News letter July
 
iGEM TU Delft
 
Hello again!
 
A month has passed and we are excited to share some updates with you. Aside from putting our game faces on and working hard, we have been able to squeeze in some time to get to know each other better and enjoy our summer! So, without further ado, let's look back at our July. 
 
July in the eyes of our Team Manager
Nick
 
 
"Over the last few weeks we have, in addition to entering the lab, been able to meet more regularly face-to-face with one another, while of course maintaining the appropriate social distancing. Now we are starting to get the first glimpses of what our hard work is creating – and it’s exciting!
While experiencing some of the “all you can eat” restaurants in Delft, we have also been able to get to know each other on a more personal level. This has been really nice as it has allowed us to enjoy the true iGEM experience; we learned about our different backgrounds and our shared passion for synthetic biology. It’s is one of the aspects that’s really bringing us together as a team.
 
 
As we approach the halfway mark of our full-time project, the team has managed to take a short holiday break here and there to help ensure everyone is refreshed and energized. We can now focus on presenting a project that encompasses everything that we have learned and is an expression of who we are as a team. As we look to the second half of the project, we are all enthusiastic and ready for the hard work ahead of us during the coming months – “bring it on!” as they say."
 
Human practices
 
During our project we try to obtain a good understanding of different perceptions of the problem and desired solution. This is crucial, as our project involves a complex network of actors and many aspects, such as biosafety, that should be very carefully considered from as many angles as possible. To this point, we have been conducting interviews with relevant scientists and organizations to understand their views and obtain feedback that we can integrate into our project. Furthermore, we have reached out to researchers about locust physiology and microbiome, (engineering) bacteriophages, (bio)pesticides, bioethics and biosafety. Additionally, through video-calling the United Nations Food and Agriculture Organization, which is responsible for global locust control efforts, and MetaMeta, which is focused on local locust control, we obtained information about how to implement our biopesticide.
Discussions with locust and bacteriophage scientists and leading experts in the field of locust control gave us multiple insights:
 
Current locust control operations make use of pesticides that are either      harmful for the environment or too slow. There is a clear need for a novel pesticide that is safe, fast and specific.

Preventing locusts from swarming is the best strategy to tackle the recurring locust crisis. PHOCUS should be applied on vegetation in remote and unpopulated areas instead of on crops, as this is where the locust swarms often start to develop.

Degregarizing locusts once they have formed a swarm may be a bad idea: You do not solve the problem, but instead spread the locusts over a larger area. As a result, you lose your target for control measures.

PHOCUS should be resistant to UV and high temperatures to survive long enough in dry and hot desert conditions.
 
 
 
 
Wet lab
 
We have continued working on the details of each module in our project, specially in modules 1 and 2.
Module 1 is a proof of concept that consists of engineering the T7 bacteriophage, which infects E.coli, with GFP in different gene positions of the phage genome. After having amplified GFP, the goal of the coming month will consist of obtaining the engineered phages.
Module 2 consists of the production of toxin molecules for locusts. In this module, there are mainly two strategies that are followed: the production of the Cry7Ca1 protein and the production of interference RNA (RNAi). The protein Cry7Ca1 is a protein from Bacillus thuringiensis (Bt), a soil bacteria that produces crystal proteins (Cry) that are shown to be toxic for insects, and in the case of Cry7Ca1 concretely to locust. On the other hand, RNAi consists of the regulation of gene expression by the interaction of RNA with messenger RNA (mRNA), the RNA transcribed from the gene DNA. Our approach is to produce double-stranded RNA (dsRNA) to target locust genes. During this month we have designed the plasmids containing the genes and constructs we want to use for these experiments.
 
 
Dry lab
 
The last month, the dry lab team has been was phocused on two specific mathematical models. The first model describes how phages interact with their target bacteria on a population level scale. The goal of this model is to determine the amount of phages required in the locust gut to produce enough toxin molecules in time to kill the locust. The second model describes a single cell in a simplified way by assuming that there are limitations in levels of cellular energy, free ribosomes, and proteins. This model allows us to study the trade-offs a cell has to make, which we can use to study how phage infection affects the behaviour of single-cells and how expressing different amounts of phage proteins influence the lysis time of these cells. Next to implementing these models in Python and sharing our code like real Git masters, we have also been analysing the models mentioned above on a more fundamental level through linear stability analysis.  Even though we do not have fixed office spots due to corona, this hasn't stopped us from setting up our dry lab camp (see picture if we have one). For each extra monitor we gain +5 productivity and for each pair of sunglasses our hacker ability gains +8 bonus point, making our dry lab team stronger than ever before.
 
 
Sponsors
 
The Department of Biotechnology engages in internationally leading, groundbreaking research and education programs in industrial and environmental biotechnology. The Department of Biotechnology covers the fields of biocatalysis, bioprocess engineering, cell systems engineering, environmental biotechnology, industrial microbiology, and biotechnology and society, thereby combining fundamental research, engineering, and design. These fields are all directed towards biotechnological process innovations.
 
 
The Faculty of Applied Sciences’ main ambition is to contribute to resolving the major social challenges of our time through its teaching and research. These challenges include a secure, safe, clean and efficient energy supply, health (e.g. effective medicines), security of food supply, green economy/bio-economy, safety and security (also in terms of information transfer) and innovation. The faculty aims to be among the best in the world in a number of research areas.
 
 
The virtual TU Delft Bioengineering Institute strengthens the campus-wide collaboration of scientists who are engineering solutions in, with or for biology, links them with external partners, and increases the visibility of the Delft University of Technology as a major partner in the international bioengineering arena.
 
 
The Department of Chemical Engineering aspires to the pursuit and dissemination of knowledge in their discipline, and to shape that discipline as they do so. Their discipline is the art-turned-science of converting molecular understanding into products and processes that benefit mankind, using a healthy dose of chemistry, mathematics, physics, biology, and material science whenever that is called for. Chemical engineering at TU Delft is eclectic by design and united by a synthetic objective.
 
 
TU Delft iGEM Phocus
Van der Maasweg 9
2629 HZ DELFT
igem@tudelft.com
Facebook
Twitter
LinkedIn
Instagram
 
 
You received this email because you are registered with iGEM TU Delft
 
 
SendinBlue
 
 
© 2020 iGEM TU Delft