Exam 3

Today we had our final exam. Stats:

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Extra activity - Genetics on the news

Students searched the news outlets for recent genetics-related articles and selected one to discuss with their classmates.  In class they met in groups of six students, commented the highlights of each article, critiqued it, and chose two to share with the rest of the class.

There was a prominence of human molecular genetics articles, mainly on the health care field.  Pharmacogenomics seems to be a field of research on the rise, or at least it seems to be catching the attention of the broad public.  Here's a list of the articles students discussed in class:

• Donor Kidney Survival Determined By Genes, Not Race
• Genetic clue to common birth defects found
• Do genes make people evil?
• Scientists discover genetic weakness in MRSA superbug wich could lead to new ways of fighting infection
• Could gene tests tell if kids can be sports stars?
• Decoding Cancer
• Single-Letter Change in DNA Code May Spell ADHD
• In a genetic research first, researchers turn zebrafish genes off and on
• Genetic Testing + Abortion = ???
• Decoding tumors in search of more effective cancer treatments
• Pharmacogenomics, the next frontier in medicine?
• Genetic testing can help predict if chemo will work
• Cancer Screening Approach Using HSV to Force Cells to Secrete Biomarker Developed
• Use Of Genetic Information May Help Predict Likelihood Of Survival Following Chemotherapy For Breast Cancer
• MicroRNA Mediates Gene-Diet Interaction Related to Obesity, Researchers Find
• Happiness linked to a gene that comes in long and short versions
• 2 unsuspected proteins may hold the key to creating artificial chromosomes
• Alzheimer's known unknowns: new genetic risk factors
• Johns Hopkins team identifies genetic link to attempted suicideTwo Unsuspected Proteins May Hold the Key to Creating Artificial Chromosomes
• U.S. researchers discover human lung stem cell
• Parents Want Genetic Testing for Kids: Study
• Electronic Records Speed Genetic Studies

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Lecture, chapter 13 - Cloning and recombinant DNA

Today we finished the chapter in cloning and recombinant DNA technology with a brief and basic overview of two of the classic techniques to analyze DNA: Southern blotting and DNA sequencing (through the dye-terminator sequencing method, a modification of the Sanger method).

• Watch a basic animation of Southern blotting
• Watch a detailed video of Southern blotting

We also had the last bioethics presentation and panel discussion.  Click here for details.

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Lab quiz 02

Today we had our second lab quiz. Stats:

(I wrote this entry on Wednesday, May 11... What's happening to Blogger?!?!?!?!?!)

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Bioethics presentations and panel discussions

Today students did a presentation of their bioethics papers and conducted panel discussions (on genetics-related topics that generate social, moral, or political controversy). The following topics were presented:

1. In vitro fertilization - Courtney, Jenny, Kwaku, Marcus
2. Genetic predisposition to alcoholism - Danielle L., Veronica, Caleb, Justin
3. Designer babies - Jeniffer, Liz, Salesha, Sarah
4. Genetically modified (GM) crops - Alex, Andre, Kevin, Mark
5. Xenotransplantation - Anabel, Jessica, Kara, Megan
6. Research using HeLa cells - Lindsay, Ben, Brent, Jordan
7. Human-animal chimeras - Andie, Danielle H., Kirstin, Maggie (on Friday, May 13)

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Lecture, chapter 13 - Cloning and recombinant DNAincluding the PCR song

Today we discussed how to use the process of cloning for building genomic library (a collection of clones containing the entire genome of an organism).  We mentioned how to find a gene, or any other sequence of interest by using labeled probes and the process to visualize the results.

Then we did an overview of the process of cloning in vitro: The polymerase chain reaction (PCR).  We mentioned the steps and some of the key ingredients, explaining why under many circumstances doing PCR is much more efficient and cheaper than cloning.

I am including a video of the PCR song, which has helped many of my molecular biology students remember the main features of the reaction.  The PCR song highlights:

• Who invented PCR
• The main reagents of PCR
• The steps of the thermal cycle
• Some important applications of PCR

Some students have even used the song as a ringtone... (Warning: Cheesy!)

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LectureChapter 11 - MutationChapter 13 - Cloning and recombinant DNA

On Wednesday we finished the mutation chapter, with a discussion on the mechanisms that cells have in place to prevent DNA changes:  The proofreading mechanism, performed by DNA polymerase as it fulfills its function, and DNA repair mechanisms, performed for several batteries of specialized enzymes, correcting mistakes that have been made during DNA replication

Today we started the chapter on cloning and recombinant DNA, with a discussion of the several modalities of cloning (cloning molecules, cells, and organisms), and the potential applications of cloning DNA and using recombinant DNA technology.

We started to describe the process of cloning DNA.

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Lab 10 - "Classic" Population Genetics IIEvolution in action

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 were considered.

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Exam 2

Today we had the second midterm exam.  Stats:

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Chapter 11 - Mutation

Following with the discussion on mutagens, we took on chemicals that cause mutations through a variety of mechanisms (base analogs, nucleotide-altering chemicals, and chemicals that bind to DNA).  We provided examples on their mechanism of action and on how they may affect the phenotype.

Then we discussed types of mutations at the nucleotide sequence level.  We described the three main categories: nucleotide substitutions, insertion/deletions (indels), and allelic expansions (a.k.a dynamic mutations).  We explained how they happen, when they alter the phenotype, and when and why they can be considered (or not) frameshift mutations.

We mentioned the mechanisms that cells have in place to fight off mutations (proofreading mechanism and repair systems) but details will be considered next week.

On Monday:  Exam 2...!

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Chapter 11 - Mutation

Today we continued the chapter on mutation, discussing how to find the origin of a mutation in a sex-linked gene.  We also talked about how calculate mutation rates in humans, when they are visible  in the phenotype.  We defined the conditions under which such calculation is possible.

We mentioned factors that determine variation in mutation rate in different genes and factors that increase such rate. We introduced the concept of radiation as a mutagen and started describing the most common sources of it and mechanisms of action.

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Lab 08 - 'Classic' population genetics

Screenshot of PopCycle, by John Herron
(click on pic for full size image)
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Today we did the "classic" population genetics lab. "Classic" as opposed to the increasingly strong trend of studying population genetics based on the coalescent theory.

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 able to observe their effect on allele frequency

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LectureChapter 10 - From proteins to phenotypesChapter 11 - Mutation

We continued a discussion on pharmacogenetics, or studying phenotypes in terms of how we react to chemicals in our bodies.

We did the popular genetic test on tasting phenylthiocarbamide (PTC), a Mendelian trait easy to diagnose. Some people have the dominant allele that manifests in being able to taste PTC (dubbed "tasters", with the genotype TT or Tt), and some people have only the recessive allele, which prevents them from tasting the chemical compound (dubbed "non-tasters", with genotype tt).  Those who can taste it perceive a bitter flavor.

In our class there were 16 'taster' vs. 6 'non-taster' students.  A fast survey revealed that tasters have a tendency to dislike foods or beverages that have chemicals similar to PTC, like dark beer (question limited to students over 21 years of age), coffee, strong cheeses, artificial sweeteners, and spicy foods. Interestingly enough, most tasters also liked vegetables like broccoli and cabbage, which should be bitter for them.  Non-tasters tended to like such foods and beverages.

We discussed the scope of ecogenetics, the field that studies our responses to chemicals in the environment.

We started the chapter on mutation by providing a definition and outlining the conditions in which a mutation that has a phenotypic effect can be detected.

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Lab 07 - Gene mapping in humans

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

In humans, we must rely on pedigrees. In this lab we considered three different pedigrees showing linkage between a genetic disorder and another trait (easily observable). 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, chapter 10 - From proteins to phenotypes

Today we started chapter 10 on how proteins can affect our phenotype.

We started with a brief discussion of protein function and then ways in which mutations can affect our phenotype by causing changes in the sequence of amino acids of enzymes (which may impact metabolic pathways), receptor proteins and transport proteins.  We provided examples using several diseases caused by such mutations.

We started a discussion on pharmacogenetics, or how we can study phenotypes in terms of how we react to chemicals in our bodies.

Up next:  Can you can you not taste phenylthiocarbamide?

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Lecture, chapter 9 - From genes to proteins

Today we discussed what cytoplasmic components are crucial for the process of translation.  We described the main characteristics of ribosomes, amino acids and tRNA.

We then described the actual process of translation, dividing in its phases of initiation, elongation and termination.  We followed with a discussion of the fate of synthesized polypeptides and the features of protein structure.

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Lab quiz 01

Today we had our first lab quiz.  Stats:

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Lab 06 - Gene mapping - Drosophila

Tuesday, April 12, 2011

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).  We did this for three genes, using a three-point test cross.

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Chapter 9 - From genes to proteins

Today we discussed the way in which genetic information is coded in DNA.  We introduced the genetic code, some of its properties and some of its implications.

Then we moved on to talk about the transcription process.  We mentioned its steps (initiation, elongation, and termination), and the processing that a mRNA molecule must undergo before being exported to the nucleus (5' capping, polyadenylation, intron splicing).

As an introduction to the process of translation, we explained what amino acids are and how they are linked into polypeptides.  On Wednesday we will talk about other cytoplasmic components important for
translation, and about the translation process itself.

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LectureChapter 8 - DNA structure and chromosomal organizationChapter 9 - From genes to proteins

Today we discussed the basics of RNA structure and pointed out basic differences between it and DNA.  We then had an overview of how DNA is condensed into chromosomes and how it is replicated.

Watch the following video or access this link to understand the main features of the DNA replication process

We also started chapter 9, on how genetic information is transcribed into mRNA and translated into proteins.  We briefly recapped how Beadle and Tatum confirmed that there was a connection between genes and proteins in the 1940sand how their famous quote ("one gene, one enzyme") has been modified, as discoveries have been made, to make it more accurate.

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Chapter 8 - DNA structure and chromosomal organization

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Rosalind Franklin and her "photo 51"
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We continued discussing the history of how the structure of DNA was discovered, including the injustice  (alleged by many) 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.

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Lab 05 - Heritability

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

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/recessiveness, polygenic interactions, and well as maternal and paternal effects.
2. Narrow sense heritability: It quantifies only the proportion of phenotypic variation explained by additive contribution of the genes that control the trait, ignoring all other genetic contributions.

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

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LectureChapter 6 - CytogeneticsChapter 8 - DNA structure and chromosomal organization

Today we finished the cytogenetics chapter, with a discussion on uniparental disomy (UPD) and fragile sites, the remaining chromosomal abnormalities.

And we started on chapter 8, on DNA structure and chromosomal organization, with a brief discussion on some science history events that led to the discovery of the structure of DNA.  On Wednesday we'll pick up on  the drama that unfolded around Rosalind Franklin's (involuntary? not-acknowledged?) involvement in the process of deciphering the structure of the now famous double helix.

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Exam 1

Friday, April 1, 2011

Stats on exam 1:

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Lecture, chapter 6 - Cytogenetics

Today we discussed the several cases of autosomal and sex chromosome aneuploidies:  Their frequency, symptoms, and consequences for an individual's life.  Polyploidies and aneuploidies are cases of alterations in chromosome number.

We also introduced the concept of chromosomal structural alterations.  We mentioned the various categories (deletions, duplications, inversions and translocations) and started discussing them.

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Lab 04 - Inheritance of complex traits

Today we practiced pedigree analysis when a trait is controlled by one or 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)

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Lecture, chapter 6 - Cytogenetics

A human karyotype
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Following with the chapter on cytogenetics we discussed the nomenclature of chromosomes, how to produce a human karyotype, including the different chromosome banding and painting techniques, and methods to obtain cells from fetuses and adults to produce a karyotype.

We introduced the topic of variations in chromosome number, including polyploidy and aneuploidy;  we discussed the most common causes for each abnormality.

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LectureChapter 5 - Polygenic and multifactorial inheritanceChapter 6 - Cytogenetics

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.

Then we started discussing the chapter on cytogenetics, a field that focuses on studying chromosomes, using karyotypes as the main tool.

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Lecture, chapter 5 - Polygenic and multifactorial inheritance

We started covering quantitative genetics, the subfield of genetics that studies polygenic and multifactorial inheritance based on observations on phenotypic variation.

We discussed the principle of regression to the mean and how statistics is used as an important tool in quantitative genetics. We focused on concepts that are specific to quantitative genetics, such as phenotypic distribution and distribution of environments.

We mentioned features of the interaction of genes and environment as preparation to discuss the concept of heritability.

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Lab 03 - Epistasis and hypothesis testing

Genetic corn

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Yesterday 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 kernels, students were able to predict the phenotypic proportions of purple and yellow kernels. The predictions were compared to the observations and tested using a chi-square test, with a significance level of 5% (0.05, numerically, but not conceptually equal to α).

When the hypothesis (observed counts = expected counts) was rejected (if it was rejected), results were explained as the consequence of an epistatic interaction that prevented the R and C genes of showing the phenotypic proportions predicted by Mendelian inheritance.

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Lecture, chapter 5 - Polygenic and multifactorial inheritance

After finishing chapter 4 on pedigree analysis (discussing age-related phenotypic expression, penetrance, and expressivity), we started chapter 5, on multifactorial and polygenic inheritance.

We discussed the differences between continuous and discontinuous traits, and how they are related to the number of genes that affect them. Discontinuous traits must be described in terms of measurements taken in a population rather than qualitatively describing individuals. We defined complex, multifactorial, and polygenic traits.

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Why are fruit flies important for us?

Audio slideshow screenshots
Clockwise: A normal fruit fly next to another with a liver disease, white-eyed mutant flies feeding, a collage of epifluorescence images of flies internal organs or systems, and a fruit fly brain with neurons that control mating, fluorescing in green

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Research in fruit flies, Drosophila, specially D. melanogaster, has been fundamental for enhancing our knowledge of genetics as a whole and of human genetics in particular, since we share about 60% of our genes with them. In lab we have used software that simulates controlled crosses of fruit flies with specific mutations, and in the next few weeks we will perform more complex simulations.

But fruit flies are also used in other areas of research. Check out this audio slideshow, produced by the BBC, on the use of fruit flies in neurophysiology research. Some of the general principles outlined by the researcher apply to genetics research too. The system to breed the flies (jars with growth media, covered with cotton or gauze) is the same as in genetics research.

BBC Audio slideshow: Fruit flies - up close

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Lecture, chapter 4 - Pedigree analysis

Today we started chapter 3, on pedigree analysis.

We discussed the reasons for which human Mendelian genetics has been traditionally studied with pedigrees rather than with more direct approaches, and what are the shortcomings of doing so.

We also listed the six modes of inheritance and described two of them: Autosomal dominant and autosomal recessive. We discussed examples of each: Cystic fibrosis and sickle cell anemia (autosomal recessive) and Marfan syndrome (autosomal dominant).

I also introduced the catalog that stores information on human Mendelian traits: Online Mendelian Inheritance In Man (OMIM). [OMIM in Wikipedia]

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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 (test crosses). By doing so students were able to demonstrate the principles of segregation and independent assortment

• Video on how to use DrosophiLab

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Chapter 3 - Mendelian genetics

Mendel, in his garden in the 1880s
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Between Friday and today we covered the chapter on Mendelian genetics.

We discussed how Mendel performed the experiments with pea plants that led him to propose his principles of segregation and independent assortment, laying the foundation of the field of genetics.

We then discussed the apparent deviations from Mendel's principles that are observed in organisms with complex phenotypes. The genes responsible for such phenotypes do, indeed, follow Mendelian principles, but the phenotypic proportions are different from those Mendel observed. The cases we discussed were:

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

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LectureChapter 1 - A perspective in human geneticsChapter 3 - Mendelian genetics

Today we finished chapter 1 with a discussion of the main ways in which genetics has impacted society in the past (mainly through eugenics) and in recent decades to the present (mainly through biotechnology).

We also started chapter 3, on Mendelian genetics, with a discussion of the steps that Mendel himself took to set up his, now considered classic, experiments.

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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 lobe
• 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. Each student surveyed such traits in their immediate family in order to perform the analyses.

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

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Pre-lab 01 - Bioethics projects topics

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. In vitro fertilization - Courtney, Jenny, Kwaku, Marcus
2. Human-animal chimeras - Andie, Danielle H., Kirstin, Maggie
3. Genetic predisposition to addiction - Danielle L., Veronica, Caleb, Justin
4. Designer babies - Jeniffer, Liz, Salesha, Sarah
5. Genetically modified (GM) crops - Alex, Andre, Kevin, Mark
6. Organ farming - Anabel, Jessica, Kara, Megan
7. Research using HeLa cells - Lindsay, Ben, Brent, Jordan

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

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Intro Genetics, Biol 210 - Spring 2011

Welcome to the Spring 2011 edition of the INTRO GENETICS course!

This blog is kept for the students' convenience. You can use it as a record of how the class progresses, and occasionally as a a platform for announcements. Feel free to make comments suggesting new ideas or asking questions.

Check out the column on the right, since they contain interesting information about the course and about a few sources of genetics-related information.

Today:

We reviewed the syllabus and started with the first chapter in the textbook: A human perspective on genetics (or, if you prefer, a perspective on human genetics).

Tomorrow:

We will assign groups and topics for the bioethics projects, and will do a basic exercise on pedigree analysis using four traits easily identifiable:

• Tongue 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

Please remember to find out what are your and your relatives' phenotypes for these traits. The lab guide will be available on the p-drive and the WebCT site.

You will form groups of four people to develop the bioethics projects. You must propose genetics-related topics that are controversial. Topics will be assigned before starting the lab.

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Exam 3 (final)

Stats on the final exam:

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Activity - Genetics on the news

Students brought genetics-related news articles (or news podcast transcripts) and discuss them in small groups. Each group summarized the main points of the articles and presented them to the rest of the class.

Topics ranged from bacterial genetic engineering gone wrong to how certain genetic defects can make people less susceptible to cancer and diabetes (click here and here).

(a few other topics were DNA repair inked to genetic mutation, genes playing a role in choosing friends, contagious cancer affecting Tasmanian devils).

Although the foci of the articles were diverse, the trend was for students to find articles more related to molecular genetics than any other genetics field.

And, we were able to enjoy a warm(ish) weather outside!

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Lab 08 - Population genetics

Screenshot of PopCycle, by John Herron
(click on pic for full size image)
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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 able to observe their effect on allele frequency

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Chapter 14 - Biotechnology

Today we finished the chapter on Biotechnology. We discussed how to use DNA microarrays (a.k.a. "Gene chip") as a tool to do genetic testing.

We then discussed how tandem repeats in the human genome can be used as markers to do some DNA profiling, mainly short tandem repeats (STRs).

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LectureChapter 13 - Cloning and recombinant DNAChapter 14 - Biotechnology

We finished chapter 13, with an overview of one of the most commonly used automated DNA sequencing methods, the dye-terminator sequencing method, a modification of the Sanger method (a.k.a. chain termination - click here for an EXCELLENT video produced by the Dolan DNA learning Center).

Then we started the chapter on biotechnology, in which we provided a definition of the field, discussed its origins with the discovery of restriction enzymes in the 1970s, and did an overview of some of the most common fields within biotechnology: biopharming and genetically modified organisms (GMOs).

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Lecture, chapter 13 - Cloning and recombinant DNA

After finishing the last bioethics presentation/panel discussion on GMOs, we briefly saw animations of PCR and restriction enzymes. Then, we discussed Southern blotting, a common technique to analyze DNA.

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"Lab" 9 - Bioethics presentations and panel discussions

Yesterday we had 5 out of the 6 bioethics presentation and discussion panels this quarter. Groups of students presented the scientific basis, the bioethical issues, and expressed their opinions on, controversial genetics-related topics. They followed by leading a discussion with their classmates. The topics, and presenters, were:

• Human cloning
  Becca, Kelly, Kandai
• Genetic screening in relation to psychiatric disorders
  Chelsey, Cara, Scott
• Prenatal genetic diagnosis
  Amanda, Sarah, Brittany
• Designer babies
  Chelsie, Daisy, Johnny
• Embryonic stem cell research
  Nicole, Amy
• Genetically modified organisms (Friday)
  John, Josh, Mohammed

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Lecture, chapter 13 - Cloning and recombinant DNA

Continuing with the chapter on cloning and recombinant DNA, we talked about how to make genomic DNA libraries, which involves cloning, in some cases by using artificial chromosomes (BACs and YACs). Then we talked about how we can find a fragment of DNA of interest in such libraries by binding the DNA to nitrocellulose or nylon paper membranes and using DNA or RNA probes.

We also discussed the process of polymerase chain reaction (PCR), with emphasis on the advantages and disadvantages it has over the traditional cloning process.

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Lecture, chapter 13 - Cloning and recombinant DNA

Today we started with chapter 13.

We discussed the concept of cloning and the different kinds of cloning: Cloning molecules, cells, and organisms. We discussed the concept of recombinant DNA molecules.

We then proceeded to discuss the basics of the cloning DNA process, including the use of restriction enzymes, vectors, and DNA ligase.

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Exam 2

Stats for exam 2

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Lecture, chapter 11 - Mutation

Today we finished the chapter on mutation.

We discussed the different types of mutations (nucleotide substitutions, insertion/deletions [indels], and allelic expansions) and their potential effects on phenotype.

We also discussed how a cell prevents most of the DNA changes from becoming mutations: By putting in place a proofreading mechanism (performed by DNA polymerase) and DNA repair systems (performed by a variety of enzyme batteries). As part of the discussion, we mentioned the possible consequences of a mutation in genes that encode DNA repair enzymes.

We briefly mentioned the effects of mutations in genes affected by genetic imprinting and the effects mutations on specific nucleotides vs. mutations on any of a number of possible nucleotides

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Lecture, chapter 11 - Mutation

Today we discussed the reasons for which radiation (electromagnetic and corpuscular) can act as a mutagen, and what are the most common sources of radiation for an average citizen of the U.S.

We then listed the different categories of mutagen chemicals and how they affect DNA.

We started discussing the kinds of mutation that can occur (indels vs. substitutions, frameshift vs. non-frameshift), and their potential effect on phenotype.

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LectureChapter 10 - From proteins to phenotypesChapter 11 - Mutation

Today we finished chapter 10 by discussing the focus of the field of ecogenetics, an area of genetics concerned with how we react to chemicals in the environment based on our genotypes (how we react is our phenotype).

We then started the chapter on mutation summarizing how mutations that are observable in the phenotype have been traditionally studied, including how their rate has been measured (a task that is easier in the case of autosomal dominant diseases).

We discussed the factors that cause different genes to have different mutation rates and introduced the main agents (mutagens) that cause mutations.

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Lab 07 - Gene mapping in humans

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

In humans, we must rely on pedigrees. In this lab we considered three different pedigrees showing linkage between a genetic disorder and another trait (easily observable). 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, chapter 10 - From proteins to phenotypes

Today we discussed the effects of genotypes on how an individual reacts to chemicals, which is the scope of pharmacogenetics, and how an individual reacts to chemicals in the environment, the scope of ecogenetics.

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Lecture, chapter10 - From proteins to phenotypes

Today we examined the role of different kinds of proteins in determining our phenotype and how mutations may affect it.

We had examples on enzymes, transport proteins and receptor proteins.

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Lab quiz 1

Lab quiz 1 stats:

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Lab 06 - Gene mapping in Drosophila

Today we did lab 06: mapping genes in Drosophila.

We discussed concepts like linkage, recombination, crossing over, and how phenotypic categories deviate from Mendelian proportions because of these phenomena. We mentioned how genes that are in the same chromosome may also be unlinked, if the distance between them (measured in centimorgans [cM]) is big enough.

Using DrosophiLab, a crossing-over simulator (from Paul Lewis' lab), and paper and pencil, students learned:

• How to determine the distance between two genes in the same chromosome (measured in cM or map units (M.U.))
• The effect of the distance between genes and the size of a chromosome in the frequency of recombinant chromosomes during meiosis
• How to map genes based on gene distances
• How to map genes and find the distances between them based on phenotypic data (resulting from simulated crosses)

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Lecture, chapter 9 - From genes to proteins

Today we covered the remaining of chapter 7, mainly focusing on the process of translation.

We discussed the importance of the remaining cytoplasmic components (ribosomes and tRNA), and then we described the actual process of translation, breaking it down in its stages (initiation, elongation, and termination).

We commented on the structure of polypeptides and the events they undergo after translation (folding and different possible types of modification).

Tomorrow

• Lab 6: Gene mapping in Drosophila (computer lab)
• Lab quiz 1 (bring a calculator)

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Lecture, chapter 9 - From genes to proteins

Today we started our chapter on how genetic information is transferred into entities that affect, or in some cases are, our phenotype: Proteins.

We discussed a little bit of the history of how the link between genes and proteins was discovered, the basics of protein structure and the genetic code, and did an overview of transcription and mRNA processing.

In the next lecture we will discuss the process of translation.

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Lab 05 - Heritability and quantitative traits

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/recessiveness, polygenic interactions, and well as maternal and paternal effects.
2. Narrow sense heritability: It quantifies only the proportion of phenotypic variation explained by additive contribution of the genes that control the trait, ignoring all other genetic contributions.

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

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Lecture, chapter 8 - Nucleic acids

Today we finished the chapter we started yesterday, on nucleic acids.

Yesterday we talked briefly about the history of the study of nucleic acids and some of the basic structure and functions of nucleic acids , including a comparison of the characteristics of DNA and RNA.

Today we talked about the implications, for the understanding of genetics, of the discovery of the structure of DNA in the 1950s, the process of DNA replication, the mechanism in which DNA is compacted into chromosomes.

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Exam 1

Stats:

(click on pic for full size image)

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Lab 04 - Inheritance of complex traits

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)

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Lecture, chapter 6 - Cytogenetics

Today we finished the chapter on cytogenetics with a discussion of the effects of abnormalities on the structure of chromosomes, rather than in the number of them.

Among structural abnormalities we focused on translocations (reciprocal and Robertsonian). We also discussed uniparental disomy (UPD) and the presence of fragile sites.

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