Lab 02 - Epistasis and hypothesis testing

We developed lab guide 02 of this quarter.

We used F2 genetic corn (corn cobs with yellow, red and purple kernels)  to test whether the phenotypic ratios  (yellow or red/purple kernels) follow the ratios expected from  Mendelian inheritance.  Any statistically significant departure from the expected values is considered as evidence of epistasis.

The hypothesis (no difference between observed and expected values) was tested using the chi-square statistic (χ^2):

χ^2 = Σ [(O-E)^2 / E ],

where O is the observed value, and E the expected value.  The degrees of freedom (d.f.) are defined as n-1, where n is the number of phenotypic categories.  The level of significance was 0.05.

The result (p < 0.05) showed a great departure from the expected values, indicating a strong epistasis.

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Lecture - Mendelian Genetics: Theme variations

We covered the last part of chapter 3, regarding variations to the Mendelian inheritance theme:

• Incomplete dominance
  
• Codominance
  
• Multiple alleles
  
• Gene interactions (including epistasis)
  

We also started talking about chapter 4: Pedigree analyses...

Quiz #2 Qs & As:

1. State Mendel’s principle of segregation

Alleles segregate during gamete formation so that only one allele per gene will be allocated in a gamete

2. State Mendel’s principle of independent assortment

During gamete formation alleles of different genes are assorted independently from each other, so that at zygote formation all possible combinations of alleles are possible (true for genes in different chromosomes)

3. What is recombinant DNA technology?

Using restriction enzymes to isolate fragments of DNA and recombine them with other fragments (usually plasmids to transform bacteria sand clone the DNA fragment) to be studied through a variety of techniques, or used in industry applications

4. What is he goal of a pedigree analysis?

Determine who is in risk of having a genetic condition (providing that it's not obvious) and determining what is the probability of having children affected by that condition (trait)

5. What is codominance?

When two different alleles of a gene are fully expressed in the phenotype

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Lecture - Mendelian genetics (and some theme variations)

We continued talking about Mendelian genetics with the overview of Mendel's classic experiments, and how they lead him to postulate the second of his famous principles

• Principle of Independent Assortment
  

We also mentioned briefly how Mendelian inheritance is studied in humans and how some complex genotypes have to be considered to make sure that some traits inherited in a Mendelian fashion are properly observed.

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Lecture - Mendelian genetics

We finished covering the last part of the 'cells and cell division' chapter (ch. 2): Gametogenesis

We started talking about Mendelian genetics (chapter 3) with  an overview of Mendel's classic experiments, and how they lead him to postulate one of the principles that has become one of the pillars of genetics:

• Principle of Segregation

Quiz # 1 Qs & As

1. What are the properties of genes?

They can mutate, be turned on and off, and recombine

2. Mention three of the approaches to studying genetics (fields of study within genetics)

Transmission genetics, cytogenetics, molecular genetics, population genetics

3. What is recombinant DNA technology?

Using restriction enzymes to isolate fragments of DNA and recombine them with other fragments (usually plasmids to transform bacteria sand clone the DNA fragment) to be studied through a variety of techniques, or used in industry applications

4. What are the stages of the cell cycle?

Interphase, mitosis, cytokinesis

5. Mention one of the principles Mendel came up with after intensively studying his pea plants

Principles of segregation and independent assortment

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Lab 01 - Human Genetics

We explained how to do simple pedigree analyses, based on family information for four traits inherited in a Mendelian fashion (independent assortment and complete dominance of one of the alleles): Hitchhiker's thumb, free/attached earlobe, folding hands, and tongue rolling.

Then, following the lab guide we simulated gametogenesis and generation of offspring according with the students' genotypes for each one of those four traits.  We compared the phenotypic outcomes with the expected proportions by having each couple of students generate 10 zygotes with the simulated gametes (on paper).  Finally, students drew their pedigrees using their own family information and also the data generated for their hypothetical offspring.

Some students even named their "babies".  No extra credit for that!

Next lab: Epistasis and hypothesis testing (no Mendelian genetics).

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Lecture - Cells and cell division

We covered most of the material on chapter 2 of the textbook.  We talked about cell organelles and their function, the cell cycle, and the processes of mitosis and meiosis.  We'll pick up with gametogenesis and will start talking about mendelian genetics (chapter 3) tomorrow before the lab sessions.

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First lab meeting

Today we had our first lab meeting.  The lab syllabus was handed out and the mechanics of the lab grading were explained.

Lab guides will be NOT handed out.  Students will be responsible of printing them out.  Find them in the class folder in the school's P-drive (a-cordoba/Intro Genetics-BIOL 210/Biol 210 Lab guides).

Teams of 3, 4, and 5 people were formed (of 3 and 5 due to the uneven distribution of students in both lab sections) and topics for a bioethics paper/debate assignment were proposed by students and/or suggested by the instructor, and subsequently discussed.  Such topics will be developed as individual research papers (week 6) and a debate (week 9).

Next week:  A lab on human genetics.  To be able to make a pedigree analysis, students must collect some information from their immediate family (as many as you can and even better if you get great-grand parents involved, if possible) (check the lab 01 guide for details):

• can they roll their tongues?
  
• do they have a free or an attached ear lobe?
  
• do they have hitchhiker's thumb?
  
• how do they fold their hands?
  

These traits (three morphological and one behavioral) are genetically determined and will be useful for our exercise.

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Lecture: A perspective on human genetics (or a human perspective of genetics)

Today we had our first lecture.  Even though there was no PowerPoint presentation due to technical problems (in my office) we were able to cover most of chapter 1 of the textbook, an introduction to the course.

We talked about what genetics and genes are, how are they studied, and how important it is to understand the theoretical background of genetic-based technologies impacting our daily lives.

I also gave out the "Blue Books" that you will be using to write the answers to the quizzes, so every body should have one by now.

Reading for Friday Dec 5th:  Finish chapter 1 and start chapter 2.

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Welcome to Intro Genetics (Biol 210) @ ONU

Welcome to Introductory Genetics (Biol 210) at ONU...!

This blog is meant to be a tool for communication between students and the instructor (Alonso Córdoba), as well as to keep track of the actual happenings of the class.  Ideas and constructive criticisms are welcome.  If there is any piece of information you would like to see in this blog, please let me know:

e-mail: a-cordoba(@onu.edu)

Office phone: 419-772-3016

Some useful information

• pdfs of the syllabi can be found in the p-drive (p-drive/a-cordoba/Intro Genetics-Biol 210/Biol 210 Syllabi)
  
• I prefer to be called just by my name:  Alonso.  Unless you feel uncomfortable, you can save the titles "Dr." or "Professor".

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