scholarly journals Sensitive whole mount in situ localization of small RNAs in plants

2016 ◽  
Author(s):  
Mouli Ghosh Dastidar ◽  
Magdalena Mosiolek ◽  
Michael D Nodine ◽  
Alexis Maizel
Keyword(s):  
Small Rnas ◽  
Direct Detection ◽  
Expression Patterns ◽  
Systematic Investigation ◽  
Indirect Detection ◽  
Whole Mount ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
In Situ Detection

Small regulatory RNAs are pivotal regulators of gene expression and play important roles in many plant processes. Although our knowledge of their biogenesis and mode of action has significantly progressed, we comparatively still know little about their biological functions. In particular, knowledge about their spatiotemporal patterns of expression rely on either indirect detection by use of reporter constructs or labor-intensive direct detection by in situ hybridization on sectioned material. None of the current approaches allows for a systematic investigation of small RNAs expression patterns.Here, we present a method for the sensitive in situ detection of micro- and siRNAs in intact plant tissues that utilizes both double-labelled probes and a specific cross linker. We determined the expression patterns of several small RNAs in plant roots and embryos.

scholarly journals Procedures for in situ monitoring of gene methylation in cancer prediction (Literature Review)

Akademos ◽  
2021 ◽  
pp. 89-95
Author(s):  
Victor Popescu ◽  
◽  
Mariana Jian ◽  
Tatiana Malcova ◽  
◽  
...  
Keyword(s):  
Literature Review ◽  
In Situ Monitoring ◽  
Gene Methylation ◽  
Cancer Prediction ◽  
Human Genes ◽  
Whole Mount ◽  
In Situ Detection

The purpose of this article is to synthesize data from the specialty literature on the best performing procedures for the in situ detection and monitoring of the phenomenon of gene methylation, to analyze the protocol for the realization of the whole mount MeFISH technology and to review the human genes that are characterized by methylation in cancer.

mRNA expression patterns of the IGF system during mouse limb bud development, determined by whole mount in situ hybridization

1998 ◽  
Vol 138 (1-2) ◽  
pp. 151-161 ◽  
Author(s):  
Marjolein van Kleffens ◽  
Cora Groffen ◽  
Roberto R. Rosato ◽  
Stefan M. van den Eijnde ◽  
Johan W. van Neck ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Mrna Expression ◽  
Expression Patterns ◽  
Limb Bud ◽  
Bud Development ◽  
Igf System ◽  
Whole Mount ◽  
Mouse Limb

scholarly journals In Situ detection of apoptosis during embryogenesis with Annexin V: From whole mount to ultrastructure

Cytometry ◽  
1997 ◽  
Vol 29 (4) ◽  
pp. 313-320 ◽  
Author(s):  
Stefan M. van den Eijnde ◽  
Antonius J.M. Luijsterburg ◽  
Lenard Boshart ◽  
Chris I. De Zeeuw ◽  
Jan Hein van Dierendonck ◽  
...  
Keyword(s):  
Annexin V ◽  
Whole Mount ◽  
In Situ Detection

scholarly journals A novel computational approach for genome-wide prediction of small RNAs in bacteria

2014 ◽  
Author(s):  
Lei Li ◽  
Hoi Shan Kwan
Keyword(s):  
Small Rnas ◽  
Computational Prediction ◽  
Transcriptional Regulators ◽  
Structural Features ◽  
Extensive Study ◽  
Bacterial Physiology ◽  
Genome Wide ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Window Approach

Small regulatory RNAs (sRNAs) are the most abundant post-transcriptional regulators in bacteria. They serve ubiquitous roles that control nearly every aspects of bacterial physiology. Identification of important features from sRNAs sequences will guide the computational prediction of new sRNA sequences for a better understanding of the pervasive sRNA-mediated regulation in bacteria. In this study, we have performed systematic analyses of many sequence and structural features that are possibly related to sRNA properties and identified a subset of significant features that effectively discriminate sRNAs sequences from random sequences. we then used a neural network model that integrated these subfeatures on unlabeled testing datasets, and it had achieved a 92.2% recall and 89.8% specificity. Finally, we applied this prediction model for genome-wide identification of sRNAs-encoded genes using a sliding-window approach. We recovered multiple known sRNAs and hundreds of predicted new sRNAs. These candidate novel sRNAs deserve extensive study to better understand the sRNA-mediated regulatory network in bacteria.

scholarly journals Expression patterns of ciliopathy genes ARL3 and CEP120 reveal roles in multisystem development

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
L. Powell ◽  
M. Barroso-Gil ◽  
G. J. Clowry ◽  
L. A. Devlin ◽  
E. Molinari ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Joubert Syndrome ◽  
Developmental Expression ◽  
Human Embryos ◽  
Jeune Syndrome ◽  
Pathogenic Variants ◽  
Normal Human ◽  
In Situ Detection ◽  
Early Human

Abstract Background Joubert syndrome and related disorders (JSRD) and Jeune syndrome are multisystem ciliopathy disorders with overlapping phenotypes. There are a growing number of genetic causes for these rare syndromes, including the recently described genes ARL3 and CEP120. Methods We sought to explore the developmental expression patterns of ARL3 and CEP120 in humans to gain additional understanding of these genetic conditions. We used an RNA in situ detection technique called RNAscope to characterise ARL3 and CEP120 expression patterns in human embryos and foetuses in collaboration with the MRC-Wellcome Trust Human Developmental Biology Resource. Results Both ARL3 and CEP120 are expressed in early human brain development, including the cerebellum and in the developing retina and kidney, consistent with the clinical phenotypes seen with pathogenic variants in these genes. Conclusions This study provides insights into the potential pathogenesis of JSRD by uncovering the spatial expression of two JSRD-causative genes during normal human development.

scholarly journals Two GacA-Dependent Small RNAs Modulate the Quorum-Sensing Response in Pseudomonas aeruginosa

2006 ◽  
Vol 188 (16) ◽  
pp. 6026-6033 ◽  
Author(s):  
Elisabeth Kay ◽  
Bérénice Humair ◽  
Valérie Dénervaud ◽  
Kathrin Riedel ◽  
Stéphanie Spahr ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Small Rnas ◽  
Homoserine Lactone ◽  
Two Component System ◽  
Bond Forming ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Chitin Binding Protein ◽  
Biofilm Development

ABSTRACT In Pseudomonas aeruginosa, the GacS/GacA two-component system positively controls the quorum-sensing machinery and the expression of extracellular products via two small regulatory RNAs, RsmY and RsmZ. An rsmY rsmZ double mutant and a gacA mutant were similarly impaired in the synthesis of the quorum-sensing signal N-butanoyl-homoserine lactone, the disulfide bond-forming enzyme DsbA, and the exoproducts hydrogen cyanide, pyocyanin, elastase, chitinase (ChiC), and chitin-binding protein (CbpD). Both mutants showed increased swarming ability, azurin release, and early biofilm development.

Corrigendum to “Whole-mount in situ detection of microRNAs on Arabidopsis tissues using Zip Nucleic Acid probes” [Anal. Biochem. 434 (2013) 60–66]

2013 ◽  
Vol 437 (1) ◽  
pp. 39
Author(s):  
M. Begheldo ◽  
F.A. Ditengou ◽  
G. Cimoli ◽  
S. Trevisan ◽  
S. Quaggiotti ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Probes ◽  
Whole Mount ◽  
In Situ Detection ◽  
Zip Nucleic Acid

scholarly journals Cytochrome P450 Expression and Chemical Metabolic Activity before Full Liver Development in Zebrafish

2020 ◽  
Vol 13 (12) ◽  
pp. 456
Author(s):  
Tasuku Nawaji ◽  
Natsumi Yamashita ◽  
Haruka Umeda ◽  
Shuangyi Zhang ◽  
Naohiro Mizoguchi ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
In Situ Hybridization ◽  
Metabolic Activity ◽  
Expression Patterns ◽  
Xenobiotic Metabolism ◽  
Liver Development ◽  
P450 Expression ◽  
Whole Mount ◽  
Metabolic Activities

Zebrafish are used widely in biomedical, toxicological, and developmental research, but information on their xenobiotic metabolism is limited. Here, we characterized the expression of 14 xenobiotic cytochrome P450 (CYP) subtypes in whole embryos and larvae of zebrafish (4 to 144 h post-fertilization (hpf)) and the metabolic activities of several representative human CYP substrates. The 14 CYPs showed various changes in expression patterns during development. Many CYP transcripts abruptly increased at about 96 hpf, when the hepatic outgrowth progresses; however, the expression of some cyp1s (1b1, 1c1, 1c2, 1d1) and cyp2r1 peaked at 48 or 72 hpf, before full liver development. Whole-mount in situ hybridization revealed cyp2y3, 2r1, and 3a65 transcripts in larvae at 55 hpf after exposure to rifampicin, phenobarbital, or 2,3,7,8-tetrachlorodibenzo-p-dioxin from 30 hpf onward. Marked conversions of diclofenac to 4′-hydroxydiclofenac and 5-hydroxydiclofenac, and of caffeine to 1,7-dimethylxanthine, were detected as early as 24 or 50 hpf. The rate of metabolism to 4’-hydroxydiclofenac was more marked at 48 and 72 hpf than at 120 hpf, after the liver had become almost fully developed. These findings reveal the expression of various CYPs involved in chemical metabolism in developing zebrafish, even before full liver development.

scholarly journals In situ detection of transcripts of the myogenic factor MyoD in whole chicken embryos

2000 ◽  
Vol 23 (1) ◽  
pp. 145-148 ◽  
Author(s):  
Jane E. Gabriel ◽  
Helena J. Alves ◽  
Lucia E. Alvares ◽  
Gilberto S. Schmidt ◽  
Luiz L. Coutinho
Keyword(s):  
In Situ Hybridization ◽  
Expression Patterns ◽  
Temporal Expression ◽  
Rt Pcr ◽  
Chicken Embryos ◽  
Myogenic Factor ◽  
Polymerase Chain ◽  
In Situ Detection ◽  
Myod Expression

In situ hybridization has provided insights into the molecular basis of skeletal myogenesis during embryonic development. In situ detection of different muscle-specific regulatory factors in whole embryos has been described. Spatial and temporal expression patterns of these factors differed among species. The expression pattern of MyoD in whole chicken embryos was studied via in situ hybridization using a probe obtained by the reverse transcription - polymerase chain reaction (RT-PCR) technique. In newly formed somites (embryos of stage 12), MyoD mRNA transcripts were detected along the anterior to posterior axis of somites immediately adjacent to the neural tube, whereas in mature somites (embryos of stage 24), MyoD transcripts were detected throughout the entire somite. These results indicate that MyoD expression is important for initiating and maintaining the avian myogenic system.

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