Announcement - Dates for lab quizzes

Lab quizzes will take place on the following dates, from 4:00-4:50 p.m.:

• Lab quiz 1: Tuesday, April 06 (week 5)
• Lab quiz 2: Tuesday, May 11 (week 10)

Each lab quiz will consist on 3-5 exercises like the ones that have been done in lab. A calculator will be required.

Rules:

• Each student will team up with a partner
• Students can talk ONLY to their partners
• Students are allowed to use notes and books
• The use of electronic devices (other than calculators) is NOT allowed (i.e. no cell phones, lap tops, net books, audio file players, etc.)

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Lecture, chapter 5 - Inheritance of complex traits

Today we continued chapter 5, on complex patterns of inheritance (polygenic and multifactorial).

We talked about how alleles in polygenic trait loci contribute to the phenotype, the characteristics of multifactorial traits, and the concept of regression to the mean.

We talked about the field of quantitative genetics; we discussed the kinds of questions it can answer and some of the most important concepts (phenotypic distribution, distribution of environments, norm of reaction)

Note:

We met in Meyer 113. We will meet in this room for the remaining lectures during this quarter.

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Lab 3 - Epistasis and hypothesis testing

Genetic corn

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In this lab we used genetic corn to test a prediction based on Mendelian principles, about the inheritance of two genes.

The color of corn kernels, although just one trait, is controlled by two separate genes (R and C) that affect pigmentation in the aleurone, which may or may not be pigmented. If transparent the color of the kernel will be yellow or white, and when pigmented it will be purple or red. In our case we only had purple and yellow kernels in cobs that were obtained as the F2 generation from a cross from double homozygote parent plants (RRCC x rrcc).

By doing a count of purple and yellow kernels, students were able to predict the phenotypic proportions of yellow and purple kernels. The predictions were compared to the observations and tested using a chi-square test, with a significance level of 5% (α=0.05).

When the hypothesis (observed values = expected values) was rejected, results were explained as the consequence of an epistatic interaction that prevented the R and C genes of showing the phenotypic proportions predicted by Mendelian inheritance.

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Lecture, chapter 4 - Pedigree analysisLecture, chapter 5 - Inheritance of complex traits

Today we finished chapter 4, on pedigree analysis.

We discussed cases in which the modes of inheritance we covered in previous lectures cannot be detected in a pedigree, because of complex gene and environmental interactions that prevent the phenotype of being fully expressed. Specifically we discussed age-related phenotypic expression, penetrance and expressivity. We provided examples of traits that show such phenomena.

We also started chapter 5, on polygenic inheritance and multifactorial traits.

We highlighted the difference between continuous and discontinuous phenotypic variation, and defined complex, polygenic and multifactorial traits.

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Lecture, chapter 4 - Pedigree analysis

Friday, March 19, 2010

Today we continued with our chapter on pedigree analysis.

We discussed several modes of inheritance

• autosomal dominant
• x-linked dominant and recessive
• y-linked (paternal)
• mitochondrial (maternal)

On Monday we will discuss cases of variations on gene expression.

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Lecture, chapter 4 - Pedigree analysis

Today we started chapter 4, on pedigree analysis.

We discussed the utility of using pedigree analysis to study human genetics. We had an overview of what the main six modes of inheritance are, and how they can be identified in a pedigree.

We discussed in detail the characteristics of the autosomal recessive mode of inheritance, and provided examples: cystic fibrosis and sickle cell anemia.

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Lab 2 - Mendelian genetics

Today we did lab 2, on Mendelian genetics.

The goal of this lab was to observe the phenotypic consequences of the principles of segregation and independent assortment. We used the free software DrosophiLab to simulate experimental crosses with fruit flies. Most of the crosses were testcrosses, meaning that one of the individuals involved in the cross was homozygous recessive for the trait being considered (in this case a homozygous recessive individual would be a mutant fly. The mutation would have an observable phenotype).

A series of three experiments considering one trait, two traits controlled by genes in different chromosomes, and one trait controlled by a gene in a sex chromosome should have shown students how to see the effects of Mendel's principles in an experiment.

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Lecture, chapter 3 - Mendelian genetics

Today we finished chapter 3, on Mendelian genetics.

We talked about how human genes do follow Mendel's principles, and talked about a few examples of traits on which Mendelian inheritance can be studied by observing phenotypes.

We also discussed how there are cases in which there are deviations from Mendelian phenotypic proportions:

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

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Lecture, chapter 3 - Mendelian genetics

Friday, March 12, 2010

Today we started covering chapter 3, on Mendelian genetics (a.k.a transmission genetics). We talked about Mendel's classic experiments with pea plants and how he ended up formulating his principles:

• Principle of segregation
• Principle of independent assortment

On Monday: Do Mendel's principles apply to humans?

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Lecture, chapter 1 - A human perspective on genetics

Today we continued with the outline of what the quarter will be.

We discussed how Mendel gave birth to the field of genetics, even before the word 'gene' was coined, what the different approaches to studying genetics are, and how genetics has impacted our lives in the past and in the present.

Note: There will be no lecture on chapter 2, but students are strongly encouraged to read it. On Friday we will start covering chapter 3 in the text book, on Mendelian genetics

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Lab 1 - Basic Human Genetics

Tuesday, March 2, 2010

After choosing teams and topics for the bioethics projects we did the first lab of the quarter, on very basic human genetics.

We covered the basics of pedigree analysis, and each student built their own family pedigrees mapping on them four traits that are inherited in a Mendelian fashion: Hitchhiker's thumb, tongue rolling, free/attached earlobe, and hand folding. Genotypes were assigned to each individual in the pedigree to the extent that the available information allowed it.

Then, using the students' genotypes for the four mentioned traits, students used pieces of paper representing chromosomes with their alleles to perform simulations of gametogenesis to illustrate Mendel's principle of segregation, and of crosses generating several offspring, to illustrate Mendel's principle of independent assortment.

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Bioethics projects

Tuesday, March 2, 2010

Today we had the first lab session of the quarter. During the first hour or so, we talked about the bioethics projects, which will be presented on the lab session of week 9.

The bioethics projects will be developed by teams of four students, and will focus on genetic-related topics that pose ethical problems and are surrounded by controversy. Each team selected a topic that members considered to be controversial and interesting enough to spark discussion with classmates.

As part of the project students will write a paper explaining the scientific basis of the issue of choice, the reasons for which it is controversial, showing the opposing views on the issue, and explaining what position they take, properly backed by a rational process.

A second component of the project will be a presentation and panel discussion during the lab session on week 9. Each team will prepare a 20-minute presentation, on a format of their choice (oral presentation, a play, a mock trial, a fake documentary, etc. You can be as creative as you want), which will be followed by a 10-minute panel discussion with the rest of the class. Each group, acting as the panel of experts in the topic, will engage their classmates and have a discussion debating different points of view.

The grade will depend on how well the scientific basis of the issue is presented, how well explained the controversial aspects are, the solidity of the reasons for taking a position in the issue, and how effectively the rest of the class is drawn into the discussion.

A first draft of the paper is due on Friday of week 6, at midnight, and the final version due on Tuesday of week 9, at noon. If a power point file is used in the presentation it will be due on the night of Monday before the day of the presentations.

TOPICS AND TEAMS

• Designer babies - Niki, Andrea, Jessica, and Katie K.
• Human-animal chimeras - Beth, Sarah, Stacy, Aimee, and Emily
• Cloning of human beings - Jamal, Jerel, Shawn, and Scott
• Genetically Modified Organisms (GMOs) - Aubrey, Liz, Nathan, and Dexter
• Stem cell research - Sonia, Katie D., Dustin, and Geoff
• Privacy of genetic information - Rachel, Amy, Anessa, and Jake

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Introduction and lecture, chapter 1 - A human perspective on genetics

Monday, March 1, 2010

Welcome to the spring quarter Introductory Genetics class...!

Today we had the introduction to the class, an overview of the syllabus and a talk about the class policies.

Then we started covering chapter 1 in the textbook, an introduction to this intro class. In this chapter we outline what the course is going to be, touching in topics like what genetics is and what the properties of genes. Other general topics will be covered on the next lecture.

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Lecture, chapter 19 - Population genetics and human evolution

Friday, February 19, 2010

Today we had a very shallow introduction to population genetics and human evolution.

We discussed the concepts of gene pool, allele frequency and genotype frequency. We talked about the Hardey-Weinberg model and how it can be used to find allele frequencies in a population, or predict genotype frequencies in a given generation based on allele frequencies.

We discussed Hardey-Weinberg equilibrium and how it can be used to test if evolutionary forces are acting upon a population.

We then discussed a little bit of human evolution and how maternal and paternal haplotype data have been used to elucidate the migration routes of humans since our origin in Africa.

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Lecture, chapter 12 - Genes and cancer

Monday, February 16, 2010

Today we finished chapter 12, on the connection between genes and cancer.

The lecture focused on the main environmental factors that can cause cancer, and on what organs or tissues.

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Lecture, chapter 12 - Genes and cancer

Today we started covering chapter 12, on the connection between genes and cancer.

We discussed the relation between mutations and tumors, both, benign and malignant (cancerous). The main kinds of genes that have a direct connection with tumors are tumor suppressing genes, and proto-oncogenes.

We mentioned study cases relating breast and colon cancer, cases in which different genes have been associated with particular modes of progression of the disease (or diseases).

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Lecture, chapter 14

Today we finished chapter 14, on biotechnology, the applications of recombinant DNA technology.

We focused on the use of tandem repeats, especially STRs on DNA profiling...

(I can't believe we spent a whole hour talking about STRs!)

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Lab 09 - Bioethics projects

Today we had the presentations/debates on a variety of genetics-related topics that present ethical issues. The presentations were lively and for the most part involved most of the students in the audience, making it clear that the topics that were chosen sparked interest and in some cases touched people in a very direct way.

The following topics were discussed:

• Designer babies
• Human cloning
• Human-animal chimeras
• Genetically modified plants
• Gene therapy
• Eugenics
• Stem cell research
• Forced sterilization
• Prenatal diagnosis

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Lecture, chapter 14 - Biotechnology

Today we covered some of chapter 14, on the applications of biotechnology.

We talked about how to use transgenic animals, especially mice, in the study and experimental treatment of human genetic diseases. We also covered the basics of genetic screening and genetic testing, focusing on some of the techniques.

The use of DNA microarrays ("gene chips") on genetic testing was featured.

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Lecture, chapter 14 - Biotechnology

Today we started covering chapter 14, on biotechnology and genomics.

We defined the concept of biotechnology and discussed some of its applications, like biopharming (the use of living organisms to produce pharmaceuticals) and genetically modified organisms (GMOs). When discussing GMOs we discussed some of the ethical issues around their use.

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