Dark-Field Hyperspectral Imaging (DF-HSI) Modalities for Characterization of Single Molecule and Cellular Processes

Author(s):  
Nishir Mehta ◽  
Sushant Sahu ◽  
Shahensha Shaik ◽  
Ram Devireddy ◽  
Manas Ranjan Gartia
2016 ◽  
Vol 216 (1) ◽  
pp. 41-51 ◽  
Author(s):  
Enrico Monachino ◽  
Lisanne M. Spenkelink ◽  
Antoine M. van Oijen

Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components.


2019 ◽  
Vol 11 (21) ◽  
pp. 2778-2784
Author(s):  
Bingquan Wang ◽  
Dan Sun ◽  
Ce Zhang ◽  
Kaige Wang ◽  
Jintao Bai

Dark-field microscopy directly detects scattered light from a sample, and therefore requires no fluorescent labeling for single molecule detection.


2020 ◽  
Vol 21 (3) ◽  
pp. 1031 ◽  
Author(s):  
Kiyoto Kamagata ◽  
Yuji Itoh ◽  
Dwiky Rendra Graha Subekti

Interactions between DNA and DNA-binding proteins play an important role in many essential cellular processes. A key function of the DNA-binding protein p53 is to search for and bind to target sites incorporated in genomic DNA, which triggers transcriptional regulation. How do p53 molecules achieve “rapid” and “accurate” target search in living cells? The search dynamics of p53 were expected to include 3D diffusion in solution, 1D diffusion along DNA, and intersegmental transfer between two different DNA strands. Single-molecule fluorescence microscopy enabled the tracking of p53 molecules on DNA and the characterization of these dynamics quantitatively. Recent intensive single-molecule studies of p53 succeeded in revealing each of these search dynamics. Here, we review these studies and discuss the target search mechanisms of p53.


Author(s):  
Songquan Sun ◽  
Richard D. Leapman

Analyses of ultrathin cryosections are generally performed after freeze-drying because the presence of water renders the specimens highly susceptible to radiation damage. The water content of a subcellular compartment is an important quantity that must be known, for example, to convert the dry weight concentrations of ions to the physiologically more relevant molar concentrations. Water content can be determined indirectly from dark-field mass measurements provided that there is no differential shrinkage between compartments and that there exists a suitable internal standard. The potential advantage of a more direct method for measuring water has led us to explore the use of electron energy loss spectroscopy (EELS) for characterizing biological specimens in their frozen hydrated state.We have obtained preliminary EELS measurements from pure amorphous ice and from cryosectioned frozen protein solutions. The specimens were cryotransfered into a VG-HB501 field-emission STEM equipped with a 666 Gatan parallel-detection spectrometer and analyzed at approximately −160 C.


2021 ◽  
Author(s):  
Lucas Domulevicz ◽  
Hyunhak Jeong ◽  
Nayan K. Paul ◽  
Juan Sebastian Gomez-Diaz ◽  
Joshua Hihath

2020 ◽  
Vol 75 (11) ◽  
pp. 913-919
Author(s):  
Frank Krumeich

AbstractSince the 1970s, high-resolution transmission electron microscopy (HRTEM) is well established as the most appropriate method to explore the structural complexity of niobium tungsten oxides. Today, scanning transmission electron microscopy (STEM) represents an important alternative for performing the structural characterization of such oxides. STEM images recorded with a high-angle annular dark field (HAADF) detector provide not only information about the cation positions but also about the distribution of niobium and tungsten as the intensity is directly correlated to the local scattering potential. The applicability of this method is demonstrated here for the characterization of the real structure of Nb7W10O47.5. This sample contains well-ordered domains of Nb8W9O47 and Nb4W7O31 besides little ordered areas according to HRTEM results. Structural models for Nb4W7O31 and twinning occurring in this phase have been derived from the interpretation of HAADF-STEM images. A remarkable grain boundary between well-ordered domains of Nb4W7O31 and Nb8W9O47 has been found that contains one-dimensionally periodic features. Furthermore, short-range order observed in less ordered areas could be attributed to an intimate intergrowth of small sections of different tetragonal tungsten bronze (TTB) based structures.


2021 ◽  
Vol 22 (14) ◽  
pp. 7390
Author(s):  
Nicole Wesch ◽  
Frank Löhr ◽  
Natalia Rogova ◽  
Volker Dötsch ◽  
Vladimir V. Rogov

Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.


Author(s):  
Tzu-Yu Lee ◽  
Yi-Ching Li ◽  
Min-Guan Lin ◽  
Chwan-Deng Hsiao ◽  
Hung-Wen Li

DNA damages lead to stalled or collapsed replication forks. Replication restart primosomes re-initiate DNA synthesis at these stalled or collapsed DNA replication forks, which is important for bacterial survival. Primosomal...


2014 ◽  
Vol 106 (2) ◽  
pp. 269a ◽  
Author(s):  
Laura Tosatto ◽  
Mathew H. Horrocks ◽  
Cremades Nunilo ◽  
Tim Guilliams ◽  
Mauro Dalla Serra ◽  
...  

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