scholarly journals 3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa

2021 ◽  
Author(s):  
Octavio Mondragón-Palomino ◽  
Roberta Poceviciute ◽  
Antti Lignell ◽  
Jessica A. Griffiths ◽  
Heli Takko ◽  
...  
Keyword(s):  
Spatial Pattern ◽  
3D Imaging ◽  
Spatial Organization ◽  
High Spatial Resolution ◽  
Bacterial Colonization ◽  
Quantitative Imaging ◽  
Taxonomic Composition ◽  
Host Tissue ◽  
Imaging Approach ◽  
Biogeographical Analysis

Improving our understanding of host-microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the 3D spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 days after recovery when overall bacterial loads returned to pre-antibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern was resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that bacterial taxa are distributed differently within crypts, with Lactobacilli laying closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.

scholarly journals Quantitative Imaging of Gut Microbiota Spatial Organization

2015 ◽  
Vol 18 (4) ◽  
pp. 478-488 ◽  
Author(s):  
Kristen A. Earle ◽  
Gabriel Billings ◽  
Michael Sigal ◽  
Joshua S. Lichtman ◽  
Gunnar C. Hansson ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Spatial Organization ◽  
Quantitative Imaging

Abstract 297: SPECT/CT Imaging of Regional Foot Perfusion Provides a Quantitative Index for Evaluation of Targeted Revascularization in the Diabetic Foot

2015 ◽  
Vol 35 (suppl_1) ◽  
Author(s):  
Mitchel R Stacy ◽  
Xenophon Papademetris ◽  
Brandon Sumpio ◽  
Bauer E Sumpio ◽  
Carlos Mena ◽  
...  
Keyword(s):  
Quantitative Imaging ◽  
Three Dimensional ◽  
Tissue Perfusion ◽  
Ct Imaging ◽  
Diabetic Patients ◽  
Three Dimensional Model ◽  
Radiotracer Uptake ◽  
Ct Attenuation ◽  
Imaging Approach ◽  
Revascularization Procedures

Introduction: No standard quantitative imaging approach exists to evaluate volumetric changes in tissue perfusion in the lower extremities following medical treatment. In this study, we develop and apply a three-dimensional model of the foot for evaluation of regional changes in perfusion following revascularization in diabetic patients with non-healing foot ulcers. We hypothesize that SPECT/CT imaging will permit quantification of regional improvements in tissue perfusion in territories of the foot that contain non-healing ulcers, allowing for quantitative evaluation of revascularization procedures. Methods: Resting 99m Tc-tetrofosmin (dose 554.0 ± 26.6 MBq) SPECT/CT was performed on diabetic patients (n=5; 64 ± 15 yrs) before and 1-3 days after lower extremity angioplasty and/or stenting. The CT attenuation scans were used to define five regions of interest (ROIs) in the foot and for quantification of relative changes in regional perfusion with 99m Tc-tetrofosmin SPECT (Fig. 1A). Radiotracer uptake for each ROI was normalized to injected dose and ROI volume, and expressed as a percent change from baseline value. Results: SPECT/CT imaging demonstrated quantitative improvements in regional tissue perfusion in ROIs containing non-healing ulcers for 4 out of 5 patients following revascularization (Fig. 1B). The single patient demonstrating a negative response (11.7% decrease in perfusion) underwent eventual amputation. Conclusions: Early changes in tissue perfusion following revascularization can be non-invasively evaluated in specific vascular territories of the foot using SPECT/CT imaging and may be associated with wound healing and limb salvage outcomes.

Fabrication and performance of a 128-element crossed-electrode relaxor array, for a novel 3D imaging approach

2017 ◽  
Author(s):  
Katherine Latham ◽  
Christopher Samson ◽  
Christopher Ceroici ◽  
Roger J. Zemp ◽  
Jeremy A. Brown
Keyword(s):  
3D Imaging ◽  
Imaging Approach ◽  
And Performance

scholarly journals Dynamic switching enables efficient bacterial colonization in flow

2018 ◽  
Vol 115 (21) ◽  
pp. 5438-5443 ◽  
Author(s):  
Anerudh Kannan ◽  
Zhenbin Yang ◽  
Minyoung Kevin Kim ◽  
Howard A. Stone ◽  
Albert Siryaporn
Keyword(s):  
Mammalian Cells ◽  
Spatial Organization ◽  
Dynamic Instability ◽  
Bacterial Colonization ◽  
Cell Types ◽  
Search Space ◽  
Flow Networks ◽  
Surface Attachment ◽  
Dynamic Switching ◽  
Two Phases

Bacteria colonize environments that contain networks of moving fluids, including digestive pathways, blood vasculature in animals, and the xylem and phloem networks in plants. In these flow networks, bacteria form distinct biofilm structures that have an important role in pathogenesis. The physical mechanisms that determine the spatial organization of bacteria in flow are not understood. Here, we show that the bacteriumP. aeruginosacolonizes flow networks using a cyclical process that consists of surface attachment, upstream movement, detachment, movement with the bulk flow, and surface reattachment. This process, which we have termed dynamic switching, distributes bacterial subpopulations upstream and downstream in flow through two phases: movement on surfaces and cellular movement via the bulk. The model equations that describe dynamic switching are identical to those that describe dynamic instability, a process that enables microtubules in eukaryotic cells to search space efficiently to capture chromosomes. Our results show that dynamic switching enables bacteria to explore flow networks efficiently, which maximizes dispersal and colonization and establishes the organizational structure of biofilms. A number of eukaryotic and mammalian cells also exhibit movement in two phases in flow, which suggests that dynamic switching is a modality that enables efficient dispersal for a broad range of cell types.

Time-of-flight sensor for getting shape model of automobiles toward digital 3D imaging approach of autonomous driving

2021 ◽  
Vol 121 ◽  
pp. 103429
Author(s):  
Ilpo Niskanen ◽  
Matti Immonen ◽  
Lauri Hallman ◽  
Genki Yamamuchi ◽  
Martti Mikkonen ◽  
...  
Keyword(s):  
3D Imaging ◽  
Time Of Flight ◽  
Autonomous Driving ◽  
Shape Model ◽  
Imaging Approach

scholarly journals A quantitative imaging-based screen reveals the exocyst as a network hub connecting endocytosis and exocytosis

2015 ◽  
Vol 26 (13) ◽  
pp. 2519-2534 ◽  
Author(s):  
Mini Jose ◽  
Sylvain Tollis ◽  
Deepak Nair ◽  
Romain Mitteau ◽  
Christophe Velours ◽  
...  
Keyword(s):  
Systems Analysis ◽  
Spatial Organization ◽  
Quantitative Imaging ◽  
Golgi Vesicle ◽  
Biological Processes ◽  
Cellular Polarity ◽  
Vesicle Dynamics ◽  
Maintenance Systems ◽  
Resolution Single ◽  
Single Vesicle

The coupling of endocytosis and exocytosis underlies fundamental biological processes ranging from fertilization to neuronal activity and cellular polarity. However, the mechanisms governing the spatial organization of endocytosis and exocytosis require clarification. Using a quantitative imaging-based screen in budding yeast, we identified 89 mutants displaying defects in the localization of either one or both pathways. High-resolution single-vesicle tracking revealed that the endocytic and exocytic mutants she4∆ and bud6∆ alter post-Golgi vesicle dynamics in opposite ways. The endocytic and exocytic pathways display strong interdependence during polarity establishment while being more independent during polarity maintenance. Systems analysis identified the exocyst complex as a key network hub, rich in genetic interactions with endocytic and exocytic components. Exocyst mutants displayed altered endocytic and post-Golgi vesicle dynamics and interspersed endocytic and exocytic domains compared with control cells. These data are consistent with an important role for the exocyst in coordinating endocytosis and exocytosis.

scholarly journals Tiling light sheet selective plane illumination microscopy using discontinuous light sheets

2018 ◽  
Author(s):  
Liang Gao
Keyword(s):  
Spatial Resolution ◽  
3D Imaging ◽  
High Spatial Resolution ◽  
Image Data ◽  
Image Plane ◽  
Light Sheet ◽  
Selective Plane Illumination Microscopy ◽  
Novel Method ◽  
Technical Details ◽  
Imaging Speed

AbstractTiling light sheet selective plane illumination microscopy (TLS-SPIM) improves 3D imaging ability of SPIM by using a real-time optimized tiling light sheet. However, the imaging speed decreases, and size of the raw image data increases proportionally to the number of tiling positions in TLS-SPIM. The decreased imaging speed and the increased raw data size could cause significant problems when TLS-SPIM is used to image large specimens at high spatial resolution. Here, we present a novel method to solve the problem. Discontinuous light sheets created by scanning coaxial beam arrays synchronized with camera exposures are used for 3D imaging to decrease the number of tiling positions required at each image plane without sacrificing the spatial resolution. We investigate the performance of the method via numerical simulation and discuss the technical details of the method.

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