Lecture, chapter 12 - Genes and cancer

Monday, February 16, 2010

Today we finished chapter 12, on the connection between genes and cancer.

The lecture focused on the main environmental factors that can cause cancer, and on what organs or tissues.

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Lecture, chapter 12 - Genes and cancer

Today we started covering chapter 12, on the connection between genes and cancer.

We discussed the relation between mutations and tumors, both, benign and malignant (cancerous). The main kinds of genes that have a direct connection with tumors are tumor suppressing genes, and proto-oncogenes.

We mentioned study cases relating breast and colon cancer, cases in which different genes have been associated with particular modes of progression of the disease (or diseases).

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Lecture, chapter 14

Today we finished chapter 14, on biotechnology, the applications of recombinant DNA technology.

We focused on the use of tandem repeats, especially STRs on DNA profiling...

(I can't believe we spent a whole hour talking about STRs!)

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Lab 09 - Bioethics projects

Today we had the presentations/debates on a variety of genetics-related topics that present ethical issues. The presentations were lively and for the most part involved most of the students in the audience, making it clear that the topics that were chosen sparked interest and in some cases touched people in a very direct way.

The following topics were discussed:

• Designer babies
• Human cloning
• Human-animal chimeras
• Genetically modified plants
• Gene therapy
• Eugenics
• Stem cell research
• Forced sterilization
• Prenatal diagnosis

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Lecture, chapter 14 - Biotechnology

Today we covered some of chapter 14, on the applications of biotechnology.

We talked about how to use transgenic animals, especially mice, in the study and experimental treatment of human genetic diseases. We also covered the basics of genetic screening and genetic testing, focusing on some of the techniques.

The use of DNA microarrays ("gene chips") on genetic testing was featured.

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Lecture, chapter 14 - Biotechnology

Today we started covering chapter 14, on biotechnology and genomics.

We defined the concept of biotechnology and discussed some of its applications, like biopharming (the use of living organisms to produce pharmaceuticals) and genetically modified organisms (GMOs). When discussing GMOs we discussed some of the ethical issues around their use.

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Exam 2

Today we had our second exam. Stats.

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Lab 8 - Population Genetics

Wednesday, February 3, 2010

Today we discussed how evolution proceeds at the population level. We introduced concepts like natural selection, adaptation, fitness, gene pool, allele frequency, and microevolution. We explained the main evolutionary forces at the population level:

• Natural selection
• Migration
• Mutation
• Genetic drift

We then discussed their relation to the Hardey-Weinberg principle and the conditions for a population to be found in Hardey-Weinberg equilibrium.

Then we proceeded to do really simple but enlightening simulations to test the effect of genetic drift and natural selection on allele frequency. Our gene pools were styrofoam cups full of red and white beans. Thrtough simulation the concepts of allele fixation and allele extinction were introduced.

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Lecture, chapter 13 - Cloning and recombninant DNA

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

We covered two of the "classic" ways to analyze DNA: Southern blots and DNA sequencing.

We covered the steps to perform a Southern blot, including the basics of agarose gel electrophoresis, and how to use RNA/DNA probes to find genes of interest.

When discussing DNA sequencing we focused on automated DNA sequencing through the dye-terminator sequencing method, which uses dideoxynucleotides with a fluorescent label.

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Lecture, chapter 13 - Cloning and recombinant DNA technology

Following with the chapter on recombinant DNA and cloning...

We discussed how to make a genomic DNA library, using vectors like bacterial plasmids, bacterial artificial chromosomes (BACs), or yeast artificial chromosomes (YACs).

We covered the basics of the polymerase chain reaction (PCR). We talked about the ingredients necessary for performing it, the steps, and some of the possible applications of this method.

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Lab 7 - Human gene mapping

In this lab we used human pedigrees to test the strength of linkage between marker genes and genes that are responsible for certain genetic conditions.

We started by discussing the basics of marker genes, gene mapping in humans linkage, and the concept of recombinant and parental individuals (based on pedigree analysis)

Then we proceeded to cal...

(entry in progress)

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Lecture, chapter 13 - Cloning and recombinant DNA technology

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

We briefly discussed techniques in which plants an animals can be cloned and the reasons to do so. We devoted most of the time, though, to how DNA molecules are cloned. We introduced the concept and the basic steps of cloning DNA, starting by how DNA is cut by using restriction enzymes. We described how DNA from different organisms or species, if it has been cut with the same restriction enzyme, can be combined into single DNA molecules: Recombinant DNA.

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Lecture, chapter 11 - Mutation

Today we finished the chapter on mutation.

Our main foci were types of mutations at the nucleotide sequence level, such as nucleotide substitutions, insertions and deletions (a.k.a. "indels"), and allelic expansions.

We also discussed the mechanisms that have evolved to correct DNA changes and prevent them from being fixed as mutations: The DNA proofreading mechanism of DNA polymerase and DNA repair (process in which many enzymes are involved).

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Lecture, chapter 11 - Mutation

Today we started the chapter on mutation.

We focused on mutations at the nucleotide sequence level since in previous chapters we have discussed mutations at the chromosome level. We talked about the most common agents that cause mutation (mutagens), such as chemical agents and ionizing radiation.

We discussed why certain mutagens can cause specific kinds of mutations mutations and what some of the possible effects in the phenotype could be. Radiation captured our attention for much of the lecture.

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Lab 06 - Gene mapping in Drosophila

Wednesday, January 20, 2010

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

We discussed concepts like linkage, recombination, crossing over, and as a consequence the existence deviations from Mendelian principles, specially from independent assortment. 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 10 - From proteins to phenotypes

Today we covered chapter 10, on how proteins can affect the phenotype of an individual, specially in humans.

We discussed effects that mutations could have in the phenotype when they alter 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 05 - Heritability and quantitative traits

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. 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 (even though this is never done with any practical purposes).

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Lecture, chapter 8 - DNA structure and chromosomal organizationLecture, chapter 9 - From genes to proteins

Today we finished chapter 8. We focused on DNA replication and the differences on how the leading and the lagging strands are synthesized in the process.

We also 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)

Tomorrow: For our heritability lab please know your height. Also find out about your siblings, parents, and grandparents' heights. All heights must be provided in inches.

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Lecture, chapter 8 - DNA structure and chromosomal organization

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

We reviewed a brief time line of discoveries that lead us o 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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