Difference between revisions of "Team:IISER-Mohali-INDIA/Co-culture"

Line 121: Line 121:
 
</table>
 
</table>
 
</center>
 
</center>
 +
<br/><br/>
 +
<section><div class="page-title"><h6>Culturing on paper</h6>
 +
<h3>The study of bacterial growth has been one of the most standard approaches in the field of microbiology
 +
and Escherichia coli as a workhorse has been considerably exploited for its use in many molecular
 +
biology techniques. The need of a nutrient rich solid or liquid medium is of utmost importance for the
 +
sustenance of bacterial growth. However, people over the past few years have tried using paper based
 +
growth supports for bacteria. Paper is a ubiquitous, inexpensive, recyclable, portable, flexible and
 +
disposable material. But paper can’t be directly used for culturing microbes due to certain constraints
 +
such as the requirement of a nutrient rich medium for growth, sample dispersion and absorption by the
 +
paper, etc. Hence, paper needs to be synthetically modified for sustaining the growth of microbes. The
 +
construction of in-vitro biological systems is a remarkable area of study in synthetic biology and has
 +
been widely exploited and implemented for this approach. These systems make use of strong promoters
 +
and translation initiation sequences for the expression of most of the individual genes encoded on the
 +
genome of interest. In this, the microbial culture after having been grown to a suitable density, is
 +
subjected to lysis and the lysate is added to the synthetically modified paper and subjected to freeze
 +
drying. At the time of use, the components on the paper can be revived by adding distilled water or a
 +
suitable buffer and heating the paper at an optimum growth temperature followed by adding the
 +
components (compatibility of the components used for the reaction is a very important factor) required
 +
for transcription-translation and the required reaction can hence be carried on the paper. Fine tuning of
 +
the circuit and improvisation in the design of the paper being used for the reaction needs to be taken
 +
care of to improve the efficiency of the reaction.</h3></section>
 +
<br/>
 
<section>
 
<section>
 
<h3>References:</h3>
 
<h3>References:</h3>
Line 136: Line 158:
 
<h4>Wolfe-Simon, F., Blum, J. S., Kulp, T. R., Gordon, G. W., Hoeft, S. E., Pett-Ridge, J., ...& Anbar, A. D. (2011). A bacterium that can grow by using arsenic instead of phosphorus. <i>science</i>, 332(6034), 1163-1166.
 
<h4>Wolfe-Simon, F., Blum, J. S., Kulp, T. R., Gordon, G. W., Hoeft, S. E., Pett-Ridge, J., ...& Anbar, A. D. (2011). A bacterium that can grow by using arsenic instead of phosphorus. <i>science</i>, 332(6034), 1163-1166.
 
</h4></section><br/><br/>
 
</h4></section><br/><br/>
−
<section><h6 class="page-title">------- Rough work done to generate above data -----</h6></section><br />
 
−
<section><h3>• Acetaldehyde</h3>
 
−
<h4>Degradation of Acetaldehyde and Its Precursors by <i>Pelobactercarbinolicus</i> and <i>P. acetylenicus</i></h4>
 
−
<h4><b>Citation</b>: Schmidt A, Frensch M, Schleheck D, Schink B, Müller N (2014) Degradation of Acetaldehyde and Its Precursors by <i>Pelobactercarbinolicus</i> and <i>P. acetylenicus</i>. PLoSONE9(12): e115902. https://doi.org/10.1371/journal.pone.0115902
 
−
</h4>
 
−
<h3>• Nitric oxide (NO) and carbon dioxide (CO2)  </h3>
 
−
<h4>Denitrifying bacteria are bacteria capable of performing denitrification as part of the nitrogen cycle. Denitrifying bacteria include several species of <i>Pseudomonas, Alkaligenes ,Bacillus</i></h4>
 
−
<h4>A marine microalga, <i>(Dunaliellatertiolecta)</i> strain NOA-113, was found to simultaneously eliminate nitric oxide (NO) and carbon dioxide (CO2)</h4>
 
−
<h4><b>Citation</b>: Chem TechnolBiotechnol 80:483–494 (2005) DOI: 10.1002/jctb.1260</h4>
 
−
<h3>• Mercury</h3>
 
−
<h4>Organisms- <i>Microbacteriumoxydans HG3, Ochrobactrum sp. strain HG16, Lysinibacillus sp. strain HG17, Bacillus sp. strain CM111, and Serratiamarcescens HG19</i></h4>
 
−
<h4><b>Citation</b>: Appl. Environ. Microbiol. February 2012 vol. 78 no. 4 1097-1106</h4>
 
−
<h3>• Xylene</h3>
 
−
<h4>Organisms- <i>Pandoraea sp.</i> strain WL1</h4>
 
−
<h4>Paper- Degradation pathway and kinetic analysis for p-xylene removal by a novel Pandoraea sp. strain WL1 and its application in a biotrickling filter</h4>
 
−
<h4><b>Citation</b>:J Hazard Mater. 2015 May 15;288:17-24. doi: 10.1016/j.jhazmat.2015.02.019. Epub 2015 Feb 7.
 
−
</h4>
 
−
<h3>• Arsenic</h3>
 
−
<h4>Organism-  <i>Halomonadaceaebacterium</i> GFAJ-1</h4>
 
−
<h4>Paper-  Arsenic-eating microbe may redefine chemistry of life (http://www.nature.com/news/2010/101202/full/news.2010.645.html)</h4>
 
−
<h3>• Carbon monoxide</h3>
 
−
<h4>Organism-<i>Clostridium formicoaceticum ,C. thermoaceticum, Chlorella vutgaris</i> (algae)</h4>
 
−
<h4><b>Citation</b>: Gabriele and Rudolf K. ThauerJ. Bacteriol. November 1978 vol. 136 no. 2 597-606</h4>
 
−
<h4>EMlVIETT W. CHAPPELLE ;Biochim. Biophys.Acta, 62 (1962) 45-62
 
−
</h4>
 
−
<h3>• Lead</h3>
 
−
<h4>Organism- Pseudomonas aeruginosa</h4>
 
−
<h4><b>Citation</b>:  Slomczynski, D. J. AND W J. DavisHoover*. CHARACTERIZATION OF PB2+ UPTAKE AND SEQUESTRATION IN <i>PSEUDOMONAS</i></h4>
 
−
<h4>AERUGINOSA, CHL004, LEAD.Presented at Third International Conference, Monterey, CA, 5/20-23/2002.</h4>
 
−
 
  
  

Revision as of 20:41, 31 October 2017

gEco
Co-culture and Growth






Co-culturing is a technique of culturing or growing two or more than two different populations of cells in the same culture plate. It is a useful way to understand the interaction between two different types of cells, making it advantageous for studies of cell-cell communication.

Here in we have the plan to co-culture our engineered strain of E.coli (which can independently detect and capture each of the noxious gases and harmful chemicals) with naturally occurring microbes which can consume these harmful gases and chemicals through their evolved metabolic pathways. This ensures the existence of a sink for these pollutants, and thereby the longevity of the synthetic microbes.

Simply introducing the metabolic pathways of qualified co-culture cells (which can consume these harmful gases and chemicals) in a synthetic microbe induces immense burden and reduces its longevity. This approach has been taken up by many teams, only to result in the non-viability of these microbes. Therefore, we have taken a novel co-culturing method which is partially synthetic and partially natural to tackle pollution in a more efficient and effective manner.

Chemical Organism
Acetaldehyde Pelobacter carbinolicus , P. acetylenicus
Nitric Oxide species of Pseudomonas, Alkaligenes , Bacillus and algae -Dunaliella tertiolecta
Mercury Microbacterium oxydans, Ochrobactrum, Lysinibacillus, Serratia marcescens
Xylene Pandoraea sp. strain WL1
Arsenic Halomonadaceaebacterium GFAJ-1
Lead Clostridium formicoaceticum ,C.thermoaceticum, algae -Chlorella vutgaris, Spirogyra
Carbon monoxide Pseudomonas aeruginosa
Uranium algae -Cladophora hutchinsiae
Chromium algae -Oedogonium hatei
Copper algae - Gelidium
Zinc algae -Gelidium


Culturing on paper

The study of bacterial growth has been one of the most standard approaches in the field of microbiology and Escherichia coli as a workhorse has been considerably exploited for its use in many molecular biology techniques. The need of a nutrient rich solid or liquid medium is of utmost importance for the sustenance of bacterial growth. However, people over the past few years have tried using paper based growth supports for bacteria. Paper is a ubiquitous, inexpensive, recyclable, portable, flexible and disposable material. But paper can’t be directly used for culturing microbes due to certain constraints such as the requirement of a nutrient rich medium for growth, sample dispersion and absorption by the paper, etc. Hence, paper needs to be synthetically modified for sustaining the growth of microbes. The construction of in-vitro biological systems is a remarkable area of study in synthetic biology and has been widely exploited and implemented for this approach. These systems make use of strong promoters and translation initiation sequences for the expression of most of the individual genes encoded on the genome of interest. In this, the microbial culture after having been grown to a suitable density, is subjected to lysis and the lysate is added to the synthetically modified paper and subjected to freeze drying. At the time of use, the components on the paper can be revived by adding distilled water or a suitable buffer and heating the paper at an optimum growth temperature followed by adding the components (compatibility of the components used for the reaction is a very important factor) required for transcription-translation and the required reaction can hence be carried on the paper. Fine tuning of the circuit and improvisation in the design of the paper being used for the reaction needs to be taken care of to improve the efficiency of the reaction.


References:

Schmidt, A., Frensch, M., Schleheck, D., Schink, B., & Müller, N. (2014).Degradation of Acetaldehyde and Its Precursors by Pelobactercarbinolicus and P. acetylenicus. PloS one, 9(12), e115902.

Jin, Y., Veiga, M. C., &Kennes, C. (2005).Bioprocesses for the removal of nitrogen oxides from polluted air. Journal of Chemical Technology and Biotechnology, 80(5), 483-494.

François, F., Lombard, C., Guigner, J. M., Soreau, P., Brian-Jaisson, F., Martino, G., ...&Peduzzi, J. (2012). Isolation and characterization of environmental bacteria capable of extracellular biosorption of mercury. Applied and environmental microbiology, 78(4), 1097-1106.

Wang, X., Wang, Q., Li, S., & Li, W. (2015). Degradation pathway and kinetic analysis for p-xylene removal by a novel Pandoraea sp. strain WL1 and its application in a biotrickling filter. Journal of hazardous materials, 288, 17-24.

Diekert, G. B., &Thauer, R. K. (1978).Carbon monoxide oxidation by Clostridium thermoaceticum and Clostridium formicoaceticum. Journal of bacteriology, 136(2), 597-606.

Chappelle, E. W. (1962). Carbon monoxide oxidation by algae. Biochimicaetbiophysicaacta, 62(1), 45-62. Slomczynski, D. J. AND W J. DavisHoover*.CHARACTERIZATION OF PB2+ UPTAKE AND SEQUESTRATION IN PSEUDOMONAS AERUGINOSA, CHL004, LEAD.Presented at Third International Conference, Monterey, CA, 5/20-23/2002.

Wolfe-Simon, F., Blum, J. S., Kulp, T. R., Gordon, G. W., Hoeft, S. E., Pett-Ridge, J., ...& Anbar, A. D. (2011). A bacterium that can grow by using arsenic instead of phosphorus. science, 332(6034), 1163-1166.