"
Team:Evry/Biology/Chassis/Pseudovibrio
From 2014.igem.org
(Difference between revisions)
| Line 12: | Line 12: | ||
</FONT> | </FONT> | ||
<br><br> | <br><br> | ||
| - | + | ||
== <b><big>From a poorly known genius, a jewel emerged</big></b> == | == <b><big>From a poorly known genius, a jewel emerged</big></b> == | ||
| - | + | ||
<br><br> | <br><br> | ||
<div align="justify"> | <div align="justify"> | ||
| - | + | ||
At first glance working on the microbiome of sponges appears like an hasardous task : 5734 articles for marine sponges, only 51 with microbiome of sponges, only 28 articles mentionning <i>Pseudovibrio genius</i>, only 5 mentionning <i>Pseudovibrio denitrificans</i>, and finally none about a genetic engineering system in it. | At first glance working on the microbiome of sponges appears like an hasardous task : 5734 articles for marine sponges, only 51 with microbiome of sponges, only 28 articles mentionning <i>Pseudovibrio genius</i>, only 5 mentionning <i>Pseudovibrio denitrificans</i>, and finally none about a genetic engineering system in it. | ||
<br><br> | <br><br> | ||
| Line 29: | Line 29: | ||
Now the thorny question is : can it be easily used in our lab ? | Now the thorny question is : can it be easily used in our lab ? | ||
| - | + | ||
<div align="center"> | <div align="center"> | ||
| - | + | ||
== <b><big>A bacterium we could work with</big></b> == | == <b><big>A bacterium we could work with</big></b> == | ||
| - | |||
<br><br> | <br><br> | ||
| + | |||
<div align="justify"> | <div align="justify"> | ||
| - | |||
In the literature <i>Pseudovibrio denitrificans </i> is described as a Gram-negative, motile by means of one to several lateral or subpolar flagella requiring NaCl for growth. It exhibits optimal growth at about 30 C°, pH 8 and 3 % NaCl, and a doubling time of 45 min in rich media. In a nutshell the conditions seem favorable for an iGEM project.</i> | In the literature <i>Pseudovibrio denitrificans </i> is described as a Gram-negative, motile by means of one to several lateral or subpolar flagella requiring NaCl for growth. It exhibits optimal growth at about 30 C°, pH 8 and 3 % NaCl, and a doubling time of 45 min in rich media. In a nutshell the conditions seem favorable for an iGEM project.</i> | ||
</p> | </p> | ||
| Line 42: | Line 41: | ||
<p> | <p> | ||
They are known to be capable of anaerobic growth by carrying out denitrifying metabolism using nitrate, nitrite or nitrous oxide as terminal electron acceptors. Being consequently a main reason for our <b><big>RNAseq</big></b> study to discover the transcripts upregulated by the presence of nitrite and clone their promoters as new sensors. | They are known to be capable of anaerobic growth by carrying out denitrifying metabolism using nitrate, nitrite or nitrous oxide as terminal electron acceptors. Being consequently a main reason for our <b><big>RNAseq</big></b> study to discover the transcripts upregulated by the presence of nitrite and clone their promoters as new sensors. | ||
| - | + | ||
<br><br> | <br><br> | ||
| - | + | ||
The following section describe the protocol use to optimize (Rich media) & control(Minimal media) growth conditions | The following section describe the protocol use to optimize (Rich media) & control(Minimal media) growth conditions | ||
| - | + | ||
<br><br> | <br><br> | ||
Revision as of 16:41, 17 October 2014
Pseudovibrio denitrificans the bacterium to modify.
== From a poorly known genius, a jewel emerged ==
At first glance working on the microbiome of sponges appears like an hasardous task : 5734 articles for marine sponges, only 51 with microbiome of sponges, only 28 articles mentionning Pseudovibrio genius, only 5 mentionning Pseudovibrio denitrificans, and finally none about a genetic engineering system in it.
Moreover with only 12 species in the genius, and 2 strains sequenced (Pseudovibrio sp. FO-BEG1, Pseudovibrio sp. JE062) we knew we would have to sequence our strain of Pseudovibrio denitrificans with a mapping to one of the 2 strains references. A formidable drawback even considering that in the first place the species was chosen because of its natural denitrification ability (cf toxic compound) and easy to sourced at DMSZ.
On the other hand Pseudovibrio denitrificans or strains related to the species has been shown as majoritary in at least six microbiomes of sponges in the mediterrean sea, where spongia officinalis reside.
Now the thorny question is : can it be easily used in our lab ?
Moreover with only 12 species in the genius, and 2 strains sequenced (Pseudovibrio sp. FO-BEG1, Pseudovibrio sp. JE062) we knew we would have to sequence our strain of Pseudovibrio denitrificans with a mapping to one of the 2 strains references. A formidable drawback even considering that in the first place the species was chosen because of its natural denitrification ability (cf toxic compound) and easy to sourced at DMSZ.
On the other hand Pseudovibrio denitrificans or strains related to the species has been shown as majoritary in at least six microbiomes of sponges in the mediterrean sea, where spongia officinalis reside.
Now the thorny question is : can it be easily used in our lab ?
== A bacterium we could work with ==
In the literature Pseudovibrio denitrificans is described as a Gram-negative, motile by means of one to several lateral or subpolar flagella requiring NaCl for growth. It exhibits optimal growth at about 30 C°, pH 8 and 3 % NaCl, and a doubling time of 45 min in rich media. In a nutshell the conditions seem favorable for an iGEM project.
They are known to be capable of anaerobic growth by carrying out denitrifying metabolism using nitrate, nitrite or nitrous oxide as terminal electron acceptors. Being consequently a main reason for our RNAseq study to discover the transcripts upregulated by the presence of nitrite and clone their promoters as new sensors.
The following section describe the protocol use to optimize (Rich media) & control(Minimal media) growth conditions
