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Researcher

Research & Initiatives

Please find below a few examples of our new projects

MAKING SENSE: SMART ENVIRONMENTAL IOT

December 2022        

1.    Background and DescriptionExtreme climate, global warming, and adverse environmental conditions risk the future of life on Earth. Can you fix it?
In this project we will build smart sensors that will measure multiple signals like earth vital signs, human vocal signals, air ingredients and many more. We will share the measurements on the cloud and encourage action. The sensor network combines standard physical sensors, novel biosensors, and public available data from the internet. It then applies AI to derive conclusions and actions.      

 


2.    Scope
The students will work closely with a new-born start-up, SenseNow, which has built an amazing global system that can sense and act locally and globally to improve the quality of our lives on earth. The students will build a sensor network in a box that will enable sensing and activating multiple outputs according to some important alerts such as local weather changes. The box will later be integrated into the big system via the internet in real time. 

 

3.    Additional information
This project will be performed by 4th year bioengineering students. It can be later expanded for master. The project will expose students to all steps of an engineering project from theory to computational tools and all the way to implementation. Basic programming, HW and probability theory knowledge are required. More information can be provided by Dr. Yuval Dorfan. Please contact him via email: dorfany@gmail.com

SenseNow logo
SenseNow heading

CYBER-BIOSECURITY & QUALITY ASSURANCE: EXPLORING THE OUTPUT OF A CODON OPTIMIZER

November 2022        

1.    Background and Description
In the past two decades DNA synthesis became widely used due to several reasons: Price dramatic decrease, advances in synthetic biology and other bio-tech fields, easy ways to ship, store and integrate DNA almost everywhere and in wide variety of organisms. Cyber-biosecurity and quality assurance became very important in order to prevent threats and innocent mistakes in the age of high volumes DNA synthesis. As important in every software related discipline, cyber becomes a critical issue in biology. Unlike engineers and computer scientists, the average biologist is naïve and unaware of these threats. One of the most interesting tools is a codon optimizer, used by many biologists before they order DNA for their research.     


2.    Scope
The students will study the field of cyber-biosecurity and then develop new computational tools to evaluate threats and issues that seem critical to resolve. From threats list they will choose a specific algorithmic challenge and suggest new SW packages that can increase the quality assurance for potential users. For example: The students can focus on the operation of a codon optimizer and explore parallel encoding that often occur. They will then have to suggest ways to prevent insertion of harmful components.

 

3.    Additional information
This project will be performed by 4th year bioengineering students. It can be later expanded for master that would like to specialize in computational biology and SynBio. The project will expose students to all steps of an engineering project from theory to computational tools and all the way to implementation. Basic programming and probability theory knowledge are required. More information can be provided by Dr. Yuval Dorfan. Please contact him via email: dorfany@gmail.com

 

4.    Initial references list
- Franz, D.R., Lilly, D., Carr, P.: " Synthetic Biology: Safety, Security, and Promise" (Book, 2016)
- Natalie Kuldell, ‎Rachel Bernstein, ‎Karen Ingram: "BioBuilder: Synthetic Biology in the Lab" (Book, 2015)

CORROSION CONTROL BY PROGRAMMING OF MICROORGANISMS
 
October 2022        

1.    Project Background and Description
Corrosion is a severe issue for many civil and defense applications, such as ships bodies. It turns out that bacteria play a major role in the corrosion process via bio-films. Synthetic biology (SynBio) is a new engineering field that enable us to program living cells according to various applications requirements. SynBio should be combined with other classical engineering disciplines (also called ‘bio-convergence’) to make sure the best solution is found.  

  
2.    Project Scope
The students will study these phenomena and then run or develop computational tools to suggest ways to increase or decrease the activity of bacteria in the bio-films. Then a computational design phase will be performed to simulate the effect of various proposed solutions. We then build experimental setup of a few solutions that are predicted to perform best in order to test them and measure the effect in the lab.

 

3.    Additional information
This project can be either performed by 4th year bio-engineering students or by master students that would like to specialized in SynBio and its combinations with classical engineering fields. The project will expose students to all steps of an engineering project from theory, to computational tools and all the way to experimental setup in the lab. 


4.    Initial references list
1.    Taleb-Berrouane, Mohammed, et al. "Model for microbiologically influenced corrosion potential assessment for the oil and gas industry." Corrosion Engineering, Science and Technology 53.5 (2018): 378-392.
2.    Kip, Nardy, and Johannes A. Van Veen. "The dual role of microbes in corrosion." The ISME journal 9.3 (2015): 542-551.

MIC_Bio_Films.jpg

Development novel healthy painting materials for rooms & offices 
 
October 2022        

1.    Project Background and Description
Fungi and other microorganisms sometimes grow very well in walls especially in wet enough conditions. Chemicals used to prevent their growth are widely used in modern painting of rooms and offices, but are sometimes not healthy for us either. Synthetic biology (SynBio) is a new engineering field that enable us to program living cells according to various applications requirements. In order to replace the commercially used chemicals we can either engineer new bacteria or use natural friendly microorganisms that make our internal space healthier and cleaner.  

  
2.    Project Scope
The students will study these phenomena and then develop new ways to decrease the fungi activity using natural bacteria. Then a computational design phase will be performed to simulate the effect of various proposed solutions. We then build experimental setup of a few solutions that are predicted to perform best in order to test them and measure the effect in the lab.

 

3.    Additional information
This project can be either performed by 4th year bio-engineering students or by master students that would like to specialized in SynBio and its combinations with classical engineering fields. The project will expose students to all steps of an engineering project from theory, to computational tools and all the way to experimental setup in the lab. 

Special lab automation:
Bio-production of cancer drugs using photogenetic 
 
February 2023        

MFB_BIO_Prod_edited.jpg

1.    Project Background and Description
Protein toxins are an important class of biomolecules, whose structure and functionality need to be understood to, on the one hand, identify potent inhibitors against their cytotoxicity and, on the other, exploit that same cytotoxicity to selectively kill desired cell populations (e.g., cancer cells). In this approach, the toxin is split into two non-toxic fragments, which are separately purified and then recombined into the full-length toxin. While this method is very attractive, it relies on cell lysis prior to the purification of the two fragments, which leads to the production of high amounts of endotoxin, which must be eliminated before the toxin can be used as a drug. Furthermore, the whole experimental procedure is not automated and requires sequential execution of all the steps. 

  
2.    Project Scope
The students will study the fields of bio-production and automation tools (Gome et al., 2019) and then develop automation new tools based on an existing patent. The project requires besides general understanding of bio-production, embedded and making skills. It is possible to learn some of these skills during the project.

3.    Additional information
This This project will be performed by 4th year bioengineering students. It can be later expanded for master that would like to specialize in SynBio & bio-convergence. The project will expose students to all steps of an engineering project from theory to automation tools and all the way to implementation. Basic prog
ramming and HW knowledge are required.

 

4. Initial references list

  1. Natalie Kuldell, ‎Rachel Bernstein, ‎Karen Ingram: "BioBuilder: Synthetic Biology in the Lab" (Book, 2015).

  2. Gome, G., Fein, Y., Waksberg, J., Maayan, Y., Grishko, A., Wald, I. Y., & Zuckerman, O. (2019). My First Biolab: A System for Hands-On Biology Experiments. Extended Abstracts of the 2019 CHI Conference on Human Factors in Computing Systems, 1–6. https://doi.org/10.1145/3290607.3313081

Pathogen detection: Tailored DNA transfer into specific bacteria

 
May 2023        

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1.    Project Background and DescriptionAn interdisciplinary project combing microbiology, synthetic biology and bioinformatics aiming to develop novel detection methods of pathogenic bacteria requires bio-engineering students with passion for problem-solving and out-of-the-box thinking to lead computational analysis of genetic data.

  
2.    Project Scope
The students’ project will focus on the prediction of genetic targets and systems in big data sets of genomic data. The project is a collaboration with Dr. Avihu Yona’s lab at the Faculty of Agriculture in Rehovot
.

3.    Additional information
This This project will be performed by 4th year bioengineering students. It can be later expanded for master that would like to specialize in SynBio & bio-convergence. The project will expose students to all steps of a SynBio project from theory to 
implementation. Basic programming and biology knowledge are required.

4. Initial references list

  1. Brophy, Jennifer AN, Alexander J. Triassi, Bryn L. Adams, Rebecca L. Renberg, Dimitra N. Stratis-Cullum, Alan D. Grossman, and Christopher A. Voigt. "Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria." Nature microbiology 3, no. 9 (2018): 1043-1053.

  2. Chemla, Yonatan, Yuval Dorfan, Adi Yannai, Dechuan Meng, Paul Cao, Sarah Glaven, D. Benjamin Gordon, Johann Elbaz, and Christopher A. Voigt. "Parallel engineering of environmental bacteria and performance over years under jungle-simulated conditions." Plos one 17, no. 12 (2022): e0278471.

SynBio Bacteria
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