Team:AFCM-Egypt

Welcome to iGEM 2018!

Your team has been approved and you are ready to start the iGEM season!

Before you start

Please read the following pages:

Styling your wiki

You may style this page as you like or you can simply leave the style as it is. You can easily keep the styling and edit the content of these default wiki pages with your project information and completely fulfill the requirement to document your project.

While you may not win Best Wiki with this styling, your team is still eligible for all other awards. This default wiki meets the requirements, it improves navigability and ease of use for visitors, and you should not feel it is necessary to style beyond what has been provided.

Uploading pictures and files

You must upload any pictures and files to the iGEM 2018 server. Remember to keep all your pictures and files within your team's namespace or at least include your team's name in the file name.

When you upload, set the "Destination Filename" to T--YourOfficialTeamName--NameOfFile.jpg. (If you don't do this, someone else might upload a different file with the same "Destination Filename", and your file would be erased!)

Wiki template information

We have created these wiki template pages to help you get started and to help you think about how your team will be evaluated. You can find a list of all the pages tied to awards here at the Pages for awards link. You must edit these pages to be evaluated for medals and awards, but ultimately the design, layout, style and all other elements of your team wiki is up to you!

Editing your wiki

On this page you can document your project, introduce your team members, document your progress and share your iGEM experience with the rest of the world!

Use WikiTools - Edit in the black menu bar to edit this page

Project Description

Role of modulation of TLR unmethylated cPG island

  • Due to the specificity of toll-like receptors -and other innate immune receptors- they cannot change with evolution. Those receptors recognize the threat associated molecules such as pathogens or cell stress and are extremely specific to them so they can never be stimulated by self-molecules that are normally expressed in the physiological conditions.
  • Some features in the pathogens are conserved to some extent and they include; cell-surface lipopolysaccharide (LPS), lipopeptides, lipoproteins and lipoarabinomannan; which are proteins such as flagellin from bacterial flagella, viral double-stranded RNA or the unmethylated CpG islands of viral and bacterial DNA, and also of the CpG islands which can be found in the eukaryotic DNA. The stereotypic inflammatory response caused by the activation of toll-like receptors raised the theories that endogenous activators of toll-like receptors may participate in the autoimmune diseases.
  • The following is how different antigens could stimulate the TLRs; The CpG islands stimulate TLR9. The pattern recognition receptor (PRR) TLR 9 which is expressed only in B cells and pasmactoid dendritic cells in humans recognizes the CpG PAMP, which is only expressed in B cells and plasmacytoid dendritic cells (pDCs) in humans. Variable sequences were found to stimulate TLR9 with variations in the number and location of CpG dimers and the precise base sequences flanking the CpG dimers; this let us find out about 5 unofficial categories of CpG ODN based on their secondary structures, sequences and their effect on human peripheral blood mononuclear cells (PBMCs). The five categories are Class A (Type D), Class B (Type K), Class C, Class P, and Class S. It is very important to realize that during the discovery process, the "categories" were defined only when it has become evident that ODN with certain characteristics could elicit specific responses.
  • Role of crispr in targeted methylation
  • Correlations between epigenetic marks and gene expression pattern form a strong base for the epigenetic studies so far. Precise epigenetic modifications and gene regulation are going on in the meanwhile due to technologies that have been specially developed for epigenome editing. Epigenetic modification is of a reversible nature, like DNA methylation, that exploited in the field of cancer therapy, yet this was done non-selectively by epigenetic inhibitors. A novel approach to selectively alter gene expression trough editing at a specific loci. CRISPR-Cas9-based tool for specific DNA methylation consisting of deactivated Cas9 (dCas9) nuclease and catalytic domain of the DNA methyltransferase DNMT3A targeted by co–expression of a guide RNA to any 20 bp DNA sequence followed by the NGG trinucleotide.targeted CpG methylation in a ∼35 bp wide region by the fusion protein. In order to enable methylation of a larger part of the promoter, guide RNAs are made multiple to target dCas9-DNMT3A multiple adjacent sites. According to the literature it was found that e.coli is in close relation to CRC; so we have searched the e.coli genome looking for motifs to use in our project using " motif finder tool". We found that our motif occurs 20 times in the e.coli genes. Among those genes was colibactin gene cluster. According to (Christine et. al ) there is a close relationship between CRC and colibactin gene cluster as they are responsible for DNA mutations. The gene cluster includes 18 genes, we found that clbj gene recorded the most frequent motif number, with a score of three times within the gene. This enlightened us with an idea, which is to make sure that we down-regulate the colibactin gene using the same methylation way that we are going to use to regulate the immune system.

Tips

This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started:

  • State your accomplishments! Tell people what you have achieved from the start.
  • Be clear about what you are doing and how you plan to do this.
  • You have a global audience! Consider the different backgrounds that your users come from.
  • Make sure information is easy to find; nothing should be more than 3 clicks away.
  • Avoid using very small fonts and low contrast colors; information should be easy to read.
  • Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the iGEM 2018 calendar
  • Have lots of fun!

Inspiration

You can also view other team wikis for inspiration! Here are some examples: