Cell Defense Crack Code

WEST LAFAYETTE, Ind. – Imagine the day when any tissue or organ can be repaired or replacements personalized to the patient.

This is one of the objectives of the work carried out by David Umulis from Purdue University and a team of scientists using artificial intelligence in biology to see how cells defend themselves against chemical or mechanical attacks and / or repair their damage using biochemical and mechanical inputs and reactions.

If that succeeds, Umulis says, scientists might have a new way to approach human health and longevity.

“If you can touch a network and change three or four locations at once, the ability to deal with disease or damage will improve because you simultaneously report all of these different biological pathways,” he says.

Unlock new potentials

Umulis uses AI in several of its biomedical engineering projects, including image quantification and the simulation of developing cells. He finds that it delivers better results, sooner and faster, and can be inexpensive compared to many hours of simulating cellular characteristics.

But he wants to innovate and push further. New Institute of Emerging Mechanisms in Robustness, Integration and Organization Biology (EMBRIO) will use AI to extend biology and engineering by exploring how cellular signals are integrated to fight off invaders or activated to repair wounds, both of which are essential for survival.

“I want the EMBRIO Institute team to be known as the research team that cracked the code on how cells organize to alter structural function to defend and repair tissue,” said Umulis, EMBRIO Project Director, Professor and Director of Purdue’s Dane A. Miller. Weldon School of Biomedical Engineering. “The network where cells make these decisions and how it is copied and replicated throughout the animal kingdom is still a big mystery. Integrating laboratory experimentation with the simulation and data acquisition approach that we have is really the best way to tackle a fundamental biological treatment issue on such a large scale. “

Purdue serves as the primary site for the EMBRIO Institute, which has received $ 12.5 million from the National Science Foundation (NSF) over five years as part of the agency’s Biology Integration Institutes (BII) program. Partner institutions are Indiana University, Morehouse College, University of Notre Dame, University of Pennsylvania, Ponce University of Health Sciences (Puerto Rico) and University of Puerto Rico at Mayagüez. Morehouse, Ponce and Mayagüez are essential in extending the contributions of traditionally under-represented populations throughout the EMBRIO Institute.

“The EMBRIO Institute illustrates the goals of the BII program by bringing together an interdisciplinary team of researchers around the common goal of understanding how the processes that sustain life and enable biological innovation operate and interact at different scales,” says Wilson Francisco , Ph. .D., Program Director in the Biological Sciences Branch, NSF. “It will also provide effective new training paradigms that are inclusive and prepare next generations of scientists to navigate various fields of biological sciences and STEM at large. By combining experimental biology, theory, computation, and modeling, along with training and educating a diverse group of students, EMBRIO has the potential to advance biology, biotechnology, and the workforce. work of biological sciences.

As Director, Umulis will coordinate and empower researchers and students to find new ways to use AI to crack cellular organization.

“We can do a lot more with a lot less,” he says. “It allows us to think about how cells calculate and then how cells are coupled, causing tissue changes on this massive scale.”

With AI, Umulis and scientists are able to use full 3D simulations of biological structures to establish predictive capabilities. This allows them to see how the shape of networks and tissues can change.

They can then link different biological systems, such as cell chemistry and chemical signaling, as well as mechanics and mechanical changes, to better predict outcomes in more complex systems.

“We’re getting to a point where we know how a tissue grows, forms and turns into something that has the right structure and function based on genotypes, genetics and signaling pathways,” Umulis explains. “Biology is able to use all of these things synchronously throughout the stages of life and development. The way they do it is incredible synchrony that can only be harnessed through the combination of simulation and AI. “

EMBRIO’s Biological Systems group immediately acquires data for simulations, such as a plant fighting invading fungi or tens of thousands of cells signaling to each other to heal a wound. However, developing models to merge the different findings will take time.

“We’re going to use each biological system to get the best data acquisition possible so that we can respond to how cells react together to fight potential attacks. How do wounds heal? How can we speed this up? How do cells orchestrate tissue remodeling processes for the development of the embryo or to repair and restore function of cells, tissues or organs? It’s the most important part of life, ”he says.

Building on the strengths of AI and biomedical engineering

The AI ​​and biology industry doubles in size every five years, which means that the biology, engineering and science students who now enter EMBRIO will be the cutting edge leaders over the next 10 years, Umulis said.

Umulis has assembled a team of specialist engineers and scientists who in turn will work with and inspire students with these new techniques and meet future workforce development needs.

One of the institutional partners involved is Morehouse College, a historically black liberal arts college and university (HBCU) in Atlanta.

Juana Mendenhall, Walter E. Massey Professor of Physical Sciences at Morehouse College. (Photo provided)

Building on the strengths of AI and biomedical engineering

The AI ​​and biology industry doubles in size every five years, which means that the biology, engineering and science students who now enter EMBRIO will be the cutting edge leaders over the next 10 years, Umulis said.

Umulis has assembled a team of specialist engineers and scientists who in turn will work with and inspire students with these new techniques and meet future workforce development needs.

One of the institutional partners involved is Morehouse College, a historically black liberal arts college and university (HBCU) in Atlanta.

Juana mendenhall, Walter E. Massey Professor of Physical Sciences at Morehouse College, is one of the research partners who will conduct research within the EMBRIO Institute in her laboratory in Morehouse. She brings to the project her expertise in the chemistry and fabrication of materials as well as in nanobiotechnology using atomic force microscopy to study biological processes.

In addition to the basic research that Mendenhall will be conducting with the institute, she also sees many positive points for her students. They can gain experiential opportunities by improving their laboratory techniques and learning new software for computer modeling and data science visualizations that will help them develop as scientists, she says.

“The ability to engage and train HBCU students in AI at the intersection of STEM while using methods used in biology and biomedical engineering is necessary for our students at Morehouse,” said Mendenhall. “Our students need to see the synergy between natural sciences, life sciences and engineering.

“Working with Purdue, Morehouse will have access to advanced technology and tools to help study these processes. This will further enhance our students’ knowledge and exposure to the emerging field of integrative biology.”

The leaders of Umulis and EMBRIO also plan to use existing open source programs, but will develop other AI and biology programs for students.

Additional IPs are Janice Evans, Chris Staiger, Stephanie Gardner and Alejandra Magana (Purdue), and site managers Mauricio Cabrera (University of Puerto Rico at Mayagüez), James Glazer (IU), Clara Isaza (Ponce Health Sciences University), Mary Mullins (Penn ), and Jérémie Zartman (Notre Dame).