scholarly journals Identification of cis -regulatory elements in the upstream regions of zebrafish runx3 through in silico analysis: implications for function

2014 ◽  
Vol 30 (4) ◽  
pp. 661-670 ◽  
Author(s):  
B. Simões ◽  
N. Conceição ◽  
R. N. Kelsh ◽  
M. L. Cancela
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Silico Analysis

scholarly journals Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10053
Author(s):  
Fernando Carlos Gómez-Merino ◽  
Libia Iris Trejo-Téllez ◽  
Atonaltzin García-Jiménez ◽  
Hugo Fernando Escobar-Sepúlveda ◽  
Sara Monzerrat Ramírez-Olvera
Keyword(s):  
Plant Growth ◽  
Plant Species ◽  
In Silico ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Plant Tissues ◽  
Promoter Regions ◽  
Root Cells ◽  
Physiological Processes ◽  
Silico Analysis

Background Silicon (Si) is categorized as a quasi-essential element for plants thanks to the benefits on growth, development and metabolism in a hormetic manner. Si uptake is cooperatively mediated by Lsi1 and Lsi2. Nevertheless, Lsi channels have not yet been identified and characterized in pepper (Capsicum annuum), while genes involved in major physiological processes in pepper are Si-regulated. Furthermore, Si and phytohormones may act together in regulating plant growth, metabolism and tolerance against stress. Our aim was to identify potential synergies between Si and phytohormones stimulating growth and metabolism in pepper, based on in silico data. Methods We established a hydroponic system to test the effect of Si (0, 60, 125 and 250 mg L−1 Si) on the concentrations of this element in different pepper plant tissues. We also performed an in silico analysis of putative Lsi genes from pepper and other species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum) and Arabidopsis thaliana, to look for cis-acting elements responsive to phytohormones in their promoter regions. With the Lsi1 and Lsi2 protein sequences from various plant species, we performed a phylogenetic analysis. Taking into consideration the Lsi genes retrieved from tomato, potato and Arabidopsis, an expression profiling analysis in different plant tissues was carried out. Expression of Si-regulated genes was also analyzed in response to phytohormones and different plant tissues and developmental stages in Arabidopsis. Results Si concentrations in plant tissues exhibited the following gradient: roots > stems > leaves. We were able to identify 16 Lsi1 and three Lsi2 genes in silico in the pepper genome, while putative Lsi homologs were also found in other plant species. They were mainly expressed in root tissues in the genomes analyzed. Both Lsi and Si-regulated genes displayed cis-acting elements responsive to diverse phytohormones. In Arabidopsis, Si-regulated genes were transcriptionally active in most tissues analyzed, though at different expressed levels. From the set of Si-responsive genes, the NOCS2 gene was highly expressed in germinated seeds, whereas RABH1B, and RBCS-1A, were moderately expressed in developed flowers. All genes analyzed showed responsiveness to phytohormones and phytohormone precursors. Conclusion Pepper root cells are capable of absorbing Si, but small amounts of this element are transported to the upper parts of the plant. We could identify putative Si influx (Lsi1) and efflux (Lsi2) channels that potentially participate in the absorption and transport of Si, since they are mainly expressed in roots. Both Lsi and Si-regulated genes exhibit cis-regulatory elements in their promoter regions, which are involved in phytohormone responses, pointing to a potential connection among Si, phytohormones, plant growth, and other vital physiological processes triggered by Si in pepper.

In silico analysis of EST and genomic sequences allowed the prediction of cis-regulatory elements for Entamoeba histolytica mRNA polyadenylation

2008 ◽  
Vol 32 (4) ◽  
pp. 256-263 ◽  
Author(s):  
Absalom Zamorano ◽  
César López-Camarillo ◽  
Esther Orozco ◽  
Christian Weber ◽  
Nancy Guillen ◽  
...  
Keyword(s):  
Entamoeba Histolytica ◽  
In Silico ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Genomic Sequences ◽  
Mrna Polyadenylation ◽  
Silico Analysis

Deciphering the cis-regulatory elements of co-expressed genes in PCOS by in silico analysis

Gene ◽  
2008 ◽  
Vol 408 (1-2) ◽  
pp. 72-84 ◽  
Author(s):  
Chiradeep Sarkar ◽  
Anurupa Maitra
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Silico Analysis

A systematic review with in silico analysis on transcriptomic profile of gallbladder carcinoma

2020 ◽  
Vol 47 (6) ◽  
pp. 398-408
Author(s):  
Sonam Tulsyan ◽  
Showket Hussain ◽  
Balraj Mittal ◽  
Sundeep Singh Saluja ◽  
Pranay Tanwar ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gallbladder Carcinoma ◽  
In Silico ◽  
In Silico Analysis ◽  
Transcriptomic Profile ◽  
Silico Analysis

In Silico Analysis of Single Nucleotide Polymorphism in Human Prothrombin Gene

2019 ◽  
Author(s):  
I. Farah ◽  
A. El-Mubark ◽  
M. Osman ◽  
A. Soliman ◽  
F. Ali ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
In Silico ◽  
In Silico Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Prothrombin Gene ◽  
Silico Analysis
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