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.

----------------------

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

----------------------

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.

______________________

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.

______________________

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)

----------------------

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.

----------------------

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.

----------------------

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.

----------------------

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.

----------------------

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?

----------------------

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

----------------------

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

----------------------

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...!

----------------------

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.

----------------------

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.

----------------------

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.

----------------------

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

----------------------

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.

----------------------

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

----------------------

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)

----------------------

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.

---------------------

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...!

----------------------