Discussion - Genetics in the news

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Today we met outdoors since we had such a nice weather, and got involved in a series of group discussions.

Students were asked to search for genetics-related news released in the last two months, and select a few that were of interest to them. Groups of 4-5 students met during 20 minutes to discuss their various articles and choose one that they wanted to share with the class at large, because of its relevance to the class or to every day life.

Then, during half hour, the whole class met and different groups brought their chosen topics to the attention of their classmates. We had discussions on such topics under the enjoyable Ohio spring sun.

Topics were mostly related to molecular genetics, ranging from epigenetics and autism, to a putative correlation between the strength of the immune system in women and their success in relationships, to the evolution of a photosynthetic slug.

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Lecture, chapter 11 - Mutation

Today we started the chapter on mutation, the source of genetic variation.

Our focus in this chapter will be on how mutations are detected and how they happen.

We discussed traditional methods to pinpoint the individual in which a mutation that affects the phenotype appears. These methods apply to mutations that produce a dominant allele of a trait controlled by one fully penetrant and expressed gene.

We also discussed how mutation rate has been traditionally estimated in humans, and then we mentioned the factors that can affect the mutation rate across genes.

NOTE:

On Friday students are to bring a printout of a genetics-related news article (from a news paper, magazine, podcast, etc.) and be ready to discuss it with the instructor and classmates. Small discussion groups will meet and then the most relevant articles will be discussed in a general forum.

(if at least 17 different topics are submitted 5 bonus points will be awarded to all students who bring an article and are involved in the discussions)

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Lab 7 - Human gene mapping

Today we discussed the importance of applying principles of gene mapping to calculating the risk of a person inheriting an allele responsible for a genetic disorder, by observing the inheritance of a marker gene (i.e. a closely linked gene with an easily observable phenotype).

Three pedigrees were analyzed, to determine the genotypes of all of the portrayed individuals and if they were parental types or recombinant types. Once this information was available the odds ratio is calculated as an estimate of how closely linked the genes are.

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Lecture, chapter 11 - From proteins to phenotypes

Today we finished the chapter in which we explained at a basic level how proteins, direct products of genes, do reflect in an individual's phenotype.

We talked about how transport proteins can be altered by mutations and have an impact, from mild to lethal, in the individual's phenotype. Our example was hemoglobin. A number of mutations can alter the genes that encode the globins (subunits of hemoglobin), producing a disease categorized as a hemoglobin variant, or could alter the genes that encode proteins that control the transcription of globin genes, producing a disease categorized as a thalassemia.

In either case the consequence of the mutation, if it is noticeable, will be anemia.

We also introduced the basic idea of the field of biochemical genetics, more specifically in the subfields of pharmacogenetics and ecogenetics. Such subfields study our phenotypes in terms of how we react to chemicals: Within our bodies (pharmacogenetics), and in the environment (ecogenetics). Active research is being conducted in such areas.

An important aspect is how the way we taste food can have an impact in health problems such as obesity (pharmacogenetics). Another important topic is how we react to chemicals used in agriculture, such as pesticides, or used in manufacturing (an example would be the effects of led used in baby toys manufactured in China)

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Lecture, chapter 10 - From proteins to phenotypes

Friday, April 16, 2010

Today we discussed translation, and how mutations can have an effect in the phenotype when altering enzymes, transport proteins, and receptor proteins.

Then we discussed the effects of genotypes on how an individual reacts to chemicals, which is the scope of pharmacogenetics, and how an individual reacts to chemicals in the environment, the scope of ecogenetics.

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Lecture, chapter 9 - From genes to proteins

Today we finished chapter 9, from genes to proteins.

We talked about translation, protein structure, and the possible modifications that a polypeptide can undergo after it has been synthesized (by translation). We also discussed the difference between a polypeptide and a protein (when there is one).

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Lab 06 - Gene mapping - Drosophila

Tuesday, April 13, 2010

Today we did lab 06, on mapping genes in Drosophila.

We discussed concepts like linkage, recombination, crossing over, and as a consequence how phenotypic categories deviate from Mendelian proportions. We mentioned how genes that are in the same chromosome may also be unlinked, if the distance between them (measured in centimorgans (cM) is big enough.

Using DrosophiLab, a crossing-over simulator (from Paul Lewis' lab), and paper and pencil, students learned:

• How to determine the distance between two genes in the same chromosome (measured in cM or map units (M.U.))
• The effect of the distance between genes and the size of a chromosome in the frequency of recombinant chromosomes during meiosis
• How to map genes based on gene distances
• How to map genes and find the distances between them based on phenotypic data (resulting from simulated crosses)

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Lecture, chapter 9 - From genes to proteins

Monday, April 12, 2010

We started chapter 9, on transcription and translation.

We covered the transcription process at a basic level, touching on its three stages (initiation, elongation, termination) and the role of different DNA sequences (promoter, gene [narrowly defined], terminator) in the process. Then we discussed mRNA processing (5'-capping, polyadenylation)

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Lecture, chapter 8 - Nucleic acids

Today we covered most of chapter 8, on DNA structure and chromosomal organization.

We reviewed a brief time line of discoveries that lead us to know what we now know about nucleic acids, from the discovery of nuclein to the structure of DNA, for which Crick, Watson, and Wilkins received the Nobel prize in 1962. We remembered the important role that Rosalind Franklin played on the discovery of the DNA double helix, and how Watson neglected to acknowledge her properly (as well as the committee in charge of awarding the Nobel prize).

We compared the basic differences between DNA and RNA, introduced important concepts to comprehend nucleic acid lingo, and discussed the basics of the mechanisms in place for a cell to supercoil DNA into densely packed chromosomes visible during metafase in cell division.

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Lecture, chapter 6 - Cytogenetics

Today we started the chapter on cytogenetics.

We discussed chromosome terminology, the steps to prepare a human karyotype, and generalities about chromosome abnormalities: Polyploidy, aneuploidy, and the most common cases and causes of each.

We then discussed structural alterations (duplications, deletions, inversions, and translocations (reciprocal and Robertsonian), and other abnormalities (Double Uniparental Disomy and fragile sites).

The details of each case of aneuploidy were covered by students as an independent reading and will be tested.

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Lab 05 - Heritability (of quantitative traits)Lab quiz 1

Today we did our lab in heritability, a calculation that can be done when dealing with quantitative traits.

Heritability: The proportion of phenotypic variation explained by genotypic variation (as opposed to environmental factors).

Broad sense heritability (H^2): Heritability taking into account all kinds of genetic interactions (additive effects of polygenes, epistasis, dominance-recessiveness, etc.)

We used finger print ridge count data to calculate the broad sense heritability of the trait. in our "population" (the class). Every student took his/her own fingerprints and did a ridge count on each one. We pooled everybody's data and proceeded with the calculation.

Narrow sense heritability (h^2)*: Heritability taking into account only the additive effects of polygenes. This measure is of interest to individuals who are interested in selection programs with the goal of shaping a population according to their interests (e.g. farmers or cattle breeders).

We used height data from students, their parents, aunts and uncles, and siblings, to calculate h^2 in a human population, since we had the data available. This kind of heritability is usually not calculated in humans.

*Actually performed a week later, on April 13.

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Lab quiz 1

During the last hour of today's lab students took the first lab quiz.

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Exam 1

Today we had our first exam. Results statistics:

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Lab 04 - Inheritance of complex traits

Wednesday, March 30, 2010

Today we practiced pedigree analysis when a trait is controlled by 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

Today we started covering chapter 6 on cytogenetics.

We talked about what a karyotype is, how it's made, what it is used for and what kinds of cells can be used to make one. We also discussed chromosome nomenclature and techniques to stain or paint chromosomes while making a karyotype.

We introduced the concepts of euploidy, polyploidy, and aneuploidy.

Reminder: First exam this Wednesday, March 31.

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Lecture, chapter 5 - Inheritance of complex traits

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.

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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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