LectureChapter 5 - Polygenic and multifactorial inheritanceChapter 6 - Cytogenetics

We finished the chapter on polygenic and multifactorial inheritance with a discussion of the importance of twin studies in studying heritability and on some human complex traits whose relative importance of genetic and environmental factors is still not completely understood: skin color, IQ, and propensity to obesity

We started the chapter on cytogenetics, with an overview of chromosome structure and nomenclature, and the process of making a human karyotype. We followed by discussing abnormalities in chromosome number: polyploidy and aneuploidy (we described some specific cases).

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

Lab 03 - Epistasis and hypothesis testing

Genetic corn

_____________________________________

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.

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

Lecture, chapter 5 - Polygenic and multifactorial inheritance

We continued the lecture we started yesterday, on polygenic and multifactorial inheritance, a field of genetics that departs from the Mendelian approach. Although individual genes behave according to Mendel's principles, traits that are controlled my more than one gene or are affected by the environment don't show Mendelian proportions in the phenotype of offspring generations.

We defined complex traits, including polygenic and multifactorial, and we introduced the concept of quantitative genetics. We discussed some concepts that are important in the field, like phenotypic distribution, distribution of environments, norm of reaction, and heritability.

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

Lecture, chapter 4 - Pedigree analysis in human genetics

Today we finished chapter 4.

We covered the remaining modes of inheritance in human mendelian genetics: X-linked recessive, Y-linked, and mitochondrial. We studied examples of some of those.

We than discussed variations in phenotypic expression, mainly age-related phenotypic expression, penetrance, and expressivity, and provided a few examples, including , interestingly enough, one of the students! (good times!)

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

Lab 02 - Mendelian genetics

Today we completed lab 2, in which principles of mendelian genetics were studied through computer simulations of fruit fly (Drosophila melanogaster) crosses.

We used DrosophiLab to simulate crosses between wild type flies and mutants for the autosomal genes vestigial wings and sepia eyes, and the X-linked gene white eyes. By doing so students were able to demonstrate the principles of segregation and independent assortment.

• Video on how to use DrosophiLab

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

Lecture, chapter 4 - Pedigree analysis

Following on the pedigree analysis chapter, we discussed the advantages of using a catalog of human Mendelian traits: The Online Mendelian Inheritance In Man (OMIM) catalog, hosted by the NCBI website. In OMIM you can find a wealth of information on human traits that are inherited in a Mendelian fashion, from the symptoms of a genetic disorder and how to diagnose it, to details in the molecular genetics and published papers on the trait or disease.

Then we introduced the several modes of inheritance of human Mendelian traits.

• Autosomal - dominant and recessive
• X-linked - dominant and recessive
• Y-linked
• Mitochondrial

We described the characteristics of the autosomal and X-linked dominant modes of inheritance.

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

LectureChapter 3 - Mendelian geneticsChapter 4 - Pedigree analysis

Yesterday we finished chapter 3, on Mendelian genetics.

We discussed more complex phenotypes that made Mendel's principles harder to study in many organisms, and how they do not conflict with them when considering the genotypes. Such phenotypic variations to Mendel's theme are:

• Incomplete dominance
• Codominance
• Multiple alleles
• Gene interactions (mainly epistasis)

We also started chapter 4, on pedigree analysis.

We briefly revisited the reasons for which human genetics cannot be studied experimentally and introduced the modes of inheritance of human Mendelian traits.

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

Lecture, chapter 3 - Mendelian Genetics

Mendel, in his garden
_______________________________________________

Today we talked about the classic experiments with which Mendel kick-started the field of genetics. We discussed the monohybrid and dihybrid crosses that lead Mendel to propose his principles:

• Principle of segregation
• Principle of independent assortment

We then discussed human traits in which Mendel's principles can be observed. On Monday we will talk about apparent deviations from Mendel's principles.

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

Buzz of the week (or the month; or the year?)

Bacteria that can use arsenic instead of phosphorus? CLICK HERE for more info...

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

Lab 01 - Human Mendelian genetics

During this first lab students learned the basics of building pedigrees to study human genetics.

Pedigrees were built for the following traits

• Free or attached ear lone
• Hitchhiker's thumb
• Tongue rolling
• Hand folding

The latter two are behavioral traits with a genetic component but they seem to be inherited in a Mendelian fashion; they were suitable for this basic exercise.

Then students did simulations of gametogenesis and offspring production to illustrate topics that will be soon studied in lecture: Mendel's principles.

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

Bioethics projects - Topics selection

Today students formed groups and chose topics for the bioethics papers and panel discussions (genetics-related topics that generate social, moral, or political controversy). The groups and chosen topics are the following:

1. Human cloning - Becca, Kelly, Kandai
2. Genetically modified organisms (GMOs) - John, Josh, Mohammed
3. Genetic screening for psychiatric disorders - Cara, Chelsey, Scott
4. Prenatal genetic diagnosis (PGD) - Amanda, Sarah, Brittany
5. Embryonic stem cell research - Amy, Nicole, Saleh
6. Designer babies - Chelsie, Daisy, Johnny

Panel discussions will take place during the lab session of week 9. Papers are due the same day.

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

Lecture, chapter 1 - A human perspective on genetics

Today we finished chapter 1.

We discussed the impact that genetics has had in society, since the 19th century when Francis Galton started a eugenics movement, to the more positive impact it has today through biotechnology.

Tomorrow:

We will do lab 1, Family pedigree analysis. Please remember to find out what are your and your relatives' phenotypes for the following traits:

• Tonge rolling - Roller vs. non-roller
• Ear lobe - Free vs. attached
• Thumb - Hitchhiker's vs. straight thumb
• Hand folding - Left thumb over right vs. right over left

The lab guide will be available on the p-drive and the WebCT site and will be e-mailed to you as well.

Remember you must form groups of three people to develop the bioethics projects. You must propose genetics-related topics that are controversial. Topics will b assigned before starting lab 1.

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

Lecture, chapter 1 - A human perspective on genetics

Today we had an introduction to the class. We talked about the organization of the course, expectations and how it's going to be graded, and started chapter 1 in the book.

Chapter 1 in the textbook, Genetics as a human endeavor, is an introduction to the course, and a dissertation on the importance of genetics for every day's life. We discussed, at a basic level, topics from the definition of genetics to the different approaches to study genetics.

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

Lecture, chapter 14 - Biotechnology

Today we covered most of chapter 14 in Biotechnology.

We discussed some of the services offered within the context of biotechnology, such as genetic testing and screening, and DNA profiling, mainly using short tandem repeats (STRs) or microsatellites.

On Friday we will discuss genetic testing via DNA microarrays, and we will have a brief discussion on population genetics.

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

Lab 10 - Population genetics II - Evolution

Today on lab 10, we performed a series of computer simulations to understand the effect of natural selection and genetic drift on the evolution of populations.

We used Jon C. Herron's AlleleA1 and EvoDots. AlleleA1 allowed us to simulate changes in allele frequency under specific conditions, since we were able to control variables such as population size, initial allele frequency, and fitness (we didn't change other variables that could be controlled as well). EvoDots allowed us to simulate the effects of predation on a population of dots which vary in certain traits (speed, size, and color). In this case the user is the predator.

The effects of natural selection and genetic drift under various conditions was considered.

Other activities:

• We had the last bioethics discussion panel (privacy of genetic information)
• We had our second lab quiz

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

Lecture, chapter 14 - Biotechnology

Today we started covering chapter 14, on Biotechnology

Biotechnology is the use of recombinant DNA technology to produce commodities or offer services.

We discussed some of the uses of biotechnology in today's society, such as biopharming (obtaining pharmaceutical products by using bacteria, animals, and plants), and Genetically Modified Organisms (GMOs).

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

Lecture, chapter 13 - Cloning and recombinant DNA technology

Today we continued with chapter 13.

We discussed the process to make genomic DNA libraries and how to screen them for DNA fragments of interest, and we introduced the basics of PCR. We talked about the reagents that are required for the reactions and the basic steps in a cycle.

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

"Lab" 9 - Bioethics discussion panels

Tuesday, May 4, 2010

Today we had our bioethics presentations and discussion panels. Students did a presentation highlighting the scientific background and ethical issues of selected genetics-related topics:

• Genetically Modified Organisms (GMOs) - Aubrey, Liz, Nathan, and Dexter
• Human-animal chimeras - Beth, Sarah, Stacy, Aimee, and Emily
• Stem cell research - Sonia, Katie D., Dustin, and Geoff
• Designer babies - Niki, Andrea, Jessica, and Katie K.
• Cloning of human beings - Jamal, Jerel, Shawn, and Scott

Next week:

• Privacy of genetic information - Rachel, Amy, Anessa, and Jake

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

Lecture, chapter 13 - Cloning and recombinant DNA technology

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

We defined cloning and clones, and provided examples in cloning plants, animals, and molecules. Then we discussed the basic steps and the rationale behind DNA cloning. We introduced concepts like restriction enzymes, vectors, recombinant DNA, ligation, and genetic transformation.

In out next meeting we will talk about details of the cloning process, with and without the use of bacteria.

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

Lecture, chapter 11 - Mutation

Today we finished the chapter on mutation.

We discussed the types of mutation at the nucleotide sequence level (nucleotide substitutions, including missense, sense, nonsense, and silent mutations, insertions and deletions [indels] and allelic expansions [a.k.a. dynamic mutations]).

We then discussed the mechanism that cells have in place to precent DNA changes from becoming mutaitons (proofreading and repair mechanisms), the consequences of these systems failing, and the concept of genomic imprinting.

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

Lab 08 - Population genetics

Today we did the population genetics lab

We introduced concepts that are key to the study of population genetics such as allele frequency, genotype frequency, gene pool, and Hardy-Weinberg principle (and equilibrium) and its assumptions. When discussing the Hardy-Weinberg principle we discussed the forces that can alter allele frequency in a population: genetic drift, selection (including sexual selection), mutation, and migration.

We then then proceeded to further study Hardy-Weinberg equilibrium by running simulations on PopCycle, a software package created by Jon Herron, from the University of Washington. PopCycle allowed us to see the conditions under which allele and genotype frequencies remain constant, and it also allow us to relax some of the assumptions. We introduced the effect of genetic drift and natural selection. Students were allowed to observe their effect on allele frequency

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

Lecture, chapter 11 - Mutation

Today we talked about agents that produce mutations (mutagens), and we focused in radiation and chemicals.

When discussion radiation we mentioned the various sources of radiation to which we are exposed and the average amounts to which the U.S. population is exposed. We also mentioned some of the variations from the average depending on people's profession, location, or whether they are undergoing medical testing or treatment.

When discussing chemicals, we talked about the classification of chemicals according to the kind of change they induce on DNA. Specifically we discussed base analogs, intercalating agents, and chemicals that alter DNA.

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

Discussion - Genetics in the news

___________________________________________________

Today we met outdoors since we had such a nice weather, and got involved in a series of group discussions.

Students were asked to search for genetics-related news released in the last two months, and select a few that were of interest to them. Groups of 4-5 students met during 20 minutes to discuss their various articles and choose one that they wanted to share with the class at large, because of its relevance to the class or to every day life.

Then, during half hour, the whole class met and different groups brought their chosen topics to the attention of their classmates. We had discussions on such topics under the enjoyable Ohio spring sun.

Topics were mostly related to molecular genetics, ranging from epigenetics and autism, to a putative correlation between the strength of the immune system in women and their success in relationships, to the evolution of a photosynthetic slug.

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

Lecture, chapter 11 - Mutation

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

Our focus in this chapter will be on how mutations are detected and how they happen.

We discussed traditional methods to pinpoint the individual in which a mutation that affects the phenotype appears. These methods apply to mutations that produce a dominant allele of a trait controlled by one fully penetrant and expressed gene.

We also discussed how mutation rate has been traditionally estimated in humans, and then we mentioned the factors that can affect the mutation rate across genes.

NOTE:

On Friday students are to bring a printout of a genetics-related news article (from a news paper, magazine, podcast, etc.) and be ready to discuss it with the instructor and classmates. Small discussion groups will meet and then the most relevant articles will be discussed in a general forum.

(if at least 17 different topics are submitted 5 bonus points will be awarded to all students who bring an article and are involved in the discussions)

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

Lab 7 - Human gene mapping

Today we discussed the importance of applying principles of gene mapping to calculating the risk of a person inheriting an allele responsible for a genetic disorder, by observing the inheritance of a marker gene (i.e. a closely linked gene with an easily observable phenotype).

Three pedigrees were analyzed, to determine the genotypes of all of the portrayed individuals and if they were parental types or recombinant types. Once this information was available the odds ratio is calculated as an estimate of how closely linked the genes are.

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

Lecture, chapter 11 - From proteins to phenotypes

Today we finished the chapter in which we explained at a basic level how proteins, direct products of genes, do reflect in an individual's phenotype.

We talked about how transport proteins can be altered by mutations and have an impact, from mild to lethal, in the individual's phenotype. Our example was hemoglobin. A number of mutations can alter the genes that encode the globins (subunits of hemoglobin), producing a disease categorized as a hemoglobin variant, or could alter the genes that encode proteins that control the transcription of globin genes, producing a disease categorized as a thalassemia.

In either case the consequence of the mutation, if it is noticeable, will be anemia.

We also introduced the basic idea of the field of biochemical genetics, more specifically in the subfields of pharmacogenetics and ecogenetics. Such subfields study our phenotypes in terms of how we react to chemicals: Within our bodies (pharmacogenetics), and in the environment (ecogenetics). Active research is being conducted in such areas.

An important aspect is how the way we taste food can have an impact in health problems such as obesity (pharmacogenetics). Another important topic is how we react to chemicals used in agriculture, such as pesticides, or used in manufacturing (an example would be the effects of led used in baby toys manufactured in China)

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

Lecture, chapter 10 - From proteins to phenotypes

Friday, April 16, 2010

Today we discussed translation, and how mutations can have an effect in the phenotype when altering 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.

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

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).

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

Lab 06 - Gene mapping - Drosophila

Tuesday, April 13, 2010

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

We discussed concepts like linkage, recombination, crossing over, and as a consequence how phenotypic categories deviate from Mendelian proportions. 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)

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

Lecture, chapter 9 - From genes to proteins

Monday, April 12, 2010

We 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)

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

Lecture, chapter 8 - Nucleic acids

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

We reviewed a brief time line of discoveries that lead us to 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.

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

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 and causes of each.

We then discussed structural alterations (duplications, deletions, inversions, and translocations (reciprocal and Robertsonian), and other abnormalities (Double Uniparental Disomy and fragile sites).

The details of each case of aneuploidy were covered by students as an independent reading and will be tested.

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

Lab 05 - Heritability (of quantitative traits)Lab quiz 1

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. in our "population" (the class). 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, since we had the data available. This kind of heritability is usually not calculated in humans.

*Actually performed a week later, on April 13.

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

Lab quiz 1

During the last hour of today's lab students took the first lab quiz.

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

Exam 1

Today we had our first exam. Results statistics:

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

Lab 04 - Inheritance of complex traits

Wednesday, March 30, 2010

Today we practiced pedigree analysis when a trait is controlled by several genes and environmental factors. Students learned how to identify a complex trait on a pedigree and to estimate the most plausible mechanism explaining the pattern of inheritance observed in a pedigree.

We introduced the concepts of threshold traits and genetic liability, and used them to calculate the risk of parents conceiving a child affected by a multifactorial disease (an example of a threshold trait)

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

Lecture, chapter 6 - Cytogenetics

Today we started covering chapter 6 on cytogenetics.

We talked about what a karyotype is, how it's made, what it is used for and what kinds of cells can be used to make one. We also discussed chromosome nomenclature and techniques to stain or paint chromosomes while making a karyotype.

We introduced the concepts of euploidy, polyploidy, and aneuploidy.

Reminder: First exam this Wednesday, March 31.

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

Lecture, chapter 5 - Inheritance of complex traits

Today we discussed one of the most important concepts in quantitative genetics.

We defined heritability and talked about some of its implications. We discussed the use of twin studies as tools the estimate heritability of different traits, and the importance of using both, monozygotic (MZ) and dizygotic (DZ) twin studies.

We discussed a few examples of multifactorial traits in humans: Skin color, IQ, and obesity.

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

Announcement - Dates for lab quizzes

Lab quizzes will take place on the following dates, from 4:00-4:50 p.m.:

• Lab quiz 1: Tuesday, April 06 (week 5)
• Lab quiz 2: Tuesday, May 11 (week 10)

Each lab quiz will consist on 3-5 exercises like the ones that have been done in lab. A calculator will be required.

Rules:

• Each student will team up with a partner
• Students can talk ONLY to their partners
• Students are allowed to use notes and books
• The use of electronic devices (other than calculators) is NOT allowed (i.e. no cell phones, lap tops, net books, audio file players, etc.)

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

Lecture, chapter 5 - Inheritance of complex traits

Today we continued chapter 5, on complex patterns of inheritance (polygenic and multifactorial).

We talked about how alleles in polygenic trait loci contribute to the phenotype, the characteristics of multifactorial traits, and the concept of regression to the mean.

We talked about the field of quantitative genetics; we discussed the kinds of questions it can answer and some of the most important concepts (phenotypic distribution, distribution of environments, norm of reaction)

Note:

We met in Meyer 113. We will meet in this room for the remaining lectures during this quarter.

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

Lab 3 - Epistasis and hypothesis testing

Genetic corn

_____________________________________

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.

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

Lecture, chapter 4 - Pedigree analysisLecture, chapter 5 - Inheritance of complex traits

Today we finished chapter 4, on pedigree analysis.

We discussed cases in which the modes of inheritance we covered in previous lectures cannot be detected in a pedigree, because of complex gene and environmental interactions that prevent the phenotype of being fully expressed. Specifically we discussed age-related phenotypic expression, penetrance and expressivity. We provided examples of traits that show such phenomena.

We also started chapter 5, on polygenic inheritance and multifactorial traits.

We highlighted the difference between continuous and discontinuous phenotypic variation, and defined complex, polygenic and multifactorial traits.

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

Lecture, chapter 4 - Pedigree analysis

Friday, March 19, 2010

Today we continued with our chapter on pedigree analysis.

We discussed several modes of inheritance

• autosomal dominant
• x-linked dominant and recessive
• y-linked (paternal)
• mitochondrial (maternal)

On Monday we will discuss cases of variations on gene expression.

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

Lecture, chapter 4 - Pedigree analysis

Today we started chapter 4, on pedigree analysis.

We discussed the utility of using pedigree analysis to study human genetics. We had an overview of what the main six modes of inheritance are, and how they can be identified in a pedigree.

We discussed in detail the characteristics of the autosomal recessive mode of inheritance, and provided examples: cystic fibrosis and sickle cell anemia.

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

Lab 2 - Mendelian genetics

Today we did lab 2, on Mendelian genetics.

The goal of this lab was to observe the phenotypic consequences of the principles of segregation and independent assortment. We used the free software DrosophiLab to simulate experimental crosses with fruit flies. Most of the crosses were testcrosses, meaning that one of the individuals involved in the cross was homozygous recessive for the trait being considered (in this case a homozygous recessive individual would be a mutant fly. The mutation would have an observable phenotype).

A series of three experiments considering one trait, two traits controlled by genes in different chromosomes, and one trait controlled by a gene in a sex chromosome should have shown students how to see the effects of Mendel's principles in an experiment.

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

Lecture, chapter 3 - Mendelian genetics

Today we finished chapter 3, on Mendelian genetics.

We talked about how human genes do follow Mendel's principles, and talked about a few examples of traits on which Mendelian inheritance can be studied by observing phenotypes.

We also discussed how there are cases in which there are deviations from Mendelian phenotypic proportions:

• Incomplete dominance
• Codominance
• Multiple alleles
• Gene interactions (including epistasis)

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

Lecture, chapter 3 - Mendelian genetics

Friday, March 12, 2010

Today we started covering chapter 3, on Mendelian genetics (a.k.a transmission genetics). We talked about Mendel's classic experiments with pea plants and how he ended up formulating his principles:

• Principle of segregation
• Principle of independent assortment

On Monday: Do Mendel's principles apply to humans?

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

Lecture, chapter 1 - A human perspective on genetics

Today we continued with the outline of what the quarter will be.

We discussed how Mendel gave birth to the field of genetics, even before the word 'gene' was coined, what the different approaches to studying genetics are, and how genetics has impacted our lives in the past and in the present.

Note: There will be no lecture on chapter 2, but students are strongly encouraged to read it. On Friday we will start covering chapter 3 in the text book, on Mendelian genetics

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

Lab 1 - Basic Human Genetics

Tuesday, March 2, 2010

After choosing teams and topics for the bioethics projects we did the first lab of the quarter, on very basic human genetics.

We covered the basics of pedigree analysis, and each student built their own family pedigrees mapping on them four traits that are inherited in a Mendelian fashion: Hitchhiker's thumb, tongue rolling, free/attached earlobe, and hand folding. Genotypes were assigned to each individual in the pedigree to the extent that the available information allowed it.

Then, using the students' genotypes for the four mentioned traits, students used pieces of paper representing chromosomes with their alleles to perform simulations of gametogenesis to illustrate Mendel's principle of segregation, and of crosses generating several offspring, to illustrate Mendel's principle of independent assortment.

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

Bioethics projects

Tuesday, March 2, 2010

Today we had the first lab session of the quarter. During the first hour or so, we talked about the bioethics projects, which will be presented on the lab session of week 9.

The bioethics projects will be developed by teams of four students, and will focus on genetic-related topics that pose ethical problems and are surrounded by controversy. Each team selected a topic that members considered to be controversial and interesting enough to spark discussion with classmates.

As part of the project students will write a paper explaining the scientific basis of the issue of choice, the reasons for which it is controversial, showing the opposing views on the issue, and explaining what position they take, properly backed by a rational process.

A second component of the project will be a presentation and panel discussion during the lab session on week 9. Each team will prepare a 20-minute presentation, on a format of their choice (oral presentation, a play, a mock trial, a fake documentary, etc. You can be as creative as you want), which will be followed by a 10-minute panel discussion with the rest of the class. Each group, acting as the panel of experts in the topic, will engage their classmates and have a discussion debating different points of view.

The grade will depend on how well the scientific basis of the issue is presented, how well explained the controversial aspects are, the solidity of the reasons for taking a position in the issue, and how effectively the rest of the class is drawn into the discussion.

A first draft of the paper is due on Friday of week 6, at midnight, and the final version due on Tuesday of week 9, at noon. If a power point file is used in the presentation it will be due on the night of Monday before the day of the presentations.

TOPICS AND TEAMS

• Designer babies - Niki, Andrea, Jessica, and Katie K.
• Human-animal chimeras - Beth, Sarah, Stacy, Aimee, and Emily
• Cloning of human beings - Jamal, Jerel, Shawn, and Scott
• Genetically Modified Organisms (GMOs) - Aubrey, Liz, Nathan, and Dexter
• Stem cell research - Sonia, Katie D., Dustin, and Geoff
• Privacy of genetic information - Rachel, Amy, Anessa, and Jake

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

Introduction and lecture, chapter 1 - A human perspective on genetics

Monday, March 1, 2010

Welcome to the spring quarter Introductory Genetics class...!

Today we had the introduction to the class, an overview of the syllabus and a talk about the class policies.

Then we started covering chapter 1 in the textbook, an introduction to this intro class. In this chapter we outline what the course is going to be, touching in topics like what genetics is and what the properties of genes. Other general topics will be covered on the next lecture.

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

Lecture, chapter 19 - Population genetics and human evolution

Friday, February 19, 2010

Today we had a very shallow introduction to population genetics and human evolution.

We discussed the concepts of gene pool, allele frequency and genotype frequency. We talked about the Hardey-Weinberg model and how it can be used to find allele frequencies in a population, or predict genotype frequencies in a given generation based on allele frequencies.

We discussed Hardey-Weinberg equilibrium and how it can be used to test if evolutionary forces are acting upon a population.

We then discussed a little bit of human evolution and how maternal and paternal haplotype data have been used to elucidate the migration routes of humans since our origin in Africa.

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

Lecture, chapter 12 - Genes and cancer

Monday, February 16, 2010

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

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

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

Lecture, chapter 12 - Genes and cancer

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

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

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

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

Lecture, chapter 14

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

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

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

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

Lab 09 - Bioethics projects

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

The following topics were discussed:

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

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

Lecture, chapter 14 - Biotechnology

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

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

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

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

Lecture, chapter 14 - Biotechnology

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

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

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

Exam 2

Today we had our second exam. Stats.

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

Lab 8 - Population Genetics

Wednesday, February 3, 2010

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

• Natural selection
• Migration
• Mutation
• Genetic drift

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

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

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

Lecture, chapter 13 - Cloning and recombninant DNA

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

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

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

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

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

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.

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

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)

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

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.

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

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).

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

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.

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

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)

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

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.

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

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).

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

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).

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

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.

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

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.

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

Exam 1

Today we had our first exam. Stats:

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

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).

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

Lecture, chapter 6 - Cytogenetics

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

© 1991 Harper Perennial

__________________________________________________

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.

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

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.

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