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Team:Calgary/Sandbox/Notebook/Journal/Reporter
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<h2>Week 1: May 1 - May 3</h2> | <h2>Week 1: May 1 - May 3</h2> | ||
<p>We examined three problems related to ferritin. Firstly, we investigated protein isolation of ferritin. We are considering the protocols created by Santambrogio et al. (1993), as they have been used by multiple other authors as well. This paper uses precipitation followed by column chromatography, and verification with spectroscopy, PAGE and SDS-PAGE (Levi 1994). Alternatively, we may consider using his-tags for Ni-NTA column purification. | <p>We examined three problems related to ferritin. Firstly, we investigated protein isolation of ferritin. We are considering the protocols created by Santambrogio et al. (1993), as they have been used by multiple other authors as well. This paper uses precipitation followed by column chromatography, and verification with spectroscopy, PAGE and SDS-PAGE (Levi 1994). Alternatively, we may consider using his-tags for Ni-NTA column purification. | ||
| - | Secondly, we examined the feasibility of using magnetism to manipulate ferritin. Commercial horse spleen ferritin was tested on a Dynabead rack, and as expected, it did not move, as the core should not be magnetic. We must thus synthesize magnetoferritin wherein the native ferrihydrite core is converted to magnetite--a paramagnetic material which can be attracted to magnetic fields (Jordan et al. 2010, Wong et al. 1998). We were able to attain some general knowledge of magnetism in nano-scale material, including a basic understanding of blocking temperatures, superparamagnetism and magnetic moments, all magnetism-related measurements. But we are ill-equipped to model this system theoretically in terms of calculated forces. We also explore the possibility of alternative magnetic particles, in the case ferritin is too small to exhibit magnetic forces significant enough to move proteins. Magnetosomes were found to be much larger, but unviable due to the complexity of their creation. The CCMV virus may also be an option, although there is currently little known about it and therefore further research into this topic is required. (Lohsse et al. 2011). | + | Secondly, we examined the feasibility of using magnetism to manipulate ferritin. Commercial horse spleen ferritin was tested on a magnetic Dynabead rack, and as expected, it did not move, as the core should not be magnetic. We must thus synthesize magnetoferritin wherein the native ferrihydrite core is converted to magnetite--a paramagnetic material which can be attracted to magnetic fields (Jordan et al. 2010, Wong et al. 1998). We were able to attain some general knowledge of magnetism in nano-scale material, including a basic understanding of blocking temperatures, superparamagnetism and magnetic moments, all magnetism-related measurements. But we are ill-equipped to model this system theoretically in terms of calculated forces. We also explore the possibility of alternative magnetic particles, in the case ferritin is too small to exhibit magnetic forces significant enough to move proteins. Magnetosomes were found to be much larger, but unviable due to the complexity of their creation. The CCMV virus may also be an option, although there is currently little known about it and therefore further research into this topic is required. (Lohsse et al. 2011). |
Because we also intend to scaffold proteins to ferritin as in our TALE DNA-binding proteins, we looked into fusions to both C- and N-terminals of ferritin. The N- and C- termini of ferritin subunits are present on the outside and inside of the nanoparticle respectively, and therefore N-terminal fusions are an obvious choice to ensure TALEs are present on the exterior of the nanoparticles (Dorner et al. 1985). | Because we also intend to scaffold proteins to ferritin as in our TALE DNA-binding proteins, we looked into fusions to both C- and N-terminals of ferritin. The N- and C- termini of ferritin subunits are present on the outside and inside of the nanoparticle respectively, and therefore N-terminal fusions are an obvious choice to ensure TALEs are present on the exterior of the nanoparticles (Dorner et al. 1985). | ||
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<h2>Week 5: May 27 - May 31</h2> | <h2>Week 5: May 27 - May 31</h2> | ||
| - | <p> | + | <p>While we are unsure of exactly how ferritin will be used in our project, any capacity in which we use it requires isolating recombinant ferritin from E. coli. We investigated which terminus to locate purification tags (eg, His tags) on ferritin subunits. Ingrassia et al. (2006) found that small amino acid additions to the C-terminus of either heavy or light chain ferritin are not deleterious to its function. Thus, we are contemplating fusing proteins to the N-terminal of ferritin as discussed last week, and using the C-terminus for tags to isolate recombinant subunits. |
| + | We also contemplated methods for controlling expression in terms of proportions of H and L subunits in completed ferritin. This could influence iron dynamics of completed ferritin. Lee et al. (2002) overcame this issue by fusing the heavy and light chains together to ensure that completed nanoparticles have a 1:1 ratio of each subunit. We are trying to determine pitfalls of this expression strategy. Finally, we investigated methods for validating nanoparticle formation. Namely, we considered fluorescence spectroscopy as tested by Parker et al. (2008), where 410nm output was indicative of iron incorporation as per assembled ferritins. | ||
| + | Apart from using magnetism to manipulate magnetoferritin to isolate pathogenic DNA, we developed a backup approach. Watt et al. (2012) constructed a nanoscale battery where ferritins with two different cores were oxidized and reduced on gold electrodes. We are contemplating using a split TALE capture system to bring ferritin into close association of an electrode. Current could then flow from ferritin into an electrode to indicate binding of pathogenic DNA. | ||
| + | Finally, we considered how we might construct a magnetic device to isolate ferritin. Bushart et al. (2006) discussed method for isolating metal chelating magnetoferritin for metal purification. However, the necessary magnetic field strengths, mesh density, or mass of isolated compounds in these systems were not explicit. Thus, we are still uncertain about the feasibility of using magnetism to isolate proteins attached to magnetoferritin. | ||
| + | </p> | ||
<h2>Week 6: June 3 - June 7</h2> | <h2>Week 6: June 3 - June 7</h2> | ||
Revision as of 15:29, 30 August 2013
Ferritin Journal
Week 1: May 1 - May 3
We examined three problems related to ferritin. Firstly, we investigated protein isolation of ferritin. We are considering the protocols created by Santambrogio et al. (1993), as they have been used by multiple other authors as well. This paper uses precipitation followed by column chromatography, and verification with spectroscopy, PAGE and SDS-PAGE (Levi 1994). Alternatively, we may consider using his-tags for Ni-NTA column purification. Secondly, we examined the feasibility of using magnetism to manipulate ferritin. Commercial horse spleen ferritin was tested on a magnetic Dynabead rack, and as expected, it did not move, as the core should not be magnetic. We must thus synthesize magnetoferritin wherein the native ferrihydrite core is converted to magnetite--a paramagnetic material which can be attracted to magnetic fields (Jordan et al. 2010, Wong et al. 1998). We were able to attain some general knowledge of magnetism in nano-scale material, including a basic understanding of blocking temperatures, superparamagnetism and magnetic moments, all magnetism-related measurements. But we are ill-equipped to model this system theoretically in terms of calculated forces. We also explore the possibility of alternative magnetic particles, in the case ferritin is too small to exhibit magnetic forces significant enough to move proteins. Magnetosomes were found to be much larger, but unviable due to the complexity of their creation. The CCMV virus may also be an option, although there is currently little known about it and therefore further research into this topic is required. (Lohsse et al. 2011). Because we also intend to scaffold proteins to ferritin as in our TALE DNA-binding proteins, we looked into fusions to both C- and N-terminals of ferritin. The N- and C- termini of ferritin subunits are present on the outside and inside of the nanoparticle respectively, and therefore N-terminal fusions are an obvious choice to ensure TALEs are present on the exterior of the nanoparticles (Dorner et al. 1985).
Week 2: May 6 - May 10
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Week 3: May 13 - May 17
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Week 4: May 20 - May 24
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Week 5: May 27 - May 31
While we are unsure of exactly how ferritin will be used in our project, any capacity in which we use it requires isolating recombinant ferritin from E. coli. We investigated which terminus to locate purification tags (eg, His tags) on ferritin subunits. Ingrassia et al. (2006) found that small amino acid additions to the C-terminus of either heavy or light chain ferritin are not deleterious to its function. Thus, we are contemplating fusing proteins to the N-terminal of ferritin as discussed last week, and using the C-terminus for tags to isolate recombinant subunits. We also contemplated methods for controlling expression in terms of proportions of H and L subunits in completed ferritin. This could influence iron dynamics of completed ferritin. Lee et al. (2002) overcame this issue by fusing the heavy and light chains together to ensure that completed nanoparticles have a 1:1 ratio of each subunit. We are trying to determine pitfalls of this expression strategy. Finally, we investigated methods for validating nanoparticle formation. Namely, we considered fluorescence spectroscopy as tested by Parker et al. (2008), where 410nm output was indicative of iron incorporation as per assembled ferritins. Apart from using magnetism to manipulate magnetoferritin to isolate pathogenic DNA, we developed a backup approach. Watt et al. (2012) constructed a nanoscale battery where ferritins with two different cores were oxidized and reduced on gold electrodes. We are contemplating using a split TALE capture system to bring ferritin into close association of an electrode. Current could then flow from ferritin into an electrode to indicate binding of pathogenic DNA. Finally, we considered how we might construct a magnetic device to isolate ferritin. Bushart et al. (2006) discussed method for isolating metal chelating magnetoferritin for metal purification. However, the necessary magnetic field strengths, mesh density, or mass of isolated compounds in these systems were not explicit. Thus, we are still uncertain about the feasibility of using magnetism to isolate proteins attached to magnetoferritin.
Week 6: June 3 - June 7
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Week 7: June 10 - June 14
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Week 8: June 17 - June 21
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Week 9: June 24 - June 28
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Week 10: July 1 - July 5
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Week 11: July 8 - July 12
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Week 12: July 15 - July 19
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Week 13: July 22 - July 26
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Week 14: July 29 - August 2
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Week 15: August 5 - August 9
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Week 16: August 12 - August 16
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Week 17: August 19 - August 23
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Week 18: August 26 - August 30
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Week 19: September 2 - September 6
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Week 20: September 9 - September 13
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Week 21: September 16 - September 20
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Week 22: September 23 - September 27
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Week 23: September 30 - October 4
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