Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 27
Filter
1.
Article in English | WPRIM | ID: wpr-922572

ABSTRACT

OBJECTIVE@#To explore the mechanisms of Dangua Recipe (DGR) in improving glycolipid metabolism based on transcriptomics.@*METHODS@#Sprague-Dawley rats with normal glucose level were divided into 3 groups according to a random number table, including a conventional diet group (Group A), a DGR group (Group B, high-calorie diet + 20.5 g DGR), and a high-calorie fodder model group (Group C). After 12 weeks of intervention, the liver tissue of rats was taken. Gene sequence and transcriptional analysis were performed to identify the key genes related to glycolipid metabolism reflecting DGR efficacy, and then gene or protein validation of liver tissue were performed. Nicotinamide phosphoribosyl transferase (Nampt) and phosphoenolpyruvate carboxykinase (PEPCK) proteins in liver tissues were detected by enzyme linked immunosorbent assay, fatty acid synthase (FASN) protein was detected by Western blot, and fatty acid binding protein 5 (FABP5)-mRNA was detected by quantitative real-time polymerase chain reaction. Furthermore, the functional verification was performed on the diabetic model rats by Nampt blocker (GEN-617) injected in vivo. Hemoglobin A@*RESULTS@#Totally, 257 differential-dominant genes of Group A vs. Group C and 392 differential-dominant genes of Group B vs. Group C were found. Moreover, 11 Gene Ontology molecular function terms and 7 Kyoto Encyclopedia of Genes and Genomes enrichment pathways owned by both Group A vs. Group C and Group C vs. Group B were confirmed. The liver tissue target validation showed that Nampt, FASN, PEPCK protein and FABP5-mRNA had the same changes consistent with transcriptome. The in vivo functional tests showed that GEN-617 increased body weight, HbA@*CONCLUSION@#Nampt activation was one of the mechanisms about DGR regulating glycolipid metabolism.


Subject(s)
Animals , Diabetes Mellitus, Experimental , Drugs, Chinese Herbal , Glycolipids , Liver , Metabolic Diseases , Rats , Rats, Sprague-Dawley , Transcriptome/genetics
2.
Article in Chinese | WPRIM | ID: wpr-879008

ABSTRACT

In order to enrich the transcriptome data of Fagopyrum dibotrys plants, analyze the genes encoding key enzyme involved in flavonoid biosynthesis pathway, and mine their functional genes, in this study, we performed RNA sequencing analysis for the rhizomes, roots, flowers, leaves and stems of F. dibotrys on the BGISEQ-500 sequencing platform. After de novo assembly of transcripts, a total of 205 619 unigenes were generated and 132 372 unigenes were obtained and annotated into seven public databases, of which, 81 327 unigenes were mapped to the GO database and most of the unigenes were annotated in cellular process, biological regulation, binding and catalytic activity. Besides, 86 922 unigenes were enriched in 136 pathways using KEGG database' and we identified 82 unigenes that encodes key enzymes involved in flavonoid biosynthesis. Comparing rhizome with root, flower, leaf or stem in F. dibotrys, 27 962 co-expressed differentially expressed genes(DEGs) were obtained. Among them, 23 515 DEGs of rhizome tissue-specific were enriched into 132 pathways and 13 unigenes were significantly enriched in biosynthesis of flavone and flavonol. In addition, we also identified 3 427 unigenes encoding 60 transcription factor(TFs) families as well as four unigenes encoding bHLH TFs were enriched in flavonoid biosynthesis. Our results greatly enriched the transcriptome database of plants, provided a reference for the analysis of key enzymes involved in flavonoid biosynthesis in plants, and will facilitate the study of the functions and regulatory mechanisms of key enzymes involved in flavonoid biosynthesis in F. dibotrys at the genetic level.


Subject(s)
Biosynthetic Pathways/genetics , Fagopyrum , Flavonoids , Flowers , Gene Expression Profiling , Gene Expression Regulation, Plant , Humans , Transcriptome/genetics
3.
Chinese Journal of Biotechnology ; (12): 1260-1276, 2021.
Article in Chinese | WPRIM | ID: wpr-878629

ABSTRACT

The unicellular green alga Haematococcus pluvialis is the best source of natural astaxanthin (AST) in the world due to its high content under stress conditions. Although high light (HL) can effectively induce AST biosynthesis, the specific mechanisms of light signal perception and transduction are unclear. In the current study, we used transcriptomic data of normal (N), high white light (W), and high blue light (B) to study the mechanisms of light inducing AST accumulation from the point of photoreceptors. The original data of 4.0 G, 3.8 G, and 3.6 G for N, W, and B were obtained, respectively, by the Illumina Hi-seq 2000 sequencing technology. Totally, 51 954 unigenes (at least 200 bp in length) were generated, of which, 20 537 unigenes were annotated into at least one database (NR, NT, KO, SwissProt, Pfam, GO, or KOG). There were 1 255 DEGs in the W vs N, 1 494 DEGs in the B vs N, and 1 008 DEGs in the both W vs N and B vs N. KEGG enrichment analysis revealed that photosynthesis, oxidative phosphorylation, carotenoid biosynthesis, fatty acids biosynthesis, DNA replication, nitrogen metabolism, and carbon metabolism were the significantly enriched pathways. Moreover, a large number of genes encoding photoreceptors and predicted interacting proteins were predicted in Haematococcus transcriptome data. These genes showed significant differences at transcriptional expression levels. In addition, 15 related DEGs were selected and tested by qRT-PCR and the results were significantly correlated with the transcriptome data. The above results indicate that the signal transduction pathway of "light signal - photoreceptors - interaction proteins - (interaction proteins - transcription factor/transcriptional regulator) - gene expression - AST accumulation" might play important roles in the regulation process, and provide reference for further understanding the transcriptional regulation mechanisms of AST accumulation under HL stress.


Subject(s)
Chlorophyta/genetics , Gene Expression Profiling , Signal Transduction/genetics , Transcriptome/genetics , Xanthophylls
4.
Chinese Journal of Biotechnology ; (12): 253-265, 2021.
Article in Chinese | WPRIM | ID: wpr-878559

ABSTRACT

Based on observing the cytological characteristics of the flower buds of the functional male sterile line (S13) and the fertile line (F142) in eggplant, it was found that the disintegration period of the annular cell clusters in S13 anther was 2 days later than that of F142, and the cells of stomiun tissue and tapetum in F142 disintegrated on the blooming day, while it did not happen in S13. The comparative transcriptomic analysis showed that there were 1 436 differential expression genes (DEGs) (651 up-regulated and 785 down-regulated) in anthers of F142 and S13 at 8, 5 days before flowering and flowering day. The significance analysis of GO enrichment indicated that there were more unigene clusters involved in single cell biological process, metabolism process and cell process, and more catalytic activity and binding function were involved in molecular functions. Through KEGG annotation we found that the common DEGs were mainly enriched in the biosynthesis of secondary metabolites, metabolic pathway, protein processing in endoplasmic reticulum, biosynthesis of amino acids, carbon metabolism and plant hormone signal transduction. The fifteen genes co-expression modules were identified from 16 465 selected genes by weighted gene co-expression network analysis (WGCNA), three of which (Plum2, Royalblue and Bisque4 modules) were highly related to S13 during flower development. KEGG enrichment showed that the specific modules could be enriched in phenylpropanoid biosynthesis, photosynthesis, porphyrin and chlorophyll metabolism, α-linolenic acid metabolism, polysaccharide biosynthesis and metabolism, fatty acid degradation and the mutual transformation of pentose and glucuronic acid. These genes might play important roles during flower development of S13. It provided a reference for further study on the mechanism of anther dehiscence in eggplant.


Subject(s)
Flowers/genetics , Gene Expression Profiling , Gene Expression Regulation, Plant , Humans , Infertility, Male , Male , Metabolic Networks and Pathways/genetics , Solanum melongena/genetics , Transcriptome/genetics
5.
Mem. Inst. Oswaldo Cruz ; 116: e200547, 2021. tab, graf
Article in English | LILACS | ID: biblio-1250365

ABSTRACT

BACKGROUND Forty percent of the world's population live in areas where they are at risk from dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. Dengue viruses are transmitted primarily by the mosquito Aedes aegypti. In Cali, Colombia, approximately 30% of field collected Ae. aegypti are naturally refractory to all four dengue serotypes. OBJECTIVES Use RNA-sequencing to identify those genes that determine refractoriness in feral mosquitoes to dengue. This information can be used in gene editing strategies to reduce dengue transmission. METHODS We employed a full factorial design, analyzing differential gene expression across time (24, 36 and 48 h post bloodmeal), feeding treatment (blood or blood + dengue-2) and strain (susceptible or refractory). Sequences were aligned to the reference Ae. aegypti genome for identification, assembled to visualize transcript structure, and analyzed for dynamic gene expression changes. A variety of clustering techniques was used to identify the differentially expressed genes. FINDINGS We identified a subset of genes that likely assist dengue entry and replication in susceptible mosquitoes and contribute to vector competence. MAIN CONCLUSIONS The differential expression of specific genes by refractory and susceptible mosquitoes could determine the phenotype, and may be used to in gene editing strategies to reduce dengue transmission.


Subject(s)
Animals , Aedes , Dengue , Dengue Virus , RNA , Colombia , Transcriptome/genetics , Mosquito Vectors/genetics
6.
Electron. j. biotechnol ; 48: 72-77, nov. 2020. tab, ilus
Article in English | LILACS | ID: biblio-1254810

ABSTRACT

BACKGROUND: To identify differentially expressed genes (DEGs) between muscle and adipose in cattle, we analyzed the data from the RNA sequencing of three Angus×Qinchuan crossbred cattle. RESULTS: Searched the Gene Expression Omnibus (GEO) for a microarray dataset of Yan yellow cattle, GSE49992. After the DEGs were identified, we used STRING and Cytoscape to construct a protein­protein interaction (PPI) network, subsequently analyzing the major modules of key genes. In total, 340 DEGs were discovered, including 21 hub genes, which were mainly enriched in muscle contraction, skeletal muscle contraction, troponin complex, lipid particle, Z disc, tropomyosin binding, and actin filament binding. CONCLUSIONS: In summary, these genes can be regarded as candidate biomarkers for the regulation of muscle and adipose development.


Subject(s)
Animals , Cattle , Adipose Tissue/growth & development , Muscle Development/genetics , Transcriptome/genetics , Gene Expression , Gene Expression Regulation, Developmental , Computational Biology , RNA-Seq
7.
Mem. Inst. Oswaldo Cruz ; 115: e190378, 2020. tab, graf
Article in English | SES-SP, LILACS, SES-SP | ID: biblio-1135284

ABSTRACT

BACKGROUND Key genes control the infectivity of the Schistosoma haematobium causing schistosomiasis. A method for understanding the regulation of these genes might help in developing new disease strategies to control schistosomiasis, such as the silencing mediated by microRNAs (miRNAs). The miRNAs have been studied in schistosome species and they play important roles in the post-transcriptional regulation of genes, and in parasite-host interactions. However, genome-wide identification and characterisation of novel miRNAs and their pathway genes and their gene expression have not been explored deeply in the genome and transcriptome of S. haematobium. OBJECTIVES Identify and characterise mature and precursor miRNAs and their pathway genes in the S. haematobium genome. METHODS Computational prediction and characterisation of miRNAs and genes involved in miRNA pathway from S. haematobium genome on SchistoDB. Conserved domain analysis was performed using PFAM and CDD databases. A robust algorithm was applied to identify mature miRNAs and their precursors. The characterisation of the precursor miRNAs was performed using RNAfold, RNAalifold and Perl scripts. FINDINGS We identified and characterised 14 putative proteins involved in miRNA pathway including ARGONAUTE and DICER in S. haematobium. Besides that, 149 mature miRNAs and 131 precursor miRNAs were identified in the genome including novel miRNAs. MAIN CONCLUSIONS miRNA pathway occurs in the S. haematobium, including endogenous miRNAs and miRNA pathway components, suggesting a role of this type of non-coding RNAs in gene regulation in the parasite. The results found in this work will open up a new avenue for studying miRNAs in the S. haematobium biology in helping to understand the mechanism of gene silencing in the human parasite Schistosome.


Subject(s)
Humans , Animals , Schistosoma haematobium/genetics , Schistosomiasis/parasitology , Gene Expression Regulation/genetics , Computational Biology/methods , MicroRNAs/genetics , Sequence Analysis, RNA , Transcriptome/genetics
8.
Mem. Inst. Oswaldo Cruz ; 115: e190413, 2020. tab, graf
Article in English | LILACS | ID: biblio-1101274

ABSTRACT

BACKGROUND The leishmaniases are complex neglected diseases caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the main etiological agent of cutaneous leishmaniasis in the New World. In recent studies, genomic changes such as chromosome and gene copy number variations (CNVs), as well as transcriptomic changes have been highlighted as mechanisms used by Leishmania species to adapt to stress situations. OBJECTIVES The aim of this study was to determine the effect of short-term minor temperature shifts in the genomic and transcriptomic responses of L. braziliensis promastigotes in vitro. METHODS Growth curves, genome and transcriptome sequencing of L. braziliensis promastigotes were conducted from cultures exposed to three different temperatures (24ºC, 28ºC and 30ºC) compared with the control temperature (26ºC). FINDINGS Our results showed a decrease in L. braziliensis proliferation at 30ºC, with around 3% of the genes showing CNVs at each temperature, and transcriptomic changes in genes encoding amastin surface-like proteins, heat shock proteins and transport proteins, which may indicate a direct response to temperature stress. MAIN CONCLUSIONS This study provides evidence that L. braziliensis promastigotes exhibit a decrease in cell density, and noticeable changes in the transcriptomic profiles. However, there were not perceptible changes at chromosome CNVs and only ~3% of the genes changed their copies in each treatment.


Subject(s)
Animals , Temperature , Leishmania braziliensis/genetics , Adaptation, Physiological/genetics , DNA Copy Number Variations/genetics , Transcriptome/genetics , Adaptation, Physiological/physiology , Gene Expression Profiling , Genetic Profile
9.
Braz. j. biol ; 79(2): 180-190, Apr.-June 2019. tab, graf
Article in English | LILACS | ID: biblio-989438

ABSTRACT

Abstract Synthetic polyploids are key breeding materials for watermelon. Compared with diploid watermelon, the tetraploid watermelon often exhibit wide phenotypic differences and differential gene expression. Digital gene expression (DGE) profile technique was performed in this study to present gene expression patterns in an autotetraploid and its progenitor diploid watermelon, and deferentially expressed genes (DEGs) related to the abiotic and biotic stress were also addressed. Altogether, 4,985 DEGs were obtained in the autotetraploid against its progenitor diploid, and 66.02% DEGs is up-regulated. GO analysis shows that these DEGs mainly distributed in 'metabolic process', 'cell' and 'catalytic activity'. KEGG analysis revealed that these DEGs mainly cover 'metabolic pathways', 'secondary metabolites' and 'ribosome'. Moreover, 134 tolerance related DEGs were identified which cover osmotic adjustment substance, protective enzymes/protein, signaling proteins and pathogenesis-related proteins. This study present the differential expression of stress related genes and global gene expression patterns at background level in autotetraploid watermelons. These new evidences could supplement the molecular theoretical basis for the better resistance after the genome doubling in the gourd family.


Resumo Poliploides sintéticos são materias fundamentais para melhoramento genético da melancia. Comparativamente ao seu homólogo diploide, a melancia tetraploide apresenta amplas diferenças genotípica e fenotípica e diferença de expressão gênica. A expressão gênica digital ou DGE (digital gene expression) foi utilizada neste estudo para representar o perfil de expressão gênica da melancia autotetraploide e seu progenitor diploide e a expressão diferencial de genes relacionados ao estresse biótico e abiótico. Os resultados mostraram que 4.985 DEGs foram observados no organismo autotetraploide, sendo que, deste total, 66.02%foram supra-regulados. A análise de ontologia gênica (GO) mostrou que estes DEGs estão relacionados principalmente com processos metabólicas, célula e atividade catalítica, abrangendo de acordo com a análise de genes e genoma (KEGG) rotas metabólicas, metabolismo secundário e ribossomos. Além disso, 134 genes de defesa foram identificados, abrangendo substâncias de ajuste osmótico, enzimas/proteínas de proteção, proteínas sinalizadoras e proteínas relacionadas à patogênese. Este estudo mostrou a expressão diferencial de genes relacionados ao estresse e o perfil global de expressão gênica de melancia autotetraploide, estes resultados podem complementar, a nível molecular, o entendimento do fator resistência após a duplicação do genoma em cucurbitáceas.


Subject(s)
Polyploidy , Genes, Plant/genetics , Gene Expression Regulation, Plant/genetics , Citrullus/genetics , Citrullus/metabolism , Transcriptome/genetics , Gene Expression Profiling , Diploidy
10.
Biol. Res ; 52: 13, 2019. graf
Article in English | LILACS | ID: biblio-1011415

ABSTRACT

BACKGROUND: Ovarian cancer is a significant cancer-related cause of death in women worldwide. The most used chemotherapeutic regimen is based on carboplatin (CBDCA). However, CBDCA resistance is the main obstacle to a better prognosis. An in vitro drug-resistant cell model would help in the understanding of molecular mechanisms underlying this drug-resistance phenomenon. The aim of this study was to characterize cellular and molecular changes of induced CBDCA-resistant ovarian cancer cell line A2780. METHODS: The cell selection strategy used in this study was a dose-per-pulse method using a concentration of 100 µM for 2 h. Once 20 cycles of exposure to the drug were completed, the cell cultures showed a resistant phenotype. Then, the ovarian cancer cell line A2780 was grown with 100 µM of CBDCA (CBDCA-resistant cells) or without CBDCA (parental cells). After, a drug sensitivity assay, morphological analyses, cell death assays and a RNA-seq analysis were performed in CBDCA-resistant A2780 cells. RESULTS: Microscopy on both parental and CBDCA-resistant A2780 cells showed similar characteristics in morphology and F-actin distribution within cells. In cell-death assays, parental A2780 cells showed a significant increase in phosphatidylserine translocation and caspase-3/7 cleavage compared to CBDCA-resistant A2780 cells (P < 0.05 and P < 0.005, respectively). Cell viability in parental A2780 cells was significantly decreased compared to CBDCA-resistant A2780 cells (P < 0.0005). The RNA-seq analysis showed 156 differentially expressed genes (DEGs) associated mainly to molecular functions. CONCLUSION: CBDCA-resistant A2780 ovarian cancer cells is a reliable model of CBDCA resistance that shows several DEGs involved in molecular functions such as transmembrane activity, protein binding to cell surface receptor and catalytic activity. Also, we found that the Wnt/3-catenin and integrin signaling pathway are the main metabolic pathway dysregulated in CBDCA-resistant A2780 cells.


Subject(s)
Humans , Female , Ovarian Neoplasms/genetics , Gene Expression Regulation, Neoplastic/drug effects , Carboplatin/pharmacology , Drug Resistance, Neoplasm/genetics , Transcriptome/drug effects , Antineoplastic Agents/pharmacology , Ovarian Neoplasms/pathology , Ovarian Neoplasms/drug therapy , Phenotype , Signal Transduction , Cell Death/drug effects , Cell Death/genetics , Sequence Analysis, RNA , Cell Line, Tumor , Transcriptome/genetics
11.
São Paulo; s.n; s.n; 2019. 186 p. tab, graf.
Thesis in Portuguese | LILACS | ID: biblio-1023443

ABSTRACT

A fumaça do cigarro apresenta mais de 8700 substâncias identificadas, as quais já foram relacionadas com o desenvolvimento das mais variadas doenças. Dentre elas, uma substância relevante neste contexto de toxicidade do cigarro é a hidroquinona (HQ), gerada após a biotransformação do benzeno inalado. A HQ apresenta atividades relacionadas com a imunossupressão das respostas imune inata e adaptativa, observados mais no contexto in vitro e parcamente no in vivo; contudo, nenhum estudo ainda trouxe a abordagem do efeito da exposição à HQ sobre a resposta induzida por vacinação. Sendo assim, será que a exposição à fumaça do cigarro ou à HQ influenciaria na resposta de células B e geração de anticorpos induzidas por imunizações com vacinas anti-virais? Observamos que, após a exposição diária com 2500 ppm de HQ (equivalente a um maço de cigarro fumado / dia) por 8 semanas e vacinação com proteína recombinante codificadora do domínio III do Envelope do vírus da Dengue sorotipo 2 (EDIII) mais o adjuvante Alum, houve uma "tendência" para menores títulos de IgG total e IgG1 específicos à EDIII em camundongos C57BL/6. Análises histológicas revelaram um menor número de folículos e redução significativa de suas áreas no baço do grupo HQ em comparação com os não expostos. Para entendermos o efeito da HQ sobre a resposta humoral, realizamos uma análise de dados públicos de transcriptoma obtidas de amostras de sangue de humanos. Curiosamente, observamos que a HQ regula positivamente genes relacionados com a ativação de células B, assim como a migração e quimiotaxia de neutrófilos e outros leucócitos. Como é sabido que existe uma população de neutrófilos (N2) com a capacidade de auxiliar as respostas de células B, hipotetizamos que essas células poderiam disparar um mecanismo imunocompensatório que aumenta os títulos de anticorpos no grupo HQ


The cigarette smoke has more than 8700 harmful substances related to the occurrence of the most varied diseases. Among them, a relevant substance is the hydroquinone (HQ), generated upon the biotransformation of inhaled benzene. In vitro and in vivo analyses have demonstrated that HQ can suppress both innate and adaptive immune responses. However, no study has approached the effect of the HQ exposure on the vaccination-induced response. Thus, would the exposure to the cigarette smoke or HQ influence the B-cell and antibody responses elicited by immunizations with antiviral vaccines? We observed a "tendency" to lower titers of IgG total and IgG1 anti-EDIII in mice daily exposed to 2,500 ppm of HQ for 8 weeks and vaccinated. Histological analyses revealed a smaller number of follicles and a significant reduction in their area in the HQ group in comparison to their counterparts. In order to understand the effect of the HQ on the humoral response, we performed an analysis of public transcriptome data derived from human blood samples. We observed that the HQ up-regulates the expression of genes related to B cell activation as well as the migration and chemotaxis of neutrophils and other leukocytes. Considering that N2 neutrophils have the ability to help the B cell response, we have hypothesized that the HQ exposure may trigger an immunocompensatory effect, increasing the humoral response


Subject(s)
Animals , Male , Mice , Vaccines/pharmacology , Dengue , Hydroquinones/analysis , Enzyme-Linked Immunosorbent Assay/methods , Enzyme-Linked Immunospot Assay/methods , Transcriptome/genetics , Tobacco Products/adverse effects
12.
Braz. j. med. biol. res ; 52(11): e8950, 2019. tab, graf
Article in English | LILACS | ID: biblio-1039256

ABSTRACT

Aortic dissection is characterized by the redirection of blood flow, which flows through an intimal tear into the aortic media. The purpose of this study was to find potential acute type A aortic dissection (AAAD)-related genes and molecular mechanisms by bioinformatics. The gene expression profiles of GSE52093 were obtained from Gene Expression Omnibus (GEO) database, including 7 AAAD samples and 5 normal samples. The differentially expressed genes (DEGs) were detected between AAAD and normal samples. The functional annotation and pathway enrichment analysis were conducted through the Database for Annotation, Visualization and Integration Discovery (DAVID). A protein-protein interaction network was established by the Search Tool for the Retrieval of Interacting Genes (STRING) software. The microRNAs (miRNAs) of these differentially expressed genes were predicted using <microRNA.org> database. Moreover, DEGs were analyzed in the comparative toxicogenomics (CTD) database to screen out the potential therapeutic small molecules. As a result, there were 172 DEGs identified in patients with AAAD. These DEGs were significantly enriched in 6 pathways, including cell cycle, oocyte meiosis, DNA replication, extracellular matrix-receptor interaction, and mineral absorption pathway. Notably, CDC20, CDK1, CHEK1, KIF20A, MCM10, PBK, PTTG1, RACGAP, and TOP2A were crucial genes with a high degree in the protein-protein interaction network. Furthermore, potential miRNAs (miR-301, miR-302 family, and miR-130 family) were identified. In addition, small molecules like azathioprine and zoledronic acid were identified to be potential drugs for AAAD.


Subject(s)
Humans , Computational Biology , Protein Interaction Mapping , Transcriptome/genetics , Aneurysm, Dissecting/genetics , Signal Transduction , Case-Control Studies , Acute Disease , Databases, Genetic
13.
Electron. j. biotechnol ; 32: 19-25, Mar. 2018. graf, ilus
Article in English | LILACS | ID: biblio-1022497

ABSTRACT

Background: Soil salinity can significantly reduce crop production, but the molecular mechanism of salinity tolerance in peanut is poorly understood. A mutant (S1) with higher salinity resistance than its mutagenic parent HY22 (S3) was obtained. Transcriptome sequencing and digital gene expression (DGE) analysis were performed with leaves of S1 and S3 before and after plants were irrigated with 250 mM NaCl. Results: A total of 107,725 comprehensive transcripts were assembled into 67,738 unigenes using TIGR Gene Indices clustering tools (TGICL). All unigenes were searched against the euKaryotic Ortholog Groups (KOG), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and these unigenes were assigned to 26 functional KOG categories, 56 GO terms, 32 KEGG groups, respectively. In total 112 differentially expressed genes (DEGs) between S1 and S3 after salinity stress were screened, among them, 86 were responsive to salinity stress in S1 and/or S3. These 86 DEGs included genes that encoded the following kinds of proteins that are known to be involved in resistance to salinity stress: late embryogenesis abundant proteins (LEAs), major intrinsic proteins (MIPs) or aquaporins, metallothioneins (MTs), lipid transfer protein (LTP), calcineurin B-like protein-interacting protein kinases (CIPKs), 9-cis-epoxycarotenoid dioxygenase (NCED) and oleosins, etc. Of these 86 DEGs, 18 could not be matched with known proteins. Conclusion: The results from this study will be useful for further research on the mechanism of salinity resistance and will provide a useful gene resource for the variety breeding of salinity resistance in peanut.


Subject(s)
Arachis/genetics , Salt-Tolerant Plants/genetics , Salt Tolerance/genetics , Transcriptome/genetics , Soil , Sodium Chloride , Sequence Analysis, RNA/methods , Gene Expression Profiling/methods , Real-Time Polymerase Chain Reaction , Mutation
14.
Biol. Res ; 51: 25, 2018. tab, graf
Article in English | LILACS | ID: biblio-950908

ABSTRACT

PURPOSE: This aim of this study was to investigate the key genes and pathways involved in the response to pain in goat and sheep by transcriptome sequencing. METHODS: Chronic pain was induced with the injection of the complete Freund's adjuvant (CFA) in sheep and goats. The animals were divided into four groups: CFA-treated sheep, control sheep, CFA-treated goat, and control goat groups (n = 3 in each group). The dorsal root ganglions of these animals were isolated and used for the construction of a cDNA library and transcriptome sequencing. Differentially expressed genes (DEGs) were identified in CFA-induced sheep and goats and gene ontology (GO) enrichment analysis was performed. RESULTS: In total, 1748 and 2441 DEGs were identified in CFA-treated goat and sheep, respectively. The DEGs identified in CFA-treated goats, such as C-C motif chemokine ligand 27 (CCL27), glutamate receptor 2 (GRIA2), and sodium voltage-gated channel alpha subunit 3 (SCN3A), were mainly enriched in GO functions associated with N-methyl-D-aspartate (NMDA) receptor, inflammatory response, and immune response. The DEGs identified in CFA-treated sheep, such as gamma-aminobutyric acid (GABA)-related DEGs (gamma-aminobutyric acid type A receptor gamma 3 subunit [GABRG3], GABRB2, and GABRB1), SCN9A, and transient receptor potential cation channel subfamily V member 1 (TRPV1), were mainly enriched in GO functions related to neuroactive ligand-receptor interaction, NMDA receptor, and defense response. CONCLUSIONS: Our data indicate that NMDA receptor, inflammatory response, and immune response as well as key DEGs such as CCL27, GRIA2, and SCN3A may regulate the process of pain response during chronic pain in goats. Neuroactive ligand-receptor interaction and NMDA receptor as well as GABA-related DEGs, SCN9A, and TRPV1 may modulate the process of response to pain in sheep. These DEGs may serve as drug targets for preventing chronic pain.


Subject(s)
Animals , Signal Transduction/genetics , Chronic Pain/genetics , Transcriptome/genetics , Ganglia, Spinal/physiopathology , Goats , Sheep , Signal Transduction/physiology , Gene Library , Adjuvants, Immunologic , Freund's Adjuvant , Pain Threshold/physiology , Gene Expression Profiling , Disease Models, Animal , Chronic Pain/physiopathology , Chronic Pain/chemically induced , Transcriptome/physiology , Gene Ontology
15.
Mem. Inst. Oswaldo Cruz ; 113(5): e170404, 2018. graf
Article in English | LILACS | ID: biblio-894928

ABSTRACT

BACKGROUND Trypanosoma cruzi is an important protozoan parasite and the causative agent of Chagas disease. A critical step in understanding T. cruzi biology is the study of cellular and molecular features exhibited during its growth curve. OBJECTIVES We aimed to acquire a global view of the gene expression profile of T. cruzi during epimastigote growth. METHODS RNA-Seq analysis of total and polysomal/granular RNA fractions was performed along the 10 days T. cruzi epimastigote growth curve in vitro, in addition to cell viability and cell cycle analyses. We also analysed the polysome profile and investigated the presence of granular RNA by FISH and western blotting. FINDINGS We identified 1082 differentially expressed genes (DEGs), of which 220 were modulated in both fractions. According to the modulation pattern, DEGs were grouped into 12 clusters and showed enrichment of important gene ontology (GO) terms. Moreover, we showed that by the sixth day of the growth curve, polysomal content declined greatly and the RNA granules content appeared to increase, suggesting that a portion of mRNAs isolated from the sucrose gradient during late growth stages was associated with RNA granules and not only polyribosomes. Furthermore, we discuss several modulated genes possibly involved in T. cruzi growth, mainly during the stationary phase, such as genes related to cell cycle, pathogenesis, metabolic processes and RNA-binding proteins.


Subject(s)
Humans , Sequence Analysis, RNA , Transcriptome/genetics , Axenic Culture , Life Cycle Stages/genetics
16.
Braz. j. med. biol. res ; 51(8): e7044, 2018. graf
Article in English | LILACS | ID: biblio-951748

ABSTRACT

In this study, we screened differentially expressed genes in a multidrug-resistant isolate strain of Clostridium perfringens by RNA sequencing. We also separated and identified differentially expressed proteins (DEPs) in the isolate strain by two-dimensional electrophoresis (2-DE) and mass spectrometry (MS). The RNA sequencing results showed that, compared with the control strain, 1128 genes were differentially expressed in the isolate strain, and these included 227 up-regulated genes and 901 down-regulated genes. Bioinformatics analysis identified the following genes and gene categories that are potentially involved in multidrug resistance (MDR) in the isolate strain: drug transport, drug response, hydrolase activity, transmembrane transporter, transferase activity, amidase transmembrane transporter, efflux transmembrane transporter, bacterial chemotaxis, ABC transporter, and others. The results of the 2-DE showed that 70 proteins were differentially expressed in the isolate strain, 45 of which were up-regulated and 25 down-regulated. Twenty-seven DEPs were identified by MS and these included the following protein categories: ribosome, antimicrobial peptide resistance, and ABC transporter, all of which may be involved in MDR in the isolate strain of C. perfringens. The results provide reference data for further investigations on the drug resistant molecular mechanisms of C. perfringens.


Subject(s)
Animals , Bacterial Proteins/genetics , Clostridium perfringens/genetics , Sequence Analysis, RNA/methods , Genes, MDR , Drug Resistance, Multiple, Bacterial/genetics , Mass Spectrometry/methods , Bacterial Proteins/metabolism , Electrophoresis, Gel, Two-Dimensional/methods , Gene Expression Regulation, Bacterial/genetics , Genome, Bacterial/genetics , Clostridium perfringens/classification , Clostridium perfringens/drug effects , Clostridium perfringens/metabolism , DNA, Complementary , Proteome/genetics , Transcriptome/genetics , Gene Ontology
17.
Appl. cancer res ; 37: 1-5, 2017. tab, ilus
Article in English | LILACS, Inca | ID: biblio-914894

ABSTRACT

Background: Cutaneous melanoma (CM) is the most aggressive subtype of skin cancer, with increasing incidence over the past several decades. DNA methylation is a key element of several biological processes such as genomic imprinting, cell differentiation and senescence, and deregulation of this mechanism has been implicated in several diseases, including cancer. In order to understand the relationship of DNA methylation in CMs, we searched for an epigenetic signature of cutaneous melanomas by comparing the DNA methylation profiles between tumours and benign melanocytes, the precursor cells of CM. Methods: We used 20 primary CMs and three primary cell cultures of melanocytes as a discovery cohort. The tumours mutational background was collected as previously reported. Methylomes were obtained using the HM450K DNA methylation assay, and differential methylation analysis was performed. DNA methylation data of CMs from TCGA were recovered to validate our findings. Results: A signature of 514 differentially methylated genes (DMGs) was evident in CMs compared to melanocytes, which was independent of the presence of driver mutations. Pathway analysis of this CM signature revealed an enrichment of proteins involved in the binding of DNA regulatory regions (hypermethylated sites), and related to transmembrane signal transducer activities (hypomethylated sites). The methylation signature was validated in an independent dataset of primary CMs, as well as in lymph node and distant metastases (correlation of DNA methylation level: r > 0,95; Pearson's test: p < 2.2e-16). Conclusions: CMs exhibited a DMGs signature, which was independent of the mutational background and possibly established prior to genetic alterations. This signature provides important insights into how epigenetic deregulation contributes to melanomagenesis in general (AU)


Subject(s)
Humans , Male , Female , Skin Neoplasms , Signal Transduction , DNA Methylation , DNA-Binding Proteins , Transcriptome/genetics , Melanoma
18.
Mem. Inst. Oswaldo Cruz ; 111(11): 686-691, Nov. 2016. graf
Article in English | LILACS | ID: biblio-829250

ABSTRACT

Trypanosomatids are parasites that cause disease in humans, animals, and plants. Most are non-pathogenic and some harbor a symbiotic bacterium. Endosymbiosis is part of the evolutionary process of vital cell functions such as respiration and photosynthesis. Angomonas deanei is an example of a symbiont-containing trypanosomatid. In this paper, we sought to investigate how symbionts influence host cells by characterising and comparing the transcriptomes of the symbiont-containing A. deanei (wild type) and the symbiont-free aposymbiotic strains. The comparison revealed that the presence of the symbiont modulates several differentially expressed genes. Empirical analysis of differential gene expression showed that 216 of the 7625 modulated genes were significantly changed. Finally, gene set enrichment analysis revealed that the largest categories of genes that downregulated in the absence of the symbiont were those involved in oxidation-reduction process, ATP hydrolysis coupled proton transport and glycolysis. In contrast, among the upregulated gene categories were those involved in proteolysis, microtubule-based movement, and cellular metabolic process. Our results provide valuable information for dissecting the mechanism of endosymbiosis in A. deanei.


Subject(s)
Humans , Animals , Gene Expression Regulation/physiology , Gene Ontology , RNA, Protozoan/genetics , Symbiosis/genetics , Transcriptome/genetics , Trypanosomatina/genetics , Bacteria/growth & development , Gene Expression Profiling , Genes, Protozoan , Genome, Protozoan , Genomics , RNA, Protozoan/isolation & purification , Trypanosomatina/metabolism
19.
São Paulo; s.n; s.n; mai. 2014. 149 p. tab, graf, ilus.
Thesis in Portuguese | LILACS | ID: biblio-836917

ABSTRACT

O presente trabalho investigou se a exposição em períodos precoces da vida à ração com alto teor de gordura animal altera o risco de câncer de mama na vida adulta em ratas. Ratas mães foram expostas à ração com alto teor de gordura (ATG) à base de banha de porco (60 % de energia proveniente de gordura) ou uma dieta controle AIN93G (16 % de energia proveniente de gordura) durante a gestação ou gestação e lactação. A prole feminina com 7 semanas de idade foi induzida a carcinogênese mamária com o carcinógeno 7,12-dimeti-benz[a]antraceno. Comparado à prole do grupo controle, observou-se menor suscetibilidade à carcinogênese mamária na prole do grupo de ratas prenhas submetidas à ração ATG durante a gestação (menor incidência de neoplasias, multiplicidade e peso das neoplasias) ou gestação e lactação (menor multiplicidade). Prole feminina de ratas exposta à ração ATG durante a gestação apresentou menor crescimento da árvore epitelial mamária, proliferação celular (Ki67) e expressão de NFkB p65 e maior expressão de p21 e níveis globais de H3K9me3 na glândula mamária. Além disso, esta apresentou uma tendência na redução da razão Rank/Rankl (p=0,09) e níveis de progesterona sérica (p=0,07). Glândula mamária da prole feminina do grupo exposto à ração ATG durante a gestação e lactação apresentou menor número de TEBs, crescimento da árvore epitelial e razão BCL-2/BAX e maiores níveis de leptina em comparação à prole do grupo controle. Análise de lipidômica das glândulas mamárias revelou que exposição à ração ATG especificamente durante a gestação apresentou pequenos efeitos no perfil de ácidos graxos na prole feminina, enquanto que a exposição à essa ração durante a gestação e lactação promoveu menor concentração de ácidos graxos saturados (exceto ácido esteárico) e maior concentração de ácidos graxos polinsaturados da série n-6, monoinsaturados e ácido linoleico conjugado (CLA). De acordo com análise de dependência de redes diferencial (DDN) dos genes diferentemente expressos pela análise de "microarray" exposição à ração ATG em períodos precoces da vida altera a rede transcricional da glândula mamária na vida adulta. Especificamente, ratas expostas à ração ATG somente durante o período fetal apresentou aumento da expressão de Hrh1 e Repin1 em comparação ao controle. A prole exposta à ração durante o período fetal e lactacional apresentou maior e menor expressão de Stra6 e Tlr1 em comparação ao contole, respectivamente e menor expressão de Crkrs em comparação à prole exposta à ração somente durante o período fetal. Nossos dados confirmam que o risco de câncer de mama da prole pode ser programado pela alimentação materna. No entanto, ao contrário do que se esperava, exposição a altos níveis de gordura animal no início da vida diminuiu a suscetibilidade ao câncer de mama na vida adulta. Dentre os possíveis mecanismos envolvidos nessa proteção encontram-se a modulação da morfologia e perfil lipídico da glândula mamária, redução da proliferação celular e aumento dos níveis proteicos de reguladores do ciclo celular, modulação de marcas epigenéticas como H3K9me3, modulação da expressão gênica global com alteração de redes de sinalização, bem como regulação de vias de sinalização específicas como RANK/RANKL/NFκB. Porém esses mecanismos são dependentes do tempo e período de exposição


The present study investigated whether early life exposure to high levels of animal fat changes breast cancer risk in adulthood in rats. Dams consumed a lard-based high-fat (HF) diet (60% fat-derived energy) or an AIN93G control diet (16% fat-derived energy) during gestation or gestation and lactation. Their 7-week-old female offspring were exposed to 7,12-dimethylbenz[a]anthracene to induce mammary tumors. Compared to the control offspring, significantly lower susceptibility to mammary cancer development was observed in the offspring of dams fed on HF diet during gestation (lower tumor incidence, multiplicity and weight), or gestation and lactation (lower tumor multiplicity only). Mammary epithelial elongation, cell proliferation (Ki67), and expression of NFkB p65 were significantly lower, and p21 expression and global H3K9me3 levels were higher in the mammary glands of rats exposed to HF lard diet in utero. They also tended to have lower Rank/Rankl ratios (p=0.09) and serum progesterone levels (p=0.07) than control offspring. In the mammary glands of offspring of dams consuming the HF diet during both gestation and lactation, the number of terminal end buds, epithelial elongation and the BCL-2/BAX ratio were significantly lower, and serum leptin levels were higher than in the controls. Lipidomic analysis on mammary glands showed that exposure to a lard-based HF diet only during gestation had little effects on fatty acids profile on offspring, whereas this exposure during gestation and lactation promoted significant changes on the offspring's mammary glands. In general, it decreased SFA (except for stearic acid) and increased n-6 PUFA, MUFA and CLA concentrations in mammary gland. According to Differential dependency network (DDN), analysis of genes differently expressed by microarray, exposure to HF diet during early life changes the transcriptional network of the mammary gland in adulthood. Specifically, rats exposed to HF diet only during the fetal period showed increased expression of Hrh1 e Repin1 compared to the control. The offspring exposed to the HF diet in utero and nursing had higher and lower expression of Stra6 and Tlr1, respectively, compared to the control and lower expression of Crkrs compared to the offspring exposed only in utero. Our data confirm that the breast cancer risk of offspring can be programmed by maternal dietary intake. However, contrary to our expectation, exposure to high levels of lard during early life decreased later susceptibility to breast cancer. The mechanisms involve modulation of mammary gland's morphology and lipid profile, decrease of cell proliferation and increase of cell cycle regulators, modulation of epigenetics marks as H3K9me3, modulation of global gene expression with alteration of transcriptional network and RANK/RANKL/NFκB pathway. However, these mechanisms are dependent on the duration and period of exposure


Subject(s)
Female , Pregnancy , Rats , Breast Neoplasms/complications , Dietary Fats/administration & dosage , Diet, High-Fat/adverse effects , Epigenetic Repression , Nutritional Status , Programming/methods , Transcriptome/genetics
20.
Mem. Inst. Oswaldo Cruz ; 109(1): 38-50, 02/2014. tab, graf
Article in English | LILACS | ID: lil-703647

ABSTRACT

Transcripts similar to those that encode the nonstructural (NS) proteins NS3 and NS5 from flaviviruses were found in a salivary gland (SG) complementary DNA (cDNA) library from the cattle tick Rhipicephalus microplus. Tick extracts were cultured with cells to enable the isolation of viruses capable of replicating in cultured invertebrate and vertebrate cells. Deep sequencing of the viral RNA isolated from culture supernatants provided the complete coding sequences for the NS3 and NS5 proteins and their molecular characterisation confirmed similarity with the NS3 and NS5 sequences from other flaviviruses. Despite this similarity, phylogenetic analyses revealed that this potentially novel virus may be a highly divergent member of the genus Flavivirus. Interestingly, we detected the divergent NS3 and NS5 sequences in ticks collected from several dairy farms widely distributed throughout three regions of Brazil. This is the first report of flavivirus-like transcripts in R. microplus ticks. This novel virus is a potential arbovirus because it replicated in arthropod and mammalian cells; furthermore, it was detected in a cDNA library from tick SGs and therefore may be present in tick saliva. It is important to determine whether and by what means this potential virus is transmissible and to monitor the virus as a potential emerging tick-borne zoonotic pathogen.


Subject(s)
Animals , Cattle , Flavivirus/chemistry , RNA, Viral/isolation & purification , Rhipicephalus/virology , Viral Nonstructural Proteins/chemistry , Brazil , Conserved Sequence/genetics , Flavivirus/classification , Flavivirus/isolation & purification , Gene Library , Hydrophobic and Hydrophilic Interactions , Phylogeny , Polymerase Chain Reaction , RNA Helicases/chemistry , Sequence Alignment/statistics & numerical data , Sequence Analysis, Protein/methods , Serine Endopeptidases/chemistry , Tissue Extracts/analysis , Transcriptome/genetics
SELECTION OF CITATIONS
SEARCH DETAIL