Today we had our final exam. Stats:
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Monday, May 16, 2011
Friday, May 13, 2011
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:
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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).
We also had the last bioethics presentation and panel discussion. Click here for details.
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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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Tuesday, May 10, 2011
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:
- 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)
Monday, May 9, 2011
Lecture, chapter 13 - Cloning and recombinant DNA
including 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:
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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Friday, May 6, 2011
Lecture
Chapter 11 - Mutation
Chapter 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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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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Tuesday, May 3, 2011
Lab 10 - "Classic" Population Genetics II
Evolution 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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Monday, May 2, 2011
Exam 2
Today we had the second midterm exam. Stats:
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Friday, April 29, 2011
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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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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Wednesday, April 27, 2011
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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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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Tuesday, April 26, 2011
Lab 08 - 'Classic' population genetics
Screenshot of PopCycle, by John Herron
(click on pic for full size image)
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(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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Wednesday, April 20, 2011
Lecture
Chapter 10 - From proteins to phenotypes
Chapter 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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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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Tuesday, April 19, 2011
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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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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Monday, April 18, 2011
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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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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Friday, April 15, 2011
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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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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Wednesday, April 13, 2011
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:
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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Monday, April 11, 2011
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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Friday, April 8, 2011
Lecture
Chapter 8 - DNA structure and chromosomal organization
Chapter 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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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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