Table of contents

1. Introduction to Genetics51m
2. Mendel's Laws of Inheritance3h 37m
3. Extensions to Mendelian Inheritance2h 41m
4. Genetic Mapping and Linkage2h 28m
5. Genetics of Bacteria and Viruses1h 21m
6. Chromosomal Variation1h 48m
7. DNA and Chromosome Structure56m
8. DNA Replication1h 10m
9. Mitosis and Meiosis1h 34m
10. Transcription1h 0m
11. Translation58m
12. Gene Regulation in Prokaryotes1h 19m
13. Gene Regulation in Eukaryotes44m
14. Genetic Control of Development44m
15. Genomes and Genomics1h 50m
16. Transposable Elements47m
17. Mutation, Repair, and Recombination1h 6m
18. Molecular Genetic Tools19m
- Genetic Cloning
  9m
- Methods for Analyzing DNA
  9m
19. Cancer Genetics29m
- Overview of Cancer
  21m
- Cancer Mutations
  7m
20. Quantitative Genetics1h 26m
21. Population Genetics50m
- Hardy Weinberg
  19m
- Allelic Frequency Changes
  31m
22. Evolutionary Genetics29m

15. Genomes and Genomics

Proteomics

Genetics

15. Genomes and Genomics

Proteomics

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2:07 minutes

Problem 13a

Textbook Question

The CBF genes of Arabidopsis are induced by exposure of the plants to low temperature. How would you examine the temporal and spatial patterns of expression after induction by low temperature?

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Design an experiment to monitor the expression of CBF genes over time and in different tissues. This can be achieved by creating transgenic Arabidopsis plants with a reporter gene (e.g., GFP or GUS) fused to the promoter of the CBF genes.

Expose the transgenic plants to low-temperature conditions to induce the expression of the CBF genes. Ensure that the temperature and duration of exposure are consistent across all samples.

Collect tissue samples from different parts of the plant (e.g., leaves, stems, roots) at various time points after the low-temperature exposure. This will allow you to study both temporal (time-based) and spatial (location-based) expression patterns.

Analyze the reporter gene activity in the collected samples. For example, if using GFP, observe fluorescence under a fluorescence microscope. If using GUS, perform a histochemical staining assay to visualize expression patterns.

Quantify the expression levels of the CBF genes using molecular techniques such as quantitative PCR (qPCR) or RNA sequencing (RNA-seq) to validate and complement the reporter gene data. This will provide precise temporal and spatial expression profiles.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

Gene Expression

Gene expression refers to the process by which information from a gene is used to synthesize functional gene products, typically proteins. In the context of the CBF genes in Arabidopsis, understanding how these genes are activated in response to low temperatures is crucial for studying plant responses to environmental stress.

Temporal and Spatial Patterns

Temporal patterns of gene expression involve measuring how gene activity changes over time, while spatial patterns refer to where in the plant the gene is expressed. Analyzing these patterns helps researchers understand the dynamics of CBF gene activation and its role in cold acclimation in Arabidopsis.

Induction Mechanisms

Induction mechanisms describe the processes that trigger the activation of specific genes in response to environmental stimuli, such as low temperature. Investigating these mechanisms can reveal the signaling pathways involved in the cold response and how plants adapt to changing climates.

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How can proteomics identify differences between the number of protein-coding genes predicted for a genome and the number of proteins expressed by a genome?

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How do high-throughput techniques such as computer-automated, next-generation sequencing, and mass spectrometry facilitate research in genomics and proteomics? Explain.

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Based on the tree of life in the following figure (Figure 16.12), would you expect human proteins to be more similar to fungal proteins or to plant proteins? Would you expect plant proteins to be more similar to fungal proteins or to human proteins?

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Textbook Question

The CBF genes of Arabidopsis are induced by exposure of the plants to low temperature. Can you design a method that would reveal these changes in gene expression in a way that a farmer could recognize them by observing plants growing in the field?

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Textbook Question

The two-hybrid method facilitates the discovery of protein–protein interactions. How does this technique work? Can you think of reasons for obtaining a false-positive result, that is, where the proteins encoded by two clones interact in the two-hybrid system but do not interact in the organism in which they naturally occur? Can you think of reasons you might obtain a false-negative result, in which the two proteins interact in vivo but fail to interact in the two-hybrid system?

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Textbook Question

Annotation of the human genome sequence reveals a discrepancy between the number of protein-coding genes and the number of predicted proteins actually expressed by the genome. Proteomic analysis indicates that human cells are capable of synthesizing more than 100,000 different proteins and perhaps three times this number. What is the discrepancy, and how can it be reconciled?

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An interactive Web site for the Human Proteome Map (HPM) is available at http://www.humanproteomemap.org. Visit this site, and then answer the question.

Use the 'Query' tab and select the 'Gene family' dropdown menu to do a search on the distribution of proteins encoded by a pathway of interest to you. Search in fetal tissues, adult tissues, or both.

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Textbook Question

An interactive Web site for the Human Proteome Map (HPM) is available at http://www.humanproteomemap.org. Visit this site, and then answer the question.

How many fetal tissues were analyzed?

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