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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Lecture, chapter 13 - Cloning and recombinant DNA

Today we started with chapter 13.

We discussed the concept of cloning and the different kinds of cloning: Cloning molecules, cells, and organisms. We discussed the concept of recombinant DNA molecules.

We then proceeded to discuss the basics of the cloning DNA process, including the use of restriction enzymes, vectors, and DNA ligase.

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Exam 2

Stats for exam 2

(Click on pic for full size image)

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Lecture, chapter 11 - Mutation

Today we finished the chapter on mutation.

We discussed the different types of mutations (nucleotide substitutions, insertion/deletions [indels], and allelic expansions) and their potential effects on phenotype.

We also discussed how a cell prevents most of the DNA changes from becoming mutations: By putting in place a proofreading mechanism (performed by DNA polymerase) and DNA repair systems (performed by a variety of enzyme batteries). As part of the discussion, we mentioned the possible consequences of a mutation in genes that encode DNA repair enzymes.

We briefly mentioned the effects of mutations in genes affected by genetic imprinting and the effects mutations on specific nucleotides vs. mutations on any of a number of possible nucleotides

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Lecture, chapter 11 - Mutation

Today we discussed the reasons for which radiation (electromagnetic and corpuscular) can act as a mutagen, and what are the most common sources of radiation for an average citizen of the U.S.

We then listed the different categories of mutagen chemicals and how they affect DNA.

We started discussing the kinds of mutation that can occur (indels vs. substitutions, frameshift vs. non-frameshift), and their potential effect on phenotype.

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LectureChapter 10 - From proteins to phenotypesChapter 11 - Mutation

Today we finished chapter 10 by discussing the focus of the field of ecogenetics, an area of genetics concerned with how we react to chemicals in the environment based on our genotypes (how we react is our phenotype).

We then started the chapter on mutation summarizing how mutations that are observable in the phenotype have been traditionally studied, including how their rate has been measured (a task that is easier in the case of autosomal dominant diseases).

We discussed the factors that cause different genes to have different mutation rates and introduced the main agents (mutagens) that cause mutations.

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Lab 07 - Gene mapping in humans

In Drosophila it is easy to find out if genes are linked, and how closely, since it can be determined by doing experimental crosses and measuring phenotypic frequencies in the offspring (see lab 06). In addition to that, we know exactly what genes are found in specific chromosomes (fruit flies have only four pairs of chromosomes).
In humans it is not that straight forward. Experimental crosses are out of the question, and humans tend to have very few offspring (even large families have very few offspring compared with the potentially thousands of offspring of a Drosophila cross).

In humans, we must rely on pedigrees. In this lab we considered three different pedigrees showing linkage between a genetic disorder and another trait (easily observable). Students learned and practiced how to identify parental and recombinant types in the offpring of each generation, and in the third exercise calculated the odds ratio to determine linkage of traits.

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Lecture, chapter 10 - From proteins to phenotypes

Today 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, chapter10 - From proteins to phenotypes

Today we examined the role of different kinds of proteins in determining our phenotype and how mutations may affect it.

We had examples on enzymes, transport proteins and receptor proteins.

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Lab quiz 1

Lab quiz 1 stats:

(click on pic for full size image)

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Lab 06 - Gene mapping in Drosophila

Today we did lab 06: mapping genes in Drosophila.

We discussed concepts like linkage, recombination, crossing over, and how phenotypic categories deviate from Mendelian proportions because of these phenomena. 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

Today we covered the remaining of chapter 7, mainly focusing on the process of translation.

We discussed the importance of the remaining cytoplasmic components (ribosomes and tRNA), and then we described the actual process of translation, breaking it down in its stages (initiation, elongation, and termination).

We commented on the structure of polypeptides and the events they undergo after translation (folding and different possible types of modification).

Tomorrow

• Lab 6: Gene mapping in Drosophila (computer lab)
• Lab quiz 1 (bring a calculator)

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