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1.
Gene ; 764: 145055, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32882332

RESUMEN

Cyanobacteria are model photosynthetic prokaryotic organisms often used in biotechnology to produce biofuels including alcohols. The effect of alcohols on cyanobacterial cell physiology and specifically on membrane fluidity is poorly understood. Previous research on various primary aliphatic alcohols found that alcohols with a short hydrocarbon chain (C1-C3) do not affect expression of genes related to membrane physical state. In addition, less water-soluble alcohols with a hydrocarbon chain longer than C8 are found to have a reduced ability to reach cellular membranes hence do not drastically change membrane physical state or induce expression of stress-responsive genes. Therefore, hexan-1-ol (C6) is suggested to have the most profound effect on cyanobacterial membrane physical state. Here, we studied the effects of hexan-1-ol on the cyanobacterium Synechocystis sp. PCC 6803 transcriptome. The transcriptome data obtained is compared to the previously reported analysis of gene expression induced by benzyl alcohol and butan-1-ol. The set of genes whose expression is induced after exposure to all three studied alcohols is identified. The expression under alcohol stress for several general stress response operons is analyzed, and examples of antisense interactions of RNA are investigated.


Asunto(s)
Membrana Celular/efectos de los fármacos , Regulación Bacteriana de la Expresión Génica/efectos de los fármacos , Hexanoles/toxicidad , Estrés Fisiológico/genética , Synechocystis/genética , 1-Butanol/toxicidad , Alcohol Bencilo/toxicidad , Operón/efectos de los fármacos , Operón/genética , ARN sin Sentido/genética , ARN sin Sentido/metabolismo , RNA-Seq , Estrés Fisiológico/efectos de los fármacos , Synechocystis/efectos de los fármacos , Transcriptoma/efectos de los fármacos
2.
Gene ; 764: 145105, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32882333

RESUMEN

Sarcoma (SARC) represents a group of highly histological and molecular heterogeneous rare malignant tumors with poor prognosis. There are few proposed classifiers for predicting patient's outcome. The Cancer Proteome Atlas (TPCA) and The Cancer Genome Atlas (TCGA) databases provide multi-omics datasets that enable a comprehensive investigation for this disease. The proteomic expression profile of SARC patients along with the clinical information was downloaded. 55 proteins were found to be associated with overall survival (OS) of patients using univariate Cox regression analysis. We developed a prognostic risk signature that comprises seven proteins (AMPKALPHA, CHK1, S6, ARID1A, RBM15, ACETYLATUBULINLYS40, and MSH6) with robust predictive performance using multivariate Cox stepwise regression analysis. Additionally, the signature could be an independent prognostic predictor after adjusting for clinicopathological parameters. Patients in high-risk group also have worse progression free intervals (PFI) than that of patients in low-risk group, but not for disease free intervals (DFI). The signature was validated using transcriptomic profile of SARC patients from TCGA. Potential mechanisms between high- and low-risk groups were identified using differentially expressed genes (DEGs) analysis. These DEGs were primarily enriched in RAS and MPAK signaling pathways. The signature protein molecules are candidate biomarkers for SARC, and the analysis of computational biology in tumor infiltrating lymphocytes and immune checkpoint molecules revealed distinctly immune landscapes of high- and low-risk patients. Together, we constructed a prognostic signature for predicting outcomes for SARC integrating proteomic and transcriptomic profiles, this might have value in guiding clinical practice.


Asunto(s)
Biomarcadores de Tumor/genética , Regulación Neoplásica de la Expresión Génica/inmunología , Pruebas Genéticas/métodos , Sarcoma/mortalidad , Microambiente Tumoral/inmunología , Antineoplásicos Inmunológicos/farmacología , Antineoplásicos Inmunológicos/uso terapéutico , Antígeno B7-H1/antagonistas & inhibidores , Antígeno B7-H1/genética , Antígeno B7-H1/inmunología , Antígeno CTLA-4/antagonistas & inhibidores , Antígeno CTLA-4/genética , Antígeno CTLA-4/inmunología , Conjuntos de Datos como Asunto , Femenino , Estudios de Seguimiento , Perfilación de la Expresión Génica , Humanos , Estimación de Kaplan-Meier , Linfocitos Infiltrantes de Tumor/inmunología , Linfocitos Infiltrantes de Tumor/metabolismo , Masculino , Persona de Mediana Edad , Valor Predictivo de las Pruebas , Pronóstico , Receptor de Muerte Celular Programada 1/antagonistas & inhibidores , Receptor de Muerte Celular Programada 1/genética , Receptor de Muerte Celular Programada 1/inmunología , Supervivencia sin Progresión , Mapeo de Interacción de Proteínas , Proteómica , Curva ROC , Sarcoma/tratamiento farmacológico , Sarcoma/genética , Sarcoma/inmunología , Transcriptoma/genética , Microambiente Tumoral/efectos de los fármacos , Microambiente Tumoral/genética
3.
Gene ; 764: 145082, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32858176

RESUMEN

Melatonin functions as a plant growth regulator in a concentration-dependent manner. In this study, we investigated the effects of melatonin on root growth and dissected underlined mechanisms. The results showed that melatonin up to 1000 µM inhibited primary root growth, but promoted lateral root development. Through RNA sequencing analysis, functions of differentially expressed genes were mainly involved in stress response, signaling transduction, transport, hormone metabolism and amino acid metabolism. Genes involving in jasmonate (JA), brassinosteroid (BR) and cytokinin (CK) biosynthesis were inhibited, but these in ethylene (ET), strigolactone (SL) and gibberellins (GA) biosynthetic pathways were activated after melatonin treatment. The majority of zinc finger proteins (ZFPs), Calmodulin-like (CMLs), NAM, ATAF1/2, and CUC2 (NACs) and ubiquitination related genes (RING/U-box and F-box) were upregulated, which possibly acted downstream of integrated hormone signals to mediate root growth. This study characterized melatonin modulated networks in regulating root growth.


Asunto(s)
Arabidopsis/fisiología , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Melatonina/metabolismo , Reguladores del Crecimiento de las Plantas/metabolismo , Raíces de Plantas/crecimiento & desarrollo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Vías Biosintéticas/genética , RNA-Seq , Transducción de Señal/genética , Factores de Transcripción/metabolismo , Transcriptoma/genética
4.
Gene ; 766: 145118, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32896588

RESUMEN

Insulin-like growth factor 1 (IGF1) is a multifunctional cell proliferation regulator that plays a critical role in regulating animal growth and development. In this study, the expression level of IGF1 gene in different tissues of Dezhou donkey in different periods was investigated by RT-qPCR. Meanwhile, two mutation sites were identified within the IGF1 gene and its effect on body size traits of Dezhou donkey was analysed. The results showed that the expression level of the adult donkey IGF1 gene in heart, liver, spleen, lung, renal and gastric tissues is higher than that of the young donkeys, but the young donkeys are significantly higher in muscle tissues than the adult donkeys. The IGF1-1 and IGF1-2 loci showed a trend that the GG mutant was larger than other genotypes in the growth traits of both male and female donkeys, among which the IGF1-1 loci had a significant association with the chest circumference and chest depth of male donkeys (P < 0.05), and the IGF1-2 loci had a significant association with the chest circumference of female donkeys. Haplotype combination Hap1Hap1 (GG-GG) showed a greater tendency than Hap2Hap2 (AA-GG) combination in terms of growth traits, reflecting that the results were consistent with the analysis results of genotypes, which also proved the analysis results of genotypes and growth traits had certain reliability. In summary, the IGF1 gene is a candidate gene for growth and development, and its polymorphisms can be used as the molecular markers for Dezhou donkey breeding.


Asunto(s)
Tamaño Corporal/genética , Equidae/genética , Factor I del Crecimiento Similar a la Insulina/genética , Transcriptoma/genética , Animales , Cruzamiento/métodos , Femenino , Genotipo , Haplotipos/genética , Masculino , Fenotipo , Polimorfismo de Nucleótido Simple/genética
5.
Gene ; 766: 145142, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32911027

RESUMEN

Rootstocks are among the primary factors that influence fruit yield and quality as well as melon development. To understand the differences in the molecular mechanisms and gene expression networks of fruit development between grafted and nongrafted plants in oriental melon, we performed a comprehensive analysis of the transcriptome and proteome dynamic gene/protein expression profiles during fruit development in oriental melon (Cucumis melo L. var. makuwa). Using pairwise comparisons between grafted and nongrafted samples by transcriptome analysis, we identified a large number of candidate genes involved in hormonal signaling pathways, transcription factors, resistance-related biosynthetic pathways and photosynthesis-related metabolic pathways. Many transcription factor-encoded genes were significantly more strongly expressed in the grafted samples, for example, AP2/ERF, C2H2, MYB, bHLH, and AUX/IAA, which are well-known participants in the regulation of developmental processes and hormonal signaling metabolism. Some differentially expressed genes (DEGs) were enriched in flavonoid biosynthesis and phenylpropanoid biosynthesis and determined plant resistance. In addition, some differentially expressed proteins (DEPs) were enriched in photosynthesis-related pathways, which could improve fruit quality and yield. Moreover, through weighted gene coexpression network analyses, we identified modules of coexpressed genes and hub genes specifically related to grafting for different fruit developmental stages. The results suggested that graft-related modules and hub genes were primarily associated with photosynthate metabolism and hormonal signaling pathways. The results obtained in this study provide a valuable resource for dissecting the role of candidate genes governing graft-related metabolism in oriental melon fruit, suggesting an interesting correlation with the effects of rootstock on fruit development.


Asunto(s)
Cucumis melo/genética , Cucurbitaceae/crecimiento & desarrollo , Cucurbitaceae/genética , Frutas/crecimiento & desarrollo , Frutas/genética , Regulación de la Expresión Génica de las Plantas/genética , Perfilación de la Expresión Génica/métodos , Redes Reguladoras de Genes/genética , Fotosíntesis/genética , Raíces de Plantas/genética , RNA-Seq/métodos , Transducción de Señal/genética , Transcriptoma/genética
6.
Gene ; 766: 145077, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32941951

RESUMEN

Newcastle disease virus (NDV) is a contagious poultry paramyxovirus, leading to substantial economic losses to the poultry industry. Here, RNA-seq was carried out to investigate the altered expression of immune-related genes in chicken thymus within 96 h in response to NDV infection. In NDV-infected chicken thymus tissues, comparative transcriptome analysis revealed 1386 differentially expressed genes (DEGs) at 24 h with 989 up- and 397 down-regulated genes, 728 DEGs at 48 h with 567 up- and 161 down-regulated genes, 1514 DEGs at 72 h with 1016 up- and 498 down-regulated genes, and 1196 DEGs at 96 h with 522 up- and 674 down-regulated genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these candidate targets mainly participate in biological processes or biochemical, metabolic and signal transduction processes. Notably, there is large enrichment in biological processes, cell components and metabolic processes, which may be related to NDV pathogenicity. In addition, the expression of five immune-related DEGs identified by RNA-seq was validated by quantitative real-time polymerase chain reaction (qRT-PCR). Our results indicated that the expression levels of AvBD5, IL16, IL22 and IL18R1 were obviously up-regulated, and Il-18 expression was also changed, but not significantly, which play key roles in the defense against NDV. Overall, we identified several candidate targets that may be involved in the regulation of NDV infection, which provide new insights into the complicated regulatory mechanisms of virus-host interactions, and explore new strategies for protecting chickens against the virus.


Asunto(s)
Pollos/genética , Pollos/inmunología , Enfermedad de Newcastle/genética , Enfermedad de Newcastle/inmunología , Virus de la Enfermedad de Newcastle/inmunología , Transcriptoma/genética , Vacunas Virales/inmunología , Animales , Pollos/virología , Regulación hacia Abajo/inmunología , Perfilación de la Expresión Génica/métodos , Enfermedad de Newcastle/virología , Enfermedades de las Aves de Corral/genética , Enfermedades de las Aves de Corral/inmunología , Enfermedades de las Aves de Corral/virología , Análisis de Secuencia de ARN/métodos , Transcriptoma/inmunología , Regulación hacia Arriba/inmunología
7.
Gene ; 766: 145119, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32946928

RESUMEN

BACKGROUND: Cervical cancer is the fourth most commonly diagnosed cancer in women worldwide. The metastasis and invasion of this type of cancer are closely related to the tumor microenvironment. Immune cells and stromal cells dominate the tumor microenvironment in cervical cancer. Therefore, we should further investigate the complex interplay between the tumor progression with immune cells or stromal cells. METHODS: We downloaded the gene expression profiles and clinical data of 307 patients with cervical cancers based on the TCGA database. Subsequently, the Estimation of Stromal and Immune cells in Malignant Tumours using Expression data (ESTIMATE) algorithm was used to calculate the scores of stromal cells and immune cells in order to uncover differential expressed genes, and we analyzed the correlation between their scores and patient survival. Then the Cell type Identification By Estimating Relative Subsets Of known RNA Transcripts (CIBERSORT) deconvolution algorithm was applied to quantify the fraction and infiltration of 22 types of immune cells in cervical cancer. Moreover, we also used R language packs and network tools to analyze GO term, gene enrichment pathway, and protein-protein relationship to trace down genes related to inflammation and immune regulation. RESULTS: The gene expression profiles and corresponding clinical data of 307 patients were obtained from TCGA database. The results showed that the scores were statistically significant between the high immunescore group and the low immunescore group. And the low immunescore group had shorter survival period than the high scores group (P = 0.035). Among the 22 types of immune cells, only T cells and mast cells were significantly related to the survival rate of cervical cancer patients. Moreover, PPI network analysis revealed that CCR5 and CXCL9, -10, -11/CXCR3 axis might be a new target for cervical cancer treatment. Finally, Kaplan-Meier survival curves found outnine representative genes significantly related to survival rate including BTNL8, CCR7, CD1E, CD6, CD27, CD79A, GRAP2, SP1B, LY9. CONCLUSIONS: These genes can be used as markers for the prognosis and diagnosis of cervical cancer and also might be used as treatment targets.


Asunto(s)
Regulación Neoplásica de la Expresión Génica/genética , Transcriptoma/genética , Microambiente Tumoral/genética , Neoplasias del Cuello Uterino/genética , Adulto , Biomarcadores de Tumor/genética , Manejo de Datos , Femenino , Perfilación de la Expresión Génica/métodos , Humanos , Estimación de Kaplan-Meier , Persona de Mediana Edad , Pronóstico , Mapas de Interacción de Proteínas/genética , Células del Estroma/patología , Neoplasias del Cuello Uterino/patología , Adulto Joven
8.
Gene ; 766: 145150, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32949695

RESUMEN

There are a few studies indicating that small molecular compounds affect the proliferation, differentiation, apoptosis, and autophagy of female germline stem cells (FGSCs). However, whether small molecular compound 28 (C28) affect development of FGSCs remains unknown. In this study, we found that C28 reduced the viability and proliferation of FGSCs, respectively. Additionally, western blotting showed that the expression of autophagy marker light chain 3 beta II (LC3B-II) was significantly increased and expression of sequestosome-1 (SQSTM1) was significantly reduced in C28-treated groups. Immunofluorescence showed that, in C28-treated groups, the number of LC3B-II-positive puncta was increased significantly. These results indicated that C28 induced autophagy of FGSCs in vitro. Furthermore, data from Chromatin Immunoprecipitation Sequencing for H3K27ac showed that autophagy-related biological processes such as regulation of mitochondrial membrane potential, Golgi vesicle transport, and cellular response to reactive oxygen species were different after C28-treated. In addition, RNA-Seq showed that the expression of genes (Trib3, DDIT3, and ATF4) related to endoplasmic reticulum (ER) stress was enhanced by C28. These results suggest that the changes of H3K27ac and ER stress might be associated with C28-induced FGSC autophagy.


Asunto(s)
Acetilación/efectos de los fármacos , Autofagia/efectos de los fármacos , Histonas/genética , Células Madre Oogoniales/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/farmacología , Transcriptoma/efectos de los fármacos , Animales , Proliferación Celular/efectos de los fármacos , Estrés del Retículo Endoplásmico/efectos de los fármacos , Femenino , Aparato de Golgi/efectos de los fármacos , Aparato de Golgi/genética , Potencial de la Membrana Mitocondrial/efectos de los fármacos , Ratones , Ratones Endogámicos C57BL , Células Madre Oogoniales/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Transducción de Señal/efectos de los fármacos
9.
Gene ; 766: 145157, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32949697

RESUMEN

Glycolytic potential (GP) calculated based on glucose, glycogen, glucose-6-phosphate, and lactate contents is a critical factor for multiple meat quality characteristics. However, the genetic basis of glycolytic metabolism is still unclear. In this study, we constructed six RNA-Seq libraries using longissimus dorsi (LD) muscles from pigs divergent for GP phenotypic values and generated the whole genome-wide gene expression profiles. Furthermore, we identified 25,880 known and 220 novel genes from these skeletal muscle libraries, and 222 differentially expressed genes (DEGs) between the higher and lower GP groups. Notably, we found that the Lactate dehydrogenase B (LDHB) and Fructose-2, 6-biphosphatase 3 (PFKFB3) expression levels were higher in the higher GP group than the lower GP group, and positively correlated with GP and lactic acid (LA), and reversely correlated with pH value at 45 min postmortem (pH45min). Besides, LDHB and PFKFB3 expression were positively correlated with drip loss measured at 48 h postmortem (DL48h) and drip loss measured at 24 h postmortem (DL24h). Collectively, we identified a serial of DEGs as the potential key candidate genes affecting GP and found that LDHB and PFKFB3 are closely related to GP and GP-related traits. Our results lay a solid basis for in-depth studies of the regulatory mechanisms on GP and GP-related traits in pigs.


Asunto(s)
Glucólisis/genética , Músculo Esquelético/metabolismo , Porcinos/genética , Transcriptoma/genética , Animales , Perfilación de la Expresión Génica/métodos , Glucosa/genética , Glucógeno/genética , Isoenzimas/genética , L-Lactato Deshidrogenasa/genética , Ácido Láctico/metabolismo , Carne , Fenotipo , Fosfofructoquinasa-2/genética , Porcinos/metabolismo
10.
Gene ; 766: 145151, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32950635

RESUMEN

Smoking tobacco is the major hazard for lung cancer in Indian subcontinent especially men, compare to woman where, other important risk factors such as air pollutions are responsible. So, the aim of the study is to compare chronic smokers (CS) and non-smokers living in areas with air quality categorized as poor (AQI 201-300) or moderate (AQI 101-200). We measured the expression of non-small cell lung cancer (NSCLC) biomarkers;. IDH1, CEA, Cyfra21-1, and TPA through quantitative Real-Time PCR (qRT-PCR) and compared the levels of upregulation of the transcripts in stage IIIa NSCLC over control benign tissues among the smoking and AQI settings. Though the all biomarkers were significantly up-regulated in tumor tissues compared to control benign tissues, the fold change increase of IDH1 and CEA was highest in CS-poor/moderate AQI, followed by non-smokers-poor AQI and non-smokers moderate AQI. This indicates the aggressiveness and poor prognosis in CS living in either poor or moderate AQI areas. The level of Cyfra21-1 was lower in in the CS groups in comparison to non-smokers in the poor AQI area. This suggest higher Lung Squamous cell carcinoma histology in non-smokers living areas with poor AQI. Hence, we conclude that poor air quality can be as injurious for lung cancers as chronic smoking.


Asunto(s)
Antígenos de Neoplasias/genética , Antígeno Carcinoembrionario/genética , Carcinoma de Pulmón de Células no Pequeñas/genética , Isocitrato Deshidrogenasa/genética , Queratina-19/genética , Neoplasias Pulmonares/genética , Fumar/genética , Contaminación del Aire , Biomarcadores de Tumor/genética , Carcinoma de Pulmón de Células no Pequeñas/patología , Carcinoma de Células Escamosas/genética , Femenino , Humanos , Neoplasias Pulmonares/patología , Masculino , Persona de Mediana Edad , No Fumadores , Pronóstico , Fumadores , Transcriptoma/genética
11.
Gene ; 764: 145090, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32861880

RESUMEN

Litopenaeus vannamei (L. vannamei) is one of the most widely cultured shrimp species in the world. The species often suffers from cold stress. To understand the molecular mechanism of cold tolerance, we performed transcriptomic analysis on two contrasting cultivars of L. vannamei, namely, cold-tolerant Guihai 2 (GH2) and cold-sensitive Guihai1 (GH1), under a control temperature (28 °C), cold stress (16 °C), and recovery to 28 °C. A total of 84.5 Gb of sequences were generated from 12 L. vannamei hepatopancreas libraries. The de-novo assembly generated a total of 143,029 unigenes with a mean size of 1,052 bp and an N50 of 2,604 bp, of which 34.08% were annotated in the Nr database. We analyzed the differentially expressed genes (DEGs) between nine comparison groups and detected a total of 21,026 DEGs. KEGG pathways, including lysosome, sphingolipid metabolism and nitrogen metabolism, were significantly enriched by DEGs between different temperatures in GH2. Furthermore, eight of the most significantly DEGs under cold stress from the transcriptomic analysis were selected for quantitative real-time PCR (qPCR) validation. Overall, we compared gene expression changes under cold stress in cold-tolerant and cold-sensitive L. vannamei for the first time. The results may further extend our understanding of the cold stress-response mechanism in L. vannamei.


Asunto(s)
Aclimatación/genética , Respuesta al Choque por Frío/genética , Hepatopáncreas/metabolismo , Penaeidae/fisiología , Mariscos , Animales , Acuicultura , China , Frío/efectos adversos , Regulación de la Expresión Génica/fisiología , Anotación de Secuencia Molecular , RNA-Seq , Reacción en Cadena en Tiempo Real de la Polimerasa , Transcriptoma/genética
12.
Gene ; 764: 145098, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32861881

RESUMEN

Neocaridina denticulate sinensis is a small freshwater economic shrimp, as well as excellent laboratory model for their short life cycle and easy availability. However, the response of N. denticulate sinensis to pervasive copper pollution in aquatic environments has not been deeply investigated yet. Herein, we preformed Illumina sequencing technology to mine the alterations of cephalothorax transcriptome under 2.5 µmol/L of Cu2+ after 48 h. 122,512 unigenes were assembled and 219 unigenes were identified as significantly differentially expressed genes (DEGs) between control and Cu2+ treatment groups. Functional enrichment analysis revealed that DEGs were mostly associated with immune responses and molting, such as endocytosis, Fc gamma R-mediated phagocytosis and chitin metabolic process. Seven genes were chosen for qPCR verification, and the results showed that the transcriptome sequencing data were consistent with the qPCR results. This is the first report of transcriptome information about N. denticulate sinensis. These results provided a direction for the future research of resistance to Cu2+ in this shrimp, and simultaneously enriched gene information of N. denticulate sinensis.


Asunto(s)
Cobre/toxicidad , Decápodos/genética , Regulación de la Expresión Génica/efectos de los fármacos , Mariscos , Contaminantes Químicos del Agua/toxicidad , Animales , Quitina/metabolismo , Decápodos/efectos de los fármacos , Decápodos/inmunología , Endocitosis/efectos de los fármacos , Endocitosis/genética , Inmunidad Innata/efectos de los fármacos , Inmunidad Innata/genética , Redes y Vías Metabólicas/efectos de los fármacos , Redes y Vías Metabólicas/genética , Anotación de Secuencia Molecular , Muda/efectos de los fármacos , Muda/genética , Fagocitosis/efectos de los fármacos , Fagocitosis/genética , RNA-Seq , Transcriptoma/efectos de los fármacos
13.
Gene ; 764: 145101, 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-32877747

RESUMEN

India is the world's largest milk producing country because of massive contribution made by cattle and buffaloes. In the present investigation, comprehensive comparative profiling of transcriptomic landscape of milk somatic cells of Sahiwal cattle and Murrah buffaloes was carried out. Genes with highest transcript abundance in both species were enriched for biological processes such as lactation, immune response, cellular oxidant detoxification and response to hormones. Analysis of differential expression identified 377 significantly up-regulated and 847 significantly down-regulated genes with fold change >1.5 in Murrah buffaloes as compared to Sahiwal cattle (padj <0.05). Marked enrichment of innate and adaptive immune response related GO terms and higher expression of genes for various host defense peptides such as lysozyme, defensin ß and granzymes were evident in buffaloes. Genes related to ECM-receptor interaction, complement and coagulation cascades, cytokine-cytokine receptor interaction and keratinization pathway showed more abundant expression in cattle. Network analysis of the up-regulated genes delineated highly connected genes representing immunity and haematopoietic cell lineage (CBL, CD28, CD247, PECAM1 and ITGA4). For the down-regulated dataset, genes with highest interactions were KRT18, FGFR1, GPR183, ITGB3 and DKK3. Our results lend support to more robust immune mechanisms in buffaloes, possibly explaining lower susceptibility to mammary infections as compared to cattle.


Asunto(s)
Búfalos/inmunología , Bovinos/inmunología , Inmunidad/genética , Transcriptoma/inmunología , Animales , Péptidos Catiónicos Antimicrobianos/genética , Búfalos/genética , Bovinos/genética , Linaje de la Célula/genética , Linaje de la Célula/inmunología , Regulación hacia Abajo/inmunología , Femenino , Hematopoyesis/genética , Hematopoyesis/inmunología , India , Lactancia/genética , Lactancia/inmunología , Leche/citología , Leche/inmunología , RNA-Seq , Transcriptoma/genética , Regulación hacia Arriba/inmunología
14.
Chemosphere ; 262: 127573, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32745791

RESUMEN

Polycyclic aromatic hydrocarbons (PAHs) are widespread, persistent environmental pollutants. They exert toxic effects at different developmental stages of plants. Plant defense mechanisms against PAHs are poorly understood. To this end, transcriptomics and widely targeted metabolomic sequencing were used to study the changes in gene expression and metabolites that occur in the roots of Salix viminalis subjected to phenanthrene stress. Significant variations in genes and metabolites were observed between treatment groups and the control group. Thirteen amino acids and key genes involved in their biosynthesis were upregulated exposed to phenanthrene. Cysteine biosynthesis was upregulated. Sucrose, inositol galactoside, and mellidiose were the main carbohydrates that were largely accumulated. Glutathione biosynthesis was enhanced in order to scavenge reactive oxygen species and detoxify the phenanthrene. Glucosinolate and flavonoid biosynthesis were upregulated. The production of pinocembrin, apigenin, and epigallocatechin increased, which may play a role in antioxidation to resist phenanthrene stress. In addition, levels of six amino acids and N,N'-(p-coumaroyl)-cinnamoyl-caffeoyl-spermidine were significantly increased, which may have helped protect the plant against phenanthrene stress. These results demonstrated that S. viminalis had a positive defense strategy in response to phenanthrene challenge. Subsequent defense-related reactions may have also occurred within 24 h of phenanthrene exposure. The findings of the present study would be useful in elucidating the molecular mechanisms regulating plant responses to PAH challenges and would help guide crop and plant breeders in enhancing PAH resistance.


Asunto(s)
Fenantrenos/toxicidad , Salix/fisiología , Contaminantes del Suelo/toxicidad , Metabolómica , Fenantrenos/metabolismo , Raíces de Plantas/metabolismo , Hidrocarburos Policíclicos Aromáticos/metabolismo , Salix/metabolismo , Contaminantes del Suelo/metabolismo , Transcriptoma
15.
Chemosphere ; 262: 127891, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32799150

RESUMEN

Fluoride generally exists in the natural environment, and has been reported to induce serious environmental hazard to animals, plants, and even humans via ecological cycle. Silkworm, Bombyx mori, which showed significant growth and reproductivity reduction when exposed to fluoride, has become a model to evaluate the toxicity of fluoride. However, the detailed mechanism underlying fluoride toxicity and corresponding transport proteins remain unclear. In this study, we performed RNA-seq of the larval midgut and fat body with fluoride exposure and normal treatment. Differential analysis showed that there were 4405 differentially expressed genes in fat body and 4430 DEGs in midgut with fluoride stress. By Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we identified several key pathways involved in the fluoride exposure and poisoning. We focused on the oxidative phosphorylation and MAPK signal pathway. QRT-PCR confirmed that oxidative phosphorylation process was remarkably inhibited by fluoride exposure and resulted in the blocking of ATP synthesis. The MAPK signal pathway was stimulated via phosphorylation signal transduction. Moreover, by protein structure analysis combined with the DEGs, we screen 36 potential membrane proteins which might take part in transporting fluoride. Taken together, the results of our study expanded the underlying mechanisms of fluoride poisoning on silkworm larval growth and development, and implied potential fluoride transport proteins in silkworm.


Asunto(s)
Bombyx/fisiología , Fluoruros/toxicidad , Sustancias Peligrosas/toxicidad , Tejido Adiposo/metabolismo , Animales , Bombyx/metabolismo , Sistema Digestivo/metabolismo , Cuerpo Adiposo/metabolismo , Perfilación de la Expresión Génica/métodos , Inactivación Metabólica , Larva/genética , Transcriptoma/fisiología
16.
Sci Total Environ ; 752: 141783, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32890828

RESUMEN

Polybrominated diphenyl ethers (PBDEs) are a class of widely used flame retardants, and their residue in the environment may threaten the ecosystem and human health. The neurodevelopmental toxic effects of PBDEs have been verified in previous studies, but the mechanisms are still unclear. Behavioral analysis and transcriptomics were performed in this study to assess the neurodevelopmental toxic effects of PBDEs on zebrafish embryos and larvae, and the potential mechanisms. The embryos were collected after fertilization and exposed to control (0.05% DMSO), 10, 50, 100 (ug/L) 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47) for 7 days. The locomotion parameters of larvae were recorded and analyzed by a behavioral analysis system (EthoVision XT, Noldus). Enrichment of functions and signaling pathways of differentially expressed genes (DEGs) were analyzed by GO and DAVID database. The comparison with the control group showed adverse developments such as low hatching rate, high mortality rate, alterative heart rate, and abnormal spontaneous tail coiling frequency of embryos (24hpf). For the zebrafish larvae, behavioral analyses results suggested decreased activities and movements of the treatment in the light-dark period at 120, 144 and 168hpf, especially the 50 and 100µg/L groups. The affected functions included steroid hormone regulation, neuro regulation, circadian regulation, cardioblast differentiation, immune-related regulation. The enrichment of KEGG pathways were Hedgehog signaling (Shh), Toll-like receptor signaling, FoxO signaling, and Steroid biosynthesis pathway. Hedgehog signaling pathway was further verified via RT-qPCR for its major role in the development of neurogenesis. The mRNA levels of Shh pathway indicated the inhibition of Shh signal in our study since shha, patched1, gli1 and gli2 genes were significantly down-regulated. In summary, PBDEs might influence the neurodevelopment of zebrafish in the early life stage by multiple toxic signaling pathways alteration.


Asunto(s)
Retardadores de Llama , Contaminantes Químicos del Agua , Animales , Ecosistema , Embrión no Mamífero , Éter , Retardadores de Llama/toxicidad , Éteres Difenilos Halogenados/toxicidad , Proteínas Hedgehog , Humanos , Larva , Transcriptoma , Contaminantes Químicos del Agua/toxicidad , Pez Cebra/genética
17.
Sci Total Environ ; 753: 141906, 2021 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-32890873

RESUMEN

Symbiodiniaceae are the source of essential coral symbionts of reef building corals. The growth and density of endosymbiotic Symbiodiniaceae within the coral host is dependent on nutrient availability, yet little is known about how Symbiodiniaceae respond to the dynamics of the nutrients, including switch between different chemical forms and changes in abundance. In this study, we investigated physiological, cytometric, and transcriptomic responses in Fugacium kawagutii to nitrogen (N)-nutrient deficiency and different chemical N forms (nitrate and ammonium) in batch culture conditions. We mainly found that ammonium was consumed faster than nitrate when provided separately, and was preferentially utilized over nitrate when both N compounds were supplied at 1:2, 1:1 and 2:1 molarity ratios. Besides, N-deficiency caused decreases in growth, energy production, antioxidative capacity and investment in photosynthate transport but increased energy consumption. Growing on ammonium produced a similar cell yield as nitrate, but with a reduced investment in nutrient transport and assimilation; yet at high concentrations ammonium exhibited inhibitory effects. These findings together have important implications in N-nutrient regulation of coral symbiosis. In addition, we identified ten highly and stably expressed genes as candidate reference genes, which will be potentially useful for gene expression studies in the future.


Asunto(s)
Compuestos de Amonio , Antozoos , Dinoflagelados , Animales , Nitratos , Transcriptoma
18.
Food Chem ; 334: 127550, 2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-32693335

RESUMEN

Potato accumulates large amounts of soluble sugar during cold storage periods. However, a system based understanding of this process is still largely unknown. Here, we compared the dynamic cold-responded transcriptome of genotypes between cold-induced sweetening resistant (CIS-R) and cold-induced sweetening sensitive (CIS-S) in tubers. Comparative transcriptome revealed that activating the pathways of starch degradation, sucrose synthesis and hydrolysis could be common strategies in response to cold in both genotypes. Moreover, the variation in sugar accumulation between genotypes may be due to genetic differences in cold response, which could be mainly explained: CIS-R genotype was active in starch synthesis and attenuated in sucrose hydrolysis by promoting the coordinate expression of aseries ofgenes involved in starch-sugar interconversion. Additionally, transcription factors, the candidate master regulators of starch-sugar interconversion, were discussed. Taken together, this work has provided an avenue for studying the mechanism involved in the regulation of the CIS resistance.


Asunto(s)
Solanum tuberosum/genética , Almidón/metabolismo , Azúcares/metabolismo , Edulcorantes/metabolismo , Transcriptoma , Frío , Regulación hacia Abajo , Genotipo , Hidrólisis , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Tubérculos de la Planta/metabolismo , Análisis de Componente Principal , Solanum tuberosum/metabolismo , Regulación hacia Arriba
19.
Zhongguo Zhong Yao Za Zhi ; 45(18): 4382-4391, 2020 Sep.
Artículo en Chino | MEDLINE | ID: mdl-33164366

RESUMEN

GDP-mannose is an important precursor for the synthesis of Codonopsis pilosula polysaccharides and involved in the synthesis of sugar chains. Phosphomannomutase(PMM)catalyzes the conversion of mannose-6-phosphate(Man-6-P)to mannose-1-phosphate(Man-1-P)to synthesize GDP-mannose. In this study, specific primers were designed based on the PMM gene sequence information in transcriptome data, and the full length of the C. pilosula PMM gene was cloned and named CpPMM. The correlation between the CpPMM gene expression and C. pilosula polysaccharide synthesis was analyzed by a series of bioinformatics analysis, prokaryotic expression and qRT-PCR. The results show that the CpPMM gene contains a 741 bp open reading frame(ORF), encoding 246 amino acids, which is highly similar to the PMM of other species and highly homologous to the Helianthus annuus from the Asteraceae family. It was predicted to be a hydrophilic non-transmembrane protein without signal peptide, which was predicted to be located in the cytoplasm with multiple phosphorylation sites. Combined with predictive analysis of conserved domains, this protein belongs to the HAD(haloacid dehalogenase)superfamily; prokaryotic expression studies show that the size of the CpPMM fusion protein is about 29 kDa, which is consistent with the relative molecular mass predicted. The target protein is an inclusion body and is partially soluble. The qRT-PCR results showed that the CpPMM gene exerted spatiotemporal expression patterns, and the expression level in fruiting period was significantly higher than that in the other three periods such as the flowering period. Along with the growth period of C. pilosula, the polysaccharide content of C. pilosula showed a gradual increase trend, reaching the highest during the harvest time. And there are significant differences in the polysaccharide content of C. pilosula in each period. In this study, the CpPMM gene was cloned from the root of C. pilosula, at the same time, the prokaryotic expression system was constructed. In addition, its gene expression level is highly correlated with the polysaccharide content of C. pilosula. It lays the foundation for further studying the function of CpPMM gene and the analysis of biosynthetic pathways of polysaccharides in medicinal plants.


Asunto(s)
Codonopsis , Plantas Medicinales , Clonación Molecular , Codonopsis/genética , Polisacáridos , Transcriptoma
20.
Zhongguo Zhong Yao Za Zhi ; 45(19): 4606-4616, 2020 Oct.
Artículo en Chino | MEDLINE | ID: mdl-33164424

RESUMEN

Prunus mume "Langmei" is a relict tree species, which fruit has good medicinal value. To understand the biosynthesis pathway of citric acid, the Illumina HiSeq XTen high-throughput sequencing technology was used to get the transcriptome from "Langmei". A total of 38 936 unigenes were obtained by assembling the fruit transcripts, of which 28 311 unigenes were successfully annotated in public databases, 15 193 unigenes were mapped to 265 KEGG metabolic pathways, and 18 908 unigenes were classified into 59 GO functional subclasses, 103 unigenes encoding 15 key enzymes involved in citric acid synthesis pathway were identified and analyzed. The structural model of citrate synthetase in "Langmei" showed that it was a homodimer and the secondary structure of each monomer was mainly composed of alpha helixes. Moreover, the residues in the active site of the citrate synthetase were highly conserved. This study provides a valuable resource for identifying candidate genes involved in the citric acid biosynthesis pathway, and will promote the development and sustainable utilization of genetic resources of "Langmei".


Asunto(s)
Ácido Cítrico , Frutas , Frutas/genética , Perfilación de la Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , Transcriptoma
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