scholarly journals Plastic embedding for precise imaging of large-scale biological tissues labeled with multiple fluorescent dyes and proteins

2021 ◽  
Author(s):  
Miao Ren ◽  
JiaoJiao Tian ◽  
Qingtao Sun ◽  
Siqi Chen ◽  
Ting Luo ◽  
...  
Keyword(s):  
Large Scale ◽  
Fluorescent Dyes ◽  
Biological Tissues ◽  
Plastic Embedding

scholarly journals Clearing and Labeling Techniques for Large-Scale Biological Tissues

2016 ◽  
Vol 39 (6) ◽  
pp. 439-446 ◽  
Author(s):  
Jinyoung Seo ◽  
Minjin Choe ◽  
Sung-Yon Kim
Keyword(s):  
Large Scale ◽  
Biological Tissues

scholarly journals Small-scale demixing in confluent biological tissues

Soft Matter ◽  
2020 ◽  
Vol 16 (13) ◽  
pp. 3325-3337 ◽  
Author(s):  
Preeti Sahu ◽  
Daniel M. Sussman ◽  
Matthias Rübsam ◽  
Aaron F. Mertz ◽  
Valerie Horsley ◽  
...  
Keyword(s):  
Interfacial Tension ◽  
Cell Shape ◽  
Large Scale ◽  
Biological Tissues ◽  
Small Scale

While interfacial tension in confluent cellular mixtures leads to large-scale demixing, cell shape disparity leads to robust small-scale demixing that is observed in experiments and can be explained via neighbor exchange barriers at an interface.

scholarly journals Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields

2020 ◽  
Author(s):  
Cheng-Wei Ju ◽  
Hanzhi Bai ◽  
Bo Li ◽  
Rizhang Liu
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Large Scale ◽  
Fluorescent Dyes ◽  
Photophysical Properties ◽  
Quantum Yields ◽  
Substitution Effects ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Fluorescent Materials

<div> <p>The development of functional organic fluorescent materials calls for fast and accurate predictions of photophysical parameters for processes such as high-throughput virtual screening, while the task is challenged by the limitations of quantum mechanical calculations. We establish a database covering >4,300 solvated organic fluorescent dyes and develop new machine learning (ML) approach aimed at efficient and accurate predictions of emission wavelength and photoluminescence quantum yield (PLQY). Our feature engineering has given rise to Functionalized Structure Descriptor (FSD) and Comprehensive General Solvent Descriptor (CGSD), whereby a highly black-box computational framework is realized with consistently good accuracy across different dye families, ability of describing substitution effects and solvent effects, efficiency for large-scale predictions and workability with on-the-fly learning. Evaluations with unseen molecules suggests a remarkable MAE of 0.13 for PLQY and 0.080 eV for emission energy, the latter comparable to time-dependent density functional theory (TD-DFT) calculations. An online prediction platform was constructed based on the ensemble model to make prediction in various solvents (https://www.chemfluor.top/). Our statistical learning methodology will complement quantum mechanical calculations as an efficient alternative approach for the prediction of these parameters.<br></p> </div><p> <br></p>

scholarly journals Highly Infectious Prions Generated by a Single Round of Microplate-Based Protein Misfolding Cyclic Amplification

mBio ◽  
2013 ◽  
Vol 5 (1) ◽  
Author(s):  
Mohammed Moudjou ◽  
Pierre Sibille ◽  
Guillaume Fichet ◽  
Fabienne Reine ◽  
Jérôme Chapuis ◽  
...  
Keyword(s):  
High Throughput ◽  
Protein Misfolding ◽  
Large Scale ◽  
Biological Tissues ◽  
Protein Misfolding Cyclic Amplification ◽  
Bodily Fluids ◽  
Sensitive Tool ◽  
Jakob Disease ◽  
Laboratory Bioassays

ABSTRACTMeasurements of the presence of prions in biological tissues or fluids rely more and more on cell-free assays. Although protein misfolding cyclic amplification (PMCA) has emerged as a valuable, sensitive tool, it is currently hampered by its lack of robustness and rapidity for high-throughput purposes. Here, we made a number of improvements making it possible to amplify the maximum levels of scrapie prions in a single 48-h round and in a microplate format. The amplification rates and the infectious titer of the PMCA-formed prions appeared similar to those derived from thein vivolaboratory bioassays. This enhanced technique also amplified efficiently prions from different species, including those responsible for human variant Creutzfeldt-Jakob disease. This new format should help in developing ultrasensitive, high-throughput prion assays for cognitive, diagnostic, and therapeutic applications.IMPORTANCEThe method developed here allows large-scale, fast, and reliable cell-free amplification of subinfectious levels of prions from different species. The sensitivity and rapidity achieved approach or equal those of other recently developed prion-seeded conversion assays. Our simplified assay may be amenable to high-throughput, automated purposes and serve in a complementary manner with other recently developed assays for urgently needed antemortem diagnostic tests, by using bodily fluids containing small amounts of prion infectivity. Such a combination of assays is of paramount importance to reduce the transfusion risk in the human population and to identify asymptomatic carriers of variant Creutzfeldt-Jakob disease.

Facile Large-Scale Synthesis of 5- and 6-Carboxyfluoresceins: Application for the Preparation of New Fluorescent Dyes

2015 ◽  
Vol 2015 (33) ◽  
pp. 7301-7309 ◽  
Author(s):  
Peter Hammershøj ◽  
E. K. Pramod Kumar ◽  
Pernille Harris ◽  
Thomas L. Andresen ◽  
Mads H. Clausen
Keyword(s):  
Large Scale ◽  
Fluorescent Dyes ◽  
Large Scale Synthesis

Different Impact of Staining Procedures Using Visible Stains and Fluorescent Dyes for Large-Scale Investigation of Proteomes by MALDI-TOF Mass Spectrometry

2006 ◽  
Vol 5 (3) ◽  
pp. 512-520 ◽  
Author(s):  
François Chevalier ◽  
Delphine Centeno ◽  
Valérie Rofidal ◽  
Marc Tauzin ◽  
Olivier Martin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Fluorescent Dyes ◽  
Maldi Tof Mass Spectrometry ◽  
Maldi Tof

scholarly journals Mesoscale substrate curvature overrules nanoscale contact guidance to direct bone marrow stromal cell migration

2018 ◽  
Vol 15 (145) ◽  
pp. 20180162 ◽  
Author(s):  
Maike Werner ◽  
Nicholas A. Kurniawan ◽  
Gabriela Korus ◽  
Carlijn V. C. Bouten ◽  
Ansgar Petersen
Keyword(s):  
Bone Marrow ◽  
Cellular Response ◽  
Large Scale ◽  
Biological Tissues ◽  
Collagen Fibrils ◽  
Contact Guidance ◽  
Cylinder Axis ◽  
Cylinder Diameter ◽  
Substrate Curvature ◽  
And Migration

The intrinsic architecture of biological tissues and of implanted biomaterials provides cells with large-scale geometrical cues. To understand how cells are able to sense and respond to complex structural environments, a deeper insight into the cellular response to multi-scale and conflicting geometrical cues is needed. In this study, we subjected human bone marrow stromal cells (hBMSCs) to mesoscale cylindrical surfaces (diameter 250–5000 µm) and nanoscale collagen fibrils (diameter 100–200 nm) that were aligned perpendicular to the cylinder axis. On flat surfaces and at low substrate curvatures (cylinder diameter d > 1000 µm), cell alignment and migration were governed by the nanoscale collagen fibrils, consistent with the contact guidance effect. With increasing surface curvature (decreasing cylinder diameter, d < 1000 µm), cells increasingly aligned and migrated along the cylinder axis, i.e. the direction of zero curvature. An increase in phosphorylated myosin light chain levels was observed with increasing substrate curvature, suggesting a link between substrate-induced cell bending and the F-actin–myosin machinery. Taken together, this work demonstrates that geometrical cues of up to 10× cell size can play a dominant role in directing hBMSC alignment and migration and that the effect of nanoscale contact guidance can even be overruled by mesoscale curvature guidance.

scholarly journals An in vivo reporter for tracking lipid droplet dynamics in transparent zebrafish

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Dianne Lumaquin ◽  
Eleanor Johns ◽  
Emily Montal ◽  
Joshua M Weiss ◽  
David Ola ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Lipid Droplet ◽  
Lipid Droplets ◽  
Large Scale ◽  
Fluorescent Dyes ◽  
Cell Types ◽  
Structural Protein ◽  
Droplet Dynamics

Lipid droplets are lipid storage organelles found in nearly all cell types from adipocytes to cancer cells. Although increasingly implicated in disease, current methods to study lipid droplets in vertebrate models rely on static imaging or the use of fluorescent dyes, limiting investigation of their rapid in vivo dynamics. To address this, we created a lipid droplet transgenic reporter in whole animals and cell culture by fusing tdTOMATO to Perilipin-2 (PLIN2), a lipid droplet structural protein. Expression of this transgene in transparent casper zebrafish enabled in vivo imaging of adipose depots responsive to nutrient deprivation and high-fat diet. Simultaneously, we performed a large-scale in vitro chemical screen of 1280 compounds and identified several novel regulators of lipolysis in adipocytes. Using our Tg(-3.5ubb:plin2-tdTomato) zebrafish line, we validated several of these novel regulators and revealed an unexpected role for nitric oxide in modulating adipocyte lipid droplets. Similarly, we expressed the PLIN2-tdTOMATO transgene in melanoma cells and found that the nitric oxide pathway also regulated lipid droplets in cancer. This model offers a tractable imaging platform to study lipid droplets across cell types and disease contexts using chemical, dietary, or genetic perturbations.

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