Salomon Garcia: Week 11

Preparation for Journal Club 3

• Link to the Journal Article:
  1. van de Mortel JE, Almar Villanueva L, Schat H, Kwekkeboom J, Coughlan S, Moerland PD, Ver Loren van Themaat E, Koornneef M, and Aarts MG. Large expression differences in genes for iron and zinc homeostasis, stress response, and lignin biosynthesis distinguish roots of Arabidopsis thaliana and the related metal hyperaccumulator Thlaspi caerulescens. Plant Physiol. 2006 Nov;142(3):1127-47. DOI:10.1104/pp.106.082073 |

     van de Mortel et al. (2006) link to full text

• Link to the Powerpoint presentation for Journal Club 3:
• Link to the Data Set: Data Set

Ten New Words from the van de Mortel paper

1. Hydroponic- the cultivation of plants by placing the roots in liquid nutrient solutions rather than in soil; soilless growth of plants.http://dictionary.reference.com/browse/hydroponic
2. Hyperaccumulator-A plant is said to be a hyperaccumulator if it can concentrate the pollutants in a minimum percentage which varies according to the pollutant involved.http://en.wikipedia.org/wiki/Hyperaccumulator#Hyperaccumulators_and_biotic_interactions
3. putative genes-a putative gene is a piece of DNA thought to be a gene based on sequence (ex. Open Reading Frame) but either the protein produced or the function of what is thought to be the expressed protein is not known.http://wiki.answers.com/Q/What_is_putative_gene
4. ethylene biosynthesis- Protein involved in the synthesis of ethylene (C2H4), an unsaturated hydrocarbon gas mainly produced in plants. It has developmental effects as a hormone, including growth inhibition, regulation of fruit development, leaf abscission and aging.http://www.uniprot.org/keywords/KW-0266
5. lignin biosynthesis-begins in the cytosol with the synthesis of glycosylated monolignols from the amino acid phenylalanine. http://en.wikipedia.org/wiki/Lignin#Biosynthesis
6. nonaccumulator-
7. defensin genes-defensin, alpha 1, is found in the microbicidal granules of neutrophils and likely plays a role in phagocyte-mediated host defense.http://en.wikipedia.org/wiki/Defensin,_alpha_1
8. vacuolar transporter-
9. suberin biosynthesis- The biosynthesis of the aliphatic monomers shares the same upstream reactions with cutin biosynthesis, and the biosynthesis of aromatics shares the same upstream reactions with lignin biosynthesis. Lignin and suberin are the only known biological polymers that are irregular. http://en.wikipedia.org/wiki/Suberin
10. lignification- a change in the character of a cell wall, by which it becomes harder. It is supposed to be due to an incrustation of lignin.http://www.biology-online.org/dictionary/Lignification

Outline

• Introduction

BIOL 398-01: Bioinformatics Lab

• Lab Journal

Salomon Garcia: Week 2	Salomon Garcia: Week 6	Salomon Garcia: Week 11
Salomon Garcia: Week 3	Salomon Garcia: Week 7	Salomon Garcia: Week 12
Salomon Garcia: Week 4	Salomon Garcia: Week 8	Salomon Garcia: Week 13
Salomon Garcia: Week 5	Salomon Garcia: Week 9	Salomon Garcia: Week 14

• Shared Journal

1. BIOL398-01/S10:Class Journal Week 2
2. BIOL398-01/S10:Class Journal Week 3
3. BIOL398-01/S10:Class Journal Week 4
4. BIOL398-01/S10:Class Journal Week 5
5. BIOL398-01/S10:Class Journal Week 6
6. BIOL398-01/S10:Class Journal Week 7
7. BIOL398-01/S10:Class Journal Week 8
8. BIOL398-01/S10:Class Journal Week 9
9. BIOL398-01/S10:Class Journal Week 11
10. BIOL398-01/S10:Class Journal Week 12
11. BIOL398-01/S10:Class Journal Week 13
12. BIOL398-01/S10:Class Journal Week 14

• Assignments

1. BIOL398-01/S10:Week 2
2. BIOL398-01/S10:Week 3
3. BIOL398-01/S10:Week 4
4. BIOL398-01/S10:Week 5
5. BIOL398-01/S10:Week 6
6. BIOL398-01/S10:Week 7
7. BIOL398-01/S10:Week 8
8. BIOL398-01/S10:Week 9
9. BIOL398-01/S10:Week 11
10. BIOL398-01/S10:Week 12
11. BIOL398-01/S10:Week 13
12. BIOL398-01/S10:Week 14

Links

• Salomon Garcia Valencia
• Bioinformatics Lab Home