scholarly journals Metabolic Profiling and Gene Expression Analysis Unveil Differences in Flavonoid and Lipid Metabolisms Between ‘Huapi’ Kumquat (Fortunella crassifolia Swingle) and Its Wild Type

2021 ◽  
Vol 12 ◽  
Author(s):  
Qiaoli Ma ◽  
Yongwei Hu ◽  
Xinghua Dong ◽  
Gaofeng Zhou ◽  
Xiao Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Metabolic Profiling ◽  
Gene Expression Analysis ◽  
Structural Genes ◽  
Wild Type ◽  
Gene Expressions ◽  
Oil Glands ◽  
Light Color ◽  
Metabolomics Analysis

To elucidate the mechanism underlying special characteristic differences between a spontaneous seedling mutant ‘Huapi’ kumquat (HP) and its wild-type ‘Rongan’ kumquat (RA), the fruit quality, metabolic profiles, and gene expressions of the peel and flesh were comprehensively analyzed. Compared with RA, HP fruit has distinctive phenotypes such as glossy peel, light color, and few amounts of oil glands. Interestingly, HP also accumulated higher flavonoid (approximately 4.1-fold changes) than RA. Based on metabolomics analysis, we identified 201 differential compounds, including 65 flavonoids and 37 lipids. Most of the differential flavonoids were glycosylated by hexoside and accumulated higher contents in the peel but lower in the flesh of HP than those of RA fruit. For differential lipids, most of them belonged to lysophosphatidycholines (LysoPCs) and lysophosphatidylethanolamines (LysoPEs) and exhibited low abundance in both peel and flesh of HP fruit. In addition, structural genes associated with the flavonoid and lipid pathways were differentially regulated between the two kumquat varieties. Gene expression analysis also revealed the significant roles of UDP-glycosyltransferase (UGT) and phospholipase genes in flavonoid and glycerophospholipid metabolisms, respectively. These findings provide valuable information for interpreting the mutation mechanism of HP kumquat.

scholarly journals An Integrated Preprocessing Approach for Exploring Single-Cell Gene Expression in Rare Cells

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Junyi Shang ◽  
David Welch ◽  
Manuela Buonanno ◽  
Brian Ponnaiya ◽  
Guy Garty ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Bystander Effect ◽  
Kinase Inhibitor ◽  
Digital Pcr ◽  
Lung Fibroblasts ◽  
Gene Expressions ◽  
Rare Cells

AbstractExploring the variability in gene expressions of rare cells at the single-cell level is critical for understanding mechanisms of differentiation in tissue function and development as well as for disease diagnostics and cancer treatment. Such studies, however, have been hindered by major difficulties in tracking the identity of individual cells. We present an approach that combines single-cell picking, lysing, reverse transcription and digital polymerase chain reaction to enable the isolation, tracking and gene expression analysis of rare cells. The approach utilizes a photocleavage bead-based microfluidic device to synthesize and deliver stable cDNA for downstream gene expression analysis, thereby allowing chip-based integration of multiple reactions and facilitating the minimization of sample loss or contamination. The utility of the approach was demonstrated with QuantStudio digital PCR by analyzing the radiation and bystander effect on individual IMR90 human lung fibroblasts. Expression levels of the Cyclin-dependent kinase inhibitor 1a (CDKN1A), Growth/differentiation factor 15 (GDF15), and Prostaglandin-endoperoxide synthase 2 (PTGS2) genes, previously shown to have different responses to direct and bystander irradiation, were measured across individual control, microbeam-irradiated or bystander IMR90 cells. In addition to the confirmation of accurate tracking of cell treatments through the system and efficient analysis of single-cell responses, the results enable comparison of activation levels of different genes and provide insight into signaling pathways within individual cells.

scholarly journals In silico gene expression analysis reveals glycolysis and acetate anaplerosis in IDH1 wild-type glioma and lactate and glutamate anaplerosis in IDH1-mutated glioma

Oncotarget ◽  
2017 ◽  
Vol 8 (30) ◽  
pp. 49165-49177 ◽  
Author(s):  
Mohammed Khurshed ◽  
Remco J. Molenaar ◽  
Krissie Lenting ◽  
William P. Leenders ◽  
Cornelis J.F. van Noorden
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
In Silico ◽  
Gene Expression Analysis ◽  
Wild Type

scholarly journals Mechanisms of Targeting the MDM2-p53-FOXM1 Axis in Well-Differentiated Intestinal Neuroendocrine Tumors

2017 ◽  
Vol 107 (1) ◽  
pp. 1-23
Author(s):  
Franziska Briest ◽  
Irina Grass ◽  
Dagmar Sedding ◽  
Markus Möbs ◽  
Friederike Christen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Western Blot ◽  
Neuroendocrine Tumors ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Neuroendocrine Neoplasms ◽  
Wild Type ◽  
Frequent Event ◽  
P53 Response

Background/Aims: The tumor suppressor p53 is rarely mutated in gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN) but they frequently show a strong expression of negative regulators of p53, rendering these tumors excellent targets for a p53 recovery therapy. Therefore, we analyzed the mechanisms of a p53 recovery therapy on intestinal neuroendocrine tumors in vitro and in vivo.Methods: By Western blot and immunohistochemistry, we found that in GEP-NEN biopsy material overexpression of MDM2 was present in intestinal NEN. Therefore, we analyzed the effect of a small-molecule inhibitor, nutlin-3a, in p53 wild-type and mutant GEP-NEN cell lines by proliferation assay, flow cytometry, immunofluorescence, Western blot, and by multiplex gene expression analysis. Finally, we analyzed the antitumor effect of nutlin-3a in a xenograft mouse model in vivo. During the study, the tumor volume was determined. Results: The midgut wild-type cell line KRJ-I responded to the treatment with cell cycle arrest and apoptosis. By gene expression analysis, we could demonstrate that nutlins reactivated an antiproliferative p53 response. KRJ-I-derived xenograft tumors showed a significantly decreased tumor growth upon treatment with nutlin-3a in vivo. Furthermore, our data suggest that MDM2 also influences the expression of the oncogene FOXM1 in a p53-independent manner. Subsequently, a combined treatment of nutlin-3a and cisplatin (as chemoresistance model) resulted in synergistically enhanced antiproliferative effects. Conclusion: In summary, MDM2 overexpression is a frequent event in p53 wild-type intestinal neuroendocrine neoplasms and therefore recovery of a p53 response might be a novel personalized treatment approach in these tumors.

scholarly journals Comparative Genetics of the rdar Morphotype in Salmonella

2006 ◽  
Vol 188 (24) ◽  
pp. 8395-8406 ◽  
Author(s):  
A. P. White ◽  
M. G. Surette
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Intergenic Region ◽  
Promoter Activity ◽  
Gene Expression Analysis ◽  
Structural Genes ◽  
Comparative Genetics ◽  
Regulatory Factors ◽  
Reference Set ◽  
Divergent Promoters

ABSTRACT The Salmonella rdar morphotype is a distinct, rough and dry colony morphology formed by the extracellular interaction of thin aggregative fimbriae (Tafi or curli), cellulose, and other polysaccharides. Cells in rdar colonies are more resistant to desiccation and exogenous stresses, which is hypothesized to aid in the passage of pathogenic Salmonella spp. between hosts. Here we analyzed the genetic and phenotypic conservation of the rdar morphotype throughout the entire Salmonella genus. The rdar morphotype was conserved in 90% of 80 isolates representing all 7 Salmonella groups; however, the frequency was only 31% in a reference set of 16 strains (Salmonella reference collection C [SARC]). Comparative gene expression analysis was used to separate cis- and trans-acting effects on promoter activity for the 16 SARC strains, focusing on the 780-bp intergenic region containing divergent promoters for the master regulator of the rdar morphotype (agfD) and the Tafi structural genes (agfB). Surprisingly, promoter functionality was conserved in most isolates, and loss of the phenotype was due primarily to defects in trans-acting regulatory factors. We hypothesize that trans differences have been caused by domestication, whereas cis differences, detected for Salmonella enterica subsp. arizonae isolates, may reflect an evolutionary change in lifestyle. Our results demonstrate that the rdar morphotype is conserved throughout the salmonellae, but they also emphasize that regulation is an important source of variability among isolates.

scholarly journals Gene Expression Analysis Indicates Divergent Mechanisms in DEN-Induced Carcinogenesis in Wild Type and Bid-Deficient Livers

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0155211 ◽  
Author(s):  
Changshun Yu ◽  
Shengmin Yan ◽  
Bilon Khambu ◽  
Xiaoyun Chen ◽  
Zheng Dong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Wild Type
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