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.

_______________

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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Lecture, chapter 3 - Mendelian genetics

Today we talked about Mendel's principles, the principle of segregation and the principle of independent assortment. We discussed how Mendel performed the experiments that lead him to formulate his principles and the implications of doing so at the time he did it. We also talked about the re-discovery of his work in the early 1900s, the connection of his findings with the discovery of chromosomes, mitosis, and meiosis, and finally set the stage to discuss some of the variations on Mendel's principles (cases other than complete dominance, multiple alleles, etc.)

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Lecture, chapter 01 - A perspective on human geneticsLecture, chapter 03 - Mendelian genetics

Today we finished chapter 01, with a discussion of the impact genetics has had and has in society, from eugenics, to biotechnology and the development of the Human Genome Project (HGP).

We started chapter 03, on inheritance of genes (transmission genetics or Mendelian genetics), with a brief discussion of the characteristics Mendel was looking for in the plants he would use for his studies. We, briefly and informally, stated the first of Mendel's principles, and set the stage to discuss the second principle.

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Lab 01 - Human genetics

Students formed groups of four people to work in the bioethics projects that we will develop during the quarter. Each group proposed one or more topics that are controversial and have a genetic basis. Topics were assigned to groups that proposed them, and in a few cases groups decided to choose a topic suggested by the instructor.

We also did exercise 01, on the basics of studying human genetics by using pedigree analyses. Students did a little mini-survey in their families to find out who had one of the alternative forms of expression of the following traits:

• Hitchhiker's thumb
• Tongue rolling
• Free/attached ear lobe
• Hand folding

Each student learned how to draw and interpret a basic pedigree using such traits in their families, and learned how to figure out the genotypes of each individual in the pedigree.

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WINTER QUARTER 2009-10Chapter 01 - A perspective on human genetics

We officially started the winter quarter today.

We went over the lecture syllabus and started covering chapter 1 in the book, 'A perspective on human genetics' (or 'a human perspective on genetics'; your choice). We talked about the very basics of what a gene is, what it does and how it is transmitted, and the different approaches to the study of genetics. All these pointing out to how important the study of genetics is in every day's life.

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Last lecture, chapters 14 and 12 - Biotechnology + Genes and cancer

We met outdoors to enjoy the weather...

We closed the chapter on biotechnology by discussing the use of short tandem repeats (STRs) in gene profiling or fingerprinting.

Then we discussed the first part of the chapter on genes and cancer. We talked about the link between cancer and mutation, the role of mechanisms that control de cell cycle, and cancer originated from mutations in genes related to DNA repair.

Tuesday, May 19: Final exam. Meyer 114, 4-6 pm.

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Lecture, chapter 14 - Biotechnology

Thursday, May 14, 2009

A gene "chip", a microarray containing an emtire human genome,
used for genetic testing
_____________________________________________________

We continued with the chapter on biotechnology.

We talked about the process of making transgenic mice to use as models of human diseases, the differences between genetic screening and genetic testing, and the main techniques of genetic testing, including those involved in what it is known as pre-implantation genetic diagnosis (PGD).

We finished discussing the possibilities to do genetic testing on an entire genome using microarrays, specifically gene "chips".

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Lecture, chapter 14 - Biotechnology

Today we started chapter 14 on biotechnology.

We discussed the most basic applications of biotechnology and how it has bben applied to replace older methodologies to produce proteins to treat human diseases (biopharming).

We also discussed the goals of genetically modifying crops, and some of the main concerns that people have about them. We also started discussing how recombinant DNA technology has been used to create transgenic animal model organisms, mainly mice, to study the development of human diseases and test possible treatments to cure them.

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Lecture, chapter 13 - Mutation

Child with xeroderma pigmentosum a disorder caused by mutations
on genes involved in DNA repair mechanisms
_____________________________________________________

Today we finished the chapter on mutation.

We talked about how insertions and deletions (indels) can affect a nucleotidic sequence depending on how many nucleotides are inserted and whether or not they change the reading frame of the sequence.

Then we discussed the basics of the proofreading and DNA repair mechanisms that cells have in place to fix DNA changes, which happen at a much greater rate than the rate of mutation (reminder: a mutation is a DNA change that gets passed to subsequent generations of cells and/or organisms; it's a DNA change that doesn't get repaired).

We also considered a third category of mutations: allelic expansions, which interestingly enough happen in only one of the alleles in a gene pair. Genes that have trinucleotide repeats undergo mutations in which the number of repeats increase to the point in which the protein they encode for is not functional any more.
We mentioned anticipation, the phenomenon in which a genetic disorder caused by an allelic expansion is expressed in a more severe way, and at earlier ages, generation after generation.

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Lecture, chapter 13 - Intro to cloning and recombinant DNA technology

Today we finished chapter 13, an introduction to the use of recombinant DNA technology.

We talked about how to clone DNA in vitro, through PCR, and how to analyze DNA that has been cloned, mainly with the techniques Southern blotting and automated DNA sequencing.

Tomorrow: We will finish the chapter on mutation (ch 11).

And now, honoring Kyle and Jackie's request, I introduce you to the cheesiest, geekiest, funniest, and learnyousomethingest song: The PCR song...!

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Lab 09 - Bioethics debates/presentations

Yesterday, Tuesday May 5, we had our 5 bioethics debates/presentations on the following topics:

• Prenatal diagnosis or screening
• Designer babies
• Genetic privacy
• Emryonic stem cell research
• Gene therapy

The style of the presentation portion ranged from a U.S. Senate hearing to a trial (including witnesses, a jury, and even a really ugly bailiff...). Students engaged in relatively gentle, but still interesting debates on different issues. They were able to express their views and opinions, but also showed to be knowledgeable in the topics they decided to research.

On Thursday: More on chapters 11 (mutation) and 13 (intro to cloning and recombinant DNA)

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Lecture, chapter 13 - Cloning and recombinant DNA

A cartoon version of how to ligate DNA into
plasmids as part of the cloning process
click image to see a full size pic
_____________________________________________________

Today we started covering chapter 13, an introduction to cloning and recombinant DNA technology. We have temporarily skipped the second half of the chapter on mutation, but we will get back to it after finishing the current chapter.

We talked about the definition of cloning, and the basic steps for cloning DNA, including the use of plasmids, YACs, and BACs. We also briefly reviewed the basics of constructing a genomic library and how to probe it when searching for a specific fragment of DNA.

On Thursday: We will talk about in vitro cloning (PCR), southern blots, and automated DNA sequencing.

Tomorrow: Bioethics debates...!!!

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Exam 02

Today we had our second midterm exam, covering materials from chapter 8 (DNA structure and chromosomal organization) to the beginning of chapter 11 (mutation - [mutation rate]).

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Lecture, chapter 11 - Mutation (causes of mutation)

Continuing with the chapter on mutation, today we talked about the main agents that act as mutagens, mainly radiation and chemicals. We discussed some of the different kinds of mutation and how mutagens promote them; also how different categories of chemicals interact with DNA witht he result of causing mutations.

Reminder: Exam 2 is tomorrow!

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Lecture, chapter 11 - Mutation

Today we started chapter 11, on mutation, the source of genetic variation.

We talked about the kind of mutations we are going to be focusing on (those that alter the nucleotidic sequence of genes), and how it is detected in humans when they are reflected in the phenotype.
We also discussed what the rate of mutation is, and how it is calculated in humans, based on the observed number mutant phenotypes in a set of births.

After lecturing we did a quick and dirty overview of a couple of execises in the Drosophila gene mapping lab. A handout in pdf format has been uploaded to both, the p-drive and the WebCT site for the class explaining how to do a three-point testcross.

Note: A three-point testcross exercise will be included in the exam this Friday.

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Lecture, chapter 10 - From proteins to phenotypes: Pharmacogenetics

Today we finished chapter 10, from proteins to genotypes. Specifically we talked about pharmacogenetics

There are phenotypes that become obvious only when people are exposed to chemicals. Whether they are drugs, chemicals in the environment, or chemicals in products we consume (food, clothing, etc.), different allele combinations make us more or less sensitive to exposure.

We talket about the first pharmcogenetic trait, discoverd in the 1930s, the ability or inability to taste PTC. This trait is trivial, but it has implications that have lead research that may find connections between sensitivity to certain tastes, diet, and obesity.
We also talkes about how between 100 and 1000 cel membrane proteins dictate our ability to smell or not smell certain chemicals. So many enzymes, most of which most likely have several alleles, and so many possible allele combinations make us virtually unique in our olfactory capacity.

In terms of sensitivity to chemicals in the environment, especially pesticides, it is ecogenetics the subfield that deals wit our genetic-based differences in sensitivity. Research is being done in many populations to determine safe levels of exposure to different chemicals. Such research involves an important genetic component.

On Monday: We will start chapter 11, on mutation as the source of genetc variation.

Reminder: Next Friday, May 01, we will have our second exam. over chapters 8, 9, 10, and 11, plus elements of our genetic mapping labs (both in human and Drosophila). Bring a calculator!

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Lecture, chapter 10 - From proteins to phenotypes

Today we covered most of chapter 10, from proteins to genotypes.

We talked about how mutations in genes that encode for transport proteins can be reflected in the phenotype. Our main example was hemoglobin. Mutations in the genes thay encode for any of the subunits of the protein can cause a variety of genetic disorders (hemoglobin variants, thalassemias) which most common symptom is anemia.

One of the better known cases is sickle cell anemia, caused by a mutation in the beta globins of hemoglobin, causing them to come become insoluble, resulting in the aggregation of the protein, therefore altering the shape of red blood cells and making them brittle.

Tomorrow: We'll finish chapter 10, covering the section on pharmacogenetics.

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Lab 07 - Human gene mapping

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

In humans, we have to rely on pedigrees. In this lab we considered three different pedigrees showing linkage between a genetic disorder and another trait. 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, chapters 9 and 10 - From genes to proteins, and from proteins to phenotypes

Today we finished chapter 9, on how genetic information is used to synthesize proteins, and started chapter 10, on how proteins are, or influence, the phenotype.

We talked about the possibilities of changing a polypeptide after it has been synthesized, thus accounting fopr the more than 100,000 enzymes in the human organism, which has just about 25,000 genes in its genome. We defined the difference between a polypeptide and a protein (hint: every protein is a polypeptide or a group of polypeptides, but not every polypeptide is a protein).
Then we talked about the levels of structure that proteins can have: Primary, secondary, tertiary, and, in some cases, quaternary. We finished the chapter by discussing some of the consequences of a mutation that alters the amino acid sequence of a protein.

We also started chapter 10, and discussed how certain mutations in the sequence of amino acids of enzymes and receptor proteins affect the phenotype of the person who bearing them.

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Lecture, chapter 9 - From genes to proteins

Today we continued covering chapter 9, on how the information stored in the genetic code gets reflected on a phenotype, specifically in proteins.

We talked about the processes of translation transcription, including the stages that each one has (initiation, elongation, and termination in both cases).

In the case of trascription we talked about the elements that are found in a gene, and how they get trnascribed into a pre-mRNA transcript, which gets modified into a mature mRNA transcript. We also discussed the different elements that make a mRNA molecule, including a 5' cap and a Poly-A tail.

In the case of translation we covered the cytoplasmatic elements that play a role in it: amino acids, ribosomes, and tRNA. We also discussed the chemical make up of amino acids, an amino, a carboxyl, and an 'R' groups, and a few of their characeristics.

On Monday: We'll finish chapter 9 and begin chapter 10.

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Lecture, chapters 8 and 9 - RNA, chromosome structure, and gene expression

Today we finished the chapter on DNA and chromosome structure. It should have been "nucleic acid and chromosome structure".

We discussed the primary and secondary structure of RNA, how DNA is coiled (and supercoiled) to from chromosomes, and then we started the next chapter in the text book, on how the information stored in DNA is used to form proteins.

Note: The draft papers on bioethical issues were returned with recommendations to improve what you have so far. Tomorrow I'll provide a handout with indications of how to cite and reference papers in a scientific fashion.

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Lab 06 - Mapping genes in Drosophila

http://www.drosophilab.com
__________________________________________________

Although the actual lab will be a take-home lab, we set the stage to do the work we need to do in the couple of mapping genes labs we will have.

We covered concepts like gene mapping, genetic linkage, and genetic distance within a chromosome, and how they are correlated. We also introduced the concept of CentiMorgan (cM), a.k.a. Map Unit (m.u.), and how it is useful to map genes, based on the results of experimental crosses.

We also used a little applet developed by Paul Lewis, from the University of Connecticut, called demonstration of crossing over. With this application we did simulations on recombination events affecting two loci separated by variable genetic distances. We then introduced the concepts of parental haplotypes/gametes and recombinant haplotypes/gametes, as part of the more practical explanation of genetic linkage.

We also did a quick demo of the software to be used in this lab: DrosophiLab. Students will download this Windows-based free software to simulate experimental crosses in Drosophila melanogaster, and calculate genetic distances between different genes. The labguide is being written and will be posted soon.

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Lecture, chapter 8 - DNA structure

________________________________________________

Rosalind Franklin and her "photo 51"
________________________________________________

Today we started covering chapter 8, on the structure of DNA and chromosomes.

We talked about a little bit of the history of how the structure of DNA was discovered, including the injustice commited towards Rosalind Franklin, who took the X-ray diffraction image known as "photo 51", which was key for Watson and Crick to resolve the structure of the double helix. Her collaborator, Maurice Wilkins showed Watson the picture, without Franklin's knowledge, and the latter failed to acknowledge the fact that HER image put him and Crick on the road to become the icons they officially are today.

Then we talked about the structure of nucleotides and how they are assembled to form the famous DNA double helix.

On Thursday: We will talk about the similarities and differences between DNA and RNA, and will cover the basics of chromosome structure.

Congratulations to Brittany Simmons, the winner of the heritability challenge...!

Have a happy Easter break!

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Lab 05 - Heritability

In today's lab we focused in calculating heritability, the proportion of phenotypic variance explained by genetic differences.

We covered two approaches to calculating heritability:

1. Broad sense heritability: It reflects all possible genetic contributions to a population's phenotypic variance like effects due to allelic variation (additive variance), dominance, or polygenic interactions, as well as matrenal and paternal effects.
2. Narrow sense heritability: It quantifies the proportion of phenotypic variation explained by allelic variation.

We calculated broad sense heritability with data collected from student's fingerprints, specifically total ridge count. And narrow sense heritability will be calculated based on students' heights in inches, as well as the heights of their siblings, parents, and parents siblings.

The heritability challenge (Thursday):

During the exercise I made a mistake when calculating broad sense heritability. Apparently no body caught it. If you can find the mistake and explain the whole exercise correctly to the rest of the class, you will have the chance to earn 5 bonus points. Be prepared, and among those who have the answer I will randomly chose some one to try to get the bonus points.

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Friday, April 3, 2009

EXAM 1

We had our first exam, covering chapters 1 through 6 in the book.

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Lab 04 - Complex patterns of inheritance

In lab 4 students analyzed pedigrees that showed patterns of inheritance that could not be explained by any one of the six modes of Mendelian inheritance covered in class. As part of the pedigree analyses they observed the incidence of incomplete penetrance and variable expressivity of traits.

Students also became familiar with concepts like genetic liability and recurrence risk, and were able to calculate the latter using specific methods that make use of the standard deviation of the population as a tool to infer such information.

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Lecture, chapter 6 - Cytogenetics

From The Cartoon Guide to Genetics
Larry Gonick & Mark Wheelis
© Harper Perennial, 1983 & 1991
____________________________________________________

We finished chapter 6, on cytogenetics.

We covered the main cases of autosomal and sex chromosome aneuploidy: Down syndrome (trisomy 21), Turner syndrome (trisomy 18), Patau symdrome (trisomy 13), Klinefelter's syndrome (XXY), and "supermale" syndrome (XYY).
We also discussed structural abnormalities in chromosomes, like deletions, additions, inversions, and translocations.

On Friday: Exam 01
On Monday: Chapter 8, on chromosomes and DNA

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Lecture, chapter 6 - Cytogenetics

A human karyotype
__________________________________________________

Today we started chapter 6 on cytogenetics.

We covered karyotypes, chromosome nomenclature, and classification of variation in chromosome number: Polyploidy and aneuploidy. We discussed triploidy and tetraploidy and on Monday we'll start discussing cases of aneuploidy.

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Our "Genetics News Friday" discussion was a failure and a dissapointment. In spite of having tools to acquire information easier than ever before, nobody brought an idea to discuss, and you can find them everywhere!
Remember, genetics is not just a class to get out of the way. It is a field that has plenty of applications and implications in the real world! Reading or listening to genetics-related news is a good exercise, for this class and for life in general.

Again: Other than the traditional sources of information you can also get information from RSS feeds (the news come TO you), and podcasts (some are literally 1 min 20 secs long...! Can it get any easier?). See Monday's entry (March 23) for some extra details.

No discussion may mean questions about genetic-related news in the quizzes. You pick.

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An RSS Feed looks like this (click for full size image)

And the link will take you to something like this (click for full size image)

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Lecture, chapter 5 - Polygenic inheritance

A gradient of skin tones
click on image for a full size pic
_________________________________________________

Today we finished covering chapter 5, on polygenic inheritance.

We discussed concepts like distribution of environmental factors, norm of reaction, and heritability. We also discussed the importance of twin studies in complex traits research, and talked about a couple of examples of polygenic traits in humans: skin color and intelligence.

Tomorrow: Chapter 6, on cytogenetics.

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Lab 03 - Epistasis and hypothesis testing

Tuesday, March 24, 2009

___________________________________________________




___________________________________________________

We did our "corny genetics" lab. Students, working in pairs, analized the expected and observed phenotypic proportions of the F2 generation from a dihybrid cross in genetic corn. They used their expectations and their observations to perchorm a chi-sqare test and relate the results to a potentially epistatic interaction.

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Lecture, chapter 5 - Polygenic inheritance

Today we started covering chapter 5, on polygenic inheritance and interaction with the environment.

We discussed the differences between continuous and discontinuous characters, the definitions of polygenic, multifactorial, and complex traits, and the most common approach to studying the inheritance of continuous variation: Quantitative genetics. Quantitative genetics uses many statistical tools as well as some concepts inherent to it, like the genetic version of regression to the mean, phenotypic distribution, norm of reaction, genetic variance, phenotypic variance, and heritability.

Tomorrow: Lab 3, on Epistasis and hypothesis testing.

On Thursday: More about chapter 5.


Note:

Given the success of the end-of-class discussion on Friday, we will continue having "genetics on the news" discussions in the future, with the possibility of including questions in quizzes. I encourage you to use on-line resources to find genetics news, or let them find you. The main sources would be RSS feeds of publications like Nature, Science, or Scientific American (among MANY others), and scientific podcasts.

Some podcasts have been uploaded to the p-drive and the WebCT site (check them out!), but you can find many more on genetics-related sites. You can get them wherever you want to.
If you don't know were to begin just use iTunes (freeware, availale in Windows and Mac OS X versions) to access the iTunes store and download/subscribe to any of the FREE scientific podcasts available.

Remember, you can find the news, and with RSS feeds and podcast subscriptions the news will find you.

Examples of sites with RSS feeds:

• Scientific American
• Nature
• Science Magazine

If you find any other interesting site, let me know.

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Lecture, chapter 4 - Modes of inheritance and variations in gene expression

_____________________________________________________________________

Polydactyly and camptodactyly,
traits with incomplete penetrance and variable expressivity
_____________________________________________________________________

Today we finished chapter 4, on pedigree analysis.

We talked about the last couple of modes of inheritance: Y-linked traits and mitochondrial inheritance. Then we talked about variations in gene expression: Age-related phenotypic expression, penetrance, and expressivity.

By the end, we had a discussion about genetics in the news. People were passionate about it and it was fun and productive. We talked about the case of the California octuplets that was recently on the news (need an update/reminder? Click here!).
It was a good exercise and it may happen again. Should we do it every Friday? Should we call it "Genetics news Friday" or something along those lines? If you read this blog comment on this. If not... We may do it any way.

You could (should) subscribe to science podcasts and/or RSS feeds to keep abreast of the latest news...there is more out there than you think.

On Monday: We will start chapter 5 in our textbook.

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Lecture, chapter 4 - Pedigree analysis

Click on image for a full size pedigree

Today we continued chapter 4 in the textbook.

We started with a little overview of, and a demonstration on how to use, the Online Mendelian Inheritance in Man (OMIM) catalogue. The catalogue of human Mendelian traits.

Then we started covering the modes of inheritance that can be inferred from pedigree analysis. We went over autosomal recessive and autosomal dominant traits, and we started sex-linked traits, with X-linked dominant and X-linked recessive traits. We examined pedigrees and observed the characteristics they exhibited.

We discussed examples of diseases inherited in each one of these modes.

Tomorrow: More about modes of inheritance, and variations of gene expression. Oh, and possibly an activity to wake up people during class...

Huh...? What is this guy doing in a genetics class blog?

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Lab 02 - Mendelian genetics

Today we did a lab in which we examined a little bit of Mendelian genetics, faking crosses in fruit flies.

We focused on monohybrid and dihybrid crosses in, both, autosomal and X-linked traits. Students did observations that illustrated the principles of segregation and independent assortment, mainly based on test crosses.

Next week: Lab 03 - Epistasis and hypothesis testing

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Lecture, chapters 3 and 4 - Mendelian inheritance and Pedigree analyses

Today we finished chapter 3 in the book, on Mendelian inheritance, covering some of the variations on Mendel's findings: codominance, multiple alleles, and gene interaction, including epistasis.

On the other hand we began chapter 4, on pedigree analysis, talking about the six modes of inheritance we will be covering, in addition to the basic reasons for which pedigrees are so important when studying human genetics.

Tomorrow in lab: Mendelian genetics. The lab is being re-written so it will be posted late, but it will be up.

For Thursday: Read the remaining of chapter 4, and access the OMIM database, to get familiar with the kind onf information you can find there

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Lecture, chapter 3 - Mendelian genetics

Today we covered most of chapter 3 in the textbook, after having our first quiz of the quarter.

We had an overview of how Mendel's experiments lead him to propose his two famous principles:

• Principle of segregation
• Principle of independent assortment

As part of the story of Mendel's progress we talked about the reception his research had when he puylished it (1866), when and why his work was redicovered by other European geneticists at about 1900, and when his results were linked to the recent (at the time) discoveries of mitosis, meiosis, and chromosomes.
We covered monohybid and dihybrid crosses, concepts of dominance and recesiveness, and phenotypic proportions resulting from each one of these.
We also started covering complex phenotypes and the phenomena that explains their patterns under the light of Mendelian inheritance.

For Monday: Read chapter 4 in the textbook...!

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Lecture, chapter 1: A human perspective on genetics

...or a perspective on human genetics.

We covered material in chapter 1 of the textbook, dealing with some general issues of the development and importance of genetics, and the impact this science has had on society in the past and the impact it has now.

The power point presentation has already been uploaded to the p-drive and the WebCT site.

Reminders:

• Chapter 2 will NOT be covered in lecture, but you must read it. It will be quizzed and included in exams 1 and 3.
• We will start with chapter 3 (Mendelian genetics) tomorrow.
  
• You MUST have a 'Blue Book' ($0.60 at the ONU bookstore) to be able to answer your quizzes.

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Lab 01: Family pedigree analysis

On Tuesday, March 10, we had the first lab of the quarter, in which we did a very basic family pedigree analysis of some traits that show a Mendelian mode of inheritance, and assigned topics for the bioethics projects.

Bioethics project assignments

We talked about the bioethics projects before the actual lab exercise. Students picked their teams (four members per team) and proposed topics they would like to work with. We discussed briefly the reasons for which people thought certain topics would be interesting, and based on such reasons and after weighting preferences topics were assigned. The following topics were picked:

• Privacy of genetic information
• Embryonic stem cell research
• Prenatal screening
• Designer babies
• Gene therapy

We then discussed some of the requirements for both, the bioethics papers and the debates, as stipulated on the lab guide for week 9.


Family pedigree analysis

Following lab guide No 1 we performed a series of family pedigree analyses for some human traits (hitchhiker's thumb, free vs. attached earlobe, tongue rolling, and hand folding or clasping). Each student surveyed such traits in their immediate family in order to perform the analyses.

Then we performed a couple od simulations (gametogenesis and fertilziation) to illustrate the Mendelian principles of segregation and independent assortment.


Fire alarm and building evacuation

It was an eventful lab. In the middle of it a fire alarm (cause still unknown to the instructor) forced us to evacuate the buiklding and stay out for about half hour. Fortunately we were able to resume activities soon enough.

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Spring Quarter 2009

Today we started the spring quarter of 2008-09.

Students introduced themselves, provided information about their motivation for taking this class and their expectations. We went over the syllabi (lecture and lab), discussed grading and attendance policies, lecture and lab mechanics, and mentioned areas upon which students would like to focus towards the end of the quarter.

Some of the areas in which students expressed interest are:

• Genetic diseases
• Speciation
• Population genetics
• Genetics and cancer
• Biotechnology
• Human evolution

I'll do my best to meet expectations regarding these topics.

Reminders:

• Get an examination book ("Blue Book") at the ONU bookstore! You will need it for your quizzes, and it's very cheap (under $1.00). You must bring your Blue Book to every lecture.
• The syllabi have been already posted to the p-drive (under 'a-cordoba') and on WebCT.
• Tomorrow we are having our first lab. Think of topics you would like to develop during your bioethics projects, and have ready the information you need to do family pedigrees (see below)

Information you must collect from your immediate family (siblings, parents, and, ideally, aunts, uncles, and grandparents):

• Can you roll your tongue? (yes/no)
• Do you have hitchhiker's thumb? (yes/no)
• What type of earlobe do you have? (free/attached)
• How do you fold (or clasp) your hands? (right thumb over left or viceversa)
  

Also, don't forget to printout the lab guide. It will be posted to the WebCT site and later on to the p-drive as well.

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Lecture - DNA. chromosomes and gene expression

Ttoday we fineshed chapter 7, about the structure of DNA and chromosomes. We talked about how nucleosomes are organized to compact DNA into chromosomes. Then we talkes about the basics of DNA replication. Among other things we mentioned the "mini-dogma" that you must remember. DNA is always synthesized in the 5'-3' direction...!

We also started chapter 8, on gene expression. Specifically how the information strored in genes is transformed into proteins.

Reminder: We have exam 2 on Monday. Last topic to be included in the exam: Chapter 7.


QUIZ #8

1. What are the components of a nucleotide? (there are three)
Phosphate group, nucleotidic base, sugar

2. The DNA strands in the double helix are antiparallel. What does that mean?
One of the strands runs in the 5'-3' direction and the other runs in the 3'-5' direction

3. List three differences between DNA and RNA
DNA is double stranded, RNA is single stranded
The sugar in DNA is deoxyribose, in RNA is ribose
DNA has T in its sequence, RNA has U instead

4. What is the name for a core of histones and the DNA wrapped around it?
Nucleosome

5. What is DNA replication?
The process through which DNA is copied in a cell prior to cell division

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Lectures - DNA structure and Chromosomal organization

Friday Jan 30 - Monday Feb 02

We are covering chapter 8 in the textbook: DNA structure and chromosomal organization.
We have been talking about a quick story of how DNA was discovered, the structure of nucleic acids, starting by nucleotides and how they can be put together to form the double stranded DNA and the single stranded RNA.

We started talking about how the large molecules of DNA can be compacted in the space of the nucleus, by wrapping DNA around histone cores to form nucleosomes.

Tomorrow we will finish chapter 8 and start chapter 9.

REMINDER: Exam 2 on Friday. It will include material in chapters 5, 6, and 8.

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Lectures - Cytogenetics

Monday Jan 26 - Friday Jan 30

We covered chapter 6 in the book: Cytogenetics.

• The most important topics of this chapter were
• Chromosome morphology
• The human karyotype
• Variations in chromosome number: Polyploidy and anueploidy
• Important chromosomal abnormalities: Autosomal and sex chromosome trisomies
• Structural alterations and other abnormalities in chromosomes

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Lab cancelled due to weather

Due to weather afternoon classes and labs have been cancelled today.

Lab 04 is about heritability and quantitative traits.

Expect information about a make up lab for both sections, with the possibility of a partial lab and the rest of it as an assignment.

I don't like to cancel class or lab and I'll do it only if it is impossible to actually do the lab (case of the Drosophila gene mapping lab), or if the school closes due to weather, like today. My apologies for those cases. We'll make up for it. And yes, you shall learn! (no joke)

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Lecture - Polygenic inheritance

Phenotypes controlled by two or more genes often show
a normal distribution (click on image for a full-size pic)

We are covering chapter 5 in the textbook, on polygenic inheritance and the influence environment has on phenotypes.

Important concepts include continuous and discontinuous variation, polygenic and multifactorial traits, complex traits, polygenic inheritance, and regression to the mean.

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Midterm survey and discussion about class

We did a survey about things that students like about this class and aspects that could be improved. After the survey we held a discussion about those same topics.

The goal of a mid-term survey is to address student concerns (as long as they are reasonable) before the quarter ends, instead of waiting to get student evaluations and make improvements for another group of students the following quarter.

A summary of the main positive aspects and concerns that students brought up follows:

Positive aspects:

• The class has a good pace and it has a relaxed atmosphere
• Instructor is approachable and available outside of class
• Instructor encourages participation
• Instructor is willing to stop and explain concepts and ideas
• Instructor actually listens to students
• Good combination of PowerPoint and board usage
  
• Power Point presentations follow the book and summarize information
• Presentations are posted on the p-drive
• Pop quizzes encourage studying the material
• "I think your pop quizzes are WONDERFUL!" (this is a direct quote)*
  

Aspects to improve:

• More organization in lab exercises
• Make lab guides available earlier
• More specific requirements for bioethics paper and lab notebook
• Include also material and concepts that are not covered in the book
  
• Upload PowerPoints to the p-drive earlier**
• "Pop quizzes are evil" (this is a direct quote)*
  

* Notice the rather interesting contrast of opinions regarding pop quizzes... It seems like about 70% of people like quizzes and the remaining 30% don't...
** I will, if I finish them soon enough...

Opinions about the textbook:

• About 90% of students like the textbook as a clear tool to understand the material, because it is easy to read and it provides helpful graphic material.
• The remaining 10% either doesn't use the book or thinks it is not challenging enough for a college-level class

Opinions about the PowerPoints:

• Easily followed
• Layed out nicely
• They summarize the lecture well
  
• Too wordy
• We go over them too fast

These points include what was written in the section where you told me what you would do different should you be teaching this class. There is a wide range of opinions and levels of satisfaction.
Many valid points were made, as well as a few unreasonable ones. I'll do my best to keep up the good things and improve the not-so-good ones. Pop quizzes are staying the way they are, perhaps with a few changes in the way questions are asked. I'll post PowerPoints to the p-drive as I make them, so you may see several incomplete versions before the final product (will that help?)
For those of you who are worried about writing down everything in the presentations... they will be posted anyway. I suggest you relax a little, pay more attention to what is being said, and then download the presentation if it is not up by the time lecture starts.

Please feel free to post comments to these results...!

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Lecture - Variations in gene expression: A conclusion to chapter 4

Today we covered the last portion of chapter 4, focused on variations of gene expression, and some examples. We explained the following key concepts:

• Age-related phenotypic expression
• Penetrance
• Expressivity

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Lecture - More about pedigree analysis

We covered the four remaining modes of inheritance of Mendelian traits in humans (chapter 4):

• X-linked dominant
• X-linked recessive
• Y-linked (paternal inheritance)
• Mitochondrial (maternal inheritance)

We introuduced the concept of variation of gene expression.

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(Friday December 19th) Lecture - Pedigree analysis

A pedigree is a graphic way to present family information using standardized symbols (mainly squares and circles). Using Mendelian principles a pedigree can be analyzed to determine if a trait is autosomal or sex-linked, dominant or recessive, and calculate the probability of parents transmitting the trait to their offspring.
Since it is unethical to do controled crosses in humans, pedigree analyses are the tool for geneticists to study transmission genetics in this case.

We covered the first part of chapter 4 in the book. We explained what a pedigree is, how Mendelian traits in humans are being catalogued in the OMIM database, and we listed the characteristics of the first modes of inheritance in humans (autosomal recessive and autosomal dominant).

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