Jessica Keenan: Biomaterials Engineering

=For Next Time Day 5= To allow the phage to align more tightly on the ITO, the phage could be engineered to have a negative region on the p3 protein (perhaps a series of glutamates). Because the change on p3 would be greater than the weak charges on the p3 coat, the tip of the phage would would readily bind to the cathode, allowing for a tighter pattern of the phage on the surface.

For transfection, we could standardize:


 * DNA efficiency
 * % of competent cells
 * Density of plated cells

=For Next Time Day 4=

MG1655 MDS43

 * MG1655 contains 4,639,675bp, and MDS43 contains 3,931,408bp
 * 743 genes have been deleted from MG1655 in MDS43
 * The gray rings are portions of the K-12 genome that are absent in other E. coli (and thus good candidates for regions that can be deleted, since they do not appear to be necessary in other E. coli).
 * Purple represents the deletions made in MDS43. I can't find it clearly stated anywhere, but it seems that the deletion of the purple regions separates MDS43 from MDS42, and the deletion of the blue regions separates MDS42 from MDS41, etc.  If this is true, then all colored regions in that ring were deleted in MDS43.

Material Transfer Agreement
I found this agreement interesting, as it seems to be focused around protecting Scarab's best interests. For example, it ensures that Scarab knows exactly what we are doing with the bacteria, and also that we must share any beneficial knowledge we discover about the bacteria with scarab. These requests seem reasonable, and it seems likely to me that they would be fulfilled even in the absence of a formal agreement, simply due to the cooperative nature of the project. However, it seems less reasonable that we could not share even very distant derivatives of the material with other labs, and that we would not receive credit for new discoveries made. While these terms seem reasonable for a teaching laboratory, I doubt that there are many other labs that would be willing to agree with them. I also really dislike how this document opposes the nature of "Open Source" information. I understand that Scarab wants to protect the product that they are selling, but it seems that the most progress on the project would be made if the material was readily available and shared with other labs. Scarab might lose sales if another lab produces more useful bacterial models, but new advances could be made that could be very beneficial.

=For Next Time Day 2=

TEM Questions
While light microscopes use light to view samples, TEM uses electrons.

How is the electron beam focused on the sample to be viewed by STEM? What does the electron beam interact with in the sample? What is the greatest magnification possible with a light microscope? What is the greatest magnification possible with a TEM? STEM is type of TEM that is able to measure the mass of samples, though it requires them to be freeze-dried. On the other hand, cryoEM can be used on samples stored on ice (more natural), but is unable to measure their mass and the contrast is lower.
 * The electron beam is focused with a magnetic lens.
 * The electron beam interacts with a detector in the sample.
 * Light microscopes can magnify up to 1000x.
 * TEMs can magnify 10 million times.
 * What are some of the difference between cryoEM, STEM and TEM?

=For Next Time Day 1=

A Synthetic Gene Network for Tuning Protein Degradation in Saccharomyces Cerevisiae

 * Grilly C, Stricker J, Pang WL, Bennett MR, Hasty J. A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae . Molecular Systems Biology 2007; 3:127
 * The authors of this article created a mechanism in yeast that uses IPTG to tune the degradation levels of proteins tagged with a specific amino acid sequence. They have also produced a predictive model for their system, making it even more useful.  It would be interesting to see if this system (or a modified version of this system) could be made to work in mammalian cells.  Eventually, such a system could be used to degrade proteins over-expressed in cancers (for example, the Her receptors in breast cancer).

Bypass of DNA Lesions Generated During Anticancer Treatment with Cisplatin by DNA Polymerase η

 * Alt A, Lammens K, Chiocchini C, Lammens A, Pieck JC, Kuch D, Hopfner KP, Carell T. Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA Polymerase η.  Science 2007; 318:967-970
 * Here the authors describe how a particular DNA polymerase is able to replicate DNA even though that DNA has been damaged by chemotherapy. Since the cell continues to replicate its mutated genome instead of dying, it is resistant to the the therapy.  RNAi could be used to study how the depletion of this gene is able to alter cancer growth.

Printing Cells

 * Calvert P. Printing Cells. Science 2007; 318:208-209
 * This article explains that modified ink jet printers can be used to print 3D materials out of cells. While there has been great success in printing bacterial and yeast cells, mammalian cells are often more difficult to work with.  It would be interesting to investigate cell-to-cell signaling within the the structures we are already able to print, or to look at how this technology could be modified to work better with mammalian cells.  Moreover, this technology could be used to build organs, so studying how a particular type of human tissue can be printed with great precision would be interesting.

Bioengineering Novel in Vitro Metabolic Pathways Using Synthetic Biology

 * Meyer A, Pellaux R, Panke S. Bioengineering novel in vitro metabolic pathways using synthetic biology. Current Opinion in Microbiology 2007; 10:245-253
 * In the past, most industrial reactions involve only one or two enzymatic steps. The authors of this article argue that with recent advances in DNA sequencing, genome engineering, and analytics, it should be possible to design multi-enzyme reactions at the industrial scale.  While there are a myriad of different multi-enzyme systems that would be beneficial to design, I think it would be particularly useful and interesting to try to design a better method for processing biomass into biofuel.

An siRNA-based Microbicide Protects Mice from Lethal Herpes Simplex Virus 2 Infection

 * Palliser D, Chowdhury D, Wang Q, Lee SJ, Bronson RT, Knipe DM, Lieberman J. An siRNA-based microbicide protects mice from lethal herpes simplex virus 2 infections. Nature 2006; 439:89-94
 * The authors of this article designed an siRNA against Herpes Simplex Virus 2 (HSV-2) genes that are essential for viral replication. They used vaginal installation of the siRNA in a lipid mixture to effectively prevent HSV-2 infection in mice.  Because HSV-2 is a cofactor necessary to transmit HIV infection, it would be interesting to see how this treatment affects the mice's ability to contract HIV.  Moreover, other siRNAs could be designed to target other sexually transmitted viruses, like hepatitis, HPV, or even HIV itself.