scholarly journals Integrative analysis of transcriptomic data related to the liver of laying hens: from physiological basics to newly identified functions

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Audrey Gloux ◽  
Michel J. Duclos ◽  
Aurélien Brionne ◽  
Marie Bourin ◽  
Yves Nys ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Sexual Maturity ◽  
Laying Hens ◽  
Clock Genes ◽  
Gene Annotation ◽  
Secreted Proteins ◽  
Avian Reproduction ◽  
Related Information ◽  
Metabolic Functions ◽  
Integrative View

Abstract Background At sexual maturity, the liver of laying hens undergoes many metabolic changes to support vitellogenesis. In published transcriptomic approaches, hundreds of genes were reported to be overexpressed in laying hens and functional gene annotation using gene ontology tools have essentially revealed an enrichment in lipid and protein metabolisms. We reanalyzed some data from a previously published article comparing 38-week old versus 10-week old hens to give a more integrative view of the functions stimulated in the liver at sexual maturity and to move beyond current physiological knowledge. Functions were defined based on information available in Uniprot database and published literature. Results Of the 516 genes previously shown to be overexpressed in the liver of laying hens, 475 were intracellular (1.23–50.72 fold changes), while only 36 were predicted to be secreted (1.35–66.93 fold changes) and 5 had no related information on their cellular location. Besides lipogenesis and protein metabolism, we demonstrated that the liver of laying hens overexpresses several clock genes (which supports the circadian control of liver metabolic functions) and was likely to be involved in a liver/brain/liver circuit (neurotransmitter transport), in thyroid and steroid hormones metabolisms. Many genes were associated with anatomical structure development, organ homeostasis but also regulation of blood pressure. As expected, several secreted proteins are incorporated in yolky follicles but we also evidenced that some proteins are likely participating in fertilization (ZP1, MFGE8, LINC00954, OVOCH1) and in thyroid hormone maturation (CPQ). We also proposed that secreted proteins (PHOSPHO1, FGF23, BMP7 but also vitamin-binding proteins) may contribute to the development of peripheral organs including the formation of medullar bones to provide labile calcium for eggshell formation. Thirteen genes are uniquely found in chicken/bird but not in human species, which strengthens that some of these genes may be specifically related to avian reproduction. Conclusions This study gives additional hypotheses on some molecular actors and mechanisms that are involved in basic physiological function of the liver at sexual maturity of hen. It also revealed some additional functions that accompany reproductive capacities of laying hens, and that are usually underestimated when using classical gene ontology approaches.

Dusk feeding in laying hens is shifted by light program via involvement of clock genes

2021 ◽  
Author(s):  
Xiaojuan Wang ◽  
Zengmin Liu ◽  
Jingpeng Zhao ◽  
Hongchao Jiao ◽  
Hai Lin
Keyword(s):  
Laying Hens ◽  
Clock Genes

scholarly journals GENETIC AND PHENOTYPIC ASSOCIATIONS OF JUVENILE BODY WEIGHTS AND EGG PRODUCTION TRAITS IN TWO STRAINS OF RHODE ISLAND CHICKENS

2021 ◽  
Vol 18 ◽  
pp. 66-70
Author(s):  
O. O. ONI ◽  
B. Y. ABUBAKAR ◽  
S. O. OGUNDIPE
Keyword(s):  
Body Weight ◽  
Rhode Island ◽  
Sexual Maturity ◽  
Egg Production ◽  
Genetic Parameters ◽  
Laying Hens ◽  
Genetic Correlations ◽  
Selection Criterion ◽  
Production Traits ◽  
Body Weights

Data on body weight at 16 (WT16); 20 (WT20) weeks of age and at sexual maturity (WTSM) weight of first egg (WT1st), age at sexual maturity (ASM) and 120-d egg production (EN)  were used to estimate genetic parameters in 636 hens of two strains of Rhode Island chikens. There were significant (P.01) differences between  the two strains for all traits except for WTSM.The heritability estimates obtained ranged from 0.05 to 0.41 and 0.04 to 0.30 for strains 1 and 2 respectively. The genetic correlations obtained for the various traits were medium to high for the two strains. The phenotypic correlations were generally low but followed the same trend. The results indicate that selected stocks of the two strains would show improvements in egg production and age   at sexual maturity if juvenile body weight (WT20) is employed as a selection criterion at housing for laying hens.

scholarly journals GAPGOM—an R package for gene annotation prediction using GO Metrics

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Casper van Mourik ◽  
Rezvan Ehsani ◽  
Finn Drabløs
Keyword(s):  
Gene Ontology ◽  
Gene Annotation ◽  
Enrichment Analysis ◽  
R Package ◽  
Prediction Performance ◽  
Gene Products ◽  
Limited Information ◽  
Non Coding Rnas ◽  
User Friendly ◽  
Go Terms

Abstract Objective Properties of gene products can be described or annotated with Gene Ontology (GO) terms. But for many genes we have limited information about their products, for example with respect to function. This is particularly true for long non-coding RNAs (lncRNAs), where the function in most cases is unknown. However, it has been shown that annotation as described by GO terms to some extent can be predicted by enrichment analysis on properties of co-expressed genes. Results GAPGOM integrates two relevant algorithms, lncRNA2GOA and TopoICSim, into a user-friendly R package. Here lncRNA2GOA does annotation prediction by co-expression, whereas TopoICSim estimates similarity between GO graphs, which can be used for benchmarking of prediction performance, but also for comparison of GO graphs in general. The package provides an improved implementation of the original tools, with substantial improvements in performance and documentation, unified interfaces, and additional features.

scholarly journals Period1 mediates rhythmic metabolism of toxins by interacting with CYP2E1

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wenhao Ge ◽  
Tao Wang ◽  
Yang Zhao ◽  
Yunxia Yang ◽  
Qi Sun ◽  
...  
Keyword(s):  
Clock Gene ◽  
Clock Genes ◽  
Biological Clock ◽  
Nutrient Metabolism ◽  
Potential Therapeutic Target ◽  
Metabolic Functions ◽  
Timing System ◽  
Almost All ◽  
Substrate Processing ◽  
Deficient Mice

AbstractThe biological clock is an endogenous biological timing system, which controls metabolic functions in almost all organs. Nutrient metabolism, substrate processing, and detoxification are circadian controlled in livers. However, how the clock genes respond to toxins and influence toxicity keeps unclear. We identified the clock gene Per1 was specifically elevated in mice exposed to toxins such as carbon tetrachloride (CCl4). Mice lacking Per1 slowed down the metabolic rate of toxins including CCl4, capsaicin, and acetaminophen, exhibiting relatively more residues in the plasma. Liver injury and fibrosis induced by acute and chronic CCl4 exposure were markedly alleviated in Per1-deficient mice. These processes involved the binding of PER1 protein and hepatocyte nuclear factor-1alpha (HNF-1α), which enhances the recruitment of HNF-1α to cytochrome P450 2E1 (Cyp2e1) promoter and increases Cyp2e1 expression, thereby promoting metabolism for toxins in the livers. These results indicate that PER1 mediates the metabolism of toxins and appropriate suppression of Per1 response is a potential therapeutic target for toxin-induced hepatotoxicity.

scholarly journals Transcriptional characterisation of the Exaiptasia pallida pedal disc

2019 ◽  
Author(s):  
Peter A Davey ◽  
Jessica L Clarke ◽  
Marcelo Rodrigues ◽  
Nick Aldred
Keyword(s):  
Gene Ontology ◽  
Marine Invertebrates ◽  
Secreted Proteins ◽  
Specific Gene ◽  
Protein Superfamily ◽  
Biological Adhesion ◽  
Ab Initio Prediction ◽  
Upregulated Genes ◽  
Exaiptasia Pallida ◽  
Pedal Disc

Abstract Background Biological adhesion (bioadhesion), enables organisms to attach to surfaces as well as to a range of other targets. Bioadhesion evolved numerous times independently and is ubiquitous throughout the kingdoms of life. To date, investigations have focussed on various taxa of animals, plants and bacteria, but the fundamental processes underlying bioadhesion and the degree of conservation in different biological systems remain poorly understood. This study had two aims: 1) To characterise tissue-specific gene regulation in the pedal disc of the model cnidarian Exaiptasia pallida, and 2) to elucidate putative genes involved in pedal disc adhesion. Results Five hundred and forty-seven genes were differentially expressed in the pedal disc compared to the rest of the animal. Four hundred and twenty-seven genes were significantly upregulated and one hundred and twenty genes were significantly downregulated. Forty-one condensed gene ontology terms and 19 protein superfamily classifications were enriched in the pedal disc. Eight condensed gene ontology terms and 11 protein superfamily classifications were depleted. Enriched superfamilies were consistent with classifications identified previously as important for the bioadhesion of unrelated marine invertebrates. A host of genes involved in regulation of extra cellular matrix generation and degradation were identified, as well as others related to development and immunity. Ab initio prediction identified 173 upregulated genes that putatively code for extracellularly secreted proteins. Conclusion The analytical workflow facilitated identification of genes putatively involved in adhesion, immunity, defence and development of the E. pallida pedal disc. When defence, immunity and development-related genes were identified, those remaining corresponded most closely to formation of the extracellular matrix (ECM), implicating ECM in the adhesion of anemones to surfaces. This study therefore provides a valuable high-throughput resource for the bioadhesion community and lays a foundation for further targeted research to elucidate bioadhesion in the Cnidaria.

scholarly journals Efficacy of signal peptide predictors in identifying signal peptides in the experimental secretome of Picrophilous torridus, a thermoacidophilic archaeon

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255826
Author(s):  
Neelja Singhal ◽  
Anjali Garg ◽  
Nirpendra Singh ◽  
Pallavi Gulati ◽  
Manish Kumar ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Signal Peptide ◽  
Carbon Metabolism ◽  
Metabolic Pathways ◽  
Protein Translocation ◽  
Mass Spectrometric ◽  
Secreted Proteins ◽  
Secretory Proteins ◽  
Signal Peptides ◽  
Microbial Adaptation

Secretory proteins are important for microbial adaptation and survival in a particular environment. Till date, experimental secretomes have been reported for a few archaea. In this study, we have identified the experimental secretome of Picrophilous torridus and evaluated the efficacy of various signal peptide predictors (SPPs) in identifying signal peptides (SPs) in its experimental secretome. Liquid chromatography mass spectrometric (LC MS) analysis was performed for three independent P. torridus secretome samples and only those proteins which were common in the three experiments were selected for further analysis. Thus, 30 proteins were finally included in this study. Of these, 10 proteins were identified as hypothetical/uncharacterized proteins. Gene Ontology, KEGG and STRING analyses revealed that majority of the sercreted proteins and/or their interacting partners were involved in different metabolic pathways. Also, a few proteins like malate dehydrogenase (Q6L0C3) were multi-functional involved in different metabolic pathways like carbon metabolism, microbial metabolism in diverse environments, biosynthesis of antibiotics, etc. Multi-functionality of the secreted proteins reflects an important aspect of thermoacidophilic adaptation of P. torridus which has the smallest genome (1.5 Mbp) among nonparasitic aerobic microbes. SPPs like, PRED-SIGNAL, SignalP 5.0, PRED-TAT and LipoP 1.0 identified SPs in only a few secreted proteins. This suggests that either these SPPs were insufficient, or N-terminal SPs were absent in majority of the secreted proteins, or there might be alternative mechanisms of protein translocation in P. torridus.

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