Large‐scale potential RNA editing profiling in different adult chicken tissues

2019 ◽  
Vol 50 (5) ◽  
pp. 460-474 ◽  
Author(s):  
H. Shafiei ◽  
M. R. Bakhtiarizadeh ◽  
A. Salehi
Keyword(s):  
Rna Editing ◽  
Large Scale ◽  
Adult Chicken ◽  
Chicken Tissues

scholarly journals Large-scale RNA editing profiling in different adult chicken tissues

2018 ◽  
Author(s):  
Hamid Shafiei ◽  
Mohammad Reza Bakhtiarizadeh ◽  
Abdolreza Salehi
Keyword(s):  
Rna Editing ◽  
Large Scale ◽  
Critical Role ◽  
Sequencing Data ◽  
Adult Chicken ◽  
Chicken Tissues ◽  
Sequencing Technologies ◽  
Synonymous Sites ◽  
Interspersed Repeats ◽  
The Brain

AbstractRNA editing is a post-transcription maturation process that diversifies genomically encoded information and can lead to diversity and complexity of transcriptome, especially in the brain. Thanks to next-generation sequencing technologies, a large number of editing sites have been identified in different species, especially in human, mouse and rat. While this mechanism is well described in mammals, only a few studies have been performed in the chicken. Here, we developed a rigorous computational strategy to identify RNA editing sites in eight different tissues of the chicken (brain, spleen, colon, lung, kidney, heart, testes and liver), based on RNA sequencing data alone. We identified 68 A-to-G editing sites in 46 genes. Only two of these were previously reported in chicken. We found no C-to-U sites, attesting the lack of this type of editing mechanism in the chicken. Similar to mammals, the editing sites were enriched in non-coding regions, rarely resulted in change of amino acids, showed a critical role in nervous system and had a low guanosine level upstream of the editing site and some enrichment downstream from the site. Moreover, in contrast to mammals, editing sites were weakly enriched in interspersed repeats and the frequency and editing ratio of non-synonymous sites were higher than those of synonymous sites.Interestingly, we found several tissue-specific edited genes including GABRA3, SORL1 and HTR1D in brain and RYR2 and FHOD3 in heart that were associated with functional processes relevant to the corresponding tissue. This finding highlighted the importance of the RNA editing in several chicken tissues, especially the brain. This study extends our understanding of RNA editing in chicken tissues and establish a foundation for further exploration of this process.

scholarly journals Automated Isoform Diversity Detector (AIDD): A pipeline for investigating transcriptome diversity of RNA-seq data

2020 ◽  
Author(s):  
Noel-Marie Plonski ◽  
Emily Johnson ◽  
Madeline Frederick ◽  
Heather Mercer ◽  
Gail Fraizer ◽  
...  
Keyword(s):  
Rna Editing ◽  
Large Scale ◽  
Neural Progenitor Cells ◽  
Viral Infections ◽  
Variant Calling ◽  
Rna Seq ◽  
Major Mechanism ◽  
Isoform Diversity ◽  
Adar Editing ◽  
Transcriptome Diversity

AbstractBackgroundAs the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. Many available tools facilitate analyses of one of the two major mechanisms of transcriptome diversity, namely, differential expression of isoforms due to alternative splicing, while the second major mechanism - RNA editing due to post-transcriptional changes of individual nucleotides – remains under-appreciated. Both these mechanisms play an essential role in physiological and diseases processes, including cancer and neurological disorders. However, elucidation of RNA editing events at transcriptome-wide level requires increasingly complex computational tools, in turn resulting in a steep entrance barrier for labs who are interested in high-throughput variant calling applications on a large scale but lack the manpower and/or computational expertise.ResultsHere we present an easy-to-use, fully automated, computational pipeline (Automated Isoform Diversity Detector, AIDD) that contains open source tools for various tasks needed to map transcriptome diversity, including RNA editing events. To facilitate reproducibility and avoid system dependencies, the pipeline is contained within a pre-configured VirtualBox environment. The analytical tasks and format conversions are accomplished via a set of automated scripts that enable the user to go from a set of raw data, such as fastq files, to publication-ready results and figures in one step. A publicly available dataset of Zika virus-infected neural progenitor cells is used to illustrate AIDD’s capabilities.ConclusionsAIDD pipeline offers a user-friendly interface for comprehensive and reproducible RNA-seq analyses. Among unique features of AIDD are its ability to infer RNA editing patterns, including ADAR editing, and inclusion of Guttman scale patterns for time series analysis of such editing landscapes. AIDD-based results show importance of diversity of ADAR isoforms, key RNA editing enzymes linked with the innate immune system and viral infections. These findings offer insights into the potential role of ADAR editing dysregulation in the disease mechanisms, including those of congenital Zika syndrome. Because of its automated all-inclusive features, AIDD pipeline enables even a novice user to easily explore common mechanisms of transcriptome diversity, including RNA editing landscapes.

scholarly journals Quantitation of two endogenous lactose-inhibitable lectins in embryonic and adult chicken tissues.

1982 ◽  
Vol 92 (1) ◽  
pp. 23-27 ◽  
Author(s):  
E C Beyer ◽  
S H Barondes
Keyword(s):  
Gel Electrophoresis ◽  
Peptide Mapping ◽  
Polyacrylamide Gel Electrophoresis ◽  
Cross Reactivity ◽  
Adult Chicken ◽  
Chicken Tissues ◽  
Adult Tissues ◽  
Embryonic Muscle ◽  
The Many ◽  
Kidney Liver

Two lactose-binding lectins from chicken tissues, chicken-lactose-lectin-1 (CLL-1) and chicken-lactose-lectin-11 (CLL-11) were quantified with a radioimmunoassay in extracts of a number of developing and adult chicken tissues. Both lectins could be measured in the same extract without separation, because they showed not significant immunological cross-reactivity. Many embryonic and adult tissues, including brain, heart, intestine, kidney, liver, lung, muscle, pancreas, and spleen, contained one or both lectins, although their concentrations differed markedly. For example, embryonic muscle, the richest source of CLL-1 contained only traces of CLL-11 whereas embryonic kidney, a very rich source of CLL-11 contained substantial CLL-1. In both muscle and kidney, lectin levels in adulthood were much lower than in the embryonic state. In contrast, CLL-1 in liver and CLL-11 in intestine were 10-fold to 30-fold more concentrated in the adult than in the 15-d embryo. CLL-1 and CLL-11 from several tissues were purified by affinity chromatography and their identity in the various tissues was confirmed by polyacrylamide gel electrophoresis, isoelectric focusing, and peptide mapping. The results suggest that these lectins might have different functions in the many developing and adult tissues in which they are found.

Large-scale prediction of ADAR-mediated effective human A-to-I RNA editing

2017 ◽  
Vol 20 (1) ◽  
pp. 102-109 ◽  
Author(s):  
Li Yao ◽  
Heming Wang ◽  
Yuanyuan Song ◽  
Zhen Dai ◽  
Hao Yu ◽  
...  
Keyword(s):  
Rna Editing ◽  
Large Scale

The distribution of sorbitol dehydrogenase in embryonic and adult chicken tissues

1979 ◽  
Vol 208 (3) ◽  
pp. 287-290 ◽  
Author(s):  
Sofía P. Defabro ◽  
David W. Bishop ◽  
Adriana Lía Goldemberg
Keyword(s):  
Sorbitol Dehydrogenase ◽  
Adult Chicken ◽  
Chicken Tissues

scholarly journals Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

2010 ◽  
Vol 38 (14) ◽  
pp. 4755-4767 ◽  
Author(s):  
Ernesto Picardi ◽  
David S. Horner ◽  
Matteo Chiara ◽  
Riccardo Schiavon ◽  
Giorgio Valle ◽  
...  
Keyword(s):  
Rna Editing ◽  
Deep Sequencing ◽  
Large Scale ◽  
Rna Deep Sequencing ◽  
Scale Detection

Antibodies to two major chicken heat shock proteins cross-react with similar proteins in widely divergent species

1982 ◽  
Vol 2 (3) ◽  
pp. 267-274
Author(s):  
P M Kelley ◽  
M J Schlesinger
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Solid Phase ◽  
Adult Chicken ◽  
Chicken Tissues ◽  
Molecular Weights ◽  
Culture Cells ◽  
Antigenic Material ◽  
Shock Proteins ◽  
The University

Three of the proteins induced by heat shock of chicken embryo fibroblasts have been purified, and rabbit antibodies have been raised against them. These antibodies have been used in radioimmune precipitation reactions and in a solid-phase immune assay to detect antigenic material in non-heat-shocked chicken tissues and in extracts of widely different species ranging from yeast to mammalian tissue culture cells and human erythrocyte ghosts. Antibodies to two of the major chicken heat shock proteins, chsp89 and chsp70, cross-reacted with proteins of similar molecular weights in normal embryonic and adult chicken tissues and in extracts from widely different organisms. These data provide further evidence for the university of the heat shock response and conservation of proteins induced by this type of stress.

scholarly journals AN EVALUATION OF METHODS FOR THE CONCENTRATION AND PURIFICATION OF INFLUENZA VIRUS

1944 ◽  
Vol 79 (3) ◽  
pp. 255-266 ◽  
Author(s):  
W. M. Stanley
Keyword(s):  
Influenza Virus ◽  
Large Scale ◽  
Allantoic Fluid ◽  
Red Cells ◽  
Virus Protein ◽  
Differential Centrifugation ◽  
Freezing And Thawing ◽  
Protein Nitrogen ◽  
Adult Chicken ◽  
Sedimentation Constant

The concentration and purification of influenza virus by means of differential centrifugation in a vacuum type centrifuge, by adsorption on and elution from adult chicken red cells, by elution of the precipitate formed on freezing and thawing of allantoic fluid, by adsorption on and elution from embryonic chick red cells, and by combinations of the first method with each of the three succeeding methods, have been studied. Over-all yields of virus of about 50 to 70 per cent were obtained by these methods and combinations of methods except for somewhat lower yields when adsorption on and elution from adult chicken red cells was employed. However, the purified products obtained by methods involving only the use of red cells or the freezing and thawing technique were found to contain about 80 per cent of non-virus protein. The purified products obtained when differential centrifugation was used either alone or in combination with any one of the other methods were found to be indistinguishable and to consist of a fairly homogeneous component having a sedimentation constant of about 600 S. Such preparations possessed about 22,000 chicken red cell agglutinating units per mg. of protein nitrogen and solutions containing only about 10–14 gm. of the materials gave 50 per cent infectivity end points in chick embryos. The Sharples centrifuge was found to be almost as efficient as the vacuum type centrifuge for the concentration and purification of influenza virus and, because of its larger capacity, is recommended for the preparation of purified virus on a large scale.

scholarly journals Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data

2020 ◽  
Vol 21 (S18) ◽  
Author(s):  
Noel-Marie Plonski ◽  
Emily Johnson ◽  
Madeline Frederick ◽  
Heather Mercer ◽  
Gail Fraizer ◽  
...  
Keyword(s):  
Rna Editing ◽  
Large Scale ◽  
Neural Progenitor Cells ◽  
Viral Infections ◽  
Variant Calling ◽  
Rna Seq ◽  
Major Mechanism ◽  
Isoform Diversity ◽  
Adar Editing ◽  
Transcriptome Diversity

Abstract Background As the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. Many available tools facilitate analyses of one of the two major mechanisms of transcriptome diversity, namely, differential expression of isoforms due to alternative splicing, while the second major mechanism—RNA editing due to post-transcriptional changes of individual nucleotides—remains under-appreciated. Both these mechanisms play an essential role in physiological and diseases processes, including cancer and neurological disorders. However, elucidation of RNA editing events at transcriptome-wide level requires increasingly complex computational tools, in turn resulting in a steep entrance barrier for labs who are interested in high-throughput variant calling applications on a large scale but lack the manpower and/or computational expertise. Results Here we present an easy-to-use, fully automated, computational pipeline (Automated Isoform Diversity Detector, AIDD) that contains open source tools for various tasks needed to map transcriptome diversity, including RNA editing events. To facilitate reproducibility and avoid system dependencies, the pipeline is contained within a pre-configured VirtualBox environment. The analytical tasks and format conversions are accomplished via a set of automated scripts that enable the user to go from a set of raw data, such as fastq files, to publication-ready results and figures in one step. A publicly available dataset of Zika virus-infected neural progenitor cells is used to illustrate AIDD’s capabilities. Conclusions AIDD pipeline offers a user-friendly interface for comprehensive and reproducible RNA-seq analyses. Among unique features of AIDD are its ability to infer RNA editing patterns, including ADAR editing, and inclusion of Guttman scale patterns for time series analysis of such editing landscapes. AIDD-based results show importance of diversity of ADAR isoforms, key RNA editing enzymes linked with the innate immune system and viral infections. These findings offer insights into the potential role of ADAR editing dysregulation in the disease mechanisms, including those of congenital Zika syndrome. Because of its automated all-inclusive features, AIDD pipeline enables even a novice user to easily explore common mechanisms of transcriptome diversity, including RNA editing landscapes.

Enhancement of Growth of Chick Host Spleens following Chorio-allantoic Membrane Grafts of Homologous Tissues1

Development ◽  
1959 ◽  
Vol 7 (4) ◽  
pp. 512-525
Author(s):  
A. M. Mun ◽  
I. L. Kosin ◽  
I. Sato
Keyword(s):  
Chick Embryo ◽  
Mitotic Index ◽  
Chick Embryos ◽  
Adult Chicken ◽  
Chicken Tissues ◽  
Chicken Spleen ◽  
Organ Specific ◽  
Excellent Tool

The phenomenon of enlargement of the host chick embryo spleen, following grafts of homologous adult chicken tissues to the chorio-allantoic membrane (CAM), affords the investigator an excellent tool for the study of growth. Initial observations of this phenomenon were made by Danchakoff (1916) and Murphy (1916). Grafts of adult chicken spleen on the chorio-allantoic membrane of 9-day-old chick embryos brought about a striking enlargement of the host spleens after 8 additional days of incubation. The phenomenon was later studied by Ebert (1951), who showed that the effect was only partially organ-specific. Grafts of thymus and liver affected the weight of the host spleen, but in each case the effect was far smaller than that observed with splenic transplants. Andres (1955) found that injected kidney and liver debris, which elicited an increased mitotic index in the homologous host organ, was not inhibited in its action by killing the cells through freezing and subsequent thawing.

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