scholarly journals Yn-situ: a robust single RNA molecule in situ detection method

2021 ◽  
Author(s):  
Yunming Wu ◽  
Wenjing Xu ◽  
Limei Ma ◽  
Zulin Yu ◽  
Yongfu Wang ◽  
...  
Keyword(s):  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
High Sensitivity ◽  
Cost Effective ◽  
Hybridization Chain Reaction ◽  
Single Pair ◽  
Rna Molecules ◽  
Key Steps ◽  
In Situ Detection

We describe a cost-effective, highly sensitive, and quantitative method for in situ detection of single RNA molecules in tissue sections. This method, dubbed Yn situ, standing for Y-branched probe in situ hybridization, uses a single-strand DNA preamplifier with multiple initiation sites that trigger hybridization chain reaction (HCR) to detect polynucleotide. We characterized the performance of this method and compared it to other approaches in the postnatal mouse olfactory epithelia. We find that the Yn situ method, in conjunction with an improved fixation step, is sensitive enough to allow detection of single molecules using a single pair of probes targeting a short nucleotide sequence. A set of 5-probes can produce quantitative results with smaller puncta and higher signal-to-noise ratio than the 20-probe sets commonly required for HCR and RNA-Scope. We show that the high sensitivity and wide dynamic range allow quantification of genes expressed at different levels in the olfactory sensory neurons. We describe key steps of this method to enable broad utility by individual laboratories.

scholarly journals Ultrastructural visualization of cytoskeletal mRNAs and their associated proteins using double-label in situ hybridization.

1989 ◽  
Vol 108 (6) ◽  
pp. 2343-2353 ◽  
Author(s):  
R H Singer ◽  
G L Langevin ◽  
J B Lawrence
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Colloidal Gold ◽  
Messenger Rna ◽  
Signal To Noise Ratio ◽  
Simultaneous Detection ◽  
Gold Particles ◽  
Rna Molecules ◽  
Nucleic Acid Molecule

We have been able to visualize cytoskeletal messenger RNA molecules at high resolution using nonisotopic in situ hybridization followed by whole-mount electron microscopy. Biotinated cDNA probes for actin, tubulin, or vimentin mRNAs were hybridized to Triton-extracted chicken embryo fibroblasts and myoblasts. The cells were then exposed to antibodies against biotin followed by colloidal gold-conjugated antibodies and then critical-point dried. Identification of mRNA was possible using a probe fragmented to small sizes such that hybridization of several probe fragments along the mRNA was detected as a string of colloidal gold particles qualitatively and quantitatively distinguishable from nonspecific background. Extensive analysis showed that when eight gold particles were seen in this iterated array, the signal to noise ratio was greater than 30:1. Furthermore, these gold particles were colinear, often spiral, or circular suggesting detection of a single nucleic acid molecule. Antibodies against actin, vimentin, or tubulin proteins were used after in situ hybridization, allowing simultaneous detection of the protein and its cognate message on the same sample. This revealed that cytoskeletal mRNAs are likely to be extremely close to actin protein (5 nm or less) and unlikely to be within 20 nm of vimentin or tubulin filaments. Actin mRNA was found to be more predominant in lamellipodia of motile cells, confirming previous results. These results indicate that this high resolution in situ hybridization approach is a powerful tool by which to investigate the association of mRNA with the cytoskeleton.

scholarly journals Methods for Voltage-Sensitive Dye Imaging of Rat Cortical Activity With High Signal-to-Noise Ratio

2007 ◽  
Vol 98 (1) ◽  
pp. 502-512 ◽  
Author(s):  
Michael T. Lippert ◽  
Kentaroh Takagaki ◽  
Weifeng Xu ◽  
Xiaoying Huang ◽  
Jian-Young Wu
Keyword(s):  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Field Potential ◽  
High Sensitivity ◽  
High Dynamic Range ◽  
High Signal ◽  
Blue Dye ◽  
Voltage Sensitive Dye ◽  
Imaging Device

We describe methods to achieve high sensitivity in voltage-sensitive dye (VSD) imaging from rat barrel and visual cortices in vivo with the use of a blue dye RH1691 and a high dynamic range imaging device (photodiode array). With an improved staining protocol and an off-line procedure to remove pulsation artifact, the sensitivity of VSD recording is comparable with that of local field potential recording from the same location. With this sensitivity, one can record from ∼500 individual detectors, each covering an area of cortical tissue 160 μm in diameter (total imaging field ∼4 mm in diameter) and a temporal resolution of 1,600 frames/s, without multiple-trial averaging. We can record 80–100 trials of intermittent 10-s trials from each imaging field before the VSD signal reduces to one half of its initial amplitude because of bleaching and wash-out. Taken together, the methods described in this report provide a useful tool for visualizing evoked and spontaneous waves from rodent cortex.

scholarly journals Nanopipette/Nanorod-Combined Quartz Tuning Fork–Atomic Force Microscope

Sensors ◽  
2019 ◽  
Vol 19 (8) ◽  
pp. 1794 ◽  
Author(s):  
Sangmin An ◽  
Wonho Jhe
Keyword(s):  
Atomic Force Microscope ◽  
Tuning Fork ◽  
High Sensitivity ◽  
Quartz Tuning Fork ◽  
Force Sensor ◽  
Au Nanoparticle ◽  
Ambient Conditions ◽  
Atomic Force ◽  
In Situ Detection

We introduce a nanopipette/quartz tuning fork (QTF)–atomic force microscope (AFM) for nanolithography and a nanorod/QTF–AFM for nanoscratching with in situ detection of shear dynamics during performance. Capillary-condensed nanoscale water meniscus-mediated and electric field-assisted small-volume liquid ejection and nanolithography in ambient conditions are performed at a low bias voltage (~10 V) via a nanopipette/QTF–AFM. We produce and analyze Au nanoparticle-aggregated nanowire by using nanomeniscus-based particle stacking via a nanopipette/QTF–AFM. In addition, we perform a nanoscratching technique using in situ detection of the mechanical interactions of shear dynamics via a nanorod/QTF–AFM with force sensor capability and high sensitivity.

A theoretical study of digital silicon photomultiplier utilization in diffuse optical imaging systems

2019 ◽  
Vol 64 (3) ◽  
pp. 357-363 ◽  
Author(s):  
Taha Haddadifam ◽  
Mohammad Azim Karami
Keyword(s):  
Optical Imaging ◽  
Continuous Wave ◽  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
High Sensitivity ◽  
High Dynamic Range ◽  
Diffuse Optical Imaging ◽  
Silicon Photomultiplier ◽  
Thoracic Imaging ◽  
Low Level

Abstract Digital silicon photomultiplier (dSiPM) is introduced for diffuse optical imaging (DOI) applications instead of conventional photomultiplier tubes and avalanche photodiodes (APDs) as a state-of-the-art detector. According to the low-level light regime in DOI applications, high sensitivity and high dynamic range (DR) image sensors are needed for DOI systems. dSiPM is proposed as a developing detector which can detect low-level lights. Also, an accurate equation is obtained for calculating the DR of dSiPMs. Different dSiPMs and the corresponding benefits are studied for DOI applications. Furthermore, a 120 dB DR dSiPM is chosen for use in DOI systems. It is shown that dSiPMs can be utilized in DOI configurations such as time domain (TD), frequency domain (FD) and continuous wave (CW) systems. Ultimately, by utilizing dSiPM in DOI systems, the DOI method can be used for thoracic imaging due to the high DR and signal-to-noise ratio (SNR) of the detector.

Rapid, targeted and culture-free viral infectivity assay in drop-based microfluidics

Lab on a Chip ◽  
2015 ◽  
Vol 15 (19) ◽  
pp. 3934-3940 ◽  
Author(s):  
Ye Tao ◽  
Assaf Rotem ◽  
Huidan Zhang ◽  
Connie B. Chang ◽  
Anindita Basu ◽  
...  
Keyword(s):  
High Throughput ◽  
Dynamic Range ◽  
High Sensitivity ◽  
Cost Effective ◽  
Serial Dilution ◽  
Viral Infectivity ◽  
Large Dynamic Range ◽  
Infectivity Assay ◽  
Dilution Experiments

We developed a rapid, targeted and culture-free infectivity assay using high-throughput drop-based microfluidics. The high sensitivity and large dynamic range of our cost effective assay alleviates the need for serial dilution experiments.

scholarly journals In situ detection of non-polyadenylated RNA molecules using Turtle Probes and target primed rolling circle PRINS

2007 ◽  
Vol 7 (1) ◽  
pp. 69 ◽  
Author(s):  
Magnus Stougaard ◽  
Jakob S Lohmann ◽  
Magdalena Zajac ◽  
Stephen Hamilton-Dutoit ◽  
Jørn Koch
Keyword(s):  
Rolling Circle ◽  
Rna Molecules ◽  
Polyadenylated Rna ◽  
In Situ Detection

scholarly journals High sensitivity fluorescence up-conversion spectroscopy of 3MLCT emission of metal-organic complexes

2019 ◽  
Vol 205 ◽  
pp. 09009 ◽  
Author(s):  
Li Liu ◽  
Damianos Agathangelou ◽  
Thomas Roland ◽  
Olivier Crégut ◽  
Thibaud Duchanois ◽  
...  
Keyword(s):  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Emission Spectra ◽  
High Sensitivity ◽  
High Signal ◽  
Triplet States ◽  
Organic Complexes ◽  
Metal Organic ◽  
Set Up ◽  
Weak Luminescence

We demonstrate the implementation of a broadband fluorescence up-conversion set-up with high signal-to-noise ratio and dynamic range allowing for the detection of weak luminescence from triplet states in Fe(II) NHC complexes. Based on the experimentally determined radiative rates and the emission spectra, these states have dominant MLCT character.

A novel approach to design electrochemical aptamer-based biosensor for ultrasensitive detecting of zearalenone as a prevalent estrogenic mycotoxin

2021 ◽  
Vol 28 ◽  
Author(s):  
Shokoufeh Hassani ◽  
Armin Salek Maghsoudi ◽  
Milad Rezaei Akmal ◽  
Shahram Shoeibi ◽  
Fatemeh Ghadipasha ◽  
...  
Keyword(s):  
Dynamic Range ◽  
Electrochemical Impedance ◽  
Fusarium Species ◽  
High Sensitivity ◽  
High Specificity ◽  
Cost Effective ◽  
Differential Pulse ◽  
Electrode Position ◽  
Novel Approach ◽  
Modified Surface

Background: Zearalenone is a well-known estrogenic mycotoxin produced by Fusarium species, a serious threat to the agricultural and food industries worldwide. Zearalenone, with its known metabolites, are biomarkers of exposure to certain fungi, primarily through food. It has considerable toxic effects on biological systems due to its carcinogenicity, mutagenicity, renal toxicity, teratogenicity, and immunotoxicity. Introduction: This study aims to design a simple, quick, precise, and cost-effective method on a biosensor platform to evaluate the low levels of this toxin in foodstuffs and agricultural products. Methods: An aptamer-based electrochemical biosensor was introduced that utilizes screen-printed gold electrodes instead of conventional electrodes. The electrode position process was employed to develop a gold nanoparticle-modified surface to enhance the electroactive surface area. Thiolated aptamers were immobilized on the surface of gold nanoparticles, and subsequently, the blocker and analyte were added to the modified surface. In the presence of a redox probe, electrochemical characterization of differential pulse voltammetry, cyclic voltammetry, and electrochemical impedance spectroscopy were used to investigate the various stages of aptasensor fabrication. Results: The proposed aptasensor for zearalenone concentration had a wide linear dynamic range covering the 0.5 pg/mL to 100 ng/mL with a 0.14 pg/mL detection limit. Moreover, this aptasensor had high specificity so that a non-specific analyte cannot negatively affect the selectivity of the aptasensor. Conclusion: Overall, due to its simple design, high sensitivity, and fast performance, this aptasensor showed a high potential for assessing zearalenone in real samples, providing a clear perspective for designing a portable and cost-effective device.

Non-enzymatic Glucose Sensor Based on Palladium Coated Nanoporous Gold Film Electrode

2013 ◽  
Vol 66 (9) ◽  
pp. 1097 ◽  
Author(s):  
Nahid Tavakkoli ◽  
Shekofe Nasrollahi
Keyword(s):  
Glucose Sensor ◽  
Dynamic Range ◽  
Gold Film ◽  
Signal To Noise Ratio ◽  
Amperometric Detection ◽  
High Sensitivity ◽  
Glucose Biosensor ◽  
Nanoporous Gold ◽  
Film Electrode ◽  
Voltammetric Detection

The non-enzymatic voltammetric and amperometric detection of glucose using a palladium coated nanoporous gold film electrode is described. The effect of surfactant on the fabrication of nanoporous gold film was also investigated. The voltammetric detection of glucose was performed by cyclic voltammetry. The sensor had good electrocatalytic activity towards oxidation of glucose, exhibited a rapid response (~6 s), and gave a linear range from 1 to 33 mM with a detection limit of 5 μM (with a signal to noise ratio of 3). The wide dynamic range, long-term stability, high sensitivity and selectivity, good reproducibility, and high resistance towards electrode fouling resulted in an ideal inexpensive amperometric glucose biosensor applicable for complex matrices.

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