LectureChapter 3 - Mendelian geneticsChapter 4 - Pedigree analysis

Yesterday we finished chapter 3, on Mendelian genetics.

We discussed more complex phenotypes that made Mendel's principles harder to study in many organisms, and how they do not conflict with them when considering the genotypes. Such phenotypic variations to Mendel's theme are:

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

We also started chapter 4, on pedigree analysis.

We briefly revisited the reasons for which human genetics cannot be studied experimentally and introduced the modes of inheritance of human Mendelian traits.

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Lecture, chapter 3 - Mendelian Genetics

Mendel, in his garden
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Today we talked about the classic experiments with which Mendel kick-started the field of genetics. We discussed the monohybrid and dihybrid crosses that lead Mendel to propose his principles:

• Principle of segregation
• Principle of independent assortment

We then discussed human traits in which Mendel's principles can be observed. On Monday we will talk about apparent deviations from Mendel's principles.

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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 lone
• 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.

Then students did simulations of gametogenesis and offspring production to illustrate topics that will be soon studied in lecture: Mendel's principles.

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Bioethics projects - Topics selection

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. Human cloning - Becca, Kelly, Kandai
2. Genetically modified organisms (GMOs) - John, Josh, Mohammed
3. Genetic screening for psychiatric disorders - Cara, Chelsey, Scott
4. Prenatal genetic diagnosis (PGD) - Amanda, Sarah, Brittany
5. Embryonic stem cell research - Amy, Nicole, Saleh
6. Designer babies - Chelsie, Daisy, Johnny

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

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Lecture, chapter 1 - A human perspective on genetics

Today we finished chapter 1.

We discussed the impact that genetics has had in society, since the 19th century when Francis Galton started a eugenics movement, to the more positive impact it has today through biotechnology.

Tomorrow:

We will do lab 1, Family pedigree analysis. Please remember to find out what are your and your relatives' phenotypes for the following traits:

• Tonge 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

The lab guide will be available on the p-drive and the WebCT site and will be e-mailed to you as well.

Remember you must form groups of three people to develop the bioethics projects. You must propose genetics-related topics that are controversial. Topics will b assigned before starting lab 1.

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Lecture, chapter 1 - A human perspective on genetics

Today we had an introduction to the class. We talked about the organization of the course, expectations and how it's going to be graded, and started chapter 1 in the book.

Chapter 1 in the textbook, Genetics as a human endeavor, is an introduction to the course, and a dissertation on the importance of genetics for every day's life. We discussed, at a basic level, topics from the definition of genetics to the different approaches to study genetics.

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Lecture, chapter 14 - Biotechnology

Today we covered most of chapter 14 in Biotechnology.

We discussed some of the services offered within the context of biotechnology, such as genetic testing and screening, and DNA profiling, mainly using short tandem repeats (STRs) or microsatellites.

On Friday we will discuss genetic testing via DNA microarrays, and we will have a brief discussion on population genetics.

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Lab 10 - Population genetics II - Evolution

Today on lab 10, we performed a series of computer simulations to understand the effect of natural selection and genetic drift on the evolution of populations.

We used Jon C. Herron's AlleleA1 and EvoDots. AlleleA1 allowed us to simulate changes in allele frequency under specific conditions, since we were able to control variables such as population size, initial allele frequency, and fitness (we didn't change other variables that could be controlled as well). EvoDots allowed us to simulate the effects of predation on a population of dots which vary in certain traits (speed, size, and color). In this case the user is the predator.

The effects of natural selection and genetic drift under various conditions was considered.

Other activities:

• We had the last bioethics discussion panel (privacy of genetic information)
• We had our second lab quiz

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Lecture, chapter 14 - Biotechnology

Today we started covering chapter 14, on Biotechnology

Biotechnology is the use of recombinant DNA technology to produce commodities or offer services.

We discussed some of the uses of biotechnology in today's society, such as biopharming (obtaining pharmaceutical products by using bacteria, animals, and plants), and Genetically Modified Organisms (GMOs).

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Lecture, chapter 13 - Cloning and recombinant DNA technology

Today we continued with chapter 13.

We discussed the process to make genomic DNA libraries and how to screen them for DNA fragments of interest, and we introduced the basics of PCR. We talked about the reagents that are required for the reactions and the basic steps in a cycle.

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"Lab" 9 - Bioethics discussion panels

Tuesday, May 4, 2010

Today we had our bioethics presentations and discussion panels. Students did a presentation highlighting the scientific background and ethical issues of selected genetics-related topics:

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

Next week:

• Privacy of genetic information - Rachel, Amy, Anessa, and Jake

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Lecture, chapter 13 - Cloning and recombinant DNA technology

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

We defined cloning and clones, and provided examples in cloning plants, animals, and molecules. Then we discussed the basic steps and the rationale behind DNA cloning. We introduced concepts like restriction enzymes, vectors, recombinant DNA, ligation, and genetic transformation.

In out next meeting we will talk about details of the cloning process, with and without the use of bacteria.

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Lecture, chapter 11 - Mutation

Today we finished the chapter on mutation.

We discussed the types of mutation at the nucleotide sequence level (nucleotide substitutions, including missense, sense, nonsense, and silent mutations, insertions and deletions [indels] and allelic expansions [a.k.a. dynamic mutations]).

We then discussed the mechanism that cells have in place to precent DNA changes from becoming mutaitons (proofreading and repair mechanisms), the consequences of these systems failing, and the concept of genomic imprinting.

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Lab 08 - Population genetics

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 allowed to observe their effect on allele frequency

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Lecture, chapter 11 - Mutation

Today we talked about agents that produce mutations (mutagens), and we focused in radiation and chemicals.

When discussion radiation we mentioned the various sources of radiation to which we are exposed and the average amounts to which the U.S. population is exposed. We also mentioned some of the variations from the average depending on people's profession, location, or whether they are undergoing medical testing or treatment.

When discussing chemicals, we talked about the classification of chemicals according to the kind of change they induce on DNA. Specifically we discussed base analogs, intercalating agents, and chemicals that alter DNA.

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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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