Difference between revisions of "Team:Korea U Seoul/Project/Biological Background/content"

Line 89: Line 89:
 
             </div>
 
             </div>
 
             <div class="content_">  
 
             <div class="content_">  
−
            <p>
+
       
 
   
 
   
−
① NADH and NADPH
+
<h2>① NADH and NADPH</h2>
−
Like an ATP (adenosine triphosphate) which serves as a convenient and versatile storage in cells, NADH (nicotinamide adenine dinucleotide) and NADPH (nicotinamide adenine dinucleotide phosphate) serve as activated carriers specialized in carrying high-energy electrons and hydrogen atoms (see Figure 1-a).  
+
<p>Like an ATP (adenosine triphosphate) which serves as a convenient and versatile storage in cells, NADH (nicotinamide adenine dinucleotide) and NADPH (nicotinamide adenine dinucleotide phosphate) serve as activated carriers specialized in carrying high-energy electrons and hydrogen atoms (see Figure 1-a).  
  
 
             </p>
 
             </p>
 +
<img src="https://static.igem.org/mediawiki/2015/4/43/KoreaUSeoul_BiologicalBackground_Figure1.jpg">
 
    
 
    
 
             </div>
 
             </div>

Revision as of 16:00, 18 September 2015

1) KEGG database

The program ‘Gil’ is a project based on KEGG (Kyoto Encyclopedia of Genesand Genomes) database (Kanehisa M., et al. 2014; and Kanehisa M., Goto S., 2000). Its information were accumulated by genome sequencing and other biological research. It offers well-combined metabolic-related pathways. Also we organized and parsed these database that provide compound, reaction, gene and enzymatic information. Especially, we built RPair, a main network in four reaction pair groups. However, there are some shortcomings in KEGG database. First, it doesn't provide thermodynamic information that is a crucial criterion to determine reaction direction. Though we cannot obtain thermodynamic information in KEGG database, we tried to compensate it by utilizing Equilibrater and anotherdatabase. Additionally KEGG database, however, show reactions in bidirectional way in which usually do not process as it is a thermodynamically unfavorable reaction. Lastly, every glycan in KEGG database is not connected with compound. By origin, glycans have G number (ex. G00000) but there are some cases that glycans have C number (ex. C00000) that kegg compounds have. Specially, they can react to compounds or glycans. However, many glycans don’t have C number, so they can not react with compounds and they even don’t have any reactions in glycans. For example, glycan named neoagarobiose in the path that has been being studying for experimental validation doesn’t have C number. So we added the information of the glycan found other databases such as “-------”* and -------** to data obtained from kegg compounds to complement kegg’s fault. * a database of chemical molecules maintained by the National Center for Biotechnology information (NCBI) (Wikipedia) ** Eun Ju Yun et al. (2015), The novel catabolic pathway of 3,6-anhydro-Lgalactose, the main component of red macroalgae, in a marine bacterium, Environmental Microbiology, 1677 – 1688p We used K12 as our E. coli model strain. It is the most commonly used E. coli strain in biological lab.

2) Thermodynamic information

Thermodynamic constrain is one of the most important factors of biological experiments. Therefore, the program ‘Gil’ provides Gibbs energy of each metabolic reaction. The program ‘Gil’ obtained thermodynamic datafrom two separated databases even though they were obtained from the same program, eQuilibrator (Flamholz A., et al. 2012). The first database is composed of Gibbs energy from standard condition—pH 7.0 and 0.1 M ionic strength. These data are correct, but the size of the database is smaller than the other one due to the lack of wetlab experiments. On the other hand, the second version is made up of values from calculation. This database has much more values than the first one, however it is hard for researchers to apply this values directly to their experiments since they are not experimentally proved. Thus, additional attention is needed to utilize the second version of data.

Thermodynamic constrain is one of the most important factors of biological experiments. Therefore, the program ‘Gil’ provides Gibbs energy of each metabolic reaction. The program ‘Gil’ obtained thermodynamic datafrom two separated databases even though they were obtained from the same program, eQuilibrator (Flamholz A., et al. 2012). The first database is composed of Gibbs energy from standard condition—pH 7.0 and 0.1 M ionic strength. These data are correct, but the size of the database is smaller than the other one due to the lack of wetlab experiments. On the other hand, the second version is made up of values from calculation. This database has much more values than the first one, however it is hard for researchers to apply this values directly to their experiments since they are not experimentally proved. Thus, additional attention is needed to utilize the second version of data.
3) Four path-scoring criteria

① NADH and NADPH

Like an ATP (adenosine triphosphate) which serves as a convenient and versatile storage in cells, NADH (nicotinamide adenine dinucleotide) and NADPH (nicotinamide adenine dinucleotide phosphate) serve as activated carriers specialized in carrying high-energy electrons and hydrogen atoms (see Figure 1-a).