scholarly journals A systems biology approach identifies new regulators of poplar root development under low nitrogen

2015 ◽  
Vol 84 (2) ◽  
pp. 335-346 ◽  
Author(s):  
Madhumita Dash ◽  
Yordan S. Yordanov ◽  
Tatyana Georgieva ◽  
Sapna Kumari ◽  
Hairong Wei ◽  
...  
Keyword(s):  
Systems Biology ◽  
Root Development ◽  
Poplar Root ◽  
Low Nitrogen

scholarly journals A network of genes associated with poplar root development in response to low nitrogen

2016 ◽  
Vol 11 (8) ◽  
pp. e1214792 ◽  
Author(s):  
Madhumita Dash ◽  
Yordan S. Yordanov ◽  
Tatyana Georgieva ◽  
Sapna Kumari ◽  
Hairong Wei ◽  
...  
Keyword(s):  
Root Development ◽  
Poplar Root ◽  
Low Nitrogen

scholarly journals Genetic networks involved in poplar root response to low nitrogen

2013 ◽  
Vol 8 (11) ◽  
pp. e27211 ◽  
Author(s):  
Hairong Wei ◽  
Yordan Yordanov ◽  
Sapna Kumari ◽  
Tatyana Georgieva ◽  
Victor Busov
Keyword(s):  
Genetic Networks ◽  
Root Response ◽  
Poplar Root ◽  
Low Nitrogen

scholarly journals A systems biology approach to root development

2006 ◽  
Vol 295 (1) ◽  
pp. 345
Author(s):  
Philip N. Benfey ◽  
Ji-Young Lee ◽  
Juliette Colinas ◽  
Hongchang Cui ◽  
Richard Twigg ◽  
...  
Keyword(s):  
Systems Biology ◽  
Root Development

A systems approach to understanding root development

2006 ◽  
Vol 84 (5) ◽  
pp. 695-701 ◽  
Author(s):  
Siobhan M. Brady ◽  
Philip N. Benfey
Keyword(s):  
Systems Biology ◽  
Systems Theory ◽  
Root Development ◽  
Evolutionary Biology ◽  
Systems Approach ◽  
Process Analysis ◽  
Model Organisms ◽  
Current Status ◽  
Data Sets ◽  
Component Identification

Systems theory has been applied to process analysis in a variety of scientific disciplines from engineering to evolutionary biology. In the recent postgenomic era, the accumulation of an enormous amount of data gained from a variety of technologies has led to a revisiting of systems theory concepts. This systems biology approach has been integral in understanding a variety of processes in a number of model organisms. This review gives an overview of systems biology approaches, from component identification to modeling of networks. Various features of the root, including its development and the availability of high resolution gene expression data sets that describe root development, make the root amenable to a systems approach. The current status of systems approaches to understanding root development is reviewed.

scholarly journals SiMYB3 in Foxtail Millet (Setaria italica) Confers Tolerance to Low-Nitrogen Stress by Regulating Root Growth in Transgenic Plants

2019 ◽  
Vol 20 (22) ◽  
pp. 5741 ◽  
Author(s):  
Linhao Ge ◽  
Yining Dou ◽  
Maomao Li ◽  
Pengju Qu ◽  
Zhang He ◽  
...  
Keyword(s):  
Root Development ◽  
Plant Root ◽  
Expression Patterns ◽  
Protein Structures ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Nitrogen Stress ◽  
Auxin Synthesis ◽  
Low Nitrogen Stress ◽  
Low Nitrogen

Foxtail millet (Setaria italica), which originated in China, has a strong tolerance to low nutrition stresses. However, the mechanism of foxtail millet tolerance to low-nitrogen stress is still unknown. In this study, the transcriptome of foxtail millet under low-nitrogen stress was systematically analyzed. Expression of 1891 genes was altered, including 1318 up-regulated genes and 573 down-regulated genes. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that 3% of these genes were involved in membrane transport and 5% were involved in redox processes. There were 74 total transcription factor (TF) genes in the DEGs (differentially expressed genes), and MYB-like transcription factors accounted for one-third (25) of the TF genes. We systematically analyzed the characteristics, expression patterns, chromosome locations, and protein structures of 25 MYB-like genes. The analysis of gene function showed that Arabidopsis and rice overexpressing SiMYB3 had better root development than WT under low-nitrogen stress. Moreover, EMSA results showed that SiMYB3 protein could specifically bind MYB elements in the promoter region of TAR2, an auxin synthesis related gene and MYB3-TAR2 regulate pair conserved in rice and foxtail millet. These results suggested that SiMYB3 can regulate root development by regulating plant root auxin synthesis under low-nitrogen conditions.

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

2019 ◽  
Vol 42 ◽  
Author(s):  
J. Alfredo Blakeley-Ruiz ◽  
Carlee S. McClintock ◽  
Ralph Lydic ◽  
Helen A. Baghdoyan ◽  
James J. Choo ◽  
...  
Keyword(s):  
Systems Biology ◽  
High Resolution ◽  
Experimental Design ◽  
Integrated Systems ◽  
Microbiome Research ◽  
Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

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