LectureChapter 8 - DNA structure and chromosomal organizationChapter 9 - From genes to proteins

Today we discussed the basics of RNA structure and pointed out basic differences between it and DNA.  We then had an overview of how DNA is condensed into chromosomes and how it is replicated.

Watch the following video or access this link to understand the main features of the DNA replication process

We also started chapter 9, on how genetic information is transcribed into mRNA and translated into proteins.  We briefly recapped how Beadle and Tatum confirmed that there was a connection between genes and proteins in the 1940sand how their famous quote ("one gene, one enzyme") has been modified, as discoveries have been made, to make it more accurate.

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Chapter 8 - DNA structure and chromosomal organization

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Rosalind Franklin and her "photo 51"
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We continued discussing the history of how the structure of DNA was discovered, including the injustice  (alleged by many) commited towards Rosalind Franklin, who took the X-ray diffraction image known as "photo 51", which was key for Watson and Crick to resolve the structure of the double helix. Her collaborator, Maurice Wilkins showed Watson the picture, without Franklin's knowledge, and the latter failed to acknowledge the fact that HER image put him and Crick on the road to become the icons they officially are today.

Then we talked about the structure of nucleotides and how they are assembled to form the famous DNA double helix.

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Lab 05 - Heritability

In today's lab we focused in calculating heritability, the proportion of phenotypic variance explained by genetic factors.

We covered two approaches to calculating heritability:

1. Broad sense heritability: It reflects all possible genetic contributions to a population's phenotypic variance like effects due to allelic variation (additive variance), dominance/recessiveness, polygenic interactions, and well as maternal and paternal effects.
2. Narrow sense heritability: It quantifies only the proportion of phenotypic variation explained by additive contribution of the genes that control the trait, ignoring all other genetic contributions.

We calculated broad sense heritability with data collected from student's fingerprints, specifically total ridge count. And narrow sense heritability was calculated based on students' heights in inches, as well as the heights of their siblings, parents, and parents' siblings.

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LectureChapter 6 - CytogeneticsChapter 8 - DNA structure and chromosomal organization

Today we finished the cytogenetics chapter, with a discussion on uniparental disomy (UPD) and fragile sites, the remaining chromosomal abnormalities.

And we started on chapter 8, on DNA structure and chromosomal organization, with a brief discussion on some science history events that led to the discovery of the structure of DNA.  On Wednesday we'll pick up on  the drama that unfolded around Rosalind Franklin's (involuntary? not-acknowledged?) involvement in the process of deciphering the structure of the now famous double helix.

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Exam 1

Friday, April 1, 2011

Stats on exam 1:

(clic pic for full size image)

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Lecture, chapter 6 - Cytogenetics

Today we discussed the several cases of autosomal and sex chromosome aneuploidies:  Their frequency, symptoms, and consequences for an individual's life.  Polyploidies and aneuploidies are cases of alterations in chromosome number.

We also introduced the concept of chromosomal structural alterations.  We mentioned the various categories (deletions, duplications, inversions and translocations) and started discussing them.

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Lab 04 - Inheritance of complex traits

Today we practiced pedigree analysis when a trait is controlled by one or several genes and environmental factors. Students learned how to identify a complex trait on a pedigree and to estimate the most plausible mechanism explaining the pattern of inheritance observed in a pedigree.

We introduced the concepts of threshold traits and genetic liability, and used them to calculate the risk of parents conceiving a child affected by a multifactorial disease (an example of a threshold trait)

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Lecture, chapter 6 - Cytogenetics

A human karyotype
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Following with the chapter on cytogenetics we discussed the nomenclature of chromosomes, how to produce a human karyotype, including the different chromosome banding and painting techniques, and methods to obtain cells from fetuses and adults to produce a karyotype.

We introduced the topic of variations in chromosome number, including polyploidy and aneuploidy;  we discussed the most common causes for each abnormality.

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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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