INTRODUCTION TO MODELLING OF AN INTACT BIOLOGICAL CELL: STRUCTURAL BIOLOGY, FLUORESCENCE MICROSCOPY AND COMPUTATIONAL METHODS

Author(s):  
THOMAS R. CECH
ACS Omega ◽  
2020 ◽  
Vol 5 (33) ◽  
pp. 21145-21161
Author(s):  
Santhosh Kumar Nagarajan ◽  
Sathya Babu ◽  
Honglae Sohn ◽  
Thirumurthy Madhavan

2019 ◽  
Vol 2 (1) ◽  
pp. 175-197 ◽  
Author(s):  
Jean-Karim Hériché ◽  
Stephanie Alexander ◽  
Jan Ellenberg

Fluorescence microscopy imaging has long been complementary to DNA sequencing- and mass spectrometry–based omics in biomedical research, but these approaches are now converging. On the one hand, omics methods are moving from in vitro methods that average across large cell populations to in situ molecular characterization tools with single-cell sensitivity. On the other hand, fluorescence microscopy imaging has moved from a morphological description of tissues and cells to quantitative molecular profiling with single-molecule resolution. Recent technological developments underpinned by computational methods have started to blur the lines between imaging and omics and have made their direct correlation and seamless integration an exciting possibility. As this trend continues rapidly, it will allow us to create comprehensive molecular profiles of living systems with spatial and temporal context and subcellular resolution. Key to achieving this ambitious goal will be novel computational methods and successfully dealing with the challenges of data integration and sharing as well as cloud-enabled big data analysis.


2013 ◽  
Author(s):  
Muhammad Mizanur Rahman ◽  
Lutz H. Schaefer ◽  
Dietwald Schuster ◽  
Chrysanthe Preza

2019 ◽  
Author(s):  
Brian C. Ross ◽  
Fabio Anaclerio ◽  
Nicola Lorusso ◽  
Mario Ventura ◽  
Jim Costello

AbstractMeasurement of in-vivo chromosome conformations (structures) in single cells is a major technological goal of structural biology. If one could identify many genetic loci in a microscope image despite the limited palette of fluorescent colors used to label them, then the conformation could be solved at some resolution by ‘connecting the dots’. Computational tools for making this reconstruction are expected to produce near-perfect reconstructions when the number of fluorescent colors is high enough, irrespective of the number of loci assayed. Here we report the first experimental test of the performance of these reconstruction algorithms and check their ability to reconstruct experimentally-measured conformations. We also demonstrate the experimental metrics needed to assess reconstruction quality. Our results indicate that current sequential FISH experiments may be close to the point where the reconstructions are nearly flawless at some distance scales.


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