scholarly journals Chromatin Organization and Radio Resistance in the Bacterium Gemmata obscuriglobus

2008 ◽  
Vol 191 (5) ◽  
pp. 1439-1445 ◽  
Author(s):  
Arnon Lieber ◽  
Andrew Leis ◽  
Ariel Kushmaro ◽  
Abraham Minsky ◽  
Ohad Medalia
Keyword(s):  
Spatial Organization ◽  
Genetic Material ◽  
Three Dimensional ◽  
Chromatin Organization ◽  
End Joining ◽  
Technological Advances ◽  
Gemmata Obscuriglobus ◽  
Membrane Bound ◽  
High Doses ◽  
Nucleoid Structure

ABSTRACT The organization of chromatin has a major impact on cellular activities, such as gene expression. For bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. Accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures. Gemmata obscuriglobus, a member of the phylum Planctomycetes, exhibits a distinctive nucleoid structure in which chromatin is encapsulated within a discrete membrane-bound compartment. Here, we show that this soil and freshwater bacterium tolerates high doses of UV and ionizing radiation. Cryoelectron tomography of frozen hydrated sections and electron microscopy of freeze-substituted cells have indicated a more highly ordered condensed-chromatin organization in actively dividing and stationary-phase G. obscuriglobus cells. These three-dimensional analyses revealed a complex network of double membranes that engulf the condensed DNA. Bioinformatics analysis has revealed the existence of a putative component involved in nonhomologous DNA end joining that presumably plays a role in maintaining chromatin integrity within the bacterium. Thus, our observations further support the notion that packed chromatin organization enhances radiation tolerance.

scholarly journals Microbial Biofilms: Structural Plasticity and Emerging Properties

2022 ◽  
Vol 10 (1) ◽  
pp. 138
Author(s):  
Arnaud Bridier ◽  
Romain Briandet
Keyword(s):  
Spatial Organization ◽  
3D Structure ◽  
Three Dimensional ◽  
Original Data ◽  
Natural Environments ◽  
Natural Ecosystems ◽  
Chronic Infections ◽  
Ecological Processes ◽  
Microbial Biofilms ◽  
Technological Advances

Microbial biofilms are found everywhere and can be either beneficial or detrimental, as they are involved in crucial ecological processes and in severe chronic infections. The functional properties of biofilms are closely related to their three-dimensional (3D) structure, and the ability of microorganisms to collectively and dynamically shape the community spatial organization in response to stresses in such biological edifices. A large number of works have shown a relationship between the modulation of the spatial organization and ecological interactions in biofilms in response to environmental fluctuations, as well as their emerging properties essential for nutrient cycling and bioremediation processes in natural environments. On the contrary, numerous studies have emphasized the role of structural rearrangements and matrix production in the increased tolerance of bacteria in biofilms toward antimicrobials. In these last few years, the development of innovative approaches, relying on recent technological advances in imaging, computing capacity, and other analytical tools, has led to the production of original data that have improved our understanding of this close relationship. However, it has also highlighted the need to delve deeper into the study of cell behavior in such complex communities during 3D structure development and maturation— from a single-cell to a multicellular scale— to better control or harness positive and negative impacts of biofilms. For this Special Issue, the interplay between biofilm emerging properties and their 3D spatial organization considering different models, from single bacteria to complex environmental communities, and various environments, from natural ecosystems to industrial and medical settings are addressed.

scholarly journals Is Micro X-ray Computer Tomography a Suitable Non-Destructive Method for the Characterisation of Dental Materials?

Polymers ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1271
Author(s):  
Andreas Koenig ◽  
Leonie Schmohl ◽  
Johannes Scheffler ◽  
Florian Fuchs ◽  
Michaela Schulz-Siegmund ◽  
...  
Keyword(s):  
Flexural Strength ◽  
Computer Tomography ◽  
Mechanical Performance ◽  
Dental Materials ◽  
Three Dimensional ◽  
X Rays ◽  
Scanning Calorimetry ◽  
X Ray ◽  
Multiple Measurements ◽  
High Doses

The aim of the study was to investigate the effect of X-rays used in micro X-ray computer tomography (µXCT) on the mechanical performance and microstructure of a variety of dental materials. Standardised bending beams (2 × 2 × 25 mm3) were forwarded to irradiation with an industrial tomograph. Using three-dimensional datasets, the porosity of the materials was quantified and flexural strength was investigated prior to and after irradiation. The thermal properties of irradiated and unirradiated materials were analysed and compared by means of differential scanning calorimetry (DSC). Single µXCT measurements led to a significant decrease in flexural strength of polycarbonate with acrylnitril-butadien-styrol (PC-ABS). No significant influence in flexural strength was identified for resin-based composites (RBCs), poly(methyl methacrylate) (PMMA), and zinc phosphate cement (HAR) after a single irradiation by measurement. However, DSC results suggest that changes in the microstructure of PMMA are possible with increasing radiation doses (multiple measurements, longer measurements, higher output power from the X-ray tube). In summary, it must be assumed that X-ray radiation during µXCT measurement at high doses can lead to changes in the structure and properties of certain polymers.

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.

Foundations of Advanced Neuroanatomy: Technical Guidelines for Specimen Preparation, Dissection, and 3D-Photodocumentation in a Surgical Anatomy Laboratory

2019 ◽  
Author(s):  
Luciano César PC Leonel ◽  
Lucas P. Carlstrom ◽  
Christopher S. Graffeo ◽  
Avital Perry ◽  
Carlos Diogenes Pinheiro-Neto ◽  
...  
Keyword(s):  
Oral Tradition ◽  
Dynamic Range ◽  
Tap Water ◽  
Three Dimensional ◽  
High Dynamic Range ◽  
Surgical Anatomy ◽  
Lessons Learned ◽  
Specimen Preparation ◽  
Technological Advances ◽  
Key Steps

Abstract Objective This study was aimed to provide a key update to the seminal works of Prof. Albert L. Rhoton Jr., MD, with particular attention to previously unpublished insights from the oral tradition of his fellows, recent technological advances including endoscopy, and high-dynamic range (HDR) photodocumentation, and, local improvements in technique, we have developed to optimize efficient neuroanatomic study. Methods Two formaldehyde-fixed cadaveric heads were injected with colored latex to demonstrate step-by-step specimen preparation for microscopic or endoscopic dissection. One formaldehyde-fixed brain was utilized to demonstrate optimal three-dimensional (3D) photodocumentation techniques. Results Key steps of specimen preparation include vessel cannulation and securing, serial tap water flushing, specimen drainage, vessel injection with optimized and color-augmented latex material, and storage in 70% ethanol. Optimizations for photodocumentation included the incorporation of dry black drop cloth and covering materials, an imaging-oriented approach to specimen positioning and illumination, and single-camera stereoscopic capture techniques, emphasizing the three-exposure-times-per-eye approach to generating images for HDR postprocessing. Recommended tools, materials, and technical nuances were emphasized throughout. Relative advantages and limitations of major 3D projection systems were comparatively assessed, with sensitivity to audience size and purpose specific recommendations. Conclusion We describe the first consolidated step-by-step approach to advanced neuroanatomy, including specimen preparation, dissection, and 3D photodocumentation, supplemented by previously unpublished insights from the Rhoton fellowship experience and lessons learned in our laboratories in the past years such that Prof. Rhoton's model can be realized, reproduced, and expanded upon in surgical neuroanatomy laboratories worldwide.

Three Dimensional Video Imaging for Endoscopic Sinus Surgery and Diagnosis

1995 ◽  
Vol 9 (4) ◽  
pp. 197-202 ◽  
Author(s):  
Anthony J. Reino ◽  
William Lawson ◽  
Baxter J. Garcia ◽  
Robert J. Greenstein
Keyword(s):  
Endoscopic Sinus Surgery ◽  
Three Dimensional ◽  
Small Diameter ◽  
Image Distortion ◽  
Sinus Surgery ◽  
Depth Of Field ◽  
Visual Fatigue ◽  
Video Imaging ◽  
Video Cameras ◽  
Technological Advances

Technological advances in video imaging over the last decade have resulted in remarkable additions to the armamentarium of instrumentation for the otolaryngologist. The use of video cameras and computer generated imaging in the operating room and office is invaluable for documentation and teaching purposes. Despite the obvious advantages of these systems, problems are evident, the most serious of which include image distortion and inability to judge depth of field. For more than 6 decades 3D imaging has been neither technically nor commercially successful. Reasons include alignment difficulties and image distortion. The result is “visual fatigue,” usually in about 15 minutes. At its extreme, this may be characterized by headache, nausea, and even vomiting. In this study, we employed the first 3D video imager to electronically manipulate a single video source to produce 3D images; therefore, neither alignment nor image distortions were produced. Of interest to the clinical surgeon, “visual fatigue” does not seem to occur; however, with prolonged procedures (greater than 2 hours) there exists the potential for physical intolerance for some individuals. This is the first unit that is compatible with any rigid or flexible videoendoscopic system and the small diameter endoscopes available for endoscopic sinus surgery. Moreover, prerecorded 2D tapes may be viewed in 3D on an existing VCR. The 3D image seems to provide enhanced anatomic awareness with less image distortion. We have found this system to be optically superior to the 2D video imagers currently available.

scholarly journals 3D Laparoscopic Monitors

2014 ◽  
Vol 5 ◽  
pp. MEI.S13342
Author(s):  
Francesca Destro ◽  
Noemi Cantone ◽  
Mario Lima
Keyword(s):  
Minimally Invasive Surgery ◽  
Minimally Invasive ◽  
Invasive Surgery ◽  
Three Dimensional ◽  
Short Paper ◽  
High Definition ◽  
Recent Introduction ◽  
Technological Advances ◽  
New Surgery

Minimally invasive surgery (MIS) is a relatively new surgery comprising various procedures performed with special miniaturized instruments and imaging reproduction systems. Technological advances have made MIS an efficient, safe, and applicable tool for pediatric surgeons with unquestionable advantages. The recent introduction of three-dimensional (3D) high definition systems has been advocated in order to overcome some of the problems related to standard MIS visual limitations. This short paper recapitulates the necessity to minimize MIS visualization limitations and reports the characteristics of new laparoscopic 3D systems.

scholarly journals Tooth-size discrepancy: A comparison between manual and digital methods

2014 ◽  
Vol 19 (4) ◽  
pp. 107-113 ◽  
Author(s):  
Gabriele Dória Cabral Correia ◽  
Fernando Antonio Lima Habib ◽  
Carlos Jorge Vogel
Keyword(s):  
Three Dimensional ◽  
Diagnostic Tools ◽  
Tooth Size ◽  
Digital Models ◽  
Linear Measurements ◽  
Length Discrepancy ◽  
Technological Advances ◽  
Size Discrepancy ◽  
Digital Methods ◽  
Plaster Models

INTRODUCTION: Technological advances in Dentistry have emerged primarily in the area of diagnostic tools. One example is the 3D scanner, which can transform plaster models into three-dimensional digital models. OBJECTIVE: This study aimed to assess the reliability of tooth size-arch length discrepancy analysis measurements performed on three-dimensional digital models, and compare these measurements with those obtained from plaster models. MATERIAL AND METHODS: To this end, plaster models of lower dental arches and their corresponding three-dimensional digital models acquired with a 3Shape R700T scanner were used. All of them had lower permanent dentition. Four different tooth size-arch length discrepancy calculations were performed on each model, two of which by manual methods using calipers and brass wire, and two by digital methods using linear measurements and parabolas. RESULTS: Data were statistically assessed using Friedman test and no statistically significant differences were found between the two methods (P > 0.05), except for values found by the linear digital method which revealed a slight, non-significant statistical difference. CONCLUSIONS: Based on the results, it is reasonable to assert that any of these resources used by orthodontists to clinically assess tooth size-arch length discrepancy can be considered reliable.

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