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1.
PLoS One ; 15(11): e0239938, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33166313

RESUMO

Mycobacterium bovis, the causative agent of bovine tuberculosis, is a pathogen that impacts both animal and human health. Consequently, there is a need to improve understanding of disease dynamics, identification of infected animals, and characterization of the basis of immune protection. This study assessed the transcriptional changes occurring in cattle during the early weeks following a M. bovis infection. RNA-seq analysis of whole blood-cell transcriptomes revealed two distinct transcriptional clusters of infected cattle at both 4- and 10-weeks post-infection that correlated with disease severity. Cattle exhibiting more severe disease were transcriptionally divergent from uninfected animals. At 4-weeks post-infection, 25 genes had commonly increased expression in infected cattle compared to uninfected cattle regardless of disease severity. Ten weeks post-infection, differential gene expression was only observed when severely-affected cattle were compared to uninfected cattle. This indicates a transcriptional divergence based on clinical status following infection. In cattle with more severe disease, biological processes and cell type enrichment analyses revealed overrepresentation of innate immune-related processes and cell types in infected animals. Collectively, our findings demonstrate two distinct transcriptional profiles occur in cattle following M. bovis infection, which correlate to clinical status.


Assuntos
Imunidade Inata/genética , Leucócitos Mononucleares/metabolismo , Mycobacterium bovis/imunologia , Transcriptoma/genética , Tuberculose Bovina/patologia , Animais , Bovinos , Expressão Gênica/genética , Perfilação da Expressão Gênica/veterinária , Leucócitos Mononucleares/citologia , Mycobacterium bovis/genética , Análise de Sequência com Séries de Oligonucleotídeos , Índice de Gravidade de Doença , Tuberculose Bovina/imunologia
2.
PLoS One ; 15(11): e0241861, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33156842

RESUMO

Macrophages are classified upon activation as classical activated M1 and M2 anti-inflammatory regulatory populations. This macrophage polarization is well characterized in humans and mice, but M1/M2 profile in cattle has been far less explored. Bos primigenius taurus (taurine) and Bos primigenius indicus (indicine) cattle display contrasting levels of resistance to infection and parasitic diseases such as C57BL/6J and Balb/c murine experimental models of parasite infection outcomes based on genetic background. Thus, we investigated the differential gene expression profile of unstimulated and LPS stimulated monocyte-derived macrophages (MDMs) from Holstein (taurine) and Gir (indicine) breeds using RNA sequencing methodology. For unstimulated MDMs, the contrast between Holstein and Gir breeds identified 163 Differentially Expressed Genes (DEGs) highlighting the higher expression of C-C chemokine receptor type five (CCR5) and BOLA-DQ genes in Gir animals. LPS-stimulated MDMs from Gir and Holstein animals displayed 1,257 DEGs enriched for cell adhesion and inflammatory responses. Gir MDMs cells displayed a higher expression of M1 related genes like Nitric Oxide Synthase 2 (NOS2), Toll like receptor 4 (TLR4), Nuclear factor NF-kappa-B 2 (NFKB2) in addition to higher levels of transcripts for proinflammatory cytokines, chemokines, complement factors and the acute phase protein Serum Amyloid A (SAA). We also showed that gene expression of inflammatory M1 population markers, complement and SAA genes was higher in Gir in buffy coat peripheral cells in addition to nitric oxide concentration in MDMs supernatant and animal serum. Co-expression analyses revealed that Holstein and Gir animals showed different transcriptional signatures in the MDMs response to LPS that impact on cell cycle regulation, leukocyte migration and extracellular matrix organization biological processes. Overall, the results suggest that Gir animals show a natural propensity to generate a more pronounced M1 inflammatory response than Holstein, which might account for a faster immune response favouring resistance to many infection diseases.


Assuntos
Cruzamento , Bovinos , Perfilação da Expressão Gênica/veterinária , Redes Reguladoras de Genes/efeitos dos fármacos , Lipopolissacarídeos/farmacologia , Macrófagos/química , Alcaloides de Pirrolizidina/metabolismo , Animais , Diferenciação Celular/efeitos dos fármacos , Regulação da Expressão Gênica/efeitos dos fármacos , Lipopolissacarídeos/efeitos adversos , Ativação de Macrófagos , Macrófagos/efeitos dos fármacos , Espécies Reativas de Oxigênio/metabolismo , Análise de Sequência de RNA/veterinária , Especificidade da Espécie
3.
PLoS One ; 15(11): e0240743, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33170837

RESUMO

BACKGROUND: Insecticide resistance is challenging the effectiveness of insecticide-based control interventions to reduce malaria burden in Africa. Understanding the molecular basis of insecticides resistance and patterns of gene flow in major malaria vectors such as Anopheles funestus are important steps for designing effective resistance management strategies. Here, we investigated the association between patterns of genetic structure and expression profiles of genes involved in the pyrethroid resistance in An. funestus across Uganda and neighboring Kenya. METHODS: Blood-fed mosquitoes An. funestus were collected across the four localities in Uganda and neighboring Kenya. A Microarray-based genome-wide transcription analysis was performed to identify the set of genes associated with permethrin resistance. 17 microsatellites markers were genotyped and used to establish patterns of genetic differentiation. RESULTS: Microarray-based genome-wide transcription profiling of pyrethroid resistance in four locations across Uganda (Arua, Bulambuli, Lira, and Tororo) and Kenya (Kisumu) revealed that resistance was mainly driven by metabolic resistance. The most commonly up-regulated genes in pyrethroid resistance mosquitoes include cytochrome P450s (CYP9K1, CYP6M7, CYP4H18, CYP4H17, CYP4C36). However, expression levels of key genes vary geographically such as the P450 CYP6M7 [Fold-change (FC) = 115.8 (Arua) vs 24.05 (Tororo) and 16.9 (Kisumu)]. In addition, several genes from other families were also over-expressed including Glutathione S-transferases (GSTs), carboxylesterases, trypsin, glycogenin, and nucleotide binding protein which probably contribute to insecticide resistance across Uganda and Kenya. Genotyping of 17 microsatellite loci in the five locations provided evidence that a geographical shift in the resistance mechanisms could be associated with patterns of population structure throughout East Africa. Genetic and population structure analyses indicated significant genetic differentiation between Arua and other localities (FST>0.03) and revealed a barrier to gene flow between Arua and other areas, possibly associated with Rift Valley. CONCLUSION: The correlation between patterns of genetic structure and variation in gene expression could be used to inform future interventions especially as new insecticides are gradually introduced.


Assuntos
Anopheles/genética , Perfilação da Expressão Gênica/veterinária , Resistência a Inseticidas , Piretrinas/farmacologia , Animais , Regulação da Expressão Gênica , Fluxo Gênico , Proteínas de Insetos/genética , Quênia , Repetições de Microssatélites , Mosquitos Vetores/genética , Uganda , Sequenciamento Completo do Exoma
4.
PLoS One ; 15(10): e0228514, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33091033

RESUMO

Coral disease outbreaks are expected to increase in prevalence, frequency and severity due to climate change and other anthropogenic stressors. This is especially worrying for the Caribbean branching coral Acropora palmata which has already seen an 80% decrease in cover primarily due to disease. Despite the importance of this keystone species, there has yet to be a characterization of its transcriptomic response to disease exposure. In this study we provide the first transcriptomic analysis of 12 A. palmata genotypes and their symbiont Symbiodiniaceae exposed to disease in 2016 and 2017. Year was the primary driver of gene expression variance for A. palmata and the Symbiodiniaceae. We hypothesize that lower expression of ribosomal genes in the coral, and higher expression of transmembrane ion transport genes in the Symbiodiniaceae indicate that a compensation or dysbiosis may be occurring between host and symbiont. Disease response was the second driver of gene expression variance for A. palmata and included a core set of 422 genes that were significantly differentially expressed. Of these, 2 genes (a predicted cyclin-dependent kinase 11b and aspartate 1-decarboxylase) showed negative Log2 fold changes in corals showing transmission of disease, and positive Log2 fold changes in corals showing no transmission of disease, indicating that these may be important in disease resistance. Co-expression analysis identified two modules positively correlated to disease exposure, one enriched for lipid biosynthesis genes, and the other enriched in innate immune genes. The hub gene in the immune module was identified as D-amino acid oxidase, a gene implicated in phagocytosis and microbiome homeostasis. The role of D-amino acid oxidase in coral immunity has not been characterized but could be an important enzyme for responding to disease. Our results indicate that A. palmata mounts a core immune response to disease exposure despite differences in the disease type and virulence between 2016 and 2017. These identified genes may be important for future biomarker development in this Caribbean keystone species.


Assuntos
Alveolados/genética , Antozoários/parasitologia , Perfilação da Expressão Gênica/veterinária , Imunidade Inata , Animais , Antozoários/genética , Antozoários/imunologia , Mudança Climática , Regulação da Expressão Gênica , Genótipo , Proteínas de Protozoários/genética , Proteínas Ribossômicas/genética , Simbiose
5.
Br Poult Sci ; 61(6): 609-614, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33012177

RESUMO

1. Ovarian transcriptomic profiling between birds showing high egg number (HEN) and birds of low egg number (LEN) in Longyan Shan-ma ducks at 71 weeks of age was carried out using Illumina Hiseq 2500 technology. 2. A total of 343 differentially expressed genes (DEGs, 269 upregulated and 74 downregulated) were identified between HEN and LEN ovaries. These DEGs were enriched in 30 Gene Ontology terms. Pathway functional analysis found that the DEGs were enriched in 10 metabolic pathways (P < 0.05), one of which was regulation of the actin cytoskeleton pathway (Q < 0.05). 3. Three integrin family genes, ITGB2, ITGB5 and ITGA8 were differentially expressed in the RNA-seq and qPCR experiments. 4. The DEGs and signalling pathways identified in ovarian tissue in this study provide new insights into high egg production in Longyan Shan-ma duck.


Assuntos
Patos , Ovário , Animais , Galinhas , Patos/genética , Feminino , Perfilação da Expressão Gênica/veterinária , Transcriptoma
6.
PLoS One ; 15(10): e0240308, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33035258

RESUMO

During recent years, China has become a hotspot for the domestication of mandarin fish, and this is of great commercial value. Although the food preference of domesticated mandarin fish has been studied, little is known about genes regulating their growth. We raised hybrid mandarin fish on artificial feed for 3 months, the results showed that the survival rate of hybrid mandarin fish was 60.00%. Their total length and body weight were 18.34 ±0.43 cm and 100.44 ±4.87 g. The absolute length and weight gain rates were 0.14 cm/d and 1.08 g/d, respectively. Finally, RNA sequencing (RNA-Seq) was performed to identify potential genes and pathways activated in response to growth performance. The transcriptome analysis generated 68, 197 transcripts and 45,871 unigenes. Among them, 1025 genes were up-regulated and 593 genes were down-regulated between the fast- and slow-growth fish. Finally, we obtained 32 differentially expressed genes, which were mainly related to fatty acid biosynthesis (e.g. FASN and ACACB), collecting duct acid secretion (e.g. ATP6E and KCC4), cell cycle (e.g. CDC20 and CCNB), and the insulin-like growth factor (IGF) system (IGFBP1). These pathways might be related to the growth of hybrid mandarin fish. In addition, more potential single nucleotide polymorphisms (SNPs) were detected in the fast-growth fish than in the slow-growth fish. The results suggest that the interaction of metabolism and abundant alleles might determine the growth of hybrid mandarin fish after food conversion.


Assuntos
Peixes/crescimento & desenvolvimento , Perfilação da Expressão Gênica/veterinária , Redes Reguladoras de Genes , Ração Animal , Animais , Peso Corporal , China , Proteínas de Peixes/genética , Pesqueiros , Peixes/genética , Regulação da Expressão Gênica no Desenvolvimento , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de RNA
7.
PLoS One ; 15(10): e0240313, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33048954

RESUMO

To convert external light into internal neural signal, vertebrates rely on a special group of proteins, the visual opsins. Four of the five types of visual opsins-short-wavelength sensitive 1 (Sws1), short-wavelength sensitive 2 (Sws2), medium-wavelength sensitive (Rh2), and long-wavelength sensitive (Lws)-are expressed in cone cells for scotopic vision, with the fifth, rhodopsin (Rh1), being expressed in rod cells for photopic vision. Fish often display differing ontogenetic cone opsin expression profiles, which may be related to dietary and/or habitat ontogenetic shift. The western mosquitofish (Gambusia affinis) is an aggressive invader that has successfully colonized every continent except Antarctica. The strong invasiveness of this species may be linked to its visual acuity since it can inhabit turbid waters better than other fishes. By genome screening and transcriptome analysis, we identify seven cone opsin genes in the western mosquitofish, including one sws1, two sws2, one rh2, and three lws. The predicted maximal absorbance wavelength (λmax) values of the respective proteins are 353 nm for Sws1, 449 nm for Sws2a, 408 nm for Sws2b, 516 nm for Rh2-1, 571 nm for Lws-1, and 519 nm for Lws-3. Retention of an intron in the lws-r transcript likely renders this visual opsin gene non-functional. Our real-time quantitative PCR demonstrates that adult male and female western mosquitofish do not differ in their cone opsin expression profiles, but we do reveal an ontogenetic shift in cone opsin expression. Compared to adults, larvae express proportionally more sws1 and less lws-1, suggesting that the western mosquitofish is more sensitive to shorter wavelengths in the larval stage, but becomes more sensitive to longer wavelengths in adulthood.


Assuntos
Opsinas dos Cones/genética , Ciprinodontiformes/genética , Perfilação da Expressão Gênica/veterinária , Sequenciamento Completo do Genoma/veterinária , Animais , Opsinas dos Cones/metabolismo , Ecossistema , Evolução Molecular , Feminino , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Regulação da Expressão Gênica , Espécies Introduzidas , Masculino , Família Multigênica , Filogenia , Reação em Cadeia da Polimerase em Tempo Real
8.
PLoS One ; 15(10): e0240935, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33119641

RESUMO

Sockeye salmon (Oncorhynchus nerka) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes-the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.


Assuntos
Perfilação da Expressão Gênica/veterinária , Cadeias Pesadas de Imunoglobulinas/genética , Salmão/genética , Sequenciamento Completo do Genoma/veterinária , Animais , Cromossomos/genética , Ecótipo , Proteínas de Peixes/genética , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala/veterinária , Salmão/classificação , Análise de Sequência de RNA/veterinária
9.
Sci Rep ; 10(1): 18275, 2020 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-33106520

RESUMO

The transcriptome of the endometrium early postpartum was profiled to determine if inflammatory gene expression was elevated in cows which subsequently developed uterine disease. Endometrial cytobrush samples were collected at 7 days postpartum (DPP) from 112 Holstein-Friesian dairy cows, from which 27 were retrospectively chosen for RNA-seq on the basis of disease classification [ten healthy and an additional 17 diagnosed with cytological endometritis (CYTO), or purulent vaginal discharge (PVD)] at 21 DPP. 297 genes were significantly differentially expressed between cows that remained healthy versus those that subsequently developed PVD, including IL1A and IL1B (adjusted p < 0.05). In contrast, only 3 genes were significantly differentially expressed in cows which subsequently developed CYTO. Accounting for the early physiological inflammatory status present in cows which do not develop disease enhanced the detection of differentially expressed genes associated with CYTO and further expression profiling in 51 additional cows showed upregulation of multiple immune genes, including IL1A, IL1B and TNFA. Despite the expected heterogeneity associated with natural infection, enhanced activation of the inflammatory response is likely a key contributory feature of both PVD and CYTO development. Prognostic biomarkers of uterine disease would be particularly valuable for seasonal-based dairy systems where any delay to conception undermines sustainability.


Assuntos
Doenças dos Bovinos/diagnóstico , Perfilação da Expressão Gênica/veterinária , Interleucina-1alfa/genética , Interleucina-1beta/genética , Fator de Necrose Tumoral alfa/genética , Doenças Uterinas/veterinária , Animais , Estudos de Casos e Controles , Bovinos , Doenças dos Bovinos/genética , Feminino , Regulação da Expressão Gênica , Período Pós-Parto , Estudos Retrospectivos , Análise de Sequência de RNA/veterinária , Doenças Uterinas/genética
10.
J Dairy Sci ; 103(11): 10321-10331, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32896393

RESUMO

Crossbreeding capitalizes on heterosis effects and results in increased performance of crossbred animals. Dominance hypothesis and overdominance hypothesis are 2 common models proposed to explain heterosis. Differential gene expression between parents and hybrids is hypothesized to be responsible for heterosis. This study aimed to investigate the heat tolerance and inheritance patterns of leukocyte transcriptomics in F1 hybrid cattle (Angus males × Droughtmaster females) and their parents Red Angus (AN) and Droughtmaster (DR) under heat stress. According to the respiratory rate and heat tolerance coefficient index, DR was better adapted to heat stress than AN. The physiological responses to heat stress of F1 hybrids were similar to AN. We identified 802 differentially expressed genes in leukocytes between AN and DR under heat stress using mRNA sequencing. Compared with AN, upregulated genes in DR were enriched in biological processes of response to stress, external and chemical stimulus, and cytokine, cell surface receptor signaling pathway, and cardiovascular system development. In contrast, upregulated genes in AN were enriched in B cell activation and regulation of B cell activation. Gene expression levels can be inherited additively or nonadditively and are classified into additive (35%), dominance (44%), and overdominance and underdominance (18%) modes in F1 hybrids and their parents. Inheritance patterns of gene expression showed that 97% (249/255) of the dominant genes were classified as paternal AN dominant in hybrids. The paternal imprinted PEG10 gene and its regulatory transcription factor MYC showed an AN dominant expression pattern. The MYC interacted with most AN dominant genes. These transcriptomic analyses revealed that DR and AN had specific cellular and humoral immunity and cardiovascular systems development function under heat stress. Inheritance pattern analyses from gene expression partly explained phenotypic differences between parents and F1 hybrids. The paternal imprinted PEG10 gene interaction with transcription factor MYC may contribute to explaining paternal dominant gene expression in hybrids.


Assuntos
Bovinos/genética , Perfilação da Expressão Gênica/veterinária , Regulação da Expressão Gênica/imunologia , Vigor Híbrido/genética , Padrões de Herança , Animais , Bovinos/fisiologia , Feminino , Resposta ao Choque Térmico , Hibridização Genética , Leucócitos/imunologia , Masculino
11.
Appl Environ Microbiol ; 86(23)2020 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-32948523

RESUMO

In recent years, various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were focused primarily on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe coevolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics was employed to investigate the metabolic potential of the fecal microbiomes of 24 mammals, and subsequent statistical analyses were performed to assess the impact of host diet and corresponding physiology of the digestive system on gut microbiota composition and functionality. Functional data were confirmed and extended through metatranscriptome assessment of gut microbial populations of eight animals, thus providing insights into the transcriptional response of gut microbiota to specific dietary lifestyles. Therefore, the analyses performed in this study support the notion that the metabolic features of the mammalian gut microbiota have adapted to maximize energy extraction from the host's diet.IMPORTANCE Diet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals by using large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the bacterial taxonomic composition of 250 fecal samples belonging to 77 host species distributed along the tree of life in order to assess how diet and host physiology impact the intestinal microbial community by selecting specific microbial players. Conversely, the application of shotgun metagenomics and metatranscriptomics approaches to a group of selected fecal samples allowed us to shed light on both metabolic features and transcriptional responses of the intestinal bacterial community based on different diets.


Assuntos
Bactérias/isolamento & purificação , Dieta/veterinária , Fezes/microbiologia , Microbioma Gastrointestinal , Mamíferos/microbiologia , Mamíferos/fisiologia , Animais , Bactérias/classificação , Perfilação da Expressão Gênica/veterinária , Metagenômica , RNA Bacteriano/análise , RNA Ribossômico 16S/análise , Especificidade da Espécie
12.
PLoS One ; 15(8): e0238189, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32841273

RESUMO

The use of reference genes is required for relative quantification in gene expression analysis and the stability of these genes can be variable depending on the experimental design. Therefore, it is indispensable to test the reliability of endogenous genes previously to their use. This study evaluated nine candidate reference genes to select the most stable genes to be used as reference in gene expression studies with the femoral cartilage of normal and epiphysiolysis-affected broilers. The femur articular cartilage of 29 male broilers with 35 days of age was collected, frozen and further submitted to RNA extraction and quantitative PCR (qPCR) analysis. The candidate reference genes evaluated were GAPDH, HMBS, HPRT1, MRPS27, MRPS30, RPL30, RPL4, RPL5, and RPLP1. For the gene stability evaluation, three software were used: GeNorm, BestKeeper and NormFinder, and a global ranking was generated using the function RankAggreg. In this study, the RPLP1 and RPL5 were the most reliable endogenous genes being recommended for expression studies with femur cartilage in broilers with epiphysiolysis and possible other femur anomalies.


Assuntos
Doenças das Aves/genética , Cartilagem Articular/metabolismo , Galinhas/genética , Epifise Deslocada/veterinária , Algoritmos , Animais , Doenças das Aves/metabolismo , Galinhas/metabolismo , Epifise Deslocada/genética , Epifise Deslocada/metabolismo , Fêmur , Expressão Gênica , Perfilação da Expressão Gênica/estatística & dados numéricos , Perfilação da Expressão Gênica/veterinária , Masculino , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reação em Cadeia da Polimerase em Tempo Real
13.
Artigo em Inglês | MEDLINE | ID: mdl-32656652

RESUMO

Vibrio alginolyticus is posting an increasing threat to survival of grouper. Classical complement cascade can trigger initiation of immunity, while complement 9 (C9) is a major complement molecule involved in final step of membrane attack complex (MAC) formation. In this study, full-length EcC9 contained an ORF sequence of 1779 bp, encoding a polypeptide of 592 amino acids. A high-level expression of EcC9 mRNA was observed in liver. Following vibrio challenge, increased expression levels of EcC1q, EcBf/C2, EcC4, EcC6, EcC7 and EcC9 mRNA were detected in liver and kidney. These results implied that elevated expression level of classical complement pathway (CCP) and terminal complement components (TCCs) may assess toxicological effect of V. alginolyticus.


Assuntos
Bass/genética , Bass/imunologia , Complemento C9/genética , Complemento C9/imunologia , Doenças dos Peixes/imunologia , Regulação da Expressão Gênica/imunologia , Imunidade Inata/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Complemento C9/química , Proteínas de Peixes/química , Proteínas de Peixes/genética , Proteínas de Peixes/imunologia , Perfilação da Expressão Gênica/veterinária , Filogenia , Alinhamento de Sequência/veterinária , Vibrio alginolyticus/fisiologia
14.
Anim Genet ; 51(5): 741-751, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32720725

RESUMO

The chicken gizzard is the primary digestive and absorptive organ regulating food intake and metabolism. Body weight is a typical complex trait regulated by an interactive polygene network which is under the control of an interacting network of polygenes. To simplify these genotype-phenotype associations, the gizzard is a suitable target organ to preliminarily explore the mechanism underlying the regulation of chicken growth through controlled food intake. This study aimed to identify key food intake-related genes through combinatorial GWAS and transcriptome analysis. We performed GWAS of body weight in an F2 intercrossed population and transcriptional profiling analysis of gizzards from chickens with different body weight. We identified a major 10 Mb quantitative trait locus (QTL) on chromosome 1 and numerous minor QTL distributed among 24 chromosomes. Combining data regarding QTL and gizzard gene expression, two hub genes, MLNR and HTR2A, and a list of core genes with small effect were found to be associated with food intake. Furthermore, the neuroactive ligand-receptor interaction pathway was found to play a key role in regulating the appetite of chickens. The present results show the major-minor gene interactions in metabolic pathways and provide insights into the genetic architecture and gene regulation during food intake in chickens.


Assuntos
Peso Corporal/genética , Galinhas/fisiologia , Ingestão de Alimentos/genética , Moela das Aves/metabolismo , Locos de Características Quantitativas , Animais , Galinhas/genética , Galinhas/crescimento & desenvolvimento , Perfilação da Expressão Gênica/veterinária , Estudo de Associação Genômica Ampla/veterinária , RNA-Seq/veterinária
15.
Sci Rep ; 10(1): 12679, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-32728087

RESUMO

Endogenous antimicrobial peptides (AMPs) are evolutionarily ancient factors of innate immunity, which are produced by all multicellular organisms and play a key role in their protection against infection. Red king crab (Paralithodes camtschaticus), also called Kamchatka crab, is widely distributed and the best known species of all king crabs belonging to the family Lithodidae. Despite their economic importance, the genetic resources of king crabs are scarcely known and no full-genome sequences are available to date. Therefore, analysis of the red king crab transcriptome and identification and characterization of its AMPs could potentially contribute to the development of novel antimicrobial drug candidates when antibiotic resistance has become a global health threat. In this study, we sequenced the P. camtschaticus transcriptomes from carapace, tail flap and leg tissues using an Illumina NGS platform. Libraries were systematically analyzed for gene expression profiles along with AMP prediction. By an in silico approach using public databases we defined 49 cDNAs encoding for AMP candidates belonging to diverse families and functional classes, including buforins, crustins, paralithocins, and ALFs (anti-lipopolysaccharide factors). We analyzed expression patterns of 27 AMP genes. The highest expression was found for Paralithocin 1 and Crustin 3, with more than 8,000 reads. Other paralithocins, ALFs, crustins and ubiquicidins were among medium expressed genes. This transcriptome data set and AMPs provide a solid baseline for further functional analysis in P. camtschaticus. Results from the current study contribute also to the future application of red king crab as a bio-resource in addition to its being a known seafood delicacy.


Assuntos
Anomuros/genética , Perfilação da Expressão Gênica/veterinária , Proteínas Citotóxicas Formadoras de Poros/genética , Animais , Proteínas de Artrópodes/genética , Simulação por Computador , Bases de Dados Genéticas , Regulação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Imunidade Inata , Análise de Sequência de RNA , Cauda/química
16.
Res Vet Sci ; 132: 318-327, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32726728

RESUMO

The molecular mechanism of stress-induced immunosuppression (SIS) in certain poultry immune organs is not completely clear. In this study, we constructed a stress immunosuppression model by selecting 180 healthy 7-day-old Gushi chickens and dividing them randomly into two groups: a D_T group and a B_T group. The D_T group was given dexamethasone, and the B_T group was given normal saline, according to the treatment method established and reported in our previous study. Thymus samples were subsequently taken from both groups. RNA-seq was used to sequence the transcriptomes of the thymus samples from both groups, and 1278 significant differentially expressed genes (DEGs) were obtained, of which 845 genes were up-regulated and 433 genes were down-regulated (padj<0.05, |FC| ≥ 2, FPKM>1). We identified immune-related gene ontology (GO) terms including immune system processes, immune system process regulation, and T cell activation. The results of KEGG (http: //www.kegg.jp) analysis showed that the DEGs are involved in a variety of immune-related pathways, such as cytokine-cytokine receptor interactions, Jak-STAT signaling pathways, and cell adhesion molecules (CAMs). The cytokine-cytokine receptor interaction pathway involves the DEGs CCR6, CCR5, CD40LG and FAS. The DEGs in the Jak-STAT signaling pathway were SPRY2, BCL2L1. These DEGS play an important role in cell apoptosis. CD40L, CD8, among other genes, are involved in the CAMs pathway. The results of this study add to existing data on the genomic study of stress affecting immune function, and provide a basis for further studies of the molecular mechanisms of stress-influenced immune function.


Assuntos
Galinhas/metabolismo , Dexametasona/farmacologia , Perfilação da Expressão Gênica/veterinária , Imunossupressão/veterinária , Timo/efeitos dos fármacos , Animais , Galinhas/genética , Regulação para Baixo , Regulação da Expressão Gênica/efeitos dos fármacos , Distribuição Aleatória , Timo/metabolismo , Transcriptoma
17.
Mol Genet Genomics ; 295(5): 1239-1252, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32529263

RESUMO

The genetic mechanisms underlying cutaneous melanoma onset and progression need to be further understood to improve patients' care. Several studies have focused on the genetic determinism of melanoma development in the MeLiM pig, a biomedical model of cutaneous melanoma. The objective of this study was to better describe the influence of a particular genomic region on melanoma progression in the MeliM model. Indeed, a large region of the Sus scrofa chromosome 1 has been identified by linkage and association analyses, but the causal mechanisms have remained elusive. To deepen the analysis of this candidate region, a dedicated SNP panel was used to fine map the locus, downsizing the interval to less than 2 Mb, in a genomic region located within a large gene desert. Transcription from this locus was addressed using a tiling array strategy and further validated by RT-PCR in a large panel of tissues. Overall, the gene desert showed an extensive transcriptional landscape, notably dominated by repeated element transcription in tumor and fetal tissues. The transcription of LINE-1 and PERVs has been confirmed in skin and tumor samples from MeLiM pigs. In conclusion, although this study still does not identify a candidate mutation for melanoma occurrence or progression, it highlights a potential role of repeated element transcriptional activity in the MeLiM model.


Assuntos
Cromossomos de Mamíferos/genética , Perfilação da Expressão Gênica/veterinária , Elementos Nucleotídeos Longos e Dispersos , Melanoma/genética , Polimorfismo de Nucleotídeo Único , Neoplasias Cutâneas/genética , Animais , Mapeamento Cromossômico , Modelos Animais de Doenças , Progressão da Doença , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , Sus scrofa , Suínos
18.
Sci Rep ; 10(1): 9668, 2020 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-32541658

RESUMO

Gymnocypris namensis, the only commercial fish in Namtso Lake of Tibet in China, is rated as nearly threatened species in the Red List of China's Vertebrates. As one of the highest-altitude schizothorax fish in China, G. namensis has strong adaptability to the plateau harsh environment. Although being an indigenous economic fish with high value in research, the biological characterization, genetic diversity, and plateau adaptability of G. namensis are still unclear. Here, we used Pacific Biosciences single molecular real time long read sequencing technology to generate full-length transcripts of G. namensis. Sequences clustering analysis and error correction with Illumina-produced short reads to obtain 319,044 polished isoforms. After removing redundant reads, 125,396 non-redundant isoforms were obtained. Among all transcripts, 103,286 were annotated to public databases. Natural selection has acted on 42 genes for G. namensis, which were enriched on the functions of mismatch repair and Glutathione metabolism. Total 89,736 open reading frames, 95,947 microsatellites, and 21,360 long non-coding RNAs were identified across all transcripts. This is the first study of transcriptome in G. namensis by using PacBio Iso-seq. The acquisition of full-length transcript isoforms might accelerate the transcriptome research of G. namensis and provide basis for further research.


Assuntos
Cyprinidae/genética , Proteínas de Peixes/genética , Perfilação da Expressão Gênica/veterinária , Imagem Individual de Molécula/veterinária , Animais , Conservação dos Recursos Naturais , Regulação da Expressão Gênica , Repetições de Microssatélites , Anotação de Sequência Molecular , Fases de Leitura Aberta , RNA Longo não Codificante/genética , Seleção Genética , Análise de Sequência de RNA/veterinária , Tibet
19.
Poult Sci ; 99(6): 2841-2851, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32475417

RESUMO

The objective of this study was to investigate differences in mRNA expression between fresh and frozen-thawed sperm in roosters. In trial 1, gene expression profiles were measured using microarray with Affymetrix GeneChip Chicken Genome Arrays. The results showed that 2,115 genes were differentially expressed between the 2 groups. Among these genes, 2,086 were significantly downregulated and 29 were significantly upregulated in the frozen-thawed sperm group. Gene Ontology (GO) analysis showed that more than 1,000 differentially expressed genes (DEG) of all significantly regulated genes were involved in GO terms including biological processes, molecular function, and cellular component. Kyoto Encyclopedia of Genes and Genomes analysis showed that DEG were significantly (P < 0.05) enriched on ribosome, oxidative phosphorylation, proteasome, cell cycle, oocyte meiosis, and spliceosome pathways. In trial 2, ejaculated semen was collected from 18 roosters and divided into 5 recombinant HSP90 protein-supplemented groups (0.01, 0.1, 0.5, 1, or 2 µg/mL) and one control group with no recombinant HSP90 protein supplementation to evaluate the effect of recombinant HSP90 protein in the extender on post-thaw quality of rooster semen. The results showed that post-thaw sperm viability and motility was significantly improved (P < 0.05) in the extender containing 0.5 and 1 µg/mL of recombinant HSP90 protein compared with the control. Our preliminary results will provide a valuable basis for understanding the potential molecular mechanisms of cryodamage in frozen-thawed sperm and theoretical guidance to improve the fertility of frozen-thawed chicken sperm.


Assuntos
Galinhas/fisiologia , Crioprotetores/farmacologia , Perfilação da Expressão Gênica/veterinária , Preservação do Sêmen/veterinária , Espermatozoides/efeitos dos fármacos , Transcriptoma , Animais , Galinhas/genética , Congelamento , Masculino , Preservação do Sêmen/métodos
20.
Poult Sci ; 99(6): 2861-2872, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32475419

RESUMO

Large ovarian follicles are primary characteristics of oviparous species. The development of such follicles is crucially governed by strict intrinsic complex regulation. Many aspects of the genetic basis of this regulation remain obscure. To identify the dominant genes controlling follicular development in the chicken, growing follicles (400-1,600 µm in diameter) were selected for RNA sequencing and bioinformatics analysis. Comparing the 400-µm follicles with 800-µm follicles identified a total of 3,627 differentially expressed genes (1,792 upregulated and 1,835 downregulated genes). Comparing the 400-µm follicles with 1,600-µm follicles revealed 9,650 differentially expressed genes (including 4,848 upregulated and 4,802 downregulated genes). Comparing 800-µm with 1,600-µm follicles revealed a total of 6,779 differentially expressed genes (3,427 upregulated and 3,352 downregulated genes). Transcriptome analysis revealed that genes related to the extracellular matrix-receptor interactions, steroid biosynthesis, cell adhesion, and phagosomes displayed remarkable differential expressions. Relative to 400-µm follicles, collagen content, production of steroid hormones, cell adhesion, and phagocytic factors were significantly increased in the 1,600-µm follicles. This study identifies the dominant genes involved in the promotion of follicular development in oviparous vertebrates and represents the extraordinary gene regulation pattern related to development of the growing follicles in poultry.


Assuntos
Galinhas/genética , Perfilação da Expressão Gênica/veterinária , Regulação da Expressão Gênica no Desenvolvimento , Folículo Ovariano/crescimento & desenvolvimento , Transcriptoma , Animais , Galinhas/crescimento & desenvolvimento , Feminino , Folículo Ovariano/metabolismo , Análise de Sequência de RNA/veterinária
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