ONU Biology 210

Exam 3

2011-05-16T14:56:00.001-07:00

Today we had our final exam. Stats:

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Extra activity - Genetics on the news

2011-05-13T15:20:00.000-07:00

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:

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Lecture, chapter 13 - Cloning and recombinant DNA

2011-05-13T14:52:00.000-07:00

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

2011-05-13T13:30:00.000-07:00

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

2011-05-10T09:57:00.001-07:00

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:

In vitro fertilization - Courtney, Jenny, Kwaku, Marcus
Genetic predisposition to alcoholism - Danielle L., Veronica, Caleb, Justin
Designer babies - Jeniffer, Liz, Salesha, Sarah
Genetically modified (GM) crops - Alex, Andre, Kevin, Mark
Xenotransplantation - Anabel, Jessica, Kara, Megan
Research using HeLa cells - Lindsay, Ben, Brent, Jordan
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

2011-05-09T19:31:00.001-07:00

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

2011-05-06T16:16:00.001-07:00

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

2011-05-03T18:48:00.000-07:00

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

2011-05-02T10:41:00.000-07:00

Today we had the second midterm exam. Stats:

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Chapter 11 - Mutation

2011-04-29T13:14:00.000-07:00

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

2011-04-27T15:15:00.001-07:00

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

2011-04-26T10:58:00.000-07:00

Screenshot of PopCycle, by John Herron
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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

2011-04-20T17:13:00.000-07:00

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

2011-04-19T14:26:00.001-07:00

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

2011-04-18T12:34:00.003-07:00

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

2011-04-15T10:25:00.000-07:00

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

2011-04-13T12:16:00.001-07:00

Today we had our first lab quiz. Stats:

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Lab 06 - Gene mapping - Drosophila

2011-04-13T12:13:00.000-07:00

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

2011-04-11T12:20:00.000-07:00

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

2011-04-08T12:59:00.000-07:00

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

2011-04-06T12:42:00.000-07:00

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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

2011-04-05T14:18:00.000-07:00

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:

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.
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

2011-04-04T14:25:00.000-07:00

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

2011-04-04T14:10:00.000-07:00

Friday, April 1, 2011

Stats on exam 1:

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Lecture, chapter 6 - Cytogenetics

2011-03-30T10:06:00.001-07:00

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

2011-03-29T15:19:00.001-07:00

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

2011-03-28T13:40:00.001-07:00

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

2011-03-25T14:54:00.000-07:00

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

2011-03-23T18:23:00.001-07:00

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

2011-03-23T10:13:00.000-07:00

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

2011-03-21T15:26:00.000-07:00

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?

2011-03-17T06:32:00.000-07:00

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

2011-03-16T12:54:00.001-07:00

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

2011-03-15T19:20:00.000-07:00

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

2011-03-14T12:44:00.000-07:00

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

2011-03-09T14:17:00.000-08:00

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

2011-03-08T14:42:00.001-08:00

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

2011-03-08T10:46:00.001-08:00

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:

In vitro fertilization - Courtney, Jenny, Kwaku, Marcus
Human-animal chimeras - Andie, Danielle H., Kirstin, Maggie
Genetic predisposition to addiction - Danielle L., Veronica, Caleb, Justin
Designer babies - Jeniffer, Liz, Salesha, Sarah
Genetically modified (GM) crops - Alex, Andre, Kevin, Mark
Organ farming - Anabel, Jessica, Kara, Megan
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

2011-03-07T14:13:00.000-08:00

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)

2011-02-24T10:21:00.000-08:00

Stats on the final exam:

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Activity - Genetics on the news

2011-02-18T19:30:00.000-08:00

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

2011-02-16T07:41:00.000-08:00

Screenshot of PopCycle, by John Herron
(click on pic for full size image)
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Today we did the population genetics lab

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Chapter 14 - Biotechnology

2011-02-15T08:37:00.001-08:00

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

2011-02-14T08:32:00.001-08:00

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

2011-02-11T07:59:00.001-08:00

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

2011-02-10T09:58:00.001-08:00

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

2011-02-08T06:58:00.001-08:00

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

2011-02-07T13:52:00.000-08:00

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

2011-02-04T05:09:00.001-08:00

Stats for exam 2

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Lecture, chapter 11 - Mutation

2011-02-01T10:14:00.001-08:00

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

2011-01-31T12:43:00.000-08:00

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

2011-01-28T08:36:00.001-08:00

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

2011-01-26T07:05:00.000-08:00

Lecture, chapter 10 - From proteins to phenotypes

2011-01-25T13:29:00.000-08:00

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

2011-01-24T21:01:00.000-08:00

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

2011-01-21T11:39:00.001-08:00

Lab quiz 1 stats:

(click on pic for full size image)

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Lab 06 - Gene mapping in Drosophila

2011-01-19T10:30:00.000-08:00

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

2011-01-18T08:39:00.001-08:00

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

2011-01-14T10:06:00.001-08:00

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

2011-01-12T20:38:00.001-08:00

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:

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.
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.

Lecture, chapter 8 - Nucleic acids

2011-01-11T16:23:00.000-08:00

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

2011-01-07T12:19:00.000-08:00

Stats:

(click on pic for full size image)

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Lab 04 - Inheritance of complex traits

2011-01-06T13:14:00.000-08:00

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.

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Lecture, chapter 6 - Cytogenetics

2011-01-03T12:51:00.001-08:00

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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LectureChapter 5 - Polygenic and multifactorial inheritanceChapter 6 - Cytogenetics

2010-12-17T10:16:00.000-08:00

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).

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Lab 03 - Epistasis and hypothesis testing

2010-12-16T14:40:00.001-08:00

Genetic corn

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In this lab we used genetic corn to test a prediction based on Mendelian principles, about the inheritance of two genes.

The color of corn kernels, although just one trait, is controlled by two separate genes (R and C) that affect pigmentation in the aleurone, which may or may not be pigmented. If transparent the color of the kernel will be yellow or white, and when pigmented it will be purple or red. In our case we only had purple and yellow kernels in cobs that were obtained as the F2 generation from a cross from double homozygote parent plants (RRCC x rrcc).

By doing a count of purple and yellow kernels, students were able to predict the phenotypic proportions of yellow and purple kernels. The predictions were compared to the observations and tested using a chi-square test, with a significance level of 5% (α=0.05).

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

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Lecture, chapter 5 - Polygenic and multifactorial inheritance

2010-12-14T13:18:00.000-08:00

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.

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Lecture, chapter 4 - Pedigree analysis in human genetics

2010-12-10T07:12:00.001-08:00

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!)

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Lab 02 - Mendelian genetics

2010-12-08T15:27:00.000-08:00

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

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Lecture, chapter 4 - Pedigree analysis

2010-12-07T13:50:00.000-08:00

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.

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LectureChapter 3 - Mendelian geneticsChapter 4 - Pedigree analysis

2010-12-07T13:43:00.000-08:00

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.

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Lecture, chapter 3 - Mendelian Genetics

2010-12-03T13:31:00.000-08:00

Mendel, in his garden
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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.

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

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

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Lab 01 - Human Mendelian genetics

2010-12-01T16:17:00.001-08:00

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.

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Bioethics projects - Topics selection

2010-12-01T16:16:00.000-08:00

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

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

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Lecture, chapter 1 - A human perspective on genetics

2010-11-30T13:20:00.000-08:00

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.

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Lecture, chapter 1 - A human perspective on genetics

2010-11-29T20:17:00.000-08:00

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.

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Lecture, chapter 14 - Biotechnology

2010-05-12T19:42:00.001-07:00

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.

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Lab 10 - Population genetics II - Evolution

2010-05-11T14:56:00.000-07:00

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.

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

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Lecture, chapter 14 - Biotechnology

2010-05-10T12:30:00.000-07:00

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).

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Lecture, chapter 13 - Cloning and recombinant DNA technology

2010-05-05T08:41:00.000-07:00

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.

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"Lab" 9 - Bioethics discussion panels

2010-05-05T08:34:00.000-07:00

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

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Lecture, chapter 13 - Cloning and recombinant DNA technology

2010-05-03T17:28:00.000-07:00

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.

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Lecture, chapter 11 - Mutation

2010-04-28T13:13:00.000-07:00

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.

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Lab 08 - Population genetics

2010-04-27T16:27:00.001-07:00

Today we did the population genetics lab

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Lecture, chapter 11 - Mutation

2010-04-26T17:44:00.000-07:00

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.

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Discussion - Genetics in the news

2010-04-23T20:21:00.001-07:00

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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.

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Lecture, chapter 11 - Mutation

2010-04-21T12:02:00.000-07:00

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)

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Lab 7 - Human gene mapping

2010-04-20T18:46:00.001-07:00

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.

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Lecture, chapter 11 - From proteins to phenotypes

2010-04-19T18:51:00.000-07:00

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)

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Lecture, chapter 10 - From proteins to phenotypes

2010-04-19T18:06:00.000-07:00

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.

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Lecture, chapter 9 - From genes to proteins

2010-04-14T14:01:00.000-07:00

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).

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Lab 06 - Gene mapping - Drosophila

2010-04-14T14:00:00.000-07:00

Tuesday, April 13, 2010

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

2010-04-14T13:58:00.000-07:00

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)

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Lecture, chapter 8 - Nucleic acids

2010-04-09T13:38:00.000-07:00

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.

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Lecture, chapter 6 - Cytogenetics

2010-04-07T18:34:00.000-07:00

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.

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

2010-04-06T07:23:00.000-07:00

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.

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Lab quiz 1

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

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Exam 1

2010-03-31T08:29:00.001-07:00

Today we had our first exam. Results statistics:

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Lab 04 - Inheritance of complex traits

2010-03-31T08:20:00.001-07:00

Wednesday, March 30, 2010

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Lecture, chapter 6 - Cytogenetics

2010-03-29T10:00:00.001-07:00

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.

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Lecture, chapter 5 - Inheritance of complex traits

2010-03-26T14:26:00.001-07:00

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

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

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