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Genes Dec 2020Pigeon belongs to altrices. Squab cannot forage independently. Nutrition can only be obtained from crop milk secreted by male and female pigeon. miRNA could regulate...
Pigeon belongs to altrices. Squab cannot forage independently. Nutrition can only be obtained from crop milk secreted by male and female pigeon. miRNA could regulate many biological events. However, the roles of miRNA and ceRNA in regulating crop milk production are still unknown. In this study, we investigated the miRNAs expression profile of female pigeon crop, explored the potential key genes, and found the regulatory mechanisms of crop milk production. A total of 71 miRNAs were identified differentially expressed significantly. Meanwhile, miR-20b-5p, miR-146b-5p, miR-21-5p, and miR-26b-5p were found to be the key miRNAs regulating lactation. Target genes of these miRNAs participated mainly in cell development; protein and lipid synthesis; and ion signaling processes, such as cell-cell adhesion, epithelial cell morphogenesis, calcium signaling pathway, protein digestion, and absorption. In the ceRNA network, miR-193-5p was located in the central position, and miR-193-5p//LOC110355588, miR-460b-5p//MSTRG.132954, and miR-193-5p//LOC110355588 regulatory axes were believed to affect lactation. Collectively, our findings enriched the miRNA expression profile of pigeon and provided novel insights into the microRNA-associated-ceRNA networks regulating crop milk production in pigeon.
Topics: Animal Nutritional Physiological Phenomena; Animals; Animals, Newborn; Avian Proteins; Columbidae; Female; Gene Expression Regulation; Gene Regulatory Networks; Lipid Metabolism; Male; MicroRNAs; Molecular Sequence Annotation; Protein Biosynthesis; RNA, Long Noncoding; Signal Transduction
PubMed: 33396684
DOI: 10.3390/genes12010039 -
Scientific Reports Nov 2022Production activities drive the replacement of original habitats with artificial ones, leading to new bird assemblages. In this study, we assessed if anthropogenic...
Production activities drive the replacement of original habitats with artificial ones, leading to new bird assemblages. In this study, we assessed if anthropogenic habitats acted as environmental filters causing functional redundancy or as promoters of functional divergence, depending on the biome. We also investigated if functional patterns derived from phylogenetic convergence or clustering. For this purpose, we computed the standardized effect sizes (SES) for avian functional and phylogenetic diversity using null models and compared the SES values among tree plantations, urban settlements (US), cattle pastures (CP), crop fields (CF) and natural habitats from two biomes: grassland and forest. We used generalized least squares models to test if functional and phylogenetic SES indicated functional redundancy or divergence, and phylogenetic convergence or clustering. We found functional redundancy in grassland and functional divergence in forest associated with environmental filtering and competitive exclusion, respectively. In grassland, functional structure was not associated with a clear phylogenetic pattern, while in forest functional divergence was caused by evolutionary convergence in CF and CP and conservation in US. The prevalences of functional redundancy and functional divergence patterns and their associated predominant mechanism of community assembly were found to depend on the biome and the regional species pool.
Topics: Cattle; Animals; Phylogeny; Ecosystem; Birds; Forests; Biological Evolution
PubMed: 36396682
DOI: 10.1038/s41598-022-24238-x -
International Journal of Molecular... Jan 2023Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple...
Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple insect-resistance against insect pests such as Asian corn borer and corn leaf aphids. Although numerous genetic loci for multiple insect-resistant traits have been identified, little is known about genetic controls regarding DIMBOA content. In this study, the best linear unbiased prediction (BLUP) values of DIMBOA content in two ecological environments across 310 maize inbred lines were calculated; and their phenotypic data and BLUP values were used for marker-trait association analysis. We identified nine SSRs that were significantly associated with DIMBOA content, which explained 4.30-20.04% of the phenotypic variation. Combined with 47 original genetic loci from previous studies, we detected 19 hot loci and approximately 11 hot loci (in Bin 1.04, Bin 2.00-2.01, Bin 2.03-2.04, Bin 4.00-4.03, Bin 5.03, Bin 5.05-5.07, Bin 8.01-8.03, Bin 8.04-8.05, Bin 8.06, Bin 9.01, and Bin 10.04 regions) supported pleiotropy for their association with two or more insect-resistant traits. Within the 19 hot loci, we identified 49 candidate genes, including 12 controlling DIMBOA biosynthesis, 6 involved in sugar metabolism/homeostasis, 2 regulating peroxidases activity, 21 associated with growth and development [(auxin-upregulated RNAs (SAUR) family member and v-myb avian myeloblastosis viral oncogene homolog (MYB)], and 7 involved in several key enzyme activities (lipoxygenase, cysteine protease, restriction endonuclease, and ubiquitin-conjugating enzyme). The synergy and antagonism interactions among these genes formed the complex defense mechanisms induced by multiple insect pests. Moreover, sufficient genetic variation was reported for DIMBOA performance and SSR markers in the 310 tested maize inbred lines, and 3 highly (DIMBOA content was 402.74-528.88 μg g FW) and 15 moderate (DIMBOA content was 312.92-426.56 μg g FW) insect-resistant genotypes were major enriched in the Reid group. These insect-resistant inbred lines can be used as parents in maize breeding programs to develop new varieties.
Topics: Animals; Zea mays; Plant Breeding; Insecta; Genetic Variation; Genetic Association Studies
PubMed: 36768464
DOI: 10.3390/ijms24032138 -
Scientific Reports Feb 2019Rapeseed proteins are described to be poorly digestible in chickens. To further identify some molecular locks that may limit their use in poultry nutrition, we conducted...
Rapeseed proteins are described to be poorly digestible in chickens. To further identify some molecular locks that may limit their use in poultry nutrition, we conducted a proteomic study on the various chicken digestive contents and proposed an integrative view of the proteins recruited in the crop, proventriculus/gizzard, duodenum, jejunum, and ileum for digestion of rapeseed by-products. Twenty-seven distinct rapeseed proteins were identified in the hydrosoluble fraction of the feed prior ingestion. The number of rapeseed proteins identified in digestive contents decreases throughout the digestion process while some are progressively solubilized in the most distal digestive segment, likely due to a combined effect of pH and activity of specific hydrolytic enzymes. Fifteen chicken proteins were identified in the hydrosoluble proventriculus/gizzard content, including chymotrypsin-like elastase and pepsin. Interestingly, on the 69 distinct proteins identified in duodenum, only 9 were proteolytic enzymes, whereas the others were associated with homeostasis, and carbohydrate, lipid, vitamin and hormone metabolisms. In contrast, chicken proteins identified in jejunal and ileal contents were mostly proteases and peptidases. The present work highlights the relevance of using integrative proteomics applied to the entire digestive tract to better appreciate the protein profile and functions of each digestive segment.
Topics: Animal Feed; Animal Nutritional Physiological Phenomena; Animals; Avian Proteins; Brassica napus; Chickens; Gastrointestinal Contents; Gastrointestinal Tract; Plant Proteins, Dietary; Proteomics
PubMed: 30816158
DOI: 10.1038/s41598-019-38725-1 -
BMC Genomics Sep 2011Both male and female pigeons have the ability to produce a nutrient solution in their crop for the nourishment of their young. The production of the nutrient solution... (Comparative Study)
Comparative Study
BACKGROUND
Both male and female pigeons have the ability to produce a nutrient solution in their crop for the nourishment of their young. The production of the nutrient solution has been likened to lactation in mammals, and hence the product has been called pigeon 'milk'. It has been shown that pigeon 'milk' is essential for growth and development of the pigeon squab, and without it they fail to thrive. Studies have investigated the nutritional value of pigeon 'milk' but very little else is known about what it is or how it is produced. This study aimed to gain insight into the process by studying gene expression in the 'lactating' crop.
RESULTS
Macroscopic comparison of 'lactating' and non-'lactating' crop reveals that the 'lactating' crop is enlarged and thickened with two very obvious lateral lobes that contain discrete rice-shaped pellets of pigeon 'milk'. This was characterised histologically by an increase in the number and depth of rete pegs extending from the basal layer of the epithelium to the lamina propria, and extensive proliferation and folding of the germinal layer into the superficial epithelium. A global gene expression profile comparison between 'lactating' crop and non-'lactating' crop showed that 542 genes are up-regulated in the 'lactating' crop, and 639 genes are down-regulated. Pathway analysis revealed that genes up-regulated in 'lactating' crop were involved in the proliferation of melanocytes, extracellular matrix-receptor interaction, the adherens junction and the wingless (wnt) signalling pathway. Gene ontology analysis showed that antioxidant response and microtubule transport were enriched in 'lactating' crop.
CONCLUSIONS
There is a hyperplastic response in the pigeon crop epithelium during 'lactation' that leads to localised cellular stress and expression of antioxidant protein-encoding genes. The differentiated, cornified cells that form the pigeon 'milk' are of keratinocyte lineage and contain triglycerides that are likely endocytosed as very low density lipoprotein (VLDL) and repackaged as triglyceride in vesicles that are transported intracellularly by microtubules. This mechanism is an interesting example of the evolution of a system with analogies to mammalian lactation, as pigeon 'milk' fulfils a similar function to mammalian milk, but is produced by a different mechanism.
Topics: Animals; Cicer; Columbidae; Crop, Avian; Epithelium; Female; Gene Expression Profiling; Gene Expression Regulation; Molecular Sequence Annotation; Oligonucleotide Array Sequence Analysis; Transcriptome
PubMed: 21929790
DOI: 10.1186/1471-2164-12-452 -
BMC Plant Biology Mar 2023Chrysanthemum is a popular ornamental plant worldwide. MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factors play an important role in everything...
BACKGROUND
Chrysanthemum is a popular ornamental plant worldwide. MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factors play an important role in everything from stress resistance to plant growth and development. However, the MYB family of chrysanthemums has not been the subject of a detailed bioinformatics and expression investigation.
RESULTS
In this study, we examined 324 CnMYB transcription factors from Chrysanthemum nankingense genome data, which contained 122 Cn1R-MYB, 183 CnR2R3-MYB, 12 Cn3R-MYB, 2 Cn4R-MYB, and 5 atypical CnMYB. The protein motifs and classification of CnMYB transcription factors were analyzed. Among them, motifs 1, 2, 3, and 4 were found to encode the MYB DNA-binding domain in R2R3-MYB proteins, while in other-MYB proteins, the motifs 1, 2, 3, 4, 5, 6, 7, and 8 encode the MYB DNA-binding domain. Among all CnMYBs, 44 genes were selected due to the presence of CpG islands, while methylation is detected in three genes, including CnMYB9, CnMYB152, and CnMYB219. We analyzed the expression levels of each CnMYB gene in ray floret, disc floret, flower bud, leaf, stem, and root tissues. Based on phylogenetic analysis and gene expression analysis, three genes appeared likely to control cellulose and lignin synthesis in stem tissue, and 16 genes appeared likely to regulate flowering time, anther, pollen development, and flower color. Fifty-one candidate genes that may be involved in stress response were identified through phylogenetic, stress-responseve motif of promoter, and qRT-PCR analyses. According to genes expression levels under stress conditions, six CnMYB genes (CnMYB9, CnMYB172, CnMYB186, CnMYB199, CnMYB219, and CnMYB152) were identified as key stress-responsive genes.
CONCLUSIONS
This research provides useful information for further functional analysis of the CnMYB gene family in chrysanthemums, as well as offers candidate genes for further study of cellulose and lignin synthesis, flowering traits, salt and drought stress mechanism.
Topics: Transcription Factors; Plant Proteins; Chrysanthemum; Lignin; Phylogeny; DNA; Gene Expression Regulation, Plant
PubMed: 36915063
DOI: 10.1186/s12870-023-04137-7 -
PloS One 2019Three artificially selected duck populations (AS), higher lean meat ratios (LTPD), higher fat ratios (FTPD) and higher quality meat (CMD), have been developed in China,...
Three artificially selected duck populations (AS), higher lean meat ratios (LTPD), higher fat ratios (FTPD) and higher quality meat (CMD), have been developed in China, providing excellent populations for investigation of artificial selection effects. However, the genetic signatures of artificial selection are unclear. In this study, we sequenced the genome sequences of these three artificially selected populations and their ancestral population (mallard, M). We then compared the genome sequences between AS and M and between LTPD and FTPD using integrated strategies such as anchoring scaffolds to pseudo-chromosomes, mutation detection, selective screening, GO analysis, qRT-PCR, and protein multiple sequences alignment to uncover genetic signatures of selection. We anchored duck scaffolds to pseudo-chromosomes and obtained 28 pseudo-chromosomes, accounting for 84% of duck genome in length. Totally 78 and 99 genes were found to be under selection between AS and M and between LTPD and FTPD. Genes under selection between AS and M mainly involved in pigmentation and heart rates, while genes under selection between LTPD and FTPD involved in muscle development and fat deposition. A heart rate regulator (HCN1), the strongest selected gene between AS and M, harbored a GC deletion in AS and displayed higher mRNA expression level in M than in AS. IGF2R, a regulator of skeletal muscle mass, was found to be under selection between FTPD and LTPD. We also found two nonsynonymous substitutions in IGF2R, which might lead to higher IGF2R mRNA expression level in FTPD than LTPD, indicating the two nonsynonymous substitutions might play a key role for the regulation of duck skeletal muscle mass. Taken together, these results of this study provide valuable insight for the genetic basis of duck artificial selection.
Topics: Adipose Tissue; Amino Acid Sequence; Animals; Avian Proteins; Body Composition; Breeding; Chromosome Mapping; Ducks; Female; Gene Expression Profiling; Gene Expression Regulation; Gene Ontology; Genome; Heart Rate; Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels; Male; Meat; Molecular Sequence Annotation; Muscle, Skeletal; Pigmentation; Receptor, IGF Type 2; Selection, Genetic; Sequence Alignment; Sequence Homology, Amino Acid
PubMed: 30735526
DOI: 10.1371/journal.pone.0211908 -
The Journal of Poultry Science Jan 2020Probiotic bacteria are known for their beneficial effects on the intestinal immune function of the host animal. However, their effects on mucosal barrier function in...
Probiotic bacteria are known for their beneficial effects on the intestinal immune function of the host animal. However, their effects on mucosal barrier function in chicks are not completely understood. The aim of this study was to determine the effects of the probiotic bacterium, (LR), on the gastrointestinal mucosal barrier function of broiler chicks. One day-old male broiler chicks were orally injected water (300 L) with or without 1 × 10 cfu of LR (5 mg FINELACT, Asahi Calpis Wellness Co. Ltd.) every morning for 7 days (day 0 to 6). The crop, duodenum, ileum, and cecum were collected on day 7 and were used for histological analysis and RNA extraction. Then, the thickness of the mucosal structures and the number of goblet cells in the digestive tract were assessed using histological analysis. The expression of Mucin 2, factors related to the formation of tight junctions (Claudin1, 5, and 16, ZO2, and JAM2), cytokines (IL-6, CXCLi2, and IL-10), and avian -defensin 10 (AvBDs) (AvBD2, 10, and 12) in the crop, duodenum, ileum, and cecum were analyzed using real-time polymerase chain reaction (PCR). Results showed that oral administration of LR increased ileal villus height and crypt depth, decreased Claudin16 level in the crop and increased JAM2 level in the crop and ileum, and decreased the expression of AvBD10 in the ileum and cecum and that of AvBD12 in the crop. It did not affect goblet cell number and Mucin 2 expression. These results suggested that LR used in this study may enhance mucosal barrier function by regulating tight junctions in the upper gastrointestinal tract.
PubMed: 32174767
DOI: 10.2141/jpsa.0190035 -
PloS One 2018The critically endangered Northern bald ibis (Geronticus eremita) is a migratory bird that became extinct in Europe centuries ago. Since 2014, the Northern bald ibis is...
The critically endangered Northern bald ibis (Geronticus eremita) is a migratory bird that became extinct in Europe centuries ago. Since 2014, the Northern bald ibis is subject to an intensive rehabilitation and conservation regime aiming to reintroduce the bird in its original distribution range in Central Europe and concurrently to maintain bird health and increase population size. Hitherto, virtually nothing is known about the microbial communities associated with the ibis species; an information pivotal for the veterinary management of these birds. Hence, the present study was conducted to provide a baseline description of the cultivable microbiota residing in the Northern bald ibis. Samples derived from the choana, trachea, crop and cloaca were examined employing a culturomic approach in order to identify microbes at each sampling site and to compare their frequency among age classes, seasonal appearances and rearing types. In total, 94 microbial species including 14 potentially new bacterial taxa were cultivated from the Northern bald ibis with 36, 58 and 59 bacterial species isolated from the choana, crop and cloaca, respectively. The microbiota of the Northern bald ibis was dominated by members of the phylum Firmicutes, followed by Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria, altogether phylotypes commonly observed within avian gut environments. Differences in relative abundances of various microbial taxa were evident among sample types indicating mucosa-specific colonisation properties and tissue tropism. Besides, results of the present study indicate that the composition of microbiota was also affected by age, season (environment) and rearing type. While the prevalence of traditional pathogenic microbial species was extremely low, several opportunists including Clostridium perfringens toxotype A were frequently present in samples indicating that the Northern bald ibis may represent an important animal reservoir for these pathogens. In summary, the presented study provides a first inventory of the cultivable microbiota residing in the critically endangered Northern bald ibis and represents a first step in a wider investigation of the ibis microbiome with the ultimate goal to contribute to the management and survival of this critically endangered bird.
Topics: Animals; Birds; Clostridium perfringens; Endangered Species; Escherichia coli; Europe; Microbiota; RNA, Bacterial; RNA, Fungal; RNA, Ribosomal, 16S; Seasons; Virulence
PubMed: 29617453
DOI: 10.1371/journal.pone.0195255 -
Frontiers in Microbiology 2017The Clermont scheme has been used for subtyping of since it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type...
Comparative Analysis of Phylogenetic Assignment of Human and Avian ExPEC and Fecal Commensal Using the (Previous and Revised) Clermont Phylogenetic Typing Methods and its Impact on Avian Pathogenic (APEC) Classification.
The Clermont scheme has been used for subtyping of since it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type commensal and pathogenic , such as extraintestinal pathogenic (ExPEC), and compare their phylogenetic assignment by pathogenicity, serogroup, distribution among ExPEC of different host species and complement of virulence and resistance traits. Here, we compare assignments of human and avian ExPEC and commensal using the old and revised Clermont schemes to determine if the new scheme provides a refined snapshot of isolate classification. 1,996 from human hosts and poultry, including 84 human neonatal meningitis isolates, 88 human vaginal , 696 human uropathogenic , 197 healthy human fecal , 452 avian pathogenic (APEC), 200 retail poultry , 80 crop and gizzard from healthy poultry at slaughter and 199 fecal from healthy birds at slaughter. All isolates were subject to phylogenetic analysis using the Clermont et al. (2000, 2013) schemes and compared to determine the effect of the new classification on strain designation. Most of the isolates' strain designation remained where they were originally assigned. Greatest designation change occurred in APEC where 53.8% of isolates were reclassified; while classification rates among human strains ranged from 8 to 14%. However, some significant changes were observed for UPEC associated strains with significant ( < 0.05) designation changes observed from A to C and D to E or F phylogenetic types; a similar designation change was noted among NMEC for D to F designation change. Among the APEC significant designation changes were observed from A to C and D to E and F. These studies suggest that the new scheme provides a tighter and more meaningful definition of some ExPEC; while the new typing scheme has a significant impact on APEC classification. A comparison of phylogenetic group assignment by content of virulence, resistance, replicon and pathogenicity island genes in APEC suggests that insertion of pathogenicity islands into the genome appears to correlate closely with revised phylogenetic assignment.
PubMed: 28280491
DOI: 10.3389/fmicb.2017.00283