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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Exam 2

Today we had our second exam. Stats.

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Lab 8 - Population Genetics

Wednesday, February 3, 2010

Today we discussed how evolution proceeds at the population level. We introduced concepts like natural selection, adaptation, fitness, gene pool, allele frequency, and microevolution. We explained the main evolutionary forces at the population level:

• Natural selection
• Migration
• Mutation
• Genetic drift

We then discussed their relation to the Hardey-Weinberg principle and the conditions for a population to be found in Hardey-Weinberg equilibrium.

Then we proceeded to do really simple but enlightening simulations to test the effect of genetic drift and natural selection on allele frequency. Our gene pools were styrofoam cups full of red and white beans. Thrtough simulation the concepts of allele fixation and allele extinction were introduced.

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Lecture, chapter 13 - Cloning and recombninant DNA

Today we finished the chapter on cloning and recombinant DNA technology.

We covered two of the "classic" ways to analyze DNA: Southern blots and DNA sequencing.

We covered the steps to perform a Southern blot, including the basics of agarose gel electrophoresis, and how to use RNA/DNA probes to find genes of interest.

When discussing DNA sequencing we focused on automated DNA sequencing through the dye-terminator sequencing method, which uses dideoxynucleotides with a fluorescent label.

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Lecture, chapter 13 - Cloning and recombinant DNA technology

Following with the chapter on recombinant DNA and cloning...

We discussed how to make a genomic DNA library, using vectors like bacterial plasmids, bacterial artificial chromosomes (BACs), or yeast artificial chromosomes (YACs).

We covered the basics of the polymerase chain reaction (PCR). We talked about the ingredients necessary for performing it, the steps, and some of the possible applications of this method.

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Lab 7 - Human gene mapping

In this lab we used human pedigrees to test the strength of linkage between marker genes and genes that are responsible for certain genetic conditions.

We started by discussing the basics of marker genes, gene mapping in humans linkage, and the concept of recombinant and parental individuals (based on pedigree analysis)

Then we proceeded to cal...

(entry in progress)

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Lecture, chapter 13 - Cloning and recombinant DNA technology

Today we started the chapter on cloning and recombinant DNA technology.

We briefly discussed techniques in which plants an animals can be cloned and the reasons to do so. We devoted most of the time, though, to how DNA molecules are cloned. We introduced the concept and the basic steps of cloning DNA, starting by how DNA is cut by using restriction enzymes. We described how DNA from different organisms or species, if it has been cut with the same restriction enzyme, can be combined into single DNA molecules: Recombinant DNA.

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Lecture, chapter 11 - Mutation

Today we finished the chapter on mutation.

Our main foci were types of mutations at the nucleotide sequence level, such as nucleotide substitutions, insertions and deletions (a.k.a. "indels"), and allelic expansions.

We also discussed the mechanisms that have evolved to correct DNA changes and prevent them from being fixed as mutations: The DNA proofreading mechanism of DNA polymerase and DNA repair (process in which many enzymes are involved).

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