scholarly journals Transcriptome profiling of peanut (Arachis hypogaea) gynophores in gravitropic response

2013 ◽  
Vol 40 (12) ◽  
pp. 1249 ◽  
Author(s):  
Hai-fen Li ◽  
Xiao-Ping Chen ◽  
Fang-he Zhu ◽  
Hai-Yan Liu ◽  
Yan-Bin Hong ◽  
...  

Peanut (Arachis hypogaea L.) produces flowers aerially, but the fruit develops underground. This process is mediated by the gynophore, which always grows vertically downwards. The genetic basis underlying gravitropic bending of gynophores is not well understood. To identify genes related to gynophore gravitropism, gene expression profiles of gynophores cultured in vitro with tip pointing upward (gravitropic stimulation sample) and downward (control) at both 6 and 12 h were compared through a high-density peanut microarray. After gravitropic stimulation, there were 174 differentially expressed genes, including 91 upregulated and 83 downregulated genes at 6 h, and 491 differentially expressed genes including 129 upregulated and 362 downregulated genes at 12 h. The differentially expressed genes identified were assigned to 24 functional categories. Twenty pathways including carbon fixation, aminoacyl-tRNA biosynthesis, pentose phosphate pathway, starch and sucrose metabolism were identified. The quantitative real-time PCR analysis was performed for validation of microarray results. Our study paves the way to better understand the molecular mechanisms underlying the peanut gynophore gravitropism.

Zootaxa ◽  
2019 ◽  
Vol 4591 (1) ◽  
pp. 1
Author(s):  
DAN LIANG ◽  
PEI WANG ◽  
LINGLING WU ◽  
XIAOLI JIANG ◽  
GUOQING WEI ◽  
...  

Actias selene (Hübner) is an important silk-spinning moth. Like other moths, it has innate immunity but no acquired immunity. However, there are few studies on immune-related genes of A. selene. Here, differential expression RNAseq experiment was employed to examine the genes related to different metabolic pathways and to explore the immune mechanism of the A. selene post Beauveria bassiana (Bb) and Micrococcus luteus (ML) stimuli. A total of 64,372,921 clean reads were obtained and 39,057 differentially expressed genes (DEGs) were identified. In the Bb vs. PBS group (PBS as the control), 9,092 genes were up-regulated and 4,438 genes were down-regulated; in the ML vs. PBS group, 5,903 genes were up-regulated and 5,175 genes were down-regulated. The KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) analyses of DEGs confirmed that many DEGs were associated with "Metabolism pathway", "cellular process", "cell" and "catalytic activity". Among them, 194 and 149 differentially expressed genes were related to immunity in the Bb vs. PBS group and ML vs. PBS group, respectively. We verified the reliability of the data with reverse transcription quantitative real-time PCR analysis of randomly selected genes. Furthermore, the phylogenetic tree results showed that HSP90, PGRP and MyD88 genes of A. selene were most closely related to Antheraea pernyi (Guérin-Méneville). These results will provide an overview of the molecular mechanism of A. selene resistance to fungal and bacterial infections as well as an evolutionary aspect of these genes. Moreover, the interrelated trophic mechanisms among different groups of organisms are vital to explore, thus this study will lay a foundation for further studies on the innate immune mechanism of saturniid moths, and provide important theoretical basis for studying the relationship between A. selene and other species.


2018 ◽  
Author(s):  
Qingqi Chen ◽  
Xiangyang Xu ◽  
Jingbin Jiang ◽  
Jingfu Li

Tomato yellow leaf curl virus (TYLCV) is one of the most devastating viruses of cultivated tomato in both tropical and subtropical regions. Five major genes (Ty-1, Ty-2, Ty-3, Ty-4 and Ty-5) from wild tomato species have been associated with resistance to TYLCV. Researchers have recently attempted to determine the functions of these resistance genes, but molecular mechanisms underlying the observed resistance remain unclear. Here, resistant (cv. CLN3212A-23, carrying Ty-5) and susceptible (cv. Moneymaker) plants were either left untreated (R and S, respectively) or artificially inoculated with TYLCV via Agrobacterium-mediated transformation (RT and ST, respectively). The transcriptomes of the plants in the four groups were then analyzed by RNA-Seq, and the results identified 8,639 differentially expressed genes (DEGs) between the R and RT groups, 2,818 DEGs between the RT and ST groups, 8,899 DEGs between the S and ST groups, and 707 DEGs between the R and S groups. The gene expression profiles in both the resistant and susceptible tomato cultivars appeared to undergo notable changes after viral inoculation, and functional classification revealed that most DEGs were associated with 18 GO terms. Moreover, the functional classification of the response of Ty-5-carrying tomato plants to TYLCV infection identified the importance of the GO term “response to stimulus” in the BP category, which is related to disease resistance. In addition, 28 genes were significantly enriched in the “Plant hormone signal transduction”, “Carbon metabolism”, “ Carbon fixation in photosynthetic organisms ” and “ Glutathione metabolism ” pathways. The differential expression levels of 12 select genes were confirmed by quantitative real-time PCR. The present study indicates that the Ty-5 gene activates the expression of multiple genes involved in the resistance process and will aid a more in-depth understanding of the effects of the Ty-5 gene on resistance based on its molecular mechanism with the aim of improving TYLCV disease management in tomato.


2020 ◽  
Author(s):  
Na Li ◽  
Ru-feng Bai ◽  
Chun Li ◽  
Li-hong Dang ◽  
Qiu-xiang Du ◽  
...  

Abstract Background: Muscle trauma frequently occurs in daily life. However, the molecular mechanisms of muscle healing, which partly depend on the extent of the damage, are not well understood. This study aimed to investigate gene expression profiles following mild and severe muscle contusion, and to provide more information about the molecular mechanisms underlying the repair process.Methods: A total of 33 rats were divided randomly into control (n = 3), mild contusion (n = 15), and severe contusion (n = 15) groups; the contusion groups were further divided into five subgroups (1, 3, 24, 48, and 168 h post-injury; n = 3 per subgroup). Then full genome microarray of RNA isolated from muscle tissue was performed to access the gene expression changes during healing process.Results: A total of 2,844 and 2,298 differentially expressed genes were identified in the mild and severe contusion groups, respectively. The analysis of the overlapping differentially expressed genes showed that there are common mechanisms of transcriptomic repair of mild and severe contusion within 48 h post-contusion. This was supported by the results of principal component analysis, hierarchical clustering, and weighted gene co‐expression network analysis of the 1,620 coexpressed genes in mildly and severely contused muscle. From these analyses, we discovered that the gene profiles in functional modules and temporal clusters were similar between the mild and severe contusion groups; moreover, the genes showed time-dependent patterns of expression, which allowed us to identify useful markers of wound age. We then performed an analysis of the functions of genes (including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation, and protein–protein interaction network analysis) in the functional modules and temporal clusters, and the hub genes in each module–cluster pair were identified. Interestingly, we found that genes downregulated within 24−48 h of the healing process were largely associated with metabolic processes, especially oxidative phosphorylation of reduced nicotinamide adenine dinucleotide phosphate, which has been rarely reported. Conclusions: These results improve our understanding of the molecular mechanisms underlying muscle repair, and provide a basis for further studies of wound age estimation.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 42-42
Author(s):  
Xiaoli Liu ◽  
Dongyue Zhang ◽  
Hao Wang ◽  
Qian Ren ◽  
Lina Wang ◽  
...  

Macrophages are important member in tissue microenvironments and play diverse physiologic and pathologic roles. Leukemia associated macrophages (LAM) are a kind of specifically activated macrophages in leukemia microenvironment, which are different from M1, M2 and TAMs. We have reported the heterogeneities in gene expression profiles of LAMs. However, MicroRNA expression profiles of LAMs and regulatory mechanism are still unknown. Here, a MLL-AF9 induced mouse acute myeloid leukemia (AML) model was used, and LAMs in the spleen and bone marrow were sorted for microRNA sequencing. The microRNA expression profiles of LAMs in bone marrow and spleen in AML mice were different from macrophages from control mice. Based on the volcano plot, more than 100 microRNAs were differentially expressed in LAMs compared with macrophages in control mice. Next, five differentially expressed microRNAs were selected and verified by qRT-PCR in LAMs from spleen. The results showed that miR-451a and miR-155-5p in spleen LAMs were significantly upregulated in LAMs from spleen. Overexpression of miR-451a altered the morphology of macrophages, enhanced the phagocytic ability of macrophages, and promotes the expression of macrophage differentiation marker CD11b. Furthermore, overexpression of miR-451a had little effect on M0 macrophages, but increased the proliferation capacity of macrophages upon stimulation toward M1 or M2 phenotype. MiR-451a overexpressed-macrophages had higher level of iNOS when stimulated with LPS or IL-4 whereas there was no difference in the expression of IL-1β, IL-6, CD206 and Arg-1 between MiR-451a overexpressed-macrophages and control macrophage. Therefore, our data revealed the characteristics of the microRNA expression profile of LAMs for the first time, and verified the effect of miR-451a on macrophage in vitro. Disclosures No relevant conflicts of interest to declare.


2020 ◽  
Author(s):  
Yanjie Han ◽  
Xinxin Li ◽  
Jiliang Yan ◽  
Chunyan Ma ◽  
Xin Wang ◽  
...  

Abstract Background: Melanoma is the most deadly tumor in skin tumors and is prone to distant metastases. The incidence of melanoma has increased rapidly in the past few decades, and current trends indicate that this growth is continuing. This study was aimed to explore the molecular mechanisms of melanoma pathogenesis and discover underlying pathways and genes associated with melanoma.Methods: We used high-throughput expression data to study differential expression profiles of related genes in melanoma. The differentially expressed genes (DEGs) of melanoma in GSE15605, GSE46517, GSE7553 and the Cancer Genome Atlas (TCGA) datasets were analyzed. Differentially expressed genes (DEGs) were identified by paired t-test. Then the DEGs were performed cluster and principal component analyses and protein–protein interaction (PPI) network construction. After that, we analyzed the differential genes through bioinformatics and got hub genes. Finally, the expression of hub genes was confirmed in the TCGA databases and collected patient tissue samples.Results: Total 144 up-regulated DEGs and 16 down-regulated DEGs were identified. A total of 17 gene ontology analysis (GO) terms and 11 pathways were closely related to melanoma. Pathway of pathways in cancer was enriched in 8 DEGs, such as junction plakoglobin (JUP) and epidermal growth factor receptor (EGFR). In the PPI networks, 9 hub genes were obtained, such as loricrin (LOR), filaggrin (FLG), keratin 5 (KRT5), corneodesmosin (CDSN), desmoglein 1 (DSG1), desmoglein 3 (DSG3), keratin 1 (KRT1), involucrin (IVL) and EGFR. The pathway of pathways in cancer and its enriched DEGs may play important roles in the process of melanoma. The hub genes of DEGs may become promising melanoma candidate genes. Five key genes FLG, DSG1, DSG3, IVL and EGFR were identified in the TCGA database and melanoma tissues.Conclusions: The results suggested that FLG, DSG1, DSG3, IVL and EGFR might play important roles and potentially be valuable in the prognosis and treatment of melanoma.


2008 ◽  
Vol 20 (1) ◽  
pp. 165
Author(s):  
X. S. Cui ◽  
X. Y. Li ◽  
T. Kim ◽  
N.-H. Kim

Trichostatin A (TSA) is an inhibitor of histone deacetylase and is able to alter gene expression patterns by interfering with the removal of acetyl groups from histones. The aim of this study was to determine the effect of TSA treatment on the development and gene expression patterns of mouse zygotes developing in vitro. The addition of 100 nm TSA to the culture medium did not affect the cleavage of mouse embryos (TSA treatment, 148/150 (99%) v. control, 107/107 (100%)); however, embryos that were treated with TSA arrested at the 2-cell stage (145/148, 98%). We estimated the number of nuclei in control and TSA-treated embryos by propidium iodide staining, taking into account the presence of any cells with two or more nuclei. At 62–63 h post-hCG stimulation, control zygotes had developed to the 4-cell stage and exhibited one nucleus in each blastomere, indicative of normal development. In contrast, we observed tetraploid nuclei in at least one blastomere in 20.8% (11/53) of the embryos that had been treated with TSA. At 28–29 h post-hCG stimulation (metaphase of the 1-cell stage), there was no difference in the mitotic index (as determined by analyzing the microtubule configuration) in the TSA group compared to the control group. At the 2-cell stage, however, we did not observe mitotic spindles and metaphase chromatin in embryos in the TSA treatment group compared to the controls. Interestingly, when embryos were cultured in TSA-free medium from 35 h post-hCG stimulation (S- or early G2-phase of the 2-cell stage) onward, almost all of them (47/50) developed to the blastocyst stage. In contrast, when embryos were cultured in TSA-free medium from 42 h post-hCG stimulation (middle G2-phase of the 2-cell stage) onward, they did not develop to the 4-cell stage. We used Illumina microarray technology to analyze the gene expression profiles in control and TSA-treated late 2-cell-stage embryos. Applied Biosystems Expression System software was used to extract assay signals and assay signal-to-noise ratio values from the microarray images. Our data showed that 897 genes were significantly (P < 0.05; 2-sample t-test) up- or down-regulated by TSA treatment compared to controls. Analysis using the PANTHER classification system (https://panther.appliedbiosystems.com) revealed that the 575 genes that were differentially expressed in the TSA group compared to the control were classified as being associated with putative biological processes or molecular function. Overall, in terms of putative biological processes, more nucleoside, nucleotide, and nucleic acid metabolism, protein metabolism and modification, signal transduction, developmental process, and cell cycle genes were differentially expressed between the TSA and control groups. In terms of putative molecular function, more nucleic acid-binding transcription factor and transferase genes were differentially expressed between the groups. The results collectively suggest that inhibition of histone acetylation in mouse embryos affects gene expression profiles at the time of zygotic genome activation, and this subsequently affects further development.


2019 ◽  
Vol 80 (04) ◽  
pp. 240-249
Author(s):  
Jiajia Wang ◽  
Jie Ma

Glioblastoma multiforme (GBM), an aggressive brain tumor, is characterized histologically by the presence of a necrotic center surrounded by so-called pseudopalisading cells. Pseudopalisading necrosis has long been used as a prognostic feature. However, the underlying molecular mechanism regulating the progression of GBMs remains unclear. We hypothesized that the gene expression profiles of individual cancers, specifically necrosis-related genes, would provide objective information that would allow for the creation of a prognostic index. Gene expression profiles of necrotic and nonnecrotic areas were obtained from the Ivy Glioblastoma Atlas Project (IVY GAP) database to explore the differentially expressed genes.A robust signature of seven genes was identified as a predictor for glioblastoma and low-grade glioma (GBM/LGG) in patients from The Cancer Genome Atlas (TCGA) cohort. This set of genes was able to stratify GBM/LGG and GBM patients into high-risk and low-risk groups in the training set as well as the validation set. The TCGA, Repository for Molecular Brain Neoplasia Data (Rembrandt), and GSE16011 databases were then used to validate the expression level of these seven genes in GBMs and LGGs. Finally, the differentially expressed genes (DEGs) in the high-risk and low-risk groups were subjected to gene ontology enrichment, Kyoto Encyclopedia of Genes and Genomes pathway, and gene set enrichment analyses, and they revealed that these DEGs were associated with immune and inflammatory responses. In conclusion, our study identified a novel seven-gene signature that may guide the prognostic prediction and development of therapeutic applications.


2010 ◽  
Vol 10 (3) ◽  
pp. 373-383 ◽  
Author(s):  
Kelly E. Caudle ◽  
Katherine S. Barker ◽  
Nathan P. Wiederhold ◽  
Lijing Xu ◽  
Ramin Homayouni ◽  
...  

ABSTRACTThe ABC transportersCandida glabrataCdr1 (CgCdr1), CgPdh1, and CgSnq2 are known to mediate azole resistance in the pathogenic fungusC. glabrata. Activating mutations inCgPDR1, a zinc cluster transcription factor, result in constitutive upregulation of these ABC transporter genes but to various degrees. We examined the genomewide gene expression profiles of two matched azole-susceptible and -resistantC. glabrataclinical isolate pairs. Of the differentially expressed genes identified in the gene expression profiles for these two matched pairs, there were 28 genes commonly upregulated withCgCDR1in both isolate sets includingYOR1,LCB5,RTA1,POG1,HFD1, and several members of theFLOgene family of flocculation genes. We then sequencedCgPDR1from each susceptible and resistant isolate and found two novel activating mutations that conferred increased resistance when they were expressed in a common background strain in whichCgPDR1had been disrupted. Microarray analysis comparing these reengineered strains to their respective parent strains identified a set of commonly differentially expressed genes, includingCgCDR1,YOR1, andYIM1, as well as genes uniquely regulated by specific mutations. Our results demonstrate that while CgPdr1 activates a broad repertoire of genes, specific activating mutations result in the activation of discrete subsets of this repertoire.


2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 475-475
Author(s):  
Stafford Vigors ◽  
Torres Sweeney

Abstract The improvement of feed efficiency is a key economic goal within the pig production industry. The objective of this study was to examine transcriptomic differences in both the liver and muscle in pigs divergent for feed efficiency, thus improving our understanding of the molecular mechanisms influencing feed efficiency and enabling the identification of candidate biomarkers. Residual feed intake (RFI) was calculated in two populations of pigs from two different farms of origin. The 6 most efficient (LRFI) and 6 least efficient (HRFI) animals in each population were selected for further analysis of Longissimus Dorsi muscle and liver. Three different analysis were performed: 1) Identification of differentially expressed genes (DE) in liver, 2) Identification of DE genes in muscle and 3) Identification of genes commonly DE in both tissues. Hierarchical clustering revealed that transcriptomic data segregated based on the RFI value of the pig rather than farm of origin. A total of 6464 genes were identified as being differentially expressed (DE) in muscle, while 964 genes were identified as being DE in liver. In the muscle-only analysis, genes associated with RNA, protein synthesis and energy metabolism were downregulated in the LRFI animals while in the liver-only analysis, genes associated with cell signalling and lipid homeostasis were upregulated in the LRFI animals. Genes that were commonly DE between muscle and liver (n = 526) were used for the joint analysis. These 526 genes were associated with protein targeting to membrane, extracellular matrix organization and immune function. There are pathways common to both muscle and liver in particular genes associated with immune function. In contrast, tissue-specific pathways contributing to differences in feed efficiency were also identified with genes associated with energy metabolism identified in muscle and lipid metabolism in liver. This study identifies key mechanisms driving changes in feed efficiency in pigs.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 193-193
Author(s):  
Yun Zhao ◽  
Allen Delaney ◽  
Afshin Raouf ◽  
Kamini Raghuram ◽  
Haiyan I Li ◽  
...  

Abstract The chronic phase of CML is sustained by rare BCR-ABL+ stem cells. These cells share many properties with normal pluripotent hematopoietic stem cells, but also differ in critical ways that alter their growth, drug responsiveness and genome stability. Understanding the molecular mechanisms underlying the biological differences between normal and CML stem cells is key to the development of more effective CML therapies. To obtain new insights into these mechanisms, we generated Long Serial Analysis of Gene Expression (SAGE) libraries from paired isolates of highly purified lin-CD34+CD45RA-CD36- CD71-CD7-CD38+ and lin-CD34+CD45RA-CD36-CD71-CD7-CD38- cells from 3 chronic phase CML patients (all with predominantly Ph+/BCR-ABL+ cells in both subsets) and from 3 control samples: a pool of 10 normal bone marrows (BMs), a single normal BM and a pool of G-CSF-mobilized blood cells from 9 donors. In vitro bioassays showed the CD34+CD38+ cells were enriched in CFCs (CML: 3–20% pure; normal: 4–19% pure) and the CD34+CD38- cells were enriched in LTC-ICs (CML: 0.2–26% pure; normal: 12–52% pure). Each of the 12 libraries was then sequenced to a depth of ~200,000 tags and tags from libraries prepared from like phenotypes were compared between genotypes using DiscoverySpace software and hierarchical clustering. 1687 (355 with clustering) and 1258 (316 with clustering) transcripts were thus identified as differentially expressed in the CML vs control CD34+CD38− and CD34+CD38+ subsets, respectively. 266 of these transcripts (11 with clustering) were differentially expressed in both subsets. The differential expression of 5 genes (GAS2, IGF2BP2, IL1R1, DUSP1 & SELL) was confirmed by real-time PCR analysis of lin-CD34+ cells isolated from an additional 5 normal BMs and 11 CMLs, and lin-CD34+CD38− cells from an additional 2 normal BMs and 2 CMLs (with dominant Ph+ cells). GAS2 and IL1R1 transcript levels were correlated with BCR-ABL transcript levels in both primitive subsets, and predicted differences in expression of IL1R1 and SELL were apparent within 3 days in CD34+ cord blood cells transduced with a lenti-BCR-ABL-IRES-GFP vs a control lenti-GFP vector (n=3). These findings support a direct role of BCR-ABL in perturbing the expression of these 3 genes. Further comparison of the meta CD34+CD38− and CD34+CD38+ CML cell libraries with most publicly accessible SAGE data revealed 69 novel tags in the CD34+ CML cells that correspond to unique but conserved genomic sequences. Nine of these were recovered by 5′- and 3′- RACE applied to cDNAs pooled from several human leukemic cell lines. These results illustrate the power of SAGE to reveal key components of the transcriptomes of rare human CML stem cell populations including transcripts of genes not previously known to exist. Continuing investigation of their biological roles in primary CML cells and primitive BCR-ABL-transduced human cells offer important strategies for delineating their potential as therapeutic targets.


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