Today we finished chapter 10, from proteins to genotypes. Specifically we talked about pharmacogenetics
There are phenotypes that become obvious only when people are exposed to chemicals. Whether they are drugs, chemicals in the environment, or chemicals in products we consume (food, clothing, etc.), different allele combinations make us more or less sensitive to exposure.
We talket about the first pharmcogenetic trait, discoverd in the 1930s, the ability or inability to taste PTC. This trait is trivial, but it has implications that have lead research that may find connections between sensitivity to certain tastes, diet, and obesity.
We also talkes about how between 100 and 1000 cel membrane proteins dictate our ability to smell or not smell certain chemicals. So many enzymes, most of which most likely have several alleles, and so many possible allele combinations make us virtually unique in our olfactory capacity.
In terms of sensitivity to chemicals in the environment, especially pesticides, it is ecogenetics the subfield that deals wit our genetic-based differences in sensitivity. Research is being done in many populations to determine safe levels of exposure to different chemicals. Such research involves an important genetic component.
On Monday: We will start chapter 11, on mutation as the source of genetc variation.
Reminder: Next Friday, May 01, we will have our second exam. over chapters 8, 9, 10, and 11, plus elements of our genetic mapping labs (both in human and Drosophila). Bring a calculator!
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Friday, April 24, 2009
Thursday, April 23, 2009
Lecture, chapter 10 - From proteins to phenotypes
Today we covered most of chapter 10, from proteins to genotypes.
We talked about how mutations in genes that encode for transport proteins can be reflected in the phenotype. Our main example was hemoglobin. Mutations in the genes thay encode for any of the subunits of the protein can cause a variety of genetic disorders (hemoglobin variants, thalassemias) which most common symptom is anemia.
One of the better known cases is sickle cell anemia, caused by a mutation in the beta globins of hemoglobin, causing them to come become insoluble, resulting in the aggregation of the protein, therefore altering the shape of red blood cells and making them brittle.
Tomorrow: We'll finish chapter 10, covering the section on pharmacogenetics.
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We talked about how mutations in genes that encode for transport proteins can be reflected in the phenotype. Our main example was hemoglobin. Mutations in the genes thay encode for any of the subunits of the protein can cause a variety of genetic disorders (hemoglobin variants, thalassemias) which most common symptom is anemia.
One of the better known cases is sickle cell anemia, caused by a mutation in the beta globins of hemoglobin, causing them to come become insoluble, resulting in the aggregation of the protein, therefore altering the shape of red blood cells and making them brittle.
Tomorrow: We'll finish chapter 10, covering the section on pharmacogenetics.
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Tuesday, April 21, 2009
Lab 07 - Human gene mapping
In Drosophila it is easy to find out how linked genes are since that can be determined by doing experimental crosses and measuring phenotypic frequencies in the offspring (see lab 06). In addition to that, we know what genes are found in specific chromosomes (fruit flies have only four pairs of chromosomes).
But in humans it is not that straight forward. Experimental crosses are out of the question, and humans tend to have very few progeny (even large families have very few offspring compared with the potentially thousands of offspring of a couple of fruit flies).
In humans, we have to rely on pedigrees. In this lab we considered three different pedigrees showing linkage between a genetic disorder and another trait. 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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But in humans it is not that straight forward. Experimental crosses are out of the question, and humans tend to have very few progeny (even large families have very few offspring compared with the potentially thousands of offspring of a couple of fruit flies).
In humans, we have to rely on pedigrees. In this lab we considered three different pedigrees showing linkage between a genetic disorder and another trait. 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 20, 2009
Lecture, chapters 9 and 10 - From genes to proteins, and from proteins to phenotypes
Today we finished chapter 9, on how genetic information is used to synthesize proteins, and started chapter 10, on how proteins are, or influence, the phenotype.
We talked about the possibilities of changing a polypeptide after it has been synthesized, thus accounting fopr the more than 100,000 enzymes in the human organism, which has just about 25,000 genes in its genome. We defined the difference between a polypeptide and a protein (hint: every protein is a polypeptide or a group of polypeptides, but not every polypeptide is a protein).
Then we talked about the levels of structure that proteins can have: Primary, secondary, tertiary, and, in some cases, quaternary. We finished the chapter by discussing some of the consequences of a mutation that alters the amino acid sequence of a protein.
We also started chapter 10, and discussed how certain mutations in the sequence of amino acids of enzymes and receptor proteins affect the phenotype of the person who bearing them.
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We talked about the possibilities of changing a polypeptide after it has been synthesized, thus accounting fopr the more than 100,000 enzymes in the human organism, which has just about 25,000 genes in its genome. We defined the difference between a polypeptide and a protein (hint: every protein is a polypeptide or a group of polypeptides, but not every polypeptide is a protein).
Then we talked about the levels of structure that proteins can have: Primary, secondary, tertiary, and, in some cases, quaternary. We finished the chapter by discussing some of the consequences of a mutation that alters the amino acid sequence of a protein.
We also started chapter 10, and discussed how certain mutations in the sequence of amino acids of enzymes and receptor proteins affect the phenotype of the person who bearing them.
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Friday, April 17, 2009
Lecture, chapter 9 - From genes to proteins
Today we continued covering chapter 9, on how the information stored in the genetic code gets reflected on a phenotype, specifically in proteins.
We talked about the processes of translation transcription, including the stages that each one has (initiation, elongation, and termination in both cases).
In the case of trascription we talked about the elements that are found in a gene, and how they get trnascribed into a pre-mRNA transcript, which gets modified into a mature mRNA transcript. We also discussed the different elements that make a mRNA molecule, including a 5' cap and a Poly-A tail.
In the case of translation we covered the cytoplasmatic elements that play a role in it: amino acids, ribosomes, and tRNA. We also discussed the chemical make up of amino acids, an amino, a carboxyl, and an 'R' groups, and a few of their characeristics.
On Monday: We'll finish chapter 9 and begin chapter 10.
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We talked about the processes of translation transcription, including the stages that each one has (initiation, elongation, and termination in both cases).
In the case of trascription we talked about the elements that are found in a gene, and how they get trnascribed into a pre-mRNA transcript, which gets modified into a mature mRNA transcript. We also discussed the different elements that make a mRNA molecule, including a 5' cap and a Poly-A tail.
In the case of translation we covered the cytoplasmatic elements that play a role in it: amino acids, ribosomes, and tRNA. We also discussed the chemical make up of amino acids, an amino, a carboxyl, and an 'R' groups, and a few of their characeristics.
On Monday: We'll finish chapter 9 and begin chapter 10.
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Thursday, April 16, 2009
Lecture, chapters 8 and 9 - RNA, chromosome structure, and gene expression
Today we finished the chapter on DNA and chromosome structure. It should have been "nucleic acid and chromosome structure".
We discussed the primary and secondary structure of RNA, how DNA is coiled (and supercoiled) to from chromosomes, and then we started the next chapter in the text book, on how the information stored in DNA is used to form proteins.
Note: The draft papers on bioethical issues were returned with recommendations to improve what you have so far. Tomorrow I'll provide a handout with indications of how to cite and reference papers in a scientific fashion.
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We discussed the primary and secondary structure of RNA, how DNA is coiled (and supercoiled) to from chromosomes, and then we started the next chapter in the text book, on how the information stored in DNA is used to form proteins.
Note: The draft papers on bioethical issues were returned with recommendations to improve what you have so far. Tomorrow I'll provide a handout with indications of how to cite and reference papers in a scientific fashion.
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Tuesday, April 14, 2009
Lab 06 - Mapping genes in Drosophila
Although the actual lab will be a take-home lab, we set the stage to do the work we need to do in the couple of mapping genes labs we will have.
We covered concepts like gene mapping, genetic linkage, and genetic distance within a chromosome, and how they are correlated. We also introduced the concept of CentiMorgan (cM), a.k.a. Map Unit (m.u.), and how it is useful to map genes, based on the results of experimental crosses.
We also used a little applet developed by Paul Lewis, from the University of Connecticut, called demonstration of crossing over. With this application we did simulations on recombination events affecting two loci separated by variable genetic distances. We then introduced the concepts of parental haplotypes/gametes and recombinant haplotypes/gametes, as part of the more practical explanation of genetic linkage.
We also did a quick demo of the software to be used in this lab: DrosophiLab. Students will download this Windows-based free software to simulate experimental crosses in Drosophila melanogaster, and calculate genetic distances between different genes. The labguide is being written and will be posted soon.
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We covered concepts like gene mapping, genetic linkage, and genetic distance within a chromosome, and how they are correlated. We also introduced the concept of CentiMorgan (cM), a.k.a. Map Unit (m.u.), and how it is useful to map genes, based on the results of experimental crosses.
We also used a little applet developed by Paul Lewis, from the University of Connecticut, called demonstration of crossing over. With this application we did simulations on recombination events affecting two loci separated by variable genetic distances. We then introduced the concepts of parental haplotypes/gametes and recombinant haplotypes/gametes, as part of the more practical explanation of genetic linkage.
We also did a quick demo of the software to be used in this lab: DrosophiLab. Students will download this Windows-based free software to simulate experimental crosses in Drosophila melanogaster, and calculate genetic distances between different genes. The labguide is being written and will be posted soon.
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Thursday, April 9, 2009
Lecture, chapter 8 - DNA structure
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Rosalind Franklin and her "photo 51"
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Rosalind Franklin and her "photo 51"
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Today we started covering chapter 8, on the structure of DNA and chromosomes.
We talked about a little bit of the history of how the structure of DNA was discovered, including the injustice 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.
On Thursday: We will talk about the similarities and differences between DNA and RNA, and will cover the basics of chromosome structure.
Congratulations to Brittany Simmons, the winner of the heritability challenge...!
Have a happy Easter break!
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Tuesday, April 7, 2009
Lab 05 - Heritability
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:
The heritability challenge (Thursday):
During the exercise I made a mistake when calculating broad sense heritability. Apparently no body caught it. If you can find the mistake and explain the whole exercise correctly to the rest of the class, you will have the chance to earn 5 bonus points. Be prepared, and among those who have the answer I will randomly chose some one to try to get the bonus points.
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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, or polygenic interactions, as well as matrenal and paternal effects.
- Narrow sense heritability: It quantifies the proportion of phenotypic variation explained by allelic variation.
The heritability challenge (Thursday):
During the exercise I made a mistake when calculating broad sense heritability. Apparently no body caught it. If you can find the mistake and explain the whole exercise correctly to the rest of the class, you will have the chance to earn 5 bonus points. Be prepared, and among those who have the answer I will randomly chose some one to try to get the bonus points.
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Tuesday, March 31, 2009
Lab 04 - Complex patterns of inheritance
In lab 4 students analyzed pedigrees that showed patterns of inheritance that could not be explained by any one of the six modes of Mendelian inheritance covered in class. As part of the pedigree analyses they observed the incidence of incomplete penetrance and variable expressivity of traits.
Students also became familiar with concepts like genetic liability and recurrence risk, and were able to calculate the latter using specific methods that make use of the standard deviation of the population as a tool to infer such information.
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Students also became familiar with concepts like genetic liability and recurrence risk, and were able to calculate the latter using specific methods that make use of the standard deviation of the population as a tool to infer such information.
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Monday, March 30, 2009
Lecture, chapter 6 - Cytogenetics
From The Cartoon Guide to Genetics
Larry Gonick & Mark Wheelis
© Harper Perennial, 1983 & 1991
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We finished chapter 6, on cytogenetics.
We covered the main cases of autosomal and sex chromosome aneuploidy: Down syndrome (trisomy 21), Turner syndrome (trisomy 18), Patau symdrome (trisomy 13), Klinefelter's syndrome (XXY), and "supermale" syndrome (XYY).
We also discussed structural abnormalities in chromosomes, like deletions, additions, inversions, and translocations.
On Friday: Exam 01
On Monday: Chapter 8, on chromosomes and DNA
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Friday, March 27, 2009
Lecture, chapter 6 - Cytogenetics
A human karyotype
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Today we started chapter 6 on cytogenetics.
We covered karyotypes, chromosome nomenclature, and classification of variation in chromosome number: Polyploidy and aneuploidy. We discussed triploidy and tetraploidy and on Monday we'll start discussing cases of aneuploidy.
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Our "Genetics News Friday" discussion was a failure and a dissapointment. In spite of having tools to acquire information easier than ever before, nobody brought an idea to discuss, and you can find them everywhere!
Remember, genetics is not just a class to get out of the way. It is a field that has plenty of applications and implications in the real world! Reading or listening to genetics-related news is a good exercise, for this class and for life in general.
Again: Other than the traditional sources of information you can also get information from RSS feeds (the news come TO you), and podcasts (some are literally 1 min 20 secs long...! Can it get any easier?). See Monday's entry (March 23) for some extra details.
No discussion may mean questions about genetic-related news in the quizzes. You pick.
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An RSS Feed looks like this (click for full size image)
And the link will take you to something like this (click for full size image)
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Thursday, March 26, 2009
Lecture, chapter 5 - Polygenic inheritance
A gradient of skin tones
click on image for a full size pic
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Today we finished covering chapter 5, on polygenic inheritance.
We discussed concepts like distribution of environmental factors, norm of reaction, and heritability. We also discussed the importance of twin studies in complex traits research, and talked about a couple of examples of polygenic traits in humans: skin color and intelligence.
Tomorrow: Chapter 6, on cytogenetics.
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Lab 03 - Epistasis and hypothesis testing
Tuesday, March 24, 2009
We did our "corny genetics" lab. Students, working in pairs, analized the expected and observed phenotypic proportions of the F2 generation from a dihybrid cross in genetic corn. They used their expectations and their observations to perchorm a chi-sqare test and relate the results to a potentially epistatic interaction.
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We did our "corny genetics" lab. Students, working in pairs, analized the expected and observed phenotypic proportions of the F2 generation from a dihybrid cross in genetic corn. They used their expectations and their observations to perchorm a chi-sqare test and relate the results to a potentially epistatic interaction.
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Monday, March 23, 2009
Lecture, chapter 5 - Polygenic inheritance
Today we started covering chapter 5, on polygenic inheritance and interaction with the environment.
We discussed the differences between continuous and discontinuous characters, the definitions of polygenic, multifactorial, and complex traits, and the most common approach to studying the inheritance of continuous variation: Quantitative genetics. Quantitative genetics uses many statistical tools as well as some concepts inherent to it, like the genetic version of regression to the mean, phenotypic distribution, norm of reaction, genetic variance, phenotypic variance, and heritability.
Tomorrow: Lab 3, on Epistasis and hypothesis testing.
On Thursday: More about chapter 5.
Note:
Given the success of the end-of-class discussion on Friday, we will continue having "genetics on the news" discussions in the future, with the possibility of including questions in quizzes. I encourage you to use on-line resources to find genetics news, or let them find you. The main sources would be RSS feeds of publications like Nature, Science, or Scientific American (among MANY others), and scientific podcasts.
Some podcasts have been uploaded to the p-drive and the WebCT site (check them out!), but you can find many more on genetics-related sites. You can get them wherever you want to.
If you don't know were to begin just use iTunes (freeware, availale in Windows and Mac OS X versions) to access the iTunes store and download/subscribe to any of the FREE scientific podcasts available.
Remember, you can find the news, and with RSS feeds and podcast subscriptions the news will find you.
Examples of sites with RSS feeds:
If you find any other interesting site, let me know.
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We discussed the differences between continuous and discontinuous characters, the definitions of polygenic, multifactorial, and complex traits, and the most common approach to studying the inheritance of continuous variation: Quantitative genetics. Quantitative genetics uses many statistical tools as well as some concepts inherent to it, like the genetic version of regression to the mean, phenotypic distribution, norm of reaction, genetic variance, phenotypic variance, and heritability.
Tomorrow: Lab 3, on Epistasis and hypothesis testing.
On Thursday: More about chapter 5.
Note:
Given the success of the end-of-class discussion on Friday, we will continue having "genetics on the news" discussions in the future, with the possibility of including questions in quizzes. I encourage you to use on-line resources to find genetics news, or let them find you. The main sources would be RSS feeds of publications like Nature, Science, or Scientific American (among MANY others), and scientific podcasts.
Some podcasts have been uploaded to the p-drive and the WebCT site (check them out!), but you can find many more on genetics-related sites. You can get them wherever you want to.
If you don't know were to begin just use iTunes (freeware, availale in Windows and Mac OS X versions) to access the iTunes store and download/subscribe to any of the FREE scientific podcasts available.
Remember, you can find the news, and with RSS feeds and podcast subscriptions the news will find you.
Examples of sites with RSS feeds:
If you find any other interesting site, let me know.
----------------------
Friday, March 20, 2009
Lecture, chapter 4 - Modes of inheritance and variations in gene expression
_____________________________________________________________________
Polydactyly and camptodactyly,
traits with incomplete penetrance and variable expressivity
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traits with incomplete penetrance and variable expressivity
_____________________________________________________________________
Today we finished chapter 4, on pedigree analysis.
We talked about the last couple of modes of inheritance: Y-linked traits and mitochondrial inheritance. Then we talked about variations in gene expression: Age-related phenotypic expression, penetrance, and expressivity.
By the end, we had a discussion about genetics in the news. People were passionate about it and it was fun and productive. We talked about the case of the California octuplets that was recently on the news (need an update/reminder? Click here!).
It was a good exercise and it may happen again. Should we do it every Friday? Should we call it "Genetics news Friday" or something along those lines? If you read this blog comment on this. If not... We may do it any way.
You could (should) subscribe to science podcasts and/or RSS feeds to keep abreast of the latest news...there is more out there than you think.
On Monday: We will start chapter 5 in our textbook.
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Thursday, March 19, 2009
Lecture, chapter 4 - Pedigree analysis
Click on image for a full size pedigree
We started with a little overview of, and a demonstration on how to use, the Online Mendelian Inheritance in Man (OMIM) catalogue. The catalogue of human Mendelian traits.
Then we started covering the modes of inheritance that can be inferred from pedigree analysis. We went over autosomal recessive and autosomal dominant traits, and we started sex-linked traits, with X-linked dominant and X-linked recessive traits. We examined pedigrees and observed the characteristics they exhibited.
We discussed examples of diseases inherited in each one of these modes.
Tomorrow: More about modes of inheritance, and variations of gene expression. Oh, and possibly an activity to wake up people during class...
Huh...? What is this guy doing in a genetics class blog?
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Tuesday, March 17, 2009
Lab 02 - Mendelian genetics
Today we did a lab in which we examined a little bit of Mendelian genetics, faking crosses in fruit flies.
We focused on monohybrid and dihybrid crosses in, both, autosomal and X-linked traits. Students did observations that illustrated the principles of segregation and independent assortment, mainly based on test crosses.
Next week: Lab 03 - Epistasis and hypothesis testing
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We focused on monohybrid and dihybrid crosses in, both, autosomal and X-linked traits. Students did observations that illustrated the principles of segregation and independent assortment, mainly based on test crosses.
Next week: Lab 03 - Epistasis and hypothesis testing
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Monday, March 16, 2009
Lecture, chapters 3 and 4 - Mendelian inheritance and Pedigree analyses
Today we finished chapter 3 in the book, on Mendelian inheritance, covering some of the variations on Mendel's findings: codominance, multiple alleles, and gene interaction, including epistasis.
On the other hand we began chapter 4, on pedigree analysis, talking about the six modes of inheritance we will be covering, in addition to the basic reasons for which pedigrees are so important when studying human genetics.
Tomorrow in lab: Mendelian genetics. The lab is being re-written so it will be posted late, but it will be up.
For Thursday: Read the remaining of chapter 4, and access the OMIM database, to get familiar with the kind onf information you can find there
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On the other hand we began chapter 4, on pedigree analysis, talking about the six modes of inheritance we will be covering, in addition to the basic reasons for which pedigrees are so important when studying human genetics.
Tomorrow in lab: Mendelian genetics. The lab is being re-written so it will be posted late, but it will be up.
For Thursday: Read the remaining of chapter 4, and access the OMIM database, to get familiar with the kind onf information you can find there
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