Arabidopsis Thaliana Essay

1758 words - 7 pages

Project Proposal:
AIMS
- Bioinformatic approach to aid gene identification and characterisation in
Arabidopsis thaliana
- Evaluate and integrate the accuracy of Arabidopsis database

INTRODUCTION:
Arabidopsis thaliana is a model plant for research and has been used wisely to study many aspects of plant biology. There is significant amount of information about this plant in the database, such as fully sequenced and annotated genomic sequence, extensive expressional data and functional characterisation data. This project aims at using such information to aid gene identification.
The project will focus on a specific region (between AGIs 18,500,000 & 19,800,000) on Chromosome V, where a gene involved in root development has been mapped.

OBJECTIVES:
The project has three types of objectives they are:
1) To identify all possible genes in the region and most importantly to check whether there are genes mis- or incorrectly-annotated using sequence analyses

2) To establish the expression patterns and regulations of the genes using available microarray data.

3) And literature search of evidence for the functional properties of the genes of their homologues. The analyses will help to build an integrated picture which shows the genes in the region together with their expression profiles and functional properties. Such information can be used to guide our experimental strategy towards the identification of the interested gene and will provide a case-study for using bioinformatics approach to aid traditional genetic approach in gene identification.
Biological Background of Arabidopsis thaliana
Arabidopsis thaliana is a unique among plant model organisms due to its short life
Cycle (Heh and Bülow 2008 ) and in having a small genome, excellent physical and genetic maps, and some amount of repetitive DNA(Lin, Kaul et al. 1999).
Arabidopsis thaliana is the first plant for which the complete genome has been sequenced. The 120 megabase genome of Arabidopsis is formed into five chromosomes and consists of an approximate 20,000 genes(Sato, Kotani et al. 1997) . In this project we will focus on a specific region on chromosome V, where a gene involved in root development has been mapped.Chromosome V is 26 mega bases long and it also the second largest regions of genome(Tabata, Kaneko et al. 2000). The entire genome of chromosome 5, excluding the centromeric and telomeric regions, was covered up by two large contigs 11.6 Mb and 14.2 Mb long separated by the centromeric region(Kotani, Sato et al. 1997).The 5,874 genes encoded on chromosome 5 reveal several new functions in plant, and the patterns of gene organization provides insights into the mechanism and extent of genome evolution in plants(Tabata, Kaneko et al. 2000).
Arabidopsis thaliana is a member of the mustard family Cruciferae or Brassicaceae with a natural distribution all around Europe, Asia, and North. Many different ecotypes have been collected from natural...

Find Another Essay On Arabidopsis Thaliana

Letter of Interest Essay

728 words - 3 pages characterisation Cloning and molecular characterization constituted a major part of my PhD research. Here I cloned and sequenced genes in B. napus homologous to genes in Arabidopsis thaliana. I developed molecular markers from these gene sequences which in addition to other marker systems (including inter simple sequence repeats, intron length polymorphism) were used in molecular characterization of more than 150 canola genotypes. Enzymology

The Impact of Chloroplast Movement in Plant Cells

729 words - 3 pages (HFR) forces the chloroplasts to move to a position where lowest possible light absorption takes place, in order to evade photo-damage. (Serlin and Roux, 1984) during high fluence irradiation the chloroplasts are situated in periphery and move onto the anticlinal walls. Secondly, chloroplast movement in plant species is revealed to be most effective under blue light. In a model study involving Arabidopsis thaliana, it was found that

Characterization of LYM Genes in Medicago Truncatula

1705 words - 7 pages , most of the annotated genomes contain at least two LYM-type proteins, with the exception of Mimulus guttatus for which in the present release (JGI release v1.0) only one could be found. For all other genomes, always at least one LYM1-like and one LYM2-like protein was detected. They were named, in accordance with the designation for the LYMs from M. truncatula and Arabidopsis thaliana, LYM1 or LYM2 if a GPI-anchor was predicted, or LYM3 and LYM4

Timeline of Biotecnology

1025 words - 4 pages map of the genome of a food plant completed: Rice2000 First complete map of a plant genome developed: Arabidopsis thaliana 108.9 million acres of biotech crops grown in 13 countries "Golden Rice" announcement allows the technology to be available to developing countries in hopes of improving the health of undernourished people and curing some forms of blindness First biotech crop field tested in Kenya: Virus resistant sweet potato

Revealing Metabolic Phenotypes in Plant

1631 words - 7 pages Biomarker Discovery and Gene Function Analysis. 2003. Springer - Kell, D. B. (2004) Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7, 296–307. - Kikuchi J, K Shinozaki, T Hirayama. . Stable Isotope Labeling of Arabidopsis thaliana for an NMR-Based Metabolomics Approach.2004 Plant Cell Physiology 45: 1099–1104. - Krishnan P, Kruger NJ, Ratcliffe RG. Metabolite fingerprinting and profiling in plants using NMR. J

A summary analysis of the article “Microarray detection of food-borne pathogens using specific probes prepared by comparative genomics.”

1823 words - 7 pages . Controls and Microarray fabrication The authors’ created positive and negative controls utilizing the putative tubulin beta-4 chain (Tb-4) and the actin-3 gene (A-3) of Arabidopsis thaliana and were amplified by PCR with appropriate primers. The PCR products were then cloned into plasmid vector pMD18-T and stored at -20°C. The sequence of the Tb-4 was used as the positive control as this sequence did not exhibit homology with any of the bacterial

Plants And Seeds Of Hybrid Corn Variety

9751 words - 39 pages (18:0) CoA (McDonough et al., 1992); a gene encoding a stearoyl-acyl carrier protein delta-9 desaturase from castor (Fox et al. 1993); Δ6- and Δ12-desaturases from the cyanobacteria Synechocystis responsible for the conversion of linoleic acid (18:2) to gamma-linolenic acid (18:3 gamma) (Reddy et al. 1993); a gene from Arabidopsis thaliana that encodes an omega-3 desaturase (Arondel et al. 1992)); plant Δ9-desaturases (PCT

Reality and Illusion in Shakespeare's Hamlet - Reality, Appearance and Deception

896 words - 4 pages Reality and Illusion in Hamlet   Shakespeare’s play, Hamlet, begins with the appearance of a ghost, an apparition, possibly a hallucination. Thus, from the beginning, Shakespeare presents the air of uncertainty, of the unnatural, which drives the action of the play and develops in the protagonist as a struggle to clarify what only seems to be absolute and what is actually reality. Hamlet's mind, therefore, becomes the central force of the

Sub-plots in Hamlet

1118 words - 4 pages Sub-plots in Hamlet   There are many things that critics say make Hamlet a "Great Work," one of which is the way that Shakespeare masterfully incorporates so many sub-plots into the story, and ties them all into the main plot of Hamlet’s revenge of his father’s murder. By the end of Act I, not only is the main plot identified, but many other sub-plots are introduced. Among the sub-plots are trust in the Ghost of King Hamlet, Fortinbras, and

Hamlet as Victim and Hero

1301 words - 5 pages Hamlet as Victim and Hero      Hamlet, Prince of Denmark, a Shakespearean tragedy, tells the story of Prince Hamlet, who gained the knowledge of a terrible incident that his kingdom had suffered. Claudius, the king of Denmark and Hamlet's uncle, had killed his own brother, the king, who was also the father of Hamlet, and married his brother's widow. Hamlet suffered these traumas to a severe degree, and his only relief was to defeat his

Essay on Light and Dark in Antigone

1188 words - 5 pages Use of Light and Dark in Antigone   The "Golden Age" of Greece is noted for its many contributions to the creative world, especially in its development of the play. These performances strived to emphasize Greek morals, and were produced principally for this purpose. Antigone, by Sophocles, is typical. The moral focused on in Antigone is the conflict between physis (nature) and nomos (law), with physis ultimately presiding over nomos

Similar Essays

Dna Replication And Heterochromatin Essay

1724 words - 7 pages Important Non-CG DNA Methylation in Arabidopsis. PLoS Genet 2: e83. 2 Dinh T.T, O’Leary M, Won S.Y, Li S, Arroyo L, Liu X, Defries A, Zheng B, Cutler S.R, Chen X. 2013. Generation of a luciferase-based reporter for CHH and CG DNA methylation in Atabidopsis thaliana. Silence 4:1. 3 Du J, Zhong X, Bernatavichute YV, Stroud H, Feng S, et al. 2012. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants

Ethylene Genetics Essay

7685 words - 31 pages Abstract Hormones play an important role in plant growth and development. Ethylene is one such hormone and the past decade has seen major components of the ethylene response pathway in plants being identified and characterized. Ethylene regulates responses at a number of levels and molecular genetic analysis of ethylene signaling in Arabidopsis thaliana has identified a number of gentic loci that encode proteins involved in the ethylene response

Dna Sequences Occurs At Many Scales Within Genomes Discussion

2417 words - 10 pages demonstrated by Seoighe and Gehring, 2004. Arabidopsis thaliana was known to have been the result of multiple rounds of genome duplication and subsequent gene deletions and modifications. In their study, Seoighe and Gehring revealed that the probability of genes being retained after whole genome duplication was higher if the genes were retained after a previous genome duplication event. By investigating the function of the genes retained, it was

The Assembly And Maintenance Of Heterochromatin

1295 words - 5 pages Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana. PLoS One. 8; 3(9):e3156. 6. Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J and Jacobsen SE. (2007). The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol. 20; 17(4):379-84. 7. Jiamu Du, Xuehua Zhong, Yana V. Bernatavichute, Hume Stroud, Suhua Feng, and Elena Caro. (2012). Dual Binding of Chromomethylase