Difference between revisions of "Team:Stony Brook/Model"

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<p>Phylogenetic analysis requires little pre-existing literature in order to construct a predictive evolutionary model, because a phylogeny’s strength of prediction is based on analysis of biological sequences, data that is now readily available. This method of modeling is favorable for novel bacteriocin research because of the limited literature available for these bacteriocins.</p>
 
<p>Phylogenetic analysis requires little pre-existing literature in order to construct a predictive evolutionary model, because a phylogeny’s strength of prediction is based on analysis of biological sequences, data that is now readily available. This method of modeling is favorable for novel bacteriocin research because of the limited literature available for these bacteriocins.</p>
 
<p>The hybrid bacteriocin lacticin Q-lacticin Z was successfully created by University of Southern Denmark’s 2016 iGEM team [1]. Because these class II lacticin bacteriocins have been hybridized before, we hypothesize that the lacticin bacteriocin, lacticin Z, will have a greater affinity for hybridization with another bacteriocin that is evolutionarily similar to itself. Through the reconstruction of a phylogenetic tree and through review of past literature, we determined two bacteriocins that are suitable for hybridization: aureocin A53 and epidermicin NI01.
 
<p>The hybrid bacteriocin lacticin Q-lacticin Z was successfully created by University of Southern Denmark’s 2016 iGEM team [1]. Because these class II lacticin bacteriocins have been hybridized before, we hypothesize that the lacticin bacteriocin, lacticin Z, will have a greater affinity for hybridization with another bacteriocin that is evolutionarily similar to itself. Through the reconstruction of a phylogenetic tree and through review of past literature, we determined two bacteriocins that are suitable for hybridization: aureocin A53 and epidermicin NI01.
<center><p><a href="#"><img src="https://static.igem.org/mediawiki/2017/0/01/T--Stony_Brook--phylogeny2.jpg" style="text-align: center;width:600px;height:604px;"/></a></p></center>
 
 
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<div style="text-align: center"><a href="#"><img src="https://static.igem.org/mediawiki/2017/0/01/T--Stony_Brook--phylogeny2.jpg" style="text-align: center;width:1000px;height:1007px;"/></a></div>
  
 
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<p>Bacteriocins can be divided on the basis of two groups: those produced by gram-negative bacteria (colicins and microcins), and those produced by gram-positive (divided into five classes). Our phylogenetic tree of 93 bacteriocin sequences was composed of 14 class I bacteriocins, 64 class II bacteriocins, 4 class III bacteriocins, 6 class V bacteriocins, and 5 colicin bacteriocins that served as an outgroup. Each color on the tree below represents a clade grouped on the basis of relative divergence time (≤ 0.17).</p>
 
<p>Bacteriocins can be divided on the basis of two groups: those produced by gram-negative bacteria (colicins and microcins), and those produced by gram-positive (divided into five classes). Our phylogenetic tree of 93 bacteriocin sequences was composed of 14 class I bacteriocins, 64 class II bacteriocins, 4 class III bacteriocins, 6 class V bacteriocins, and 5 colicin bacteriocins that served as an outgroup. Each color on the tree below represents a clade grouped on the basis of relative divergence time (≤ 0.17).</p>
<a href="#"><img src="https://static.igem.org/mediawiki/2017/0/01/T--Stony_Brook--phylogeny2.jpg" style="text-align: center;width:1000px;height:1007px;"/></a>
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<a href="#"><img src="https://static.igem.org/mediawiki/2017/0/01/T--Stony_Brook--phylogeny2.jpg" style="text-align: center;width:700px;height:705px;"/></a>
 
<p>Class II bacteriocins, which are small, unmodified membrane-active peptides, can be further divided into four subclasses. There was a correlation between subclass and homology for class IIa and class IId bacteriocins, but not for class IIb and class IIc. For example, all class IIa bacteriocins related to the pediocin family, such as enterocins, had very close divergence times (yellow to orange region). The protein structural analysis supports these results, as all these bacteriocins contain the conserved N-terminal sequence KYYGNGVXCXXXXCXV(D/N)WGXA, with the sequence between the two cysteines consisting of one or two charged residues, and a serine or threonine residue [2]. Class IId bacteriocins, which are leaderless peptides that are synthesized and secreted without a further processing [3], were especially important because this subclass includes our starting bacteriocin, lacticin Z. Fortunately, like class IIa, most of these bacteriocins shared homology (cyan to light-green region).
 
<p>Class II bacteriocins, which are small, unmodified membrane-active peptides, can be further divided into four subclasses. There was a correlation between subclass and homology for class IIa and class IId bacteriocins, but not for class IIb and class IIc. For example, all class IIa bacteriocins related to the pediocin family, such as enterocins, had very close divergence times (yellow to orange region). The protein structural analysis supports these results, as all these bacteriocins contain the conserved N-terminal sequence KYYGNGVXCXXXXCXV(D/N)WGXA, with the sequence between the two cysteines consisting of one or two charged residues, and a serine or threonine residue [2]. Class IId bacteriocins, which are leaderless peptides that are synthesized and secreted without a further processing [3], were especially important because this subclass includes our starting bacteriocin, lacticin Z. Fortunately, like class IIa, most of these bacteriocins shared homology (cyan to light-green region).
 
</p>
 
</p>

Revision as of 22:46, 27 October 2017

Stony Brook 2017

Phylogenetic analysis requires little pre-existing literature in order to construct a predictive evolutionary model, because a phylogeny’s strength of prediction is based on analysis of biological sequences, data that is now readily available. This method of modeling is favorable for novel bacteriocin research because of the limited literature available for these bacteriocins.

The hybrid bacteriocin lacticin Q-lacticin Z was successfully created by University of Southern Denmark’s 2016 iGEM team [1]. Because these class II lacticin bacteriocins have been hybridized before, we hypothesize that the lacticin bacteriocin, lacticin Z, will have a greater affinity for hybridization with another bacteriocin that is evolutionarily similar to itself. Through the reconstruction of a phylogenetic tree and through review of past literature, we determined two bacteriocins that are suitable for hybridization: aureocin A53 and epidermicin NI01.