Team:AFCM-Egypt/integrated
Integrated Human Practices
Sarafina Nance
Astrophysicist and Women's Health Advocate Sarafina Nance.
Sarafina is an egyptian american eminent scientist MSc and a Ph.D candidate who is extravagantly talented with science communication. As a breast cancer previvor, she learned the importance of advocating for herself and she creatively started using media to encourage other women to advocate for themselves as well.
We knew about Sarafina through her twitter account which is always packed with scientific content and later reached out to her through her website https://starafina.com/. On the 8th of june 2021, we held an online meeting with her where we discussed various topics related to science communication and we focused mainly on the following:
- Possible ways to promote science communication in Egypt.
- Learning more about the use of media to spread awareness and to publicize our platform.
- How the system in the U.S runs the therapeutic programs once a patient is diagnosed with breast cancer all the way throughout different levels of treatment.
Our meeting with Sarafina helped in forming a deeper vision on different reasons behind the high prevalence of breast cancer and late diagnosis in Egypt. Furthermore, she explained to us how different countries implement the therapeutic journey for their patients; this helped us to recognise the drawbacks of our healthcare system when it comes to fighting breast cancer. One thing we learned was the importance of knowing all treatment options available for the patients to choose from based on their condition, thereby boosting their compliance and survival rates. However, the essentiality of genetic counselling suggested by Sarafina came as the chief insight of the meeting, as she stated that "Genetic counselling is basically step zero" of the process. Upon this meeting, we wanted to raise more awareness about the importance of genetic counselling, therefore, we added a question to our “Vector Vaccine” survey in order to assess the public knowledge of genetic counselling. Moreover, we included a talk about genetic counselling in all of our outreaches and awareness activities that came later on.
Dr. Ahmed Badran
Fellow of the Broad Institute of MIT & Harvard
Dr. Ahmed Badran is a fellow in the Broad Fellows program at the Broad Institute of MIT and Harvard, and is a member of the institute’s Infectious Disease & Microbiome (IDM) and Chemical Biology & Therapeutic Sciences (CBTS) programs. Dr. Badran's research integrates principles of protein engineering, synthetic biology, genome editing, and directed evolution to enable an improved understanding of the cellular translation machinery and its role in resource allocation. Badran has contributed to the evolution of novel functions across numerous, unrelated protein activities, including DNA-binding domain, protein-protein interactions, proteases, and genome editing agents.
On the 28th of september we had the pleasure to have a zoom meeting with Dr. Badran in which we presented our project, especially the directed evolution part which is his speciality. Dr. Badran’s feedback concerning our methodology included:
- Enabling the user to enter the structure for example from PDB as an input to reduce searching space in our programmed notebook which would be a beneficial point in colab notebook.
- He suggested doing molecular dynamic simulations on some proteins as a filtering process to model and simulate the most fit structures.
- Dr. Badran sent us some datasets regarding directed evolution of antibiotics resistance which give us the opportunity to test and validate our results with experimental data.
- He recommended using Pearson correlation coefficient to calculate the correlation between our results and the previous experimental datasets.
Dr. Daniel R. Woldring
Among the benefits we had through attending Michigan State University collaboration workshop was the chance to meet Dr. Daniel R. Woldring, assistant professor in the chemical engineering and materials science department. His research expands on the fundamental understanding of protein-protein interactions as a means of exploring complex biological systems and developing novel, effective therapeutics. He presented a lecture regarding modeling and molecular dynamics. And, we had the chance to present our project regarding design, engineering, and modeling parts. Accordingly, He gave us his feedback in regards to some needed improvements and pointed out some issues that needed reassessment that include:
- Concerning antibodies directed evolutions, he helped us in increasing the accuracy of the process by suggesting inducing the mutations in specific positions like CDR or protein binding sites instead of inducing the mutations in random positions which enhances the process and helps in ignoring invaluable mutations.
- As we have modeled one VLP chain only via Alphafold2, he recommended modeling the whole structure and the capsid in order to simulate the final product and test it accordingly.
- He advised us to determine a fitness cutoff or fitness scale in order to control nominating the most fit post-mutated proteins and ignoring non-beneficial ones. Therefore, controlling reiterating rounds.
Professor Ebtehal El-Demerdash
Professor & Head of Pharmacology and Toxicology Department, Faculty of Pharmacy, Ain Shams University, Egypt
Professor Ebtehal is an Egyptian pharmacist with more than 60 peer reviews in the field of life sciences published in international ISI-rated journals since 2000. Her research serves several medical fields. Moreover, she is a member of the Egyptian Drug Authority (EDA) with a vast experience in drug development and production and luckily for us she enjoys helping students attain their goals. All these qualities made her the perfect candidate to teach us more about the legal regulations of launching drugs to the market, a step that we will need to study in the near future.
1) In-Vivo studies to assess safety and effectiveness prior to registration in EDA. Dr. Ebtehal offered us to start our preclinical studies at her labs at the University of Ain Shams under her supervision.
2) Applying for funds. She introduced us to the Mounir Armanious Research Center (MARC) which grants up to 3 million EGP for immunotherapy research in Egypt. We applied for the grant and currently we are waiting for the response.
Resolutions for societal religious and ethical concerns
Earlier in July, our team was handing out surveys to collect information on how people working in the medical field viewed the matter of gene manipulation and to what extent they accepted applications of synbio and genetic engineering.
One of the questions aimed to help us find out why this field is hindered in Egypt and to come up with solutions based on the data we collected.
The question was about the reason people might have to reject applications of synthetic biology and genetic engineering.
According to the results displayed in the pie chart , fear of religious and ethical concerns contributed to more than 40% of the reasons why people in our local society might abstain from taking part in the field and thus hamper its development.
Therefore, to reassure people that beneficially using synbio does not break any ethical or religious principles, we interviewed a Sheikh with a degree in Islamic studies, and a priest to educate us on the religious point of view regarding gene therapy, genetic engineering and synthetic biology to help us transfer this perspective to the public through our awareness channels. Since muslims and christians form the majority of religious groups in Egypt; we chose to start with those two religions. However, in the future we are planning to include the insights of more religions. From the sessions we learned that using the science of genetics to help benefit the world and find solutions for its problems does not contradict with any religious teachings and so we conveyed this to our respondents.
