Team:Wash U/Project

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== '''Analysis''' ==
== '''Analysis''' ==
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The tissue flask experiment was an interesting way to observe the effects of a full knockout of the Light Harvesting Antenna Complex 2 (LH2) vs the Wild Type in array of photobioreactors.  A couple of interesting conclusions can be drawn from this data regarding the optimization of Light Harvesting Antenna size for photobioreactors.  <br>
+
The tissue flask experiment was an interesting way to observe the effects of a full knockout of the Light Harvesting Antenna Complex 2 (LH2) vs the Wild Type in array of photobioreactors.  A couple of interesting conclusions can be drawn from this data regarding the optimization of Light Harvesting Antenna size for photobioreactors.  <br><br>
-
The most striking difference between the Wild Type Rhodobacter Sphaeroides 2.41 and DBCOmega (LH2 knockout) growth patterns is that the first flask in the WT (closest to the light source) grew less than the second flask, while the converse was true in DBCOmega'''(3D bar graphs)'''.  This can be attributed to the photosystem saturation curves for the respective cultures.  The Wild Type has an LH2 complex, meaning that their antenna size is larger and that their photosystem will be saturated at lower light intensities than the LH2 deficient mutant.  We observed that the incident light intensity used in this experiment led to oversaturation for the first WT tissue flask and resulted in growth-inhibiting photodamage, as is evidenced by its lesser growth relative to the second culture.  In contrast, photodamage was not observed in DBCOmega as is evidenced by the first tissue flask that grew at the fastest respective rate.  Furthermore, it appears that this photodamage slowed the growth of the first WT tissue flask to the point that the OD of this tissue flask was nearly equal to that of DBCOmega after 5 days of growth(.987 vs. .967) '''(flask 1 graph)'''. This effect of photodamage under high light intensities is one that we sought to minimize in the design of our synthetic regulation for the pucB/A genes.  <br>
+
The most striking difference between the Wild Type Rhodobacter Sphaeroides 2.41 and DBCOmega (LH2 knockout) growth patterns is that the first flask in the WT (closest to the light source) grew less than the second flask, while the converse was true in DBCOmega'''(3D bar graphs)'''.  This can be attributed to the photosystem saturation curves for the respective cultures.  The Wild Type has an LH2 complex, meaning that their antenna size is larger and that their photosystem will be saturated at lower light intensities than the LH2 deficient mutant.  We observed that the incident light intensity used in this experiment led to oversaturation for the first WT tissue flask and resulted in growth-inhibiting photodamage, as is evidenced by its lesser growth relative to the second culture.  In contrast, photodamage was not observed in DBCOmega as is evidenced by the first tissue flask that grew at the fastest respective rate.  Furthermore, it appears that this photodamage slowed the growth of the first WT tissue flask to the point that the OD of this tissue flask was nearly equal to that of DBCOmega after 5 days of growth(.987 vs. .967) '''(flask 1 graph)'''. This effect of photodamage under high light intensities is one that we sought to minimize in the design of our synthetic regulation for the pucB/A genes.  <br><br>
-
A second interesting observation from a comparison of the WT and DBCOmega experiments is that the 3rd tissue flask in each had almost identical growth rates '''(3rd tissue flask)''', while the DBCOmega 4th and 5th tissue flask outperformed that of the WT '''(4th and 5th tissue flask graphs)'''.  This can simply be attributed to the higher density of cells in the 1st and 2nd flask of the WT that led to an overall lesser quantity of photons passing through to the 4th and 5th flasks in the WT experiment and likely resulting in heterotrophic growth.  This can be seen by viewing the absolute irradiance data (incident light intensity at a given wavelength) after the third culture for the WT '''(point 3, WT Irradiance)'''.  This decrease in irradiance is the most pronounced for the LH2 absorption bands at 800 and 850 nm, as was expected. <br>
+
A second interesting observation from a comparison of the WT and DBCOmega experiments is that the 3rd tissue flask in each had almost identical growth rates '''(3rd tissue flask)''', while the DBCOmega 4th and 5th tissue flask outperformed that of the WT '''(4th and 5th tissue flask graphs)'''.  This can simply be attributed to the higher density of cells in the 1st and 2nd flask of the WT that led to an overall lesser quantity of photons passing through to the 4th and 5th flasks in the WT experiment and likely resulting in heterotrophic growth.  This can be seen by viewing the absolute irradiance data (incident light intensity at a given wavelength) after the third culture for the WT '''(point 3, WT Irradiance)'''.  This decrease in irradiance is the most pronounced for the LH2 absorption bands at 800 and 850 nm, as was expected. <br><br>
-
'''Thomas, add is some further comments about the sprectroradiometer stuff.  Specifically about how it changes in the WT vs. that of DBCOmega using some specific examples on the graphs'''<br>
+
'''Thomas, add is some further comments about the sprectroradiometer stuff.  Specifically about how it changes in the WT vs. that of DBCOmega using some specific examples on the graphs'''<br><br>
-
Overall, the cumulative culture growth of the WT exceeded that of DBCOmega '''(The 2d bar graphs)''' due to the performance of the second tissue flask of the WT relative to that of DBCOmega '''(Graph of tissue flask 2)''' despite and partly due to the photodamage that occurred in tissue flask 1 for the WT.  <br>
+
Overall, the cumulative culture growth of the WT exceeded that of DBCOmega '''(The 2d bar graphs)''' due to the performance of the second tissue flask of the WT relative to that of DBCOmega '''(Graph of tissue flask 2)''' despite and partly due to the photodamage that occurred in tissue flask 1 for the WT.  <br><br>
'''It is an interesting exercise to model how our mutant system would perform under these same conditions: Thomas add in some comments about that referencing that diagram (and upload it when you are done with it).'''
'''It is an interesting exercise to model how our mutant system would perform under these same conditions: Thomas add in some comments about that referencing that diagram (and upload it when you are done with it).'''
<br>
<br>

Revision as of 00:44, 20 October 2009


Introduction

Our project goal is to maximize the photosynthetic productivity for a series of photobioreactors containing Rhodobacter sphaeroides under both high and low light intensities by synthetically regulating the size of the light-harvesting antenna complex LH2. We chose to undertake such a project in R. sphaeroides due to its well-characterized photosynthetic and genetic system.

The antenna system functions to expand the spectrum of light available for photosynthesis by absorbing different wavelengths than that of the reaction center. Essentially, it is like the dish around the main receiver of any antenna. Marine bacteria, such as R. sphaeroides, evolved very large antenna complexes to absorb light in a natural environment where there is great competition for photons. As a result, the photosynthetic machinery is saturated at low light intensities in a synthetic non-competitive environment, such as a bioreactor. This causes up to 95% of incidental photons to be dissipated as heat or fluorescence by bacteria through a process called Non-Photochemical Quenching (NPQ) (Mussgnug et al., 2007). In essence, these photons are being wasted as NPQ reduces light penetration into and across bioreactors and starves the shaded cells for for photons. One method that has been shown to improve photosynthetic efficiency is the reduction of light-harvesting antenna sizes (Polle et al., 2002, Mussgnug et al., 2007). Though, current approaches to this end are difficult to precisely control from the perspective of biological engineering and synthetic biology.

Our intention is to create a dynamic system to vary antenna size that is dependent on incident light intensity and that can be readily optimized using bioengineering principles. This synthetic regulation of the LH2 complex should result in the bacteria grown under high light intensities expressing fewer LH2 complexes than the cells that are more shaded, leading to a reduction of wasted incident photons while maintaining a high overall absorbance across subsequent bioreactors. Consequently, we expect to see an increase in the total photosynthetic productivity for our mutant Rhodobacter sphaeroides when compared to the wild type grown under similar conditions.


Slide10.jpg Slide09.jpg



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Organism

Rhodobacter sphaeroides is a purple Alphaproteobacteria. It is flexible metabolically and can grow heterotrophically via aerobic and anaerobic respiration, as well as phototrophically under anaerobic conditions with light.

R. sphaeroides is one of the best understood photosynthetic organisms. The photosystem is located in intracytoplasmic membrane invaginations and the main components are the Light Haresting Complex 2 (LH2), Light Harvesting Complex 1 (LH1), and the Reaction Center (RC). These pigment-protein complexes non-covalently bind bacteriochlorophylls and carotenoids. LH1 and RC make up the core complex and are often found in the ratio 1:1. LH2 is more peripheral and naturally ranges in the ratio to LH1/RC of 3.0:1 to 6.7:1 under varying light conditions (Scheuring et al., 2005). LH2 absorbs photons maximally at the wavelength of 842 nm and funnels its energy to LH1 and the reaction center for photochemistry. (Scheuring et al., 2005).

The two subunits of LH2 are coded for by the pucB/A genes and are naturally promoted by the puc promoter.

R sphaeroides photosystem.png source:Sener et al.2007



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Online Resources for R. sphaeroides

[http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=272943 Codon Usage Table for R. sphaeroides 2.41]
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=18843 R. sphaeroides 2.41 NCBI Genome Tools]
[http://archaea.ucsc.edu/cgi-bin/hgPcr?wp_target=&db=0&org=Rhodobacter+sphaeroides+2+4+1&wp_f=&wp_r=&wp_size=2000&wp_perfect=15&wp_good=15&wp_showPage=true&hgsid=159191 In silico PCR of R. sphaeroides 2.41 genome]

Regulation

full report
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Results

Tissue Flask 1.png Tissue Flask 2.png Tissue Flask 3.png Tissue Flask 4.png Tissue Flask 5.png
3D 241.png 3D DBCOmega.png Bar 241.png Bar DBCOmega.png




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Analysis

The tissue flask experiment was an interesting way to observe the effects of a full knockout of the Light Harvesting Antenna Complex 2 (LH2) vs the Wild Type in array of photobioreactors. A couple of interesting conclusions can be drawn from this data regarding the optimization of Light Harvesting Antenna size for photobioreactors.

The most striking difference between the Wild Type Rhodobacter Sphaeroides 2.41 and DBCOmega (LH2 knockout) growth patterns is that the first flask in the WT (closest to the light source) grew less than the second flask, while the converse was true in DBCOmega(3D bar graphs). This can be attributed to the photosystem saturation curves for the respective cultures. The Wild Type has an LH2 complex, meaning that their antenna size is larger and that their photosystem will be saturated at lower light intensities than the LH2 deficient mutant. We observed that the incident light intensity used in this experiment led to oversaturation for the first WT tissue flask and resulted in growth-inhibiting photodamage, as is evidenced by its lesser growth relative to the second culture. In contrast, photodamage was not observed in DBCOmega as is evidenced by the first tissue flask that grew at the fastest respective rate. Furthermore, it appears that this photodamage slowed the growth of the first WT tissue flask to the point that the OD of this tissue flask was nearly equal to that of DBCOmega after 5 days of growth(.987 vs. .967) (flask 1 graph). This effect of photodamage under high light intensities is one that we sought to minimize in the design of our synthetic regulation for the pucB/A genes.

A second interesting observation from a comparison of the WT and DBCOmega experiments is that the 3rd tissue flask in each had almost identical growth rates (3rd tissue flask), while the DBCOmega 4th and 5th tissue flask outperformed that of the WT (4th and 5th tissue flask graphs). This can simply be attributed to the higher density of cells in the 1st and 2nd flask of the WT that led to an overall lesser quantity of photons passing through to the 4th and 5th flasks in the WT experiment and likely resulting in heterotrophic growth. This can be seen by viewing the absolute irradiance data (incident light intensity at a given wavelength) after the third culture for the WT (point 3, WT Irradiance). This decrease in irradiance is the most pronounced for the LH2 absorption bands at 800 and 850 nm, as was expected.

Thomas, add is some further comments about the sprectroradiometer stuff. Specifically about how it changes in the WT vs. that of DBCOmega using some specific examples on the graphs

Overall, the cumulative culture growth of the WT exceeded that of DBCOmega (The 2d bar graphs) due to the performance of the second tissue flask of the WT relative to that of DBCOmega (Graph of tissue flask 2) despite and partly due to the photodamage that occurred in tissue flask 1 for the WT.

It is an interesting exercise to model how our mutant system would perform under these same conditions: Thomas add in some comments about that referencing that diagram (and upload it when you are done with it).
Final conclusion




Future Work

-tissue flask w mutant -characterize puc promoter under light conditions and additional oxygen tensions

  • What we tried to do?
  1. What actually happened?
  • Ways to improve, redo parts of our experiment differently
  • What further should be done to our end product to further its development, related back to what we initially tried to do?
  • What are possible biofuel applications and how could our system be used to improve existing biofuels?


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References

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