Long-term genome-wide blood RNA expression profiles yield novel molecular response candidates for IFN-β-1b treatment in relapsing remitting MS

2010 ◽  
Vol 11 (2) ◽  
pp. 147-161 ◽  
Author(s):  
Robert H Goertsches ◽  
Michael Hecker ◽  
Dirk Koczan ◽  
Pablo Serrano-Fernandez ◽  
Steffen Moeller ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Rna Expression ◽  
Molecular Response ◽  
Genome Wide ◽  
Relapsing Remitting

Genome-wide analysis of long non-coding RNA expression profiles in keratinocytes from psoriasis skin

2021 ◽  
Author(s):  
Longlong Luo ◽  
Nupur khera ◽  
Andor Pivarcsi ◽  
Ankit Srivastava ◽  
Lorenzo Pasquali ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Rna Expression ◽  
Genome Wide Analysis ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Long Non Coding Rna

scholarly journals Transcriptome signature of E. coli under a prolonged starvation environment

2020 ◽  
Author(s):  
Sotaro Takano ◽  
Hiromi Takahashi ◽  
Yoshie Yama ◽  
Ryo Miyazaki ◽  
Saburo Tsuru
Keyword(s):  
Stationary Phase ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Physiological State ◽  
Exponential Growth Phase ◽  
Transcriptional Responses ◽  
E Coli ◽  
Viable Cells ◽  
Genome Wide

ABSTRACTBackground“Non-growing” is a dominant life form of microorganisms in nature, where available nutrients and resources are extremely limited. However, the knowledge of the manner in which microorganisms resist nutrient deficiency is still rudimentary compared to those of the growing cells. In laboratory culture, Escherichia coli can survive for several years under starvation, denoted as long-term stationary phase (LSP), where a small fraction of the cells survive by recycling resources released from the starved nonviable cells and constitute a model system for understanding survival mechanisms under long-term starvation. Although the physiology by which viable cells in LSP adapt to long-term starvation is of great interest, their genome-wide response has not yet been fully understood.ResultsTo understand the physiological state of viable cells in the LSP environment, we analyzed the transcriptional profiles of cells exposed to the supernatant of LSP culture. We found that high expression of transporter genes and low expression of biosynthesis genes are the primary responses of the cells in the LSP supernatant compared to growing cells, which display similar responses to cells entering the stationary phase from the exponential growth phase. We also revealed some specific transcriptional responses in the LSP supernatant, such as higher expression of stress-response genes and lower expression of translation-related genes, compared to other non-growing conditions. This suggests that cells in LSP are highly efficient in terms of cellular survival and maintenance functions under starvation conditions. We also found population-density-dependent gene expression profiles in LSP, which are also informative to understand the survival mechanism of bacterial population.ConclusionOur current comprehensive analysis of the transcriptome of E. coli cells provides an overview of the genome-wide response to the long-term starvation environment. We detected both common and distinctive responses in the primary transcriptional changes between the short- and long-term stationary phase cultures, which could provide clues to understand the possible molecular mechanisms underlying survivability in the starved environment.

COMPUTATIONAL STRATEGY FOR DISCOVERING DRUGGABLE GENE NETWORKS FROM GENOME-WIDE RNA EXPRESSION PROFILES

2005 ◽  
Author(s):  
SEIYA IMOTO ◽  
YOSHINORI TAMADA ◽  
HIROMITSU ARAKI ◽  
KAORI YASUDA ◽  
CRISTIN G. PRINT ◽  
...  
Keyword(s):  
Gene Networks ◽  
Expression Profiles ◽  
Rna Expression ◽  
Genome Wide ◽  
Computational Strategy

scholarly journals Genome-Wide Analysis of HAK/KUP/KT Potassium Transporter Genes in Banana (Musa Acuminata L.) and Their Tissue-Specific Expression Profiles Under Potassium Stress

2021 ◽  
Author(s):  
Siwen Liu ◽  
Bangting Wu ◽  
Yanling Xie ◽  
Sijun Zheng ◽  
Jianghui Xie ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Specific Expression ◽  
Genome Wide ◽  
Low Potassium ◽  
Duplication Events ◽  
Osmotic Balance ◽  
Short And Long Term ◽  
Low K

Abstract Potassium is one of the most essential inorganic cations for plant growth and development. The high affinity K+ (HAK)/K+ uptake (KUP)/K+ transporter (KT) family plays essential roles in the regulation of cellular K+ levels and the maintenance of osmotic balance. However, the roles of these genes in the responses of bananas to low-potassium stress are unclear. In this study, 24 HAK/KUP/KT (MaHAK) genes were identified from banana genomic data. These genes were further classified into four groups based on phylogenetic analysis, gene structure and conserved domain analysis. Segmental duplication events played an important role in the expansion of the MaHAK gene family. Transcriptome analysis revealed the expression patterns of MaHAKs in various tissues under different K+ conditions. MaHAK14b was upregulated under both short- and long-term K+-deficient conditions, suggesting that it plays crucial roles in K+ uptake at low K+ concentrations. Furthermore, MaHAK14b mediated K+ uptake when it was heterologously expressed in the yeast mutant R5421 on low K+ medium. Collectively, these findings provide a foundation for further functional analysis of MaHAK genes, which may be used to improve stress resistance in bananas.

scholarly journals Genome-wide analysis of long noncoding RNA expression profiles in patients with non-alcoholic fatty liver disease

IUBMB Life ◽  
2015 ◽  
Vol 67 (11) ◽  
pp. 847-852 ◽  
Author(s):  
Chuanzheng Sun ◽  
Xunyang Liu ◽  
Zhongjie Yi ◽  
Xuefei Xiao ◽  
Mingshi Yang ◽  
...  
Keyword(s):  
Liver Disease ◽  
Long Noncoding Rna ◽  
Fatty Liver Disease ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Rna Expression ◽  
Alcoholic Fatty Liver ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Alcoholic Fatty Liver Disease

Genome-Wide Analysis of Long Noncoding RNA Expression Profiles in Human Xuanwei Lung Cancer

2015 ◽  
Vol 61 (10/2015) ◽  
Author(s):  
Qing Li ◽  
Chunyan Wu ◽  
Guibo Song ◽  
Hui Zhang ◽  
Bin Shan ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Rna Expression ◽  
Genome Wide Analysis ◽  
Genome Wide
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