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2.
Gene ; 732: 144350, 2020 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-31935505

RESUMEN

THO complex is a multisubunit family with a function in transcription and mRNA export. In the present study, transcripts of THO complex (thoc) were identified in developing ovary of common carp and their role during ovarian development and growth has been characterized for the first time in a teleost using expression profiling and transient siRNA silencing. Thoc expression revealed a spatiotemporal pattern in the gonads with high levels at 120 days post-hatch, with moderately high levels thereafter. In situ hybridization and immunohistochemical localization revealed the presence of thoc3 in follicular layer of stage-III/IV oocytes. High levels of thoc3, thoc5, and thoc7 genes in the follicular layer suggest a possible role in ovarian growth. Reduced levels of serum estradiol-17ß and 17α, 20ß-dihydroxypregn-4-en-3-one after thoc3 transient silencing indicated differential action on steroidogenic enzyme, transcription factor, and growth factor genes. Furthermore, transient silencing of thoc3, in vivo and in vitro, downregulated ad4bp/sf1, amh, cyp19a1a, foxl2, hsd3b, hsd11b1, hsd20b, hsd17b1, rspo1, and vtg. Incidentally, gdf9 and igf1 were upregulated, while no change was seen in esr1/2, nanos, and vasa. These observations imply that thoc3 seems to regulate ovarian function including steroidogenesis, either directly or indirectly.


Asunto(s)
Carpas/genética , Perfilación de la Expresión Génica/veterinaria , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Ovario/crecimiento & desarrollo , Animales , Núcleo Celular/genética , Estradiol/metabolismo , Evolución Molecular , Femenino , Proteínas de Peces/genética , Proteínas de Peces/metabolismo , Regulación del Desarrollo de la Expresión Génica , Folículo Ovárico , Ovario/química , ARN Interferente Pequeño/farmacología , Diferenciación Sexual
3.
Gene ; 732: 144336, 2020 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-31935514

RESUMEN

In the present study, we aimed to evaluate effects of autologous mesenchymal stem cells (MSCs) intravenous administration on the response of B cells, BAFF, APRIL, and their receptors on the surface of B cells at 1, 6, and 12 month follow-up periods in refractory rheumatoid arthritis (RA) patients. Thirteen patients with refractory RA received autologous MSCs. Plasma levels of BAFF and APRIL were measured employing ELISA method, followed by estimating B cell population and BAFFRs evaluation by flow cytometry technique. Gene expression of BAFF, APRIL, and their receptors on B cell surface in PBMCs was evaluated by SYBR Green real-time PCR technique. Plasma concentration of BAFF significantly decreased 1 and 6 months after the MSCT (MSCs Transplantation). Plasma concentration of APRIL significantly decreased 1 month after the MSCT. Percentages of CD19 + B cells in the PBMC population significantly decreased 12 months after the MSCT. Percentages of BR3 + CD19 + B cells and BCMA + CD19 + B cells significantly decreased at the 12th month after the MSCT. The gene expression of BAFF in the PBMC population significantly decreased during 6, and 12 months after the MSCT. The gene expression of APRIL significantly decreased on month 6 after the MSCT. The gene expression of BR3 significantly decreased during 1, 6, and 12 months after the MSCT. The MSCT seems to decrease B cells response because of the reduced production of BAFF and APRIL cytokines and decrease the expression of their receptors on the surface of B cells.


Asunto(s)
Artritis Reumatoide/terapia , Factor Activador de Células B/metabolismo , Receptor del Factor Activador de Células B/metabolismo , Regulación hacia Abajo , Trasplante de Células Madre Mesenquimatosas/métodos , Miembro 13 de la Superfamilia de Ligandos de Factores de Necrosis Tumoral/metabolismo , Administración Intravenosa , Adulto , Antígenos CD19/metabolismo , Artritis Reumatoide/genética , Artritis Reumatoide/inmunología , Factor Activador de Células B/genética , Receptor del Factor Activador de Células B/genética , Linfocitos B/inmunología , Femenino , Perfilación de la Expresión Génica , Humanos , Persona de Mediana Edad , Resultado del Tratamiento , Miembro 13 de la Superfamilia de Ligandos de Factores de Necrosis Tumoral/genética
4.
Plant Mol Biol ; 102(3): 323-337, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31900819

RESUMEN

KEY MESSAGE: There is a link between PAP/SAL retrograde pathway, ethylene signaling and Fe metabolism in Arabidopsis. Nuclear gene expression is regulated by a diversity of retrograde signals that travel from organelles to the nucleus in a lineal or classical model. One such signal molecule is 3'-phosphoadenisine-5'-phosphate (PAP) and it's in vivo levels are regulated by SAL1/FRY1, a phosphatase enzyme located in chloroplast and mitochondria. This metabolite inhibits the action of a group of exorribonucleases which participate in post-transcriptional gene expression regulation. Transcriptome analysis of Arabidopsis thaliana mutant plants in PAP-SAL1 pathway revealed that the ferritin genes AtFER1, AtFER3, and AtFER4 are up-regulated. In this work we studied Fe metabolism in three different mutants of the PAP/SAL1 retrograde pathway. Mutant plants showed increased Fe accumulation in roots, shoots and seeds when grown in Fe-sufficient condition, and a constitutive activation of the Strategy I Fe uptake genes. As a consequence, they grew more vigorously than wild type plants in Fe-deficient medium. However, when mutant plants grown in Fe-deficient conditions were sprayed with Fe in their leaves, they were unable to deactivate root Fe uptake. Ethylene synthesis inhibition revert the constitutive Fe uptake phenotype. We propose that there is a link between PAP/SAL pathway, ethylene signaling and Fe metabolism.


Asunto(s)
Adenosina Difosfato/metabolismo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Hierro/metabolismo , Monoéster Fosfórico Hidrolasas/metabolismo , Transducción de Señal , Adenosina Difosfato/genética , Arabidopsis/genética , Arabidopsis/crecimiento & desarrollo , Proteínas de Arabidopsis/genética , Clorofila , Cloroplastos/metabolismo , Ferritinas/genética , Ferritinas/metabolismo , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genes de Plantas/genética , Homeostasis , Mitocondrias/metabolismo , Mutación , Monoéster Fosfórico Hidrolasas/genética , Hojas de la Planta/metabolismo , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/metabolismo
5.
Medicine (Baltimore) ; 99(2): e18676, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31914060

RESUMEN

Adenoid cystic carcinoma (ACC) is one of the most frequent malignancies of salivary glands. The objective of this study was to identify key genes and potential mechanisms during ACC samples.The gene expression profiles of GSE88804 data set were downloaded from Gene Expression Omnibus. The GSE88804 data set contained 22 samples, including 15 ACC samples and 7 normal salivary gland tissues. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were constructed, and protein-protein interaction network of differentially expressed genes (DEGs) was performed by Cytoscape. The top 10 hub genes were analyzed based on Gene Expression Profiling Interactive Analysis. Then, DEGs between ACC samples and normal salivary gland samples were analyzed by gene set enrichment analysis. Furthermore, miRTarBase and Cytoscape were used for visualization of miRNA-mRNA regulatory network. KEGG pathway analysis was undertaken using DIANA-miRPath v3.0.In total, 382 DEGs were identified, including 119 upregulated genes and 263 downregulated genes. GO analysis showed that DEGs were mainly enriched in extracellular matrix organization, extracellular matrix, and calcium ion binding. KEGG pathway analysis showed that DEGs were mainly enriched in p53 signaling pathway and salivary secretion. Expression analysis and survival analysis showed that ANLN, CCNB2, CDK1, CENPF, DTL, KIF11, and TOP2A are all highly expressed, which all may be related to poor overall survival. Predicted miRNAs of 7 hub DEGs mainly enriched in proteoglycans in cancer and pathways in cancer.This study indicated that identified DEGs and hub genes might promote our understanding of molecular mechanisms, which might be used as molecular targets or diagnostic biomarkers for ACC.


Asunto(s)
Carcinoma Adenoide Quístico/genética , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica/fisiología , Neoplasias de las Glándulas Salivales/genética , Matriz Extracelular/metabolismo , Ontología de Genes , Redes Reguladoras de Genes , Humanos , MicroARNs/genética , Transcriptoma
6.
J Insect Sci ; 20(1)2020 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-31925425

RESUMEN

Diaphania caesalis (Walker) is an important boring insect mainly distributed in subtropical and tropical areas and attacked tropical woody grain crops, such as starchy plants of Artocarpus. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful approach for investigating target genes expression profiles at the transcriptional level. However, the identification and selection of internal reference genes, which is often overlooked, is the most vital step before the analysis of target gene expression by qRT-PCR. So far, the reliable internal reference genes under a certain condition of D. caesalis have not been investigated. Therefore, this study evaluated the expression stability of eight candidate reference genes including ACT, ß-TUB, GAPDH, G6PDH, RPS3a, RPL13a, EF1α, and EIF4A in different developmental stages, tissues and sexes using geNorm, NormFinder and BestKeeper algorithms. To verify the stability of the recommended internal reference genes, the expression levels of DcaeOBP5 were analyzed under different treatment conditions. The results indicated that ACT, RPL13a, ß-TUB, RPS3a, and EF1α were identified as the most stable reference genes for further studies on target gene expression involving different developmental stages of D. caesalis. And ACT and EIF4A were recommended as stable reference genes for different tissues. Furthermore, ACT, EF1α, and RPS3a were ranked as the best reference genes in different sexes based on three algorithms. Our research represents the critical first step to normalize qRT-PCR data and ensure the accuracy of expression of target genes involved in phylogenetic and physiological mechanism at the transcriptional level in D. caesalia.


Asunto(s)
Expresión Génica , Genes de Insecto , Mariposas Nocturnas/genética , Animales , Perfilación de la Expresión Génica , Larva/genética , Larva/crecimiento & desarrollo , Mariposas Nocturnas/crecimiento & desarrollo , Óvulo/crecimiento & desarrollo , Pupa/genética , Pupa/crecimiento & desarrollo , Reacción en Cadena en Tiempo Real de la Polimerasa
7.
Anticancer Res ; 40(1): 177-190, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31892566

RESUMEN

BACKGROUND/AIM: The chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII) regulates cancer cell proliferation and invasion via complex molecular mechanisms. We aimed to investigate whether COUP-TFII modulates proliferation and invasion of the colorectal adenocarcinoma cell line HT-29. MATERIALS AND METHODS: HT-29 cells were stably tranfected with COUP-TFII shRNA plasmid to knock-down COUP-TFII (COUP-TFII shRNA-HT-29 cells). Cell proliferation, colony formation assay, invasion assay, microarray assays and western blot analyses were performed. RESULTS: Cell proliferation and invasion were significantly enhanced in COUP-TFII shRNA-HT-29 cells. The protein levels of forkhead box C1 (FOXC1), p-Akt, p-glycogen synthase kinase-3ß (p-GSK-3ß), and ß-catenin, which are known to be involved in cell proliferation and invasion, were significantly increased in COUP-TFII shRNA-HT-29 cells. Akt inhibitor IV and dominant negative (DN)-Akt expression vector transfection reversed the increased proliferation and invasion, which was accompanied by decreased protein levels of p-Akt, p-GSK-3ß, ß-catenin and FOXC1. CONCLUSION: COUP-TFII knock-down promoted proliferation and invasion via activation of Akt/GSK-3ß/ß-catenin and up-regulation of FOXC1. Further studies on the molecular mechanism of interaction between ß-catenin and FOXC1 expression may reveal novel target molecules for metastatic colorectal cancer therapy.


Asunto(s)
Factor de Transcripción COUP II/genética , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/metabolismo , Factores de Transcripción Forkhead/genética , Regulación Neoplásica de la Expresión Génica , Proteínas Proto-Oncogénicas c-akt/metabolismo , Transducción de Señal , Factor de Transcripción COUP II/metabolismo , Línea Celular Tumoral , Movimiento Celular , Proliferación Celular , Neoplasias Colorrectales/patología , Perfilación de la Expresión Génica , Técnicas de Silenciamiento del Gen , Humanos , ARN Interferente Pequeño/genética
8.
Zhonghua Yi Xue Za Zhi ; 100(2): 104-109, 2020 Jan 14.
Artículo en Chino | MEDLINE | ID: mdl-31937048

RESUMEN

Objective: To investigate differential genes (DEGs) between no/mild and severe emphysema by bioinformatics analysis. Methods: The microarray dataset GSE1650, of lung tissue in no/mild and severe emphysema, was downloaded from the GEO database, and DEGs were obtained by t test. Analysis of DEGs based on DAVID database was used to obtain gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway. The protein-protein interaction network (PPI) was established using STRING database to identify hub genes. Results: A total of 76 DEGs were obtained, of which 62 genes were up-regulated and 14 genes were down-regulated in severe emphysema group. Gene ontology showed that the DEGs were mainly involved in neutrophil chemotaxis, cellular response to interleukin-1, extracellular matrix organization, immune response, and KEGG pathway involved cytokine-cytokine receptor interaction, ECM-receptor interaction, PI3K-Akt signaling pathway, platelet activation. Seventeen hub genes were recognized by PPI analysis, including CXCL8, RRAD, CLU, TIMP1, SEPP1, ISLR, BGN, COL1A1, COLIA2, ACTA2, ACTN1, FIGF, TPM1, TPM2, LUM, COL6A3 and TAGLN. Among them, fifteen genes (CLU, TIMP1, SEPP1, ISLR, BGN, COLIA2, COL1A1, ACTA2, ACTN1, FIGF, TPM1, TPM2, LUM, COL6A3, TAGLN) were up-regulated and two genes (CXCL8, RRAD) were down-regulated. Conclusion: Bioinformatics analysis based on GEO database showed that there were DEGs between non/mild and severe emphysema patients.


Asunto(s)
Biología Computacional , Enfisema , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Humanos , Fosfatidilinositol 3-Quinasas , Proteínas ras
9.
Nat Commun ; 11(1): 538, 2020 Jan 27.
Artículo en Inglés | MEDLINE | ID: mdl-31988323

RESUMEN

Lymphatic endothelial cells (LECs) chemoattract naïve T cells and promote their survival in the lymph nodes, and can cross-present antigens to naïve CD8+ T cells to drive their proliferation despite lacking key costimulatory molecules. However, the functional consequence of LEC priming of CD8+ T cells is unknown. Here, we show that while many proliferating LEC-educated T cells enter early apoptosis, the remainders comprise a long-lived memory subset, with transcriptional, metabolic, and phenotypic features of central memory and stem cell-like memory T cells. In vivo, these memory cells preferentially home to lymph nodes and display rapid proliferation and effector differentiation following memory recall, and can protect mice against a subsequent bacterial infection. These findings introduce a new immunomodulatory role for LECs in directly generating a memory-like subset of quiescent yet antigen-experienced CD8+ T cells that are long-lived and can rapidly differentiate into effector cells upon inflammatory antigenic challenge.


Asunto(s)
Linfocitos T CD8-positivos/inmunología , Células Endoteliales/fisiología , Animales , Proliferación Celular , Células Endoteliales/inmunología , Perfilación de la Expresión Génica , Memoria Inmunológica , Ratones Endogámicos C57BL , Ratones Transgénicos
10.
Cancer Treat Rev ; 82: 101925, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31785413

RESUMEN

Immune checkpoint inhibitors targeting the programmed cell death 1 (PD-1)/programmed cell death ligand 1 (PD-L1) pathway improve clinical outcomes in patients with locally advanced/metastatic urothelial carcinoma (UC). PD-L1 complementary or companion diagnostic assays are now available for anti-PD-1 and anti-PD-L1 antibodies and these assays enable testing at diagnosis. The role of PD-L1 testing in UC is, however, the subject of much discussion within the medical community, particularly in light of recent restrictions on recruitment of PD-L1-low patients in clinical trials of atezolizumab and pembrolizumab as first-line therapy, and the European Medicines Agency and US Food and Drug Administration limiting use of these agents as first-line therapy in cisplatin-ineligible patients to those with high PD-L1 expression. We explore the evolving evidence for PD-L1 expression testing in UC and the role of PD-L1 expression in both tumor cells and tumor-infiltrating immune cells. We review clinical data on the prognostic and predictive value of PD-L1 expression in response to anti-PD-1/PD-L1 agents as first- and second-line therapy, considering issues such as the differences among complementary diagnostic assays in terms of the type of cells scored, antibodies used, and cutoff values. We consider how PD-L1 testing fits into decision-making and the potential of emerging biomarkers in UC. We conclude that, based on the scientific rationale for its use and evidence from clinical trials, PD-L1 testing provides enriched information on the patients most likely to benefit from immune checkpoint blockade and should be routinely offered to patients with metastatic UC.


Asunto(s)
Anticuerpos Monoclonales Humanizados/farmacología , Antígeno B7-H1 , Carcinoma de Células Transicionales , Perfilación de la Expresión Génica/métodos , Neoplasias Urológicas , Anticuerpos Monoclonales Humanizados/clasificación , Antineoplásicos Inmunológicos/farmacología , Antígeno B7-H1/antagonistas & inhibidores , Antígeno B7-H1/genética , Biomarcadores de Tumor/antagonistas & inhibidores , Biomarcadores de Tumor/genética , Carcinoma de Células Transicionales/tratamiento farmacológico , Carcinoma de Células Transicionales/patología , Humanos , Metástasis de la Neoplasia , Estadificación de Neoplasias , Selección de Paciente , Valor Predictivo de las Pruebas , Pronóstico , Neoplasias Urológicas/tratamiento farmacológico , Neoplasias Urológicas/patología
11.
Gene ; 728: 144279, 2020 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-31821871

RESUMEN

AIM OF THE STUDY: Chronic glomerulonephritis (CGN) is the most common form of primary glomerular disease. Qi Teng Xiao Zhuo granules have been proposed as a prescription of traditional Chinese medicine (TCM) for treatment of CGN, however,the comprehensive molecular mechanism underlying this therapeutic effectremains unclear to date. Our study aimed to evaluate and analyze the possible roles and molecular mechanisms of Qi Teng Xiao Zhuo granule-mediated treatment of CGN induced by adriamycin in rats. MATERIALS AND METHODS: RNA-sequencing and real-time polymerase chain reaction (RT-PCR) were applied to identify specifically expressed long noncoding RNAs (lncRNAs) in glomerular tissues of rats from the control group, adriamycin-induced group, and Qi Teng Xiao Zhuo granules group (n = 3). Differentially expressed lncRNAs and mRNAs (messengerRNAs) were screened out among the 3 groups. Gene ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways for mRNAs. LncRNA-mRNA co-expression network was constructed to analyse for the genes. The protein-protein interaction (PPI) network was visualized. RESULTS: A total of 473 significantly up and down-regulated lncRNAs, 753 up and down-regulated mRNAs were identified. Additionally, it is worth noting that TOP2a (topoisomerase (DNA) II alpha), with the highest connectivity degree in PPI network, was enriched in variouskinds of pathways. Coding-non-coding gene co-expression networks (CNC network) were drawn based on the correlation analysis between lncRNAs and mRNAs. Ten lncRNAs, NONRATT009275.2, NONRATT025409.2, NONRATT025419.2, MSTRG.7681.1, ENSRNOT00000084373, NONRATT000512.2, NONRATT006734.2, ENSRNOT00000084386, NONRATT021738.2, ENSRNOT00000084080, were selected to analyse the relationship between LncRNAs and Qi Teng Xiao Zhuo granules via the CNC network (Coding-non-coding gene co-expression networks) and GO analysis. Real-time PCR results confirmed that the six lncRNAs were specifically expressed in the Qi Teng Xiao Zhuo granules rats. CONCLUSIONS: The ten lncRNAs might play important roles in the Qi Teng Xiao Zhuo granules treatment of CGN. Key genes, such as Ptprc (protein tyrosine phosphatase, receptor type, C), TOP2a, Fos (FBJ osteosarcoma oncogene), Myc (myelocytomatosis oncogene), etc, may be crucial biomarkers for Qi Teng Xiao Zhuo granules.


Asunto(s)
Biomarcadores/análisis , Medicamentos Herbarios Chinos/farmacología , Perfilación de la Expresión Génica , Regulación de la Expresión Génica/efectos de los fármacos , Glomerulonefritis/genética , ARN Largo no Codificante/genética , Animales , Enfermedad Crónica , Glomerulonefritis/tratamiento farmacológico , Masculino , Mapas de Interacción de Proteínas , ARN Largo no Codificante/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Ratas , Ratas Sprague-Dawley
12.
Gene ; 726: 144168, 2020 Feb 05.
Artículo en Inglés | MEDLINE | ID: mdl-31759986

RESUMEN

Methods based around statistics and linear algebra have been increasingly used in attempts to address emerging questions in microarray literature. Microarray technology is a long-used tool in the global analysis of gene expression, allowing for the simultaneous investigation of hundreds or thousands of genes in a sample. It is characterized by a low sample size and a large feature number created a non-square matrix, and by the incomplete rank, that can generate countless more solution in classifiers. To avoid the problem of the 'curse of dimensionality' many authors have performed feature selection or reduced the size of data matrix. In this work, we introduce a new logistic regression-based model to classify breast cancer tumor samples based on microarray expression data, including all features of gene expression and without reducing the microarray data matrix. If the user still deems it necessary to perform feature reduction, it can be done after the application of the methodology, still maintaining a good classification. This methodology allowed the correct classification of breast cancer sample data sets from Gene Expression Omnibus (GEO) data series GSE65194, GSE20711, and GSE25055, which contain the microarray data of said breast cancer samples. Classification had a minimum performance of 80% (sensitivity and specificity), and explored all possible data combinations, including breast cancer subtypes. This methodology highlighted genes not yet studied in breast cancer, some of which have been observed in Gene Regulatory Networks (GRNs). In this work we examine the patterns and features of a GRN composed of transcription factors (TFs) in MCF-7 breast cancer cell lines, providing valuable information regarding breast cancer. In particular, some genes whose αi ∗ associated parameter values revealed extreme positive and negative values, and, as such, can be identified as breast cancer prediction genes. We indicate that the PKN2, MKL1, MED23, CUL5 and GLI genes demonstrate a tumor suppressor profile, and that the MTR, ITGA2B, TELO2, MRPL9, MTTL1, WIPI1, KLHL20, PI4KB, FOLR1 and SHC1 genes demonstrate an oncogenic profile. We propose that these may serve as potential breast cancer prediction genes, and should be prioritized for further clinical studies on breast cancer. This new model allows for the assignment of values to the αi ∗ parameters associated with gene expression. It was noted that some αi ∗ parameters are associated with genes previously described as breast cancer biomarkers, as well as other genes not yet studied in relation to this disease.


Asunto(s)
Neoplasias de la Mama/genética , Regulación Neoplásica de la Expresión Génica/genética , Redes Reguladoras de Genes/genética , Biomarcadores de Tumor/genética , Línea Celular Tumoral , Progresión de la Enfermedad , Femenino , Perfilación de la Expresión Génica/métodos , Humanos , Modelos Logísticos , Células MCF-7 , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Factores de Transcripción/genética
13.
Mol Genet Genomics ; 295(1): 233-249, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31673754

RESUMEN

In Chinese cabbage, hybrid seed production is performed using male sterility lines, an important approach to heterosis utilization. In this study, a stably inherited male sterile mutant msm was obtained from the 'FT'-doubled haploid line of Chinese cabbage using isolated microspore culture combined with 60Co γ-ray mutagenesis. The genetic backgrounds of 'FT' and msm were highly consistent; however, compared with wild-type 'FT', msm exhibited completely degenerated stamens and no pollen phenotype. Other characters showed no significant differences. Cytological observations revealed that stamen abortion in msm begins during the tetrad period and that tapetum cells were abnormally expanded and highly vacuolated, leading to microspore abortion. Genetic analysis indicated that the msm mutant phenotype is controlled by a single recessive nuclear gene. Comparative transcriptome analysis of 'FT' and msm flower buds using RNA-Seq technology revealed 1653 differentially expressed genes, among which, a large number associated with male sterility were detected, including 64 pollen development- and pollen tube growth-related genes, 94 pollen wall development-related genes, 11 phytohormone-related genes, and 16 transcription factor-related genes. An overwhelming majority of these genes were down-regulated in msm compared with 'FT'. Furthermore, KEGG pathway analysis indicated that a variety of carbohydrate metabolic and lipid metabolic pathways were significantly enriched, which may be related to pollen abortion. The expression patterns of 24 male sterility-related genes were analyzed using qRT-PCR. In addition, 24,476 single-nucleotide polymorphisms and 413,073 insertion-deletion events were specifically detected in msm. These results will facilitate elucidation of the regulatory mechanisms underlying male sterility in Chinese cabbage.


Asunto(s)
Brassica/genética , Genes de Plantas/genética , Infertilidad Vegetal/genética , Flores/genética , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica de las Plantas/genética , Genes Recesivos/genética , Reguladores del Crecimiento de las Plantas/genética , Proteínas de Plantas/genética , Polen/genética , Transcriptoma/genética , Secuenciación del Exoma Completo/métodos
14.
Fitoterapia ; 140: 104412, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31698060

RESUMEN

Aconitum carmichaelii has been used in traditional Chinese medicine for treating various diseases for several thousand years. Based on the biosynthetic pathway of some alkaloids such as C19-diterpenoid alkaloids and obvious differences in alkaloid content between leaves of two A. carmichaelii varieties has been reported, we performed leaves transcriptome analysis of two A. carmichaelii varieties. Besides we characterized the biosynthetic pathway of salsolinol. A total of 56 million raw reads (8.28 G) and 55 million clean reads (8.24 G) were obtained from two varieties (Z175 and R184) leaves transcriptome, respectively, and 176,793 unigenes were annotated. 281 and 843 unigenes are involved in the salsolinol biosynthetic pathway and the formation of C19-diterpenoid alkaloids respectively. And including 34 and 24 unigenes are the differentially expressed genes (DEGs) in the biosynthesis pathway for C19-diterpenoid alkaloids and salsolinol between Z175 and R184 respectively, which were target genes to explore differences in C19-diterpenoid alkaloid and salsolinol biosynthesis in Z175 and R184. Thus genes involved in alkaloid biosynthesis and accumulation differ between varieties leaves. The mechanisms underlying the differences and their relevance require further exploration. The results expand our knowledge of alkaloids biosynthesis in A. carmichaelii leaves, and provide a theoretical basis for analysis differences in alkaloids biosynthesis patterns in different varieties.


Asunto(s)
Aconitum/química , Vías Biosintéticas , Isoquinolinas/química , Transcriptoma , Alcaloides/biosíntesis , China , Diterpenos/química , Perfilación de la Expresión Génica , Fitoquímicos/aislamiento & purificación , Fitoquímicos/farmacología , Hojas de la Planta/química , Plantas Medicinales/química
15.
Arch Virol ; 165(1): 127-135, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31741097

RESUMEN

In clinical virome research, whole-genome/transcriptome amplification is required when starting material is limited. An improved method, named "template-dependent multiple displacement amplification" (tdMDA), has recently been developed in our lab (Wang et al. in BioTechniques 63:21-25. https://doi.org/10.2144/000114566, 2017). In combination with Illumina sequencing and bioinformatics pipelines, its application in virome sequencing was explored using a serum sample from a patient with chronic hepatitis C virus (HCV) infection. In comparison to an amplification-free procedure, virome sequencing via tdMDA showed a 9.47-fold enrichment for HCV-mapped reads and, accordingly, an increase in HCV genome coverage from 28.5% to 70.1%. Eight serum samples from acute patients liver failure (ALF) with or without known etiology were then used for virome sequencing with an average depth at 94,913x. Both similarity-based (mapping, NCBI BLASTn, BLASTp, and profile hidden Markov model analysis) and similarity-independent methods (machine-learning algorithms) identified viruses from multiple families, including Herpesviridae, Picornaviridae, Myoviridae, and Anelloviridae. However, their commensal nature and cross-detection ruled out an etiological interpretation. Together with a lack of detection of novel viruses in a comprehensive analysis at a resolution of single reads, these data indicate that viral agents might be rare in ALF cases with indeterminate etiology.


Asunto(s)
Biología Computacional/métodos , Hepatitis C Crónica/diagnóstico , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Fallo Hepático Agudo/virología , Suero/virología , Anelloviridae/aislamiento & purificación , Anelloviridae/fisiología , Perfilación de la Expresión Génica/métodos , Hepacivirus/genética , Hepacivirus/aislamiento & purificación , Hepatitis C Crónica/sangre , Herpesviridae/aislamiento & purificación , Herpesviridae/fisiología , Humanos , Fallo Hepático Agudo/sangre , Myoviridae/aislamiento & purificación , Myoviridae/fisiología , Picornaviridae/aislamiento & purificación , Picornaviridae/fisiología , Especificidad de la Especie , Simbiosis , Secuenciación Completa del Genoma/métodos
16.
Arch Insect Biochem Physiol ; 103(2): e21629, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31599031

RESUMEN

Parasitoids serve as effective biocontrol agents for agricultural pests. However, they face constant challenges from host immune defense and numerous pathogens and must develop potent immune defense against these threats. Despite the recent advances in innate immunity, little is known about the immunological mechanisms of parasitoids. Here, we identified and characterized potential immune-related genes of the endoparasitoid, Pteromalus puparum, which act in regulating populations of some members of the Pieridae. We identified 216 immune-related genes based on interrogating the P. puparum genome and transcriptome databases. We categorized the cognate gene products into recognition molecules, signal moieties and effector proteins operating in four pathways, Toll, IMD, JAK/STAT, and JNK. Comparative analyses of immune-related genes from seven insect species indicate that recognition molecules and effector proteins are more expanded and diversified than signaling genes in these signal pathways. There are common 1:1 orthologs between the endoparasitoid P. puparum and its relative, the ectoparasitoid Nasonia vitripennis. The developmental expression profiles of immune genes randomly selected from the transcriptome analysis were verified by a quantitative polymerase chain reaction. Our work provides comprehensive analyses of P. puparum immune genes, some of which may be exploited in advancing parasitoid-based biocontrol technologies.


Asunto(s)
Proteínas Portadoras/genética , Inmunidad Innata/genética , Proteínas de Insectos/genética , Transducción de Señal/inmunología , Avispas/genética , Secuencia de Aminoácidos , Animales , Proteínas Portadoras/química , Proteínas Portadoras/metabolismo , Embrión no Mamífero/química , Embrión no Mamífero/metabolismo , Femenino , Perfilación de la Expresión Génica , Proteínas de Insectos/química , Proteínas de Insectos/metabolismo , Larva/genética , Larva/metabolismo , Masculino , Filogenia , Pupa/genética , Pupa/metabolismo , Alineación de Secuencia , Avispas/crecimiento & desarrollo , Avispas/metabolismo , Avispas/fisiología
17.
Arch Insect Biochem Physiol ; 103(2): e21628, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31599036

RESUMEN

The multifunctional insect cuticle serves as the exoskeleton, determines body shape, restricts water loss, provides attachment sites for muscles and internal organs and is a formidable barrier to invaders. It is morphologically divided into three layers, including envelope, epicuticle, and procuticle and is composed of chitin and cuticular proteins (CPs). Annotation of CPs and their cognate genes may help understand the structure and functions of insect cuticles. In this paper, we interrogated the genome of Pteromalus puparum, an endoparasitoid wasp that parasitizes Pieris rapae and Papilio xuthus pupae, and identified 82 genes encoding CPs belonging to six CP families, including 62 in the CPR family, 8 in CPAP3, 5 in CPF/CPFL, 2 low complexity proteins, 2 in TWDL, and 3 in Apidermin. We used six RNA-seq libraries to determine CP gene expression profiles through development and compared the cuticle hydrophobicity between the P. puparum and the ectoparasitoid Nasonia vitripennis based on GRAVY values of CPR sequences. In the Nasonia-Pteromalus comparison, we found in both N. vitripennis and P. puparum, the peak of their CPR hydrophobicity displayed at their pupal stage, whereas their adult stage showed the lowest level. Except at the adult stage, the CPR hydrophobicity in N. vitripennis is always higher than P. puparum. Finally, we identified three novel Apidermin genes, a family found solely in Hymenoptera and revealed a new sequence feature of this family. This new information contributes to a broader understanding of insect CPs generally.


Asunto(s)
Proteínas de Insectos/genética , Avispas/genética , Secuencia de Aminoácidos , Animales , Embrión no Mamífero/química , Embrión no Mamífero/metabolismo , Femenino , Perfilación de la Expresión Génica , Proteínas de Insectos/química , Proteínas de Insectos/metabolismo , Larva/genética , Larva/metabolismo , Masculino , Filogenia , Pupa/genética , Pupa/metabolismo , Transcriptoma , Avispas/crecimiento & desarrollo , Avispas/metabolismo
18.
Arch Virol ; 165(1): 11-20, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31620899

RESUMEN

Southern tomato virus (STV) is often found infecting healthy tomato plants (Solanum lycopersicum). In this study, we compared STV-free and STV-infected plants of cultivar M82 to determine the effect of STV infection on the host plant. STV-free plants exhibited a short and bushy phenotype, whereas STV-infected plants were taller. STV-infected plants produced more fruit than STV-free plants, and the germination rate of seeds from STV-infected plants was higher than that of seeds from STV-free plants. This phenotypic difference was also observed in progeny plants (siblings) derived from a single STV-infected plant in which the transmission rate of STV to progeny plants via the seeds was approximately 86%. These results suggest that the interaction between STV and host plants is mutualistic. Transcriptome analysis revealed that STV infection affects gene expression in the host plant and results in downregulation of genes involved in ethylene biosynthesis and signaling. STV-infected tomato plants might thus be artificially selected due to their superior traits as a crop.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Lycopersicon esculentum/crecimiento & desarrollo , Proteínas de Plantas/genética , Virus de Plantas/fisiología , Infecciones Asintomáticas , Etilenos/biosíntesis , Frutas/crecimiento & desarrollo , Frutas/virología , Regulación de la Expresión Génica de las Plantas , Germinación , Lycopersicon esculentum/genética , Lycopersicon esculentum/virología , Fenotipo , Transducción de Señal , Simbiosis
19.
Arch Insect Biochem Physiol ; 103(2): e21632, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31621105

RESUMEN

Biogenic amines (BAs), such as octopamine, tyramine, dopamine, serotonin, and acetylcholine regulate various behaviors and physiological functions in insects. Here, we identified seven genes encoding BA biosynthetic enzymes and 16 genes encoding BA G protein-coupled receptors in the genome of the endoparasitoid wasp, Pteromalus puparum. We compared the genes with their orthologs in its host Pieris rapae and the related ectoparasitic wasp Nasonia vitripennis. All the genes show high (>90%) identity to orthologs in N. vitripennis. P. puparum and N. vitripennis have the smallest number of BA receptor genes among the insect species we investigated. We then analyzed the expression profiles of the genes, finding those acting in BA biosynthesis were highly expressed in adults and larvae and those encoding BA receptors are highly expressed in adults than immatures. Octα1R and 5-HT7 genes were highly expressed in salivary glands, and a high messenger RNA level of 5-HT1A was found in venom apparatuses. We infer that BA signaling is a fundamental component of the organismal organization, homeostasis and operation in parasitoids, some of the smallest insects.


Asunto(s)
Aminas Biogénicas/metabolismo , Mariposas Diurnas/genética , Proteínas de Insectos/genética , Avispas/genética , Secuencia de Aminoácidos , Animales , Mariposas Diurnas/química , Mariposas Diurnas/metabolismo , Mariposas Diurnas/parasitología , Embrión no Mamífero/química , Embrión no Mamífero/metabolismo , Femenino , Perfilación de la Expresión Génica , Interacciones Huésped-Parásitos , Proteínas de Insectos/química , Proteínas de Insectos/metabolismo , Larva/genética , Larva/metabolismo , Masculino , Filogenia , Pupa/genética , Pupa/metabolismo , Alineación de Secuencia , Avispas/enzimología , Avispas/crecimiento & desarrollo , Avispas/metabolismo
20.
Mol Genet Genomics ; 295(1): 107-120, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31506717

RESUMEN

The oriental gall wasp Dryocosmus kuriphilus represents a limiting pest for the European Chestnut (Castanea sativa, Fagaceae) as it creates severe yield losses. The European Chestnut is a deciduous tree, having major social, economic and environmental importance in Southern Europe, covering an area of 2.53 million hectares, including 75,000 ha devoted to fruit production. Cultivars show different susceptibility and very few are resistant to gall wasp. To deeply investigate the plant response and understand which factors can lead the plant to develop or not the gall, the study of transcriptome is basic (fundamental). To date, little transcriptomic information are available for C. sativa species. Hence, we present a de novo assembly of the chestnut transcriptome of the resistant Euro-Japanese hybrid 'Bouche de Bétizac' (BB) and the susceptible cultivar 'Madonna' (M), collecting RNA from buds at different stages of budburst. The two transcriptomes were assembled into 34,081 (BB) and 30,605 (M) unigenes, respectively. The former was used as a reference sequence for further characterization analyses, highlighting the presence of 1444 putative resistance gene analogs (RGAs) and about 1135 unigenes, as putative MiRNA targets. A global quantitative transcriptome profiling comparing the resistant and the susceptible cultivars, in the presence or not of the gall wasp, revealed some GO enrichments as "response to stimulus" (GO:0050896), and "developmental processes" (e.g., post-embryonic development, GO:0009791). Many up-regulated genes appeared to be transcription factors (e.g., RAV1, AP2/ERF, WRKY33) or protein regulators (e.g., RAPTOR1B) and storage proteins (e.g., LEA D29) involved in "post-embryonic development". Our analysis was able to provide a large amount of information, including 7k simple sequence repeat (SSR) and 335k single-nucleotide polymorphism (SNP)/INDEL markers, and generated the first reference unigene catalog for the European Chestnut. The transcriptome data for C. sativa will contribute to understand the genetic basis of the resistance to gall wasp and will provide useful information for next molecular genetic studies of this species and its relatives.


Asunto(s)
Fagaceae/genética , Transcriptoma/genética , Avispas/patogenicidad , Animales , Europa (Continente) , Fagaceae/parasitología , Perfilación de la Expresión Génica/métodos , Repeticiones de Microsatélite/genética , Anotación de Secuencia Molecular/métodos , Enfermedades de las Plantas/parasitología , Polimorfismo de Nucleótido Simple/genética , Factores de Transcripción/genética , Árboles/genética , Árboles/parasitología , Regulación hacia Arriba/genética
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