Overview
Atoms Turkiye view human practice as an avenue to serve mankind. The new sublime rule, Novel Approach enforced us to deeply question what it is that be should done to form a connection between our project and humanity on the long run. Besides accomplishing the classical outreach methods as a form of human practice, we have developed a triple thriller called SynPhilo, SynArt and SynSafe. Our aim is to open a new window for our generation which will enable them to look at creation and synthetic biology through unique perspectives such as philosophy and art.
Novel Approaches
- SynPhilo: A bridge connecting philosophy to Synthetic Biology
- SynArt: A different perspective to Synthetic Biology.
- SynSafe: A unique route to enhancing Safety.
- Game: A chance to live the journeys of a cancer and a normal cell.
- High School: First Runner up: AUC Turkey. An invaluable result.
- Outreach: Tha classical with the worthy.
SynPhilo
'Learn to look, look to recognize, recognize the similarity.'
SynPhilo: Synthetic Philosophy is a new approach to evaluate scientific research. As young scientists, we abundantly have evolved to think that research is only alive in the zone of laboratory; once we take off our lab coats and leave, the research remains there. Though when cancer is taken into consideration, there is an undeniable truth that nearly most of us individuals have encountered a close relative suffering from this heartbreaking disease. Decades have been spent trying to devise a ground breaking treatment for cancer and the obstinate work is still forging. Let’s question the number of cancer contemplators from the window of philosophy. How many have intensely analysed cancers behaviour, to discover its roots to comment on its existence? More substantially go on a journey to identify the connection between human nature and cancer through philosophy?
SynPhilo’s first conference ‘Know your cell, Know yourself’ intended to take the audience on a discovery of the behaviour of cancer and its connection to the humans through our organised activities and an act play scripted by our team members. The play was based on a scientist who looks at cancer from one direction only and a student who looks into the deeper end of the pool. Cancer, once a normally functioning cell, becomes uncontrollable when a slight error of gene replication occurs. From our perspective, we apprehend that cancer cell begins to swirl into a route where it becomes selfish, greedy, anarchistic, wasting and arrogant. It takes other cells’ glucose, deceives the immune system, bypasses its alerts and decides to form its own blood vessels to do metastasis and more. When deeply thought it is inevitable that the behaviour of cancer is somewhat linked to the inner feelings that most of us have whether hidden or not. SynPhilo conference analysed every movement of cancer first scientifically then reasoned its behaviour morally and found the interrelation of cancer with us humans, teaching us how to react through seeing a live example such as cancer that lives within us and slowly pulls the body to death as well as itself.
Let’s imagine the human body as a country’s government and cancer as the villain. The human body naturally attacks the cancer cells as soon as it identifies its invasion. When observing this process in the body, we can comprehend that there is a unique similarity between the duty of a country’s government and the body itself. So why not learn how to act by reading into ourselves or simply finding the similarities between us and cancer, in some aspects forming a bridge between the two to take lessons?
For more information on the content of the conference please click here.
Future Plan
Atoms Turkiye is planning to continue the SynPhilo conferences, trying its best to evolve and grow nationally and internationally, implementing scientists and the public to not limit its eyesight with the results attained in the laboratory. On a wider aspect train ourselves to look at general situations from different points of view.
To begin our future plans we booked an appointment with Assoc. Prof. Dr. Sinan Canan who is greatly popular with his captivating conferences such as [N]Brain. We discussed our ideas and noted his advises and was honoured upon his offer of collaborating with him on our next conference.
SynArt
100 years ago our ancestors invented laboratories to ease the observation of creation; to enhance our knowledge and develop for the better so a new renascence began. Today, SynArt may introduce a second renascence where science will work together as one wit art. ATOMS Turkiye believe that laboratories may be unsatisfactory to fathom creation itself. For this reason, SynArt will allow us to perceive synthetic biology from an artist’s standpoint. In order to take the first step, we contacted the other European iGEM teams and invited them to send their valuable artworks for the 2-day SynArt exhibition that was held in our university. We asked what the viewers’ interpretations were and their choice of favourite.
- Imperial College
- UCL
- Grenoble
- Edinburgh
- York
Below the photos are the names of the teams that have sent us their work with an explanation of what it is. You can also view our gallery of the exhibition event.
SynSafe
We aim to transfer the outcomes attained in laboratories to our daily lives by implementing it on a larger scale and alterations of organisms whether genetical or epigenetical is one way to do this. However this is not always possible as we cannot predict how an altered organism will adapt to the natural environment and what it’s effects on the ecosystem will be. Hence, safety and security occupy a great space of importance when it comes to devising projects for iGEM; risks must be lowered at a maximal level.
‘Two heads are better than one’ is the best saying to depict our approach on safety. This year, we read the abstracts and e-mailed most European iGEM teams to question and discuss the safety of their projects. Scroll down to view the answers of Grenoble-EMSE-LSU and METU-Turkey. Besides collaborating, we tried to increase each teams safety by preparing them for the obvious that can be questioned. With the support of iGEM, our aim is to form a biosafety congress in the future years because synthetic biology is like a potential limitless world source to anything that can be imagined by us. If Synthetic Biology is used for the right purposes then it serves possibilities from treating the untreatable illnesses to erasing the word poverty from our dictionaries via feeding the hungry. Yet, it can also result in mass slaughter or the production of dangerous weapons such as atomic bombs or even worse. Hence, strict rules and regulations of safety is a must in this field and ATOMS-Turkiye decided to take the first step with SynSafe to raise awareness of its importance once again.
Our mail to Grenoble IGEM team
Dear Grenoble İGEM team,
With a great project comes a great responsibility of finding the best solution to the safety issues we encounter and most oftenly, figuring the main safety areas that needs concentrating on can be pretty difficult. This year iGEM has introduced strict rules and regulations for safety which is a clear indication of how much effort and importance they are expecting us to show!
So, why dont we gather and see safety as a way to benefit eachother? Because not only will this open new doors for our future safety plans but will also increase the probability of reaching our aimed destinations. The Lyon jamborees is a great opportunity to form a platform where we can discuss our safety issues, what we have done to overcome them and the main parts that have challenged us the most.
After reading your abstract a few questions on the safety of your projects popped into our minds. If you are interested in forming a discussion platform, we would be delighted receive your answers as this, on the day of the platform will enable your team to see how much progression was made with safety from today onwards.
We would be really grateful to read your questions on the safety of our project too J
iGEM cares about safety, so do we! Lets take a step together and make a change in how we handle this caseJ
Questions
1-) Does this protein have any effect on human or other living organisms health? Have you thought of it being possibly poisonous to them?
Their Response
Dear ATOMS-TÜRKİYE iGEM Team 2013,
I am Stewart Humble, a member of the iGEM Grenoble-EMSE-LSU Team for 2013. I was asked to give a quick informal overview and comparison with our project and my previous research at LSU to address some of the biosafety issues and questions that may arise for our team.
As an undergraduate at LSU, I performed my thesis work on the synthesis and cellular investigations of a specific photosensitizer that is a chlorophyll derivative called Chlorin e6. My work concentrated on the applications of this photosensitizer in the clinical process known as photodynamic therapy (PDT). PDT is used to destroy tumors, and involves three key components: a photosensitizer, light, and tissue oxygen.
By modifying this derivative through the addition of positively charged amino acids (lysine), I was able to give strengthen its amphiphilic characteristics. Amphiphilicity is a measure of the extent to which a molecule can behave in both a polar and nonpolar way. This gives these molecules the ability to dissolve in the blood and also to pass through hydrophobic cell membranes. After biological studies, I found that the molecular photosensitizer I constructed was very potent in terms of phototoxicity, which means that even at very low concentration there was destruction of the cancer cells.
In terms of biosafety, I want to focus on the basic principles of biochemistry and cell-photosensitizer interaction. In general, my photosensitizer was much more of a safety risk due to its ability to uptaken into individual cells from the extracellular space. Additionally, it is not heavily altered by spending time in the extracellular space due to its amphiphilic characteristics.
KillerRed, however, is a "genetic" photosensitizer that is created within a cell of interest and (as far as we know) can only act upon that individual cell. This is due to the very unique fact that KillerRed is a protein that folds to form a chromophore that produces 10-fold more reactive oxygen species (ROS) than other fluorescent proteins such as GFP. All proteins have unique foldings that can be quite sensitive to its surroundings (pH, temperature, etc.) and if a cell containing KillerRed were to lyse and release the photosensitizer, I believe that no other cells would be greatly (if al all) affected due to two main points:
1.) The KillerRed protein may become denatured (unfolded) due to a change in environment, breaking apart the chromophore and rendering all ROS production to null
2.) The KillerRed protein maintained its proper folding, but fails to enter any nearby cells due to its size (macromolecule) and inability to be uptaken into other cells (lack of receptors, etc to trigger any other form of uptake)
I hope this explanation will help to address some of the safety concerns we will be collaborating upon for the iGEM Competition. Please let our team know if anything further is needed. Thanks!
Our mail to METU IGEM team
Dear Metu İGEM team,
With a great project comes a great responsibility of finding the best solution to the safety issues we encounter and most oftenly, figuring the main safety areas that needs concentrating on can be pretty difficult. This year iGEM has introduced strict rules and regulations for safety which is a clear indication of how much effort and importance they are expecting us to show!
So, why dont we gather and see safety as a way to benefit eachother? Because not only will this open new doors for our future safety plans but will also increase the probability of reaching our aimed destinations. The Lyon jamborees is a great opportunity to form a platform where we can discuss our safety issues, what we have done to overcome them and the main parts that have challenged us the most.
After reading your abstract a few questions on the safety of your projects popped into our minds. If you are interested in forming a discussion platform, we would be delighted receive your answers as this, on the day of the platform will enable your team to see how much progression was made with safety from today onwards.
We would be really grateful to read your questions on the safety of our project too J
iGEM cares about safety, so do we! Lets take a step together and make a change in how we handle this caseJ
Questions
1) When you change the genetic information of bacteria in bees’ guts this may have the possibility of changing the genetic material of most bacterial flora. Have you thought about a possible solution to this?
2) Will this change effect the bees honey production and so affect humans and animals health?
3) How will you manage the amount of Coumaric Acid produced?
4) Will coumaric acid affect plants which the bees’ touch?
Metu hope your project is going well. It's a pitty we couldn't make it to the national re-union in Istanbul but do hope you made the most of it :)
ATOMS Turkiye
Their Response
Hi ATOMS Turkiye,
For the first question, we will introduce our gene construct to the bacteria before hand and then introduce it to the host bee via food (a process called paratransgenesis), so it is highly unlikely for the other bacteria to get this part. Also, our system is optimized for b. subtilis, the promoters we used and the products as a whole have slim to no chance of functioning anywhere else.
For the second question, the bacillus strain we selected is native to the bees' gut. It is normally not found in the honey stomach of the bee, even if the bacteria were to get into honey, it will still be in the natural levels. Other than that, according to literature, IPTG is never traced in honey, so our little germs, even if they can make it into honey, will be killed because of our kill switch.
The third question was a hard one because there is actually no real data about the p-coumaric acid levels let alone it is not known if such a thing as p-coumaric acid overdose exists. We used in our system a constitutive promoter for the production of it too. What we expect and what we could argue from literature is that having p-coumaric acid is in all cases preferable. Maybe exceeding levels could cause increased energy consumption and maybe even acid accumulation, a decrease in tyrosine(a precursor of p-coumaric acid) etc. What most probably will happen (and what we actually hope for) is that the natural feedback mechanism will be triggered and control the process. But you are right, a inductive system would have been prettier :)
For the last question, p-coumaric acid is mostly produced by plants. Even vanilla production and cinnamon flavour begins with p-coumaric acid. Many plants produce p-coumaric acid so p-coumaric acid exposure should not cause any harm to them. Besides, p-coumaric acid will be produced in the midgut of the bee, so it is unlikely for p-coumaric acid to find its way directly to the plant.
Kind regards,
Oguz Bolgi on behalf of METU-Turkey
Outreach
Scientists
During the proceedings of our experiments, we contacted variety of scientists to discuss the contents of our project and question its safety. Prof. Dr. Aladin Szalay, founder of genelux corperation is a scientist who spent many years performing researches using the Nissle 1917 bacteria. Initially we gathered some questions on Nissle and e-mailed Prof. Szalay in which he offered to make a skype chat for a more in-depth talk. The one hour long conversation was based on iGEM following with our project in which we informed Prof. Szalay on our project and questioned him on how safe it is to use Nissle as our choice of bacteria. Prof. Szalay kindly answered each of our questions and also explained his current promising researches which enabled us to think on a larger scale and improve our project. We have also been invited for a two week training in his science research centre.
On the other hand, our faculty’s immunology specialist Prof. Dr. Bulent Bozkurt spared some time off his deadly full schedule to listen to our project where he asked questions that forced us to think deeper and seek answers for the unanswered questions; this enabled us to strengthen our weak points.
University
Three sets of presentations were held in our university where iGEM and our project was explained. Our intention was to enable each individual studying in our university to discover the intriguing contents of iGEM and what it feels like to be a member of such a rewarding organisation. In total, approximately 400 people including 1st, 2nd and 3rd year medical students listened to us. Many students then asked the following questions: What is application criteria for iGEM? How can I guarantee a place in next year’s team?
Congress
FATUBAT is a prominent congress which has a record breaking attendant number of 1,500 participants each year. Seeing this as a valuable opportunity, we introduced iGEM to the congress attendants and acquainted them on our previous project. Additionally, two workshops on Synthetic Biology and IGEM were held. Our intention in issuing the workshops was to gather the more interested individuals, divert and persuade them to become a member of the synthetic biology community. Different activities such as playing the Canvas Town game designed by Fatih Medical 2011 iGEM team, watching videos and holding a question-answer platform took place which enabled us to exchange ideas and maybe spark a light of interest.
The Dean and Doctors
Our faculty’s dean was only familiar to the word iGEM and nothing else. Therefore a meeting was organised with the university hospital doctors and the dean. Upon listening to our presentation of iGEM and Oncoli, some doctors offered the opportunity of working with tissues they will specially design for oncoli in which we will be able to continue our experiments. Their enthusiasm and support was essential and motivating.
National Union
We attended the national union organised by the METU-Turkey team and presented our project. This enabled us to practice for the jamboree as well as answering the questions asked by them. Following this a discussion panel was held on how to spread Synthetic Biology in Turkey.
High School Achievement
Auc Turkey, the high school iGEM team trained by Atoms Turkiye member Mustafa Elitok has achieved the non-other 1st runner up prize in the 2013 jamboree which can be viewed on the link https://2013hs.igem.org/Main_Page. Despite joining for the second year, their achievements was an inexplicable joy for us and our university. Our high school student Furkan Bestepe who has undergone a training period of two years has become a member of our team Atoms Turkiye. Below:
AUC Turkey Project Description.
Big budgets and significant amounts of energy are annually allocated to cooling systems. Also, these cooling processes are one of the factors of environmental distruption. The aim of our project, BactoCooler, is to accomplish a highly efficient and low cost cooling without distrupting nature’s magnificient balance through the usage of the most common form of life on Earth, bacteria. BactoCooler contains a special RNA Thermometer which allows translation after a specific temperature. This initiates the production of the urease enzyme which is responsible in the breakdown of urea. This organic endothermic reaction results in the significant cooldown of the environment.
For more information please visit high school website: https://2013hs.igem.org/Team:AUC_TURKEY
To view their poster:
https://2013hs.igem.org/files/presentation/AUC_TURKEY.pdf
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