glioblastoma

2021 ◽  
Vol 3 (Supplement_2) ◽  
pp. ii2-ii2
Author(s):  
Radhika Mathur ◽  
Qixuan Wang ◽  
Patrick Schupp ◽  
Stephanie Hilz ◽  
Chibo Hong ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Spatial Location ◽  
Cell Types ◽  
Intratumoral Heterogeneity ◽  
Tumor Evolution ◽  
Open Chromatin ◽  
Spatial Characterization

Abstract Treatment failure in glioblastoma is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and selection of therapy-resistant clones. While genomic alterations are known contributors to ITH, emerging studies highlight functional roles for epigenomic ITH which integrates differentiation status, stochastic events, and microenvironmental inputs. Here, we have established a novel platform for integrative characterization of genomic and epigenomic ITH of glioblastoma in three-dimensional (3-D) space. In collaboration with neurosurgeons and biomedical imaging experts, we utilize 3-D surgical neuro-navigation to safely acquire ~10 tumor samples per patient representing maximal anatomical diversity. We conduct whole-exome sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-Seq) on each sample. The spatial location of each sample is mapped by its 3-D coordinates, allowing 360-degree visualization of genomic and epigenomic ITH for each patient. We demonstrate this approach on 8 patients with primary IDH-WT glioblastoma (83 spatially mapped samples), providing unprecedented insight into their spatial organization at the genomic and epigenomic levels. We link genetically defined tumor subclones to patterns of open chromatin and gene regulation, revealing underlying transcription factor binding at active promoters and enhancers. We also identify ITH in whole-genome doubling and focal oncogene amplification events in multiple patients, which we then link with epigenomic ITH. Further, to study microenvironmental inputs and their contribution to epigenomic ITH, we conduct deconvolution of RNA sequencing and ATAC-Seq data by analyzing feature co-variation. We resolve the 3-D spatial organization of immune, neural, and other nontumor cell types present in glioblastoma, characterizing their functional states and interactions with tumor cells. This work provides the most comprehensive spatial characterization of genomic and epigenomic ITH to date in glioblastoma. As a resource for further investigation, we have developed an interactive data sharing platform – The 3D Glioma Atlas – that enables 360-degree visualization of both genomic and epigenomic ITH.

scholarly journals A New Organotypic Culture of Adipose Tissue Fragments Maintains Viable Mature Adipocytes for a Long Term, Together with Development of Immature Adipocytes and Mesenchymal Stem Cell-Like Cells

Endocrinology ◽  
2008 ◽  
Vol 149 (10) ◽  
pp. 4794-4798 ◽  
Author(s):  
Emiko Sonoda ◽  
Shigehisa Aoki ◽  
Kazuyoshi Uchihashi ◽  
Hidenobu Soejima ◽  
Sachiko Kanaji ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Organotypic Culture ◽  
Three Dimensional ◽  
Collagen Gel ◽  
Cell Types ◽  
Ppar Γ ◽  
Tnf Α ◽  
Multiple Cell ◽  
Related Agent

Adipose tissue that consists of mature and immature adipocytes is suggested to contain mesenchymal stem cells (MSCs), but a culture system for analyzing their cell types within the tissue has not been established. Here we show that three-dimensional collagen gel culture of rat sc adipose tissue fragments maintained viable mature adipocytes for a long term, producing immature adipocytes and MSC-like cells from the fragments, using immunohistochemistry, ELISA, and real time RT-PCR. Bromodeoxyuridine uptake of mature adipocytes was detected. Adiponectin and leptin, and adipocyte-specific genes of adiponectin, leptin, and PPAR-γ were detected in culture assembly, whereas the lipogenesis factor insulin (20 mU/ml) and inflammation-related agent TNF-α (2 nm) increased and decreased, respectively, all of their displays. Both spindle-shaped cell types with oil red O-positive lipid droplets and those with expression of MSC markers (CD105 and CD44) developed around the fragments. The data indicate that adipose tissue-organotypic culture retains unilocular structure, proliferative ability, and some functions of mature adipocytes, generating both immature adipocytes and CD105+/CD44+ MSC-like cells. This suggests that our method will open up a new way for studying both multiple cell types within adipose tissue and the cell-based mechanisms of obesity and metabolic syndrome.

scholarly journals Three-dimensional organization of Drosophila melanogaster interphase nuclei. II. Chromosome spatial organization and gene regulation.

1987 ◽  
Vol 104 (6) ◽  
pp. 1471-1483 ◽  
Author(s):  
M Hochstrasser ◽  
J W Sedat
Keyword(s):  
Gene Regulation ◽  
Drosophila Melanogaster ◽  
Nuclear Envelope ◽  
Spatial Organization ◽  
Polytene Chromosomes ◽  
Three Dimensional ◽  
Nucleolar Organizer ◽  
Cell Types ◽  
Functional Changes ◽  
Specific Subset

In the preceding article we compared the general organization of polytene chromosomes in four different Drosophila melanogaster cell types. Here we describe experiments aimed at testing for a potential role of three-dimensional chromosome folding and positioning in modulating gene expression and examining specific chromosome interactions with different nuclear structures. By charting the configurations of salivary gland chromosomes as the cells undergo functional changes, it is shown that loci are not repositioned within the nucleus when the pattern of transcription changes. Heterologous loci show no evidence of specific physical interactions with one another in any of the cell types. However, a specific subset of chromosomal loci is attached to the nuclear envelope, and this subset is extremely similar in at least two tissues. In contrast, no specific interactions between any locus and the nucleolus are found, but the base of the X chromosome, containing the nucleolar organizer, is closely linked to this organelle. These results are used to evaluate models of gene regulation that involve the specific intranuclear positioning of gene sequences. Finally, data are presented on an unusual class of nuclear envelope structures, filled with large, electron-dense particles, that are usually associated with chromosomes.

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 Generation of rat lungs by blastocyst complementation in Fgfr2b-deficient mouse model

2022 ◽  
Author(s):  
Shunsuke Yuri ◽  
Yuki Murase ◽  
Aayako Isotani
Keyword(s):  
Mouse Model ◽  
Three Dimensional ◽  
Cell Types ◽  
Lung Epithelial Cells ◽  
Developmental Timing ◽  
Deficient Mouse ◽  
Blastocyst Complementation ◽  
Multiple Cell ◽  
Species Specific

Regenerative medicine is a tool to compensate for the shortage of lungs for transplantation, but it remains difficult to construct a lung in vitro due to the complex three-dimensional structures and multiple cell types required. A blastocyst complementation method using interspecies chimeric animals has been attracting attention as a way to create complex organs in animals, but successful lung formation has not yet been achieved. Here, we applied a reverse-blastocyst complementation method to clarify the conditions required to form lungs in an Fgfr2b-deficient mouse model. We then successfully formed a rat-derived lung in the mouse model without generating a mouse line by applying a tetraploid-based organ-complementation method. Importantly, rat lung epithelial cells retained their developmental timing even in the mouse body. This result provides useful insights regarding the need to overcome the barrier of species-specific developmental timing in order to generate functional lungs in interspecies chimeras.

Designing an Interchangeable Multi-Material Nozzle System for 3D Bioprinting Process

2021 ◽  
Author(s):  
Cartwright Nelson ◽  
Slesha Tuladhar ◽  
Md Ahasan Habib
Keyword(s):  
Rheological Properties ◽  
Structural Integrity ◽  
Three Dimensional ◽  
Cell Types ◽  
3D Bioprinting ◽  
Print Head ◽  
Functional Tissue ◽  
Multiple Cell ◽  
Continuous Deposition ◽  
Bio Material

Abstract Three-dimensional bioprinting is a rapidly growing field attempting to recreate functional tissues for medical and pharmaceutical purposes. Development of functional tissue requires deposition of multiple biomaterials encapsulating multiple cell types i.e. bio-ink necessitating switching ability between bio-inks. Existing systems use more than one print head to achieve this complex interchangeable deposition, which decreases efficiency, structural integrity, and accuracy. In this research, we developed a nozzle system capable of switching between multiple bio-inks with continuous deposition ensuring the minimum transition distance so that precise deposition transitioning can be achieved. Finally, the effect of rheological properties of different bio-material compositions on the transition distance is investigated by fabricating the sample scaffolds.

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