scholarly journals Mixed Transcriptome Analysis Revealed the Possible Interaction Mechanisms between Zizania latifolia and Ustilago esculenta Inducing Jiaobai Stem-Gall Formation

2021 ◽  
Vol 22 (22) ◽  
pp. 12258
Author(s):  
Zhi-Ping Zhang ◽  
Si-Xiao Song ◽  
Yan-Cheng Liu ◽  
Xin-Rui Zhu ◽  
Yi-Feng Jiang ◽  
...  
Keyword(s):  
Host Plant ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Hormonal Control ◽  
Transcriptional Analysis ◽  
Gall Formation ◽  
Specific Expression ◽  
Zizania Latifolia ◽  
Stem Gall ◽  
Ustilago Esculenta

The smut fungus Ustilago esculenta infects Zizania latifolia and induces stem expansion to form a unique vegetable named Jiaobai. Although previous studies have demonstrated that hormonal control is essential for triggering stem swelling, the role of hormones synthesized by Z. latifolia and U. esculenta and the underlying molecular mechanism are not yet clear. To study the mechanism that triggers swollen stem formation, we analyzed the gene expression pattern of both interacting organisms during the initial trigger of culm gall formation, at which time the infective hyphae also propagated extensively and penetrated host stem cells. Transcriptional analysis indicated that abundant genes involving fungal pathogenicity and plant resistance were reprogrammed to maintain the subtle balance between the parasite and host. In addition, the expression of genes involved in auxin biosynthesis of U. esculenta obviously decreased during stem swelling, while a large number of genes related to the synthesis, metabolism and signal transduction of hormones of the host plant were stimulated and showed specific expression patterns, particularly, the expression of ZlYUCCA9 (a flavin monooxygenase, the key enzyme in indole-3-acetic acid (IAA) biosynthesis pathway) increased significantly. Simultaneously, the content of IAA increased significantly, while the contents of cytokinin and gibberellin showed the opposite trend. We speculated that auxin produced by the host plant, rather than the fungus, triggers stem swelling. Furthermore, from the differently expressed genes, two candidate Cys2-His2 (C2H2) zinc finger proteins, GME3058_g and GME5963_g, were identified from U. esculenta, which may conduct fungus growth and infection at the initial stage of stem-gall formation.

Acute Myeloid Leukemia with Translocation t(8;16) Demonstrates Specific Cytomorphological, Cytogenetic, and Gene Expression Characteristics and Can Clearly Be Discriminated from Other AML with Balanced Translocations.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2897-2897
Author(s):  
Torsten Haferlach ◽  
Helmut Loeffler ◽  
Alexander Kohlmann ◽  
Martin Dugas ◽  
Wolfgang Hiddemann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Who Classification ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Support Vector ◽  
Gene Expression Patterns ◽  
Down Regulation ◽  
Specific Expression ◽  
Balanced Translocations

Abstract Balanced chromosomal rearrangements leading to fusion genes on the molecular level define distinct biological subsets in AML. The four balanced rearrangements (t(15;17), t(8;21), inv(16), and 11q23/MLL) show a close correlation to cytomorphology and gene expression patterns. We here focused on seven AML with t(8;16)(p11;p13). This translocation is rare (7/3515 cases in own cohort). It is more frequently found in therapy-related AML than in de novo AML (3/258 t-AML, and 4/3287 de novo, p=0.0003). Cytomorphologically, AML with t(8;16) is characterized by striking features: In all 7 cases the positivity for myeloperoxidase on bone marrow smears was >70% and intriguingly, in parallel >80% of blast cells stained strongly positive for non-specific esterase (NSE) in all cases. Thus, these cases can not be classified according to FAB categories. These data suggest that AML-t(8;16) arise from a very early stem cell with both myeloid and monoblastic potential. Furthermore, we detected erythrophagocytosis in 6/7 cases that was described as specific feature in AML with t(8;16). Four pts. had chromosomal aberrations in addition to t(8;16), 3 of these were t-AML all showing aberrations of 7q. Survival was poor with 0, 1, 1, 2, 20 and 18+ (after alloBMT) mo., one lost to follow-up, respectively. We then analyzed gene expression patterns in 4 cases (Affymetrix U133A+B). First we compared t(8;16) AML with 46 AML FAB M1, 41 M4, 9 M5a, and 16 M5b, all with normal karyotype. Hierachical clustering and principal component analyses (PCA) revealed that t(8;16) AML were intercalating with FAB M4 and M5b and did not cluster near to M1. Thus, monocytic characteristics influence the gene expression pattern stronger than myeloid. Next we compared the t(8;16) AML with the 4 other balanced subtypes according to the WHO classification (t(15;17): 43; t(8;21): 40; inv(16): 49; 11q23/MLL-rearrangements: 50). Using support vector machines the overall accuracy for correct subgroup assignment was 97.3% (10-fold CV), and 96.8% (2/3 training and 1/3 test set, 100 runs). In PCA and hierarchical cluster analysis the t(8;16) were grouped in the vicinity of the 11q23 cases. However, in a pairwise comparison these two subgroups could be discriminated with an accuracy of 94.4% (10-fold CV). Genes with a specific expression in AML-t(8;16) were further investigated in pathway analyses (Ingenuity). 15 of the top 100 genes associated with AML-t(8;16) were involved in the CMYC-pathway with up regulation of BCOR, COXB5, CDK10, FLI1, HNRPA2B1, NSEP1, PDIP38, RAD50, SUPT5H, TLR2 and USP33, and down regulation of ERG, GATA2, NCOR2 and RPS20. CEBP beta, known to play a role in myelomonocytic differentiation, was also up-regulated in t(8;16)-AML. Ten additional genes out of the 100 top differentially expressed genes were also involved in this pathway with up-regulation of DDB2, HIST1H3D, NSAP1, PTPNS1, RAN, USP4, TRIM8, ZNF278 and down regulation of KIT and MBD2. In conclusion, AML with t(8;16) is a specific subtype of AML with unique characteristics in morphology and gene expression patterns. It is more frequently found in t-AML, outcome is inferior in comparison to other AML with balanced translocations. Due to its unique features, it is a candidate for inclusion into the WHO classification as a specific entity.

scholarly journals GEsture: an online hand-drawing tool for gene expression pattern search

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4927 ◽  
Author(s):  
Chunyan Wang ◽  
Yiqing Xu ◽  
Xuelin Wang ◽  
Li Zhang ◽  
Suyun Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Pattern Search ◽  
Clustering Methods ◽  
Specific Expression ◽  
Time Series Gene Expression ◽  
Specific Expression Pattern

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users’ requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.

scholarly journals RNA-Seq Analyses Identify Additivity as the Predominant Gene Expression Pattern in F1 Chicken Embryonic Brain and Liver

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 27 ◽  
Author(s):  
Zhu Zhuo ◽  
Susan J. Lamont ◽  
Behnam Abasht
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Pairwise Comparison ◽  
Intermediate Phenotype ◽  
Superior Performance ◽  
Rna Seq ◽  
Specific Expression ◽  
Parental Lines

The superior performance of hybrids to parents, termed heterosis, has been widely utilized in animal and plant breeding programs, but the molecular mechanism underlying heterosis remains an enigma. RNA-Seq provides a novel way to investigate heterosis at the transcriptome-wide level, because gene expression functions as an intermediate phenotype that contributes to observable traits. Here we compared embryonic gene expression between chicken hybrids and their inbred parental lines to identify inheritance patterns of gene expression. Inbred Fayoumi and Leghorn were crossed reciprocally to obtain F1 fertile eggs. RNA-Seq was carried out using 24 brain and liver samples taken from day 12 embryos, and the differentially expressed (DE) genes were identified by pairwise comparison among the hybrids, parental lines, and mid-parent expression values. Our results indicated the expression levels of the majority of the genes in the F1 cross are not significantly different from the mid-parental values, suggesting additivity as the predominant gene expression pattern in the F1. The second and third prevalent gene expression patterns are dominance and over-dominance. Additionally, we found only 7–20% of the DE genes exhibit allele-specific expression in the F1, suggesting that trans regulation is the main driver for differential gene expression and thus contributes to heterosis effect in the F1 crosses.

Deeper Understanding of the Mechanism Promoting Gall Formation of Zizania latifolia under Fenaminosulf Treatment

2020 ◽  
Author(s):  
Fang Li ◽  
Juefeng Zhang ◽  
Haiying Zhong ◽  
Jianming Chen
Keyword(s):  
Genetic Manipulation ◽  
Inhibitory Effect ◽  
Fungal Endophyte ◽  
Gall Formation ◽  
High Concentration ◽  
Zizania Latifolia ◽  
Strong Inhibitory Effect ◽  
Ustilago Esculenta ◽  
Plant Pathogen Interactions

Abstract Zizania latifolia is a popular aquatic vegetable in China because of its enlarged edible stems resulting from persistent infection by a fungal endophyte, Ustilago esculenta. Fenaminosulf (FM) is a common fungicide and microbicide. In Z. latifolia fields, appropriate spraying of FM not just controls diseases, but also promotes an earlier harvest of Z. latifolia. In this study, we show that the timing of gall formation was advanced and the plant’s yield was increased significantly under a high concentration treatment of FM. Yet FM had a strong inhibitory effect on the growth of U. esculenta in vitro, while the transcript levels of some growth-related genes were all substantially downregulated. Through a transcriptome analysis, we found that FM directly affected the growth of Z. latifolia by altering the expression level of genes involved in plant-pathogen interactions, plant hormone signal transduction, and some metabolism pathways. By contrast, FM had little effect on U. esculenta growing inside of Z. latifolia. Taken together, these results provide a more in-depth understanding of the molecular processes that promote gall formation in Z. latifolia, while also identifying potential targets for genetic manipulation to improve the yield and quality of Z. latifolia, in a safer and more effective way.

scholarly journals Genome-wide identification of the tobacco GDSL family and apical meristem-specific expression conferred by the GDSL promoter

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jing Lv ◽  
Chang-Bo Dai ◽  
Wei-Feng Wang ◽  
Yu-He Sun
Keyword(s):  
Apical Meristem ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Axillary Buds ◽  
Axillary Bud ◽  
Lethal Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Gdsl Family

Abstract Background GDSL esterases/lipases are a large protein subfamily defined by the distinct GDSL motif, and play important roles in plant development and stress responses. However, few studies have reported on the role of GDSLs in the growth and development of axillary buds. This work aims to identify the GDSL family members in tobacco and explore whether the NtGDSL gene contributes to development of the axillary bud in tobacco. Results One hundred fifty-nine GDSL esterase/lipase genes from cultivated tobacco (Nicotiana tabacum) were identified, and the dynamic changes in the expression levels of 93 of these genes in response to topping, as assessed using transcriptome data of topping-induced axillary shoots, were analysed. In total, 13 GDSL esterase/lipase genes responded with changes in expression level. To identify genes and promoters that drive the tissue-specific expression in tobacco apical and axillary buds, the expression patterns of these 13 genes were verified using qRT-PCR. GUS activity and a lethal gene expression pattern driven by the NtGDSL127 promoter in transgenic tobacco demonstrated that NtGDSL127 is specifically expressed in apical buds, axillary buds, and flowers. Three separate deletions in the NtGDSL127 promoter demonstrated that a minimum upstream segment of 235 bp from the translation start site can drive the tissue-specific expression in the apical meristem. Additionally, NtGDSL127 responded to phytohormones, providing strategies for improving tobacco breeding and growth. Conclusion We propose that in tobacco, the NtGDSL127 promoter directs expression specifically in the apical meristem and that expression is closely correlated with axillary bud development.

scholarly journals Transcriptome Analysis Reveals the Symbiotic Mechanism of Ustilago esculenta-Induced Gall Formation of Zizania latifolia

2021 ◽  
pp. MPMI-05-20-0126
Author(s):  
Jie Li ◽  
Zhiyuan Lu ◽  
Yang Yang ◽  
Jinfeng Hou ◽  
Lingyun Yuan ◽  
...  
Keyword(s):  
Cell Wall ◽  
High Performance ◽  
Molecular Mechanisms ◽  
Zeatin Riboside ◽  
Gall Formation ◽  
Cell Wall Loosening ◽  
Zizania Latifolia ◽  
Ontology Term ◽  
Ustilago Esculenta ◽  
Wall Loosening

Zizania latifolia is a perennial aquatic vegetable, whose symbiosis with the fungus Ustilago esculenta (member of Basidiomycota, class Ustilaginaceae) results in the establishment of swollen gall formations. Here, we analyzed symbiotic relations of Z. latifolia and U. esculenta, using a triadimefon (TDF) treatment and transcriptome sequencing (RNA-seq). Specifically, accurately identify the whole growth cycle of Z. latifolia. Microstructure observations showed that the presence of U. esculenta could be clearly observed after gall formation but was absent after the TDF treatment. A total of 17,541 differentially expressed genes (DEGs) were identified, based on the transcriptome. According to gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway results, plant hormone signal transduction, and cell wall–loosening factors were all significantly enriched due to U. esculenta infecting Z. latifolia; relative expression levels of hormone-related genes were identified, of which downregulation of indole 3-acetic acid (IAA)-related DEGs was most pronounced in JB_D versus JB_B. The ultra–high performance liquid chromatography analysis revealed that IAA, zeatin+trans zeatin riboside, and gibberellin 3 were increased under U. esculenta infection. Based on our results, we proposed a hormone–cell wall loosening model to study the symbiotic mechanism of gall formation after U. esculenta infects Z. latifolia. Our study thus provides a new perspective for studying the physiological and molecular mechanisms of U. esculenta infection of Z. latifolia causing swollen gall formations as well as a theoretical basis for enhancing future yields of cultivated Z. latifolia. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CCO “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.

Ustilago esculenta. [Descriptions of Fungi and Bacteria].

1991 ◽  
Author(s):  
J. E. M. Mordue
Keyword(s):  
Geographical Distribution ◽  
Vegetative Propagation ◽  
Wild Rice ◽  
Distribution Map ◽  
Zizania Latifolia ◽  
Novosibirsk Region ◽  
Zizania Aquatica ◽  
Stem Gall ◽  
Ustilago Esculenta ◽  
North Vietnam

Abstract A description is provided for Ustilago esculenta. Information is included on the disease caused by the organism, its transmission, geographical distribution, and hosts. HOSTS: Zizania latifolia[Zizania aquatica] (including Z. caduciflora). DISEASE: Stem gall smut of Manchurian wild rice. The first three to four nodes beneath the apical growing point of infected culms become enlarged and the culms fail to flower. The young galls, prior to the development of ustilospores, are used as a vegetable (Gau sun, kah-peh-sung or water shoot). GEOGRAPHICAL DISTRIBUTION: Asia: China, India (Manipur), Hong Kong, Japan, North Vietnam, Taiwan, USSR (Novosibirsk region). Recorded once in USA in glasshouses, but not established in native wild rice. (IMI Distribution Map 628, 1991). TRANSMISSION: Ustilospores are disseminated by wind and water. The smut is systemic and can be transmitted by vegetative propagation of infected plants. Transmission by inoculation of cuttings with suspensions of ustilospores or of sporidia from culture has been demonstrated.

Tissue-specific expression patterns of nuclear receptors

2013 ◽  
Author(s):  
AL Bookout ◽  
Y Jeong ◽  
M Downes ◽  
RT Yu ◽  
RM Evans ◽  
...  
Keyword(s):  
Nuclear Receptors ◽  
Expression Patterns ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

scholarly journals Overexpression of the Oral Mucosa-Specific microRNA-31 Promotes Skin Wound Closure

2019 ◽  
Vol 20 (15) ◽  
pp. 3679 ◽  
Author(s):  
Lin Chen ◽  
Alyne Simões ◽  
Zujian Chen ◽  
Yan Zhao ◽  
Xinming Wu ◽  
...  
Keyword(s):  
Wound Healing ◽  
Oral Mucosa ◽  
Wound Closure ◽  
Expression Patterns ◽  
Skin Wound ◽  
Skin Wound Healing ◽  
Specific Expression ◽  
Keratinocyte Proliferation

Wounds within the oral mucosa are known to heal more rapidly than skin wounds. Recent studies suggest that differences in the microRNAome profiles may underlie the exceptional healing that occurs in oral mucosa. Here, we test whether skin wound-healing can be accelerating by increasing the levels of oral mucosa-specific microRNAs. A panel of 57 differentially expressed high expresser microRNAs were identified based on our previously published miR-seq dataset of paired skin and oral mucosal wound-healing [Sci. Rep. (2019) 9:7160]. These microRNAs were further grouped into 5 clusters based on their expression patterns, and their differential expression was confirmed by TaqMan-based quantification of LCM-captured epithelial cells from the wound edges. Of these 5 clusters, Cluster IV (consisting of 8 microRNAs, including miR-31) is most intriguing due to its tissue-specific expression pattern and temporal changes during wound-healing. The in vitro functional assays show that ectopic transfection of miR-31 consistently enhanced keratinocyte proliferation and migration. In vivo, miR-31 mimic treatment led to a statistically significant acceleration of wound closure. Our results demonstrate that wound-healing can be enhanced in skin through the overexpression of microRNAs that are highly expressed in the privileged healing response of the oral mucosa.

scholarly journals Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Leyla A. Erozenci ◽  
Sander R. Piersma ◽  
Thang V. Pham ◽  
Irene V. Bijnsdorp ◽  
Connie R. Jimenez
Keyword(s):  
Expression Patterns ◽  
Interaction Network ◽  
Extracellular Vesicle ◽  
Protein Signaling ◽  
Protein Patterns ◽  
Specific Expression ◽  
Non Invasive ◽  
Data Independent Acquisition ◽  
Time Period ◽  
Using Data

AbstractThe protein content of urinary extracellular vesicles (EVs) is considered to be an attractive non-invasive biomarker source. However, little is known about the consistency and variability of urinary EV proteins within and between individuals over a longer time-period. Here, we evaluated the stability of the urinary EV proteomes of 8 healthy individuals at 9 timepoints over 6 months using data-independent-acquisition mass spectrometry. The 1802 identified proteins had a high correlation amongst all samples, with 40% of the proteome detected in every sample and 90% detected in more than 1 individual at all timepoints. Unsupervised analysis of top 10% most variable proteins yielded person-specific profiles. The core EV-protein-interaction network of 516 proteins detected in all measured samples revealed sub-clusters involved in the biological processes of G-protein signaling, cytoskeletal transport, cellular energy metabolism and immunity. Furthermore, gender-specific expression patterns were detected in the urinary EV proteome. Our findings indicate that the urinary EV proteome is stable in longitudinal samples of healthy subjects over a prolonged time-period, further underscoring its potential for reliable non-invasive diagnostic/prognostic biomarkers.

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