Introduction to Genomics Activity

INTRODUCTION TO GENOMICS ACTIVITY

Post-AP DNA/Genetics ~ INVESTIGATING THE COMPLEXITY OF SPECIES ~ A closer look into the numbers of chromosomes and genes in organisms Background With advancements in biotechnology has come the ability to decode the genetic information of organisms: What instructions are written in the DNA of chromosomes? If the diploid number of chromosomes in an organism is known by studying its cells under a microscope, can we then deduce approximately how many genes are found in that species and therefore have an idea of the overall complexity of that species? Let’s investigate!

Purpose To investigate whether or not there is a correlation between the number of chromosomes in a species and the total estimated number of genes in that species.

Pre-Lab Brainstorming (Record Your Response in your lab journal) A) After reading the information provided so far in this activity, what variables will you be investigating in this exercise? (Hint: They are both referred to as “dependent” variables in this activity).

Variables:

B) Discuss with your lab partner(s) what your thoughts are regarding a relationship between the number of chromosomes in a species and the number of genes in that species. Write your hypothesis in the space provided below.

Hypothesis:

C) Do you feel that the number of genes is a good indicator of species’ complexity? Explain why or why not.

Procedure

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(Though you may be working with a partner in this investigation, you are individually responsible for having all of the data and information recorded on your own lab journal.)

1. In this investigation, you will be researching genetic information on the various species described below and recording two pieces of critical information: 1) the number of diploid chromosomes found in that species, and 2) the estimated number of total genes found in that species. Create a data table in your lab journal suitable for recording this data on the ten different organisms.

Species to Investigate:

Escherichia coli (often abbreviated as E. coli) are a type of large and diverse group of bacteria that are commonly found in the lower intestines of warm blooded organisms (like you!). Though most strains are harmless, some can make you very sick.

Saccharomyces cerevisiae is commonly called “baker’s yeast” or “brewer’s yeast”. Yeast are single-celled fungi which ferment sugars, such as those present in bread dough or grain mixtures when creating alcohol. The yeast release carbon dioxide and ethanol during fermentation.

Drosophila melanogaster is a two-winged insect commonly known as a fruit fly and is one of the most commonly used model organisms in biology (including studies in genetics, physiology and life history evolution).

Caenorhabditis elegans is a microscopic (~1 mm) nematode (roundworm) that normally lives in soil. It has become one of the "model" organisms in biology.

Paracentrotus lividus is a globe-shaped sea urchin covered with spines that are long, thick and smooth. Its color can vary between violet, green and brown. It is found in the Atlantic Ocean up to West Ireland and also in the Mediterranean Sea.

Arabidopsis thaliana is small flowering plant native to Europe, Asia, and northwestern Africa. Arabidopsis is a popular model organism in plant biology and genetics and is a common tool used for understanding the molecular biology of many plant traits, including flower development and light sensing.

Oryza sativa, or rice, is a staple for a large part of the world's human population, especially in tropical Latin America and Asia. It is the second-most consumed cereal grain and has the potential to improve nutrition, boost food security, foster rural development and support sustainable land care globally. Rice provides more than one fifth of the calories consumed worldwide by humans.

Mus musculus, also known as the “house mouse”, is a small mammal and a rodent. In most parts of the world, they live in close proximity to humans. They are by far the most commonly used laboratory mammal and are some of the most important model organisms in biology and medicine.

Canis familiaris is the scientific name of dogs, which are a domesticated subspecies of the wolf. The domestic dog has been one of the most widely kept working and companion animals in human history, as well as being a food source in some cultures. There are estimated to be 400 million dogs in the world.

Homo sapiens, or humans, are bipedal (stand on 2 feet) primates in the family Hominidae. Humans have a highly developed brain that is capable of abstract reasoning, language, introspection, and emotion. DNA evidence indicates that modern humans originated in Africa about 250,000 years ago.

2. Once you have read the descriptions of the species that you are responsible for investigating, use the Internet to research the critical information that is needed on each of the organisms. (Some sites

- 6 - INTRODUCTION TO GENOMICS ACTIVITY you may find beneficial in your search are http://en.wikipedia.org/wiki/Gene and http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html).

*Create a list below of every website you and your partner(s) found useful in your lab journal:

3. Once you have finished your research, review and discuss with you partner(s) the data you’ve collected and whether or not you feel your initial hypothesis regarding a correlation between chromosome number and number of genes was supported by your findings.

Briefly describe your ideas regarding this relationship in your lab journal:

4. In-depth Analysis: In order to understand data sets more clearly and determine whether patterns or relationships exist that may not be clearly evident, statistical tests have been devised to help researchers make conclusions on the data that has been collected. How do we know if there is a significant correlation between chromosome number in a species and the number of genes in that species? We must subject this data to a statistical test…

Statistical Analysis:

You will be using a test referred to as the Sign Test (Correlation) that will allow you to understand if there actually is a correlation between your two variables, or if there is no predictable pattern to the variables at all. The steps for performing the test follow…

Sign Test (Correlation)

Purpose: The sign test for correlation is used to determine if a significant positive or negative relationship exists between two variables from a single sample.

What are your “two variables”?______( in your lab journal)

What is each “sample” in your investigation?______( in your lab journal)

- You have been provided with a data table below to statistically analyze your data. Use your previous data table to fill in the required values in columns 1, 2, and 3 in this table.

- To perform this test, the individual data values are coded based on their relative positions to the medians of each variable. To determine the medians in your data, order all of the chromosome numbers that you collected from smallest to largest: The “median” value is the number directly in the

middle of the list. However, since there is an even number of values in your list, the median is then determined by finding the average of the two values found in the middle. Record the median value for chromosome number in the data table (M = ____ ). Next, use these same steps to determine the median value for the gene number for the species and record this value in the data table (M = ____ ).

Sign Test (Correlation) Data Table:

Name of Chromosome Number of Chromosome Gene Number Sign Score Organism Number Genes Number Code Code (+, -, 0) M = M =

- To determine the codes for the variables of each organism, fill in the chart appropriately with the following symbols:

< for values less than the median, > for values greater than the median, and = for values equal to the median.

- Then the data pair codes for each experimental unit are evaluated and given a “Sign Score”:

 If both codes are the same inequality symbol (i.e., < and <, or > and >), this indicates a positive correlation and is scored as a 'plus' (+),

 If either code is =, this indicates no correlation and is scored as a 'zero' (0),

 If the two codes are different inequality symbols (i.e., < and >, or > and <), this indicates a negative correlation and is scored as a 'minus' (-).

The numbers of 'plus' and 'minus' scores are used with a Sign Test Lookup Table to determine the statistical significance of the data (tables are supplied at end of lab). An “X” in the specific box corresponding to your values means the correlation between chromosome number and number of genes in species is statistically significant (for example, a higher chromosome number indicates a greater number of genes). If no “X” is seen in the corresponding box, the data does not indicate a correlation between the two variables. In this case, the null hypothesis (which is the expectation that there is no correlation) cannot be rejected.

Analysis and Conclusions

1. Define the terms chromosome and gene. Is either a valid indicator of species’ complexity?

2. Describe how it is possible that an organism can have a small number of chromosomes yet a very large number of genes.

3. What do your data and analysis allow you to conclude regarding the initial purpose of this lab investigation? Explain how this conclusion compares to your initial hypothesis.

4. Explain using your Sign Test (correlation) data table and Sign Lookup Table what it means for the data to be “statistically significant.” In other words, how does this test show whether or not a correlation between variables exists?

5. Genes encode proteins within cells. They are the “instruction books” on all the proteins that can be made. Hypothesize how it may be possible that the human “proteome” (the total amount of different types of proteins made in body) may be much larger than our “genome” (the total amount of protein- encoding genes within the body). Refer to the information found at http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HGP.html if you’re really stuck!

Sign Test Lookup Tables One-Tailed Table: look up larger value in columns & smaller value in rows; an X indicates a statistically significant difference (P < 0.05) *Use this table if there was a “directionality” to your expectations (hypothesis) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 0 X X X X X X X X X X X X X X X X X X X X X X X X X X 1 X X X X X X X X X X X X X X X X X X X X X X X X 2 X X X X X X X X X X X X X X X X X X X X X X 3 X X X X X X X X X X X X X X X X X X X X X

4 X X X X X X X X X X X X X X X X X X X 5 X X X X X X X X X X X X X X X X X X 6 X X X X X X X X X X X X X X X X 7 X X X X X X X X X X X X X X 8 X X X X X X X X X X X X X 9 X X X X X X X X X X X X 10 X X X X X X X X X X X 11 X X X X X X X X X 12 X X X X X X X X 13 X X X X X X X 14 X X X X X 15 X X X X 16 X X X 17 X 18

Two-Tailed Table: look up larger value in columns & smaller value in rows; an X indicates a statistically significant difference (P < 0.05) *Use this table if there was no “directionality” to your expectations (hypothesis)

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 0 X X X X X X X X X X X X X X X X X X X X X X X X X 1 X X X X X X X X X X X X X X X X X X X X X X 2 X X X X X X X X X X X X X X X X X X X X X 3 X X X X X X X X X X X X X X X X X X X 4 X X X X X X X X X X X X X X X X X X 5 X X X X X X X X X X X X X X X X 6 X X X X X X X X X X X X X X 7 X X X X X X X X X X X X X 8 X X X X X X X X X X X 9 X X X X X X X X X X 10 X X X X X X X X 11 X X X X X X X 12 X X X X X X 13 X X X X 14 X X X 15 X X 16 Suggested data table instead of creating their own: (below)

Sample Data Table:

Name of Organism Number of chromosomes Number of estimated in species genes in species

*This investigation was designed in 2008 using current genetic information that was available online. If in the future adjustments are made to the accepted numbers of genes in various species, the results of the Sign Test of Correlation may be different than what is seen here.

Results: Estimated number of genes in species, along with the diploid chromosome number…

References -

1. http://www.cdc.gov/nczved/dfbmd/disease_listing/stec_gi.html#1

2. http://www.microbiologybytes.com/video/Scerevisiae.html

3. http://en.wikipedia.org/wiki/Drosophila_melanogaster

4. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Caen.elegans.html

5. http://www.european-marine-life.org/30/paracentrotus-lividus.php

6. http://en.wikipedia.org/wiki/Arabidopsis_thaliana

7. http://en.wikipedia.org/wiki/Rice

8. http://en.wikipedia.org/wiki/Mus_musculus

9. http://en.wikipedia.org/wiki/Dog

10. http://en.wikipedia.org/wiki/Human

11. http://en.wikipedia.org/wiki/Gene

12. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html

13. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HGP.html

14. Kent, B. (2008) LFSC 725 – Statistics and Experimental Design. UMD Image References -

Chromosome: http://www.accessexcellence.org/RC/VL/GG/images/genes.gif

E. Coli: http://www.cdc.gov/nczved/dfbmd/disease_listing/stec_gi.html#1

Yeast: http://www.chateauneuf.dk/artikler/vini15.jpg

Fruit fly: http://www.life.uiuc.edu/hing/research/Fly%20Figures/fig-1.jpg

Roundworm: http://www.mun.ca/biology/scarr/4241_Devo_Caenorhabditis%20elegans.jpg

Sea Urchin: http://www.marlin.ac.uk/imgs/Species/Echinodermata/o_parliv.jpg

Arabidopsis thaliana: http://www.delawarewildflowers.org/arabidopsis_thaliana.jpg

Rice: http://botany.cs.tamu.edu/FLORA/dcs420/fa07/fa07090.jpg

Mouse: http://www.dkimages.com/discover/previews/976/80071075.JPG

Dog: http://www.petfoodindustry.com/uploadedImages/Petfood_Industry/Petfood_Industry_Articles/0709PETgene2_opt(1).jpg

Humans: http://www.3dscience.com/img/Resources/Human-anatomy-zygote.jpg