For amiRNA projects we will synthesize the amiRNAs as Gateway entry vectors by including truncated attL arms in the synthesized genes. As a group you need to think about a control for this approach - how will you know that this works? Have a look at this article for some ideas. Here are the amiRNA designer links for BOB2 alone and for BOB1 and BOB2 as targets.
For sHSP:GFP projects we will PCR genomic sHSP clones with a CACC tail for directional cloning into pENTR/D-TOPO. A list of heat induced sHSPs can be found below. Use the Affy-ID to find a gene locus identifier using this tool. Once you have identified your gene, click through to the locus detail page and then click on the sequence viewer link (under the map links category). Click on the sequence ruler bar above your gene to retrieve a coded genomic sequence. Copy and paste the genomic region starting at the upstream gene into Primer3 (link below) and design primers which amplify the promoter and gene. Make sure that you add a CACC on the 5' end and that you remove the stop codon.
Once entry vectors have been created they will be recombined into pFAST destination vectors using an LR reaction.
Primers will be designed using Primer3. Adjust parameters so that the Tm is 65 degrees.
Week 13 - Phytoremediation and perennialization
Ben will present a pair of paper investigation the use of plant for remediation of mercury and selenium pollution.
Jesse will present an overview of perennialization and a pair of papers (to be posted soon) investigating the scientific issues involved in breeding for this trait.
Week 12 - Glyphosate and glyphosate resistance and an investigation of mapping approaches which can be used for MAS
Michael will present a pair of papers and a short review investigating the mechanism of glyphosate action and how plants evolve resistance to this important herbicide.
Elan will present a pair of QTL papers and compare and contrast this approach to the NAM design from the Buckler lab.
Week 11 - Biofortification of Vitamin A
Rosalie and Camille will discuss a variety of approaches for Vitamin A biofortification. Technologies used include both transgenic as well as MAB strategies, which in turn require association mapping and QTL data.
Week 10 - Abiotic stress Julia and Omer will present a series of papers investigating the role of the DREB family of TFs in responses to abiotic stresses including drought, salt, and high and low temperatures. Background reading about abiotic stress in plants and the role of the plant hormone ABA can be found in Plant Physiology by Taiz and Zeiger.
Week 9 - Energy II
Rosalie will present a pair of papers looking at lignin modification in trees and the effects of these modifications on the feeding preference and growth performance of insect herbivores.
Camille will present a pair of papers about photosynthesis - the source of all of the biological energy we are discussing in the course. The first paper discusses increasing photosynthetic efficiency by optimizing the amount of light harvesting complexes produced in green algae. The second paper involves using nanotechnology to directly harvest high-energy electrons from the thylakoid membrane. It's been a while since Bio25, so you may be thinking to yourself "What is a thylakoid membrane?". A good review of the light reactions of photosynthesis can be found in chapter 7 of Plant Physiology by Taiz and Zeiger (QK711.2 .T35 2006 in the oversize section). I also have a copy of this book which you can borrow from me.
Week 8 (after fall break) - Energy I
Jesse will present an overview of current and next generation biofuels (Gressel) . He will focus on Jatropha as a next generation oil seed plant and how Jatropha yields might be improved by manipulating BR signaling. Please read the review as well as the two research papers - one is quite short and straightforward.
Elan will present a pair of papers showing how modification of lignin biosynthesis can improve biofuel yields.
The Sticklen review provides a good overview of the technical problems involved in producing cellulosic biofuels. This is an optional reading which I would strongly encourage you to read if you have any questions about cellulosic biofuels.
Week 5 - Nitrogen
Ben will tell us about one of the normal functions of alanine aminotransferases (AlaAT) as well as about improving NUE by expressing AlaAT in the root, where nitrogen is absorbed from the ground.
Omer will tell us about increasing NUE by expressing and early nodulation gene. What is an early nodulation gene (ENOD) you may ask? He'll tell us about that too.
Week 4 - Biotic stress
Michael will present a pair of papers about resistance to the brown planthopper, a very serious rice pest. The resistance is mediated by callose deposition and requires Bph14, a gene which confers planthopper resistance as a transgene.
Julia will present a pair of papers about resistance to plum pox virus (discussed in Tomorrow's Table pp. 165-167). The first paper (Tang et al.) investigates the molecular events that mediate PTGS, the second (Hily et al.) shows how PTGS can be used to engineer virus resistant plum strains.
Week 3 - The devil is in the details - the Monarch butterfly story
This week we will discuss the Monarch butterfly/Bt corn story as a way of investigating the importance of the specific details when trying to assess the possible ecological effects of transgenic technologies.
- Everyone should read Losey et al., Jesse and Obrycki, and Gatehouse et al.
- Everyone should bring in an example of popular press coverage of this issue from 1999 for discussion.
- Come prepared to present the key points of two of the shared papers. The shared papers are:
Hellmich et al. (Omer, Rosalie, Camille),
Oberhauser et al. (Camille, Amy, Elan, Michael),
Pleasants et al. (Jesse, Elan, Julia),
Sears et al. (Amy, Ben),
Stanley-Horn et al. (Ben, Jesse, Rosalie), and
Zangerl et al. (Omer, Julia, Michael)
- If you are interested in reading more about risk assessment, you can find more information in Andow and Zwahlen (completely optional reading).
Week 2 - Short talks on a variety of topics
Week 1 - Biotechnology and sustainability overview (Nick)
An evolving list of possible topics for your presentations during the semester. Each topic has an attached review to get you started finding the relevant literature. If you have something to add to this list please email it to Nick and I will add more as I find them.