Date of Publication

7-2022

Document Type

Master's Thesis

Degree Name

Master of Science in Biology

Subject Categories

Biology

College

College of Science

Department/Unit

Biology

Thesis Advisor

Mark Christian Felipe R. Redillas

Defense Panel Chair

Esperanza Maribel G. Agoo

Defense Panel Member

Chona Camille V. Abeledo
Maria Ellenita G. De Castro

Abstract/Summary

Proper monitoring of nitrogen is important in maintaining healthy and productive crops. Hence, this study aimed to design a molecular-based sensor to monitor exogenous nitrogen by employing the principle of Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP). To identify candidate genes for the RT-LAMP assay, a new algorithm was presented to identify genes that are sensitive to nitrogen starvation by adapting the fuzzy logic approach in RNA sequencing data that describes the response of rice to nitrogen stimuli. The algorithm, consisting of a two-step screening method, was designed based on the patterns of gene expression and the changes in expression to generate a list of candidate genes. Using this approach, a total of 27 genes from leaf tissues were identified to be responsive to nitrogen availability. In the absence of nitrogen, 89% of these genes were upregulated with at least a 72% change in expression. When nitrogen was re-supplied, these genes were downregulated with at least a 73% change in expression. These genes also showed association with other stressors, such as heat, drought, metal, wounds, and disease. Among them are three upregulated genes (OsCIP, DnaJ, LTPL104) and three downregulated genes, encoding a transcriptional repressor, tRNA-synthase and a hypothetical protein, that were selected for the design of the molecular sensor. LAMP primers were prepared for these candidate genes which will serve as part of the nitrogen sensor.

Abstract Format

html

Language

English

Format

Electronic

Physical Description

xi, 124 leaves

Keywords

Nitrogen; Nucleotide sequence

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Embargo Period

6-21-2023

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