Analysis of amino acid in albumen and circular RNAs in ovaries of laying hens by chromatographic analysis and RNA-seq

Abstract Background Prestin (SLC26A5) is responsible for acute sensitivity and frequency selectivity in the vertebrate auditory system. Limited knowledge of prestin is from experiments using site-directed mutagenesis or domain-swapping techniques after the amino acid residues were identified by comparing the sequence of prestin to those of its paralogs and orthologs. Frog prestin is the only representative in amphibian lineage and the studies of it were quite rare with only one species identified. Results Here we report a new coding sequence of SLC26A5 for a frog species, Rana catesbeiana (the American bullfrog). In our study, the SLC26A5 gene of Rana has been mapped, sequenced and cloned successively using RNA-Seq. We measured the nonlinear capacitance (NLC) of prestin both in the hair cells of Rana’s inner ear and HEK293T cells transfected with this new coding gene. HEK293T cells expressing Rana prestin showed electrophysiological features similar to that of hair cells from its inner ear. Comparative studies of zebrafish, chick, Rana and an ancient frog species showed that chick and zebrafish prestin lacked NLC. Ancient frog’s prestin was functionally different from Rana. Conclusions We mapped and sequenced the SLC26A5 of the Rana catesbeiana from its inner ear cDNA using RNA-Seq. The Rana SLC26A5 cDNA was 2292 bp long, encoding a polypeptide of 763 amino acid residues, with 40% identity to mammals. This new coding gene could encode a functionally active protein conferring NLC to both frog HCs and the mammalian cell line. While comparing to its orthologs, the amphibian prestin has been evolutionarily changing its function and becomes more advanced than avian and teleost prestin.

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Variability of amino acid digestibility of lupin and pea grains in caecectomised laying hens

British Poultry Science ◽

10.1080/00071668.2018.1556389 ◽

2019 ◽

Vol 60 (3) ◽

pp. 229-240 ◽

Cited By ~ 1

Author(s):

T. Zuber ◽

W. Siegert ◽

H. Salehi ◽

F. Hummel ◽

M. Rodehutscord

Keyword(s):

Amino Acid ◽

Laying Hens

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DEBKS: A Tool to Detect Differentially Expressed Circular RNA

10.1101/2020.10.14.336982 ◽

2020 ◽

Author(s):

Zelin Liu ◽

Huiru Ding ◽

Jianqi She ◽

Chunhua Chen ◽

Weiguang Zhang ◽

...

Keyword(s):

Open Source ◽

Rna Sequencing ◽

Open Source Software ◽

Simulated Data ◽

Circular Rna ◽

Host Gene ◽

Circular Rnas ◽

Biological Processes ◽

Rna Seq ◽

Disease Pathogenesis

AbstractCircular RNAs (circRNAs) are involved in various biological processes and in disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that circRNA is formed from the host gene by back-splicing (BS). To distinguish between expression originating from BS and that from the host gene, we present DEBKS, a software program to streamline the discovery of differential BS between two rRNA-depleted RNA sequencing (RNA-seq) sample groups. By applying real and simulated data and employing RT-qPCR for validation, we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups. DEBKS is available at https://github.com/yangence/DEBKS as open-source software.

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Identification and Characterization of Circular RNAs in Longissimus Dorsi Muscle Tissue from Two Goat Breeds using RNA-Seq

10.21203/rs.3.rs-944970/v1 ◽

2021 ◽

Author(s):

Jiyuan Shen ◽

Huimin Zhen ◽

Lu Li ◽

Yuting Zhang ◽

Jiqing Wang ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Fiber ◽

Muscle Development ◽

Production Performance ◽

Differentially Expressed ◽

Circular Rnas ◽

Longissimus Dorsi ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Fiber Size

Abstract Background: Circular RNAs (circRNAs) are a class of non-coding RNA that play crucial roles in the development of skeletal muscle. However, little is known about the role of circRNAs in caprine skeletal muscle. In this study, the muscle fiber size and expression profiles of circRNAs were compared in Longissimus dorsi muscle of Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with significant phenotypic differences in meat production performance, using hematoxylin and eosin staining and RNA-Seq, respectively.Results: The muscle fiber size in LC goats were larger than those in ZB goats (P < 0.05). A total of 10,875 circRNAs were identified and 214 of these were differentially expressed between the two caprine breeds. The authentication and expression levels of 20 circRNAs were confirmed using reverse transcriptase-polymerase chain reaction (RT-PCR) and DNA sequencing. The parent genes of differentially expressed circRNAs were mainly enriched in connective tissue development, Rap1, cGMP-PKG, cAMP and Ras signaling pathway. Some miRNAs reportedly associated with skeletal muscle development and intramuscular fat deposition would be targeted by several differentially expressed circRNAs and the most highly expressed circRNA (circ_001086).Conclusion: These results provide an improved understanding of the functions of circRNAs in skeletal muscle development of goats.

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Global accumulation of circRNAs during aging in Caenorhabditis elegans

10.1101/175026 ◽

2017 ◽

Author(s):

Mariela Cortés-López ◽

Matthew Gruner ◽

Daphne A. Cooper ◽

Hannah N. Gruner ◽

Alexandru-Ioan Voda ◽

...

Keyword(s):

Global Scale ◽

Circular Rnas ◽

Rna Seq ◽

Aging Research ◽

C Elegans ◽

Fourth Larval Stage ◽

Functional Consequences ◽

Exceptional Stability ◽

Massive Accumulation

SummaryCircular RNAs (CircRNAs) are a newly appreciated class of RNAs that lack free 5´ and 3´ ends, are expressed by the thousands in diverse forms of life, and are mostly of enigmatic function. Ostensibly due to their resistance to exonucleases, circRNAs are known to be exceptionally stable. Here, we examined the global profile of circRNAs in C. elegans during aging by performing ribo-depleted total RNA-seq from the fourth larval stage (L4) through 10-day old adults. Using stringent bioinformatic criteria and experimental validation, we annotated 1,166 circRNAs, including 575 newly discovered circRNAs. These circRNAs were derived from 797 genes with diverse functions, including genes involved in the determination of lifespan. A massive accumulation of circRNAs during aging was uncovered. Many hundreds of circRNAs were significantly increased among the aging time-points and increases of select circRNAs by over 40-fold during aging were quantified by qRT-PCR. The age-accumulation of circRNAs was not accompanied by increased expression of linear RNAs from the same host genes. We attribute the global scale of circRNA age-accumulation to the high composition of postmitotic cells in adult C. elegans, coupled with the high resistance of circRNAs to decay. These findings suggest that the exceptional stability of circRNAs might explain age-accumulation trends observed from neural tissues of other organisms, which also have a high composition of post-mitotic cells. Given the suitability of C. elegans for aging research, it is now poised as an excellent model system to determine if there are functional consequences of circRNA accumulation during aging.

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Transcriptomics and Transmission Ultrastructural Examination Reveals the Nephrotoxicity of Cadmium in Laying Hens

10.21203/rs.3.rs-609271/v1 ◽

2021 ◽

Author(s):

Man Zhao ◽

Wenbo He ◽

Can Tao ◽

Beiyu Zhang ◽

Shuai Wang ◽

...

Keyword(s):

Laying Hens ◽

Basal Diet ◽

Ultrastructural Changes ◽

Control Group ◽

Renal Tubules ◽

Rna Seq ◽

Ultrastructural Examination ◽

Treatment Groups ◽

Kegg Pathway Analysis ◽

Transcriptome Expression

Abstract The objective of this study was to reveal the effects of cadmium (Cd) on ultrastructural changes, oxidative stress, and transcriptome expression in the kidneys of laying hens. Seventy-two healthy Hy-Line brown laying hens at 41 weeks old were randomly allocated to four treatment groups with six replicates. The control group received a basal diet without additional Cd incorporation, and the other three treatment groups received diets supplemented with 15, 30, or 60 mg Cd /kg of feed. After 6 weeks of exposure the results show that administration of 60 mg/kg Cd significantly reduced (P < 0.05) eggshell thickness. With an increase in the Cd concentration in feed, the concentrations of renal Zn, Fe also had changed. Renal histopathology and ultrastructure also showed aggravated damage to glomeruli and renal tubules, and the deformation of nuclei and mitochondria in all Cd treatment groups. With an increase in Cd in feed, the activity of GPX and CAT was significantly reduced (P＜0.05), while the activity of T-AOC was decreased (P＜0.05) only in the 60 mg/kg Cd group. RNA-seq analysis revealed that 410 genes displayed differential expression (≥ 1.5-fold) in the 60 mg/kg supplementation group, compared to the control group. GO and KEGG pathway analysis results showed that Cd affected many genes involved in mitochondria and ion transport. In conclusion, this study elaborates the mechanisms underlying renal toxicity caused by Cd, which might provide target candidate genes for alleviating Cd poisoning in laying hens.

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