Registration/Questionnaire: 20.109 Fall 2007
20 - Biological Engineering 15 - Management
Year of Graduation
jtan_87 AT mit DOT edu
Have you taken
7.05/5.07 (Biochemistry) - YES 7.06 (Cell Biology) - NO 7.02 (General Biology Lab) - NO 5.310 (General Chemistry Lab) - NO
Do you have any experience culturing cells (mammalian, yeast or microbial)?
Do you have any experience in molecular biology (electrophoresis, PCR, etc)?
Please briefly describe any previous laboratory experience
In high school, I did a lot of biochemistry research. When I arrived at MIT, I worked at the Langer Lab doing tissue engineering research, specifically with regards to the osteogenic stem cell line. Finally, throughout my sophomore year, I worked in the Hamad-Schifferli lab designing temperature-sensitive biomedical devices for drug delivery.
Anything else you would like us to know?
I am really excited to be in this class! Although I have already had significant experience working in lab, I would really like to diversify the types of research that I do since I haven't really found a "passion" in any of the work that I've done in the past. I am also very enthusiastic about improving my oral/writing skills since it is something that I have always struggled with in the past.
M13 Re-Engineering Ideas
|I||Assembly||Re-engineering of PI will undoubtedly cause some very drastic changes since it works in conjunction with several other genes (PIV and PXI) in the assembly process. Perhaps by altering the C-terminals of PI (and PXI) in interacting with pIV, we can alter the channels with which the phages are secreted and analyze the potential consequences of having a larger/smaller channel on the rate of secretion.|
|II||Replication of DNA + strand||From 7.03, I learned of various pathways that can control promoter sequences. If the natural promoter on M13 can be altered to become inducible, the rate
of M13 replication within the host bacteria could potentially be controlled. Consequently, this will also have an impact on the life-cycle of M13 | | bacteriophage.
|III||Phage tail protein (5 copies)||Since PIII is responsible for the initial binding of M13 to the bacteria at the TolA of the F Pilus, if this protein-binding process can be modified to bind in more varied conditions, we can potentially construct an M13 bacteriophage that can bind to bacteria without the F Pilus factor.|
|IV||Assembly||In the same way as PI, re-engineering of PIV will undoubtedly cause some very drastic changes since it works in conjunction with several other genes (PI and PXI) in the assembly process. Perhaps by altering the N-terminal of PI in interacting with pI and PXI, we can alter the channels with which the phages are secreted and analyze the potential consequences of having a larger/smaller channel on the rate of secretion.|
|V||Binds ssDNA||Altering this gene will have a very profound effect upon the efficiency of DNA replication. I would be very interested to see the differences that might arise by changing the ratio between sequestered ssDNA and the formation of dsDNA. Perhaps we can optimize the level of phage production...|
|VI||Phage tail protein (5 copies)||Since PVI is only an accessory protein for PIII, we can test the stability of PIII in performing its function with decreased/increased levels of PVI production. My guess is that it works to make the process more efficient...|
|VII||Phage head protein (5 copies)||In the same way as PVI as an accessory protein for pXI, we can test with varying amounts of its expression to analyze its effects upon the efficiency of p9's function.|
|VIII||Phage coat protein (2700 copies)||Since PVIII surrounds the cells protein coat, I think it would be a great idea to alter the surface charge density of the protein coat. That way, we can compare M13 to its evolutionary relatives (fd and fl) to determine whether the difference in charge densities is really a fundamental difference between them and the way they function.|
|IX||Phage head protein (5 copies)||I could be curious to see the effect of removing the "blunt end" entirely and replacing it with the same "rounded tip" encoded by PIII. Will the M13 bacteriophage still be recognized by the F Pilus of the bacteria? Would it make things any more/less efficient?|
|X||DNA replication||I would simply like to leave this unaltered and then analyze the effects of changing the promoter sequence on PII on the relative functionality/importance of pX. Perhaps pX is the mechanism which controls the rate of the promoter on PII...|
|XI||Assembly||In the same way as PI (and PIV), re-engineering of PXI will undoubtedly cause some very drastic changes since it works in conjunction with several other genes in the assembly process. Perhaps by altering the C-terminals of PXI (and PI) in interacting with pIV, we can alter the channels with which the phages are secreted and analyze the potential consequences of having a larger/smaller channel on the rate of secretion.|
M13’s Closest evolutionary relatives
M13’s closest relatives are the bacteriophages fd and fl. Although they originate from the same bacteriophage family, Inoviridae, and exhibit the same circular single-stranded-DNA components, M13 differs from fd and fl in their protein coats. Whereas fd and fl both have carboxyl groups from aspartate, M13 has an amide group from its attached asparagine. As a result, M13 has a lower charge density along its surface than its bacteriophage relatives.
”Bba_M1307 is not a standard biological part and does not belong in the registry”
The M1307 sequence has been modified to include an origin of replication from the pACYC177 sequence as well as a kanamycin resistance gene so that it can propagate on Kan(+) plates. Hence, it has obviously been biologically engineered for in-vitro substrate building. However, a unique aspect of its function exists in the presence of other phage plasmids, whereyby it adopts an indirect “helper phage” role (i.e. providing the protein coat while allowing another phage plasmid (if present) into the phage capsid/host bacteria for substrate building.
Amendment: After the discussion in lecture, a potential reason for removing the sequence from the registry could be that it provides reliable "functional" composition (for another phage plasmid) instead of physical composition, which seems to be a property for the other biologically-engineering parts in the registry.
Revision: After the discussion from lecture on Thursday, I would contend that M13K07 does not always operate within the “standard” definition of a “biological part” – i.e. basic biological functions that can be encoded as genetic material (DNA). In the presence of a second plasmid with the M13 packaging sequence and origin, M13K07 serves only as a "helper phage" (not a basic function) by providing the necessary proteins for the phage coat “but allowing the alternative plasmid to be preferentially placed in the phage capsid”.
Phillip & Justin's research proposal
Magnetically-Induced Nanoparticles for biodetoxification of hydrophobic or non-ionizable toxins
Brief Project Overview
Using the concept of injectable magnetic nanospheres that can be magnetically filtered out of the body, we want to combine this concept with current approaches to detoxification through the use of nanoemulsion-encapsulated nanoparticles that have an affinity to hydrophic/non-ionizable toxins.
Nanoemulsions have already been shown to uptake toxins such as bupivacaine (local anaesthetic associated with cardiotoxicity) and sequester it within the blood pool. Using magnetic nanoparticles, we propose a method of functionalizing this compound for removal.
Original Paper link: [In vitro studies of functionalized magnetic nanospheres for selective removal of a simulant biotoxin, http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TJJ-4FM59V2-B&_user=501045&_coverDate=05%2F31%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=09ba98a9398555f546beea20609001f2]
This article demonstrates the ability to use nanoparticles as an effective method for removing specific molecules from blood.
Statement of Research Problem & Goals
The use of functionalized nanoparticles offers many potential, biomedical applications due to the versatility of applied receptors or encapsulation of drugs for targeted delivery. Although nanoparticles have already been extensively applied to methods of drug delivery, their ability to serve as complex-forming inducers to remove biotoxic agents from tissues is a new area with vast potential to clinical applications. Using nanocarriers as “toxin-sinks” by which to lower toxic-tissue concentration and prevent chemical poisoning, these synthetic biological components can act as an alternative to current non-specific treatments.
We hope to improve upon the capability of using this toxin sinks towards clinical applications by coupling them with magnetically-induced nanoparticles.
Project Details & Methods
Joncheray, T. J. et al. Electrochemical and spectroscopic characterization of organic compound uptake in silica core-shell nanocapsules. Langmuir 22, 8684–8689 (2006).
Underhill, R. S. et al. Oil-filled silica nanocapsules for lipophilic drug uptake: implications for drug detoxification therapy. Chem. Mater. 14, 4919–4925 (2002).
Jovanovic, A. V. et al. Surface modification of silica core-shell nanocapsules: biomedical implications. Biomacromolecules 7, 945–949 (2006).
These papers address the development of nanocapsules to facilitate drug uptake for detoxification as well as to improve the capability for clinical applications (compatibility/interaction with blood components and biodegradeability)
Leroux, J-C. Injectable nanocarriers for biodetoxification: Nature Nanotechnology 2, 679 - 684 (2007)
The above article presents current approaches to sequestering toxins in the body using nanocarriers.