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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Exam 1

Today we had our first exam. Stats:

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Lab 04 - Complex patterns of inhertance

Today students did the lab on complex patterns of inheritance, under the direction of Dr. Rod Anderson (since I was out of town).

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Lecture, chapter 6 - Cytogenetics

From Larry Gonick and Mark Wheelis' The cartoon guide to Genetics

© 1991 Harper Perennial

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Today we finished the chapter on cytogenetics.

We discussed cases of aneuploidy in sex chromosomes (Turner (X), Klinefelter (XXY), and "super male" (XYY) syndromes), structural alterations (duplications, deletions, inversions, and translocations (reciprocal and Robertsonian), and other abnormalities (Double Uniparental Disomy and fragile sites)

Reminders:

• Our first exam is on Friday. Lecture and lab topics will be included. There will be 40 multiple choice questions and 4 short essay questions.
• The first draft of the bioethics paper is due on Wednesday Jan 13.

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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 of each.

Emphasis was made on some cases of aneuploidy: (Patau syndrome (trisomy 13), Edwards syndrome (trisomy 18), and Down syndrome (trisomy 21)). Maternal age as a risk factor for the occurrence of trisomies was also discussed.

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Lecture, chapter 5 - Polygenes and multifactorial inheritanceAssigned reading - Quantitative genetics

Today we finished chapter 5, on polygenic and multifactorial inheritance, and on quantitative genetics.

We discussed concepts as norm of reaction, phenotypic distribution, distribution of environments, and heritability.

Please refer to the handout 'quantitative genetics' (file name: PhenDist+NormReaction.pdf) for the theoretical background required to understand this lecture, lacking in the text book. The handout is available in pdf format in the p-drive and WebCT.

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Lab 02 - Mendelian genetics

Today we did a practical exercise to illustrate the principles of segregation and independent assortment.

We used DrosophiLab, a free software package that allows for virtual crosses among fruit flies that can be set as homozygous or heterozygous for a variety of genes. On each cross one can generate anywhere from 1 to 50,000 offspring and perform different observations, including chi-square tests.

Following certain procedures students were able to test predictions (Punnet squares) by generating generations of flies, that were explained by Mendelian principles.

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Lecture, chapter 5 - Polygenic and multifactorial inheritance

Today we finished chapter 4 (pedigree analysis) and started chapter 5, on polygenic and multifactorial inheritance.

We introduced the main differences between continuous and discontinuous variation, and discussed why to study the former we need to make use of statistics, studying large samples (populations) under the scope of quantitative genetics. In the next meeting we will introduce some important concepts in quantitative genetics.

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Lecture, chapter 04 - Pedigree analysis in human genetics

Pedigree showing inheritance of an autosomal dominant trait
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We covered most of chapter 4, on pedigree analysis.

We discussed the several inheritance modes that can be studied by pedigree analyses (autosomal dominant and recessive, X-linked dominant and recessive, Y-linked, and mitochondrial), and we introduced the concepts of penetrance and expressivity.

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Lab 03 - Epistasis and hypothesis testing

Wednesday, December 09, 2009

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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Tissue layers on a corn kernel. When the aleurone

is transparent the kernel will show the color of

the endosperm (white or yellow)

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