scholarly journals Three-Dimensional Cellular Raman Analysis: Evidence of Highly Ordered Lipids Within Cell Nuclei

2018 ◽  
Vol 66 (12) ◽  
pp. 889-902 ◽  
Author(s):  
Bhagavathi Ramamurthy ◽  
Stanley Cohen ◽  
Mark Canales ◽  
Frederick D. Coffman
Keyword(s):  
Spatial Organization ◽  
Three Dimensional ◽  
Metastatic Potential ◽  
Cell Nuclei ◽  
Interphase Cell ◽  
Raman Analysis ◽  
Nuclear Interior ◽  
Interphase Cells ◽  
Cellular Lipids ◽  
Molecular Components

Striking levels of spatial organization exist among and within interphase cell chromosomes, raising the possibility that other nuclear molecular components may also be organized in ways that facilitate nuclear function. To further examine molecular distributions and organization within cell nuclei, we utilized Raman spectroscopy to map distributions of molecular components, with a focus on cellular lipids. Although the vast majority of cellular lipids are associated with membranes, mapping the 2870/2850 cm−1 lipid peak ratios revealed that the most highly ordered lipids within interphase cells are found within cell nuclei. This finding was seen in cells from multiple tissue types, noncancerous cells, and in cancer cell lines of different metastatic potential. These highly ordered lipids colocalize with nuclear chromatin, are present throughout the nuclear volume, and remain colocalized with chromatin through mitosis, when the nuclear envelope has dissociated. Phosphatidylinositol is a major component of the highly ordered lipids. The presence of phosphatidylinositol and other lipids in the nuclear interior is well established, but their highly ordered packing has not been reported and represents a unique finding. The molecular interactions involved in the formation and maintenance of these highly ordered lipids, and their potential effects on nuclear activities, remain to be discovered.

scholarly journals Detection of 11q13 rearrangements in hematologic neoplasias by double- color fluorescence in situ hybridization

Blood ◽  
1996 ◽  
Vol 87 (4) ◽  
pp. 1512-1519 ◽  
Author(s):  
LJ Coignet ◽  
E Schuuring ◽  
RE Kibbelaar ◽  
TK Raap ◽  
KK Kleiverda ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Hematologic Malignancies ◽  
Current Data ◽  
Lymphocytic Leukemia ◽  
Cell Nuclei ◽  
Interphase Cell ◽  
Interphase Cells ◽  
Chromosomal Breaks

Rearrangements within the chromosome 11q13 region are frequent in hematologic malignancies. 50% of 75% of mantle cell lymphomas (MCLs) carry a translocation t(11;14) (q13;q32). Using Southern blot analysis, a BCL1 breakpoint can be detected in approximately 50% of MCLs. It is not known whether other MCLs harbor also breakpoints at 11q13. Breakpoints in this region not involved in t(11;14), are detected in chronic lymphocytic leukemia and acute myeloid leukemia. To detect and localize breakpoints at 11q13 more accurately, we have developed fluorescence in situ hybridization using two probe sets of differently labeled cosmids, symmetrically localized at either side of the major translocation cluster of BCL1. These probes span a region of 450 to 750 kb. We applied this assay to a series of hematologic malignancies with 11q13 abnormalities identified by classical cytogenetics. All four samples with a t(11;14) (q13;q32) showed dissociation of the differently colored signals in metaphase and interphase cells, thereby indicating a chromosomal break in the region defined by the probe sets. The frequency of abnormal metaphase and interphase cells was comparable with that observed in any of the 13 malignancies with other chromosomal 11q13 abnormalities, indicating that these chromosomal breaks occurred outside the 450- to 750-kb region covered by the probes. One patient showed triplication and one patient showed monoallelic loss of this region. The current data show that double-color fluorescence in situ hybridization is a simple and reliable method for detection of the t(11;14)(q13;q32) in interphase cell nuclei and that is can be used to distinguish this translocation from other 11q13 rearrangements in hematologic malignancies.

scholarly journals Locus-specific gene repositioning in prostate cancer

2016 ◽  
Vol 27 (2) ◽  
pp. 236-246 ◽  
Author(s):  
Marc Leshner ◽  
Michelle Devine ◽  
Gregory W. Roloff ◽  
Lawrence D. True ◽  
Tom Misteli ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Normal Tissue ◽  
Spatial Organization ◽  
Human Prostate ◽  
Specific Gene ◽  
Pathological Changes ◽  
Cell Nuclei ◽  
Prostate Hyperplasia ◽  
Interphase Cell ◽  
Prostate Disease

Genes occupy preferred spatial positions within interphase cell nuclei. However, positioning patterns are not an innate feature of a locus, and genes can alter their localization in response to physiological and pathological changes. Here we screen the radial positioning patterns of 40 genes in normal, hyperplasic, and malignant human prostate tissues. We find that the overall spatial organization of the genome in prostate tissue is largely conserved among individuals. We identify three genes whose nuclear positions are robustly altered in neoplastic prostate tissues. FLI1 and MMP9 position differently in prostate cancer than in normal tissue and prostate hyperplasia, whereas MMP2 is repositioned in both prostate cancer and hyperplasia. Our data point to locus-specific reorganization of the genome during prostate disease.

A tilting device for three-dimensional microscopy: Application to in situ imaging of interphase cell nuclei

1992 ◽  
Vol 168 (1) ◽  
pp. 47-57 ◽  
Author(s):  
Joachim Bradl ◽  
Michael Hausmann ◽  
Volker Ehemann ◽  
Dymitr Komitowski ◽  
Christoph Cremer
Keyword(s):  
Three Dimensional ◽  
Cell Nuclei ◽  
Interphase Cell ◽  
In Situ Imaging

scholarly journals Simultaneous genotypic and immunophenotypic analysis of interphase cells using dual-color fluorescence: a demonstration of lineage involvement in polycythemia vera

Blood ◽  
1992 ◽  
Vol 80 (4) ◽  
pp. 1033-1038 ◽  
Author(s):  
CM Price ◽  
EJ Kanfer ◽  
SM Colman ◽  
N Westwood ◽  
AJ Barrett ◽  
...  
Keyword(s):  
Polycythemia Vera ◽  
Fluorescent In Situ Hybridization ◽  
Chromosomal Abnormalities ◽  
Myeloproliferative Disorders ◽  
Chromosome 8 ◽  
Dual Fluorescence ◽  
Interphase Cell ◽  
Molecular Alterations ◽  
Interphase Cells

Abstract Fluorescent in situ hybridization has become a useful technique by which chromosomal abnormalities may be shown in interphase cells. We present a dual-fluorescence method whereby a chromosomal and immunophenotypic marker can be visualized simultaneously in the same interphase cell. Two patients with the myeloproliferative disorder polycythemia vera and trisomy for chromosome 8 have been studied using this technique and selective involvement of the myeloid and erythrocyte lineages has been shown by the detection of the trisomy in immunophenotyped cells. Simultaneous analysis of genotype and immunophenotype in individual cells from patients with myeloproliferative disorders or leukemia may help identify the developmental and lineage status of cells in which molecular alterations have resulted in clonal advantage.

scholarly journals EPCO-31. EPIGENOMIC INTRATUMORAL HETEROGENEITY OF GLIOBLASTOMA IN THREE-DIMENSIONAL SPACE

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii76-ii76
Author(s):  
Radhika Mathur ◽  
Sriranga Iyyanki ◽  
Stephanie Hilz ◽  
Chibo Hong ◽  
Joanna Phillips ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Spatial Location ◽  
Therapy Resistance ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Intratumoral Heterogeneity ◽  
Tumor Evolution ◽  
Open Chromatin

Abstract Treatment failure in glioblastoma is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and generation of therapy-resistant clones. While ITH in glioblastoma has been well-characterized at the genomic and transcriptomic levels, the extent of ITH at the epigenomic level and its biological and clinical significance are not well understood. In collaboration with neurosurgeons, neuropathologists, and biomedical imaging experts, we have established a novel topographical approach towards characterizing epigenomic ITH in three-dimensional (3-D) space. We utilize pre-operative MRI scans to define tumor volume and then utilize 3-D surgical neuro-navigation to intra-operatively acquire 10+ samples representing maximal anatomical diversity. The precise spatial location of each sample is mapped by 3-D coordinates, enabling tumors to be visualized in 360-degrees and providing unprecedented insight into their spatial organization and patterning. For each sample, we conduct assay for transposase-accessible chromatin using sequencing (ATAC-Seq), which provides information on the genomic locations of open chromatin, DNA-binding proteins, and individual nucleosomes at nucleotide resolution. We additionally conduct whole-exome sequencing and RNA sequencing for each spatially mapped sample. Integrative analysis of these datasets reveals distinct patterns of chromatin accessibility within glioblastoma tumors, as well as their associations with genetically defined clonal expansions. Our analysis further reveals how differences in chromatin accessibility within tumors reflect underlying transcription factor activity at gene regulatory elements, including both promoters and enhancers, and drive expression of particular gene expression sets, including neuronal and immune programs. Collectively, this work provides the most comprehensive characterization of epigenomic ITH to date, establishing its importance for driving tumor evolution and therapy resistance in glioblastoma. As a resource for further investigation, we have provided our datasets on an interactive data sharing platform – The 3D Glioma Atlas – that enables 360-degree visualization of both genomic and epigenomic ITH.

scholarly journals New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1819
Author(s):  
Tatyana Karamysheva ◽  
Svetlana Romanenko ◽  
Alexey Makunin ◽  
Marija Rajičić ◽  
Alexey Bogdanov ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Sex Chromosomes ◽  
Interphase Nucleus ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Dna Probes ◽  
B Chromosomes ◽  
Apodemus Flavicollis ◽  
Yellow Necked Mouse

The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.

scholarly journals Three-dimensional positioning of genes in mouse cell nuclei

Chromosoma ◽  
2008 ◽  
Vol 117 (6) ◽  
pp. 535-551 ◽  
Author(s):  
Claudia Hepperger ◽  
Alexander Mannes ◽  
Julia Merz ◽  
Jürgen Peters ◽  
Steffen Dietzel
Keyword(s):  
Three Dimensional ◽  
Mouse Cell ◽  
Cell Nuclei

Three-dimensional approaches to the residual structure of histone-depleted HeLa cell nuclei

1984 ◽  
Vol 87 (2) ◽  
pp. 112-123 ◽  
Author(s):  
Dominique Bouvier ◽  
Jean Hubert ◽  
Annie-Pierre Seve ◽  
Michel Bouteille ◽  
Peter B. Moens
Keyword(s):  
Hela Cell ◽  
Three Dimensional ◽  
Cell Nuclei ◽  
Residual Structure

scholarly journals Influence of extract from shoots of Taxus baccata var. elegantissima on ultrastructure and tubulin cytoskeleton of meristematic cells of Allium cepa L. roots

2014 ◽  
Vol 71 (3) ◽  
pp. 211-221 ◽  
Author(s):  
Agnieszka Majewska ◽  
Mirosława Furmanowa ◽  
Kazimierz Głowniak ◽  
Joanna Guzewska ◽  
Alicja Zobel ◽  
...  
Keyword(s):  
Allium Cepa ◽  
Chromatin Condensation ◽  
Preprophase Band ◽  
Taxus Baccata ◽  
Cell Nuclei ◽  
Root Tips ◽  
Meristematic Cells ◽  
Allium Cepa L ◽  
Interphase Cells ◽  
Average Size

We investigated the influence of extract from <em>Taxus baccata</em> var. Elegantissima (TbE) shoots in 1:8 dilution, containing paclitaxel in concentration of 81,6 µg/g fresh mass on ultrastructure and tubulin cytoskeleton of meristematic cells of <em>Allium cepa</em> L. root tips. Incubation time 3, 6, 12 and 24 h was followed with postincubation in water for 12 and 24 h. During shorter incubation (till 12 h) the surface of the cell nuclei decreased and chromatin became condensed (in comparison to control) but after 24 h the average surface increased and chromatin condensation decreased. In the course of incubation the average size of plastids and vacuoles increased. Moreover, after treatment mitochondria and plastids showed degradation of ultrastructure, which was reversed after 12 h of postincubation. Immunocytochemical assays demonstrated that in the course of incubation in the ThE extract, the tubulin cytoskeleton became partially disorganised. In most interphase cells, cortical microtubules (MTs) lost their oval transverse orientation. The preprophase band (PPB) position in the cell was often asymmetrical. The MTs array of the karyokinetic spindle and phragmoplast was also disturbed. These alterations were completely reversed during postincubation.

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