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Animals : An Open Access Journal From... Jun 2023This study investigated the effect of three commercial water acidifiers on the performance, gut health, and colonization in experimentally challenged broiler chicks. A...
This study investigated the effect of three commercial water acidifiers on the performance, gut health, and colonization in experimentally challenged broiler chicks. A total of 192 one-day-old broiler chicks (Ross 308) were randomly allocated into 6 treatment groups with 4 replicates according to the following experimental design: group A, birds were not challenged and received tap water; group B, birds were challenged and received tap water; groups C, D, E, and F, birds were challenged and received tap water treated with 0.1% / SPECTRON, with 0.1-0.2% / ProPhorce™ SA Exclusive, with 0.1-0.2% / Premium acid, and with 0.1-0.2% / Salgard Liquid, respectively. The continuous water acidification evoked undesirable effects on broilers' performance and to an increased number of birds with ulcers and erosions in the oral cavity and the upper esophageal area. ProPhorce™ SA Exclusive and Premium acid significantly reduced the counts in the crop, whereas Salgard Liquid significantly reduced the counts in the ceca of birds. At slaughter age, only Premium acid significantly reduced counts in the ceca of birds. All the tested products ameliorated the changes induced by infection in the pH in the ceca of birds. It can be concluded that besides the effectiveness of the tested products in controlling in broilers, their continuous application evoked undesirable effects on broilers' performance, leading to the need to modify the dosage scheme in future investigations.
PubMed: 37370547
DOI: 10.3390/ani13122037 -
PLoS Genetics Jun 2023Pigeons (Columba livia) are among a select few avian species that have developed a specialized reproductive mode wherein the parents produce a 'milk' in their crop to...
Pigeons (Columba livia) are among a select few avian species that have developed a specialized reproductive mode wherein the parents produce a 'milk' in their crop to feed newborn squabs. Nonetheless, the transcriptomic dynamics and role in the rapid transition of core crop functions during 'lactation' remain largely unexplored. Here, we generated a de novo pigeon genome assembly to construct a high resolution spatio-temporal transcriptomic landscape of the crop epithelium across the entire breeding stage. This multi-omics analysis identified a set of 'lactation'-related genes involved in lipid and protein metabolism, which contribute to the rapid functional transitions in the crop. Analysis of in situ high-throughput chromatin conformation capture (Hi-C) sequencing revealed extensive reorganization of promoter-enhancer interactions linked to the dynamic expression of these 'lactation'-related genes between stages. Moreover, their expression is spatially localized in specific epithelial layers, and can be correlated with phenotypic changes in the crop. These results illustrate the preferential de novo synthesis of 'milk' lipids and proteins in the crop, and provides candidate enhancer loci for further investigation of the regulatory elements controlling pigeon 'lactation'.
Topics: Animals; Female; Transcriptome; Columbidae; Gene Expression Profiling; Milk; Lactation
PubMed: 37289658
DOI: 10.1371/journal.pgen.1010746 -
Environmental Pollution (Barking, Essex... Jun 2023Mechanistic effect models are increasingly recommended as tools for refining evaluations of risk from exposure to pesticides. In the context of bird and mammal risk...
Mechanistic effect models are increasingly recommended as tools for refining evaluations of risk from exposure to pesticides. In the context of bird and mammal risk assessments, DEB-TKTD models have been recommended for characterizing sublethal effects at lower tiers. However, there are currently no such models. Currently, chronic, multi-generational studies are performed to characterize potential effects of pesticides on avian reproduction, but it is has not been established to what extent results from these studies can inform effect models. Here, a standard Dynamic Energy Budget (DEB) model was extended to account for the avian toxicity endpoints observed in regulatory studies. We linked this new implementation to a toxicological module to capture observed pesticide effects on reproduction via a decreased efficiency of egg production. We analysed ten reproduction studies with five different pesticides conducted with the mallard (Anas platyrhynchos) and the northern bobwhite (Colinus virginianus). The new model implementation accurately distinguished between effects on egg production from direct mechanism of toxicity and from food avoidance. Due to the specific nature of regulatory studies, model applicability for risk refinement is currently limited. We provide suggestions for next steps in model development.
Topics: Animals; Pesticides; Birds; Reproduction; Colinus; Risk Assessment; Mammals
PubMed: 37011778
DOI: 10.1016/j.envpol.2023.121477 -
PloS One 2023Information about seed dispersal effectiveness (SDE) for plant species of conservation concern is rarely available to inform management strategies and actions. For...
Information about seed dispersal effectiveness (SDE) for plant species of conservation concern is rarely available to inform management strategies and actions. For Lindera subcoriacea (bog spicebush, Lauraceae), a rare endemic dioecious shrub of the southeastern United States, we examined the influence of two intrinsic and five extrinsic drivers on the number and proportion of seeds either dispersed, or predated pre- and post-dispersal. The number of seeds dispersed characterizes the quantitative component of SDE, while pre- and post-dispersal seed predation can affect the qualitative component of SDE. Using fruit counts, seed traps, and seed removal depots over multiple years, we estimated that approximately 28% of L. subcoriacea seeds are lost to pre-dispersal predation, 69% of seeds are dispersed, 3% of seeds fail to disperse, and 65% of dispersed seeds are predated post-dispersal. We observed substantial variation in these three processes among individuals. We also found that both intrinsic (plant height, crop size) and extrinsic (understory cover, time since last fire, conspecific fruiting neighborhood, substrate) drivers differentially influenced the three processes. We identified four generalist, seasonally frugivorous, avian visitors at fruiting individuals that likely act as variably effective dispersers, while the Northern Cardinal (Cardinalis cardinalis L.) is a seed predator. Rodent granivores were important pre- and post-dispersal seed predators. The magnitude of our pre-dispersal and post-dispersal seed predation estimates suggest that, given the low fecundity of L. subcoriacea, conservation strategies should emphasize facilitating dispersal and reducing the effects of seed predation.
Topics: Animals; Seed Dispersal; Lindera; Fruit; Seeds; Passeriformes; Rodentia; Feeding Behavior
PubMed: 37000816
DOI: 10.1371/journal.pone.0283810 -
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 -
Sensors (Basel, Switzerland) Jan 2023In the last decade, deep learning has enjoyed its spotlight as the game-changing addition to smart farming and precision agriculture. Such development has been...
In the last decade, deep learning has enjoyed its spotlight as the game-changing addition to smart farming and precision agriculture. Such development has been predominantly observed in developed countries, while on the other hand, in developing countries most farmers especially ones with smallholder farms have not enjoyed such wide and deep adoption of this new technologies. In this paper we attempt to improve the image classification part of smart farming and precision agriculture. Agricultural commodities tend to possess certain textural details on their surfaces which we attempt to exploit. In this work, we propose a deep learning based approach called Selective Context Adaptation Network (SCANet). SCANet performs feature enhancement strategy by leveraging level-wise information and employing context selection mechanism. In exploiting contextual correlation feature of the crop images our proposed approach demonstrates the effectiveness of the context selection mechanism. Our proposed scheme achieves 88.72% accuracy and outperforms the existing approaches. Our model is evaluated on the cocoa bean dataset constructed from the real cocoa bean industry scene in Indonesia.
PubMed: 36772398
DOI: 10.3390/s23031358 -
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 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 -
PloS One 2022The avian influenza virus (AIV) causes significant economic losses by infecting poultry and occasional spillover to humans. Backyard farms are vulnerable to AIV... (Observational Study)
Observational Study
BACKGROUND
The avian influenza virus (AIV) causes significant economic losses by infecting poultry and occasional spillover to humans. Backyard farms are vulnerable to AIV epidemics due to poor health management and biosecurity practices, threatening rural households' economic stability and nutrition. We have limited information about the risk factors associated with AIV infection in backyard poultry in Bangladesh. Hence, we conducted a cross-sectional survey comprising epidemiological and anthropological investigations to understand the poultry rearing practices and risk factors of AIV circulation among backyard poultry in selected rural communities.
METHODS
We sampled 120 poultry from backyard farms (n = 30) of the three selected communities between February 2017 and January 2018. We tested swab samples for the matrix gene (M gene) followed by H5, H7, and H9 subtypes using real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). We applied multivariable logistic regression for risk factor analysis. Furthermore, we conducted an observational study (42 hours) and informal interviews (n = 30) with backyard farmers to record poultry-raising activities in rural communities.
RESULTS
We detected that 25.2% of the backyard poultry tested positive for AIV, whereas 5% tested positive for H5N1 and 10.8% tested positive for H9N2. Results showed that scavenging in both household garden and other crop fields has higher odds of AIV than scavenging in the household garden (AOR: 24.811; 95% CI: 2.11-292.28), and keeping a cage inside the house has higher odds (AOR:14.5; 95% CI: 1.06-198.51) than keeping it in the veranda, cleaning the cage twice a week or weekly has a higher risk than cleaning daily (AOR: 34.45; 95% CI: 1.04-1139.65), dumping litter or droppings (AOR: 82.80; 95% CI: 3.91-1754.59) and dead birds or wastage (AOR: 109.92, 95% CI: 4.34-2785.29) near water bodies and bushes have a higher risk than burring in the ground, slaughtering and consuming sick birds also had a higher odd of AIV (AOR: 73.45, 95% CI: 1.56-3457.73) than treating the birds. The anthropological investigation revealed that household members had direct contact with the poultry in different ways, including touching, feeding, slaughtering, and contacting poultry feces. Poultry is usually kept inside the house, sick poultry are traditionally slaughtered and eaten, and most poultry raisers do not know that diseases can transmit from backyard poultry to humans.
CONCLUSIONS
This study showed the circulation of H5N1 and H9N2 virus in backyard poultry in rural communities; associated with species, scavenging area of the poultry, location of the poultry cage, the practice of litter, wastage, droppings, and dead bird disposal, and practice of handling sick poultry. We suggest improving biosecurity practices in backyard poultry and mass awareness campaigns to reduce incidences of AIV in household-level poultry farms in rural communities in Bangladesh.
Topics: Animals; Chickens; Cross-Sectional Studies; Ducks; Humans; Influenza A Virus, H5N1 Subtype; Influenza A Virus, H9N2 Subtype; Influenza in Birds; Poultry; Poultry Diseases; RNA-Directed DNA Polymerase; Risk Factors; Rural Population; Water
PubMed: 36219598
DOI: 10.1371/journal.pone.0275852 -
Frontiers in Physiology 2022The nutrient availability and supplementation of dietary phosphorus (P) and calcium (Ca) in avian feed, especially in laying hens, plays a vital role in phytase...
The nutrient availability and supplementation of dietary phosphorus (P) and calcium (Ca) in avian feed, especially in laying hens, plays a vital role in phytase degradation and mineral utilization during the laying phase. The required concentration of P and Ca peaks during the laying phase, and the direct interaction between Ca and P concentration shrinks the availability of both supplements in the feed. Our goal was to characterize the active microbiota of the entire gastrointestinal tract (GIT) (crop, gizzard, duodenum, ileum, caeca), including digesta- and mucosa-associated communities of two contrasting high-yielding breeds of laying hens (Lohmann Brown Classic, LB; Lohmann LSL-Classic, LSL) under different P and Ca supplementation levels. Statistical significances were observed for breed, GIT section, Ca, and the interaction of GIT section x breed, P x Ca, Ca x breed and P x Ca x breed ( < 0.05). A core microbiota of five species was detected in more than 97% of all samples. They were represented by an uncl. (average relative abundance (av. abu.) 12.1%), (av. abu. 10.8%), (av. abu. 6.8%), (av. abu. 4.5%), and an uncl. (av. abu. 1.1%). Our findings indicated that Ca and P supplementation levels 20% below the recommendation have a minor effect on the microbiota compared to the strong impact of the bird's genetic background. Moreover, a core active microbiota across the GIT of two high-yielding laying hen breeds was revealed for the first time.
PubMed: 36213242
DOI: 10.3389/fphys.2022.951350