Between last monday and today we have finished the section on DNA repair and have covered most of the section on control of gene expression.
Last Monday (Jan 26) we closed the DNA repair section, covering the concept of emergency DNA repair: When extensive damage in the DNA is detected by RNA polymerase and is repaired not just by the regular DNA polymerase, but also by a battery of DNA polymerases that are less accurate, but more specific for a type of damage. They also lack proofrweading capacity, so the likelihood that there will be mistakes during the repair process is higher than with other DNA repair mechanisms.
Between Friday (Jan 30) and today, we have been studying the basics of control of gene expression. So far we have focused on transcriptional control, and on Monday we will focus on mechanisms of post-transcriptional control.
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Monday, February 2, 2009
Lab 12 - Small-scale plasmid DNA purification (minipreps)
Thursday Jan 29 2009
We went back to the bacterial cultures we had of transformed bacteria (E. coli), to reverse (in a way) the process we started. In this case we want to isolate the plasmid (Bio-Rad's pGLO) that we used to genetically transform the bacteria. In the process of cloning DNA this is one of the steps you follow to study the DNA segement of interest, in our case the GFP gene contained in the pGLO plasmid. We made zillions of copies of it, and now we have to extract it from the bacteria to analyze it.
We used Promega's Wizard® Plus SV minipreps DNA purification system. An easy to use kit to purify plasmid DNA in a lab like the one we have available.
Next week we'll run a confirmation gel and perfomr a restriction enzyme digestion (RED) of the pGLO plasmid.
----------------------
We went back to the bacterial cultures we had of transformed bacteria (E. coli), to reverse (in a way) the process we started. In this case we want to isolate the plasmid (Bio-Rad's pGLO) that we used to genetically transform the bacteria. In the process of cloning DNA this is one of the steps you follow to study the DNA segement of interest, in our case the GFP gene contained in the pGLO plasmid. We made zillions of copies of it, and now we have to extract it from the bacteria to analyze it.
We used Promega's Wizard® Plus SV minipreps DNA purification system. An easy to use kit to purify plasmid DNA in a lab like the one we have available.
Next week we'll run a confirmation gel and perfomr a restriction enzyme digestion (RED) of the pGLO plasmid.
----------------------
Lab 11 - Polyacrylamide Gel Electrophoresis (PAGE) of GFP samples
Thursday Jan 29 2009
This lab should have taken place on Wednesday Jan 28, but classes were cancelled due to weather.
Polyacrylamide Gel Electrophoresis (PAGE) is a technique used for separating polynucleotides or polypeptides that are very similar in size, providing greater resolution than with an agarose gel.
We used PAGE to measure the size of a protein, GFP. If we follow the series of "make believe" in which we are dealing with a new protein, this would be a step to find more information about it. Protein size is quantified in Daltons (Da), a measure of molecular mass. One Dalton is defined as the mass of a hydrogen atom, which is 1.66 x 10-24grams (g).
PAGE is used for separating proteins ranging in size from 5 to 2,000 kDa due to the uniform pore size provided by the polyacrylamide gel. Agarose gels can also be used to separate proteins, but they do not have a uniform pore size, so they are optimal only for electrophoresis of proteins that are larger than 200 kDa. We ran two types of PAGEs: Native and denaturing (a.k.a. SDS)
Proteins can have varying charges and complex shapes, therefore they may not migrate into the gel at similar rates, or at all. In native gel electrophoresis the proteins being separated differ in molecular mass and intrinsic charge and experience different electrophoretic forces dependent on the ratio of the two. Because of different charges and tertiary structure proteins of the same mass may migrate at different rates.
In SDS gel electrophoresis proteins are denatured (linearized) in the presence of a detergent such as Sodium Dodecyl Sulfate (SDS) that coats the proteins with a negative charge. The resulting denatured proteins have an overall negative charge, and all the proteins have a similar charge to mass ratio. Since denatured proteins act like long rods instead of having a complex tertiary shape, the rate at which they migrate in the gel is relative only to its size (molecular weight) and not its charge or shape.
We will be able to compare teh results in both gels, and if GFP has any activity in either one of them (through pictures taken under UV light).
----------------------
This lab should have taken place on Wednesday Jan 28, but classes were cancelled due to weather.
Polyacrylamide Gel Electrophoresis (PAGE) is a technique used for separating polynucleotides or polypeptides that are very similar in size, providing greater resolution than with an agarose gel.
We used PAGE to measure the size of a protein, GFP. If we follow the series of "make believe" in which we are dealing with a new protein, this would be a step to find more information about it. Protein size is quantified in Daltons (Da), a measure of molecular mass. One Dalton is defined as the mass of a hydrogen atom, which is 1.66 x 10-24grams (g).
PAGE is used for separating proteins ranging in size from 5 to 2,000 kDa due to the uniform pore size provided by the polyacrylamide gel. Agarose gels can also be used to separate proteins, but they do not have a uniform pore size, so they are optimal only for electrophoresis of proteins that are larger than 200 kDa. We ran two types of PAGEs: Native and denaturing (a.k.a. SDS)
Proteins can have varying charges and complex shapes, therefore they may not migrate into the gel at similar rates, or at all. In native gel electrophoresis the proteins being separated differ in molecular mass and intrinsic charge and experience different electrophoretic forces dependent on the ratio of the two. Because of different charges and tertiary structure proteins of the same mass may migrate at different rates.
In SDS gel electrophoresis proteins are denatured (linearized) in the presence of a detergent such as Sodium Dodecyl Sulfate (SDS) that coats the proteins with a negative charge. The resulting denatured proteins have an overall negative charge, and all the proteins have a similar charge to mass ratio. Since denatured proteins act like long rods instead of having a complex tertiary shape, the rate at which they migrate in the gel is relative only to its size (molecular weight) and not its charge or shape.
We will be able to compare teh results in both gels, and if GFP has any activity in either one of them (through pictures taken under UV light).
----------------------
Saturday, January 24, 2009
Lecture - DNA repair
Yesterday we covered most of the DNA repair section in chapter 5.
We talked about the most common spontaneous DNA changes (e.g. depurination and deamination), the importance of having genetic information coded in a double helix, the main mechanisms of DNA repair (base excision repair, and nucleotide excision repair), and transcription-coupled repair.
On Monday we'll talk about emergency DNA repair and repairing double strand breakes.
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Monday, December 15, 2008
Lecture - Genome evolution
We covered the topic of genome evolution (p. 245-260).
We talked about the most common cases of mutations that promote genome evolution, what happens when genomes diverge, the relationship between the degree of divergence and phylogeny, why genome sizes in vertebrates can vary so much, and questions you can solve by comparing multiple genomes anf their rate of evolution.
We talked about the most common cases of mutations that promote genome evolution, what happens when genomes diverge, the relationship between the degree of divergence and phylogeny, why genome sizes in vertebrates can vary so much, and questions you can solve by comparing multiple genomes anf their rate of evolution.
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Friday, December 12, 2008
Lecture - Overview on chromosomes and PCR
We revisited some of the topics we covered on Monday and elaborated on some othres. We talked about how the DNA is packed in chromosomes, and how chromosomes compare accross related species.
We also covered some details of PCR, which we have been actually performing in lab... which reminds me, there is a video you should see, more than once. I recommend learning the lyrics. Yes they are cheesie, but they are useful!
They are nerds, and they obviously grew up in the 80's... oh, and it's a Bio-Rad ad, in case you haven't have enough of them with our lab kits... The PCR song.
We also covered some details of PCR, which we have been actually performing in lab... which reminds me, there is a video you should see, more than once. I recommend learning the lyrics. Yes they are cheesie, but they are useful!
They are nerds, and they obviously grew up in the 80's... oh, and it's a Bio-Rad ad, in case you haven't have enough of them with our lab kits... The PCR song.
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Thursday, December 11, 2008
Lab 04 - Detecting genetic modifications in food
Bio-Rad's GMO Investigator Kit
In this lab we are trying to find evidence of genes that have been inserted into a plant's genome. There are two ways of finding out:
Testing for the presence of proteins that the trans-genes produce
Amplifying a fragment of DNA that contains the trans-gene via PCR
Since we need a lot of fresh tissue and a kit to test for several of the proteins that the most common trans-genes code for, materials that we don't have, we are using the almighty PCR.
Most trans-genes have the 35S promoter from the cauliflower mosaic virus (CMV 35S), and the nopaline synthase (NOS) terminator from Agrobacterium tumefaciens. These sequences come from totally different organisms from that used to isolate the actual trans-gene, but they are recognized by the plant cell machinery (mainly its polymerase), so they can actually produce the product that the gene is intended for. Even if the gene is in the genome, it will NOT work if there are no promoters AND terminators that the plant can recognize. Since there is a number of genes that have been inserted in crops in the U.S., it's easier to go after the promoter and the terminator when using PCR. CMV 35S and NOS have been use in over 85% of the GMOs, so if we have primers to amplify them, we don't have to worry about which gene was inserted (as long as the question doesn't involve knowing the specific gene).
We extracted DNA from vending machine snacks that we presume have been made from genetically modified crops, and from a certified non-GMO food control provided by Bio Rad, the manufacturers of the kit we use. The master mixes we used include primers for both CMV35S and NOS in the same mix, and in addition to those we are using a separate master mix with primers that will amplify a 455 bp region of the photosystem II (PSII) chloroplast gene, common to most plants. This will be a control to ensure we have successfully extracted DNA, so even non-GM plants should have the band present.
In this lab we are trying to find evidence of genes that have been inserted into a plant's genome. There are two ways of finding out:
Testing for the presence of proteins that the trans-genes produce
Amplifying a fragment of DNA that contains the trans-gene via PCR
Since we need a lot of fresh tissue and a kit to test for several of the proteins that the most common trans-genes code for, materials that we don't have, we are using the almighty PCR.
Most trans-genes have the 35S promoter from the cauliflower mosaic virus (CMV 35S), and the nopaline synthase (NOS) terminator from Agrobacterium tumefaciens. These sequences come from totally different organisms from that used to isolate the actual trans-gene, but they are recognized by the plant cell machinery (mainly its polymerase), so they can actually produce the product that the gene is intended for. Even if the gene is in the genome, it will NOT work if there are no promoters AND terminators that the plant can recognize. Since there is a number of genes that have been inserted in crops in the U.S., it's easier to go after the promoter and the terminator when using PCR. CMV 35S and NOS have been use in over 85% of the GMOs, so if we have primers to amplify them, we don't have to worry about which gene was inserted (as long as the question doesn't involve knowing the specific gene).
We extracted DNA from vending machine snacks that we presume have been made from genetically modified crops, and from a certified non-GMO food control provided by Bio Rad, the manufacturers of the kit we use. The master mixes we used include primers for both CMV35S and NOS in the same mix, and in addition to those we are using a separate master mix with primers that will amplify a 455 bp region of the photosystem II (PSII) chloroplast gene, common to most plants. This will be a control to ensure we have successfully extracted DNA, so even non-GM plants should have the band present.
-----------------------
Wednesday, December 10, 2008
Lab 03 - Human DNA extraction and PCR targeting the PV92 locus
Today we extracted DNA from our cheek cells, and then set up a PCR (Polymerase Chain Reaction) targeting the PV92 locus.
PV92 is found in chromosome 16 in humans. We all have two copies of each chromosome, so we have two chromosomes 16, and therefore we have two copies of the PV92 locus.
What does PV92 do? Nothing! It does not code for any thing, just as the 95% of the human genome. Only about 5% of our genome actually encodes some sort of product. This locus was named in the old days of karyiotyping, when we didn't really know what different areas stained in a chromosome did. After we sequenced the human genome, we figured out that the names given to many loci didn't actually correspond to a functional gene. For practical purposes we'll consider PV92 a gene, with a couple of "alleles" (see below).
The nice thing of having a locus that doesn't do any thing at all is that it is not influenced by natural selection. So when we think about mating in primate populations, PV92 reflects the mating patterns, since the allele frequency is not going to be incluenced by selection. So? Well... in population genetics a lot of hypothesis testing is based on the premise of random mating in a given population. PV92 has been used for a lot of human population genetics studies.
There is another nice thing about PV92. Some people have an Alu sequence inserted in the very middle of the PV92 locus. This Alu insert (which could be an intron should PV92 be a real gene. An intron is a DNA fragment found in between coding regions of a gene, that doesn't code for any thing and that it's spliced during transcription) makes PV92 300 bases longer, which is a difference big enough to be visualized in an agarose gel (originally PV92 is about 600 base pairs long).
An Alu sequence is a retrotransposon (a DNA fragment that has been inserted in a location where it doesn't belong via reverse transcription, i.e. mRNA actually writes a sequence into the genome) found throughout primate genomes. There are thousands of copies of Alu sequences found in a single genome.
PCR, the Polymerase Chain Reaction, a method to amplify (make many copies of) specific DNA fragments, is used to generate enough DNA that it can be studied with a variety of thechniques. Using PCR we will amplify our PV92 loci to see if we have the Alu sequence insert in any of our copies of PV92. Each one of us may have 0, 1, or 2 alu inserts in our PV92 copies and we will find out through PCR and gel electrophoresis.
Today we extracted our own DNA. We scraped our cheeks to get some epithelial cells, we neutralized ions (with the InstaGel) that may be used as cofactors by DNases to chop out DNA, and then we bursted our cells open (with the water baths) to extract the DNA from the nuclei.
We added our DNA, plus three positive controls, to a master mix with all the constituents of a PCR: buffer, nucleotides, Taq polymerase, magnesium, and primers (synthesized single stranded oligonucleotide sequences) and put the tubes into the thermocycler.
Tomorrow we'll run a gel electrophoresis to figure out who among us has the Alu insert in his/her PV92 locus, and if it is a single copy or two.
----------------------
PV92 is found in chromosome 16 in humans. We all have two copies of each chromosome, so we have two chromosomes 16, and therefore we have two copies of the PV92 locus.
What does PV92 do? Nothing! It does not code for any thing, just as the 95% of the human genome. Only about 5% of our genome actually encodes some sort of product. This locus was named in the old days of karyiotyping, when we didn't really know what different areas stained in a chromosome did. After we sequenced the human genome, we figured out that the names given to many loci didn't actually correspond to a functional gene. For practical purposes we'll consider PV92 a gene, with a couple of "alleles" (see below).
The nice thing of having a locus that doesn't do any thing at all is that it is not influenced by natural selection. So when we think about mating in primate populations, PV92 reflects the mating patterns, since the allele frequency is not going to be incluenced by selection. So? Well... in population genetics a lot of hypothesis testing is based on the premise of random mating in a given population. PV92 has been used for a lot of human population genetics studies.
There is another nice thing about PV92. Some people have an Alu sequence inserted in the very middle of the PV92 locus. This Alu insert (which could be an intron should PV92 be a real gene. An intron is a DNA fragment found in between coding regions of a gene, that doesn't code for any thing and that it's spliced during transcription) makes PV92 300 bases longer, which is a difference big enough to be visualized in an agarose gel (originally PV92 is about 600 base pairs long).
An Alu sequence is a retrotransposon (a DNA fragment that has been inserted in a location where it doesn't belong via reverse transcription, i.e. mRNA actually writes a sequence into the genome) found throughout primate genomes. There are thousands of copies of Alu sequences found in a single genome.
PCR, the Polymerase Chain Reaction, a method to amplify (make many copies of) specific DNA fragments, is used to generate enough DNA that it can be studied with a variety of thechniques. Using PCR we will amplify our PV92 loci to see if we have the Alu sequence insert in any of our copies of PV92. Each one of us may have 0, 1, or 2 alu inserts in our PV92 copies and we will find out through PCR and gel electrophoresis.
Today we extracted our own DNA. We scraped our cheeks to get some epithelial cells, we neutralized ions (with the InstaGel) that may be used as cofactors by DNases to chop out DNA, and then we bursted our cells open (with the water baths) to extract the DNA from the nuclei.
We added our DNA, plus three positive controls, to a master mix with all the constituents of a PCR: buffer, nucleotides, Taq polymerase, magnesium, and primers (synthesized single stranded oligonucleotide sequences) and put the tubes into the thermocycler.
Tomorrow we'll run a gel electrophoresis to figure out who among us has the Alu insert in his/her PV92 locus, and if it is a single copy or two.
----------------------
Tuesday, December 9, 2008
Lecture - Talking about chromosomes
Yesterday we started talking about chromosomes, their structure and some characteristics found after some whole genome research has been done in several organisms, including humans. On Friday we will continue with this topic and very likely will start with genome evolution.
Readings to come: p. 233-244 (chromosomes) and p. 245-260 (genome evolution)
Wednesday's lab: Extraction of human DNA and set up of the PV92 PCRs. It corresponds to "Exercise 4&5" in the old lab manual.
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Friday, December 5, 2008
Lecture - Introduction to the course
Today we continued with the introduction we started on Monday. We talked about some generic information about the structure and function of nucleic acids, the processes of transcription and translation (make sure to know the difference!), mechanisms of control of gene expression, and talked a little about the reaches and developments of recombinant DNA technology. We even mentioned what the field of genomics and proteomics can do.
Next class: On Monday we will be talking about chromosomes (p. 233-244) and hopefully also about genome evolution (p. 245-260).
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Thursday, December 4, 2008
Lab 02 - Restriction Enzyme Digestions (REDs) and analysis of lambda DNA
A micrograph of multiple bacteriopagesRestriction enzymes are one of the most basic and important tools in molecular biology. They evolved in bacteria to attack and cut (cleave) foreign DNA, mostly from bacteriophages (viruses that "eat" bacteria). But hey have been isolated to be used in the lab, and are useful to cut any kind of DNA, not just viral.
Cleaving DNA is the first step in any technique that involves recombinant DNA technology. There are techniques that use special enzymes to paste (ligate) different fragments of DNA. For instance a gene can be ligated into a plasmid that can be inserted into bacteria to make many copies of it via bacterial reproduction (cloning), something we will do in a few weeks.
Today we used lambda DNA (DNA from the common lambda bacteriophage) as the substrate to be cleaved with three different restriction enzymes: EcoRI, HindIII, and PstI.
We then ran our first agarose gel electrophoreses of the quarter (there shall be many more), and here are the results. Click on each pic to get a full size image of each gel:
For the lab report:
- The lab report is due Thursday Dec 11th.
- If you can answer the questions on page 44 of "exercise 3" in the lab manual you'll have a solid discussion of results section. Use them as a guide to get ideas to discuss.
- In one of the four posted pictures the samples are significantly smeared. In your discussion include your thoughts (or findings) on what may have caused this.
- Include a picture of your gel. If you turn in the one printed in the lab (on thermal paper) you can label the lanes with an ultrafine point permanent marker (sharpies and the like).
- A pdf file of a semi-log paper page will be e-mailed to you for your convinience.
Research questions
- The gels we used were pre-poured for us. They were 1% agarose gels. What does this mean?
- If you want to improve the resolution of the gel (making bands sharper, improving separation of bands of similar size) what can you do different when preparing the gel?
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Wednesday, December 3, 2008
Lab 01 - Playing with micropipettes
Today we had our first lab meeting of the quarter. Lab manuals, lab notebooks, "blue books" (for lecture quizzes), and disposable lab coats were distributed. We talked about how to behave in the lab and went over the first and most simple lab exercise: getting acquainted (or re-acquainted) with micropipettes. The report for this lab was handed in at the very end of the lab.
Tomorrow: Lab 2 ("Exercise 3" in the lab manual), Restriction Enzyme Digests (REDs) and gel electrophoreses.
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Tuesday, December 2, 2008
Winter 08-09 quarter
Welcome to the Winter 08-09 Intro to Molecular Biology class at ONU...!
This blog is meant to be a tool to improve communication between students and the instructor of the class (Alonso Córdoba) and to keep track of the actual happenings in the class throughout the quarter. Feel free to browse through old entries (Fall 08 quarter) to get an idea of the kind of information you can get by reading this blog.
An interesting feature is the fact that you can find questions and answers to old quizzes. You can use this tool to get used to the quiz format or even to study for upcoming quizzes and exams.
Is there something you would like to see posted on this blog? Just let me know. I am open to new ideas, suggestions, and constructive criticism. Just drop me a line or give me a call (contact info on the column to the right of entries).
I hope you enjoy this quarter...! (stay warm!)
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Random pics... (a Fall 2008 lab)
A little Ice Man? I clearly didn't give students enough to do that day in lab... I'll have to be a little tougher in the future....
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Wednesday, November 19, 2008
Final exam
The final exam took place between 8:00 and 10:00 am at Meyer Hall 128.
Toughest questions (statistically):
13 & 20. If two genes in an individual are derived from a single ancestral gene, they are called
c & d. Paralogs
Comment: The questions were phrased slightly differently, but the essence of the question and the answer were the same. If an indidual has two (or more) genes in its genome, originated from gene duplications, the are called paralogs or paralogous genes. Orthologs or orthologous genes, the alternative, are genes, in genomes of different species, that have evolved from the same gene in an ancestor. They are the same gene, in different species, not a product of a gene duplication.
43. What is an operon?
a. a series of genes transcribed into a single mRNA in prokaryotes
Comment: Not just they are transcribed into a single mRNA, but are controlled by a single promoter. They are not found in eukaryotes, where each individual gene has its own promoter, and it's transcribed into a separate mRNA.
49. What is an mediator?
d. a complex of proteins that function as an intermediary between transcription factors and RNA polymerase
Comment: There are cases, in complex genetic switches, when having the right transcription factors in place is not enough to start trasncription. The mediator (a complex of 24 subunits), acts as an intermediary (or a coordinator, if you will) between them and the polymerase. It's not a transcription factor per se, but just as important.
57. What is an gene control region?
b. a region of DNA containing elements that control and initiate gene transcription
Comment: The DNA control region can be even longer than the actal gene (introns included). It has several elements that will have to act in coordination to start gene transcription. The gene control region is what makes complex genetic switches complex.
72. If mutation rate cannot be masured experimentally it can be estimated by...
c. comparing the genomes of multiple species
Comment: When generation times are too long to wait around and see how high mutation rate is, the only option is estimating it from the differences found in sequence alignments. There are algorithms that allow the use of nucleotide or amino acid sequence differences as the basis dor such calculation.
84. Describe RNAi. Include the steps in the process and explain its goal
Read pages 493-496 in the text book
Comment: Even though we didn't cover it in class, we did talk about the importance of such process for the cell and in terms of a research tool. I did tell you to read about it and it was specifically mentioned in the study guide as one of the potential topics for open questions.
RNA interference (RNAi) has become an imnportant molecular technique to study patterns of gene expression.
It is worth 100 points. There were 80 multiple-choice questions, worth 1 point each, and 6 short essay questions. 4 questions were worth 4 points, and 2 of them were worth 2 points.
Exam stats
- Mean score: 79 (exam 1: 86; exam 2: 79)
- Standard deviation: 15.3 (exam 1: 8.8; exam 2: 10.9)
- Mode: 77 (exam 1: 90; exam 2: 82)
Although the average was steady compared to exam 2, the mode decreased and the standard deviation increased. The likely reason is that the new material that was heavily weighted compared with exam 1 was difficult for some people. But some people had very high scores. Maybe studying more at the beginning of the semester crated a solid base to build upon?
Score frequency distribution
Toughest questions (statistically):
13 & 20. If two genes in an individual are derived from a single ancestral gene, they are called
c & d. Paralogs
Comment: The questions were phrased slightly differently, but the essence of the question and the answer were the same. If an indidual has two (or more) genes in its genome, originated from gene duplications, the are called paralogs or paralogous genes. Orthologs or orthologous genes, the alternative, are genes, in genomes of different species, that have evolved from the same gene in an ancestor. They are the same gene, in different species, not a product of a gene duplication.
43. What is an operon?
a. a series of genes transcribed into a single mRNA in prokaryotes
Comment: Not just they are transcribed into a single mRNA, but are controlled by a single promoter. They are not found in eukaryotes, where each individual gene has its own promoter, and it's transcribed into a separate mRNA.
49. What is an mediator?
d. a complex of proteins that function as an intermediary between transcription factors and RNA polymerase
Comment: There are cases, in complex genetic switches, when having the right transcription factors in place is not enough to start trasncription. The mediator (a complex of 24 subunits), acts as an intermediary (or a coordinator, if you will) between them and the polymerase. It's not a transcription factor per se, but just as important.
57. What is an gene control region?
b. a region of DNA containing elements that control and initiate gene transcription
Comment: The DNA control region can be even longer than the actal gene (introns included). It has several elements that will have to act in coordination to start gene transcription. The gene control region is what makes complex genetic switches complex.
72. If mutation rate cannot be masured experimentally it can be estimated by...
c. comparing the genomes of multiple species
Comment: When generation times are too long to wait around and see how high mutation rate is, the only option is estimating it from the differences found in sequence alignments. There are algorithms that allow the use of nucleotide or amino acid sequence differences as the basis dor such calculation.
84. Describe RNAi. Include the steps in the process and explain its goal
Read pages 493-496 in the text book
Comment: Even though we didn't cover it in class, we did talk about the importance of such process for the cell and in terms of a research tool. I did tell you to read about it and it was specifically mentioned in the study guide as one of the potential topics for open questions.
RNA interference (RNAi) has become an imnportant molecular technique to study patterns of gene expression.
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Friday, November 14, 2008
Course evaluations
Here's the website for filling in the course evaluations:
http://onuapp1.onu.edu/courseval/ets/et.asp?nxappid=WCQ&nxmid=start
http://onuapp1.onu.edu/courseval/ets/et.asp?nxappid=WCQ&nxmid=start
Use your user name and the last 4 digits of your social as your password. At least that's what it's supposed to be. If it's not, they will e-mail you the correct password.
Update (Nov 17 08): 22 out of 24 people filled in course evaluations
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Thursday, November 13, 2008
Meeting @ McIntosh - Last presentations + class conversation
We met at McIntosh 204 instead of at the regular lab to be able to use a projector and have the last 4 talks of Tuesday's symposium:
_____________________________________________________
TRANSGENIC PLANT VACCINES: A REVIEW FROM BOTANICAL AND HUMAN PERSPECTIVES
Josh Holloway and Eric Schultz
MODERN ADVANCEMENTS IN THE PRODUCTION AND SCREENING OF GENETICALLY MODIFIED CROPS
Stuart Collins and Matt Vemich
THE USE OF DNA IN RELEASING INNOCENT PRISONERS
Brandon Vieira and John Jacobs
RECOMBINANT DNA TECHNOLOGIES IN FORENSIC SCIENCES
Katie Elsass and Jonathan Digby
_____________________________________________________
After the talks, each lab section had a separate meeting to talk about impressions about the class and how it could be improved to accommodate the needs of students. Students gave input and made several recommendations, most of which will be implemented in the winter quarter.
_____________________________________________________
TRANSGENIC PLANT VACCINES: A REVIEW FROM BOTANICAL AND HUMAN PERSPECTIVES
Josh Holloway and Eric Schultz
MODERN ADVANCEMENTS IN THE PRODUCTION AND SCREENING OF GENETICALLY MODIFIED CROPS
Stuart Collins and Matt Vemich
THE USE OF DNA IN RELEASING INNOCENT PRISONERS
Brandon Vieira and John Jacobs
RECOMBINANT DNA TECHNOLOGIES IN FORENSIC SCIENCES
Katie Elsass and Jonathan Digby
_____________________________________________________
After the talks, each lab section had a separate meeting to talk about impressions about the class and how it could be improved to accommodate the needs of students. Students gave input and made several recommendations, most of which will be implemented in the winter quarter.
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Wednesday, November 12, 2008
MEETING AT McINTOSH 204 - Thursday the 13th
Tomorrow, Thursday the 13th, we will be meeting at the McINTOSH CENTER, CONFERENCE ROOM 204!
We will meet at the regular lab times to finish the remaining presentations and have a little bit of lecture.
Presentations section 1 (8:00 am):
Presentations section 2 (10:00 am):
We will meet at the regular lab times to finish the remaining presentations and have a little bit of lecture.
Presentations section 1 (8:00 am):
- Josh Holloway and Eric Schultz
- Stuart Collins and Matt Vemich
Presentations section 2 (10:00 am):
- Brandon Vieira and John Jacobs
- Jonathan Digby and Katie Elsass
Tuesday, November 11, 2008
Introductory Molecular Biology Symposium
This symposium featured students in the class presenting the results of their bibliographic research summarized in review papers on molecular biology topics. Papers will be compiled in the proceedings for the symposium.
Presentations, ordered as scheduled, were:
__________________________________________________
__________________________________________________
PLANT DEFENSE MECHANISMS : AN UNEXPECTED ARSENAL
Josh Judkins and Jackie Champa
Josh Judkins and Jackie Champa
ETIOLOGY AND EVOLUTION OF MRSA
Katie Somes and CJ Jewel
THE USE OF DNA IN FORENSICS
Mike Breckenridge and David Cassidy
GENETIC MODIFICATION IN HUMANS
Amy Mattern and Ryan Wheaton
DNA FINGERPRINTING OF DISASTER VICTIMS
Anessa Storer and Chloé Seiller
GENE THERAPEUTICS: A BRIEF REVIEW OF THE HISTORY, TECHNIQUES, AND APPLICATIONS OF A POTENTIALLY DISEASE-CURING PROCESS
Kyle Stinehart and Courtney Zupancic
TRANSGENIC PLANT VACCINES: A REVIEW FROM BOTANICAL AND HUMAN PERSPECTIVES
Josh Holloway and Eric Schultz
CUSTOM DRUGS BASED ON GENETIC PROFILE
Amanda Blandford and Jackie Trumpower
MODERN ADVANCEMENTS IN THE PRODUCTION AND SCREENING OF GENETICALLY MODIFIED CROPS
Stuart Collins and Matt Vemich
EFFECTS AND DETECTION OF DIGEORGE SYNDROME (22Q11.2 DELETION SYNDROME)
Phil Schulze and Krystal DeMonte
Katie Somes and CJ Jewel
THE USE OF DNA IN FORENSICS
Mike Breckenridge and David Cassidy
GENETIC MODIFICATION IN HUMANS
Amy Mattern and Ryan Wheaton
DNA FINGERPRINTING OF DISASTER VICTIMS
Anessa Storer and Chloé Seiller
GENE THERAPEUTICS: A BRIEF REVIEW OF THE HISTORY, TECHNIQUES, AND APPLICATIONS OF A POTENTIALLY DISEASE-CURING PROCESS
Kyle Stinehart and Courtney Zupancic
TRANSGENIC PLANT VACCINES: A REVIEW FROM BOTANICAL AND HUMAN PERSPECTIVES
Josh Holloway and Eric Schultz
CUSTOM DRUGS BASED ON GENETIC PROFILE
Amanda Blandford and Jackie Trumpower
MODERN ADVANCEMENTS IN THE PRODUCTION AND SCREENING OF GENETICALLY MODIFIED CROPS
Stuart Collins and Matt Vemich
EFFECTS AND DETECTION OF DIGEORGE SYNDROME (22Q11.2 DELETION SYNDROME)
Phil Schulze and Krystal DeMonte
THE USE OF DNA IN RELEASING INNOCENT PRISONERS
Brandon Vieira and John Jacobs
RECOMBINANT DNA TECHNOLOGIES IN FORENSIC SCIENCES
Katie Elsass and Jonathan Digby
___________________________________________________
Brandon Vieira and John Jacobs
RECOMBINANT DNA TECHNOLOGIES IN FORENSIC SCIENCES
Katie Elsass and Jonathan Digby
___________________________________________________
Monday, November 10, 2008
Complex genetic switches and post-transcriptional control
We covered pages 439-447 regarding complex genetic switches, specifically in Eukaryota. We did a short comparison between prokaryot and eukaryot genetic switches. The concept of mediator, absent in prokaryots but present in eukaryots was introduced.
We studied a typical eukaryotic gene control region. Several elements within such region were discussed (spacers, regulatory sequences, TATA box, promoter), as well as related proteins (regulatory proteins, general trasncription factors, RNA polymerase II).
On pages 477-497 post-transcriptional gene expression controls were discussed. Our discussion was not detailed but we talked about transcription attenuation, riboswitches, alternative RNA splicing, RNA editing, and RNA interference (RNAi).
Quiz #14 Q&As
1. In DNA-Binding proteins, what is the difference between α-helices and β-sheets? (other than the helical and non-helical structure)
An α-helix is made of a single polypeptide. β-sheets are made by several polypeptides
2. What is a promoter?
A region of regualtory DNA where RNA polymerase binds
3. What is an operon?
A series of adjacent genes controlled by a single promoter
4. What is an operator?
A short regulatory DNA sequence within a promoter recognized by a represor
5. What is a complex genetic “switch”?
A a genetic switch controlled by multiple gene regulatory poteins
6. What is a repressor?
A protein that binds to an operator to repress the expression of a gene
7. What is an activator? (hint: it does more than just turning a gene on)
It's a protein that increases the transcription efficiency of a gene
We studied a typical eukaryotic gene control region. Several elements within such region were discussed (spacers, regulatory sequences, TATA box, promoter), as well as related proteins (regulatory proteins, general trasncription factors, RNA polymerase II).
On pages 477-497 post-transcriptional gene expression controls were discussed. Our discussion was not detailed but we talked about transcription attenuation, riboswitches, alternative RNA splicing, RNA editing, and RNA interference (RNAi).
Quiz #14 Q&As
1. In DNA-Binding proteins, what is the difference between α-helices and β-sheets? (other than the helical and non-helical structure)
An α-helix is made of a single polypeptide. β-sheets are made by several polypeptides
2. What is a promoter?
A region of regualtory DNA where RNA polymerase binds
3. What is an operon?
A series of adjacent genes controlled by a single promoter
4. What is an operator?
A short regulatory DNA sequence within a promoter recognized by a represor
5. What is a complex genetic “switch”?
A a genetic switch controlled by multiple gene regulatory poteins
6. What is a repressor?
A protein that binds to an operator to repress the expression of a gene
7. What is an activator? (hint: it does more than just turning a gene on)
It's a protein that increases the transcription efficiency of a gene
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