Description


Our team members made a suggestion through our Integrated Human Practices meetings that the issue we seek to solve is one that does require a solution. We think it is critical to take into account professors’ suggestions at each level of project development, convey our project's knowledge, and information in a thoughtful manner.

We took advice from professors in our faculty and discussed with them each step we have reached. In order to improve our project, we have taken into account their feedback and suggestions. Our team members have spoken with many academic and medical experts over the past few months to gain perspective and feedback on our project design. These conversations have allowed us to develop our project further in a way that will help in our project success. We have learned more about Alzheimer's Disease along with the current treatments in clinical settings and these revelations have played a crucial role in our suggested switchable systems.

We were inspired and we decided to inspire others as well. Our main goal wasn’t only to focus on Cairo University but also, all Egyptian universities, schools, and our society through TV, Journal, magazine articles, social media, and even kindergartens about synthetic biology and the competition in various creative ways. Here we are showing how far we have gone.

Our meetings’ goal was to develop the basic idea of a therapeutic treatment for Alzheimer's Disease. First, we had meetings with our university professors to know more about Alzheimer's Disease and how to optimize our protocols so that we can choose the best expression method for the proteins and to know what tools to use in the dry lab. Then, we tried to focus more on the disease itself, its reasons, symptoms, and how to deal with it. We organised online and offline meetings with neurologists to know more about Alzheimer's Disease as a type of dementia and its treatments.

TA. Ahmed Samir

Teaching assistant at faculty of Science, Department of Biophysics


Recommended a proteomics book called (Chapman & Hall) for the Dry-Labmembers. Told us to focus more on WHO website to read about more different diseases. Helped us on how we can pave our way to formulate our project idea by advising us to divide the team into small subteams and each subteam can work on different ideas till we reach one. Shared some docking tools with the Dry-Lab members, in addition to different visualisation softwares such as pymol (for example)

Our response:

We began to form small subteams and work on different ideas as he suggested, this truly helped us in the formation of our idea.



Prof.Dr. Salwa Thabet

Prof.Dr. at Faculty of Science Department of zoology


Advised us to carefully prepare the experimental design before starting lab work.
Shared her experience with us about how to treat Animal models.

Dr. Heba Mohamed Fahmy

Assistant Professor at Biophysics Department, Faculty of Science, Cairo University.


Using Nanocarriers instead of liposomes because of their lower preparation cost, tunable physical and chemical properties, and its capability to cross the blood-brain barrier.
Searching more about mesoporous silica nanocarriers, as she had previous work that proved the ability of this type of nanocarriers to cross the blood-brain barrier and distribute with adequate concentrations in different brain areas.
Aluminium is not the best method for AD induction in animal models.

Our response:


We replaced liposomes with nanocarriers.
We started to search more about the drug delivery system, including mesoporous silica and other types of carriers, comparing them to choose the best one and considering the synbio approach, and searching in iGEM how to synthesise the chosen nanocarrier, which was Chitosan and PEG.

"Another meeting with Dr. Heba"

We validated our search about mesoporous silica (biocompatible, biodegradable, high surface area, its size can be controlled, low toxicity, and has the ability to cross the BBB). Metal nanocarriers are not preferable because they induce severe oxidative stress.
How the body deals with the nanocarrier.
Biodistribution test to know the concentration of the drug inside the brain.
How to load our drug into the mesoporous silica nanoparticle.
Chitosan has a low yield and is difficult to load.
PEG is efficient in coating.


Prof.Dr. Wael El Menofy

Prof.Dr. at Faculty of Science, researcher at AGERI


The protocol of the baculovirus expression system, and insect expression system.
Gave us chloramphenicol, Xba1 enzyme, BL21 and Top10 chassis.


Prof.Dr. Mahmoud Saleh

Prof.Dr at Department of Microbiology and Botany, Faculty of Science, Cairo University.


Discussed with us the yeast transformation protocol, and cleared up some misunderstood points by explaining them to us.
The homologous recombination method is more preferable in yeast transformation.
Offered us the yeast transformation kit.


Dr. Hytham Mohamed

Senior Researcher of Agricultural Genetic Engineering Research Institute, Cairo (AGERI)


-Disccus with us the protocol of yeast transformation.
-Gave us Dh5a wildtype.
-disscuss Homologous recombination & plasmid method in yeast transformation.

Our response:

We decided not to use yeast as the protocol would not be suitable for us to carry out.

Prof.Dr. Emad Elzayat

Prof.Dr at Department of Zoology, Faculty of Science, Cairo University.


Research in AD.
He talked with us about transcendence animals and how hard it is to obtain them in Egypt.

Our response:

We decided not to test our treatments on transcendence animals.


Dr. John

He shared his experience in dementia types, causes, symptoms, and mechanisms.
Told us about Delta trep which is a new approved cure for Alzahimer targeting beta amyloid aggregation.

Prof.Dr. Sara Ahmed Khaled

Professor of Geriatric Medicine -Ain Shams University


Types of Alzheimer's Disease especially the ones that could be treated.
Psychological state of Alzheimer’s Disease patients is very important.
In the progress of Alzheimer’s the patient become as a baby that doesn’t know anything, he doesn’t even know about his disease.


Dr. Nourhan Belal Atef Mohammed

Assistant lecturer of Neurology, Ain Shams university hospitals Master's degree of Neurology and Psychiatry


Difference between Alzheimer's Disease and other dementia types.
The beginning of the disease starts in the temporal lobe (recent memories begin to be lost) then anterior temporal lobe ( he does not answer normal questions) after that, losing languages and finally at the late stage, he may have .
In early stages all people think that it is a problem in the eyes or nerves but they don't imagine that it is Alzheimer’s Disease.
During the last stage he can’t recognize anyone and starts to behave abnormally.
Acetylcholinesterase inhibitors based cures increase the amount of acetylcholine and is responsible for treating the symptoms only.
Control risk factors (head injury, stimuli, no activity, obesity,....)
Memory impairment (losing things a lot or losing recent things ) but an Alzheimer patient doesn't know that he is losing his memory, he tries to fill the gap by making up scenarios.
Advised us to make a book for awareness about Alzheimer’s Disease.
There are 3 types of studies (not approved yet only in research phase) 1)biomarkers may detect if the person will suffer from Alzheimer’s or not 2)giving vaccination (immunisation against the accumulation of tau proteins) 3) Degradation of tau accumulations by monoclonal antibodies.
Awareness about Alzheimer’s in non-medical places and poor places (to make common people know more about Alzheimer)
Assessment every 6 months or 1 year check up

Suggested other contacts :
Dr. Tarek Okasha who owns a charity for Alzheimer patients in Egypt.

Advice :
To have a cure we must know the medical part,the location of each protein, how it is affected and read about different scans (CT) for parts in the brain.



Dr. Brian Jimenez

Lightdock software developer


Telling us how to optimise the software algorithm according to our needs How to optimise the number of swarms.
How to optimise the number of glowworms.
We should put or remove hydrogens according to the contributions of the hydrogen in the interaction itself.
What scoring function should we use.
How to rank produced models.
Github repository scoring codes.
Best pdb file number to chose.



Dr. Sameh Magd Al-din

Head of proteomics and metabolomics research program at 57357 hospital


Concerning protein protein interaction:
Offered us making to carry out western protocol in his lab and BCA instead of Bradford.
Western is better than ELISA.
Offered to do staining then measuring band intensity with elisa reader in his lab.
He will provide us with Anti-Ub and Anti-Tau.


Dr. Mahmoud Sameh

Research assistant in proteomics and metabolomics research program at 57357 hospital


ATP types.
Recommended the kit of ADP-assay kit.
Warned that calcium buffer may affect the chromatography during pull down assay.

Dr. Sameh Saad

Head of Tumour Biology Research Program at 57357 Children Cancer Hospitals


Offered to help us in using the reader of fluorescence and illuminance



Dr. Per hammarstrom

Supervisor of Linkoping_Sweden team


Ensured us of the steps of tau extraction, and recommended the addition of boiling step.
Tau isoforms.
Transformation, induction optimum and best conditions.
Protein extraction buffer + Boiling .
aggregates (How & Characterization) , He ensured us that the aggregates could be characterised by THT assay His study for tau (reason of study).
Denaturation using urea.

He offered us to ask for a transformation protocol from liu team, they provided us the protocol for tau transformation and expression For protein-protein interaction we can use:

1-chemical cross-linking then mass spectroscopy.
2-actually bind using isothermal calorimetry.

Prof.Dr. Mohamed Gamal

Prof.Dr. at Chemistry Department, Faculty of Science, Cairo University


We discussed the enzyme activity and kinetics equations with him, then he recommended using the arrhenius equation to solve the equation of the trim and HTRA1 system, and follow the activated complex theory to build the code structure.

Response: we begin using activated complex theory throughout the enzymatic activity measurement script.

Andrew Waterhouse

Senior Scientific Software Developer at the Swiss Institute of Bioinformatics


Swiss Structure Assessment has been an essential part of the Dry-Lab pipeline when designing our systems and filtering our libraries, there were hundreds of models generated continuously with different software which needed to be analyzed and compared in order to choose the best fit model.

The Structure Assessment server provided us with the needed service that would calculate parameters like QMEAN, Molprobity, etc. Therefore, when automating our pipeline, we wanted to facilitate access to this service instead of manually uploading your models, downloading the results, and filing them to be ranked by our quality assessment code.

So, we contacted Swiss Model, to see if they could provide us with an API to be a part of our pipeline that allows users to upload their 3D structures locally through our code, and they were really cooperative in that matter, but since there was not enough time to finish the API, we had a meeting with Andrew so that we could find a quick solution.

1-We told him more about our project and iGEM, and he actually mentioned that they had no prior knowledge of the competition until we contacted them, so they searched about it and started to get familiar with iGEM.
2-He offered to write us a simple script that would allow the upload of models and their structure assessment, and we added it to our pipeline (PharaohSuite).
3-We also agreed to do further collaboration as they could provide us with an API for their modeling services