Team:NYMU-Taipei/background-review

From 2011.igem.org

(Difference between revisions)

Latest revision as of 17:15, 12 April 2012

Slide Down Box Menu with jQuery and CSS3

               CLAIMS FOR POTENTIAL CONFLICT OF INTEREST
                               ...with those COOLEST guys around the world

Q1: What are magnetotactic bacteria?

One Sentence In Brief:

File:AMB-1.gif

Magnetospirillum magneticum AMB-1 under cryotomography and 3-D reconstruction

Magnetotactic bacteria, also known as magnetic bacteria, are an evolutionarily diverse group http://www.sciencemag.org/content/259/5096/803.short 1 of motile, Gram-negative eubacteria expressing magnetotaxis.

Q2: Community Yearning for The Strain?
We weren't wrong, were we?: )

During our review on past iGem projects, we concluded, to more or less an extend, teams dreaming for magnetotaxis have concluded in using this strain......yet only two team ever actually tried. One of them was Duke University 2006, the other being us.

Below are several arguments about the choice of this strain and reasons stopping previous iGem teams / supporting us in standing soundly on this step.

(1) So Let's Talk About The iGem History

Throughout the history of iGem, we have gained notice from exhaustive online searching that a remarkable number of previous iGem teams have continually proposed projects related to magnetosome, magnetospirillum, and magnetotaxis every year around the world.

Among these respectful pioneers, Duke University had made their magnetotactic bacteria-based project to the official jamboree titled “Bacterial Dynamo”, focusing on the use of AMB-1 as AC voltage generator http://www.duke.edu/~fr7/2007_Reza_et_al_IET_Synthetic_Biology.pdf 2, but somehow limited by the lack of genetic manipulation toolkits for Magentospirillum magneticum AMB-1.

What’s worth mentioning was the diversity of ideas regarding the application of magnetotactic bacteria proposed by a great variety of iGem teams (See Table 1). This even led to one mentioning on 2009 iGem official website about “magnetic bacteria” as one of the Ideas for Bacteria.

File:Table 1.gif

Table 1: Magneto-related iGem teams in the history.

(2) Obstacle 1: Hard to Cultivate Yes, we have heard your voice fellow iGemers. We knew from your previous/current brainstorming pages that the main reason for your giving in lies mostly in the STRINGENT growth conditions required to successfully cultivating these bacteria. It is a good reason, indeed.

There are only a few magnetotactic strains capable of pure culture. Among them, Magnetospirillum magnetotacticum MS-1 http://jb.asm.org/cgi/content/abstract/140/2/720 2, Magnetospirillum gryphiswalden MSR-1 http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=ENV&recid=3741674&q=The+isolation+of+a+new+magnetic+spirillum.&uid=791101605&setcookie=yes 3, and Magnetospirillum magneticum AMB-1 http://www.springerlink.com/content/x942j5lw60j48865/ 4 are used most frequently in research on magnetotactic bacteria. In recent years, significantly improved cultivating methods for MS-1 http://nopr.niscair.res.in/bitstream/123456789/8487/1/IJEB 48(5) 518-523.pdf 5, MSR-1 http://www.microbialcellfactories.com/content/9/1/99 6, and AMB-1 http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=104444 7 have also been achieved. These have lead to the field buzzing about the realization of applications spanning fMRI reporting, tumor targeting, etc., using magnetites produced by these cells [[http://www.nature.com/news/2004/040906/full/news040906-11.html 8], [http://ijr.sagepub.com/content/28/4/571.short 9], [http://onlinelibrary.wiley.com/doi/10.1002/mrm.21606/pdf 10], [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5627105 11]].

To be honest, we also encountered some problems in cultivating strain AMB-1, but finally a complete cultivating method has been established here. See Chassis for more details.

(3) Obstacle 2: Lack of Genetic Toolbox Sadly, for previous iGemers, there were way too many obstacles in front of their magnetic fantasies. This has lead to the fact that few precedents ever proceeded into thinking and encountering the BIG questions, that is, the lack of ANY available genetic tools in Parts Registry!

File:Tranformation of MG, MM, and AMB-1.gif

Fig.1 Transformation of MSR-1, AMB-1 and MS-1, plated on ACA medium http://www.springerlink.com/content/w5jvl853xhyrwdny/ 12

To this date, provided with our utmost efforts in literature study, we've found, from previous research on magnetotactic bacteria, two strains are capable of undergoing transformation--MSR-1 http://www.springerlink.com/content/w5jvl853xhyrwdny/ 12, and AMB-1 http://jb.asm.org/cgi/content/abstract/174/9/2748 13.

For the genetic manipulating system on MSR-1, Dr. Dirk Schüler, et al. has developed a stable and efficient method by conjugation with Escherichia coli S17-1. Plasmids used in the system are derivatives of pBBR1MCS (broad-host-range vectorhttp://www.sciencedirect.com/science/article/pii/0378111995005841 14)

In AMB-1, Dr. Long-Fei Wu used pBBR111, a pBBR1MCS derivative harboring strong, inducible promoter P_tac, to construct an expression vector http://www.sciencedirect.com/science/article/pii/S0022283610004900 15, achieving transformation by conjugation between Escherchia coli WM3064 and AMB-1 (a method developed by Arash Komeili, et al.)http://www.pnas.org/content/101/11/3839 16.

Those great examples truly set lights on successfully establishing a new chassis for magnetism in Parts Registry.

                                          BUT WE AIM EVEN HIGHER!

Works from Matsunaga's lab revealed that transformation of AMB-1 by electroporation is feasible http://aem.asm.org/cgi/content/short/69/7/4274 17. They enable a door to faster expression platform, avoiding drawbacks with conjugation, such as but not limited to: time consumption, mob gene and oriT restriction, requirement of specific E. coli strain, etc...

Furthermore, compared with the relatively adventurous adaptation of P_tac as promoter for exogenous gene expression, endogenous promoters identified from genomic DNA of magnetotactic strains provide more reliable and efficient ways. Recently identified endogenous promoters from MSR-1 http://aem.asm.org/cgi/content/abstract/75/12/4206 18 still lack thorough verification. Yet another endogeneous promoters system in AMB-1 http://www.sciencedirect.com/science/article/pii/S0006291X0502440X 19 has been well characterized [[http://aem.asm.org/cgi/content/abstract/76/4/1152 20], [http://aem.asm.org/cgi/content/abstract/72/1/465 21], [http://aem.asm.org/cgi/content/abstract/70/5/2880 22], [http://aem.asm.org/cgi/content/abstract/74/11/3342 23], [http://aem.asm.org/cgi/content/abstract/76/17/5785 24]]. See Chassis for elaborations.

Equipped with these knowledge bases, we are now confident in saying that "the world is ready for a new chassis"!

**Q3: What's The Scientific Niche For Our Project? We ARE serious about that...**

(1) People Are Whispering About Opto, Bac, and Remote!

Okay, let's proceed to the core part of this page. Now, let us show you the scientific context of our project and related or competitive neuroscientific achievements we indispensably need to compare ours with.

(2) The Whole Field Is Buzzing

Let us show you these four references published very recently.

[http://www.nature.com/neuro/journal/v14/n2/abs/nn.2730.html A wireless multi-channel neural amplifier for freely moving animals]
[http://www.sciencemag.org/content/332/6037/1571.abstract Inducing Sleep by Remote Control Facilitates Memory Consolidation in Drosophila]
[http://news.sciencemag.org/sciencenow/2011/08/mind-altering-bugs.html?ref=hp Mind-Altering Bugs]
[http://www.sciencemag.org/content/322/5900/395.abstract Optical Switches for Remote and Noninvasive Control of Cell Signaling]

Stop now. Please go back and click on those links. Three of them are from Science, the other one, Nature Neuroscience.

Take a deep consideration. What CORRELATIONS do you see from them?

Fig.2 Fantastic quratet, four researches showing interconnected scientific fantasies that contextualizes our project.

To us, they collectively mean that a whole story is currently divided into four parts, with different experts focusing on diverse issues, however laterally interconnected, or to say, interfaced, to weave a complete scientific fantasy.

Systems neuroscientists tried to develop a wireless recording module which also equips itself with multi-channel characteristics.

Neurophysiologists had the same dream on being wireless, but shifting from "recording" to "inducing (stimulating)".

Microbiologists ran into discovering "gut feelings" with mind-altering bacteria living on mammalian intestinal lumen.

Finally, Cell Biologists linked the whole story in a subtle manner, providing optogenetic systems on manipulating cell signalling.

They interface with each other on concepts of being wireless, stimulative, bacterial, and light-associated. However, they provided no direct link between bacteria and optogenetics. This leaves space for us to fit in the last of the five missing puzzles.

From this point on, an "optogenetics-facilitated neurostimulting system using wireless-controlled bacterial species as light source" will make the whole story complete.

(3) Among The Field Of Optogenetics: From 2-D to genuine 3-D matrices

File:2D matrix stimulators.gif

In the graph shown above, neuroscientists along with electronic engineers have developed an 2-dimensional optogenetic stimulation matrix using aligned LED arrays. This has been one of the greatest frontiers in neuroscientific methodologies.

However, The completion of project "Tailoring Your Avatar" (i. e., optomagnetic bacteria) will enable 3-dimensional presentation of stimulation-enabling optomagnetic bacteria by use of 2-D injection matrices with deep penetration following inject-and-withdraw cycles.

Retrieved from "http://2011.igem.org/Team:NYMU-Taipei/background-review"

@@ Line 1: / Line 1: @@
-{{:Team:NYMU-Taipei/Templates/idea/Header}}
+{{:Team:NYMU-Taipei/Templates/Header/menubar}}
-----
-----
-----
-  '''<font color=red><font size=5>CLAIM FOR POTENTIAL CONFLICT OF INTEREST</font></font><font color=gray>...with the</font> <font color=blue>COOLEST</font> <font color=gray>guys around the world</font>'''
-----
-----
-----
-='''<font size=4>What are magnetotactic bacteria? Why do we choose ''Magnetospirillum magneticum'' AMB-1?</font>'''=
 ----
-==<font color=blue>'''Brief in One Sentence:'''</font>==
-Magnetotactic bacteria, also known as magnetic bacteria, are an evolutionarily diverse group [[http://www.sciencemag.org/content/259/5096/803.short 1]] of motile, Gram-negative eubacteria presenting magnetotaxis.
+                '''<font color=red><font size=6>CLAIMS FOR POTENTIAL CONFLICT OF INTEREST</font></font>
+                                <font color=gray>...with those</font> <font color=blue>COOLEST</font> <font color=gray>guys around the world</font>'''
-----
+=='''<font size=5><font color=crimson>Q1: What are magnetotactic bacteria?</font></font>'''==
-=='''Hard to Cultivate?!!'''==
+<font size=4><font color=GREEN>'''One Sentence In Brief:'''</font></font>
-However, strains capable of pure culture are only a few. Among them, ''Magnetospirillum magnetotacticum'' MS-1 [[http://jb.asm.org/cgi/content/abstract/140/2/720 2]], ''Magnetospirillum gryphiswalden'' MSR-1 [[http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=ENV&recid=3741674&q=The+isolation+of+a+new+magnetic+spirillum.&uid=791101605&setcookie=yes 3]], and ''Magnetospirillum magneticum'' AMB-1 [[http://www.springerlink.com/content/x942j5lw60j48865/ 4]] are used most frequently in researches on magnetotactic bacteria. In recent years, improved cultivation of ''Magnetospirillum magnetotacticum'' MS-1 [[http://nopr.niscair.res.in/bitstream/123456789/8487/1/IJEB%2048(5)%20518-523.pdf 5]], ''Magnetospirillum gryphiswalden'' MSR-1 [[http://www.microbialcellfactories.com/content/9/1/99 6]], and ''Magnetospirillum magneticum'' AMB-1 [[http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=104444 7]] have also been achieved, respectively. These have lead to the field buzzing about the realization of applications spanning fMRI reporting, tumor targeting, etc., using magnetites produced by these cells [[http://www.nature.com/news/2004/040906/full/news040906-11.html 8], [http://ijr.sagepub.com/content/28/4/571.short 9], [http://onlinelibrary.wiley.com/doi/10.1002/mrm.21606/pdf 10], [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5627105 11]].
+[[Image: AMB-1.gif|thumb|300px|right|''Magnetospirillum magneticum'' AMB-1 under cryotomography and 3-D reconstruction]]
+Magnetotactic bacteria, also known as magnetic bacteria, are an evolutionarily diverse group [[http://www.sciencemag.org/content/259/5096/803.short 1]] of motile, Gram-negative eubacteria expressing magnetotaxis.
-----
+==<font size=5><font color=crimson>'''Q2: Community Yearning for The Strain?'''</font></font>'''<font size=4><font color=gray><br><center>We weren't wrong, were we?<font color=orange>: )</font></center></font></font>'''==
-=='''Wait! Let's Look Back in the iGem History.'''==
+During our review on past iGem projects, we concluded, to more or less an extend, teams dreaming for magnetotaxis have concluded in using this strain......yet only two team ever actually tried. One of them was '''''[https://2006.igem.org/Duke_2006 Duke University 2006]''''', the other being '''''us'''''.
+Below are several arguments about the choice of this strain and reasons stopping previous iGem teams / supporting us in standing soundly on this step.
+<font size=4><font color=GREEN>'''(1) So Let's Talk About The iGem History'''</font></font>
+Throughout the history of iGem, we have gained notice from exhaustive online searching that a remarkable number of previous iGem teams have continually proposed projects related to '''magnetosome''', '''magnetospirillum''', and '''magnetotaxis''' every year around the world.
+Among these respectful pioneers, Duke University had made their magnetotactic bacteria-based project to the official jamboree titled “Bacterial Dynamo”, focusing on the use of AMB-1 as AC voltage generator [[http://www.duke.edu/~fr7/2007_Reza_et_al_IET_Synthetic_Biology.pdf 2]], but somehow limited by the lack of genetic manipulation toolkits for ''Magentospirillum magneticum'' AMB-1.
+What’s worth mentioning was the diversity of ideas regarding the application of magnetotactic bacteria proposed by a great variety of iGem teams (See Table 1). This even led to one mentioning on 2009 iGem official website about “magnetic bacteria” as one of the [https://2009.igem.org/Ideas_for_Bacteria. Ideas for Bacteria].
+[[Image: Table_1.gif|thumb|center|700px|Table 1: Magneto-related iGem teams in the history.]]
+<font size=4><font color=green>'''(2) Obstacle 1: Hard to Cultivate'''</font></font>
+Yes, we have heard your voice fellow iGemers. We knew from your previous/current brainstorming pages that the main reason for your giving in lies mostly in the '''''STRINGENT''''' growth conditions required to successfully cultivating these bacteria. It is a good reason, indeed.
+There are only a few magnetotactic strains capable of pure culture. Among them, ''Magnetospirillum magnetotacticum'' MS-1 [[http://jb.asm.org/cgi/content/abstract/140/2/720 2]], ''Magnetospirillum gryphiswalden'' MSR-1 [[http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=ENV&recid=3741674&q=The+isolation+of+a+new+magnetic+spirillum.&uid=791101605&setcookie=yes 3]], and ''Magnetospirillum magneticum'' AMB-1 [[http://www.springerlink.com/content/x942j5lw60j48865/ 4]] are used most frequently in research on magnetotactic bacteria. In recent years, significantly improved cultivating methods for MS-1 [[http://nopr.niscair.res.in/bitstream/123456789/8487/1/IJEB%2048(5)%20518-523.pdf 5]], MSR-1 [[http://www.microbialcellfactories.com/content/9/1/99 6]], and AMB-1 [[http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=104444 7]] have also been achieved. These have lead to the field buzzing about the realization of applications spanning fMRI reporting, tumor targeting, etc., using magnetites produced by these cells [[http://www.nature.com/news/2004/040906/full/news040906-11.html 8], [http://ijr.sagepub.com/content/28/4/571.short 9], [http://onlinelibrary.wiley.com/doi/10.1002/mrm.21606/pdf 10], [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5627105 11]].
+To be honest, we also encountered some problems in cultivating strain AMB-1, but finally a complete cultivating method has been established here. See '''[https://2011.igem.org/Team:NYMU-Taipei/chassis Chassis]''' for more details.
+<font size=4><font color=green>'''(3) Obstacle 2: Lack of Genetic Toolbox'''</font></font>
+Sadly, for previous iGemers, there were way too many obstacles in front of their magnetic fantasies. This has lead to the fact that few precedents ever proceeded into thinking and encountering the '''BIG''' questions, that is, the lack of <font color=red>'''''ANY'''''</font> available genetic tools in Parts Registry!
+[[Image:tranformation of MG, MM, and AMB-1.gif|thumb|right|300px||'''Fig.1''' Transformation of MSR-1, AMB-1 and MS-1, plated on ACA medium [[http://www.springerlink.com/content/w5jvl853xhyrwdny/ 12]]]]
+To this date, provided with our utmost efforts in literature study, we've found, from previous research on magnetotactic bacteria, two strains are capable of <font color=blue>'''''undergoing transformation'''''</font>--'''MSR-1''' [[http://www.springerlink.com/content/w5jvl853xhyrwdny/ 12]], and '''AMB-1''' [[http://jb.asm.org/cgi/content/abstract/174/9/2748 13]].
+For the genetic manipulating system on MSR-1, Dr. Dirk Schüler,'' et al.'' has developed a stable and efficient method by conjugation with ''Escherichia coli'' S17-1. Plasmids used in the system are derivatives of pBBR1MCS (broad-host-range vector[[http://www.sciencedirect.com/science/article/pii/0378111995005841 14]])
+In AMB-1, Dr. Long-Fei Wu used pBBR111, a pBBR1MCS derivative harboring strong, inducible promoter P<sub>tac</sub>, to construct an expression vector [[http://www.sciencedirect.com/science/article/pii/S0022283610004900 15]], achieving transformation by conjugation between ''Escherchia coli'' WM3064 and AMB-1 (a method developed by Arash Komeili'', et al.'')[[http://www.pnas.org/content/101/11/3839 16]].
+Those great examples truly set lights on successfully establishing a new chassis for magnetism in Parts Registry.
+                                           <font color=magenta>'''BUT WE AIM EVEN HIGHER!'''</font>
+Works from Matsunaga's lab revealed that transformation of AMB-1 by <font color=blue>'''electroporation is feasible'''</font> [[http://aem.asm.org/cgi/content/short/69/7/4274 17]]. They enable a door to faster expression platform, avoiding drawbacks with conjugation, such as but not limited to: time consumption, mob gene and oriT restriction, requirement of specific ''E. coli'' strain, etc...
+Furthermore, compared with the relatively adventurous adaptation of P<sub>tac</sub> as promoter for exogenous gene expression, endogenous promoters identified from genomic DNA of magnetotactic strains provide more reliable and efficient ways. Recently identified endogenous promoters from MSR-1 [[http://aem.asm.org/cgi/content/abstract/75/12/4206 18]] still lack thorough verification. Yet another endogeneous promoters system in AMB-1 [[http://www.sciencedirect.com/science/article/pii/S0006291X0502440X 19]] has been well characterized [[http://aem.asm.org/cgi/content/abstract/76/4/1152 20], [http://aem.asm.org/cgi/content/abstract/72/1/465 21], [http://aem.asm.org/cgi/content/abstract/70/5/2880 22], [http://aem.asm.org/cgi/content/abstract/74/11/3342 23], [http://aem.asm.org/cgi/content/abstract/76/17/5785 24]]. See '''''[https://2011.igem.org/Team:NYMU-Taipei/chassis Chassis]''''' for elaborations.
+Equipped with these knowledge bases, we are now confident in saying that <font color=red>'''"the world is ready for a new chassis"'''</font>!
+=='''<font size=5><font color=crimson>Q3: What's The ''Scientific Niche'' For Our Project?</font></font>'''     '''<font size=4><font color=gray> We ''ARE'' serious about that...</font></font>'''==
+<font size=4><font color=Green>'''(1) People Are Whispering About ''Opto'', ''Bac'', and ''Remote''!'''</font></font>
+Okay, let's proceed to the core part of this page. Now, let us show you the scientific context of our project and related or competitive neuroscientific achievements we indispensably need to compare ours with.
+<font size=4><font color=Green>'''(2) The Whole Field Is Buzzing'''</font></font>
+Let us show you these four references published very recently.
+#<font size=4>'''[http://www.nature.com/neuro/journal/v14/n2/abs/nn.2730.html A wireless multi-channel neural amplifier for freely moving animals]'''</font>
+#<font size=4>'''[http://www.sciencemag.org/content/332/6037/1571.abstract Inducing Sleep by Remote Control Facilitates Memory Consolidation in Drosophila]'''</font>
+#<font size=4>'''[http://news.sciencemag.org/sciencenow/2011/08/mind-altering-bugs.html?ref=hp Mind-Altering Bugs]'''</font>
+#<font size=4>'''[http://www.sciencemag.org/content/322/5900/395.abstract Optical Switches for Remote and Noninvasive Control of Cell Signaling]'''</font>
+'''Stop now.''' Please go back and click on those links. Three of them are from ''Science'', the other one, ''Nature Neuroscience''.
+Take a deep consideration. What <font color=red>'''''CORRELATIONS'''''</font> do you see from them?
+[[Image:fantastic quartet.jpg|thumb|right|600px||'''Fig.2'''  Fantastic quratet, four researches showing interconnected scientific fantasies that contextualizes our project.]]
+To us, they collectively mean that a whole story is currently divided into four parts, with different experts focusing on diverse issues, however laterally interconnected, or to say, interfaced, to weave a complete scientific fantasy.
+<font color=olive>'''Systems neuroscientists'''</font> tried to develop a <font color=olive>'''wireless'''</font> recording module which also equips itself with <font color=olive>'''multi-channel'''</font> characteristics.
+<font color=MediumVioletRed>'''Neurophysiologists'''</font> had the same dream on being <font color=MediumVioletRed>'''wireless'''</font>, but shifting from '''"recording"''' to '''"inducing (stimulating)"'''.
+<font color=maroon>'''Microbiologists'''</font> ran into  discovering '''"gut feelings"''' with <font color=maroon>'''mind'''</font>-altering <font color=maroon>'''bacteria'''</font> living on mammalian intestinal lumen.
+Finally, <font color=Indigo>'''Cell Biologists'''</font> linked the whole story in a subtle manner, providing <font color=Indigo>'''optogenetic'''</font> systems on manipulating <font color=Indigo>'''cell signalling'''</font>.
+They interface with each other on concepts of being '''wireless''', '''stimulative''', '''bacterial''', and '''light-associated'''. However, they provided '''no direct link''' between bacteria and optogenetics. This leaves space for us to fit in the last of the five missing puzzles.
+From this point on, an <font size=4><font color=navy>"'''optogenetics'''-facilitated '''neurostimulting''' system using '''wireless'''-controlled '''bacterial''' species as light source"</font></font> will make the whole story complete.
+<font size=4><font color=green>'''(3) Among The Field Of Optogenetics: <font color=darkslategray>From 2-D to ''genuine'' 3-D matrices</font>'''</font></font>
+[[Image: 2D matrix stimulators.gif|thumb|center|400px|]]
+In the graph shown above, neuroscientists along with electronic engineers have developed an 2-dimensional optogenetic stimulation matrix using aligned LED arrays. This has been one of the greatest frontiers in neuroscientific methodologies.
+However, The completion of project "'''Tailoring Your Avatar'''" (i. e., optomagnetic bacteria) will enable 3-dimensional presentation of stimulation-enabling optomagnetic bacteria by use of 2-D injection matrices with deep penetration following inject-and-withdraw cycles.