scholarly journals Small RNA In Situ Hybridizations on Sections of Arabidopsis Embryos

2020 ◽  
pp. 87-99
Author(s):  
Katalin Páldi ◽  
Magdalena Mosiolek ◽  
Michael D. Nodine
Keyword(s):  
In Situ Hybridization ◽  
Small Rna ◽  
Specific Cell ◽  
Posttranscriptional Gene Silencing ◽  
Regulatory Processes ◽  
Cellular Resolution ◽  
Gene Regulatory ◽  
Hybridization Protocol ◽  
In Situ Hybridizations

AbstractSmall RNAs mediate posttranscriptional gene silencing in plants and animals. This often occurs in specific cell or tissue types and can be necessary for their differentiation. Determining small RNA (sRNA) localization patterns at cellular resolution can therefore provide information on the corresponding gene regulatory processes they are involved in. Recent improvements with in situ hybridization methods have allowed them to be applied to sRNAs. Here we describe an in situ hybridization protocol to detect sRNAs from sections of early staged Arabidopsis thaliana (Arabidopsis) embryos.

scholarly journals Methods to Enhance Signal Using Isotopic In Situ Hybridization

2002 ◽  
Vol 50 (8) ◽  
pp. 1031-1037 ◽  
Author(s):  
Betty Ky ◽  
Paul J. Shughrue
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Cell Types ◽  
Oxytocin Receptor ◽  
Specific Cell ◽  
Rat Hypothalamus ◽  
Low Levels ◽  
Tuberoinfundibular Peptide ◽  
Cryostat Sections

Isotopic in situ hybridization (ISH) has been established as a uniquely powerful tool for the study of gene expression in specific cell types. This technique allows the visualization and quantification of gene expression and gene expression changes in cells. In our study of biological and molecular phenomena, we have increasingly encountered the need to detect small changes in gene expression as well as genes of low abundance, such as the oxytocin receptor (OTR) and the tuberoinfundibular peptide of 39 residues (Tip39). To increase the sensitivity of isotopic ISH for detection of rare mRNAs, we performed ISH on cryostat sections of rat hypothalamus and thalamus with 35S-labeled riboprobes and amplified the signal by hybridizing over 2 nights as well as labeling the probe with both [35S]-UTP and [35S]-ATP. These two methods of enhancement independently and in combination demonstrated a dramatic increase in signal, allowing the visualization of low levels of gene expression previously undetectable by conventional methods.

scholarly journals Marine Planktonic Archaea Take Up Amino Acids

2000 ◽  
Vol 66 (11) ◽  
pp. 4829-4833 ◽  
Author(s):  
Cleber C. Ouverney ◽  
Jed A. Fuhrman
Keyword(s):  
Amino Acids ◽  
In Situ Hybridization ◽  
Cell Types ◽  
Similar Proportion ◽  
Specific Cell ◽  
Natural Conditions ◽  
The Pacific ◽  
The Pacific Ocean ◽  
Archaeal Communities

ABSTRACT Archaea are traditionally thought of as “extremophiles,” but recent studies have shown that marine planktonic Archaea make up a surprisingly large percentage of ocean midwater microbial communities, up to 60% of the total prokaryotes. However, the basic physiology and contribution of Archaea to community microbial activity remain unknown. We have studied Archaea from 200-m depths of the northwest Mediterranean Sea and the Pacific Ocean near California, measuring the archaeal activity under simulated natural conditions (8 to 17°C, dark and anaerobic) by means of a method called substrate tracking autoradiography fluorescence in situ hybridization (STARFISH) that simultaneously detects specific cell types by 16S rRNA probe binding and activity by microautoradiography. In the 200-m-deep Mediterranean and Pacific samples, cells binding the archaeal probes made up about 43 and 14% of the total countable cells, respectively. Our results showed that the Archaea are active in the uptake of dissolved amino acids from natural concentrations (nanomolar) with about 60% of the individuals in the archaeal communities showing measurable uptake. Bacteria showed a similar proportion of active cells. We concluded that a portion of these Archaea is heterotrophic and also appears to coexist successfully with Bacteria in the same water.

scholarly journals Catalyzed Reported Deposition-Fluorescence In Situ Hybridization Protocol To Evaluate Phagotrophy in Mixotrophic Protists

2005 ◽  
Vol 71 (11) ◽  
pp. 7321-7326 ◽  
Author(s):  
Juan M. Medina-Sánchez ◽  
Marisol Felip ◽  
Emilio O. Casamayor
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Signal Amplification ◽  
Cell Attachment ◽  
Cell Loss ◽  
Alexa Fluor ◽  
Hybridization Protocol ◽  
Card Fish ◽  
First Time

ABSTRACT We describe a catalyzed reported deposition-fluorescence in situ hybridization (CARD-FISH) protocol particularly suited to assess the phagotrophy of mixotrophic protists on prokaryotes, since it maintains cell and plastid integrity, avoids cell loss and egestion of prey, and allows visualization of labeled prey against plastid autofluorescence. This protocol, which includes steps such as Lugol's-formaldehyde-thiosulfate fixation, agarose cell attachment, cell wall permeabilization with lysozyme plus achromopeptidase, and signal amplification with Alexa-Fluor 488, allowed us to detect almost 100% of planktonic prokaryotes (Bacteria and Archaea) and, for the first time, to show archaeal cells ingested by mixotrophic protists.

scholarly journals Small RNA Detection by in Situ Hybridization Methods

2015 ◽  
Vol 16 (12) ◽  
pp. 13259-13286 ◽  
Author(s):  
Martyna Urbanek ◽  
Anna Nawrocka ◽  
Wlodzimierz Krzyzosiak
Keyword(s):  
In Situ Hybridization ◽  
Small Rna ◽  
Rna Detection

Higher axial-resolution and sensitivity pachytene fluorescence in situ hybridization protocol in tetraploid cotton

2009 ◽  
Vol 17 (8) ◽  
pp. 1041-1050 ◽  
Author(s):  
Kai Wang ◽  
Zaijie Yang ◽  
Changshen Shu ◽  
Jing Hu ◽  
Qiuyun Lin ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Tetraploid Cotton ◽  
Axial Resolution ◽  
Hybridization Protocol

Double-Network Interpenetrating Bone Cement via in situ Hybridization Protocol

2010 ◽  
Vol 20 (22) ◽  
pp. 3997-4011 ◽  
Author(s):  
Jing Wang ◽  
Changsheng Liu ◽  
Yufei Liu ◽  
Shuo Zhang
Keyword(s):  
In Situ Hybridization ◽  
Bone Cement ◽  
Double Network ◽  
Hybridization Protocol

A versatile fluorometric in situ hybridization method for the quantitation of hairpin conformations in DNA self-assembled monolayers

The Analyst ◽  
2020 ◽  
Vol 145 (13) ◽  
pp. 4522-4531
Author(s):  
Jiale He ◽  
Xiaochen Hu ◽  
Xiaoyi Gao ◽  
Chenchen Meng ◽  
Yunchao Li ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Detection Performance ◽  
Self Assembled Monolayers ◽  
Optimal Detection ◽  
Hybridization Method ◽  
Assembled Monolayers ◽  
The Creation ◽  
Self Assembled ◽  
Hybridization Protocol

We report a versatile fluorometric in-situ hybridization protocol for quantifying hairpin conformations in DNA self-assembled monolayers on substrates, which facilitates the creation of hpDNA-based biosensors with optimal detection performance.

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