scholarly journals Density Distribution Maps: A Novel Tool for Subcellular Distribution Analysis and Quantitative Biomedical Imaging

Sensors ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 1009
Author(s):  
Ilaria De Santis ◽  
Michele Zanoni ◽  
Chiara Arienti ◽  
Alessandro Bevilacqua ◽  
Anna Tesei
Keyword(s):  
Density Distribution ◽  
Large Scale ◽  
Super Resolution ◽  
Spatial Location ◽  
Relative Displacement ◽  
Distribution Analysis ◽  
Laboratory Equipment ◽  
Imaging Device ◽  
Distribution Maps ◽  
Super Resolution Microscopy

Subcellular spatial location is an essential descriptor of molecules biological function. Presently, super-resolution microscopy techniques enable quantification of subcellular objects distribution in fluorescence images, but they rely on instrumentation, tools and expertise not constituting a default for most of laboratories. We propose a method that allows resolving subcellular structures location by reinforcing each single pixel position with the information from surroundings. Although designed for entry-level laboratory equipment with common resolution powers, our method is independent from imaging device resolution, and thus can benefit also super-resolution microscopy. The approach permits to generate density distribution maps (DDMs) informative of both objects’ absolute location and self-relative displacement, thus practically reducing location uncertainty and increasing the accuracy of signal mapping. This work proves the capability of the DDMs to: (a) improve the informativeness of spatial distributions; (b) empower subcellular molecules distributions analysis; (c) extend their applicability beyond mere spatial object mapping. Finally, the possibility of enhancing or even disclosing latent distributions can concretely speed-up routine, large-scale and follow-up experiments, besides representing a benefit for all spatial distribution studies, independently of the image acquisition resolution. DDMaker, a Software endowed with a user-friendly Graphical User Interface (GUI), is also provided to support users in DDMs creation.

Modeling large-scale dynamic processes in the cell: polarization, waves, and division

2014 ◽  
Vol 47 (3) ◽  
pp. 221-248 ◽  
Author(s):  
David Sept ◽  
Anders E. Carlsson
Keyword(s):  
Large Scale ◽  
Super Resolution ◽  
Cell Polarization ◽  
Fluorescent Labeling ◽  
Detailed Knowledge ◽  
Biophysical Modeling ◽  
Quantitative Understanding ◽  
Actin Waves ◽  
Super Resolution Microscopy ◽  
Compare And Contrast

AbstractThe past decade has witnessed significant developments in molecular biology techniques, fluorescent labeling, and super-resolution microscopy, and together these advances have vastly increased our quantitative understanding of the cell. This detailed knowledge has concomitantly opened the door for biophysical modeling on a cellular scale. There have been comprehensive models produced describing many processes such as motility, transport, gene regulation, and chemotaxis. However, in this review we focus on a specific set of phenomena, namely cell polarization, F-actin waves, and cytokinesis. In each case, we compare and contrast various published models, highlight the relevant aspects of the biology, and provide a sense of the direction in which the field is moving.

scholarly journals Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging?

2021 ◽  
Vol 22 (13) ◽  
pp. 6730
Author(s):  
Paweł Matryba ◽  
Kacper Łukasiewicz ◽  
Monika Pawłowska ◽  
Jacek Tomczuk ◽  
Jakub Gołąb
Keyword(s):  
Large Scale ◽  
Rapid Development ◽  
Super Resolution ◽  
Molecular Probes ◽  
Dimensional Structure ◽  
Fluorescence Signal ◽  
Microscopy Imaging ◽  
Optical Clearing ◽  
Super Resolution Microscopy ◽  
Tissue Optical Clearing

The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.

scholarly journals Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 233 ◽  
Author(s):  
Emma Touizer ◽  
Christian Sieben ◽  
Ricardo Henriques ◽  
Mark Marsh ◽  
Romain F. Laine
Keyword(s):  
Influenza Virus ◽  
Host Cell ◽  
Virus Replication ◽  
Large Scale ◽  
Super Resolution ◽  
Living Cells ◽  
Influenza Viruses ◽  
Animal Populations ◽  
Influenza Virus Replication ◽  
Super Resolution Microscopy

With an estimated three to five million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society, and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance, how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated, providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are providing new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.

scholarly journals Co-Density Distribution Maps for Advanced Molecule Colocalization and Co-Distribution Analysis

Sensors ◽  
2021 ◽  
Vol 21 (19) ◽  
pp. 6385
Author(s):  
Ilaria De Santis ◽  
Luca Lorenzini ◽  
Marzia Moretti ◽  
Elisa Martella ◽  
Enrico Lucarelli ◽  
...  
Keyword(s):  
Density Distribution ◽  
Relative Position ◽  
Signal Intensity ◽  
Visual Inspection ◽  
Correlation Coefficients ◽  
Distribution Analysis ◽  
Important Indicator ◽  
Distribution Maps ◽  
Local Abundance ◽  
Potential Improvement

Cellular and subcellular spatial colocalization of structures and molecules in biological specimens is an important indicator of their co-compartmentalization and interaction. Presently, colocalization in biomedical images is addressed with visual inspection and quantified by co-occurrence and correlation coefficients. However, such measures alone cannot capture the complexity of the interactions, which does not limit itself to signal intensity. On top of the previously developed density distribution maps (DDMs), here, we present a method for advancing current colocalization analysis by introducing co-density distribution maps (cDDMs), which, uniquely, provide information about molecules absolute and relative position and local abundance. We exemplify the benefits of our method by developing cDDMs-integrated pipelines for the analysis of molecules pairs co-distribution in three different real-case image datasets. First, cDDMs are shown to be indicators of colocalization and degree, able to increase the reliability of correlation coefficients currently used to detect the presence of colocalization. In addition, they provide a simultaneously visual and quantitative support, which opens for new investigation paths and biomedical considerations. Finally, thanks to the coDDMaker software we developed, cDDMs become an enabling tool for the quasi real time monitoring of experiments and a potential improvement for a large number of biomedical studies.

scholarly journals The WAVE complex associates with sites of saddle membrane curvature

2021 ◽  
Vol 220 (8) ◽  
Author(s):  
Anne Pipathsouk ◽  
Rachel M. Brunetti ◽  
Jason P. Town ◽  
Brian R. Graziano ◽  
Artù Breuer ◽  
...  
Keyword(s):  
Cell Shape ◽  
Large Scale ◽  
Super Resolution ◽  
Membrane Curvature ◽  
Cell Morphogenesis ◽  
Cell Behaviors ◽  
Complex Forms ◽  
Super Resolution Microscopy ◽  
Wave Complex ◽  
Organizing Principles

How local interactions of actin regulators yield large-scale organization of cell shape and movement is not well understood. Here we investigate how the WAVE complex organizes sheet-like lamellipodia. Using super-resolution microscopy, we find that the WAVE complex forms actin-independent 230-nm-wide rings that localize to regions of saddle membrane curvature. This pattern of enrichment could explain several emergent cell behaviors, such as expanding and self-straightening lamellipodia and the ability of endothelial cells to recognize and seal transcellular holes. The WAVE complex recruits IRSp53 to sites of saddle curvature but does not depend on IRSp53 for its own localization. Although the WAVE complex stimulates actin nucleation via the Arp2/3 complex, sheet-like protrusions are still observed in ARP2-null, but not WAVE complex-null, cells. Therefore, the WAVE complex has additional roles in cell morphogenesis beyond Arp2/3 complex activation. Our work defines organizing principles of the WAVE complex lamellipodial template and suggests how feedback between cell shape and actin regulators instructs cell morphogenesis.

scholarly journals A toolbox of anti-mouse and rabbit IgG secondary nanobodies

2017 ◽  
Author(s):  
Tino Pleiner ◽  
Mark Bates ◽  
Dirk Görlich
Keyword(s):  
Large Scale ◽  
Ethical Problem ◽  
Super Resolution ◽  
Superior Performance ◽  
Affinity Tags ◽  
Site Specific ◽  
E Coli ◽  
Rabbit Igg ◽  
Secondary Antibodies ◽  
Super Resolution Microscopy

AbstractPolyclonal anti-IgG secondary antibodies are essential tools for many molecular biology techniques and diagnostic tests. Their animal-based production is, however, a major ethical problem. Here, we introduce a sustainable alternative, namely nanobodies against all mouse IgG subclasses and rabbit IgG. They can be produced at large scale in E. coli and could thus make secondary antibody-production in animals obsolete. Their recombinant nature allows fusion with affinity tags or reporter enzymes as well as efficient maleimide chemistry for fluorophore-coupling. We demonstrate their superior performance in Western Blotting, both in peroxidase- and fluorophore-linked form. Their site-specific labeling with multiple fluorophores creates bright imaging reagents for confocal and super-resolution microscopy with much smaller label displacement than traditional secondary antibodies. They also enable simpler and faster immunostaining protocols and even allow multi-target localization with primary IgGs from the same species and of the same class.

Prevalence and geographic distribution of haemophilia in Costa Rica

2010 ◽  
Vol 30 (S 01) ◽  
pp. S28-S31 ◽  
Author(s):  
J. Arroyo ◽  
L. Salazar-Sánchez ◽  
G. Jiménez-Cruz ◽  
P. Chaverri ◽  
E. Arrieta-Bolaños ◽  
...  
Keyword(s):  
Costa Rica ◽  
Survival Rates ◽  
Coagulation Factors ◽  
Developed Countries ◽  
Health Centers ◽  
Distribution Analysis ◽  
Distribution Maps ◽  
Immunodeficiency Virus ◽  
The Many ◽  
Low Prevalence

SummaryHaemophilia is the most frequent hereditary haemorrhagic illness and it is due to the deficiency of coagulation factors VIII (haemophilia A, HA) or IX (haemophilia B, HB).The prevalence of this disease varies according to the country, those having better survival rates having also higher prevalences. Specifically in Costa Rica, there are around 130 HA and 30 HB families. This study reports the prevalence and a spatial distribution analysis of both types of the disease in this country. The prevalence of haemophilia in this country is 7 cases per 100 000 men, for HA it is 6 cases per 100 000 and for HB it is 1 case per 100 000 male inhabitants. The prevalence of this disease is low when compared with other populations. This low prevalence could be due to the many patients that have died because of infection with human immunodeficiency virus during the 1980s. The prevalence of haemophilia in Costa Rica is almost one half of that present in developed countries. Nevertheless, the ratio between HA and HB follows world tendency: 5 : 1. In this study, nationwide geographical distribution maps were drawn in order to visualize the origin of severe cases and how this influences the pattern of distribution for both types of haemophilia. By means of these maps, it was possible to state that there is no association between the sites of maximum prevalence of mutated alleles and ethnicity. With this study, haemophilia prevalence distribution maps can be used to improve efforts for the establishment of hemophilia clinics or specialized health centers in those areas which hold the highest prevalences in this country. Also, this knowledge can be applied to improve treatment skills and offer the possibility of developing focused genetic counseling for these populations.

Super-Resolution Microscopy in Studying the Structure and Function of the Cell Nucleus

Acta Naturae ◽  
2017 ◽  
Vol 9 (4) ◽  
pp. 42-51
Author(s):  
S. S. Ryabichko ◽  
◽  
A. N. Ibragimov ◽  
L. A. Lebedeva ◽  
E. N. Kozlov ◽  
...  
Keyword(s):  
Cell Nucleus ◽  
Super Resolution ◽  
Structure And Function ◽  
And Function ◽  
Super Resolution Microscopy

Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins

2019 ◽  
Author(s):  
Jeffrey Chang ◽  
Matthew Romei ◽  
Steven Boxer
Keyword(s):  
Rational Design ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Super Resolution ◽  
Unit Cell Size ◽  
Chlorine Substituent ◽  
Gfp Chromophore ◽  
The One ◽  
Green Fluorescent ◽  
Super Resolution Microscopy

<p>Double-bond photoisomerization in molecules such as the green fluorescent protein (GFP) chromophore can occur either via a volume-demanding one-bond-flip pathway or via a volume-conserving hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization would inform the rational design of photoswitchable GFPs as improved tools for super-resolution microscopy. In this communication, we reveal the photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving crystal structures of <i>cis</i> and <i>trans</i> rsEGFP2 containing a monochlorinated chromophore. The position of the chlorine substituent in the <i>trans</i> state breaks the symmetry of the phenolate ring of the chromophore and allows us to distinguish the two pathways. Surprisingly, we find that the pathway depends on the arrangement of protein monomers within the crystal lattice: in a looser packing, the one-bond-flip occurs, whereas in a tighter packing (7% smaller unit cell size), the hula-twist occurs.</p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p> <p> </p>

Sign in / Sign up

Export Citation Format

Share Document