scholarly journals De Novo Foliar Transcriptome of Chenopodium amaranticolor and Analysis of Its Gene Expression During Virus-Induced Hypersensitive Response

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e45953 ◽  
Author(s):  
Yongqiang Zhang ◽  
Xinwu Pei ◽  
Chao Zhang ◽  
Zifeng Lu ◽  
Zhixing Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hypersensitive Response ◽  
De Novo ◽  
Chenopodium Amaranticolor ◽  
Its Gene

Gene Expression Profile of Acute Myeloid Leukemia (AML) with t(8;16)(p11;p13) and MYST3/CREBBP Rearrangement.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2054-2054
Author(s):  
Mireia Camos ◽  
Jordi Esteve ◽  
Pedro Jares ◽  
Maria Rozman ◽  
Dolors Colomer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
De Novo ◽  
Normal Karyotype ◽  
Genetic Profile ◽  
Transferase Activity ◽  
Internal Tandem Duplication ◽  
Its Gene ◽  
Differential Expression Profile

Abstract Translocation t(8;16)(p11;p13) is an infrequent chromosomal abnormality in de novo and secondary AML cases, leading to the fusion of MYST3 (MOZ) and CREBBP (CBP) genes, both of them harboring histone lysine acetyl-transferase activity. This AML variety displays specific clinical and biological features, although its gene expression profile is currently unknown. In this study, the genetic signature of AML cases with MYST3/CREBBP rearrangement was compared with the genetic profile of other well-defined AML subtypes. Genotypic analyses using oligonucleotide U133A arrays (Affymetrix) were performed on RNA of 19 AML samples, including t(8;16)-AML (n=3), t(15;17) (n=3), t(8;21) (n=2), inv(16)/t(16;16) (n=3), t(9;11) with AF9/MLL rearrangement (n=2), 3 cases with normal karyotype and flt-3 internal tandem duplication (flt-3 ITD), the three remaining samples corresponding to monocytic cases (M4/M5) without MLL rearrangement nor flt-3 ITD. After unsupervised analysis, cases of AML with t(8;16) clustered together, displaying a differential expression profile. Supervised analysis allowed the identification of the top 53 up-regulated and 28 down-regulated genes. Among the set of genes overexpressed, genes involved in chromatin remodelling and transcription (HOXA9, HOXA10, MEIS1, CHD3, SATB1) and protooncogenes (RET, flt-3, LMO2) were identified. In contrast, CREBBP gene and several members of the JAK-STAT pathway (STAT3, STAT5B, JAK2) were underexpressed. Interestingly, overexpression of multiple homeobox genes was detected in flt-3 ITD cases, some of them as a distinctive finding (HOXA2, HOXA3, HOXB6), and others (HOXA9, HOXA10, MEIS1) were found to be highly expressed in MYST3/CREBBP and MLL-rearranged samples. In conclusion, AML with t(8;16) and MYST3/CREBBP rearrangement shows a distinctive gene expression profile, with some similarities with MLL rearranged leukemias and flt-3 ITD AML cases, thus suggesting a partially common leukemogenic pathway.

scholarly journals De Novo Characterization of Japanese Scallop Mizuhopecten yessoensis Transcriptome and Analysis of Its Gene Expression following Cadmium Exposure

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e64485 ◽  
Author(s):  
Xiao-lin Meng ◽  
Mei Liu ◽  
Ke-yong Jiang ◽  
Bao-jie Wang ◽  
Xue Tian ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Cadmium Exposure ◽  
Japanese Scallop ◽  
Mizuhopecten Yessoensis ◽  
Its Gene

scholarly journals De novo characterization of a whitefly transcriptome and analysis of its gene expression during development

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 400 ◽  
Author(s):  
Xiao-Wei Wang ◽  
Jun-Bo Luan ◽  
Jun-Min Li ◽  
Yan-Yuan Bao ◽  
Chuan-Xi Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Its Gene

scholarly journals Transcriptomic landscape of Dendrobium huoshanense and its genes related to polysaccharide biosynthesis

2018 ◽  
Vol 87 (1) ◽  
Author(s):  
Rongchun Han ◽  
Dongmei Xie ◽  
Xiaohui Tong ◽  
Wei Zhang ◽  
Gang Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Average Length ◽  
Cultivated Plants ◽  
Polysaccharide Biosynthesis ◽  
Fastq Format ◽  
Its Gene ◽  
Dendrobium Huoshanense ◽  
Morphological Differences ◽  
Illumina Hiseq4000

<em>Dendrobium huoshanense</em> has long been used to treat various diseases in oriental medicine. In order to study its gene expression profile, transcripts involved in the biosynthesis of precursors of polysaccharides, as well as mechanisms underlining morphological differences between wild and cultivated plants, three organs of both wild type and cultivated <em>D. huoshanense</em> were collected and sequenced by Illumina HiSeq4000 platform, yielding 919,409,540 raw reads in FASTQ format. After Trinity de novo assembly and quality control, 241,242 nonredundant contigs with the average length of 967.5 bp were generated. qRT-PCR experiment on the selected transcripts showed the transcriptomic data were reliable. BLASTx was conducted against NR, SwissProt, String, Pfam, and KEGG. Gene ontology annotation revealed more than 40,000 contigs assigned to catalytic activity and metabolic process, suggesting its dynamic physiological activities. By searching KEGG pathway, six genes potentially involved in mannose biosynthetic pathway were retrieved. Gene expression analysis for stems between wild and cultivated <em>D. huoshanense</em> resulted in 956 genes differentially expressed. Simple sequence repeats (SSRs) analysis revealed 143 SSRs with the unit size of 4 and 3,437 SSRs the size of 3. The obtained SSRs are the potential molecular markers for discriminating distinct cultivars of <em>D. huoshanense</em>.

scholarly journals AAV-Mediated CRISPRi and RNAi Based Gene Silencing in Mouse Hippocampal Neurons

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 324
Author(s):  
Matthias Deutsch ◽  
Anne Günther ◽  
Rodrigo Lerchundi ◽  
Christine R. Rose ◽  
Sabine Balfanz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Initiation ◽  
Hippocampal Neurons ◽  
De Novo ◽  
Protein Biosynthesis ◽  
Physiological Role ◽  
High Specificity ◽  
Hcn Channels ◽  
Proliferating Cells ◽  
Neuronal Tissues

Uncovering the physiological role of individual proteins that are part of the intricate process of cellular signaling is often a complex and challenging task. A straightforward strategy of studying a protein’s function is by manipulating the expression rate of its gene. In recent years, the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9-based technology was established as a powerful gene-editing tool for generating sequence specific changes in proliferating cells. However, obtaining homogeneous populations of transgenic post-mitotic neurons by CRISPR/Cas9 turned out to be challenging. These constraints can be partially overcome by CRISPR interference (CRISPRi), which mediates the inhibition of gene expression by competing with the transcription machinery for promoter binding and, thus, transcription initiation. Notably, CRISPR/Cas is only one of several described approaches for the manipulation of gene expression. Here, we targeted neurons with recombinant Adeno-associated viruses to induce either CRISPRi or RNA interference (RNAi), a well-established method for impairing de novo protein biosynthesis by using cellular regulatory mechanisms that induce the degradation of pre-existing mRNA. We specifically targeted hyperpolarization-activated and cyclic nucleotide-gated (HCN) channels, which are widely expressed in neuronal tissues and play essential physiological roles in maintaining biophysical characteristics in neurons. Both of the strategies reduced the expression levels of three HCN isoforms (HCN1, 2, and 4) with high specificity. Furthermore, detailed analysis revealed that the knock-down of just a single HCN isoform (HCN4) in hippocampal neurons did not affect basic electrical parameters of transduced neurons, whereas substantial changes emerged in HCN-current specific properties.

scholarly journals Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2273
Author(s):  
Menelaos Kavouras ◽  
Emmanouil E. Malandrakis ◽  
Ewout Blom ◽  
Kyriaki Tsilika ◽  
Theodoros Danis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
De Novo ◽  
Close Association ◽  
Ionic Channels ◽  
Long Term Potentiation ◽  
General Term ◽  
The Difference ◽  
Common Sole

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)–plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones.

scholarly journals GhKWL1 Upregulates GhERF105 but Its Function Is Impaired by Binding with VdISC1, a Pathogenic Effector of Verticillium dahliae

2021 ◽  
Vol 22 (14) ◽  
pp. 7328
Author(s):  
Yang Chen ◽  
Mi Zhang ◽  
Lei Wang ◽  
Xiaohan Yu ◽  
Xianbi Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transgenic Plants ◽  
Gossypium Hirsutum ◽  
Verticillium Wilt ◽  
Verticillium Dahliae ◽  
Defense Response ◽  
Upland Cotton ◽  
Effector Protein ◽  
Positive Regulator ◽  
Its Gene

Verticillium wilt, caused by Verticillium dahliae, is a devastating disease for many important crops, including cotton. Kiwellins (KWLs), a group of cysteine-rich proteins synthesized in many plants, have been shown to be involved in response to various phytopathogens. To evaluate genes for their function in resistance to Verticillium wilt, we investigated KWL homologs in cotton. Thirty-five KWL genes (GhKWLs) were identified from the genome of upland cotton (Gossypium hirsutum). Among them, GhKWL1 was shown to be localized in nucleus and cytosol, and its gene expression is induced by the infection of V. dahliae. We revealed that GhKWL1 was a positive regulator of GhERF105. Silencing of GhKWL1 resulted in a decrease, whereas overexpression led to an increase in resistance of transgenic plants to Verticillium wilt. Interestingly, through binding to GhKWL1, the pathogenic effector protein VdISC1 produced by V. dahliae could impair the defense response mediated by GhKWL1. Therefore, our study suggests there is a GhKWL1-mediated defense response in cotton, which can be hijacked by V. dahliae through the interaction of VdISC1 with GhKWL1.

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