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1.
Gene ; 807: 145952, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-34500049

RESUMEN

Extreme temperature is one of the serious threats to crop production in present and future scenarios of global climate changes. Lentil (Lens culinaris) is an important crop, and there is a serious lack of genetic information regarding environmental and temperature stresses responses. This study is the first report of evaluation of key genes and molecular mechanisms related to temperature stresses in lentil using the RNA sequencing technique. De novo transcriptome assembly created 44,673 contigs and differential gene expression analysis revealed 7494 differentially expressed genes between the temperature stresses and control group. Basic annotation of generated transcriptome assembly in our study led to the identification of 2765 novel transcripts that have not been identified yet in lentil genome draft v1.2. In addition, several unigenes involved in mechanisms of temperature sensing, calcium and hormone signaling and DNA-binding transcription factor activity were identified. Also, common mechanisms in response to temperature stresses, including the proline biosynthesis, the photosynthetic light reactions balancing, chaperone activity and circadian rhythms, are determined by the hub genes through the protein-protein interaction networks analysis. Deciphering the mechanisms of extreme temperature tolerance would be a new way for developing crops with enhanced plasticity against climate change. In general, this study has identified set of mechanisms and various genes related to cold and heat stresses which will be useful in better understanding of the lentil's reaction to temperature stresses.


Asunto(s)
Lens (Planta)/crecimiento & desarrollo , Lens (Planta)/genética , Estrés Fisiológico/genética , Cambio Climático , Frío/efectos adversos , Respuesta al Choque por Frío/genética , Productos Agrícolas/genética , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica de las Plantas/genética , Respuesta al Choque Térmico/genética , Respuesta al Choque Térmico/fisiología , Calor/efectos adversos , Anotación de Secuencia Molecular/métodos , Fotosíntesis , Mapas de Interacción de Proteínas/genética , Temperatura , Transcriptoma/genética
2.
Gene ; 807: 145960, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-34509581

RESUMEN

Opsin is a fellow of the G protein-coupled receptors (GPCRs) superfamily. It can be divided into visual and non-visual opsin according to whether it is directly involved in visual imaging. Opsin plays an important role in visual image formation and the regulation of non-image forming functions such as circadian entrainment in the growth, development and evolution of fish. Crimson snapper belongs to Perciforme mainly found in the Indo-West Pacific and the South China Sea. It is one of the most influential economic fishes in the South China Sea. In order to study the existence and expression of opsin gene in Crimson snapper, we sequenced the genome and tissue sample transcriptome of Crimson snapper. In this study, 32 opsin genes were identified from the genome of Crimson snapper. The length of these genes ranged from 1061 bp to 86203 bp and were distributed on 15 different chromosomes. The analysis of opsin gene family of Crimson snapper showed that the sws2 had two extra copies as compared with that of Zebrafish. Domain and motif analysis revealed that all the 32 opsin genes have seven-(pass)-transmembrane domain receptors (7TM receptors) each, and the opsin family contained 10 common motifs. The expression level of opsin gene, confirmed by RT-qPCR, was analyzed by using nine tissues transcriptome databases of Crimson snapper. The results showed that almost all opsin genes were highly expressed in the retina and brain, except opn7a and opn7b which were expressed in intestine and red skin, and almost no expression in other tissues. Our results provide a comprehensive basic knowledge for the opsin gene family of Crimson snapper, which has significance for the study of the function of opsin in Lutjanidaes.


Asunto(s)
Opsinas/genética , Perciformes/genética , Animales , Secuencia de Bases/genética , China , Clonación Molecular/métodos , Enfermedades de los Peces/genética , Expresión Génica/genética , Opsinas/metabolismo , Perciformes/metabolismo , Receptores Acoplados a Proteínas G/genética , Transcriptoma/genética
3.
Gene ; 807: 145930, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-34461151

RESUMEN

Mitogen-activated protein kinase (MAPK) cascades have a universal cell signaling mechanism in eukaryotes. A typical MAPK signal transduction module comprises three kinds of sequentially phosphorylated protein kinases: MAPK, Mitogen-activated protein kinase kinase (MAPKK), and Mitogen-activated protein kinase kinase kinase (MAPKKK). However, little is known regarding the genes involved in MAPK cascades in Ophiocordyceps sinensis. Nine genes (three MAPK, three MAPKK, and three MAPKKK) were identified in this study. The MAPK, MAPKK, and MAPKKK genes were divided into three subfamilies, according to the phylogenetic analysis. TEY and TGY represented the activation domains of the MAPKs; the corresponding domains in MAPKKs were SDIWS and SDVWS, and those in the MAPKKs were GSVFYWMAPEV and GTPMYMSPEV. Transcription data analysis and quantitative real-time polymerase chain reaction showed that the MAPK cascade was related to the growth of the fruiting body. This is the first study to report a genome-wide identification of the MAPK, MAPKK, and MAPKK gene families in O. sinensis.


Asunto(s)
Cordyceps/genética , Cordyceps/metabolismo , Proteínas Serina-Treonina Quinasas/genética , Análisis de Datos , Expresión Génica/genética , Perfilación de la Expresión Génica/métodos , Técnicas Genéticas , Estudio de Asociación del Genoma Completo/métodos , Quinasas Quinasa Quinasa PAM/genética , Sistema de Señalización de MAP Quinasas/genética , Quinasas de Proteína Quinasa Activadas por Mitógenos/genética , Proteínas Quinasas Activadas por Mitógenos/genética , Filogenia , Proteínas Serina-Treonina Quinasas/metabolismo , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Saccharomyces cerevisiae/genética , Transducción de Señal/genética , Transcriptoma/genética
4.
Food Chem ; 368: 130822, 2022 Jan 30.
Artículo en Inglés | MEDLINE | ID: mdl-34411853

RESUMEN

Lei bamboo (Phyllostachys violascens) shoots are delicious food in Asia. Here, the molecular basis of lignification in postharvest Lei bamboo shoots under low temperature (LT) is revealed by transcriptomic and metabolomics analyses for the first time. We identified substantial accumulations of jasmonates (JAs) and major lignin biosynthesis precursors (coumarin, trans-4-coumaric acid, trans-ferulic acid and L-phenylalanine). Transcriptome analysis indicated that some regulatory genes were significantly differentially expressed, and the expression patterns of them were highly consistent with the changes in the key lignin precursors or JA profiles. Co-expression analysis showed that the LT responsive genes PvCRPK-4/-5, PvICE2-1/2, PvDREB2B might form a network module with the lignin (PvC3H-2/3, PvC4H-2/4, PvCAD-1/2/3/4, etc.) or JA biosynthesis genes (PvOPR2, PvJAZ-4 and PvPEX5, etc.), indicating a LT-lignification or LT-JA-lignification regulatory pathway in Lei bamboo shoots. Above all, our findings provide new an insight into the LT-associated lignification in postharvest bamboo shoots.


Asunto(s)
Redes Reguladoras de Genes , Transcriptoma , Regulación de la Expresión Génica de las Plantas , Lignina/metabolismo , Metabolómica , Temperatura
5.
Gene ; 806: 145929, 2022 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-34461150

RESUMEN

The body color of Neocaridina denticulate sinensis is a compelling phenotypic trait, in which a cascade of carotenoid metabolic processes plays an important role. The study was conducted to compare the transcriptome of cephalothoraxes among three pigmentation phenotypes (red, blue, and chocolate) of N. denticulate sinensis. The purpose of this study was to explore the candidate genes associated with different colors of N. denticulate sinensis. Nine cDNA libraries in three groups were constructed from the cephalothoraxes of shrimps. After assembly, 75022 unigenes were obtained in total with an average length of 1026 bp and N50 length of 1876 bp. There were 45977, 25284, 23605, 21913 unigenes annotated in the Nr, Swissprot, KOG, and KEGG databases, respectively. Differential expression analysis revealed that there were 829, 554, and 3194 differentially expressed genes (DEGs) in RD vs BL, RD vs CH, and BL vs CH, respectively. These DEGs may play roles in the absorption, transport, and metabolism of carotenoids. We also emphasized that electron transfer across the inner mitochondrial membrane (IMM) was a key process in pigment metabolism. In addition, a total of 6328 simple sequence repeats (SSRs) were also detected in N. denticulate sinensis. The results laid a solid foundation for further research on the molecular mechanism of integument pigmentation in the crustacean and contributed to developing more attractive aquatic animals.


Asunto(s)
Proteínas de Artrópodos/genética , Carotenoides/metabolismo , Decápodos/genética , Pigmentación/genética , Transcriptoma , Animales , Organismos Acuáticos , Proteínas de Artrópodos/clasificación , Proteínas de Artrópodos/metabolismo , Transporte Biológico , Color , Bases de Datos Genéticas , Decápodos/anatomía & histología , Decápodos/metabolismo , Agua Dulce , Regulación de la Expresión Génica , Biblioteca de Genes , Ontología de Genes , Repeticiones de Microsatélite , Mitocondrias/metabolismo , Membranas Mitocondriales/metabolismo , Anotación de Secuencia Molecular , Carácter Cuantitativo Heredable
6.
Food Chem ; 366: 130583, 2022 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-34303203

RESUMEN

Terpenoid metabolism at different developmental stages of Carya cathayensis was elucidated based on LC-MS/MS analysis and multi-omics. Terpenoid metabolites 2-hydroxy-1,4-naphoquinone and 3-hydroxybenzoic acid reached the maximum at 105 days after pollination (DAP) (P2 stage). To reveal the complex mechanism of C. cathayensis embryogenesis in relation to terpenoid metabolites (90-165 DAP), a metabolomic and transcriptional co-expression analysis was conducted. Based on RNA-Seq analysis, 679 genes of 1144 terpenoid biosynthesis were differentially expressed. Six terpenoid metabolites and 86 differentially expressed genes related to terpenoquinone metabolism were identified. Comprehensive analysis of metabolome and transcriptional data revealed that terpenoquinone accumulated in the early phase was active in the later phase. Overall, we profiled the transcriptome and metabolome changes in C. cathayensis during the developmental phase to investigate the metabolic pathways and candidate genes underlying the changes at different growth stages.


Asunto(s)
Carya , Cromatografía Liquida , Perfilación de la Expresión Génica , Espectrometría de Masas en Tándem , Terpenos , Transcriptoma
7.
Meat Sci ; 183: 108642, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34390898

RESUMEN

Improving meat quality is a crucial purpose of commercial production and breeding systems. In this study, multiomics techniques were used to investigate the molecular mechanisms that impact the excessive diversity of meat quality in Enshi black pigs. The results suggest that 120 differentially expressed genes (DEGs) and 171 significantly changed metabolites (SCMs) contribute to the content of intramuscular fat (IMF) through the processes of fat accumulation and regulation of lipolysis. A total of 141 DEGs and 47 SCMs may regulate meat color through the processes of nicotinate and nicotinamide metabolism. Herein, we found some candidate genes associated with IMF and meat color. We also presented a series of metabolites that are potentially available biological indicators to measure meat quality. This research provides further insight into the detection of intramuscular fat accumulation and meat color variation and provides a reference for molecular mechanisms in the regulation of IMF and meat color.


Asunto(s)
Músculo Esquelético/metabolismo , Carne de Cerdo/análisis , Sus scrofa/metabolismo , Tejido Adiposo/metabolismo , Animales , Color , Calidad de los Alimentos , Lipólisis , Metaboloma , Músculo Esquelético/química , Niacina/metabolismo , Niacinamida/metabolismo , Sus scrofa/genética , Transcriptoma
8.
Gene ; 807: 145934, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-34478820

RESUMEN

Residual feed intake (RFI) is a measurement of feed efficiency, and is inversely correlated with feed efficiency. The differentially expressed genes (DEGs) associated with RFI vary substantially among studies, posing great challenges in finding the RFI-related marker genes. This study attempted to resolve this issue by integrating and comparing the multiple transcriptome sequencing data associated with RFI in the cattle liver, using differential, functional enrichment, protein-protein interaction (PPI) network, weighted co-expression network (WGCNA), and gene set enrichment analyses (GSEA) to identify the candidate genes and functional enrichment pathways that are closely associated with RFI. Four candidate genes namely SHC1, GPX4, ACADL, and IGF1 were identified and validated as the marker genes for RFI. Four functional enrichment pathways, namely the fatty acid metabolism, sugar metabolism, energy metabolism, and protein ubiquitination were also found to be closely related to RFI. This study identified several genes and signaling pathways with shared characteristics, which will provide new insights into the molecular mechanisms related to the regulation of feed efficiency, and provide basis for molecular markers related to feed efficiency in beef cattle.


Asunto(s)
Ingestión de Alimentos/genética , Metabolismo Energético/genética , Hígado/metabolismo , Alimentación Animal/análisis , Animales , Bovinos , Bases de Datos Genéticas , Factor I del Crecimiento Similar a la Insulina/genética , Metabolismo de los Lípidos/genética , Hígado/fisiología , Fosfolípido Hidroperóxido Glutatión Peroxidasa/genética , Mapas de Interacción de Proteínas/genética , Transducción de Señal/genética , Proteína Transformadora 1 que Contiene Dominios de Homología 2 de Src/genética , Transcriptoma/genética , Ubiquitinación/genética , Secuenciación del Exoma Completo/métodos
9.
Sci Total Environ ; 802: 149913, 2022 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-34474298

RESUMEN

Reports have highlighted the presence of PCBs and their metabolites, OH-PCBs, in human serum as well as their endocrine-disrupting effects on reproductive function through direct interactions with the androgen receptor (AR) and estrogen receptor (ER). However, the molecular mechanisms directly linking the actions of PCBs and OH-PCBs on the AR and ER to induce reproductive impairment remain poorly understood. In this study, we characterized the cellular response to PCBs and OH-PCBs acting on AR and ER transactivation at the transcriptome level coupled with bioinformatics analysis to identify the downstream pathways of androgen and estrogen signaling that leads to reproductive dysfunction. We first confirmed the agonistic and antagonistic effects of several PCBs and OH-PCBs on AR- and ER-mediated reporter gene activity using the androgen-responsive LNCaP and estrogen-responsive MCF-7 cell lines, respectively. Anti-estrogenic activity was not detected among the tested compounds; however, we found that in addition to anti-androgenic and estrogenic activity, PCB 28 and PCB 138 exhibited androgenic activity, while most of the tested OH-PCBs showed a synergistic effect on DHT-mediated transactivation of the AR. Bioinformatics analysis of transcriptome profiles from selected PCBs and OH-PCBs revealed various pathways that were dysregulated depending on their agonistic, antagonistic, or synergistic effects. The OH-PCBs with estrogenic activity affected pathways including vitamin metabolism and calcium transport. Other notable dysregulated pathways include cholesterol transport in response to androgenic PCBs, thyroid hormone metabolism in response to anti-androgenic PCBs, and antioxidant pathways in response to androgen-synergistic OH-PCBs. Our results demonstrate that PCBs and OH-PCBs directly alter specific pathways through androgen- or estrogen-mediated signaling, thereby providing additional insights into the mechanisms by which these compounds cause reproductive dysfunction.


Asunto(s)
Bifenilos Policlorados , Reproducción , Estrógenos , Humanos , Células MCF-7 , Bifenilos Policlorados/toxicidad , Receptores Androgénicos , Receptores de Estrógenos/genética , Reproducción/efectos de los fármacos , Transducción de Señal , Transcriptoma
10.
Food Chem ; 370: 131270, 2022 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-34788951

RESUMEN

In this study, combining metabolome and transcriptome, color related attributes and phenolic compositions of Tunisian pomegranate arils from 7 Chinese regions at same developing stage were studied. The total anthocyanin (TAC), flavonoids, and percent polymeric color (PPC) were ranged at 8.93-28.41 mg/100 g arils, 37.55-69.72 mg/100 g arils, and 3.38-21.96%, respectively. In total, 51 phenolic compounds were characterized, most of which were markedly higher in reddish-purple pomegranate arils than those levels in reddish pomegranate arils. In contrast, the accumulation of tannins was significantly higher in reddish pomegranate arils. Among the 49 differentially expressed genes, 8 and 5 genes were matched to ß-glucosidase and peroxidase, respectively. Correlation analysis showed that PPC was negatively correlated with 10 phenolic metabolites and TAC, positively correlated with L*, polymeric color, and 1 gene (|r| > 0.7, p < 0.01). Our results provide new insights for understanding the difference in coloration of pomegranate arils.


Asunto(s)
Granada (Fruta) , Antocianinas , Antioxidantes , Frutas/genética , Metaboloma , Semillas , Transcriptoma
11.
Chemosphere ; 286(Pt 2): 131715, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34388874

RESUMEN

The biological impacts of residual pharmaceuticals in the complex wastewater effluents have not been fully understood. Here, we investigated changes in the transcriptomic responses of hepatobrastoma (HepG2) cells exposed to a single or partially combined three common non-steroidal anti-inflammatory drugs (NSAIDs); ketoprofen (KPF), mefenamic acid (MFA) and diclofenac (DCF), in domestic wastewater effluents. After 48 h sub-lethal exposure to single compounds, the DNA microarray analysis identified 57-184 differently expressed genes (DEGs). The hierarchical clustering analysis and GO enrichment of the DEGs showed that gene expression profiles of the NSAIDs were distinct from each other although they are classified into the same therapeutic category. Four maker genes (i.e., EGR1, AQP3, SQSTM1, and NAG1) were further selected from the common DEGs, and their expressions were quantified by qPCR assay in a dose-dependent manner (ranging from µg/L to mg/L). The results revealed the insignificant induction of the marker genes at 1 µg/L of KPF, MFA, and DCF, suggesting negligible biological impacts of the NSAIDs on gene expression (early cellular responses) of HepG2 at typical concentration levels found in the actual wastewater effluents. Based on the quantitative expression analysis of the selected marker genes, the present study indicated that the presence of wastewater effluent matrix may mitigate the potentially adverse cellular impacts of the NSAIDs.


Asunto(s)
Cetoprofeno , Preparaciones Farmacéuticas , Contaminantes Químicos del Agua , Antiinflamatorios no Esteroideos/toxicidad , Diclofenaco/toxicidad , Células Hep G2 , Humanos , Cetoprofeno/toxicidad , Ácido Mefenámico/toxicidad , Transcriptoma , Aguas Residuales , Contaminantes Químicos del Agua/análisis , Contaminantes Químicos del Agua/toxicidad
12.
Chemosphere ; 286(Pt 3): 131831, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34411925

RESUMEN

Microplastics (MPs) are pollutants that are widely distributed in the aquatic environment. Fish are directly exposed to water and are at risk of ingesting a large amount of MPs. In the present study, the grass carp were exposed to two concentrations of MPs (1000 and 100 µg/L) and fluorescence signals were detected in the liver digestion solution. Grass carp exposed to MPs for 21-days showed liver cytoplasmic vacuolation and inhibited growth. At the end of the exposure period, the fish treated with MPs exhibited inhibition of the antioxidant system and enhancement oxidative stress in comparison with the control group. The transcriptome analysis of grass carp was then performed to reveal the molecular mechanism of the response to MPs. In total, 1554 differentially expressed genes (DEGs) were identified. The results of GO and KEGG pathway analysis of the DEGs identified energy metabolism-related pathways and peroxisome proliferator-activated receptor (PPAR) signaling pathway. Taken together, the present study not only highlighted oxidative stress and metabolism disorders related to MP ingestion, but also determined the risk of MP exposure to teleost.


Asunto(s)
Carpas , Animales , Carpas/genética , Proteínas de Peces/genética , Microplásticos , Plásticos/toxicidad , Transcriptoma
13.
Gene ; 807: 145964, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-34530087

RESUMEN

AIMS: We aimed to investigate the role of G protein subunit alpha Z(GNAZ) in the progression and prognosis of patients with hepatocellular carcinoma (HCC). METHODS: Oncomine, GEO, TCGA, GEPIA2, Kaplan-Meier Plotter, TIMER2, Metascape, CCLE, LinkedOmics, and UALCAN databases were used to analyze the differential expression of GNAZ in HCC and normal liver tissues, relationship between GNAZ expression and prognosis of patients with HCC, and expression of GNAZ in common human HCC cell lines. Western blotting was performed to analyze GNAZ expression, while the Cell Counting Kit 8 assay was used to determine cell proliferation, and flow cytometry was used to evaluate the cell cycle and apoptosis. Wound healing and transwell invasion assays were used to investigate cell metastasis and invasion. RESULTS: Using Oncomine, Gene Expression Omnibus (GEO), and GEPIA2 databases, GNAZ was found to be overexpressed in HCC tissues compared with that in adjacent normal liver tissues, and western blotting analysis showed GNAZ overexpression in seven patients with HCC who underwent surgical resection of HCC and para-cancerous tissues (p < 0.01). Survival analysis revealed that high GNAZ expression was negatively associated with overall survival (OS), recurrence-free survival, progression-free survival, and disease-specific survival in patients with HCC (p < 0.05). GNAZ overexpression was associated with worse 4- month, 6- month, 12- month, 24- month, 36- month, 48- month, and 60-month OS, as well as with different clinicopathological characteristics of patients with HCC, including hepatitis virus infection state; alcohol consumption state; male; female; Asian; microvascular invasion, Stage I-II, Stage II-III, and Stage III-IV; and grade II (Cox regression, p < 0.05). KEGG/GO biological process enrichment indicated that the genes similar to GNAZ in HCC were mainly enriched in the cell cycle, cell cycle phase transition, DNA replication checkpoint, and regulation of G0 to G1 transition. siRNA-GNAZ significantly reduced the viability of JHH-2 and SNU-761 cells from 12 to 96 h; increased the percentage of cells in the G0/G1 phase and decreased that of cells in the S and G2/M phases (p < 0.05); and markedly downregulated the expression of cyclin D, cyclin E, and CDK2 protein. siRNA-GNAZ also significantly increased the percentage of JHH-2 and SNU-761 cell apoptosis at late stages, while the number of surviving cells decreased (p < 0.05), and upregulated the expression of apoptosis-related proteins Bax and caspase 3 protein. Furthermore, siRNA-GNAZ remarkably reduced the healing of scratch wounds in JHH-2 and SNU-761 cells and the number of invasive cells compared with that in the control group (p < 0.001). CONCLUSION: Our study demonstrated that GNAZ plays a pivotal role as a potential oncogene and predicts poor prognosis in patients with HCC. It promotes tumor proliferation via cell cycle arrest, apoptosis, migration, and invasion. Thus, GNAZ may be a potential candidate biomarker providing useful insight into hepatocarcinogenesis and aggressiveness.


Asunto(s)
Carcinoma Hepatocelular/genética , Puntos de Control de la Fase G1 del Ciclo Celular/genética , Subunidades alfa de la Proteína de Unión al GTP/genética , Anciano , Apoptosis/genética , Grupo de Ascendencia Continental Asiática/genética , Biomarcadores de Tumor/genética , Carcinoma Hepatocelular/mortalidad , Ciclo Celular/genética , Proteínas de Ciclo Celular/genética , Línea Celular Tumoral , Movimiento Celular/genética , Proliferación Celular/genética , China , Femenino , Subunidades alfa de la Proteína de Unión al GTP/metabolismo , Expresión Génica/genética , Regulación Neoplásica de la Expresión Génica/genética , Células Hep G2 , Humanos , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/mortalidad , Masculino , Persona de Mediana Edad , Pronóstico , Receptores Acoplados a Proteínas G/genética , Receptores Acoplados a Proteínas G/metabolismo , Transcriptoma/genética
14.
Sci Total Environ ; 804: 150254, 2022 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-34798758

RESUMEN

Although the toxicity of neonicotinoid insecticides has been demonstrated in several studies, the information on metabolism, behavior, and health risk remains limited and has raised concerns about its potential toxicity. Thus, in this study we assessed the effects of nitenpyram using different sublethal concentrations (one-third and one-tenth of the acute LC50 values) on various developmental and metabolic parameters from gene expression regulation in Drosophila melanogaster (model system used worldwide in ecotoxicological studies). As a result, nitenpyram sublethal concentrations prolonged the developmental time for both pupation and eclosion. Additionally, nitenpyram sublethal concentrations significantly decreased the lifespan, pupation rate, eclosion rate, and production of eggs of D. melanogaster. Moreover, the mRNA expression of genes relevant for development and metabolism was significantly elevated after exposure. Mixed function oxidase enzymes (Cyp12d1), (Cyp9f2), and (Cyp4ae1), hemocyte proliferation (RyR), and immune response (IM4) genes were upregulated, whereas lifespan (Atg7), male mating behavior (Ple), female fertility (Ddc), and lipid metabolism (Sxe2) genes were downregulated. These findings support a solid basis for further research to determine the hazardous effects of nitenpyram on health and the environment.


Asunto(s)
Proteínas de Drosophila , Drosophilidae , Insecticidas , Plaguicidas , Animales , Proteína 7 Relacionada con la Autofagia , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Drosophilidae/metabolismo , Femenino , Insecticidas/toxicidad , Masculino , Neonicotinoides , Reproducción , Transcriptoma
15.
BMC Genomics ; 22(1): 796, 2021 Nov 05.
Artículo en Inglés | MEDLINE | ID: mdl-34740333

RESUMEN

BACKGROUND: Mastitis is an economically important disease of dairy cows with Staphylococcus aureus a major cause worldwide. Challenge of Holstein-Friesian cows demonstrated that S. aureus strain MOK124, which belongs to Clonal Complex (CC)151, caused clinical mastitis, while strain MOK023, belonging to CC97, caused mild or subclinical mastitis. The aim of this study was to elucidate the molecular mechanisms of the host immune response utilising a transcriptomic approach. Milk somatic cells were collected from cows infected with either S. aureus MOK023 or MOK124 at 0, 24, 48, 72 and 168 h post-infection (hpi) and analysed for differentially expressed (DE) genes in response to each strain. RESULTS: In response to MOK023, 1278, 2278, 1986 and 1750 DE genes were found at 24, 48, 72 and 168 hpi, respectively, while 2293, 1979, 1428 and 1544 DE genes were found in response to MOK124 at those time points. Genes involved in milk production (CSN1, CSN10, CSN1S2, CSN2, a-LACTA and PRLR) were downregulated in response to both strains, with a more pronounced decrease in the MOK124 group. Immune response pathways such as NF-κB and TNF signalling were overrepresented in response to both strains at 24 hpi. These immune pathways continued to be overrepresented in the MOK023 group at 48 and 72 hpi, while the Hippo signalling, extracellular matrix interaction (ECM) and tight junction pathways were overrepresented in the MOK124 group between 48 and 168 hpi. Cellular composition analysis demonstrated that a neutrophil response was predominant in response to MOK124, while M1 macrophages were the main milk cell type post-infection in the MOK023 group. CONCLUSIONS: A switch from immune response pathways to pathways involved in maintaining the integrity of the epithelial cell layer was observed in the MOK124 group from 48 hpi, which coincided with the occurrence of clinical signs in the infected animals. The higher proportion of M1 macrophages in the MOK023 group and lack of substantial neutrophil recruitment in response to MOK023 may indicate immune evasion by this strain. The results of this study highlight that the somatic cell transcriptomic response to S. aureus is dependent on the genotype of the infecting strain.


Asunto(s)
Mastitis Bovina , Infecciones Estafilocócicas , Animales , Bovinos , Femenino , Genotipo , Mastitis Bovina/genética , Leche , Infecciones Estafilocócicas/genética , Infecciones Estafilocócicas/veterinaria , Staphylococcus aureus/genética , Transcriptoma
16.
Planta ; 254(6): 115, 2021 Nov 06.
Artículo en Inglés | MEDLINE | ID: mdl-34743252

RESUMEN

MAIN CONCLUSION: The banana development was inhibited under the long-term magnesium deficiency (MD) stress, resulting in the leaf chlorosis. MYB108 and WRKY75 are involved in regulating the growth and development of banana leaves and roots under long-term MD. Magnesium deficiency (MD) causes plant growth inhibition, ageing acceleration, yield reduction and quality decline of banana (Musa paradisiaca AA), but the molecular regulatory mechanisms underlying the changes in response to long-term MD conditions remain unknown. In this study, a long-term MD experiment was performed with banana seedlings at the four-leaf stage. Compared to those in the control group, the growth of leaves and roots of seedlings in the long-term MD treatment experimental groups was inhibited, and the Mg content and chlorophyll contents were decreased. Leaves and roots of seedlings from the control and experimental groups were subsequently collected for RNA sequencing to identify the genes that respond to long-term MD. More than 50 million reads were identified from each sample, resulting in the detection of 3500 and 948 differentially expressed genes (DEGs) in the leaves and roots, respectively. MYB and WRKY transcription factors (TFs) involved in plant stress responses were selected for further analysis, and 102 MYB and 149 WRKY TFs were differentially expressed. Furthermore, two highly differentially expressed candidate genes, MYB108 and WRKY75, were functionally analyzed using Arabidopsis mutants grown under long-term MD conditions. The results showed that the density of root hairs on the wild type (WT) was than that on the myb108 and wrky75 mutants under MD, implying that the mutants were more sensitive to MD than the WT. This research broadens our understanding the underlying molecular mechanism of banana seedlings adapted to the long-term MD condition.


Asunto(s)
Deficiencia de Magnesio , Musa , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Musa/genética , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Transcriptoma/genética
17.
BMC Genomics ; 22(1): 810, 2021 Nov 10.
Artículo en Inglés | MEDLINE | ID: mdl-34758725

RESUMEN

BACKGROUND: The gut is the first barrier to infection by viruses that are internally borne and transmitted persistently by arthropod vectors to plant and animal hosts. Tomato spotted wilt virus (TSWV), a plant-pathogenic virus, is transmitted exclusively by thrips vectors in a circulative-propagative manner. Frankliniella occidentalis (western flower thrips), the principal thrips vector of TSWV, is transmission-competent only if the virus is acquired by young larvae. To begin to understand the larval gut response to TSWV infection and accumulation, a genome-assisted, transcriptomic analysis of F. occidentalis gut tissues of first (early L1) and second (early L2 and late L2) instar larvae was conducted using RNA-Seq to identify differentially-expressed transcripts (DETs) in response to TSWV compared to non-exposed cohorts. RESULTS: The larval gut responded in a developmental stage-dependent manner, with the majority of DETs (71%) associated with the early L1 stage at a time when virus infection is limited to the midgut epithelium. Provisional annotations of these DETs inferred roles in digestion and absorption, insect innate immunity, and detoxification. Weighted gene co-expression network analysis using all assembled transcripts of the gut transcriptome revealed eight gene modules that distinguish larval development. Intra-module interaction network analysis of the three most DET-enriched modules revealed ten central hub genes. Droplet digital PCR-expression analyses of select network hub and connecting genes revealed temporal changes in gut expression during and post exposure to TSWV. CONCLUSIONS: These findings expand our understanding of the developmentally-mediated interaction between thrips vectors and orthotospoviruses, and provide opportunities for probing pathways for biomarkers of thrips vector competence.


Asunto(s)
Thysanoptera , Tospovirus , Animales , Larva/genética , Enfermedades de las Plantas , Thysanoptera/genética , Tospovirus/genética , Transcriptoma
18.
BMC Genomics ; 22(1): 809, 2021 Nov 10.
Artículo en Inglés | MEDLINE | ID: mdl-34758728

RESUMEN

BACKGROUND: Single-cell RNA sequencing (scRNA-seq) provides new insights to address biological and medical questions, and it will benefit more from the ultralow input RNA or subcellular sequencing. RESULTS: Here, we present a highly sensitive library construction protocol for ultralow input RNA sequencing (ulRNA-seq). We systematically evaluate experimental conditions of this protocol, such as reverse transcriptase, template-switching oligos (TSO), and template RNA structure. It was found that Maxima H Minus reverse transcriptase and rN modified TSO, as well as all RNA templates capped with m7G improved the sequencing sensitivity and low abundance gene detection ability. RNA-seq libraries were successfully prepared from total RNA samples as low as 0.5 pg, and more than 2000 genes have been identified. CONCLUSIONS: The ability of low abundance gene detection and sensitivity were largely enhanced with this optimized protocol. It was also confirmed in single-cell sequencing, that more genes and cell markers were identified compared to conventional sequencing method. We expect that ulRNA-seq will sequence and transcriptome characterization for the subcellular of disease tissue, to find the corresponding treatment plan.


Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento , Transcriptoma , Animales , Encéfalo , Perfilación de la Expresión Génica , Biblioteca de Genes , Ratones , RNA-Seq , Análisis de Secuencia de ARN , Análisis de la Célula Individual
19.
Pestic Biochem Physiol ; 179: 104971, 2021 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-34802521

RESUMEN

Haemaphysalis longicornis is an ixodid tick species of medical and veterinary importance. Investigation into the acaricidal activities of botanicals have increased recently but information about their molecular mechanism of action is scarce. Here, RNA-seq analysis of the ticks exposed to Cymbopogon citratus essential oil and citronellal was performed and the responsive genes were identified. More than 6.39 G clean reads with Q20 ≥ 94.88% were obtained for each H. longicornis sample, with an average GC content of 50.94%. Using the Trinity method, 166,710 unigenes with a mean length of 869 bp and a maximum contig length of 29,156 bp were obtained. The upregulation of genes was concentration-dependent in most of the treated groups. Many genes responsive to C. citratus oil and citronellal were stress-related and they include genes associated with adrenergic signaling/calcium channels, cGMP-PKG signaling, apoptosis, focal adhesion, ECM-receptor interaction, ubiquitin-mediated proteolysis, mTOR signaling pathway, and longevity regulating pathway. The upregulation of genes (CACNAID, ADCY9, TPM1, and MYH6) associated with calcium channels suggests a neurotoxic mode of action, whereas, the upregulation of apoptosis-associated genes (CYC, DRONC, CASP7, CASP9, BCL2L1, bcl-xL, etc.) suggests a cytotoxic mode of action. The metabolism of C. citratus essential oil generates oxidative stress which increases the intra-mitochondrial free Ca2+ and triggers the formation of reactive oxygen species (ROS) that culminates to mitochondrial depolarization, ATP depletion, and either necrotic or apoptotic death. The neurotoxic and cytotoxic effects exhibited by the monoterpenes in H. longicornis is vital and could be exploited for the advancement of acaricide development and eco-friendly tick control.


Asunto(s)
Cymbopogon , Ixodidae , Aceites Volátiles , Monoterpenos Acíclicos , Aldehídos , Animales , Aceites Volátiles/toxicidad , Transcriptoma
20.
BMC Res Notes ; 14(1): 418, 2021 Nov 18.
Artículo en Inglés | MEDLINE | ID: mdl-34794498

RESUMEN

OBJECTIVE: Transcriptional profiling of immune cells is an indispensable tool in biomedical research; however, heterogenous sample types routinely used in transcriptomic studies may mask important cell type-specific transcriptional differences. Techniques to isolate desired cell types are used to overcome this limitation. We sought to evaluate the use of immunomagnetic B cell isolation on RNA quality and transcriptional output. Additionally, we aimed to develop a B cell gene signature representative of a freshly isolated B cell population to be used as a tool to verify isolation efficacy and to provide a transcriptional standard for evaluating maintenance or deviation from traditional B cell identity. RESULTS: We found RNA quality and RNA-sequencing output to be comparable between donor-matched PBMC, whole blood, and B cells following negative selection by immunomagnetic B cell isolation. Transcriptional analysis enabled the development of an 85 gene B cell signature. This signature effectively clustered isolated B cells from heterogeneous sample types in our study and naïve and memory B cells when applied to transcriptional data from a published source. Additionally, by identifying B cell signature genes whose functional role in B cells is currently unknown, our gene signature has uncovered areas for future investigation.


Asunto(s)
Linfocitos B , Leucocitos Mononucleares , Separación Celular , Perfilación de la Expresión Génica , ARN , Transcriptoma
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