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
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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

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Rosalind Franklin and her "photo 51"
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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
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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
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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
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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

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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

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Polydactyly and camptodactyly,
traits with incomplete penetrance and variable expressivity
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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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