Nanopipette-Based SERS Aptasensor for Subcellular Localization of Cancer Biomarker in Single Cells

2017 ◽  
Vol 89 (18) ◽  
pp. 9911-9917 ◽  
Author(s):  
Sumaira Hanif ◽  
Hai-Ling Liu ◽  
Saud Asif Ahmed ◽  
Jin-Mei Yang ◽  
Yue Zhou ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Single Cells ◽  
Cancer Biomarker

scholarly journals Accurate classification of protein subcellular localization from high throughput microscopy images using deep learning

2016 ◽  
Author(s):  
Tanel Pärnamaa ◽  
Leopold Parts
Keyword(s):  
Deep Learning ◽  
Subcellular Localization ◽  
High Throughput ◽  
Single Cells ◽  
Cellular Compartment ◽  
Cell Localization ◽  
Image Characteristics ◽  
Basic Image ◽  
Training Examples

High throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held out images. We confirm that low-level network features correspond to basic image characteristics, while deeper layers separate localization classes. Using this network as a feature calculator, we train standard classifiers that assign proteins to previously unseen compartments after observing only a small number of training examples. Our results are the most accurate subcellular localization classifications to date, and demonstrate the usefulness of deep learning for high throughput microscopy.

scholarly journals High-throughput precision measurement of subcellular localization in single cells

2017 ◽  
Vol 91 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Tyler J. Burns ◽  
Andreas P. Frei ◽  
Pier F. Gherardini ◽  
Felice A. Bava ◽  
Jake E. Batchelder ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
High Throughput ◽  
Precision Measurement ◽  
Single Cells

A Two-Stage Dissociation System for Multilayer Imaging of Cancer Biomarker-Synergic Networks in Single Cells

2017 ◽  
Vol 129 (17) ◽  
pp. 4880-4883 ◽  
Author(s):  
Ruo-Can Qian ◽  
Yue Cao ◽  
Li-Jun Zhao ◽  
Zhen Gu ◽  
Yi-Tao Long
Keyword(s):  
Single Cells ◽  
Cancer Biomarker ◽  
Two Stage

A Two-Stage Dissociation System for Multilayer Imaging of Cancer Biomarker-Synergic Networks in Single Cells

2017 ◽  
Vol 56 (17) ◽  
pp. 4802-4805 ◽  
Author(s):  
Ruo-Can Qian ◽  
Yue Cao ◽  
Li-Jun Zhao ◽  
Zhen Gu ◽  
Yi-Tao Long
Keyword(s):  
Single Cells ◽  
Cancer Biomarker ◽  
Two Stage

scholarly journals Visualizing adenosine to inosine RNA editing in single mammalian cells

2016 ◽  
Author(s):  
Ian A. Mellis ◽  
Rohit K. Gupte ◽  
Arjun Raj ◽  
Sara H. Rouhanifard
Keyword(s):  
Subcellular Localization ◽  
Rna Editing ◽  
Nuclear Localization ◽  
Mammalian Cells ◽  
Single Cells ◽  
Frequent Type ◽  
Rna Fish

AbstractConversion of adenosine bases to inosine in RNA is a frequent type of RNA editing, but important details about its biology, including subcellular localization, remain unknown due to a lack of imaging tools. We developed an RNA FISH strategy we called inoFISH that enables us to directly visualize and quantify adenosine-to-inosine edited transcripts in situ. Applying this tool to three edited transcripts (GRIA2, EIF2AK2 and NUP43), we found that editing of these transcripts is not correlated with nuclear localization nor paraspeckle association, and that NUP43 exhibits constant editing rates between single cells while the rates for GRIA2 vary.

scholarly journals Expression patterns and different subcellular localization of the growth factors HDGF (hepatoma-derived growth factor) and HRP-3 (HDGF-related protein-3) suggest functions in addition to their mitogenic activity

2004 ◽  
Vol 378 (1) ◽  
pp. 169-176 ◽  
Author(s):  
Mekky M. ABOUZIED ◽  
Stephan L. BAADER ◽  
Frank DIETZ ◽  
Joachim KAPPLER ◽  
Volkmar GIESELMANN ◽  
...  
Keyword(s):  
Growth Factors ◽  
Growth Factor ◽  
Subcellular Localization ◽  
Single Cells ◽  
Expression Patterns ◽  
Primary Cultures ◽  
Brain Slices ◽  
Adult Brain ◽  
Differentiated Cells ◽  
C Terminus

HDGF (hepatoma-derived growth factor) and the HRPs (HDGF-related proteins) comprise a family of six proteins which display high identity in their N-terminus, but differ at the C-terminus. Here we investigate the patterns of expression of HDGF and HRP-3, by generating antisera specifically recognizing each growth factor. Whereas HRP-3 protein is expressed only in brain, HDGF can be found in a broad range of tissues, with highest levels in brain, testis, lung and spleen. The expression of HDGF and HRP-3 was found to be regulated during brain development, with highest levels around birth, followed by a decline until postnatal day 9. Interestingly, expression of HRP-3 increases again in adult brain. In situ hybridization and immunohistochemistry of cerebellar, cerebral and hippocampal brain slices showed that expression of both growth factors is not limited to areas of high proliferative activity. Both mRNAs and proteins are expressed in neuronal as well as glial cells. Immunocytochemistry of cultured neocortical neurons revealed that HDGF and HRP-3 can be found in the nucleus as well as the cytoplasm. HDGF is restricted to the neuronal soma, whereas HRP-3 can also be found in neurites. Thus the expression of HDGF and HRP-3 in differentiated cells, post-mitotic neurons and primary cultures of rat neocortex points to functions in brain that might not be limited to proliferation. In addition, their simultaneous expression in the same cell and their different subcellular localization in cultured neurons suggest different functions of HDGF and HRP-3 within single cells.

Effects of carbamylcholine on chick embryo aggregate retina cell cultures

1988 ◽  
Vol 46 ◽  
pp. 350-351
Author(s):  
Glenn M. Cohen ◽  
Radharaman Ray
Keyword(s):  
Cell Cultures ◽  
Single Cells ◽  
Retinal Cell ◽  
Cell Aggregates ◽  
High Concentration ◽  
In Ovo ◽  
Sterile Culture ◽  
Retinal Tissue ◽  
Synaptic Junctions ◽  
And Control

Retinal,cell aggregates develop in culture in a pattern similar to the in ovo retina, forming neurites first and then synapses. In the present study, we continuously exposed chick retinal cell aggregates to a high concentration (1 mM) of carbamylcholine (carbachol), an acetylcholine (ACh) analog that resists hydrolysis by acetylcholinesterase (AChE). This situation is similar to organophosphorus anticholinesterase poisoning in which the ACh level is elevated at synaptic junctions due to inhibition of AChE, Our objective was to determine whether continuous carbachol exposure either damaged cholino- ceptive neurites, cell bodies, and synaptic elements of the aggregates or influenced (hastened or retarded) their development.The retinal tissue was isolated aseptically from 11 day embryonic White Leghorn chicks and then enzymatically (trypsin) and mechanically (trituration) dissociated into single cells. After washing the cells by repeated suspension and low (about 200 x G) centrifugation twice, aggregate cell cultures (about l0 cells/culture) were initiated in 1.5 ml medium (BME, GIBCO) in 35 mm sterile culture dishes and maintained as experimental (containing 10-3 M carbachol) and control specimens.

Selective Staining of Acid Mucopolysaccharides By Ruthenium Red

1968 ◽  
Vol 26 ◽  
pp. 38-39
Author(s):  
J. H. Luft
Keyword(s):  
Electron Microscope ◽  
Light Microscopy ◽  
Light Microscope ◽  
Osmium Tetroxide ◽  
Single Cells ◽  
Ruthenium Red ◽  
Collagen Fibers ◽  
Selective Staining ◽  
Pectic Substances ◽  
Solid Tissues

Ruthenium red is one of the few completely inorganic dyes used to stain tissues for light microscopy. This novelty is enhanced by ignorance regarding its staining mechanism. However, its continued usefulness in botany for demonstrating pectic substances attests to selectivity of some sort. Whether understood or not, histochemists continue to be grateful for small favors.Ruthenium red can also be used with the electron microscope. If single cells are exposed to ruthenium red solution, sufficient mass can be bound to produce observable density in the electron microscope. Generally, this effect is not useful with solid tissues because the contrast is wasted on the damaged cells at the block surface, with little dye diffusing more than 25-50 μ into the interior. Although these traces of ruthenium red which penetrate between and around cells are visible in the light microscope, they produce negligible contrast in the electron microscope. However, its presence can be amplified by a reaction with osmium tetroxide, probably catalytically, to be easily visible by EM. Now the density is clearly seen to be extracellular and closely associated with collagen fibers (Fig. 1).

Fluorescent potentiometric dyes for membrane-potential imaging

1994 ◽  
Vol 52 ◽  
pp. 166-167
Author(s):  
Leslie M. Loew
Keyword(s):  
Membrane Potential ◽  
Single Cells ◽  
Quantitative Imaging ◽  
Optical Recording ◽  
Biological Processes ◽  
Major Focus ◽  
The Past ◽  
Excitable Systems ◽  
Major Application ◽  
The Impact

A major application of potentiometric dyes has been the multisite optical recording of electrical activity in excitable systems. After being championed by L.B. Cohen and his colleagues for the past 20 years, the impact of this technology is rapidly being felt and is spreading to an increasing number of neuroscience laboratories. A second class of experiments involves using dyes to image membrane potential distributions in single cells by digital imaging microscopy - a major focus of this lab. These studies usually do not require the temporal resolution of multisite optical recording, being primarily focussed on slow cell biological processes, and therefore can achieve much higher spatial resolution. We have developed 2 methods for quantitative imaging of membrane potential. One method uses dual wavelength imaging of membrane-staining dyes and the other uses quantitative 3D imaging of a fluorescent lipophilic cation; the dyes used in each case were synthesized for this purpose in this laboratory.

Investigating the functional link between TMEM165 and SPCA1

2019 ◽  
Vol 476 (21) ◽  
pp. 3281-3293 ◽  
Author(s):  
Elodie Lebredonchel ◽  
Marine Houdou ◽  
Hans-Heinrich Hoffmann ◽  
Kateryna Kondratska ◽  
Marie-Ange Krzewinski ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Complete Loss ◽  
Protein Family ◽  
Uncharacterized Protein ◽  
Functional Link ◽  
P Type

TMEM165 was highlighted in 2012 as the first member of the Uncharacterized Protein Family 0016 (UPF0016) related to human glycosylation diseases. Defects in TMEM165 are associated with strong Golgi glycosylation abnormalities. Our previous work has shown that TMEM165 rapidly degrades with supraphysiological manganese supplementation. In this paper, we establish a functional link between TMEM165 and SPCA1, the Golgi Ca2+/Mn2+ P-type ATPase pump. A nearly complete loss of TMEM165 was observed in SPCA1-deficient Hap1 cells. We demonstrate that TMEM165 was constitutively degraded in lysosomes in the absence of SPCA1. Complementation studies showed that TMEM165 abundance was directly dependent on SPCA1's function and more specifically its capacity to pump Mn2+ from the cytosol into the Golgi lumen. Among SPCA1 mutants that differentially impair Mn2+ and Ca2+ transport, only the Q747A mutant that favors Mn2+ pumping rescues the abundance and Golgi subcellular localization of TMEM165. Interestingly, the overexpression of SERCA2b also rescues the expression of TMEM165. Finally, this paper highlights that TMEM165 expression is linked to the function of SPCA1.

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