LectureChapter 5 - Polygenic and multifactorial inheritanceChapter 6 - Cytogenetics

Today we discussed one of the most important concepts in quantitative genetics.

We defined heritability and talked about some of its implications. We discussed the use of twin studies as tools the estimate heritability of different traits, and the importance of using both, monozygotic (MZ) and dizygotic (DZ) twin studies.

We discussed a few examples of multifactorial traits in humans: Skin color, IQ, and obesity.

Then we started discussing the chapter on cytogenetics, a field that focuses on studying chromosomes, using karyotypes as the main tool.

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Lecture, chapter 5 - Polygenic and multifactorial inheritance

We started covering quantitative genetics, the subfield of genetics that studies polygenic and multifactorial inheritance based on observations on phenotypic variation.

We discussed the principle of regression to the mean and how statistics is used as an important tool in quantitative genetics. We focused on concepts that are specific to quantitative genetics, such as phenotypic distribution and distribution of environments.

We mentioned features of the interaction of genes and environment as preparation to discuss the concept of heritability.

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Lab 03 - Epistasis and hypothesis testing

Genetic corn

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Yesterday 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 kernels, students were able to predict the phenotypic proportions of purple and yellow kernels. The predictions were compared to the observations and tested using a chi-square test, with a significance level of 5% (0.05, numerically, but not conceptually equal to α).

When the hypothesis (observed counts = expected counts) was rejected (if it 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 5 - Polygenic and multifactorial inheritance

After finishing chapter 4 on pedigree analysis (discussing age-related phenotypic expression, penetrance, and expressivity), we started chapter 5, on multifactorial and polygenic inheritance.

We discussed the differences between continuous and discontinuous traits, and how they are related to the number of genes that affect them. Discontinuous traits must be described in terms of measurements taken in a population rather than qualitatively describing individuals. We defined complex, multifactorial, and polygenic traits.

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Why are fruit flies important for us?

Audio slideshow screenshots
Clockwise: A normal fruit fly next to another with a liver disease, white-eyed mutant flies feeding, a collage of epifluorescence images of flies internal organs or systems, and a fruit fly brain with neurons that control mating, fluorescing in green

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Research in fruit flies, Drosophila, specially D. melanogaster, has been fundamental for enhancing our knowledge of genetics as a whole and of human genetics in particular, since we share about 60% of our genes with them. In lab we have used software that simulates controlled crosses of fruit flies with specific mutations, and in the next few weeks we will perform more complex simulations.

But fruit flies are also used in other areas of research. Check out this audio slideshow, produced by the BBC, on the use of fruit flies in neurophysiology research. Some of the general principles outlined by the researcher apply to genetics research too. The system to breed the flies (jars with growth media, covered with cotton or gauze) is the same as in genetics research.

BBC Audio slideshow: Fruit flies - up close

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Lecture, chapter 4 - Pedigree analysis

Today we started chapter 3, on pedigree analysis.

We discussed the reasons for which human Mendelian genetics has been traditionally studied with pedigrees rather than with more direct approaches, and what are the shortcomings of doing so.

We also listed the six modes of inheritance and described two of them: Autosomal dominant and autosomal recessive. We discussed examples of each: Cystic fibrosis and sickle cell anemia (autosomal recessive) and Marfan syndrome (autosomal dominant).

I also introduced the catalog that stores information on human Mendelian traits: Online Mendelian Inheritance In Man (OMIM). [OMIM in Wikipedia]

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Lab 02 - Mendelian genetics

Today we completed lab 2, in which principles of mendelian genetics were studied through computer simulations of fruit fly (Drosophila melanogaster) crosses.

We used DrosophiLab to simulate crosses between wild type flies and mutants for the autosomal genes vestigial wings and sepia eyes, and the X-linked gene white eyes (test crosses). By doing so students were able to demonstrate the principles of segregation and independent assortment

• Video on how to use DrosophiLab

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Chapter 3 - Mendelian genetics

Mendel, in his garden in the 1880s
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Between Friday and today we covered the chapter on Mendelian genetics.

We discussed how Mendel performed the experiments with pea plants that led him to propose his principles of segregation and independent assortment, laying the foundation of the field of genetics.

We then discussed the apparent deviations from Mendel's principles that are observed in organisms with complex phenotypes. The genes responsible for such phenotypes do, indeed, follow Mendelian principles, but the phenotypic proportions are different from those Mendel observed. The cases we discussed were:

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

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LectureChapter 1 - A perspective in human geneticsChapter 3 - Mendelian genetics

Today we finished chapter 1 with a discussion of the main ways in which genetics has impacted society in the past (mainly through eugenics) and in recent decades to the present (mainly through biotechnology).

We also started chapter 3, on Mendelian genetics, with a discussion of the steps that Mendel himself took to set up his, now considered classic, experiments.

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Lab 01 - Human (Mendelian) genetics

During this first lab students learned the basics of building pedigrees to study human genetics. Pedigrees were built for the following traits

• Free or attached ear lobe
• Hitchhiker's thumb
• Tongue rolling
• Hand folding

The latter two are behavioral traits with a genetic component but they seem to be inherited in a Mendelian fashion; they were suitable for this basic exercise. Each student surveyed such traits in their immediate family in order to perform the analyses.

Then we performed a couple of simulations (gametogenesis and fertilziation) to illustrate the Mendelian principles of segregation and independent assortment.

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Pre-lab 01 - Bioethics projects topics

Today students formed groups and chose topics for the bioethics papers and panel discussions (genetics-related topics that generate social, moral, or political controversy). The groups and chosen topics are the following:

1. In vitro fertilization - Courtney, Jenny, Kwaku, Marcus
2. Human-animal chimeras - Andie, Danielle H., Kirstin, Maggie
3. Genetic predisposition to addiction - Danielle L., Veronica, Caleb, Justin
4. Designer babies - Jeniffer, Liz, Salesha, Sarah
5. Genetically modified (GM) crops - Alex, Andre, Kevin, Mark
6. Organ farming - Anabel, Jessica, Kara, Megan
7. Research using HeLa cells - Lindsay, Ben, Brent, Jordan

Panel discussions will take place during the lab session of week 9. Papers are due the same day.

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Intro Genetics, Biol 210 - Spring 2011

Welcome to the Spring 2011 edition of the INTRO GENETICS course!

This blog is kept for the students' convenience. You can use it as a record of how the class progresses, and occasionally as a a platform for announcements. Feel free to make comments suggesting new ideas or asking questions.

Check out the column on the right, since they contain interesting information about the course and about a few sources of genetics-related information.

Today:

We reviewed the syllabus and started with the first chapter in the textbook: A human perspective on genetics (or, if you prefer, a perspective on human genetics).

Tomorrow:

We will assign groups and topics for the bioethics projects, and will do a basic exercise on pedigree analysis using four traits easily identifiable:

• Tongue rolling - Roller vs. non-roller
• Ear lobe - Free vs. attached
• Thumb - Hitchhiker's vs. straight thumb
• Hand folding - Left thumb over right vs. right over left

Please remember to find out what are your and your relatives' phenotypes for these traits. The lab guide will be available on the p-drive and the WebCT site.

You will form groups of four people to develop the bioethics projects. You must propose genetics-related topics that are controversial. Topics will be assigned before starting the lab.

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Exam 3 (final)

Stats on the final exam:

(click on pic for a full size image)

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Activity - Genetics on the news

Students brought genetics-related news articles (or news podcast transcripts) and discuss them in small groups. Each group summarized the main points of the articles and presented them to the rest of the class.

Topics ranged from bacterial genetic engineering gone wrong to how certain genetic defects can make people less susceptible to cancer and diabetes (click here and here).

(a few other topics were DNA repair inked to genetic mutation, genes playing a role in choosing friends, contagious cancer affecting Tasmanian devils).

Although the foci of the articles were diverse, the trend was for students to find articles more related to molecular genetics than any other genetics field.

And, we were able to enjoy a warm(ish) weather outside!

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Lab 08 - Population genetics

Screenshot of PopCycle, by John Herron
(click on pic for full size image)
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Today we did the population genetics lab

We introduced concepts that are key to the study of population genetics such as allele frequency, genotype frequency, gene pool, and Hardy-Weinberg principle (and equilibrium) and its assumptions. When discussing the Hardy-Weinberg principle we discussed the forces that can alter allele frequency in a population: genetic drift, selection (including sexual selection), mutation, and migration.

We then then proceeded to further study Hardy-Weinberg equilibrium by running simulations on PopCycle, a software package created by Jon Herron, from the University of Washington. PopCycle allowed us to see the conditions under which allele and genotype frequencies remain constant, and it also allow us to relax some of the assumptions. We introduced the effect of genetic drift and natural selection. Students were able to observe their effect on allele frequency

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Chapter 14 - Biotechnology

Today we finished the chapter on Biotechnology. We discussed how to use DNA microarrays (a.k.a. "Gene chip") as a tool to do genetic testing.

We then discussed how tandem repeats in the human genome can be used as markers to do some DNA profiling, mainly short tandem repeats (STRs).

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LectureChapter 13 - Cloning and recombinant DNAChapter 14 - Biotechnology

We finished chapter 13, with an overview of one of the most commonly used automated DNA sequencing methods, the dye-terminator sequencing method, a modification of the Sanger method (a.k.a. chain termination - click here for an EXCELLENT video produced by the Dolan DNA learning Center).

Then we started the chapter on biotechnology, in which we provided a definition of the field, discussed its origins with the discovery of restriction enzymes in the 1970s, and did an overview of some of the most common fields within biotechnology: biopharming and genetically modified organisms (GMOs).

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Lecture, chapter 13 - Cloning and recombinant DNA

After finishing the last bioethics presentation/panel discussion on GMOs, we briefly saw animations of PCR and restriction enzymes. Then, we discussed Southern blotting, a common technique to analyze DNA.

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"Lab" 9 - Bioethics presentations and panel discussions

Yesterday we had 5 out of the 6 bioethics presentation and discussion panels this quarter. Groups of students presented the scientific basis, the bioethical issues, and expressed their opinions on, controversial genetics-related topics. They followed by leading a discussion with their classmates. The topics, and presenters, were:

• Human cloning
  Becca, Kelly, Kandai
• Genetic screening in relation to psychiatric disorders
  Chelsey, Cara, Scott
• Prenatal genetic diagnosis
  Amanda, Sarah, Brittany
• Designer babies
  Chelsie, Daisy, Johnny
• Embryonic stem cell research
  Nicole, Amy
• Genetically modified organisms (Friday)
  John, Josh, Mohammed

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Lecture, chapter 13 - Cloning and recombinant DNA

Continuing with the chapter on cloning and recombinant DNA, we talked about how to make genomic DNA libraries, which involves cloning, in some cases by using artificial chromosomes (BACs and YACs). Then we talked about how we can find a fragment of DNA of interest in such libraries by binding the DNA to nitrocellulose or nylon paper membranes and using DNA or RNA probes.

We also discussed the process of polymerase chain reaction (PCR), with emphasis on the advantages and disadvantages it has over the traditional cloning process.

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