scholarly journals MicroCT-Based Phenomics in the Zebrafish Skeleton Reveals Virtues of Deep Phenotyping in a Distributed Organ System

Zebrafish ◽  
2018 ◽  
Vol 15 (1) ◽  
pp. 77-78 ◽  
Author(s):  
Matthew Hur ◽  
Charlotte A. Gistelinck ◽  
Philippe Huber ◽  
Jane Lee ◽  
Marjorie H. Thompson ◽  
...  
Keyword(s):  
Organ System ◽  
Deep Phenotyping

scholarly journals MicroCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Matthew Hur ◽  
Charlotte A Gistelinck ◽  
Philippe Huber ◽  
Jane Lee ◽  
Marjorie H Thompson ◽  
...  
Keyword(s):  
Axial Skeleton ◽  
Thyroid Stimulating Hormone ◽  
Organ System ◽  
Genetic Screens ◽  
Spatially Distributed ◽  
Functional Understanding ◽  
Increase Productivity ◽  
Brittle Bone Disease ◽  
Mutant Phenotypes ◽  
Deep Phenotyping

Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of phenotypic measures comprised of morphological and densitometric traits at a large number of sites within the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes associated with human brittle bone disease and thyroid stimulating hormone receptor hyperactivity. Finally, we develop allometric models and show their potential to aid in the discrimination of mutant phenotypes masked by alterations in growth. Our studies demonstrate virtues of deep phenotyping in a spatially distributed organ system. Analyzing phenotypic patterns may increase productivity in genetic screens, and facilitate the study of genetic variants associated with smaller effect sizes, such as those that underlie complex diseases.

scholarly journals Author response: MicroCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system

2017 ◽  
Author(s):  
Matthew Hur ◽  
Charlotte A Gistelinck ◽  
Philippe Huber ◽  
Jane Lee ◽  
Marjorie H Thompson ◽  
...  
Keyword(s):  
Organ System ◽  
Author Response ◽  
Deep Phenotyping

Tissue section lifting for electron microscopy

1978 ◽  
Vol 36 (2) ◽  
pp. 86-87
Author(s):  
Adrian F. van Dellen
Keyword(s):  
Infectious Disease ◽  
Electron Microscopy ◽  
Tissue Culture ◽  
Organ System ◽  
Surrounding Tissue ◽  
Paraffin Sections ◽  
Surface Areas ◽  
Specific Determination ◽  
High Degree ◽  
Accuracy And Repeatability

The morphologic pathologist may require information on the ultrastructure of a non-specific lesion seen under the light microscope before he can make a specific determination. Such lesions, when caused by infectious disease agents, may be sparsely distributed in any organ system. Tissue culture systems, too, may only have widely dispersed foci suitable for ultrastructural study. In these situations, when only a few, small foci in large tissue areas are useful for electron microscopy, it is advantageous to employ a methodology which rapidly selects a single tissue focus that is expected to yield beneficial ultrastructural data from amongst the surrounding tissue. This is in essence what "LIFTING" accomplishes. We have developed LIFTING to a high degree of accuracy and repeatability utilizing the Microlift (Fig 1), and have successfully applied it to tissue culture monolayers, histologic paraffin sections, and tissue blocks with large surface areas that had been initially fixed for either light or electron microscopy.

scholarly journals Science for the Next Century: Deep Phenotyping

2021 ◽  
pp. 002203452110018
Author(s):  
J.T. Wright ◽  
M.C. Herzberg
Keyword(s):  
Health Care ◽  
Human Health ◽  
Care Delivery ◽  
The Past ◽  
Large Populations ◽  
Health And Disease ◽  
Methodological Approaches ◽  
Omic Data ◽  
Precision Health ◽  
Deep Phenotyping

Our ability to unravel the mysteries of human health and disease have changed dramatically over the past 2 decades. Decoding health and disease has been facilitated by the recent availability of high-throughput genomics and multi-omics analyses and the companion tools of advanced informatics and computational science. Understanding of the human genome and its influence on phenotype continues to advance through genotyping large populations and using “light phenotyping” approaches in combination with smaller subsets of the population being evaluated using “deep phenotyping” approaches. Using our capability to integrate and jointly analyze genomic data with other multi-omic data, the knowledge of genotype-phenotype relationships and associated genetic pathways and functions is being advanced. Understanding genotype-phenotype relationships that discriminate human health from disease is speculated to facilitate predictive, precision health care and change modes of health care delivery. The American Association for Dental Research Fall Focused Symposium assembled experts to discuss how studies of genotype-phenotype relationships are illuminating the pathophysiology of craniofacial diseases and developmental biology. Although the breadth of the topic did not allow all areas of dental, oral, and craniofacial research to be addressed (e.g., cancer), the importance and power of integrating genomic, phenomic, and other -omic data are illustrated using a variety of examples. The 8 Fall Focused talks presented different methodological approaches for ascertaining study populations and evaluating population variance and phenotyping approaches. These advances are reviewed in this summary.

scholarly journals Educational Case: Thymoma

2021 ◽  
Vol 8 ◽  
pp. 237428952110219
Author(s):  
Gregory Chandler ◽  
Isaac E. McCool ◽  
Alison R. Huppmann
Keyword(s):  
Medical Education ◽  
Organ System ◽  
Learning Objectives ◽  
National Standards ◽  
Learning Tool ◽  
Full List ◽  
Additional Information ◽  
Disease Mechanisms ◽  
Basic Competencies ◽  
Diagnostic Medicine

The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040 . 1

scholarly journals Educational Case: AA Amyloidosis Complicating Common Variable Immunodeficiency

2021 ◽  
Vol 8 ◽  
pp. 237428952199423
Author(s):  
Meghan E. Kapp ◽  
Mark A. Lusco ◽  
Aaron C. Shaver
Keyword(s):  
Medical Education ◽  
Organ System ◽  
Learning Objectives ◽  
National Standards ◽  
Aa Amyloidosis ◽  
Full List ◽  
Additional Information ◽  
Disease Mechanisms ◽  
Basic Competencies ◽  
Common Variable

The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040 .1

scholarly journals Evaluation of the Addictions Neuroclinical Assessment (ANA) framework through deep phenotyping of problem drinkers

2021 ◽  
Vol 221 ◽  
pp. 108603
Author(s):  
Steven J. Nieto ◽  
Erica N. Grodin ◽  
ReJoyce Green ◽  
Lara A. Ray
Keyword(s):  
Problem Drinkers ◽  
Deep Phenotyping
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