scholarly journals Interphase Human Chromosome Exhibits Out of Equilibrium Glassy Dynamics

2017 ◽  
Author(s):  
Guang Shi ◽  
Lei Liu ◽  
Changbong Hyeon ◽  
D. Thirumalai
Keyword(s):  
Ostwald Ripening ◽  
Imaging Techniques ◽  
Mean Square Displacement ◽  
Super Resolution ◽  
Spatial Distance ◽  
Base Pairs ◽  
Glassy Dynamics ◽  
Distance Information ◽  
Contact Maps ◽  
Super Resolution Microscopy

AbstractThe structural organization of the condensed chromosomes is being revealed using chromosome conformation capture experiments and super-resolution imaging techniques. Fingerprints of their three-dimensional organization on length scale from about hundred kilo base pairs to millions of base pairs have emerged using advances in Hi-C and super-resolution microscopy. To determine the poorly understood dynamics of human interphase chromosomes, we created the Chromosome Copolymer Model (CCM) by representing the chromosomes as a self-avoiding polymer with two loci types corresponding to euchromatin and heterochromatin. Using advanced clustering algorithms we establish quantitatively that the simulated contact maps for chromosomes 5 and 10 and those inferred from Hi-C experiments are in agreement. Ward Linkage Matrix (WLM), constructed from spatial distance information, shows that the Topologically Associated Domains (TADs) and compartments predicted from simulations are in agreement with inferred WLM computed using data from super-resolution microscopy experiments. Glassy dynamics is manifested in the stretched exponential relaxation of the structure factor and caging in the mean square displacement of individual loci, ∆i(t) ∼ tα with 0 < α < 1. Remarkably, the distribution of α, is extremely broad suggestive of highly heterogeneous dynamics, which is also reflected in the large cell-to-cell variations in the contact maps. Chromosome organization is hierarchical involving the formation of chromosome droplets (CDs) on short genomic scale followed by coalescence of the CDs, reminiscent of Ostwald ripening. We propose that glassy landscapes for the condensed active chromosomes might provide a balance between genomic conformational stability and biological functions.

scholarly journals Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes

2021 ◽  
Vol 22 (4) ◽  
pp. 1903
Author(s):  
Ivona Kubalová ◽  
Alžběta Němečková ◽  
Klaus Weisshart ◽  
Eva Hřibová ◽  
Veit Schubert
Keyword(s):  
Single Molecule ◽  
Imaging Techniques ◽  
Chromatin Condensation ◽  
Super Resolution ◽  
Stimulated Emission ◽  
Wide Field ◽  
Structured Illumination Microscopy ◽  
Metaphase Chromosomes ◽  
Localization Microscopy ◽  
Super Resolution Microscopy

The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.

scholarly journals TDP-43 proteinopathy impairs neuronal mRNP granule mediated postsynaptic local translation and mRNA metabolism

2019 ◽  
Author(s):  
Chia-En Wong ◽  
Kuen-Jer Tsai
Keyword(s):  
Imaging Techniques ◽  
Super Resolution ◽  
Protein Translation ◽  
Local Protein Synthesis ◽  
Mrna Metabolism ◽  
Molecular Approaches ◽  
Super Resolution Microscopy ◽  
First Time ◽  
Activity Dependent ◽  
Local Protein

AbstractLocal protein synthesis and mRNA metabolism mediated by mRNP granules in the dendrites and the postsynaptic compartments is essential for synaptic remodelling and plasticity in the neuronal cells. Misregulation in these processes caused by TDP-43 proteinopathy lead to neurodegenerative diseases such frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Using biochemical analysis and imaging techniques including super-resolution microscopy, we provide evidences for the first time of the postsynaptic localization of TDP-43 in the mammalian synapses; and we show TDP-43 as a component of neuronal mRNP granules. With activity stimulation and different molecular approaches, we further demonstrate activity-dependent mRNP granule dynamics involving disassembly of mRNP granules, release of mRNAs, and activation of local protein translation as long as impairments in models of TDP-43 proteinopathy. This study elucidates the interplay between TDP-43 and neuronal mRNP granules in normal physiology and TDP-43 proteinopathy in regulation of local protein translation and mRNA metabolism in the postsynaptic compartment.

Expansion Microscopy: Scalable and Convenient Super-Resolution Microscopy

2019 ◽  
Vol 35 (1) ◽  
pp. 683-701 ◽  
Author(s):  
Paul W. Tillberg ◽  
Fei Chen
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Resolving Power ◽  
Relative Ease ◽  
Nanoscale Structures ◽  
Physical Form ◽  
Tissue Specimens ◽  
Super Resolution Microscopy

Expansion microscopy (ExM) is a physical form of magnification that increases the effective resolving power of any microscope. Here, we describe the fundamental principles of ExM, as well as how recently developed ExM variants build upon and apply those principles. We examine applications of ExM in cell and developmental biology for the study of nanoscale structures as well as ExM's potential for scalable mapping of nanoscale structures across large sample volumes. Finally, we explore how the unique anchoring and hydrogel embedding properties enable postexpansion molecular interrogation in a purified chemical environment. ExM promises to play an important role complementary to emerging live-cell imaging techniques, because of its relative ease of adoption and modification and its compatibility with tissue specimens up to at least 200 μm thick.

scholarly journals Fast widefield scan provides tunable and uniform illumination optimizing super-resolution microscopy on large fields

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Adrien Mau ◽  
Karoline Friedl ◽  
Christophe Leterrier ◽  
Nicolas Bourg ◽  
Sandrine Lévêque-Fort
Keyword(s):  
Single Molecule ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Uniform Illumination ◽  
Optical Sectioning ◽  
Coated Pits ◽  
Laser Illumination ◽  
Quantitative Analyses ◽  
Super Resolution Microscopy ◽  
Single Molecule Localization Microscopy

AbstractNon-uniform illumination limits quantitative analyses of fluorescence imaging techniques. In particular, single molecule localization microscopy (SMLM) relies on high irradiances, but conventional Gaussian-shaped laser illumination restricts the usable field of view to around 40 µm × 40 µm. We present Adaptable Scanning for Tunable Excitation Regions (ASTER), a versatile illumination technique that generates uniform and adaptable illumination. ASTER is also highly compatible with optical sectioning techniques such as total internal reflection fluorescence (TIRF). For SMLM, ASTER delivers homogeneous blinking kinetics at reasonable laser power over fields-of-view up to 200 µm × 200 µm. We demonstrate that ASTER improves clustering analysis and nanoscopic size measurements by imaging nanorulers, microtubules and clathrin-coated pits in COS-7 cells, and β2-spectrin in neurons. ASTER’s sharp and quantitative illumination paves the way for high-throughput quantification of biological structures and processes in classical and super-resolution fluorescence microscopies.

scholarly journals Recent Advances in Organelle-Targeted Fluorescent Probes

Molecules ◽  
2021 ◽  
Vol 26 (1) ◽  
pp. 217
Author(s):  
Na-Eun Choi ◽  
Ji-Yu Lee ◽  
Eun-Chae Park ◽  
Ju-Hee Lee ◽  
Jiyoun Lee
Keyword(s):  
Fluorescent Probes ◽  
Molecular Level ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Structural Features ◽  
Future Directions ◽  
Cellular Processes ◽  
Biochemical Pathways ◽  
Recent Advances ◽  
Super Resolution Microscopy

Recent advances in fluorescence imaging techniques and super-resolution microscopy have extended the applications of fluorescent probes in studying various cellular processes at the molecular level. Specifically, organelle-targeted probes have been commonly used to detect cellular metabolites and transient chemical messengers with high precision and have become invaluable tools to study biochemical pathways. Moreover, several recent studies reported various labeling strategies and novel chemical scaffolds to enhance target specificity and responsiveness. In this review, we will survey the most recent reports of organelle-targeted fluorescent probes and assess their general strategies and structural features on the basis of their target organelles. We will discuss the advantages of the currently used probes and the potential challenges in their application as well as future directions.

scholarly journals Nanoscopy on the Chea(i)p

2020 ◽  
Author(s):  
Benedict Diederich ◽  
Øystein Helle ◽  
Patrick Then ◽  
Pablo Carravilla ◽  
Kay Oliver Schink ◽  
...  
Keyword(s):  
Single Molecule ◽  
Imaging Techniques ◽  
Low Cost ◽  
Super Resolution ◽  
Image Sensor ◽  
Optical Diffraction ◽  
Sensor Technology ◽  
Safety Level ◽  
Resolution Imaging ◽  
Super Resolution Microscopy

AbstractSuper-resolution microscopy allows for stunning images with a resolution well beyond the optical diffraction limit, but the imaging techniques are demanding in terms of instrumentation and software. Using scientific-grade cameras, solid-state lasers and top-shelf microscopy objective lenses drives the price and complexity of the system, limiting its use to well-funded institutions. However, by harnessing recent developments in CMOS image sensor technology and low-cost illumination strategies, super-resolution microscopy can be made available to the mass-markets for a fraction of the price. Here, we present a 3D printed, self-contained super-resolution microscope with a price tag below 1000 $ including the objective and a cellphone. The system relies on a cellphone to both acquire and process images as well as control the hardware, and a photonic-chip enabled illumination. The system exhibits 100nm optical resolution using single-molecule localization microscopy and can provide live super-resolution imaging using light intensity fluctuation methods. Furthermore, due to its compactness, we demonstrate its potential use inside bench-top incubators and high biological safety level environments imaging SARS-CoV-2 viroids. By the development of low-cost instrumentation and by sharing the designs and manuals, the stage for democratizing super-resolution imaging is set.

scholarly journals Structured illumination microscopy and its new developments

2016 ◽  
Vol 09 (03) ◽  
pp. 1630010 ◽  
Author(s):  
Jianling Chen ◽  
Caimin Qiu ◽  
Minghai You ◽  
Xiaogang Chen ◽  
Hongqin Yang ◽  
...  
Keyword(s):  
Optical Microscopy ◽  
Spatial Resolution ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Living Cells ◽  
The Other ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Recent Developments ◽  
Super Resolution Microscopy

Optical microscopy allows us to observe the biological structures and processes within living cells. However, the spatial resolution of the optical microscopy is limited to about half of the wavelength by the light diffraction. Structured illumination microscopy (SIM), a type of new emerging super-resolution microscopy, doubles the spatial resolution by illuminating the specimen with a patterned light, and the sample and light source requirements of SIM are not as strict as the other super-resolution microscopy. In addition, SIM is easier to combine with the other imaging techniques to improve their imaging resolution, leading to the developments of diverse types of SIM. SIM has great potential to meet the various requirements of living cells imaging. Here, we review the recent developments of SIM and its combination with other imaging techniques.

scholarly journals Imaging the kidney: from light to super-resolution microscopy

2019 ◽  
Vol 36 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Maria Lucia Angelotti ◽  
Giulia Antonelli ◽  
Carolina Conte ◽  
Paola Romagnani
Keyword(s):  
Electron Microscopy ◽  
Kidney Diseases ◽  
Imaging Techniques ◽  
Imaging Mass Spectrometry ◽  
Multiphoton Microscopy ◽  
Three Dimensional ◽  
Super Resolution ◽  
Classification Systems ◽  
Fluorescence Lifetime Imaging ◽  
Super Resolution Microscopy

Abstract The important achievements in kidney physiological and pathophysiological mechanisms can largely be ascribed to progress in the technology of microscopy. Much of what we know about the architecture of the kidney is based on the fundamental descriptions of anatomic microscopists using light microscopy and later by ultrastructural analysis provided by electron microscopy. These two techniques were used for the first classification systems of kidney diseases and for their constant updates. More recently, a series of novel imaging techniques added the analysis in further dimensions of time and space. Confocal microscopy allowed us to sequentially visualize optical sections along the z-axis and the availability of specific analysis software provided a three-dimensional rendering of thicker tissue specimens. Multiphoton microscopy permitted us to simultaneously investigate kidney function and structure in real time. Fluorescence-lifetime imaging microscopy allowed to study the spatial distribution of metabolites. Super-resolution microscopy increased sensitivity and resolution up to nanoscale levels. With cryo-electron microscopy, researchers could visualize the individual biomolecules at atomic levels directly in the tissues and understand their interaction at subcellular levels. Finally, matrix-assisted laser desorption/ionization imaging mass spectrometry permitted the measuring of hundreds of different molecules at the same time on tissue sections at high resolution. This review provides an overview of available kidney imaging strategies, with a focus on the possible impact of the most recent technical improvements.

scholarly journals Theranostics with radiation-induced ultrasound emission (TRUE)

2018 ◽  
Vol 11 (03) ◽  
pp. 1830002
Author(s):  
Elijah Robertson ◽  
Liangzhong Xiang
Keyword(s):  
Radiation Dosimetry ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Optical Diffraction ◽  
Cellular Structures ◽  
Fluorescence Labeling ◽  
X Ray ◽  
Radiation Induced ◽  
Ray Projection ◽  
Super Resolution Microscopy

Two novel ultrasound imaging techniques with imaging contrast mechanisms are in the works: X-ray-induced acoustic computed tomography (XACT), and nanoscale photoacoustic tomography (nPAT). XACT has incredible potential in: (1) biomedical imaging, through which a 3D image can be generated using only a single X-ray projection, and (2) radiation dosimetry. nPAT as a new alternative of super-resolution microscopy can break through the optical diffraction limit and is capable of exploring sub-cellular structures without reliance on fluorescence labeling. We expect these new imaging techniques to find widespread applications in both pre-clinical and clinical biomedical research.

scholarly journals Innovative affinitätsbasierte Markierungen für die High-End-Mikroskopie

BIOspektrum ◽  
2021 ◽  
Vol 27 (7) ◽  
pp. 709-712
Author(s):  
Vladimir Khayenko ◽  
Hans Michael Maric
Keyword(s):  
Imaging Techniques ◽  
Life Sciences ◽  
Super Resolution ◽  
Tissue Imaging ◽  
Protein Labelling ◽  
Free Protein ◽  
Endogenous Proteins ◽  
Super Resolution Microscopy

AbstractAdvanced tissue imaging techniques and super resolution microscopy are opening new avenues of investigations in life sciences. These mainly instrumentation-driven innovations require the development of appropriate molecular labelling tools. Here, we discuss currently used and upcoming manipulation-free protein labelling strategies and their potential for the precise and interference-free visualization of endogenous proteins.

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